# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 08:47:41 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cnc(N)c(O[C@H]2CN(CC2(F)F)C(=O)Cc3ccc(OC(F)(F)F)cc3)c1
#
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
 GOD  GOD  6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide  ligand  52  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOD
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
 GOD  C4    C  CR16  0  -0.103   -7.0055   1.0780  -0.9379
 GOD  C5    C  CR6   0   0.271   -4.4166   1.1619  -0.1297
 GOD  C8    C  CR6   0   0.393   -5.1524   2.3345  -0.4512
 GOD  C15   C  C     0   0.583    1.4232   0.0269   0.2820
 GOD  C20   C  CR16  0  -0.285    5.4972  -1.6055  -0.8748
 GOD  C21   C  CR6   0   0.297    6.3640  -0.8125  -0.1433
 GOD  C22   C  CR16  0  -0.284    5.9303  -0.0943   0.9568
 GOD  C1    C  CR6   0  -0.135   -6.3807  -0.1154  -0.6308
 GOD  C2    C  C     0   0.527   -7.0239  -1.4496  -0.7524
 GOD  C3    C  CR16  0  -0.274   -5.0379  -0.0527  -0.2228
 GOD  N6    N  N     0  -0.445   -6.4146   2.2648  -0.8471
 GOD  O7    O  O2    0  -0.496   -3.1327   1.3857   0.2482
 GOD  C9    C  CH1   0  -0.128   -2.1899   0.3534   0.2116
 GOD  N10   N  NH2   0  -0.821   -4.5612   3.5479  -0.3989
 GOD  C11   C  CH2   0  -0.256   -0.8125   0.9193  -0.1251
 GOD  C12   C  CT    0   0.724   -1.9415  -0.3160   1.5608
 GOD  N13   N  NT    0  -0.502    0.0987  -0.0118   0.5238
 GOD  C14   C  CH2   0  -0.378   -0.5709  -0.9435   1.4135
 GOD  C16   C  CH2   0  -0.710    2.2539  -1.0241   0.9979
 GOD  O17   O  O     0  -0.478    1.9103   0.8562  -0.4680
 GOD  C18   C  CR6   0   0.176    3.6981  -0.9547   0.6051
 GOD  C19   C  CR16  0  -0.300    4.1657  -1.6697  -0.4925
 GOD  C23   C  CR16  0  -0.304    4.5950  -0.1725   1.3241
 GOD  C25   C  CT    0   1.071    8.1255   0.1316  -1.3563
 GOD  F26   F  F     0  -0.278    9.4314  -0.0161  -1.5152
 GOD  F27   F  F     0  -0.300    7.5414   0.0058  -2.5499
 GOD  F28   F  F     0  -0.300    7.8909   1.3793  -0.9443
 GOD  F29   F  F     0  -0.325   -2.8863  -1.2196   1.9160
 GOD  F30   F  F     0  -0.334   -1.9362   0.6318   2.5355
 GOD  O31   O  O     0  -0.500   -6.3504  -2.4692  -0.8627
 GOD  N32   N  NH1   0  -0.645   -8.3650  -1.4789  -0.7404
 GOD  C33   C  CH3   0  -0.513   -9.1060  -2.7084  -0.8920
 GOD  HC4   H  HCR6  0   0.257   -8.0277   1.1023  -1.3002
 GOD  HC20  H  HCR6  0   0.279    5.8531  -2.1800  -1.7199
 GOD  HC22  H  HCR6  0   0.280    6.6225   0.5062   1.5319
 GOD  HC3   H  HCR6  0   0.278   -4.5223  -0.9722   0.0177
 GOD  HC9   H  HCH1  0   0.297   -2.4572  -0.4177  -0.5198
