# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:14:59 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 3-(5-{[4-(aminomethyl)piperidin-1-yl]methyl}-1H-indol-2-yl)quinolin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(CC1)Cc2ccc3[nH]c(cc3c2)C4=Cc5ccccc5NC4=O
#
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
 373  373  3-(5-{[4-(aminomethyl)piperidin-1-yl]methyl}-1H-indol-2-yl)quinolin-2(1H)-one  ligand  55  29  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_373
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
 373  C1    C  CR66  0   0.063  -2.5683  -10.2019   4.1694
 373  C2    C  CR16  0  -0.321  -1.7700  -11.3548   4.2095
 373  C3    C  CR16  0  -0.261  -2.3476  -12.6035   4.2492
 373  C4    C  CR16  0  -0.258  -3.7424  -12.7235   4.2517
 373  C5    C  CR16  0  -0.311  -4.5497  -11.6060   4.2159
 373  C6    C  CR66  0   0.382  -3.9624  -10.3392   4.1746
 373  N11   N  NR16  0  -0.751  -4.7240   -9.2023   4.1400
 373  C12   C  CR6   0   0.512  -4.2677   -7.9130   4.0957
 373  C13   C  CR6   0  -0.192  -2.8061   -7.7694   4.0762
 373  C14   C  CR16  0  -0.223  -2.0280   -8.8840   4.1250
 373  C16   C  CR5   0   0.384  -2.2290   -6.4360   3.9951
 373  N17   N  NR15  0  -0.762  -0.9215   -6.2708   3.5961
 373  C18   C  CR56  0   0.334  -0.5931   -4.9485   3.6201
 373  C19   C  CR56  0   0.104  -1.7259   -4.2383   4.0723
 373  C20   C  CR15  0  -0.450  -2.7523   -5.2006   4.2984
 373  C24   C  CR16  0  -0.302   0.5886   -4.3007   3.2721
 373  C25   C  CR16  0  -0.333   0.6149   -2.9238   3.3894
 373  C26   C  CR6   0   0.069  -0.4932   -2.1870   3.8471
 373  C27   C  CR16  0  -0.385  -1.6608   -2.8455   4.1883
 373  C31   C  CH2   0  -0.318  -0.3990   -0.6858   3.9689
 373  N32   N  NT    0  -0.410  -1.5517   -0.0066   3.4138
 373  C35   C  CH2   0  -0.271  -1.6313   -0.1739   1.9739
 373  C36   C  CH2   0  -0.427  -2.8997    0.4464   1.4125
 373  C37   C  CH1   0  -0.257  -2.9980    1.9257   1.7692
 373  C38   C  CH2   0  -0.424  -2.8337    2.0807   3.2780
 373  C39   C  CH2   0  -0.276  -1.5681    1.3991   3.7750
 373  C48   C  CH2   0  -0.276  -4.2999    2.5664   1.2867
 373  N50   N  NH2   0  -0.795  -4.5458    2.5433  -0.1468
 373  O1    O  OC    0  -0.468  -5.0599   -6.9817   4.0713
 373  H2    H  HCR6  0   0.265  -0.6924  -11.2467   4.2067
 373  H3    H  HCR6  0   0.264  -1.7277  -13.4890   4.2782
 373  H4    H  HCR6  0   0.269  -4.1971  -13.7049   4.2825
 373  H5    H  HCR6  0   0.279  -5.6282  -11.7026   4.2186
 373  HN11  H  HNR6  0   0.418  -5.7306   -9.3077   4.1470
 373  H14   H  HCR6  0   0.270  -0.9476   -8.7989   4.1437
 373  HN17  H  HNR5  0   0.412  -0.3315   -6.9951   3.2218
 373  H20   H  HCR5  0   0.251  -3.7456   -4.9998   4.6586
 373  H24   H  HCR6  0   0.257   1.4512   -4.8466   2.9118
 373  H25   H  HCR6  0   0.244   1.5159   -2.3906   3.1096
 373  H27   H  HCR6  0   0.234  -2.5231   -2.2810   4.5229
 373  H311  H  HCH2  0   0.242  -0.3279   -0.4117   5.0268
