# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:12:14 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 5-chloro-N-[(1S)-1-(4-fluorobenzyl)-2-(4-hydroxypiperidin-1-yl)-2-oxoethyl]-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN(CC1)C(=O)[C@H](Cc2ccc(F)cc2)NC(=O)c3[nH]c4ccc(Cl)cc4c3
#
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
 CHI  CHI  5-chloro-N-[(1S)-1-(4-fluorobenzyl)-2-(4-hydroxypiperidin-1-yl)-2-oxoethyl]-1H-indole-2-carboxamide  ligand  54  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CHI
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
 CHI  CL1   CL  CL    0  -0.140  -2.0387  -1.0090  -7.5354
 CHI  C1    C   CR6   0  -0.049  -1.6187  -0.4421  -5.9460
 CHI  C2    C   CR16  0  -0.236  -1.5937   0.9450  -5.7221
 CHI  C3    C   CR16  0  -0.307  -1.2777   1.4455  -4.4779
 CHI  C4    C   CR56  0   0.358  -0.9898   0.5305  -3.4659
 CHI  N1    N   NR15  0  -0.743  -0.6626   0.7354  -2.1608
 CHI  C5    C   CR56  0   0.062  -1.0003  -0.8633  -3.6911
 CHI  C6    C   CR16  0  -0.302  -1.3284  -1.3564  -4.9609
 CHI  C7    C   CR15  0  -0.397  -0.6399  -1.4825  -2.4620
 CHI  C8    C   CR5   0   0.221  -0.4425  -0.4768  -1.5557
 CHI  C9    C   C     0   0.536  -0.0654  -0.6343  -0.1359
 CHI  O1    O   O     0  -0.467   0.4779  -1.6568   0.2508
 CHI  N2    N   NH1   0  -0.655  -0.3705   0.4079   0.6613
 CHI  C10   C   CH1   0  -0.227   0.0284   0.4914   2.0396
 CHI  C11   C   C     0   0.574  -1.1797   0.9057   2.8828
 CHI  O2    O   O     0  -0.493  -2.1147   1.4819   2.3415
 CHI  N3    N   NT    0  -0.448  -1.1299   0.6706   4.2055
 CHI  C12   C   CH2   0  -0.347  -0.1251  -0.1248   4.8942
 CHI  C13   C   CH2   0  -0.449  -0.7216  -1.4380   5.3843
 CHI  C14   C   CH1   0   0.068  -1.9263  -1.1737   6.2744
 CHI  O3    O   OH1   0  -0.671  -2.4747  -2.4177   6.6486
 CHI  C15   C   CH2   0  -0.476  -2.9325  -0.2863   5.5473
 CHI  C16   C   CH2   0  -0.332  -2.2662   0.9940   5.0561
 CHI  C17   C   CH2   0  -0.525   1.1647   1.5243   2.2071
 CHI  C18   C   CR6   0   0.137   2.3537   1.1568   1.3689
 CHI  C19   C   CR16  0  -0.298   2.5326   1.6961   0.0991
 CHI  C20   C   CR16  0  -0.396   3.5994   1.3133  -0.7030
 CHI  C21   C   CR6   0   0.511   4.4891   0.3786  -0.2128
 CHI  F1    F   F     0  -0.318   5.5272   0.0016  -0.9792
 CHI  C22   C   CR16  0  -0.397   4.3495  -0.1780   1.0442
 CHI  C23   C   CR16  0  -0.276   3.2748   0.2175   1.8256
 CHI  H21   H   HCR6  0   0.278  -1.8268   1.6234  -6.5313
 CHI  H31   H   HCR6  0   0.276  -1.2601   2.5127  -4.3008
 CHI  HN1   H   HNR5  0   0.414  -0.4720   1.6391  -1.7589
 CHI  H61   H   HCR6  0   0.275  -1.3518  -2.4201  -5.1571
 CHI  H7    H   HCR5  0   0.264  -0.5604  -2.5386  -2.2610
 CHI  HN2   H   HNH1  0   0.398  -0.9787   1.1402   0.3275
 CHI  H101  H   HCH1  0   0.294   0.3895  -0.4961   2.3270
 CHI  H121  H   HCH2  0   0.261   0.2395   0.4595   5.7442