 GOD  H10B  H  HNH2  0   0.401   -3.7090   3.6709   0.1191
 GOD  H10A  H  HNH2  0   0.395   -5.1570   4.3559  -0.4661
 GOD  H11B  H  HCH2  0   0.277   -0.6486   0.9558  -1.2010
 GOD  H11A  H  HCH2  0   0.266   -0.6998   1.9318   0.2722
 GOD  H14B  H  HCH2  0   0.296   -0.0725  -1.0397   2.3786
 GOD  H14A  H  HCH2  0   0.285   -0.6637  -1.9398   0.9724
 GOD  H16A  H  HCH2  0   0.304    2.1461  -0.8875   2.0782
 GOD  H16B  H  HCH2  0   0.301    1.8468  -2.0154   0.7775
 GOD  HC19  H  HCR6  0   0.263    3.4850  -2.2943  -1.0572
 GOD  HC23  H  HCR6  0   0.262    4.2545   0.3817   2.1900
 GOD  HN32  H  HNH1  0   0.408   -8.8818  -0.6473  -0.5123
 GOD  H33B  H  HCH3  0   0.236   -8.9559  -3.3866  -0.0504
 GOD  H33C  H  HCH3  0   0.250  -10.1630  -2.4652  -0.9509
 GOD  H33A  H  HCH3  0   0.240   -8.8233  -3.2298  -1.8059
 GOD  O24   O  O2    0  -0.523    7.7153  -0.7904  -0.4787

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
 GOD  C33  N32   single    1.444  0.020  1.444
 GOD  N32  C2    single    1.341  0.020  1.341
 GOD  C2   O31   double    1.227  0.020  1.227
 GOD  C2   C1    single    1.486  0.020  1.486
 GOD  C4   C1    aromatic  1.382  0.020  1.382
 GOD  C4   N6    aromatic  1.329  0.020  1.329
 GOD  C1   C3    aromatic  1.405  0.020  1.405
 GOD  N6   C8    aromatic  1.325  0.020  1.325
 GOD  C3   C5    aromatic  1.368  0.020  1.368
 GOD  C8   C5    aromatic  1.421  0.020  1.421
 GOD  C8   N10   single    1.351  0.020  1.351
 GOD  C5   O7    single    1.357  0.020  1.357
 GOD  O7   C9    single    1.399  0.020  1.399
 GOD  F30  C12   single    1.360  0.020  1.360
 GOD  C9   C12   single    1.526  0.020  1.526
 GOD  C9   C11   single    1.527  0.020  1.527
 GOD  C12  F29   single    1.355  0.020  1.355
 GOD  C12  C14   single    1.515  0.020  1.515
 GOD  C11  N13   single    1.455  0.020  1.455
 GOD  C14  N13   single    1.452  0.020  1.452
 GOD  N13  C15   single    1.347  0.020  1.347
 GOD  C15  O17   double    1.220  0.020  1.220
 GOD  C15  C16   single    1.519  0.020  1.519
 GOD  C16  C18   single    1.498  0.020  1.498
 GOD  C18  C23   aromatic  1.390  0.020  1.390
 GOD  C18  C19   aromatic  1.391  0.020  1.391
 GOD  C23  C22   aromatic  1.387  0.020  1.387
 GOD  C19  C20   aromatic  1.387  0.020  1.387
 GOD  C22  C21   aromatic  1.384  0.020  1.384
 GOD  C20  C21   aromatic  1.384  0.020  1.384
 GOD  C21  O24   single    1.392  0.020  1.392
 GOD  F27  C25   single    1.335  0.020  1.335
 GOD  O24  C25   single    1.337  0.020  1.337
 GOD  C25  F28   single    1.335  0.020  1.335
 GOD  C25  F26   single    1.324  0.020  1.324
 GOD  C4   HC4   single    0.930  0.020  1.080