 373  H312  H  HCH2  0   0.204   0.5421   -0.3432   3.5038
 373  H351  H  HCH2  0   0.239  -1.6096   -1.2396   1.7393
 373  H352  H  HCH2  0   0.181  -0.7532    0.2778   1.4748
 373  H361  H  HCH2  0   0.222  -2.9087    0.3038   0.3292
 373  H362  H  HCH2  0   0.211  -3.7700   -0.0847   1.8152
 373  H37   H  HCH1  0   0.206  -2.1609    2.4467   1.2824
 373  H381  H  HCH2  0   0.211  -3.7007    1.6433   3.7859
 373  H382  H  HCH2  0   0.227  -2.8032    3.1383   3.5541
 373  H391  H  HCH2  0   0.181  -0.6879    1.9303   3.3676
 373  H392  H  HCH2  0   0.231  -1.5049    1.4802   4.8636
 373  H481  H  HCH2  0   0.217  -4.3219    3.6096   1.6177
 373  H482  H  HCH2  0   0.208  -5.1421    2.0737   1.7842
 373  H501  H  HNH2  0   0.343  -4.6147    1.5866  -0.4700
 373  H502  H  HNH2  0   0.338  -3.7496    2.9395  -0.6323

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
 373  C1   C6    aromatic  1.401  0.020  1.401
 373  C1   C14   aromatic  1.425  0.020  1.425
 373  C1   C2    aromatic  1.403  0.020  1.403
 373  C2   C3    aromatic  1.376  0.020  1.376
 373  C2   H2    single    0.930  0.020  1.080
 373  C3   C4    aromatic  1.400  0.020  1.400
 373  C3   H3    single    0.930  0.020  1.080
 373  C4   C5    aromatic  1.379  0.020  1.379
 373  C4   H4    single    0.930  0.020  1.080
 373  C5   C6    aromatic  1.397  0.020  1.397
 373  C5   H5    single    0.930  0.020  1.080
 373  C6   N11   aromatic  1.369  0.020  1.369
 373  N11  C12   aromatic  1.368  0.020  1.368
 373  N11  HN11  single    0.860  0.020  1.020
 373  C12  O1    double    1.223  0.020  1.223
 373  C12  C13   aromatic  1.469  0.020  1.469
 373  C13  C16   single    1.455  0.020  1.455
 373  C13  C14   aromatic  1.360  0.020  1.360
 373  C14  H14   single    0.930  0.020  1.080
 373  C16  N17   aromatic  1.377  0.020  1.377
 373  C16  C20   aromatic  1.376  0.020  1.376
 373  N17  C18   aromatic  1.363  0.020  1.363
 373  N17  HN17  single    0.860  0.020  1.020
 373  C18  C24   aromatic  1.392  0.020  1.392
 373  C18  C19   aromatic  1.411  0.020  1.411
 373  C19  C27   aromatic  1.399  0.020  1.399
 373  C19  C20   aromatic  1.425  0.020  1.425
 373  C20  H20   single    0.930  0.020  1.080
 373  C24  C25   aromatic  1.382  0.020  1.382
 373  C24  H24   single    0.930  0.020  1.080
 373  C25  C26   aromatic  1.407  0.020  1.407
 373  C25  H25   single    0.930  0.020  1.080
 373  C26  C31   single    1.509  0.020  1.509
 373  C26  C27   aromatic  1.383  0.020  1.383
 373  C27  H27   single    0.930  0.020  1.080
 373  C31  N32   single    1.449  0.020  1.449
 373  C31  H311  single    0.970  0.020  1.090
 373  C31  H312  single    0.970  0.020  1.090
 373  N32  C35   single    1.452  0.020  1.452
 373  N32  C39   single    1.451  0.020  1.451
 373  C35  C36   single    1.519  0.020  1.519
 373  C35  H351  single    0.970  0.020  1.090
 373  C35  H352  single    0.970  0.020  1.090
 373  C36  C37   single    1.525  0.020  1.525
 373  C36  H361  single    0.970  0.020  1.090
