# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 18:26:17 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-[(2~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c2[nH]ccc2c1CN3CCCC[C@H]3c4ccc(cc4)C(O)=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
 MVK  MVK  '4-[(2~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid'  ligand  52  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MVK
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
 MVK  C1   C  CR6    0   0.062  -1.7373  -1.4795   0.8662
 MVK  C2   C  CR16   0  -0.401  -2.8767  -2.2378   1.2026
 MVK  C3   C  CR6    0   0.063  -4.0890  -2.1298   0.5453
 MVK  C11  C  CR15   0  -0.443  -3.4368   0.4047  -1.9541
 MVK  C12  C  CR15   0  -0.034  -4.7474   0.1055  -2.1923
 MVK  C14  C  CH2    0  -0.274  -1.4025   2.2291   0.5316
 MVK  C15  C  CH2    0  -0.432  -1.1241   3.3227   1.5480
 MVK  C16  C  CH2    0  -0.444   0.1165   4.1099   1.1597
 MVK  C17  C  CH2    0  -0.424   1.2753   3.1488   0.9509
 MVK  C18  C  CH1    0  -0.106   0.9233   2.0473  -0.0539
 MVK  C19  C  CR6    0   0.100   2.1086   1.1302  -0.2314
 MVK  C20  C  CR16   0  -0.312   2.8225   1.1233  -1.4242
 MVK  C21  C  CR16   0  -0.275   3.9339   0.3067  -1.5871
 MVK  C22  C  CR6    0  -0.115   4.3614  -0.5312  -0.5623
 MVK  C23  C  CR16   0  -0.278   3.6449  -0.5212   0.6340
 MVK  C24  C  CR16   0  -0.270   2.5395   0.2978   0.7999
 MVK  C25  C  C      0   0.392   5.5747  -1.4323  -0.7447
 MVK  C4   C  CR56   0   0.306  -4.1283  -1.2029  -0.4977
 MVK  C5   C  CR56   0   0.050  -3.0115  -0.4257  -0.8678
 MVK  C6   C  CR6    0  -0.017  -1.7947  -0.5631  -0.1770
 MVK  C7   C  CH3    0  -0.737  -5.2920  -2.9404   0.9190
 MVK  C8   C  CH2    0  -0.364  -0.5980   0.2581  -0.5765
 MVK  N9   N  NT     0  -0.402  -0.2747   1.3236   0.3686
 MVK  C10  C  CH3    0  -0.752  -0.4673  -1.6905   1.6437
 MVK  N13  N  NR15   0  -0.687  -5.1650  -0.8575  -1.3205
 MVK  O26  O  O      0  -0.596   6.1550  -1.3717  -1.8463
 MVK  O27  O  OC    -1  -0.596   5.8854  -2.1554   0.2220
 MVK  H1   H  HCR6   0   0.230  -2.7976  -2.9465   2.0205
 MVK  H2   H  HCR5   0   0.240  -2.8487   1.1330  -2.4885
 MVK  H3   H  HCR5   0   0.276  -5.4256   0.5127  -2.9250
 MVK  H4   H  HCH2   0   0.243  -2.2695   1.6524   0.8553
 MVK  H5   H  HCH2   0   0.177  -1.6772   2.6950  -0.4336
 MVK  H6   H  HCH2   0   0.229  -1.9982   3.9743   1.6166
 MVK  H7   H  HCH2   0   0.214  -0.9842   2.8719   2.5352
 MVK  H8   H  HCH2   0   0.211  -0.0736   4.6628   0.2335
 MVK  H9   H  HCH2   0   0.232   0.3657   4.8517   1.9218
 MVK  H10  H  HCH2   0   0.235   2.1612   3.6758   0.5899
 MVK  H11  H  HCH2   0   0.220   1.5460   2.6866   1.9055
