# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:18:34 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(CNCC2CCN(CC2)c3ncc(cn3)C(=O)NO)c4ccccc14
#
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
 GOK  GOK  2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide  ligand  55  29  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOK
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
 GOK  N1   N  NH1   0  -0.388  -7.3588  -2.0709  -0.8420
 GOK  O3   O  O     0  -0.475  -7.5212  -0.1619  -2.0369
 GOK  C5   C  CR6   0   0.653  -3.4505   0.5727   0.5925
 GOK  C8   C  CR6   0  -0.247  -5.6891  -0.3970  -0.5585
 GOK  C9   C  CR16  0   0.015  -5.4178   0.9680  -0.4677
 GOK  C14  C  CH2   0  -0.316  -1.2820   0.2053   1.6799
 GOK  N15  N  NT    0  -0.474  -2.3581   1.0558   1.2048
 GOK  C16  C  CH2   0  -0.321  -2.0172   2.4677   1.2095
 GOK  C34  C  CR56  0   0.372   6.4805  -0.9837  -0.0484
 GOK  C2   C  C     0   0.500  -6.9255  -0.8550  -1.2272
 GOK  O4   O  OH1   0  -0.538  -8.3630  -2.6827  -1.5249
 GOK  N6   N  N     0  -0.469  -3.5964  -0.7615   0.5220
 GOK  C7   C  CR16  0  -0.004  -4.6926  -1.2201  -0.0394
 GOK  N10  N  N     0  -0.467  -4.3361   1.4548   0.0939
 GOK  C13  C  CH2   0  -0.436  -0.0371   0.3863   0.8190
 GOK  C17  C  CH2   0  -0.420  -0.7991   2.7194   0.3295
 GOK  C18  C  CH1   0  -0.261   0.3889   1.8536   0.7480
 GOK  C27  C  CH2   0  -0.244   1.5637   2.0739  -0.1965
 GOK  N29  N  NH1   0  -0.601   2.7679   1.3946   0.2417
 GOK  C30  C  CH2   0  -0.373   3.8958   1.6465  -0.6475
 GOK  C31  C  CR5   0  -0.020   5.0726   0.8001  -0.2990
 GOK  N32  N  NR5   0  -0.521   7.0453   0.1132   0.5370
 GOK  C33  C  CR15  0  -0.080   6.1959   1.1746   0.3823
 GOK  C35  C  CR56  0   0.042   5.2340  -0.5936  -0.5863
 GOK  C36  C  CR16  0  -0.384   4.4509  -1.5453  -1.2489
 GOK  C37  C  CR16  0  -0.268   4.9224  -2.8393  -1.3599
 GOK  C38  C  CR16  0  -0.282   6.1651  -3.2063  -0.8179
 GOK  C39  C  CR16  0  -0.315   6.9607  -2.2881  -0.1581
 GOK  C44  C  CH3   0  -0.527   8.3366   0.1434   1.1768
 GOK  H1   H  HNH1  0   0.421  -6.8775  -2.6574  -0.1773
 GOK  H2   H  HCR6  0   0.275  -6.1218   1.6913  -0.8662
 GOK  H4   H  HCH2  0   0.273  -1.6077  -0.8299   1.6867
 GOK  H5   H  HCH2  0   0.273  -2.8697   3.0521   0.8783
 GOK  H6   H  HCH2  0   0.241  -1.7954   2.7588   2.2417
 GOK  H7   H  HOH1  0   0.479  -9.1796  -2.4741  -1.0523
 GOK  H8   H  HCR6  0   0.269  -4.7658  -2.3024  -0.0986
 GOK  H9   H  HCH2  0   0.239   0.7588  -0.2323   1.2411
 GOK  H10  H  HCH2  0   0.224  -0.2378   0.0091  -0.1904
 GOK  H11  H  HCH2  0   0.223  -1.0625   2.5126  -0.7136
 GOK  H12  H  HCH2  0   0.240  -0.5329   3.7779   0.3883
 GOK  H13  H  HCH1  0   0.221   0.6992   2.1644   1.7541
