# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:59:50 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-(4-fluorophenyl)-N-[3-(piperidin-4-yl)-1H-indol-5-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CC(=O)Nc2ccc3[nH]cc(C4CCNCC4)c3c2)cc1
#
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
 7AH  7AH  2-(4-fluorophenyl)-N-[3-(piperidin-4-yl)-1H-indol-5-yl]acetamide  ligand  48  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7AH
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
 7AH  O     O  O     0  -0.464   2.5520  -0.6169   0.8301
 7AH  C5    C  C     0   0.543   2.1859   0.1788  -0.0150
 7AH  C4    C  CH2   0  -0.696   3.0504   1.3467  -0.4649
 7AH  C3    C  CR6   0   0.142   4.5132   1.0795  -0.2791
 7AH  C2    C  CR16  0  -0.277   5.2428   0.4273  -1.2692
 7AH  C1    C  CR16  0  -0.398   6.5952   0.1608  -1.1096
 7AH  C19   C  CR16  0  -0.290   5.1687   1.4593   0.8872
 7AH  C20   C  CR16  0  -0.399   6.5214   1.2058   1.0678
 7AH  C     C  CR6   0   0.511   7.2107   0.5584   0.0616
 7AH  F     F  F     0  -0.318   8.5222   0.3130   0.2245
 7AH  N     N  NH1   0  -0.740   0.9781   0.1357  -0.6239
 7AH  C6    C  CR6   0   0.350  -0.0860  -0.7398  -0.3203
 7AH  C18   C  CR16  0  -0.471  -1.3705  -0.2258  -0.3033
 7AH  C17   C  CR56  0   0.025  -2.4477  -1.0844  -0.0624
 7AH  C9    C  CR56  0   0.352  -2.1949  -2.4516   0.1816
 7AH  C8    C  CR16  0  -0.302  -0.9031  -2.9721   0.1656
 7AH  C7    C  CR16  0  -0.318   0.1438  -2.1112  -0.0941
 7AH  C11   C  CR5   0   0.070  -3.8666  -0.8937  -0.0009
 7AH  C10   C  CR15  0  -0.095  -4.3948  -2.1255   0.2755
 7AH  N1    N  NR15  0  -0.691  -3.3989  -3.0552   0.3894
 7AH  C12   C  CH1   0  -0.359  -4.6017   0.3981  -0.1740
 7AH  C16   C  CH2   0  -0.407  -5.8876   0.2484  -0.9892
 7AH  C15   C  CH2   0  -0.296  -6.5957   1.5881  -1.1247
 7AH  N2    N  NH1   0  -0.596  -6.8903   2.1304   0.1900
 7AH  C14   C  CH2   0  -0.296  -5.6770   2.3751   0.9504
 7AH  C13   C  CH2   0  -0.403  -4.9241   1.0704   1.1668
 7AH  H41C  H  HCH2  0   0.284   2.8345   1.5961  -1.5061
 7AH  H42C  H  HCH2  0   0.303   2.7445   2.2162   0.1252
 7AH  H     H  HNH1  0   0.410   0.7577   0.8955  -1.2497
 7AH  H2    H  HCR6  0   0.262   4.7530   0.1215  -2.1858
 7AH  H19   H  HCR6  0   0.262   4.6219   1.9709   1.6695
 7AH  H1    H  HCR6  0   0.279   7.1580  -0.3438  -1.8841
 7AH  H20   H  HCR6  0   0.279   7.0283   1.5113   1.9737
 7AH  H18   H  HCR6  0   0.251  -1.5321   0.8319  -0.4806
 7AH  H7    H  HCR6  0   0.260   1.1487  -2.5031  -0.1373
 7AH  H8    H  HCR6  0   0.261  -0.7179  -4.0249   0.3358
 7AH  HA    H  HNR5  0   0.407  -3.5446  -4.0361   0.5571
 7AH  H10   H  HCR5  0   0.278  -5.4246  -2.4197   0.4046
 7AH  H12   H  HCH1  0   0.222  -3.9492   1.0847  -0.7300
 7AH  H161  H  HCH2  0   0.231  -5.6609  -0.1533  -1.9796
 7AH  H162  H  HCH2  0   0.213  -6.5606  -0.4620  -0.4990
 7AH  H131  H  HCH2  0   0.213  -5.5336   0.3916   1.7720
 7AH  H132  H  HCH2  0   0.229  -4.0035   1.2629   1.7235
 7AH  H151  H  HCH2  0   0.184  -5.9578   2.2619  -1.7223
 7AH  H152  H  HCH2  0   0.230  -7.5312   1.4651  -1.6748
 7AH  HB    H  HNH1  0   0.350  -7.4012   2.9974   0.0873