 GOD  C20  HC20  single    0.930  0.020  1.080
 GOD  C22  HC22  single    0.930  0.020  1.080
 GOD  C3   HC3   single    0.930  0.020  1.080
 GOD  C9   HC9   single    0.970  0.020  1.090
 GOD  N10  H10B  single    0.890  0.020  1.040
 GOD  N10  H10A  single    0.890  0.020  1.040
 GOD  C11  H11B  single    0.970  0.020  1.090
 GOD  C11  H11A  single    0.970  0.020  1.090
 GOD  C14  H14B  single    0.970  0.020  1.090
 GOD  C14  H14A  single    0.970  0.020  1.090
 GOD  C16  H16A  single    0.970  0.020  1.090
 GOD  C16  H16B  single    0.970  0.020  1.090
 GOD  C19  HC19  single    0.930  0.020  1.080
 GOD  C23  HC23  single    0.930  0.020  1.080
 GOD  N32  HN32  single    0.860  0.020  1.020
 GOD  C33  H33B  single    0.970  0.020  1.090
 GOD  C33  H33C  single    0.970  0.020  1.090
 GOD  C33  H33A  single    0.970  0.020  1.090

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
 GOD  HC4   C4   N6    114.95  3.000
 GOD  HC4   C4   C1    121.31  3.000
 GOD  N6    C4   C1    123.73  3.000
 GOD  O7    C5   C3    126.54  3.000
 GOD  O7    C5   C8    114.64  3.000
 GOD  C3    C5   C8    118.83  3.000
 GOD  N10   C8   N6    118.41  3.000
 GOD  N10   C8   C5    120.39  3.000
 GOD  N6    C8   C5    121.17  3.000
 GOD  O17   C15  C16   122.81  3.000
 GOD  C16   C15  N13   115.68  3.000
 GOD  O17   C15  N13   121.51  3.000
 GOD  HC20  C20  C19   120.44  3.000
 GOD  HC20  C20  C21   120.73  3.000
 GOD  C19   C20  C21   118.83  3.000
 GOD  O24   C21  C22   119.18  3.000
 GOD  O24   C21  C20   119.32  3.000
 GOD  C22   C21  C20   121.42  3.000
 GOD  HC22  C22  C23   120.43  3.000
 GOD  HC22  C22  C21   120.68  3.000
 GOD  C23   C22  C21   118.89  3.000
 GOD  C3    C1   C2    118.52  3.000
 GOD  C3    C1   C4    117.27  3.000
 GOD  C2    C1   C4    124.17  3.000
 GOD  N32   C2   O31   122.10  3.000
 GOD  O31   C2   C1    121.06  3.000
 GOD  N32   C2   C1    116.84  3.000
 GOD  HC3   C3   C1    118.85  3.000
 GOD  HC3   C3   C5    121.56  3.000
 GOD  C1    C3   C5    119.59  3.000
 GOD  C8    N6   C4    119.41  3.000
 GOD  C9    O7   C5    120.59  3.000
 GOD  HC9   C9   C12   108.72  3.000
 GOD  HC9   C9   C11   109.49  3.000
 GOD  C12   C9   C11   102.16  3.000
 GOD  HC9   C9   O7    111.86  3.000
 GOD  C11   C9   O7    109.90  3.000
 GOD  C12   C9   O7    114.22  3.000
 GOD  H10A  N10  H10B  116.01  3.000
 GOD  H10A  N10  C8    117.36  3.000
 GOD  H10B  N10  C8    120.07  3.000
 GOD  H11A  C11  H11B  108.21  3.000
 GOD  H11A  C11  N13   111.46  3.000
 GOD  H11B  C11  N13   111.57  3.000
 GOD  H11A  C11  C9    110.86  3.000
 GOD  H11B  C11  C9    111.48  3.000
 GOD  N13   C11  C9    103.26  3.000
