data_LVR
# 
_chem_comp.id                                    LVR 
_chem_comp.name                                  "1-{[2-({6-[(2-aminoethyl)amino]-5,10-dioxo-5,10-dihydrobenzo[g]isoquinolin-9-yl}amino)ethyl]amino}-1,2-dideoxy-5-O-(dihydroxyphosphanyl)-L-threo-pentitol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H30 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-03-07 
_chem_comp.pdbx_modified_date                    2023-03-21 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        523.476 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LVR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7U38 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
LVR OP1   O1  O 0 1 N N N 44.685 41.718 32.098 10.715 -1.157 -1.168 OP1   LVR 1  
LVR P     P1  P 0 1 N N N 43.554 40.764 32.056 10.600 -0.002 -0.250 P     LVR 2  
LVR OP2   O2  O 0 1 N N N 42.264 41.087 32.679 11.629 1.150  -0.706 OP2   LVR 3  
LVR "O5'" O3  O 0 1 N N N 43.217 40.358 30.503 9.097  0.573  -0.297 "O5'" LVR 4  
LVR "C5'" C1  C 0 1 N N N 44.295 40.011 29.661 7.946  -0.237 -0.049 "C5'" LVR 5  
LVR "C4'" C2  C 0 1 N N S 43.825 39.551 28.258 6.684  0.618  -0.172 "C4'" LVR 6  
LVR "O4'" O4  O 0 1 N N N 42.414 39.395 28.192 6.677  1.610  0.857  "O4'" LVR 7  
LVR "C3'" C3  C 0 1 N N S 44.509 38.232 27.965 5.448  -0.273 -0.030 "C3'" LVR 8  
LVR "O3'" O5  O 0 1 N N N 43.599 37.290 27.433 5.524  -1.001 1.197  "O3'" LVR 9  
LVR "C2'" C4  C 0 1 N N N 45.699 38.420 27.029 4.189  0.598  -0.029 "C2'" LVR 10 
LVR "C1'" C5  C 0 1 N N N 46.294 37.122 26.545 2.950  -0.299 -0.012 "C1'" LVR 11 
LVR NAT   N1  N 0 1 N N N 47.598 37.069 26.439 1.741  0.537  -0.011 NAT   LVR 12 
LVR CAP   C6  C 0 1 N N N 48.048 35.665 26.313 0.528  -0.292 0.005  CAP   LVR 13 
LVR CAR   C7  C 0 1 N N N 48.105 34.988 27.660 -0.706 0.612  0.006  CAR   LVR 14 
LVR NAV   N2  N 0 1 N N N 49.228 34.029 27.691 -1.916 -0.215 0.022  NAV   LVR 15 
LVR CAZ   C8  C 0 1 Y N N 50.450 34.392 28.039 -3.166 0.386  0.025  CAZ   LVR 16 
LVR CAJ   C9  C 0 1 Y N N 50.778 35.729 27.851 -3.276 1.774  0.148  CAJ   LVR 17 
LVR CAI   C10 C 0 1 Y N N 52.058 36.141 28.107 -4.500 2.378  0.152  CAI   LVR 18 
LVR CBF   C11 C 0 1 Y N N 51.371 33.401 28.528 -4.319 -0.394 -0.100 CBF   LVR 19 
LVR CBB   C12 C 0 1 N N N 51.034 32.027 28.797 -4.224 -1.858 -0.235 CBB   LVR 20 
LVR OAB   O6  O 0 1 N N N 49.910 31.565 28.580 -3.156 -2.386 -0.481 OAB   LVR 21 
LVR CBD   C13 C 0 1 Y N N 51.972 31.141 29.334 -5.442 -2.676 -0.067 CBD   LVR 22 
LVR CAX   C14 C 0 1 Y N N 51.618 29.806 29.575 -5.371 -4.056 0.090  CAX   LVR 23 
LVR NAH   N3  N 0 1 Y N N 52.595 28.886 30.098 -6.474 -4.766 0.238  NAH   LVR 24 
