# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:23:13 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-[(4-aminobutyl)amino]-1,2-dimethyl-3-[(4-nitrophenoxy)methyl]-1H-indole-4,7-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(C)c(COc2ccc(cc2)[N+]([O-])=O)c3C(=O)C(=CC(=O)c13)NCCCCN
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 O73  O73  5-[(4-aminobutyl)amino]-1,2-dimethyl-3-[(4-nitrophenoxy)methyl]-1H-indole-4,7-dione  ligand  54  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O73
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 O73  C1    C  CR16   0  -0.252   4.1498   2.1025  -1.3145
 O73  C2    C  CR16   0  -0.344   3.2109   1.0977  -1.3179
 O73  C3    C  CR6    0   0.428   3.0450   0.2746  -0.1959
 O73  C4    C  CR16   0  -0.378   3.8436   0.4802   0.9324
 O73  C5    C  CR16   0  -0.251   4.7867   1.4911   0.9357
 O73  C6    C  CR6    0   0.225   4.9377   2.2982  -0.1822
 O73  N7    N  N      1   0.328   5.9246   3.3507  -0.1729
 O73  O8    O  O      0  -0.391   6.0481   4.0295  -1.1684
 O73  O9    O  O     -1  -0.391   6.5861   3.5096   0.8292
 O73  O10   O  O2     0  -0.449   2.1164  -0.6738  -0.2968
 O73  C11   C  CH2    0  -0.339   1.8110  -1.4732   0.8472
 O73  C12   C  CR5    0   0.030   0.6413  -2.3193   0.5073
 O73  C13   C  CR5    0   0.296   0.6329  -3.6817   0.2973
 O73  N14   N  NR5    0  -0.532  -0.6508  -4.0658   0.0022
 O73  C15   C  CR56   0   0.261  -1.4585  -2.9792   0.0089
 O73  C16   C  CR56   0  -0.094  -0.6908  -1.8769   0.3203
 O73  C17   C  CR6    0   0.391  -2.9027  -2.9217  -0.2617
 O73  C18   C  CR16   0  -0.576  -3.4873  -1.6056  -0.1810
 O73  C19   C  CR6    0   0.340  -2.7620  -0.4859   0.1239
 O73  C20   C  CR6    0   0.248  -1.2734  -0.5619   0.4132
 O73  C21   C  CH3    0  -0.760   1.7557  -4.6548   0.3528
 O73  C22   C  CH3    0  -0.528  -1.0602  -5.4299  -0.2794
 O73  O23   O  O      0  -0.447  -3.5539  -3.9247  -0.5357
 O73  O24   O  O      0  -0.382  -0.6620   0.4479   0.7010
 O73  N25   N  NH1    0  -0.656  -3.2608   0.7437   0.1942
 O73  C26   C  CH2    0  -0.250  -4.6460   1.0672  -0.0497
 O73  C27   C  CH2    0  -0.473  -4.8799   2.5651   0.0431
 O73  C28   C  CH2    0  -0.429  -6.3337   2.9282  -0.2266
 O73  C29   C  CH2    0  -0.271  -6.5781   4.4282  -0.1606
 O73  N30   N  NH2    0  -0.801  -7.9777   4.7380  -0.4142
 O73  H1    H  HCR6   0   0.297   4.2612   2.7276  -2.1883
 O73  H2    H  HCR6   0   0.283   2.5911   0.9376  -2.1902
 O73  H4    H  HCR6   0   0.301   3.7527  -0.1388   1.8135
 O73  H5    H  HCR6   0   0.299   5.3978   1.6357   1.8147
 O73  H11   H  HCH2   0   0.254   2.6749  -2.0870   1.1159
 O73  H11A  H  HCH2   0   0.252   1.5853  -0.8269   1.6995
 O73  H18   H  HCR6   0   0.272  -4.5493  -1.5366  -0.3782
 O73  H21   H  HCH3   0   0.265   1.5954  -5.4195   1.1143
 O73  H21A  H  HCH3   0   0.266   1.8997  -5.1620  -0.6027
 O73  H21B  H  HCH3   0   0.271   2.6867  -4.1469   0.5929
 O73  H22   H  HCH3   0   0.266  -1.8498  -5.7402   0.3985
 O73  H22A  H  HCH3   0   0.265  -1.4144  -5.5213  -1.3030
 O73  H22B  H  HCH3   0   0.272  -0.2108  -6.0903  -0.1462
 O73  HN25  H  HNH1   0   0.404  -2.6244   1.4886   0.4389
 O73  H26   H  HCH2   0   0.239  -4.9334   0.7023  -1.0422
 O73  H26A  H  HCH2   0   0.240  -5.2803   0.5415   0.6732
