# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 04:41:55 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5,7-dimethyl-4-[[(2~{S})-2-phenylpiperidin-1-yl]methyl]-1~{H}-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c2[nH]ccc2c1CN3CCCC[C@H]3c4ccccc4
#
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
 MVW  MVW  5,7-dimethyl-4-[[(2~{S})-2-phenylpiperidin-1-yl]methyl]-1~{H}-indole  ligand  50  24  .  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_MVW
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
 MVW  C1   C  CH2   0  -0.433   0.7063  -2.8879  -1.7247
 MVW  C2   C  CR56  0   0.305  -3.6599   0.3578   0.4411
 MVW  C3   C  CR56  0   0.051  -2.3784  -0.0968   0.8165
 MVW  C11  C  CH2   0  -0.366   0.1397  -0.0097   0.6264
 MVW  C15  C  CH2   0  -0.275   0.0505  -2.0244  -0.6627
 MVW  C16  C  CH1   0  -0.107   2.1703  -1.1709   0.0920
 MVW  C17  C  CH2   0  -0.426   2.8975  -2.0520  -0.9296
 MVW  C18  C  CH2   0  -0.445   2.1002  -3.2977  -1.2791
 MVW  C19  C  CR6   0   0.108   3.0076   0.0573   0.3649
 MVW  C20  C  CR16  0  -0.323   3.6656   0.2089   1.5805
 MVW  C21  C  CR16  0  -0.241   4.4808   1.3095   1.8197
 MVW  C22  C  CR16  0  -0.273   4.6428   2.2793   0.8408
 MVW  C23  C  CR16  0  -0.242   3.9884   2.1375  -0.3778
 MVW  C24  C  CR16  0  -0.280   3.1805   1.0351  -0.6133
 MVW  C4   C  CR15  0  -0.445  -2.5819  -1.0976   1.8211
 MVW  C5   C  CR15  0  -0.033  -3.9303  -1.2007   2.0102
 MVW  N6   N  NR15  0  -0.687  -4.5787  -0.3277   1.1869
 MVW  C7   C  CR16  0  -0.401  -2.7107   1.8375  -1.1189
 MVW  C8   C  CR6   0   0.059  -1.4121   1.4154  -0.7712
 MVW  C9   C  CR6   0  -0.016  -1.2327   0.4423   0.2048
 MVW  C10  C  CR6   0   0.065  -3.8592   1.3361  -0.5341
 MVW  N12  N  NT    0  -0.402   0.8269  -0.8280  -0.3684
 MVW  H1   H  HCH2  0   0.230   0.0793  -3.7618  -1.9150
 MVW  H2   H  HCH2  0   0.215   0.7664  -2.3260  -2.6620
 MVW  H3   H  HCH2  0   0.252   0.7529   0.8727   0.8240
 MVW  H4   H  HCH2  0   0.215   0.0708  -0.5462   1.5876
 MVW  H5   H  HCH3  0   0.233   0.4238   2.5557  -0.7651
 MVW  H6   H  HCH3  0   0.248   0.3746   1.2879  -1.9674
 MVW  H7   H  HCH3  0   0.240  -0.5563   2.7682  -2.2105
 MVW  H8   H  HCH3  0   0.242  -5.7868   2.1726  -0.0540
 MVW  H9   H  HCH3  0   0.251  -5.1915   2.5897  -1.6580
 MVW  H10  H  HCH3  0   0.244  -5.8243   0.9775  -1.3393
 MVW  H11  H  HCH2  0   0.243  -0.9418  -1.7197  -0.9975
 MVW  H12  H  HCH2  0   0.178  -0.0978  -2.6312   0.2502
 MVW  H13  H  HCH1  0   0.198   2.1039  -1.7444   1.0374
 MVW  H14  H  HCH2  0   0.222   3.0788  -1.4680  -1.8372
 MVW  H15  H  HCH2  0   0.237   3.8763  -2.3146  -0.5219
 MVW  H16  H  HCH2  0   0.212   2.0293  -3.9497  -0.4023
 MVW  H17  H  HCH2  0   0.232   2.6112  -3.8703  -2.0564
 MVW  H18  H  HCR6  0   0.245   3.5386  -0.5416   2.3524
 MVW  H19  H  HCR6  0   0.252   4.9822   1.4105   2.7740