LVR CAG   C15 C 0 1 Y N N 53.911 29.334 30.336 -7.672 -4.215 0.245  CAG   LVR 25 
LVR CAW   C16 C 0 1 Y N N 54.225 30.686 30.109 -7.836 -2.846 0.094  CAW   LVR 26 
LVR CBC   C17 C 0 1 Y N N 53.263 31.565 29.588 -6.705 -2.053 -0.064 CBC   LVR 27 
LVR CBA   C18 C 0 1 N N N 53.605 32.893 29.369 -6.804 -0.586 -0.226 CBA   LVR 28 
LVR OAA   O7  O 0 1 N N N 54.759 33.218 29.664 -7.875 -0.063 -0.464 OAA   LVR 29 
LVR CBE   C19 C 0 1 Y N N 52.660 33.836 28.840 -5.585 0.230  -0.096 CBE   LVR 30 
LVR CAY   C20 C 0 1 Y N N 52.976 35.213 28.604 -5.669 1.620  0.034  CAY   LVR 31 
LVR NAU   N4  N 0 1 N N N 54.204 35.652 28.915 -6.907 2.245  0.040  NAU   LVR 32 
LVR CAQ   C21 C 0 1 N N N 54.538 37.094 28.945 -6.989 3.707  0.030  CAQ   LVR 33 
LVR CAO   C22 C 0 1 N N N 55.043 37.518 27.560 -8.458 4.136  0.040  CAO   LVR 34 
LVR NAS   N5  N 0 1 N N N 56.390 38.115 27.656 -8.540 5.602  0.029  NAS   LVR 35 
LVR H2    H2  H 0 1 N N N 42.309 41.950 33.073 12.556 0.873  -0.701 H2    LVR 36 
LVR H3    H3  H 0 1 N N N 44.860 39.192 30.130 7.908  -1.048 -0.776 H3    LVR 37 
LVR H4    H4  H 0 1 N N N 44.949 40.888 29.545 8.005  -0.654 0.957  H4    LVR 38 
LVR H5    H5  H 0 1 N N N 44.158 40.295 27.520 6.670  1.106  -1.147 H5    LVR 39 
LVR H6    H6  H 0 1 N N N 41.994 40.227 28.377 6.689  1.246  1.753  H6    LVR 40 
LVR H7    H7  H 0 1 N N N 44.900 37.845 28.918 5.406  -0.971 -0.865 H7    LVR 41 
LVR H8    H8  H 0 1 N N N 42.866 37.186 28.028 5.565  -0.442 1.985  H8    LVR 42 
LVR H9    H9  H 0 1 N N N 46.478 38.982 27.565 4.189  1.235  0.856  H9    LVR 43 
LVR H10   H10 H 0 1 N N N 45.366 38.998 26.154 4.176  1.219  -0.924 H10   LVR 44 
LVR H11   H11 H 0 1 N N N 45.871 36.913 25.551 2.950  -0.936 -0.896 H11   LVR 45 
LVR H12   H12 H 0 1 N N N 45.986 36.333 27.247 2.963  -0.920 0.883  H12   LVR 46 
LVR H13   H13 H 0 1 N N N 48.012 37.476 27.253 1.738  1.168  -0.798 H13   LVR 47 
LVR H15   H15 H 0 1 N N N 47.345 35.119 25.667 0.512  -0.929 -0.879 H15   LVR 48 
LVR H16   H16 H 0 1 N N N 49.050 35.649 25.860 0.525  -0.913 0.900  H16   LVR 49 
LVR H17   H17 H 0 1 N N N 48.250 35.746 28.444 -0.690 1.249  0.890  H17   LVR 50 
LVR H18   H18 H 0 1 N N N 47.162 34.451 27.839 -0.702 1.233  -0.890 H18   LVR 51 
LVR H19   H19 H 0 1 N N N 48.960 33.305 28.326 -1.843 -1.182 0.030  H19   LVR 52 
LVR H20   H20 H 0 1 N N N 50.034 36.433 27.508 -2.384 2.376  0.240  H20   LVR 53 
LVR H21   H21 H 0 1 N N N 52.353 37.165 27.928 -4.566 3.451  0.248  H21   LVR 54 
LVR H22   H22 H 0 1 N N N 50.613 29.468 29.369 -4.410 -4.549 0.091  H22   LVR 55 
LVR H23   H23 H 0 1 N N N 54.667 28.648 30.688 -8.542 -4.843 0.369  H23   LVR 56 