 GOD  F30   C12  F29   106.25  3.000
 GOD  F29   C12  C14   112.35  3.000
 GOD  F30   C12  C14   110.80  3.000
 GOD  C14   C12  C9    104.06  3.000
 GOD  F29   C12  C9    114.25  3.000
 GOD  F30   C12  C9    109.19  3.000
 GOD  C14   N13  C11   113.26  3.000
 GOD  C14   N13  C15   125.59  3.000
 GOD  C11   N13  C15   121.15  3.000
 GOD  H14A  C14  H14B  108.39  3.000
 GOD  H14A  C14  N13   112.12  3.000
 GOD  H14B  C14  N13   112.84  3.000
 GOD  H14A  C14  C12   109.87  3.000
 GOD  H14B  C14  C12   111.35  3.000
 GOD  N13   C14  C12   102.18  3.000
 GOD  H16B  C16  H16A  105.98  3.000
 GOD  H16B  C16  C18   110.35  3.000
 GOD  H16A  C16  C18   110.37  3.000
 GOD  H16B  C16  C15   109.17  3.000
 GOD  H16A  C16  C15   108.97  3.000
 GOD  C18   C16  C15   111.81  3.000
 GOD  C23   C18  C19   118.71  3.000
 GOD  C19   C18  C16   120.48  3.000
 GOD  C23   C18  C16   120.81  3.000
 GOD  HC19  C19  C18   119.78  3.000
 GOD  HC19  C19  C20   119.11  3.000
 GOD  C18   C19  C20   121.11  3.000
 GOD  HC23  C23  C18   119.91  3.000
 GOD  HC23  C23  C22   119.04  3.000
 GOD  C18   C23  C22   121.05  3.000
 GOD  F28   C25  F27   106.69  3.000
 GOD  F28   C25  F26   108.34  3.000
 GOD  F27   C25  F26   108.29  3.000
 GOD  F26   C25  O24   107.72  3.000
 GOD  F28   C25  O24   112.83  3.000
 GOD  F27   C25  O24   112.81  3.000
 GOD  HN32  N32  C33   117.68  3.000
 GOD  HN32  N32  C2    119.86  3.000
 GOD  C33   N32  C2    122.06  3.000
 GOD  H33A  C33  H33C  108.31  3.000
 GOD  H33A  C33  H33B  108.29  3.000
 GOD  H33C  C33  H33B  108.35  3.000
 GOD  H33A  C33  N32   111.25  3.000
 GOD  H33C  C33  N32   108.33  3.000
 GOD  H33B  C33  N32   112.19  3.000
 GOD  C25   O24  C21   117.82  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
 GOD  CONST_01  C5    C3   C1   C4     0.00   0.0  0
 GOD  CONST_02  C5    C8   N6   C4     0.00   0.0  0
 GOD  CONST_03  C1    C4   N6   C8     0.00   0.0  0
 GOD  CONST_04  C1    C3   C5   C8     0.00   0.0  0
 GOD  CONST_05  C23   C18  C19  C20    0.00   0.0  0
 GOD  CONST_06  C23   C22  C21  C20    0.00   0.0  0
 GOD  CONST_07  C18   C23  C22  C21    0.00   0.0  0
 GOD  CONST_08  C18   C19  C20  C21    0.00   0.0  0
 GOD  CONST_09  C19   C18  C23  C22    0.00   0.0  0
 GOD  CONST_10  C19   C20  C21  C22    0.00   0.0  0
 GOD  CONST_11  N6    C4   C1   C3     0.00   0.0  0
 GOD  CONST_12  N6    C8   C5   C3     0.00   0.0  0
 GOD  CONST_13  N10   C8   N6   C4   180.00   0.0  0
 GOD  CONST_14  C2    C1   C3   C5   180.00   0.0  0
 GOD  CONST_15  C16   C18  C19  C20  180.00   0.0  0
 GOD  CONST_16  C16   C18  C23  C22  180.00   0.0  0