 MVW  H20  H  HCR6  0   0.252   5.2744   3.1393   1.0238
 MVW  H21  H  HCR6  0   0.251   4.1101   2.8887  -1.1481
 MVW  H22  H  HCR6  0   0.246   2.6732   0.9370  -1.5649
 MVW  H23  H  HCR5  0   0.239  -1.8335  -1.6749   2.3397
 MVW  H24  H  HCR5  0   0.277  -4.4861  -1.8411   2.6761
 MVW  H25  H  HNR5  0   0.408  -5.5781  -0.2281   1.1295
 MVW  H26  H  HCR6  0   0.230  -2.8127   2.6016  -1.8822
 MVW  C13  C  CH3   0  -0.747  -0.2346   2.0396  -1.4670
 MVW  C14  C  CH3   0  -0.740  -5.2338   1.7937  -0.9163

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
 MVW  C22  C23  aromatic  1.390  0.020  1.390
 MVW  C22  C21  aromatic  1.387  0.020  1.387
 MVW  C23  C24  aromatic  1.387  0.020  1.387
 MVW  C21  C20  aromatic  1.390  0.020  1.390
 MVW  C24  C19  aromatic  1.394  0.020  1.394
 MVW  C20  C19  aromatic  1.391  0.020  1.391
 MVW  C5   C4   aromatic  1.366  0.020  1.366
 MVW  C5   N6   aromatic  1.364  0.020  1.364
 MVW  C4   C3   aromatic  1.433  0.020  1.433
 MVW  C19  C16  single    1.511  0.020  1.511
 MVW  N6   C2   aromatic  1.368  0.020  1.368
 MVW  C3   C2   aromatic  1.411  0.020  1.411
 MVW  C3   C9   aromatic  1.406  0.020  1.406
 MVW  C16  C17  single    1.533  0.020  1.533
 MVW  C16  N12  single    1.461  0.020  1.461
 MVW  C17  C18  single    1.520  0.020  1.520
 MVW  C2   C10  aromatic  1.396  0.020  1.396
 MVW  C11  N12  single    1.460  0.020  1.460
 MVW  C11  C9   single    1.505  0.020  1.505
 MVW  N12  C15  single    1.456  0.020  1.456
 MVW  C9   C8   aromatic  1.390  0.020  1.390
 MVW  C10  C14  single    1.498  0.020  1.498
 MVW  C10  C7   aromatic  1.383  0.020  1.383
 MVW  C18  C1   single    1.520  0.020  1.520
 MVW  C15  C1   single    1.518  0.020  1.518
 MVW  C8   C7   aromatic  1.409  0.020  1.409
 MVW  C8   C13  single    1.503  0.020  1.503
 MVW  C1   H1   single    0.970  0.020  1.090
 MVW  C1   H2   single    0.970  0.020  1.090
 MVW  C11  H3   single    0.970  0.020  1.090
 MVW  C11  H4   single    0.970  0.020  1.090
 MVW  C13  H5   single    0.970  0.020  1.090
 MVW  C13  H6   single    0.970  0.020  1.090
 MVW  C13  H7   single    0.970  0.020  1.090
 MVW  C14  H8   single    0.970  0.020  1.090
 MVW  C14  H9   single    0.970  0.020  1.090
 MVW  C14  H10  single    0.970  0.020  1.090
 MVW  C15  H11  single    0.970  0.020  1.090
 MVW  C15  H12  single    0.970  0.020  1.090
 MVW  C16  H13  single    0.970  0.020  1.090
 MVW  C17  H14  single    0.970  0.020  1.090
 MVW  C17  H15  single    0.970  0.020  1.090
 MVW  C18  H16  single    0.970  0.020  1.090
 MVW  C18  H17  single    0.970  0.020  1.090
 MVW  C20  H18  single    0.930  0.020  1.080
 MVW  C21  H19  single    0.930  0.020  1.080
 MVW  C22  H20  single    0.930  0.020  1.080
 MVW  C23  H21  single    0.930  0.020  1.080
 MVW  C24  H22  single    0.930  0.020  1.080
 MVW  C4   H23  single    0.930  0.020  1.080