LVR H24   H24 H 0 1 N N N 55.215 31.051 30.338 -8.822 -2.406 0.100  H24   LVR 57 
LVR H25   H25 H 0 1 N N N 54.404 35.299 29.829 -7.718 1.713  0.051  H25   LVR 58 
LVR H26   H26 H 0 1 N N N 55.322 37.276 29.695 -6.488 4.105  0.913  H26   LVR 59 
LVR H27   H27 H 0 1 N N N 53.641 37.675 29.204 -6.504 4.092  -0.867 H27   LVR 60 
LVR H28   H28 H 0 1 N N N 54.350 38.258 27.134 -8.958 3.737  -0.843 H28   LVR 61 
LVR H29   H29 H 0 1 N N N 55.085 36.635 26.905 -8.942 3.751  0.937  H29   LVR 62 
LVR H30   H30 H 0 1 N N N 56.701 38.385 26.745 -8.042 5.987  -0.759 H30   LVR 63 
LVR H31   H31 H 0 1 N N N 56.356 38.920 28.248 -9.500 5.911  0.035  H31   LVR 64 
LVR OP3   OP3 O 0 1 N Y N ?      ?      ?      10.949 -0.471 1.250  OP3   LVR 65 
LVR HO3   HO3 H 0 1 N Y N ?      ?      ?      10.894 0.236  1.906  HO3   LVR 66 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
LVR CAP   NAT   SING N N 1  
LVR CAP   CAR   SING N N 2  
LVR NAT   "C1'" SING N N 3  
LVR "C1'" "C2'" SING N N 4  
LVR "C2'" "C3'" SING N N 5  
LVR "O3'" "C3'" SING N N 6  
LVR CAO   NAS   SING N N 7  
LVR CAO   CAQ   SING N N 8  
LVR CAR   NAV   SING N N 9  
LVR NAV   CAZ   SING N N 10 
LVR CAJ   CAZ   DOUB Y N 11 
LVR CAJ   CAI   SING Y N 12 
LVR "C3'" "C4'" SING N N 13 
LVR CAZ   CBF   SING Y N 14 
LVR CAI   CAY   DOUB Y N 15 
LVR "O4'" "C4'" SING N N 16 
LVR "C4'" "C5'" SING N N 17 
LVR CBF   CBB   SING N N 18 
LVR CBF   CBE   DOUB Y N 19 
LVR OAB   CBB   DOUB N N 20 
LVR CAY   CBE   SING Y N 21 
LVR CAY   NAU   SING N N 22 
LVR CBB   CBD   SING N N 23 
LVR CBE   CBA   SING N N 24 
LVR NAU   CAQ   SING N N 25 
LVR CBD   CAX   DOUB Y N 26 
LVR CBD   CBC   SING Y N 27 
LVR CBA   CBC   SING N N 28 
LVR CBA   OAA   DOUB N N 29 
LVR CAX   NAH   SING Y N 30 
LVR CBC   CAW   DOUB Y N 31 
LVR "C5'" "O5'" SING N N 32 
LVR NAH   CAG   DOUB Y N 33 
LVR CAW   CAG   SING Y N 34 
LVR "O5'" P     SING N N 35 
LVR P     OP1   DOUB N N 36 
LVR P     OP2   SING N N 37 
LVR OP2   H2    SING N N 38 
LVR "C5'" H3    SING N N 39 
LVR "C5'" H4    SING N N 40 
LVR "C4'" H5    SING N N 41 
LVR "O4'" H6    SING N N 42 
LVR "C3'" H7    SING N N 43 
LVR "O3'" H8    SING N N 44 
LVR "C2'" H9    SING N N 45 
LVR "C2'" H10   SING N N 46 
LVR "C1'" H11   SING N N 47 
LVR "C1'" H12   SING N N 48 
LVR NAT   H13   SING N N 49 
LVR CAP   H15   SING N N 50 
LVR CAP   H16   SING N N 51 
LVR CAR   H17   SING N N 52 
LVR CAR   H18   SING N N 53 
LVR NAV   H19   SING N N 54 
LVR CAJ   H20   SING N N 55 
LVR CAI   H21   SING N N 56 
LVR CAX   H22   SING N N 57 
LVR CAG   H23   SING N N 58 
LVR CAW   H24   SING N N 59 
LVR NAU   H25   SING N N 60 
LVR CAQ   H26   SING N N 61 