 GOD  CONST_17  O7    C5   C3   C1   180.00   0.0  0
 GOD  CONST_18  N6    C4   C1   C2   180.00   0.0  0
 GOD  CONST_19  N10   C8   C5   C3   180.00   0.0  0
 GOD  CONST_20  O7    C5   C8   N6   180.00   0.0  0
 GOD  CONST_21  O24   C21  C20  C19  180.00   0.0  0
 GOD  CONST_22  O24   C21  C22  C23  180.00   0.0  0
 GOD  CONST_23  HC3   C3   C1   C4   180.00   0.0  0
 GOD  CONST_24  HC4   C4   N6   C8   180.00   0.0  0
 GOD  CONST_25  HC22  C22  C21  C20  180.00   0.0  0
 GOD  CONST_26  HC23  C23  C22  C21  180.00   0.0  0
 GOD  CONST_27  HC19  C19  C20  C21  180.00   0.0  0
 GOD  CONST_28  HC20  C20  C21  C22  180.00   0.0  0
 GOD  CONST_29  O17   C15  N13  C11    0.00   0.0  0
 GOD  CONST_30  C16   C15  N13  C11  180.00   0.0  0
 GOD  CONST_31  O17   C15  N13  C14  180.00   0.0  0
 GOD  CONST_32  C16   C15  N13  C14    0.00   0.0  0
 GOD  CONST_34  H10A  N10  C8   C5   180.00   0.0  0
 GOD  CONST_35  C33   N32  C2   C1   180.00   0.0  0
 GOD  CONST_36  HN32  N32  C2   C1     0.00   0.0  0
 GOD  CONST_37  C33   N32  C2   O31    0.00   0.0  0
 GOD  Var_01    N13   C14  C12  C9    32.55  30.0  1
 GOD  Var_02    C14   N13  C11  C9   -10.33  30.0  1
 GOD  Var_03    C12   C14  N13  C11  -13.92  30.0  1
 GOD  Var_04    N32   C2   C1   C4   -21.94  30.0  2
 GOD  Var_05    C23   C18  C16  C15   91.22  30.0  2
 GOD  Var_06    C18   C16  C15  N13  176.58  30.0  3
 GOD  Var_07    F27   C25  O24  C21  -61.29  30.0  3
 GOD  Var_08    H33B  C33  N32  C2    66.13  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
 GOD  chir_01  C9  O7  C12  C11  positiv

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
 GOD  plan-1  C4    0.020
 GOD  plan-1  C5    0.020
 GOD  plan-1  C8    0.020
 GOD  plan-1  C1    0.020
 GOD  plan-1  C2    0.020
 GOD  plan-1  C3    0.020
 GOD  plan-1  N6    0.020
 GOD  plan-1  O7    0.020
 GOD  plan-1  N10   0.020
 GOD  plan-1  HC4   0.020
 GOD  plan-1  HC3   0.020
 GOD  plan-2  C20   0.020
 GOD  plan-2  C21   0.020
 GOD  plan-2  C22   0.020
 GOD  plan-2  C16   0.020
 GOD  plan-2  C18   0.020
 GOD  plan-2  C19   0.020
 GOD  plan-2  C23   0.020
 GOD  plan-2  HC20  0.020
 GOD  plan-2  HC22  0.020
 GOD  plan-2  HC19  0.020
 GOD  plan-2  HC23  0.020
 GOD  plan-2  O24   0.020
 GOD  plan-3  C1    0.020
 GOD  plan-3  C2    0.020
 GOD  plan-3  O31   0.020
 GOD  plan-3  N32   0.020
 GOD  plan-3  C33   0.020
 GOD  plan-3  HN32  0.020
 GOD  plan-4  C8    0.020
 GOD  plan-4  N10   0.020
 GOD  plan-4  H10B  0.020
 GOD  plan-4  H10A  0.020
 GOD  plan-5  C15   0.020
 GOD  plan-5  C11   0.020
 GOD  plan-5  N13   0.020
 GOD  plan-5  C14   0.020
 GOD  plan-5  C16   0.020
 GOD  plan-5  O17   0.020