 GOK  H14  H  HCH2  0   0.186   1.2612   1.7815  -1.2174
 GOK  H15  H  HCH2  0   0.223   1.7820   3.1461  -0.2410
 GOK  H16  H  HNH1  0   0.339   2.5999   0.3958   0.2657
 GOK  H18  H  HCH2  0   0.199   3.6293   1.4786  -1.7039
 GOK  H19  H  HCH2  0   0.235   4.1656   2.7036  -0.5681
 GOK  H20  H  HCR5  0   0.285   6.4631   2.1450   0.7739
 GOK  H21  H  HCR6  0   0.240   3.4910  -1.2749  -1.6739
 GOK  H22  H  HCR6  0   0.246   4.3282  -3.5851  -1.8720
 GOK  H23  H  HCR6  0   0.249   6.5066  -4.2283  -0.9196
 GOK  H24  H  HCR6  0   0.263   7.9187  -2.5771   0.2551
 GOK  H25  H  HCH3  0   0.251   9.1317  -0.0918   0.4687
 GOK  H26  H  HCH3  0   0.263   8.5140   1.1388   1.5744
 GOK  H27  H  HCH3  0   0.252   8.3814  -0.5686   2.0010
 GOK  H3   H  HCH2  0   0.242  -1.0591   0.4917   2.7131

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
 GOK  C36  C37  aromatic  1.382  0.020  1.382
 GOK  C36  C35  aromatic  1.399  0.020  1.399
 GOK  C37  C38  aromatic  1.405  0.020  1.405
 GOK  C30  N29  single    1.458  0.020  1.458
 GOK  C30  C31  single    1.491  0.020  1.491
 GOK  N29  C27  single    1.450  0.020  1.450
 GOK  C17  C16  single    1.524  0.020  1.524
 GOK  C17  C18  single    1.528  0.020  1.528
 GOK  C35  C31  aromatic  1.432  0.020  1.432
 GOK  C35  C34  aromatic  1.412  0.020  1.412
 GOK  C16  N15  single    1.452  0.020  1.452
 GOK  C31  C33  aromatic  1.366  0.020  1.366
 GOK  C38  C39  aromatic  1.382  0.020  1.382
 GOK  C27  C18  single    1.523  0.020  1.523
 GOK  C18  C13  single    1.530  0.020  1.530
 GOK  C34  C39  aromatic  1.394  0.020  1.394
 GOK  C34  N32  aromatic  1.366  0.020  1.366
 GOK  N6   C7   aromatic  1.314  0.020  1.314
 GOK  N6   C5   aromatic  1.344  0.020  1.344
 GOK  C33  N32  aromatic  1.368  0.020  1.368
 GOK  N15  C5   single    1.342  0.020  1.342
 GOK  N15  C14  single    1.452  0.020  1.452
 GOK  C7   C8   aromatic  1.393  0.020  1.393
 GOK  N32  C44  single    1.441  0.020  1.441
 GOK  C5   N10  aromatic  1.346  0.020  1.346
 GOK  C13  C14  single    1.524  0.020  1.524
 GOK  N1   O4   single    1.360  0.020  1.360
 GOK  N1   C2   single    1.347  0.020  1.347
 GOK  C8   C2   single    1.478  0.020  1.478
 GOK  C8   C9   aromatic  1.395  0.020  1.395
 GOK  N10  C9   aromatic  1.312  0.020  1.312
 GOK  C2   O3   double    1.221  0.020  1.221
 GOK  N1   H1   single    0.860  0.020  1.020
 GOK  C9   H2   single    0.930  0.020  1.080
 GOK  C14  H3   single    0.970  0.020  1.090
 GOK  C14  H4   single    0.970  0.020  1.090
 GOK  C16  H5   single    0.970  0.020  1.090
 GOK  C16  H6   single    0.970  0.020  1.090
 GOK  O4   H7   single    0.850  0.020  0.980
 GOK  C7   H8   single    0.930  0.020  1.080
 GOK  C13  H9   single    0.970  0.020  1.090