 373  C36  H362  single    0.970  0.020  1.090
 373  C37  C48   single    1.529  0.020  1.529
 373  C37  C38   single    1.526  0.020  1.526
 373  C37  H37   single    0.970  0.020  1.090
 373  C38  C39   single    1.521  0.020  1.521
 373  C38  H381  single    0.970  0.020  1.090
 373  C38  H382  single    0.970  0.020  1.090
 373  C39  H391  single    0.970  0.020  1.090
 373  C39  H392  single    0.970  0.020  1.090
 373  C48  N50   single    1.455  0.020  1.455
 373  C48  H481  single    0.970  0.020  1.090
 373  C48  H482  single    0.970  0.020  1.090
 373  N50  H501  single    0.890  0.020  1.040
 373  N50  H502  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
 373  C14   C1   C6    117.91  3.000
 373  C14   C1   C2    123.04  3.000
 373  C6    C1   C2    119.05  3.000
 373  H2    C2   C3    120.54  3.000
 373  H2    C2   C1    118.95  3.000
 373  C3    C2   C1    120.50  3.000
 373  H3    C3   C4    120.07  3.000
 373  H3    C3   C2    120.21  3.000
 373  C4    C3   C2    119.73  3.000
 373  H4    C4   C5    119.32  3.000
 373  H4    C4   C3    119.76  3.000
 373  C5    C4   C3    120.92  3.000
 373  H5    C5   C6    119.98  3.000
 373  H5    C5   C4    120.71  3.000
 373  C6    C5   C4    119.31  3.000
 373  N11   C6   C5    121.33  3.000
 373  N11   C6   C1    118.18  3.000
 373  C5    C6   C1    120.49  3.000
 373  HN11  N11  C12   115.46  3.000
 373  HN11  N11  C6    117.82  3.000
 373  C12   N11  C6    126.72  3.000
 373  O1    C12  C13   124.75  3.000
 373  C13   C12  N11   115.11  3.000
 373  O1    C12  N11   120.14  3.000
 373  C16   C13  C14   121.74  3.000
 373  C14   C13  C12   119.25  3.000
 373  C16   C13  C12   119.01  3.000
 373  H14   C14  C13   120.43  3.000
 373  H14   C14  C1    116.74  3.000
 373  C13   C14  C1    122.83  3.000
 373  C20   C16  N17   108.50  3.000
 373  C20   C16  C13   131.29  3.000
 373  N17   C16  C13   120.18  3.000
 373  HN17  N17  C18   124.31  3.000
 373  HN17  N17  C16   125.32  3.000
 373  C18   N17  C16   109.89  3.000
 373  C24   C18  C19   121.83  3.000
 373  C19   C18  N17   107.49  3.000
 373  C24   C18  N17   130.68  3.000
 373  C27   C19  C20   133.83  3.000
 373  C20   C19  C18   106.81  3.000
 373  C27   C19  C18   119.35  3.000
 373  H20   C20  C19   126.32  3.000
 373  H20   C20  C16   126.36  3.000
 373  C19   C20  C16   107.31  3.000
 373  H24   C24  C25   121.03  3.000
 373  H24   C24  C18   121.67  3.000
 373  C25   C24  C18   117.29  3.000
 373  H25   C25  C26   118.75  3.000
 373  H25   C25  C24   118.95  3.000
 373  C26   C25  C24   122.29  3.000
 373  C31   C26  C27   120.42  3.000
 373  C27   C26  C25   119.71  3.000
 373  C31   C26  C25   119.87  3.000
 373  H27   C27  C26   120.00  3.000
 373  H27   C27  C19   120.47  3.000
 373  C26   C27  C19   119.52  3.000
 373  H312  C31  H311  105.89  3.000
 373  H312  C31  N32   111.80  3.000
 373  H311  C31  N32   107.73  3.000
 373  H312  C31  C26   109.14  3.000
 373  H311  C31  C26   109.33  3.000