 MVK  H12  H  HCH1   0   0.196   0.7379   2.5382  -1.0292
 MVK  H13  H  HCR6   0   0.237   2.5021   1.7621  -2.2403
 MVK  H14  H  HCR6   0   0.238   4.4732   0.3156  -2.5252
 MVK  H15  H  HCR6   0   0.237   3.9605  -1.1652   1.4446
 MVK  H16  H  HCR6   0   0.238   1.9962   0.2839   1.7369
 MVK  H17  H  HCH3   0   0.244  -6.1013  -2.3094   1.2937
 MVK  H18  H  HCH3   0   0.241  -5.6879  -3.4917   0.0633
 MVK  H19  H  HCH3   0   0.250  -5.0539  -3.6651   1.6961
 MVK  H20  H  HCH2   0   0.253   0.2684  -0.4021  -0.6530
 MVK  H21  H  HCH2   0   0.213  -0.7587   0.6665  -1.5888
 MVK  H23  H  HCH3   0   0.234   0.3183  -2.1340   1.0267
 MVK  H24  H  HCH3   0   0.249  -0.0718  -0.7484   2.0203
 MVK  H25  H  HCH3   0   0.240  -0.6293  -2.3584   2.4890
 MVK  H26  H  HNR5   0   0.409  -6.0926  -1.2458  -1.2972

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
 MVK  C15  C16  single    1.520  0.020  1.520
 MVK  C15  C14  single    1.519  0.020  1.519
 MVK  C16  C17  single    1.520  0.020  1.520
 MVK  C17  C18  single    1.532  0.020  1.532
 MVK  C14  N9   single    1.456  0.020  1.456
 MVK  C18  N9   single    1.462  0.020  1.462
 MVK  C18  C19  single    1.509  0.020  1.509
 MVK  C24  C19  aromatic  1.394  0.020  1.394
 MVK  C24  C23  aromatic  1.386  0.020  1.386
 MVK  N9   C8   single    1.460  0.020  1.460
 MVK  C19  C20  aromatic  1.390  0.020  1.390
 MVK  C23  C22  aromatic  1.394  0.020  1.394
 MVK  C12  C11  aromatic  1.365  0.020  1.365
 MVK  C12  N13  aromatic  1.365  0.020  1.365
 MVK  C11  C5   aromatic  1.432  0.020  1.432
 MVK  N13  C4   aromatic  1.368  0.020  1.368
 MVK  C20  C21  aromatic  1.389  0.020  1.389
 MVK  C5   C4   aromatic  1.410  0.020  1.410
 MVK  C5   C6   aromatic  1.406  0.020  1.406
 MVK  C22  C21  aromatic  1.391  0.020  1.391
 MVK  C22  C25  single    1.522  0.020  1.522
 MVK  C8   C6   single    1.505  0.020  1.505
 MVK  C4   C3   aromatic  1.396  0.020  1.396
 MVK  C6   C1   aromatic  1.390  0.020  1.390
 MVK  O26  C25  deloc     1.247  0.020  1.247
 MVK  C3   C7   single    1.498  0.020  1.498
 MVK  C3   C2   aromatic  1.383  0.020  1.383
 MVK  C1   C2   aromatic  1.409  0.020  1.409
 MVK  C1   C10  single    1.504  0.020  1.504
 MVK  C25  O27  deloc     1.247  0.020  1.247
 MVK  C2   H1   single    0.930  0.020  1.080
 MVK  C11  H2   single    0.930  0.020  1.080
 MVK  C12  H3   single    0.930  0.020  1.080
 MVK  C14  H4   single    0.970  0.020  1.090
 MVK  C14  H5   single    0.970  0.020  1.090
 MVK  C15  H6   single    0.970  0.020  1.090
 MVK  C15  H7   single    0.970  0.020  1.090
 MVK  C16  H8   single    0.970  0.020  1.090
 MVK  C16  H9   single    0.970  0.020  1.090