LVR CAQ   H27   SING N N 62 
LVR CAO   H28   SING N N 63 
LVR CAO   H29   SING N N 64 
LVR NAS   H30   SING N N 65 
LVR NAS   H31   SING N N 66 
LVR P     OP3   SING N N 67 
LVR OP3   HO3   SING N N 68 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
LVR SMILES           ACDLabs              12.01 "O=P(O)(O)OCC(O)C(O)CCNCCNc1ccc(NCCN)c2c1C(=O)c1cnccc1C2=O"                                                                                                                                                 
LVR InChI            InChI                1.06  "InChI=1S/C22H30N5O8P/c23-5-8-26-15-1-2-16(20-19(15)21(30)13-3-6-25-11-14(13)22(20)31)27-10-9-24-7-4-17(28)18(29)12-35-36(32,33)34/h1-3,6,11,17-18,24,26-29H,4-5,7-10,12,23H2,(H2,32,33,34)/t17-,18-/m0/s1" 
LVR InChIKey         InChI                1.06  BJAOHGRBCOQHHR-ROUUACIJSA-N                                                                                                                                                                                 
LVR SMILES_CANONICAL CACTVS               3.385 "NCCNc1ccc(NCCNCC[C@H](O)[C@@H](O)CO[P](O)(O)=O)c2C(=O)c3cnccc3C(=O)c12"                                                                                                                                    
LVR SMILES           CACTVS               3.385 "NCCNc1ccc(NCCNCC[CH](O)[CH](O)CO[P](O)(O)=O)c2C(=O)c3cnccc3C(=O)c12"                                                                                                                                       
LVR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c2c(c1NCCN)C(=O)c3ccncc3C2=O)NCCNCC[C@@H]([C@H](COP(=O)(O)O)O)O"                                                                                                                                      
LVR SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c2c(c1NCCN)C(=O)c3ccncc3C2=O)NCCNCCC(C(COP(=O)(O)O)O)O"                                                                                                                                               
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
LVR "SYSTEMATIC NAME" ACDLabs              12.01 "1-{[2-({6-[(2-aminoethyl)amino]-5,10-dioxo-5,10-dihydrobenzo[g]isoquinolin-9-yl}amino)ethyl]amino}-1,2-dideoxy-5-O-phosphono-L-threo-pentitol"                
LVR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S})-5-[2-[[6-(2-azanylethylamino)-5,10-bis(oxidanylidene)benzo[g]isoquinolin-9-yl]amino]ethylamino]-2,3-bis(oxidanyl)pentyl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
LVR "Create component"   2022-03-07 RCSB 
LVR "Initial release"    2023-03-15 RCSB 
LVR "Other modification" 2023-03-21 RCSB 
# 