 7AH  H141  H  HCH2  0   0.184  -5.0028   3.0895   0.4465
 7AH  H142  H  HCH2  0   0.230  -5.9453   2.8175   1.9123

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
 7AH  O    C5    double    1.217  0.020  1.217
 7AH  C5   C4    single    1.521  0.020  1.521
 7AH  C5   N     single    1.353  0.020  1.353
 7AH  C4   C3    single    1.499  0.020  1.499
 7AH  C3   C2    aromatic  1.392  0.020  1.392
 7AH  C3   C19   aromatic  1.391  0.020  1.391
 7AH  C2   C1    aromatic  1.388  0.020  1.388
 7AH  C1   C     aromatic  1.382  0.020  1.382
 7AH  C19  C20   aromatic  1.388  0.020  1.388
 7AH  C20  C     aromatic  1.381  0.020  1.381
 7AH  C    F     single    1.344  0.020  1.344
 7AH  N    C6    single    1.411  0.020  1.411
 7AH  C6   C18   aromatic  1.384  0.020  1.384
 7AH  C6   C7    aromatic  1.409  0.020  1.409
 7AH  C18  C17   aromatic  1.398  0.020  1.398
 7AH  C17  C9    aromatic  1.412  0.020  1.412
 7AH  C17  C11   aromatic  1.433  0.020  1.433
 7AH  C9   C8    aromatic  1.393  0.020  1.393
 7AH  C9   N1    aromatic  1.363  0.020  1.363
 7AH  C8   C7    aromatic  1.380  0.020  1.380
 7AH  C11  C10   aromatic  1.369  0.020  1.369
 7AH  C11  C12   single    1.496  0.020  1.496
 7AH  C10  N1    aromatic  1.367  0.020  1.367
 7AH  C12  C16   single    1.530  0.020  1.530
 7AH  C12  C13   single    1.534  0.020  1.534
 7AH  C16  C15   single    1.521  0.020  1.521
 7AH  C15  N2    single    1.452  0.020  1.452
 7AH  N2   C14   single    1.453  0.020  1.453
 7AH  C14  C13   single    1.522  0.020  1.522
 7AH  C4   H41C  single    0.970  0.020  1.090
 7AH  C4   H42C  single    0.970  0.020  1.090
 7AH  N    H     single    0.860  0.020  1.020
 7AH  C2   H2    single    0.930  0.020  1.080
 7AH  C19  H19   single    0.930  0.020  1.080
 7AH  C1   H1    single    0.930  0.020  1.080
 7AH  C20  H20   single    0.930  0.020  1.080
 7AH  C18  H18   single    0.930  0.020  1.080
 7AH  C7   H7    single    0.930  0.020  1.080
 7AH  C8   H8    single    0.930  0.020  1.080
 7AH  N1   HA    single    0.860  0.020  1.020
 7AH  C10  H10   single    0.930  0.020  1.080
 7AH  C12  H12   single    0.970  0.020  1.090
 7AH  C16  H161  single    0.970  0.020  1.090
 7AH  C16  H162  single    0.970  0.020  1.090
 7AH  C13  H131  single    0.970  0.020  1.090
 7AH  C13  H132  single    0.970  0.020  1.090
 7AH  C15  H151  single    0.970  0.020  1.090
 7AH  C15  H152  single    0.970  0.020  1.090
 7AH  N2   HB    single    0.890  0.020  1.040
 7AH  C14  H141  single    0.970  0.020  1.090
 7AH  C14  H142  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
 7AH  N     C5   C4    113.49  3.000
 7AH  N     C5   O     124.06  3.000
 7AH  C4    C5   O     122.44  3.000
 7AH  H42C  C4   H41C  106.10  3.000
 7AH  H42C  C4   C3    110.34  3.000
 7AH  H41C  C4   C3    110.60  3.000
 7AH  H42C  C4   C5    106.95  3.000
 7AH  H41C  C4   C5    110.18  3.000
 7AH  C3    C4   C5    112.41  3.000
 7AH  C19   C3   C2    118.52  3.000
 7AH  C19   C3   C4    121.02  3.000
 7AH  C2    C3   C4    120.46  3.000
 7AH  H2    C2   C1    118.93  3.000
 7AH  H2    C2   C3    119.80  3.000
 7AH  C1    C2   C3    121.26  3.000