 MVK  C17  H10  single    0.970  0.020  1.090
 MVK  C17  H11  single    0.970  0.020  1.090
 MVK  C18  H12  single    0.970  0.020  1.090
 MVK  C20  H13  single    0.930  0.020  1.080
 MVK  C21  H14  single    0.930  0.020  1.080
 MVK  C23  H15  single    0.930  0.020  1.080
 MVK  C24  H16  single    0.930  0.020  1.080
 MVK  C7   H17  single    0.970  0.020  1.090
 MVK  C7   H18  single    0.970  0.020  1.090
 MVK  C7   H19  single    0.970  0.020  1.090
 MVK  C8   H20  single    0.970  0.020  1.090
 MVK  C8   H21  single    0.970  0.020  1.090
 MVK  C10  H23  single    0.970  0.020  1.090
 MVK  C10  H24  single    0.970  0.020  1.090
 MVK  C10  H25  single    0.970  0.020  1.090
 MVK  N13  H26  single    0.860  0.020  1.020

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
 MVK  C10  C1   C6   121.03  3.000
 MVK  C10  C1   C2   118.93  3.000
 MVK  C6   C1   C2   120.03  3.000
 MVK  H1   C2   C3   118.23  3.000
 MVK  H1   C2   C1   118.19  3.000
 MVK  C3   C2   C1   123.58  3.000
 MVK  C7   C3   C4   121.54  3.000
 MVK  C7   C3   C2   122.89  3.000
 MVK  C4   C3   C2   115.57  3.000
 MVK  H2   C11  C5   127.29  3.000
 MVK  H2   C11  C12  125.83  3.000
 MVK  C5   C11  C12  106.88  3.000
 MVK  H3   C12  N13  120.55  3.000
 MVK  H3   C12  C11  129.76  3.000
 MVK  N13  C12  C11  109.69  3.000
 MVK  H5   C14  H4   106.52  3.000
 MVK  H5   C14  N9   110.90  3.000
 MVK  H4   C14  N9   108.68  3.000
 MVK  H5   C14  C15  109.03  3.000
 MVK  H4   C14  C15  109.14  3.000
 MVK  N9   C14  C15  112.39  3.000
 MVK  H7   C15  H6   106.94  3.000
 MVK  H7   C15  C16  109.85  3.000
 MVK  H6   C15  C16  111.12  3.000
 MVK  H7   C15  C14  109.30  3.000
 MVK  H6   C15  C14  108.96  3.000
 MVK  C16  C15  C14  110.59  3.000
 MVK  H9   C16  H8   106.66  3.000
 MVK  H9   C16  C17  110.57  3.000
 MVK  H8   C16  C17  109.60  3.000
 MVK  H9   C16  C15  111.09  3.000
 MVK  H8   C16  C15  109.62  3.000
 MVK  C17  C16  C15  109.27  3.000
 MVK  H11  C17  H10  106.94  3.000
 MVK  H11  C17  C18  108.98  3.000
 MVK  H10  C17  C18  108.45  3.000
 MVK  H11  C17  C16  109.62  3.000
 MVK  H10  C17  C16  111.02  3.000
 MVK  C18  C17  C16  111.69  3.000
 MVK  H12  C18  N9   109.68  3.000
 MVK  H12  C18  C19  107.29  3.000
 MVK  N9   C18  C19  112.13  3.000
 MVK  H12  C18  C17  107.30  3.000
 MVK  C19  C18  C17  109.49  3.000
 MVK  N9   C18  C17  110.78  3.000
 MVK  C24  C19  C20  118.24  3.000
 MVK  C20  C19  C18  120.49  3.000
 MVK  C24  C19  C18  121.25  3.000
 MVK  H13  C20  C21  119.63  3.000
 MVK  H13  C20  C19  119.40  3.000
 MVK  C21  C20  C19  120.97  3.000
 MVK  H14  C21  C22  119.37  3.000
 MVK  H14  C21  C20  119.72  3.000