 GOK  C13  H10  single    0.970  0.020  1.090
 GOK  C17  H11  single    0.970  0.020  1.090
 GOK  C17  H12  single    0.970  0.020  1.090
 GOK  C18  H13  single    0.970  0.020  1.090
 GOK  C27  H14  single    0.970  0.020  1.090
 GOK  C27  H15  single    0.970  0.020  1.090
 GOK  N29  H16  single    0.890  0.020  1.040
 GOK  C30  H18  single    0.970  0.020  1.090
 GOK  C30  H19  single    0.970  0.020  1.090
 GOK  C33  H20  single    0.930  0.020  1.080
 GOK  C36  H21  single    0.930  0.020  1.080
 GOK  C37  H22  single    0.930  0.020  1.080
 GOK  C38  H23  single    0.930  0.020  1.080
 GOK  C39  H24  single    0.930  0.020  1.080
 GOK  C44  H25  single    0.970  0.020  1.090
 GOK  C44  H26  single    0.970  0.020  1.090
 GOK  C44  H27  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
 GOK  H1   N1   O4   114.94  3.000
 GOK  H1   N1   C2   124.04  3.000
 GOK  O4   N1   C2   120.00  3.000
 GOK  N10  C5   N6   124.05  3.000
 GOK  N10  C5   N15  117.95  3.000
 GOK  N6   C5   N15  118.01  3.000
 GOK  C7   C8   C2   125.72  3.000
 GOK  C2   C8   C9   119.69  3.000
 GOK  C7   C8   C9   114.52  3.000
 GOK  H2   C9   N10  116.40  3.000
 GOK  H2   C9   C8   120.15  3.000
 GOK  N10  C9   C8   123.45  3.000
 GOK  H4   C14  H3   107.74  3.000
 GOK  H4   C14  C13  111.21  3.000
 GOK  H3   C14  C13  109.61  3.000
 GOK  H4   C14  N15  109.78  3.000
 GOK  H3   C14  N15  107.85  3.000
 GOK  C13  C14  N15  110.55  3.000
 GOK  C16  N15  C14  113.23  3.000
 GOK  C14  N15  C5   122.80  3.000
 GOK  C16  N15  C5   122.85  3.000
 GOK  H6   C16  H5   107.67  3.000
 GOK  H6   C16  C17  109.79  3.000
 GOK  H5   C16  C17  111.27  3.000
 GOK  H6   C16  N15  108.00  3.000
 GOK  H5   C16  N15  109.75  3.000
 GOK  C17  C16  N15  110.27  3.000
 GOK  C39  C34  C35  122.16  3.000
 GOK  C39  C34  N32  129.99  3.000
 GOK  C35  C34  N32  107.84  3.000
 GOK  C8   C2   O3   122.15  3.000
 GOK  O3   C2   N1   123.04  3.000
 GOK  C8   C2   N1   114.79  3.000
 GOK  H7   O4   N1   106.34  3.000
 GOK  C7   N6   C5   117.35  3.000
 GOK  H8   C7   N6   115.29  3.000
 GOK  H8   C7   C8   121.35  3.000
 GOK  N6   C7   C8   123.35  3.000
 GOK  C9   N10  C5   117.24  3.000
 GOK  H10  C13  H9   107.11  3.000
 GOK  H10  C13  C18  109.77  3.000
 GOK  H9   C13  C18  110.98  3.000
 GOK  H10  C13  C14  109.25  3.000
 GOK  H9   C13  C14  108.03  3.000
 GOK  C18  C13  C14  111.57  3.000
 GOK  H12  C17  H11  107.02  3.000
 GOK  H12  C17  C18  110.16  3.000
 GOK  H11  C17  C18  109.91  3.000
 GOK  H12  C17  C16  108.88  3.000
 GOK  H11  C17  C16  109.06  3.000
 GOK  C18  C17  C16  111.69  3.000
 GOK  H13  C18  C27  108.01  3.000
 GOK  H13  C18  C17  108.07  3.000
 GOK  C27  C18  C17  110.35  3.000