 O73  H27   H  HCH2   0   0.235  -4.5894   2.9177   1.0375
 O73  H27A  H  HCH2   0   0.235  -4.2328   3.0756  -0.6770
 O73  H28   H  HCH2   0   0.221  -6.6340   2.5588  -1.2116
 O73  H28A  H  HCH2   0   0.219  -6.9757   2.4261   0.5054
 O73  H29   H  HCH2   0   0.189  -6.2132   4.8060   0.8059
 O73  H29A  H  HCH2   0   0.214  -5.9751   4.9212  -0.9281
 O73  HN30  H  HNH2   0   0.337  -8.5404   4.3908   0.3532
 O73  HN3A  H  HNH2   0   0.346  -8.1061   5.7419  -0.4094

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 O73  C1   C2    aromatic  1.375  0.020  1.375
 O73  C1   C6    aromatic  1.393  0.020  1.393
 O73  C1   H1    single    0.930  0.020  1.080
 O73  C2   C3    aromatic  1.401  0.020  1.401
 O73  C2   H2    single    0.930  0.020  1.080
 O73  C3   C4    aromatic  1.398  0.020  1.398
 O73  C3   O10   single    1.331  0.020  1.331
 O73  C4   C5    aromatic  1.382  0.020  1.382
 O73  C4   H4    single    0.930  0.020  1.080
 O73  C5   C6    aromatic  1.387  0.020  1.387
 O73  C5   H5    single    0.930  0.020  1.080
 O73  C6   N7    single    1.443  0.020  1.443
 O73  N7   O8    double    1.211  0.020  1.211
 O73  N7   O9    single    1.211  0.020  1.211
 O73  O10  C11   single    1.429  0.020  1.429
 O73  C11  C12   single    1.483  0.020  1.483
 O73  C11  H11   single    0.970  0.020  1.090
 O73  C11  H11A  single    0.970  0.020  1.090
 O73  C12  C13   aromatic  1.379  0.020  1.379
 O73  C12  C16   aromatic  1.416  0.020  1.416
 O73  C13  N14   aromatic  1.372  0.020  1.372
 O73  C13  C21   single    1.487  0.020  1.487
 O73  N14  C15   aromatic  1.354  0.020  1.354
 O73  N14  C22   single    1.452  0.020  1.452
 O73  C15  C16   aromatic  1.379  0.020  1.379
 O73  C15  C17   single    1.470  0.020  1.470
 O73  C16  C20   single    1.441  0.020  1.441
 O73  C17  C18   single    1.442  0.020  1.442
 O73  C17  O23   double    1.227  0.020  1.227
 O73  C18  C19   double    1.368  0.020  1.368
 O73  C18  H18   single    0.930  0.020  1.080
 O73  C19  C20   single    1.518  0.020  1.518
 O73  C19  N25   single    1.329  0.020  1.329
 O73  C20  O24   double    1.215  0.020  1.215
 O73  C21  H21   single    0.970  0.020  1.090
 O73  C21  H21A  single    0.970  0.020  1.090
 O73  C21  H21B  single    0.970  0.020  1.090
 O73  C22  H22   single    0.970  0.020  1.090
 O73  C22  H22A  single    0.970  0.020  1.090
 O73  C22  H22B  single    0.970  0.020  1.090
 O73  N25  C26   single    1.443  0.020  1.443
 O73  N25  HN25  single    0.860  0.020  1.020
 O73  C26  C27   single    1.519  0.020  1.519
 O73  C26  H26   single    0.970  0.020  1.090
 O73  C26  H26A  single    0.970  0.020  1.090
 O73  C27  C28   single    1.523  0.020  1.523
 O73  C27  H27   single    0.970  0.020  1.090
 O73  C27  H27A  single    0.970  0.020  1.090
 O73  C28  C29   single    1.521  0.020  1.521
 O73  C28  H28   single    0.970  0.020  1.090
 O73  C28  H28A  single    0.970  0.020  1.090
 O73  C29  N30   single    1.456  0.020  1.456
 O73  C29  H29   single    0.970  0.020  1.090
 O73  C29  H29A  single    0.970  0.020  1.090
 O73  N30  HN30  single    0.890  0.020  1.040
 O73  N30  HN3A  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 O73  H1    C1   C6    121.19  3.000
 O73  H1    C1   C2    119.42  3.000
 O73  C6    C1   C2    119.39  3.000