 MVK  C22  C21  C20  120.91  3.000
 MVK  C25  C22  C23  121.10  3.000
 MVK  C25  C22  C21  120.88  3.000
 MVK  C23  C22  C21  118.02  3.000
 MVK  H15  C23  C24  119.64  3.000
 MVK  H15  C23  C22  119.24  3.000
 MVK  C24  C23  C22  121.12  3.000
 MVK  H16  C24  C23  119.74  3.000
 MVK  H16  C24  C19  119.52  3.000
 MVK  C23  C24  C19  120.74  3.000
 MVK  O27  C25  O26  126.69  3.000
 MVK  O27  C25  C22  116.68  3.000
 MVK  O26  C25  C22  116.62  3.000
 MVK  N13  C4   C5   107.65  3.000
 MVK  C5   C4   C3   122.67  3.000
 MVK  N13  C4   C3   129.68  3.000
 MVK  C6   C5   C4   120.18  3.000
 MVK  C6   C5   C11  133.35  3.000
 MVK  C4   C5   C11  106.47  3.000
 MVK  C8   C6   C5   120.29  3.000
 MVK  C8   C6   C1   121.74  3.000
 MVK  C5   C6   C1   117.97  3.000
 MVK  H19  C7   H18  107.60  3.000
 MVK  H19  C7   H17  107.55  3.000
 MVK  H18  C7   H17  106.96  3.000
 MVK  H19  C7   C3   111.26  3.000
 MVK  H18  C7   C3   111.65  3.000
 MVK  H17  C7   C3   111.59  3.000
 MVK  H21  C8   H20  105.96  3.000
 MVK  H21  C8   N9   110.85  3.000
 MVK  H20  C8   N9   108.11  3.000
 MVK  H21  C8   C6   109.24  3.000
 MVK  H20  C8   C6   108.63  3.000
 MVK  N9   C8   C6   113.72  3.000
 MVK  C8   N9   C18  110.83  3.000
 MVK  C8   N9   C14  110.78  3.000
 MVK  C18  N9   C14  111.06  3.000
 MVK  H25  C10  H24  108.42  3.000
 MVK  H25  C10  H23  107.22  3.000
 MVK  H24  C10  H23  106.58  3.000
 MVK  H25  C10  C1   111.20  3.000
 MVK  H24  C10  C1   111.35  3.000
 MVK  H23  C10  C1   111.84  3.000
 MVK  H26  N13  C4   125.99  3.000
 MVK  H26  N13  C12  124.71  3.000
 MVK  C4   N13  C12  109.30  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
 MVK  CONST_01  C11  C5   C6   C1   180.00   0.0  0
 MVK  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 MVK  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 MVK  CONST_04  N13  C4   C3   C2   180.00   0.0  0
 MVK  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 MVK  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 MVK  CONST_07  C12  N13  C4   C3   180.00   0.0  0
 MVK  CONST_08  C11  C5   C4   C3   180.00   0.0  0
 MVK  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 MVK  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 MVK  CONST_11  C4   N13  C12  C11    0.00   0.0  0
 MVK  CONST_12  N13  C4   C5   C11    0.00   0.0  0
 MVK  CONST_13  C4   C5   C11  C12    0.00   0.0  0
 MVK  CONST_14  C6   C5   C11  C12  180.00   0.0  0
 MVK  CONST_15  C5   C4   N13  C12    0.00   0.0  0
 MVK  CONST_16  C22  C23  C24  C19    0.00   0.0  0
 MVK  CONST_17  C22  C21  C20  C19    0.00   0.0  0
 MVK  CONST_18  C23  C24  C19  C20    0.00   0.0  0
 MVK  CONST_19  C23  C22  C21  C20    0.00   0.0  0