 GOK  H13  C18  C13  107.92  3.000
 GOK  C27  C18  C13  112.48  3.000
 GOK  C17  C18  C13  109.86  3.000
 GOK  H15  C27  H14  106.04  3.000
 GOK  H15  C27  N29  107.78  3.000
 GOK  H14  C27  N29  112.51  3.000
 GOK  H15  C27  C18  108.69  3.000
 GOK  H14  C27  C18  108.88  3.000
 GOK  N29  C27  C18  112.66  3.000
 GOK  H16  N29  C30  108.25  3.000
 GOK  H16  N29  C27  109.34  3.000
 GOK  C30  N29  C27  112.15  3.000
 GOK  H19  C30  H18  106.05  3.000
 GOK  H19  C30  C31  109.69  3.000
 GOK  H18  C30  C31  109.17  3.000
 GOK  H19  C30  N29  108.27  3.000
 GOK  H18  C30  N29  111.78  3.000
 GOK  C31  C30  N29  111.71  3.000
 GOK  C35  C31  C33  105.91  3.000
 GOK  C33  C31  C30  127.59  3.000
 GOK  C35  C31  C30  126.49  3.000
 GOK  C44  N32  C33  126.17  3.000
 GOK  C44  N32  C34  125.29  3.000
 GOK  C33  N32  C34  108.53  3.000
 GOK  H20  C33  N32  120.16  3.000
 GOK  H20  C33  C31  129.09  3.000
 GOK  N32  C33  C31  110.75  3.000
 GOK  C36  C35  C31  133.93  3.000
 GOK  C31  C35  C34  106.97  3.000
 GOK  C36  C35  C34  119.10  3.000
 GOK  H21  C36  C37  120.28  3.000
 GOK  H21  C36  C35  120.77  3.000
 GOK  C37  C36  C35  118.95  3.000
 GOK  H22  C37  C38  119.22  3.000
 GOK  H22  C37  C36  119.74  3.000
 GOK  C38  C37  C36  121.04  3.000
 GOK  H23  C38  C39  119.37  3.000
 GOK  H23  C38  C37  119.31  3.000
 GOK  C39  C38  C37  121.32  3.000
 GOK  H24  C39  C38  120.94  3.000
 GOK  H24  C39  C34  121.63  3.000
 GOK  C38  C39  C34  117.43  3.000
 GOK  H27  C44  H26  108.36  3.000
 GOK  H27  C44  H25  108.68  3.000
 GOK  H26  C44  H25  108.43  3.000
 GOK  H27  C44  N32  111.02  3.000
 GOK  H26  C44  N32  109.14  3.000
 GOK  H25  C44  N32  111.12  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
 GOK  CONST_01  C8   C7   N6   C5      0.00   0.0  0
 GOK  CONST_02  C8   C9   N10  C5      0.00   0.0  0
 GOK  CONST_03  N6   C7   C8   C9      0.00   0.0  0
 GOK  CONST_04  N6   C5   N10  C9      0.00   0.0  0
 GOK  CONST_05  C37  C36  C35  C34     0.00   0.0  0
 GOK  CONST_06  C33  C31  C35  C34     0.00   0.0  0
 GOK  CONST_07  C37  C38  C39  C34     0.00   0.0  0
 GOK  CONST_08  C31  C33  N32  C34     0.00   0.0  0
 GOK  CONST_09  N10  C5   N6   C7      0.00   0.0  0
 GOK  CONST_10  N10  C9   C8   C7      0.00   0.0  0
 GOK  CONST_11  C37  C36  C35  C31   180.00   0.0  0
 GOK  CONST_12  C39  C34  C35  C31   180.00   0.0  0
 GOK  CONST_13  N32  C34  C35  C31     0.00   0.0  0
 GOK  CONST_14  C36  C35  C34  N32   180.00   0.0  0
 GOK  CONST_15  C38  C39  C34  N32   180.00   0.0  0
 GOK  CONST_16  C35  C31  C33  N32     0.00   0.0  0
 GOK  CONST_17  C36  C35  C31  C33   180.00   0.0  0
 GOK  CONST_18  C35  C34  N32  C33     0.00   0.0  0
 GOK  CONST_19  C39  C34  N32  C33   180.00   0.0  0