 O73  H2    C2   C3    119.39  3.000
 O73  H2    C2   C1    120.08  3.000
 O73  C3    C2   C1    120.53  3.000
 O73  O10   C3   C4    124.38  3.000
 O73  O10   C3   C2    116.13  3.000
 O73  C4    C3   C2    119.49  3.000
 O73  H4    C4   C5    118.31  3.000
 O73  H4    C4   C3    121.73  3.000
 O73  C5    C4   C3    119.95  3.000
 O73  H5    C5   C6    121.08  3.000
 O73  H5    C5   C4    119.06  3.000
 O73  C6    C5   C4    119.86  3.000
 O73  N7    C6   C5    119.59  3.000
 O73  N7    C6   C1    119.64  3.000
 O73  C5    C6   C1    120.77  3.000
 O73  O9    N7   O8    123.43  3.000
 O73  O9    N7   C6    118.33  3.000
 O73  O8    N7   C6    118.24  3.000
 O73  C11   O10  C3    119.15  3.000
 O73  H11A  C11  H11   107.67  3.000
 O73  H11A  C11  C12   110.68  3.000
 O73  H11   C11  C12   111.06  3.000
 O73  H11A  C11  O10   109.73  3.000
 O73  H11   C11  O10   110.00  3.000
 O73  C12   C11  O10   107.71  3.000
 O73  C16   C12  C13   106.43  3.000
 O73  C16   C12  C11   126.44  3.000
 O73  C13   C12  C11   127.12  3.000
 O73  C21   C13  N14   122.10  3.000
 O73  C21   C13  C12   129.53  3.000
 O73  N14   C13  C12   108.37  3.000
 O73  C22   N14  C15   125.93  3.000
 O73  C22   N14  C13   124.65  3.000
 O73  C15   N14  C13   109.42  3.000
 O73  C17   C15  C16   123.85  3.000
 O73  C17   C15  N14   128.06  3.000
 O73  C16   C15  N14   108.09  3.000
 O73  C20   C16  C15   121.26  3.000
 O73  C20   C16  C12   131.05  3.000
 O73  C15   C16  C12   107.69  3.000
 O73  O23   C17  C18   122.91  3.000
 O73  O23   C17  C15   122.03  3.000
 O73  C18   C17  C15   115.05  3.000
 O73  H18   C18  C19   120.56  3.000
 O73  H18   C18  C17   116.47  3.000
 O73  C19   C18  C17   122.97  3.000
 O73  N25   C19  C20   113.84  3.000
 O73  N25   C19  C18   124.75  3.000
 O73  C20   C19  C18   121.41  3.000
 O73  O24   C20  C19   119.79  3.000
 O73  O24   C20  C16   124.76  3.000
 O73  C19   C20  C16   115.45  3.000
 O73  H21B  C21  H21A  107.31  3.000
 O73  H21B  C21  H21   107.40  3.000
 O73  H21A  C21  H21   107.75  3.000
 O73  H21B  C21  C13   110.43  3.000
 O73  H21A  C21  C13   111.78  3.000
 O73  H21   C21  C13   111.95  3.000
 O73  H22B  C22  H22A  108.65  3.000
 O73  H22B  C22  H22   108.60  3.000
 O73  H22A  C22  H22   109.08  3.000
 O73  H22B  C22  N14   109.12  3.000
 O73  H22A  C22  N14   110.70  3.000
 O73  H22   C22  N14   110.64  3.000
 O73  HN25  N25  C26   118.72  3.000
 O73  HN25  N25  C19   117.31  3.000
 O73  C26   N25  C19   123.97  3.000
 O73  H26A  C26  H26   106.61  3.000
 O73  H26A  C26  C27   110.10  3.000
 O73  H26   C26  C27   110.08  3.000
 O73  H26A  C26  N25   109.66  3.000
 O73  H26   C26  N25   109.27  3.000
 O73  C27   C26  N25   111.01  3.000
 O73  H27A  C27  H27   106.90  3.000
 O73  H27A  C27  C28   109.68  3.000
 O73  H27   C27  C28   109.73  3.000
 O73  H27A  C27  C26   109.19  3.000
 O73  H27   C27  C26   109.41  3.000
 O73  C28   C27  C26   111.81  3.000
 O73  H28A  C28  H28   106.62  3.000
 O73  H28A  C28  C29   109.20  3.000
 O73  H28   C28  C29   109.14  3.000
 O73  H28A  C28  C27   109.38  3.000
 O73  H28   C28  C27   109.94  3.000
 O73  C29   C28  C27   112.39  3.000
 O73  H29A  C29  H29   106.19  3.000
 O73  H29A  C29  N30   108.18  3.000
 O73  H29   C29  N30   113.51  3.000
 O73  H29A  C29  C28   108.99  3.000
 O73  H29   C29  C28   108.88  3.000