 CHI  H122  H   HCH2  0   0.272   0.7389  -0.3110   4.2635
 CHI  H131  H   HCH2  0   0.252   0.0424  -1.9946   5.9316
 CHI  H132  H   HCH2  0   0.233  -1.0232  -2.0458   4.5252
 CHI  H14   H   HCH1  0   0.194  -1.5747  -0.6253   7.1629
 CHI  HO3   H   HOH1  0   0.449  -3.2322  -2.2555   7.2197
 CHI  H151  H   HCH2  0   0.234  -3.3511  -0.8285   4.6940
 CHI  H152  H   HCH2  0   0.247  -3.7627  -0.0272   6.2107
 CHI  H161  H   HCH2  0   0.250  -1.9022   1.5821   5.9043
 CHI  H162  H   HCH2  0   0.273  -2.9690   1.6144   4.5086
 CHI  H171  H   HCH2  0   0.273   0.7855   2.5091   1.9229
 CHI  H172  H   HCH2  0   0.273   1.4493   1.5896   3.2595
 CHI  H191  H   HCR6  0   0.258   1.8360   2.4361  -0.2753
 CHI  H201  H   HCR6  0   0.278   3.7343   1.7373  -1.6895
 CHI  H221  H   HCR6  0   0.278   5.0645  -0.9044   1.4079
 CHI  H231  H   HCR6  0   0.259   3.1565  -0.2171   2.8115

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
 CHI  CL1  C1    single    1.739  0.020  1.739
 CHI  C1   C2    aromatic  1.405  0.020  1.405
 CHI  C1   C6    aromatic  1.375  0.020  1.375
 CHI  C2   C3    aromatic  1.378  0.020  1.378
 CHI  C2   H21   single    0.930  0.020  1.080
 CHI  C3   C4    aromatic  1.394  0.020  1.394
 CHI  C3   H31   single    0.930  0.020  1.080
 CHI  C4   N1    aromatic  1.361  0.020  1.361
 CHI  C4   C5    aromatic  1.412  0.020  1.412
 CHI  N1   C8    aromatic  1.373  0.020  1.373
 CHI  N1   HN1   single    0.860  0.020  1.020
 CHI  C5   C6    aromatic  1.401  0.020  1.401
 CHI  C5   C7    aromatic  1.423  0.020  1.423
 CHI  C6   H61   single    0.930  0.020  1.080
 CHI  C7   C8    aromatic  1.368  0.020  1.368
 CHI  C7   H7    single    0.930  0.020  1.080
 CHI  C8   C9    single    1.477  0.020  1.477
 CHI  C9   O1    double    1.221  0.020  1.221
 CHI  C9   N2    single    1.347  0.020  1.347
 CHI  N2   C10   single    1.437  0.020  1.437
 CHI  N2   HN2   single    0.860  0.020  1.020
 CHI  C10  C11   single    1.530  0.020  1.530
 CHI  C10  C17   single    1.545  0.020  1.545
 CHI  C10  H101  single    0.970  0.020  1.090
 CHI  C11  O2    double    1.224  0.020  1.224
 CHI  C11  N3    single    1.344  0.020  1.344
 CHI  N3   C12   single    1.455  0.020  1.455
 CHI  N3   C16   single    1.456  0.020  1.456
 CHI  C12  C13   single    1.523  0.020  1.523
 CHI  C12  H121  single    0.970  0.020  1.090
 CHI  C12  H122  single    0.970  0.020  1.090
 CHI  C13  C14   single    1.521  0.020  1.521
 CHI  C13  H131  single    0.970  0.020  1.090
 CHI  C13  H132  single    0.970  0.020  1.090
 CHI  C14  O3    single    1.410  0.020  1.410
 CHI  C14  C15   single    1.526  0.020  1.526
 CHI  C14  H14   single    0.970  0.020  1.090
 CHI  O3   HO3   single    0.850  0.020  0.980
 CHI  C15  C16   single    1.525  0.020  1.525
 CHI  C15  H151  single    0.970  0.020  1.090
 CHI  C15  H152  single    0.970  0.020  1.090