 GOK  CONST_20  C38  C37  C36  C35     0.00   0.0  0
 GOK  CONST_21  C38  C39  C34  C35     0.00   0.0  0
 GOK  CONST_22  C39  C38  C37  C36     0.00   0.0  0
 GOK  CONST_23  C39  C34  C35  C36     0.00   0.0  0
 GOK  CONST_24  N15  C5   N10  C9    180.00   0.0  0
 GOK  CONST_25  C7   N6   C5   N15   180.00   0.0  0
 GOK  CONST_26  C30  C31  C35  C34   180.00   0.0  0
 GOK  CONST_27  N6   C7   C8   C2    180.00   0.0  0
 GOK  CONST_28  N10  C9   C8   C2    180.00   0.0  0
 GOK  CONST_29  C36  C35  C31  C30     0.00   0.0  0
 GOK  CONST_30  N32  C33  C31  C30   180.00   0.0  0
 GOK  CONST_31  C44  N32  C33  C31   180.00   0.0  0
 GOK  CONST_32  C44  N32  C34  C35   180.00   0.0  0
 GOK  CONST_33  C44  N32  C34  C39     0.00   0.0  0
 GOK  CONST_34  H8   C7   N6   C5    180.00   0.0  0
 GOK  CONST_35  H2   C9   N10  C5    180.00   0.0  0
 GOK  CONST_36  H21  C36  C35  C34   180.00   0.0  0
 GOK  CONST_37  H23  C38  C39  C34   180.00   0.0  0
 GOK  CONST_38  H20  C33  N32  C34   180.00   0.0  0
 GOK  CONST_39  H24  C39  C34  N32     0.00   0.0  0
 GOK  CONST_40  H22  C37  C36  C35   180.00   0.0  0
 GOK  CONST_41  O4   N1   C2   C8    180.00   0.0  0
 GOK  CONST_42  H1   N1   C2   C8      0.00   0.0  0
 GOK  CONST_43  O4   N1   C2   O3      0.00   0.0  0
 GOK  Var_01    C17  C16  N15  C5   -109.17  30.0  1
 GOK  Var_02    C13  C14  N15  C5    109.26  30.0  1
 GOK  Var_03    N6   C5   N15  C14     5.73  30.0  2
 GOK  Var_04    C18  C17  C16  N15   -55.37  30.0  1
 GOK  Var_05    C18  C13  C14  N15    54.97  30.0  1
 GOK  Var_06    C7   C8   C2   N1     27.35  30.0  1
 GOK  Var_07    C35  C31  C30  N29    76.17  30.0  2
 GOK  Var_08    H25  C44  N32  C34    61.93  30.0  2
 GOK  Var_09    C30  N29  C27  C18  -178.22  30.0  1
 GOK  Var_10    C31  C30  N29  C27  -172.14  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
 GOK  chir_01  C18  C17  C27  C13  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
 GOK  plan-1  C5   0.020
 GOK  plan-1  C8   0.020
 GOK  plan-1  C9   0.020
 GOK  plan-1  N15  0.020
 GOK  plan-1  C2   0.020
 GOK  plan-1  N6   0.020
 GOK  plan-1  C7   0.020
 GOK  plan-1  N10  0.020
 GOK  plan-1  H2   0.020
 GOK  plan-1  H8   0.020
 GOK  plan-2  C34  0.020
 GOK  plan-2  C30  0.020
 GOK  plan-2  C31  0.020
 GOK  plan-2  N32  0.020
 GOK  plan-2  C33  0.020
 GOK  plan-2  C35  0.020
 GOK  plan-2  C36  0.020
 GOK  plan-2  C37  0.020
 GOK  plan-2  C38  0.020
 GOK  plan-2  C39  0.020
 GOK  plan-2  C44  0.020
 GOK  plan-2  H20  0.020
 GOK  plan-2  H21  0.020
 GOK  plan-2  H22  0.020
 GOK  plan-2  H23  0.020
 GOK  plan-2  H24  0.020
 GOK  plan-3  N1   0.020
 GOK  plan-3  O3   0.020
 GOK  plan-3  C8   0.020
 GOK  plan-3  C2   0.020
 GOK  plan-3  O4   0.020
 GOK  plan-3  H1   0.020