 373  N32   C31  C26   112.69  3.000
 373  C39   N32  C35   110.97  3.000
 373  C39   N32  C31   111.57  3.000
 373  C35   N32  C31   111.69  3.000
 373  H352  C35  H351  106.62  3.000
 373  H352  C35  C36   109.22  3.000
 373  H351  C35  C36   109.62  3.000
 373  H352  C35  N32   110.91  3.000
 373  H351  C35  N32   108.94  3.000
 373  C36   C35  N32   111.41  3.000
 373  H362  C36  H361  107.12  3.000
 373  H362  C36  C37   109.44  3.000
 373  H361  C36  C37   110.98  3.000
 373  H362  C36  C35   109.22  3.000
 373  H361  C36  C35   108.66  3.000
 373  C37   C36  C35   111.32  3.000
 373  H37   C37  C48   108.05  3.000
 373  H37   C37  C38   107.92  3.000
 373  C48   C37  C38   111.18  3.000
 373  H37   C37  C36   107.88  3.000
 373  C38   C37  C36   108.84  3.000
 373  C48   C37  C36   112.81  3.000
 373  H382  C38  H381  106.92  3.000
 373  H382  C38  C39   109.13  3.000
 373  H381  C38  C39   109.15  3.000
 373  H382  C38  C37   110.55  3.000
 373  H381  C38  C37   109.42  3.000
 373  C39   C38  C37   111.55  3.000
 373  H392  C39  H391  106.57  3.000
 373  H392  C39  C38   109.89  3.000
 373  H391  C39  C38   109.07  3.000
 373  H392  C39  N32   108.60  3.000
 373  H391  C39  N32   111.38  3.000
 373  C38   C39  N32   111.22  3.000
 373  H482  C48  H481  106.02  3.000
 373  H482  C48  N50   108.09  3.000
 373  H481  C48  N50   108.04  3.000
 373  H482  C48  C37   108.84  3.000
 373  H481  C48  C37   108.72  3.000
 373  N50   C48  C37   116.63  3.000
 373  H502  N50  H501  105.67  3.000
 373  H502  N50  C48   109.46  3.000
 373  H501  N50  C48   109.96  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
 373  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 373  CONST_02  C12   N11  C6   C1     0.00   0.0  0
 373  CONST_03  C12   C13  C14  C1     0.00   0.0  0
 373  CONST_04  C16   C13  C14  C1   180.00   0.0  0
 373  CONST_05  C4    C3   C2   C1     0.00   0.0  0
 373  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 373  CONST_07  N11   C6   C1   C2   180.00   0.0  0
 373  CONST_08  C13   C14  C1   C2   180.00   0.0  0
 373  CONST_09  C5    C4   C3   C2     0.00   0.0  0
 373  CONST_10  C6    C1   C2   C3     0.00   0.0  0
 373  CONST_11  C14   C1   C2   C3   180.00   0.0  0
 373  CONST_12  C6    C5   C4   C3     0.00   0.0  0
 373  CONST_13  N11   C6   C5   C4   180.00   0.0  0
 373  CONST_14  C14   C1   C6   C5   180.00   0.0  0
 373  CONST_15  C12   N11  C6   C5   180.00   0.0  0
 373  CONST_16  C13   C14  C1   C6     0.00   0.0  0
 373  CONST_17  C13   C12  N11  C6     0.00   0.0  0
 373  CONST_18  C14   C1   C6   N11    0.00   0.0  0
 373  CONST_19  C16   C13  C12  N11  180.00   0.0  0
 373  CONST_20  C14   C13  C12  N11    0.00   0.0  0
 373  CONST_23  C18   N17  C16  C13  180.00   0.0  0
 373  CONST_24  C19   C20  C16  C13  180.00   0.0  0
 373  CONST_27  C24   C18  N17  C16  180.00   0.0  0
 373  CONST_28  C19   C18  N17  C16    0.00   0.0  0
 373  CONST_29  C18   C19  C20  C16    0.00   0.0  0