 7AH  H1    C1   C     120.61  3.000
 7AH  H1    C1   C2    120.94  3.000
 7AH  C     C1   C2    118.45  3.000
 7AH  H19   C19  C20   118.97  3.000
 7AH  H19   C19  C3    119.80  3.000
 7AH  C20   C19  C3    121.23  3.000
 7AH  H20   C20  C     120.57  3.000
 7AH  H20   C20  C19   120.92  3.000
 7AH  C     C20  C19   118.51  3.000
 7AH  F     C    C20   118.97  3.000
 7AH  F     C    C1    119.00  3.000
 7AH  C20   C    C1    122.03  3.000
 7AH  H     N    C6    115.85  3.000
 7AH  H     N    C5    116.76  3.000
 7AH  C6    N    C5    126.58  3.000
 7AH  C7    C6   C18   120.74  3.000
 7AH  C7    C6   N     121.03  3.000
 7AH  C18   C6   N     118.18  3.000
 7AH  H18   C18  C17   120.81  3.000
 7AH  H18   C18  C6    119.91  3.000
 7AH  C17   C18  C6    119.29  3.000
 7AH  C11   C17  C9    107.39  3.000
 7AH  C11   C17  C18   133.51  3.000
 7AH  C9    C17  C18   119.11  3.000
 7AH  N1    C9   C8    130.96  3.000
 7AH  N1    C9   C17   107.29  3.000
 7AH  C8    C9   C17   121.74  3.000
 7AH  H8    C8   C7    120.43  3.000
 7AH  H8    C8   C9    121.36  3.000
 7AH  C7    C8   C9    118.20  3.000
 7AH  H7    C7   C8    119.16  3.000
 7AH  H7    C7   C6    119.92  3.000
 7AH  C8    C7   C6    120.91  3.000
 7AH  C12   C11  C10   127.65  3.000
 7AH  C12   C11  C17   126.61  3.000
 7AH  C10   C11  C17   105.73  3.000
 7AH  H10   C10  N1    119.99  3.000
 7AH  H10   C10  C11   129.65  3.000
 7AH  N1    C10  C11   110.35  3.000
 7AH  HA    N1   C10   124.86  3.000
 7AH  HA    N1   C9    125.83  3.000
 7AH  C10   N1   C9    109.25  3.000
 7AH  H12   C12  C13   107.06  3.000
 7AH  H12   C12  C16   106.90  3.000
 7AH  C13   C12  C16   109.38  3.000
 7AH  H12   C12  C11   107.85  3.000
 7AH  C13   C12  C11   112.36  3.000
 7AH  C16   C12  C11   112.96  3.000
 7AH  H162  C16  H161  107.15  3.000
 7AH  H162  C16  C15   108.98  3.000
 7AH  H161  C16  C15   109.86  3.000
 7AH  H162  C16  C12   109.98  3.000
 7AH  H161  C16  C12   110.16  3.000
 7AH  C15   C16  C12   110.64  3.000
 7AH  H152  C15  H151  106.92  3.000
 7AH  H152  C15  N2    108.92  3.000
 7AH  H151  C15  N2    112.30  3.000
 7AH  H152  C15  C16   110.14  3.000
 7AH  H151  C15  C16   108.47  3.000
 7AH  N2    C15  C16   110.03  3.000
 7AH  HB    N2   C14   109.31  3.000
 7AH  HB    N2   C15   109.30  3.000
 7AH  C14   N2   C15   111.54  3.000
 7AH  H142  C14  H141  106.85  3.000
 7AH  H142  C14  C13   110.09  3.000
 7AH  H141  C14  C13   108.52  3.000
 7AH  H142  C14  N2    108.90  3.000
 7AH  H141  C14  N2    112.34  3.000
 7AH  C13   C14  N2    110.07  3.000
 7AH  H132  C13  H131  107.26  3.000
 7AH  H132  C13  C14   109.76  3.000
 7AH  H131  C13  C14   109.56  3.000
 7AH  H132  C13  C12   110.20  3.000
 7AH  H131  C13  C12   109.18  3.000
 7AH  C14   C13  C12   110.81  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
 7AH  CONST_01  C    C1   C2   C3     0.00   0.0  0
 7AH  CONST_02  C    C20  C19  C3     0.00   0.0  0
 7AH  CONST_03  C20  C19  C3   C2     0.00   0.0  0
 7AH  CONST_04  C20  C    C1   C2     0.00   0.0  0
 7AH  CONST_05  C19  C3   C2   C1     0.00   0.0  0
 7AH  CONST_06  C19  C20  C    C1     0.00   0.0  0
 7AH  CONST_07  C9   C17  C18  C6     0.00   0.0  0