 CHI  C16  H161  single    0.970  0.020  1.090
 CHI  C16  H162  single    0.970  0.020  1.090
 CHI  C17  C18   single    1.500  0.020  1.500
 CHI  C17  H171  single    0.970  0.020  1.090
 CHI  C17  H172  single    0.970  0.020  1.090
 CHI  C18  C19   aromatic  1.391  0.020  1.391
 CHI  C18  C23   aromatic  1.393  0.020  1.393
 CHI  C19  C20   aromatic  1.389  0.020  1.389
 CHI  C19  H191  single    0.930  0.020  1.080
 CHI  C20  C21   aromatic  1.380  0.020  1.380
 CHI  C20  H201  single    0.930  0.020  1.080
 CHI  C21  F1    single    1.344  0.020  1.344
 CHI  C21  C22   aromatic  1.382  0.020  1.382
 CHI  C22  C23   aromatic  1.386  0.020  1.386
 CHI  C22  H221  single    0.930  0.020  1.080
 CHI  C23  H231  single    0.930  0.020  1.080

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
 CHI  C6    C1   C2    122.58  3.000
 CHI  C6    C1   CL1   119.28  3.000
 CHI  C2    C1   CL1   118.15  3.000
 CHI  H21   C2   C3    119.82  3.000
 CHI  H21   C2   C1    119.74  3.000
 CHI  C3    C2   C1    120.43  3.000
 CHI  H31   C3   C4    121.67  3.000
 CHI  H31   C3   C2    120.66  3.000
 CHI  C4    C3   C2    117.67  3.000
 CHI  C5    C4   N1    107.66  3.000
 CHI  C5    C4   C3    122.04  3.000
 CHI  N1    C4   C3    130.30  3.000
 CHI  HN1   N1   C8    125.89  3.000
 CHI  HN1   N1   C4    124.28  3.000
 CHI  C8    N1   C4    109.17  3.000
 CHI  C7    C5   C6    133.56  3.000
 CHI  C7    C5   C4    106.86  3.000
 CHI  C6    C5   C4    119.58  3.000
 CHI  H61   C6   C5    121.03  3.000
 CHI  H61   C6   C1    121.28  3.000
 CHI  C5    C6   C1    117.69  3.000
 CHI  H7    C7   C8    125.87  3.000
 CHI  H7    C7   C5    127.32  3.000
 CHI  C8    C7   C5    106.79  3.000
 CHI  C9    C8   C7    126.52  3.000
 CHI  C9    C8   N1    123.97  3.000
 CHI  C7    C8   N1    109.52  3.000
 CHI  N2    C9   O1    124.14  3.000
 CHI  N2    C9   C8    115.37  3.000
 CHI  O1    C9   C8    120.49  3.000
 CHI  HN2   N2   C10   116.26  3.000
 CHI  HN2   N2   C9    120.15  3.000
 CHI  C10   N2   C9    123.34  3.000
 CHI  H101  C10  C17   109.48  3.000
 CHI  H101  C10  C11   111.19  3.000
 CHI  C17   C10  C11   109.87  3.000
 CHI  H101  C10  N2    106.99  3.000
 CHI  C17   C10  N2    110.30  3.000
 CHI  C11   C10  N2    108.97  3.000
 CHI  N3    C11  O2    123.06  3.000
 CHI  N3    C11  C10   117.74  3.000
 CHI  O2    C11  C10   119.12  3.000
 CHI  C16   N3   C12   112.58  3.000
 CHI  C16   N3   C11   120.47  3.000
 CHI  C12   N3   C11   125.94  3.000
 CHI  H122  C12  H121  106.13  3.000
 CHI  H122  C12  C13   110.52  3.000
 CHI  H121  C12  C13   109.93  3.000
 CHI  H122  C12  N3    111.61  3.000
 CHI  H121  C12  N3    107.82  3.000
 CHI  C13   C12  N3    110.68  3.000
 CHI  H132  C13  H131  107.64  3.000
 CHI  H132  C13  C14   109.73  3.000
 CHI  H131  C13  C14   110.45  3.000
 CHI  H132  C13  C12   109.51  3.000
 CHI  H131  C13  C12   109.06  3.000
 CHI  C14   C13  C12   110.40  3.000