 MVW  C5   H24  single    0.930  0.020  1.080
 MVW  N6   H25  single    0.860  0.020  1.020
 MVW  C7   H26  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
 MVW  H2   C1   H1   107.04  3.000
 MVW  H2   C1   C18  109.83  3.000
 MVW  H1   C1   C18  111.22  3.000
 MVW  H2   C1   C15  109.32  3.000
 MVW  H1   C1   C15  109.21  3.000
 MVW  C18  C1   C15  110.16  3.000
 MVW  C10  C2   N6   129.53  3.000
 MVW  C10  C2   C3   122.79  3.000
 MVW  N6   C2   C3   107.68  3.000
 MVW  C9   C3   C4   133.52  3.000
 MVW  C9   C3   C2   120.05  3.000
 MVW  C4   C3   C2   106.42  3.000
 MVW  H4   C11  H3   105.68  3.000
 MVW  H4   C11  N12  110.52  3.000
 MVW  H3   C11  N12  108.17  3.000
 MVW  H4   C11  C9   109.46  3.000
 MVW  H3   C11  C9   108.65  3.000
 MVW  N12  C11  C9   114.00  3.000
 MVW  H12  C15  H11  106.53  3.000
 MVW  H12  C15  N12  110.81  3.000
 MVW  H11  C15  N12  108.51  3.000
 MVW  H12  C15  C1   108.87  3.000
 MVW  H11  C15  C1   109.71  3.000
 MVW  N12  C15  C1   112.24  3.000
 MVW  H13  C16  N12  109.59  3.000
 MVW  H13  C16  C19  107.45  3.000
 MVW  N12  C16  C19  112.06  3.000
 MVW  H13  C16  C17  107.44  3.000
 MVW  N12  C16  C17  111.18  3.000
 MVW  C19  C16  C17  108.94  3.000
 MVW  H15  C17  H14  106.82  3.000
 MVW  H15  C17  C18  111.03  3.000
 MVW  H14  C17  C18  109.48  3.000
 MVW  H15  C17  C16  108.34  3.000
 MVW  H14  C17  C16  108.95  3.000
 MVW  C18  C17  C16  112.06  3.000
 MVW  H17  C18  H16  106.73  3.000
 MVW  H17  C18  C17  110.36  3.000
 MVW  H16  C18  C17  109.75  3.000
 MVW  H17  C18  C1   111.21  3.000
 MVW  H16  C18  C1   109.64  3.000
 MVW  C17  C18  C1   109.12  3.000
 MVW  C24  C19  C20  118.58  3.000
 MVW  C20  C19  C16  120.57  3.000
 MVW  C24  C19  C16  120.80  3.000
 MVW  H18  C20  C21  119.62  3.000
 MVW  H18  C20  C19  119.44  3.000
 MVW  C21  C20  C19  120.94  3.000
 MVW  H19  C21  C22  120.17  3.000
 MVW  H19  C21  C20  119.80  3.000
 MVW  C22  C21  C20  120.03  3.000
 MVW  H20  C22  C23  120.25  3.000
 MVW  H20  C22  C21  120.28  3.000
 MVW  C23  C22  C21  119.48  3.000
 MVW  H21  C23  C24  119.74  3.000
 MVW  H21  C23  C22  119.99  3.000
 MVW  C24  C23  C22  120.27  3.000
 MVW  H22  C24  C23  119.61  3.000
 MVW  H22  C24  C19  119.68  3.000
 MVW  C23  C24  C19  120.71  3.000
 MVW  H23  C4   C5   125.35  3.000
 MVW  H23  C4   C3   127.79  3.000
 MVW  C5   C4   C3   106.87  3.000
 MVW  H24  C5   N6   120.53  3.000
 MVW  H24  C5   C4   129.75  3.000
 MVW  N6   C5   C4   109.73  3.000
 MVW  H25  N6   C5   124.76  3.000
 MVW  H25  N6   C2   125.92  3.000
 MVW  C5   N6   C2   109.30  3.000
 MVW  H26  C7   C10  118.35  3.000
 MVW  H26  C7   C8   118.11  3.000
 MVW  C10  C7   C8   123.54  3.000
 MVW  C9   C8   C7   120.13  3.000
 MVW  C7   C8   C13  118.90  3.000
 MVW  C9   C8   C13  120.98  3.000
 MVW  C8   C9   C11  121.64  3.000
 MVW  C8   C9   C3   117.96  3.000
 MVW  C11  C9   C3   120.39  3.000