 7AH  CONST_08  C11  C17  C18  C6   180.00   0.0  0
 7AH  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 7AH  CONST_10  C8   C7   C6   C18    0.00   0.0  0
 7AH  CONST_11  C8   C9   C17  C18    0.00   0.0  0
 7AH  CONST_12  N1   C9   C17  C18  180.00   0.0  0
 7AH  CONST_13  C10  C11  C17  C18  180.00   0.0  0
 7AH  CONST_14  C7   C6   C18  C17    0.00   0.0  0
 7AH  CONST_15  C7   C8   C9   C17    0.00   0.0  0
 7AH  CONST_16  C10  N1   C9   C17    0.00   0.0  0
 7AH  CONST_17  N1   C10  C11  C17    0.00   0.0  0
 7AH  CONST_18  C10  C11  C17  C9     0.00   0.0  0
 7AH  CONST_19  C11  C10  N1   C9     0.00   0.0  0
 7AH  CONST_20  C11  C17  C9   C8   180.00   0.0  0
 7AH  CONST_21  C10  N1   C9   C8   180.00   0.0  0
 7AH  CONST_22  N1   C9   C8   C7   180.00   0.0  0
 7AH  CONST_23  N1   C9   C17  C11    0.00   0.0  0
 7AH  CONST_24  C12  C11  C17  C18    0.00   0.0  0
 7AH  CONST_25  C12  C11  C17  C9   180.00   0.0  0
 7AH  CONST_26  C12  C11  C10  N1   180.00   0.0  0
 7AH  CONST_27  C1   C2   C3   C4   180.00   0.0  0
 7AH  CONST_28  C20  C19  C3   C4   180.00   0.0  0
 7AH  CONST_29  F    C    C1   C2   180.00   0.0  0
 7AH  CONST_30  F    C    C20  C19  180.00   0.0  0
 7AH  CONST_31  C17  C18  C6   N    180.00   0.0  0
 7AH  CONST_32  C8   C7   C6   N    180.00   0.0  0
 7AH  CONST_33  H1   C1   C2   C3   180.00   0.0  0
 7AH  CONST_34  H20  C20  C19  C3   180.00   0.0  0
 7AH  CONST_35  H19  C19  C3   C2   180.00   0.0  0
 7AH  CONST_36  H2   C2   C3   C19  180.00   0.0  0
 7AH  CONST_37  H8   C8   C7   C6   180.00   0.0  0
 7AH  CONST_38  H7   C7   C6   C18  180.00   0.0  0
 7AH  CONST_39  HA   N1   C9   C17  180.00   0.0  0
 7AH  CONST_40  H10  C10  C11  C17  180.00   0.0  0
 7AH  CONST_41  H18  C18  C17  C9   180.00   0.0  0
 7AH  CONST_45  C6   N    C5   O      0.00   0.0  0
 7AH  CONST_46  C6   N    C5   C4   180.00   0.0  0
 7AH  Var_01    N2   C15  C16  C12  -57.75  30.0  1
 7AH  Var_02    N2   C14  C13  C12   57.04  30.0  1
 7AH  Var_03    C14  N2   C15  C16   61.81  30.0  1
 7AH  Var_04    C13  C14  N2   C15  -61.43  30.0  1
 7AH  Var_05    C2   C3   C4   C5    86.79  30.0  2
 7AH  Var_06    C3   C4   C5   O     26.09  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
 7AH  chir_01  C12  C11  C16  C13  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
 7AH  plan-1  C4   0.020
 7AH  plan-1  C3   0.020
 7AH  plan-1  C2   0.020
 7AH  plan-1  C1   0.020
 7AH  plan-1  C19  0.020
 7AH  plan-1  C20  0.020
 7AH  plan-1  C    0.020
 7AH  plan-1  F    0.020
 7AH  plan-1  H2   0.020
 7AH  plan-1  H19  0.020
 7AH  plan-1  H1   0.020
 7AH  plan-1  H20  0.020
 7AH  plan-2  N    0.020
 7AH  plan-2  C6   0.020
 7AH  plan-2  C18  0.020
 7AH  plan-2  C17  0.020
 7AH  plan-2  C9   0.020
 7AH  plan-2  C8   0.020
 7AH  plan-2  C7   0.020
 7AH  plan-2  C11  0.020
 7AH  plan-2  C10  0.020
 7AH  plan-2  N1   0.020
 7AH  plan-2  C12  0.020
 7AH  plan-2  H18  0.020
 7AH  plan-2  H7   0.020
 7AH  plan-2  H8   0.020
 7AH  plan-2  HA   0.020
 7AH  plan-2  H10  0.020
 7AH  plan-3  O    0.020
 7AH  plan-3  C5   0.020
 7AH  plan-3  C4   0.020
 7AH  plan-3  N    0.020
 7AH  plan-3  C6   0.020
 7AH  plan-3  H    0.020