 CHI  H14   C14  C15   107.77  3.000
 CHI  H14   C14  O3    110.44  3.000
 CHI  C15   C14  O3    112.52  3.000
 CHI  H14   C14  C13   107.80  3.000
 CHI  C15   C14  C13   110.15  3.000
 CHI  O3    C14  C13   108.06  3.000
 CHI  HO3   O3   C14   108.35  3.000
 CHI  H152  C15  H151  107.46  3.000
 CHI  H152  C15  C16   109.16  3.000
 CHI  H151  C15  C16   109.39  3.000
 CHI  H152  C15  C14   110.45  3.000
 CHI  H151  C15  C14   109.62  3.000
 CHI  C16   C15  C14   110.71  3.000
 CHI  H162  C16  H161  107.40  3.000
 CHI  H162  C16  C15   111.07  3.000
 CHI  H161  C16  C15   110.30  3.000
 CHI  H162  C16  N3    109.72  3.000
 CHI  H161  C16  N3    108.22  3.000
 CHI  C15   C16  N3    110.05  3.000
 CHI  H172  C17  H171  106.69  3.000
 CHI  H172  C17  C18   110.27  3.000
 CHI  H171  C17  C18   110.51  3.000
 CHI  H172  C17  C10   109.64  3.000
 CHI  H171  C17  C10   108.61  3.000
 CHI  C18   C17  C10   111.01  3.000
 CHI  C23   C18  C19   118.41  3.000
 CHI  C23   C18  C17   120.41  3.000
 CHI  C19   C18  C17   121.12  3.000
 CHI  H191  C19  C20   118.87  3.000
 CHI  H191  C19  C18   119.85  3.000
 CHI  C20   C19  C18   121.28  3.000
 CHI  H201  C20  C21   120.57  3.000
 CHI  H201  C20  C19   120.95  3.000
 CHI  C21   C20  C19   118.47  3.000
 CHI  C22   C21  F1    118.92  3.000
 CHI  C22   C21  C20   122.05  3.000
 CHI  F1    C21  C20   119.03  3.000
 CHI  H221  C22  C23   120.94  3.000
 CHI  H221  C22  C21   120.62  3.000
 CHI  C23   C22  C21   118.43  3.000
 CHI  H231  C23  C22   118.88  3.000
 CHI  H231  C23  C18   119.77  3.000
 CHI  C22   C23  C18   121.36  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
 CHI  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CHI  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CHI  CONST_03  C7    C5   C6   C1    180.00   0.0  0
 CHI  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 CHI  CONST_05  N1    C4   C3   C2    180.00   0.0  0
 CHI  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 CHI  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 CHI  CONST_08  C8    N1   C4   C3    180.00   0.0  0
 CHI  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 CHI  CONST_10  C7    C5   C4   C3    180.00   0.0  0
 CHI  CONST_11  C7    C8   N1   C4      0.00   0.0  0
 CHI  CONST_12  C8    C7   C5   C4      0.00   0.0  0
 CHI  CONST_13  C6    C5   C4   N1    180.00   0.0  0
 CHI  CONST_14  C7    C5   C4   N1      0.00   0.0  0
 CHI  CONST_15  C5    C7   C8   N1      0.00   0.0  0
 CHI  CONST_16  C8    N1   C4   C5      0.00   0.0  0
 CHI  CONST_17  C8    C7   C5   C6    180.00   0.0  0
 CHI  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 CHI  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 CHI  CONST_20  C22   C23  C18  C19     0.00   0.0  0
 CHI  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 CHI  CONST_22  C23   C18  C19  C20     0.00   0.0  0