 MVK  CONST_20  C24  C19  C20  C21    0.00   0.0  0
 MVK  CONST_21  C24  C23  C22  C21    0.00   0.0  0
 MVK  CONST_22  N13  C12  C11  C5     0.00   0.0  0
 MVK  CONST_23  N13  C4   C5   C6   180.00   0.0  0
 MVK  CONST_24  C23  C24  C19  C18  180.00   0.0  0
 MVK  CONST_25  C21  C20  C19  C18  180.00   0.0  0
 MVK  CONST_26  C7   C3   C2   C1   180.00   0.0  0
 MVK  CONST_27  C8   C6   C1   C2   180.00   0.0  0
 MVK  CONST_28  C10  C1   C2   C3   180.00   0.0  0
 MVK  CONST_29  C8   C6   C5   C11    0.00   0.0  0
 MVK  CONST_30  C25  C22  C21  C20  180.00   0.0  0
 MVK  CONST_31  C25  C22  C23  C24  180.00   0.0  0
 MVK  CONST_32  C8   C6   C5   C4   180.00   0.0  0
 MVK  CONST_33  C7   C3   C4   C5   180.00   0.0  0
 MVK  CONST_34  C10  C1   C6   C5   180.00   0.0  0
 MVK  CONST_35  N13  C4   C3   C7     0.00   0.0  0
 MVK  CONST_36  H26  N13  C4   C3     0.00   0.0  0
 MVK  CONST_37  H16  C24  C19  C18    0.00   0.0  0
 MVK  CONST_38  H13  C20  C19  C18    0.00   0.0  0
 MVK  CONST_39  H15  C23  C24  C19  180.00   0.0  0
 MVK  CONST_40  H14  C21  C20  C19  180.00   0.0  0
 MVK  CONST_41  H3   C12  N13  C4   180.00   0.0  0
 MVK  CONST_42  H2   C11  C5   C4   180.00   0.0  0
 MVK  CONST_43  H1   C2   C3   C4   180.00   0.0  0
 MVK  Var_01    C17  C16  C15  C14  -53.67  30.0  1
 MVK  Var_02    C18  C17  C16  C15   54.10  30.0  1
 MVK  Var_03    C18  N9   C14  C15  -58.55  30.0  1
 MVK  Var_04    N9   C14  C15  C16   56.88  30.0  1
 MVK  Var_05    N9   C8   C6   C1   -73.17  30.0  2
 MVK  Var_06    C6   C8   N9   C14  -58.36  30.0  3
 MVK  Var_07    O26  C25  C22  C21    0.26  30.0  2
 MVK  Var_08    H17  C7   C3   C2   115.13  30.0  2
 MVK  Var_09    H23  C10  C1   C2   113.00  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
 MVK  chir_01  C18  C17  N9  C19  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
 MVK  plan-1  C18  0.020
 MVK  plan-1  C19  0.020
 MVK  plan-1  C20  0.020
 MVK  plan-1  C21  0.020
 MVK  plan-1  C22  0.020
 MVK  plan-1  C23  0.020
 MVK  plan-1  C24  0.020
 MVK  plan-1  C25  0.020
 MVK  plan-1  H13  0.020
 MVK  plan-1  H14  0.020
 MVK  plan-1  H15  0.020
 MVK  plan-1  H16  0.020
 MVK  plan-2  C1   0.020
 MVK  plan-2  C2   0.020
 MVK  plan-2  C3   0.020
 MVK  plan-2  C11  0.020
 MVK  plan-2  C12  0.020
 MVK  plan-2  C4   0.020
 MVK  plan-2  C5   0.020
 MVK  plan-2  C6   0.020
 MVK  plan-2  C7   0.020
 MVK  plan-2  C8   0.020
 MVK  plan-2  C10  0.020
 MVK  plan-2  N13  0.020
 MVK  plan-2  H1   0.020
 MVK  plan-2  H2   0.020
 MVK  plan-2  H3   0.020
 MVK  plan-2  H26  0.020
 MVK  plan-3  C22  0.020
 MVK  plan-3  C25  0.020
 MVK  plan-3  O26  0.020
 MVK  plan-3  O27  0.020