 373  CONST_30  C27   C19  C20  C16  180.00   0.0  0
 373  CONST_31  C19   C20  C16  N17    0.00   0.0  0
 373  CONST_32  C25   C24  C18  N17  180.00   0.0  0
 373  CONST_33  C27   C19  C18  N17  180.00   0.0  0
 373  CONST_34  C20   C19  C18  N17    0.00   0.0  0
 373  CONST_35  C20   C16  N17  C18    0.00   0.0  0
 373  CONST_36  C26   C25  C24  C18    0.00   0.0  0
 373  CONST_37  C26   C27  C19  C18    0.00   0.0  0
 373  CONST_38  C25   C24  C18  C19    0.00   0.0  0
 373  CONST_39  C25   C26  C27  C19    0.00   0.0  0
 373  CONST_40  C24   C18  C19  C20  180.00   0.0  0
 373  CONST_41  C26   C27  C19  C20  180.00   0.0  0
 373  CONST_42  C27   C19  C18  C24    0.00   0.0  0
 373  CONST_43  C27   C26  C25  C24    0.00   0.0  0
 373  CONST_44  O1    C12  N11  C6   180.00   0.0  0
 373  CONST_45  O1    C12  C13  C14  180.00   0.0  0
 373  CONST_46  O1    C12  C13  C16    0.00   0.0  0
 373  CONST_47  C31   C26  C27  C19  180.00   0.0  0
 373  CONST_48  C31   C26  C25  C24  180.00   0.0  0
 373  CONST_49  H5    C5   C6   C1   180.00   0.0  0
 373  CONST_50  HN11  N11  C6   C1   180.00   0.0  0
 373  CONST_51  H3    C3   C2   C1   180.00   0.0  0
 373  CONST_52  H14   C14  C1   C2     0.00   0.0  0
 373  CONST_53  H4    C4   C3   C2   180.00   0.0  0
 373  CONST_54  H2    C2   C3   C4   180.00   0.0  0
 373  CONST_55  HN17  N17  C16  C13    0.00   0.0  0
 373  CONST_56  H20   C20  C16  C13    0.00   0.0  0
 373  CONST_57  H24   C24  C18  N17    0.00   0.0  0
 373  CONST_58  H25   C25  C24  C18  180.00   0.0  0
 373  CONST_59  H27   C27  C19  C18  180.00   0.0  0
 373  Var_01    C37   C36  C35  N32   56.95  30.0  1
 373  Var_02    C37   C38  C39  N32  -56.67  30.0  1
 373  Var_03    C38   C39  N32  C35   59.05  30.0  1
 373  Var_04    C39   N32  C35  C36  -59.32  30.0  1
 373  Var_05    N32   C31  C26  C25  133.96  30.0  2
 373  Var_06    C35   N32  C31  C26  -66.58  30.0  3
 373  Var_07    H501  N50  C48  C37   62.33  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 373  chir_01  C37  C36  C48  C38  negativ

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
 373  plan-1  C13   0.020
 373  plan-1  C16   0.020
 373  plan-1  N17   0.020
 373  plan-1  C18   0.020
 373  plan-1  C19   0.020
 373  plan-1  C20   0.020
 373  plan-1  C24   0.020
 373  plan-1  C25   0.020
 373  plan-1  C26   0.020
 373  plan-1  C27   0.020
 373  plan-1  C31   0.020
 373  plan-1  HN17  0.020
 373  plan-1  H20   0.020
 373  plan-1  H24   0.020
 373  plan-1  H25   0.020
 373  plan-1  H27   0.020
 373  plan-2  C1    0.020
 373  plan-2  C2    0.020
 373  plan-2  C3    0.020
 373  plan-2  C4    0.020
 373  plan-2  C5    0.020
 373  plan-2  C6    0.020
 373  plan-2  N11   0.020
 373  plan-2  C12   0.020
 373  plan-2  C13   0.020
 373  plan-2  C14   0.020
 373  plan-2  C16   0.020
 373  plan-2  O1    0.020
 373  plan-2  H2    0.020
 373  plan-2  H3    0.020
 373  plan-2  H4    0.020
 373  plan-2  H5    0.020
 373  plan-2  HN11  0.020
 373  plan-2  H14   0.020