 CHI  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 CHI  CONST_24  C3    C2   C1   CL1   180.00   0.0  0
 CHI  CONST_25  C5    C6   C1   CL1   180.00   0.0  0
 CHI  CONST_26  C9    C8   N1   C4    180.00   0.0  0
 CHI  CONST_27  C9    C8   C7   C5    180.00   0.0  0
 CHI  CONST_28  C20   C19  C18  C17   180.00   0.0  0
 CHI  CONST_29  C22   C23  C18  C17   180.00   0.0  0
 CHI  CONST_30  F1    C21  C20  C19   180.00   0.0  0
 CHI  CONST_31  C23   C22  C21  F1    180.00   0.0  0
 CHI  CONST_32  H31   C3   C2   C1    180.00   0.0  0
 CHI  CONST_33  H61   C6   C1   C2    180.00   0.0  0
 CHI  CONST_34  HN1   N1   C4   C3      0.00   0.0  0
 CHI  CONST_35  H21   C2   C3   C4    180.00   0.0  0
 CHI  CONST_36  H7    C7   C5   C4    180.00   0.0  0
 CHI  CONST_37  H201  C20  C19  C18   180.00   0.0  0
 CHI  CONST_38  H221  C22  C23  C18   180.00   0.0  0
 CHI  CONST_39  H231  C23  C18  C19   180.00   0.0  0
 CHI  CONST_40  H191  C19  C20  C21   180.00   0.0  0
 CHI  CONST_41  C12   N3   C11  C10     0.00   0.0  0
 CHI  CONST_42  C16   N3   C11  C10   180.00   0.0  0
 CHI  CONST_43  C12   N3   C11  O2    180.00   0.0  0
 CHI  CONST_44  C16   N3   C11  O2      0.00   0.0  0
 CHI  CONST_45  C10   N2   C9   C8    180.00   0.0  0
 CHI  CONST_46  HN2   N2   C9   C8      0.00   0.0  0
 CHI  CONST_47  C10   N2   C9   O1      0.00   0.0  0
 CHI  Var_01    C14   C13  C12  N3    -56.17  30.0  1
 CHI  Var_02    C14   C15  C16  N3     56.36  30.0  1
 CHI  Var_03    C15   C16  N3   C12   -59.41  30.0  1
 CHI  Var_04    C16   N3   C12  C13    59.56  30.0  1
 CHI  Var_05    O1    C9   C8   N1   -159.01  30.0  2
 CHI  Var_06    C19   C18  C17  C10    94.99  30.0  2

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
 CHI  chir_01  C10  N2  C11  C17  positiv
 CHI  chir_02  C14  O3  C13  C15  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
 CHI  plan-1  C17   0.020
 CHI  plan-1  C18   0.020
 CHI  plan-1  C19   0.020
 CHI  plan-1  C20   0.020
 CHI  plan-1  C21   0.020
 CHI  plan-1  F1    0.020
 CHI  plan-1  C22   0.020
 CHI  plan-1  C23   0.020
 CHI  plan-1  H191  0.020
 CHI  plan-1  H201  0.020
 CHI  plan-1  H221  0.020
 CHI  plan-1  H231  0.020
 CHI  plan-2  CL1   0.020
 CHI  plan-2  C1    0.020
 CHI  plan-2  C2    0.020
 CHI  plan-2  C3    0.020
 CHI  plan-2  C4    0.020
 CHI  plan-2  N1    0.020
 CHI  plan-2  C5    0.020
 CHI  plan-2  C6    0.020
 CHI  plan-2  C7    0.020
 CHI  plan-2  C8    0.020
 CHI  plan-2  C9    0.020
 CHI  plan-2  H21   0.020
 CHI  plan-2  H31   0.020
 CHI  plan-2  HN1   0.020
 CHI  plan-2  H61   0.020
 CHI  plan-2  H7    0.020
 CHI  plan-3  C10   0.020
 CHI  plan-3  C11   0.020
 CHI  plan-3  O2    0.020
 CHI  plan-3  N3    0.020
 CHI  plan-3  C12   0.020
 CHI  plan-3  C16   0.020
 CHI  plan-4  C8    0.020
 CHI  plan-4  C9    0.020
 CHI  plan-4  O1    0.020
 CHI  plan-4  N2    0.020
 CHI  plan-4  C10   0.020
 CHI  plan-4  HN2   0.020