 O73  N30   C29  C28   110.90  3.000
 O73  HN3A  N30  HN30  105.43  3.000
 O73  HN3A  N30  C29   109.40  3.000
 O73  HN30  N30  C29   109.21  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 O73  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 O73  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 O73  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 O73  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 O73  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 O73  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 O73  CONST_07  C15   N14  C13  C12     0.00   0.0  0
 O73  CONST_08  N14   C15  C16  C12     0.00   0.0  0
 O73  CONST_09  C15   C16  C12  C13     0.00   0.0  0
 O73  CONST_10  C16   C15  N14  C13     0.00   0.0  0
 O73  CONST_11  C16   C12  C13  N14     0.00   0.0  0
 O73  CONST_12  O10   C3   C2   C1    180.00   0.0  0
 O73  CONST_13  N7    C6   C1   C2    180.00   0.0  0
 O73  CONST_14  N7    C6   C5   C4    180.00   0.0  0
 O73  CONST_15  O10   C3   C4   C5    180.00   0.0  0
 O73  CONST_16  N14   C13  C12  C11   180.00   0.0  0
 O73  CONST_17  C15   C16  C12  C11   180.00   0.0  0
 O73  CONST_18  C20   C16  C12  C11     0.00   0.0  0
 O73  CONST_19  C22   N14  C13  C12   180.00   0.0  0
 O73  CONST_20  C21   C13  N14  C15   180.00   0.0  0
 O73  CONST_21  C21   C13  C12  C16   180.00   0.0  0
 O73  CONST_22  C22   N14  C15  C16   180.00   0.0  0
 O73  CONST_23  C22   N14  C15  C17     0.00   0.0  0
 O73  CONST_24  H5    C5   C6   C1    180.00   0.0  0
 O73  CONST_25  H4    C4   C3   C2    180.00   0.0  0
 O73  CONST_26  H1    C1   C2   C3    180.00   0.0  0
 O73  CONST_27  H2    C2   C3   C4    180.00   0.0  0
 O73  CONST_28  O8    N7   C6   C1      0.00   0.0  0
 O73  CONST_29  O9    N7   C6   C1    180.00   0.0  0
 O73  CONST_30  O8    N7   C6   C5    180.00   0.0  0
 O73  CONST_31  O9    N7   C6   C5      0.00   0.0  0
 O73  Var_01    C12   C11  O10  C3    173.03  30.0  3
 O73  Var_02    C13   C12  C11  O10   109.11  30.0  2
 O73  Var_03    C26   N25  C19  C18    -0.29  30.0  2
 O73  Var_04    H21   C21  C13  C12   119.23  30.0  2
 O73  Var_05    H22   C22  N14  C13   123.57  30.0  2
 O73  Var_06    C27   C26  N25  C19  -177.22  30.0  3
 O73  Var_07    C28   C27  C26  N25   179.37  30.0  3
 O73  Var_08    C29   C28  C27  C26  -179.02  30.0  3
 O73  Var_09    N30   C29  C28  C27  -179.63  30.0  3
 O73  Var_10    HN30  N30  C29  C28    67.80  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 O73  plan-1  C1   0.020
 O73  plan-1  C2   0.020
 O73  plan-1  C3   0.020
 O73  plan-1  C4   0.020
 O73  plan-1  C5   0.020
 O73  plan-1  C6   0.020
 O73  plan-1  N7   0.020
 O73  plan-1  O10  0.020
 O73  plan-1  H1   0.020
 O73  plan-1  H2   0.020
 O73  plan-1  H4   0.020
 O73  plan-1  H5   0.020
 O73  plan-2  C11  0.020
 O73  plan-2  C12  0.020
 O73  plan-2  C13  0.020
 O73  plan-2  N14  0.020
 O73  plan-2  C15  0.020
 O73  plan-2  C16  0.020
 O73  plan-2  C17  0.020
 O73  plan-2  C18  0.020
 O73  plan-2  C19  0.020
 O73  plan-2  C20  0.020
 O73  plan-2  C21  0.020
 O73  plan-2  C22  0.020
 O73  plan-2  O23  0.020
 O73  plan-2  O24  0.020
 O73  plan-2  N25  0.020
 O73  plan-2  H18  0.020
 O73  plan-3  C6   0.020
 O73  plan-3  N7   0.020
 O73  plan-3  O8   0.020
 O73  plan-3  O9   0.020