 MVW  C7   C10  C14  122.91  3.000
 MVW  C7   C10  C2   115.53  3.000
 MVW  C14  C10  C2   121.56  3.000
 MVW  C16  N12  C15  111.17  3.000
 MVW  C15  N12  C11  110.32  3.000
 MVW  C16  N12  C11  110.47  3.000
 MVW  H7   C13  H6   108.25  3.000
 MVW  H7   C13  H5   107.49  3.000
 MVW  H6   C13  H5   106.51  3.000
 MVW  H7   C13  C8   111.23  3.000
 MVW  H6   C13  C8   111.35  3.000
 MVW  H5   C13  C8   111.77  3.000
 MVW  H10  C14  H9   107.67  3.000
 MVW  H10  C14  H8   106.93  3.000
 MVW  H9   C14  H8   107.69  3.000
 MVW  H10  C14  C10  111.49  3.000
 MVW  H9   C14  C10  111.19  3.000
 MVW  H8   C14  C10  111.65  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
 MVW  CONST_01  C4   C5   N6   C2     0.00   0.0  0
 MVW  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 MVW  CONST_03  C8   C9   C3   C2     0.00   0.0  0
 MVW  CONST_04  C8   C7   C10  C2     0.00   0.0  0
 MVW  CONST_05  N6   C5   C4   C3     0.00   0.0  0
 MVW  CONST_06  C5   N6   C2   C3     0.00   0.0  0
 MVW  CONST_07  C7   C10  C2   C3     0.00   0.0  0
 MVW  CONST_08  C7   C8   C9   C3     0.00   0.0  0
 MVW  CONST_09  C22  C23  C24  C19    0.00   0.0  0
 MVW  CONST_10  C22  C21  C20  C19    0.00   0.0  0
 MVW  CONST_11  C23  C22  C21  C20    0.00   0.0  0
 MVW  CONST_12  C23  C24  C19  C20    0.00   0.0  0
 MVW  CONST_13  C24  C23  C22  C21    0.00   0.0  0
 MVW  CONST_14  C24  C19  C20  C21    0.00   0.0  0
 MVW  CONST_15  N6   C2   C3   C4     0.00   0.0  0
 MVW  CONST_16  C10  C2   C3   C4   180.00   0.0  0
 MVW  CONST_17  C8   C9   C3   C4   180.00   0.0  0
 MVW  CONST_18  C9   C3   C4   C5   180.00   0.0  0
 MVW  CONST_19  C10  C2   N6   C5   180.00   0.0  0
 MVW  CONST_20  C9   C3   C2   N6   180.00   0.0  0
 MVW  CONST_21  C7   C10  C2   N6   180.00   0.0  0
 MVW  CONST_22  C10  C2   C3   C9     0.00   0.0  0
 MVW  CONST_23  C10  C7   C8   C9     0.00   0.0  0
 MVW  CONST_24  C23  C24  C19  C16  180.00   0.0  0
 MVW  CONST_25  C21  C20  C19  C16  180.00   0.0  0
 MVW  CONST_26  C11  C9   C3   C2   180.00   0.0  0
 MVW  CONST_27  C14  C10  C2   C3   180.00   0.0  0
 MVW  CONST_28  C13  C8   C9   C3   180.00   0.0  0
 MVW  CONST_29  C4   C3   C9   C11    0.00   0.0  0
 MVW  CONST_30  C7   C8   C9   C11  180.00   0.0  0
 MVW  CONST_31  C10  C7   C8   C13  180.00   0.0  0
 MVW  CONST_32  N6   C2   C10  C14    0.00   0.0  0
 MVW  CONST_33  C8   C7   C10  C14  180.00   0.0  0
 MVW  CONST_34  H24  C5   N6   C2   180.00   0.0  0
 MVW  CONST_35  H23  C4   C3   C2   180.00   0.0  0
 MVW  CONST_36  H26  C7   C10  C2   180.00   0.0  0
 MVW  CONST_37  H25  N6   C2   C3   180.00   0.0  0
 MVW  CONST_38  H22  C24  C19  C16    0.00   0.0  0
 MVW  CONST_39  H18  C20  C19  C16    0.00   0.0  0
 MVW  CONST_40  H21  C23  C24  C19  180.00   0.0  0
 MVW  CONST_41  H19  C21  C20  C19  180.00   0.0  0
 MVW  CONST_42  H20  C22  C21  C20  180.00   0.0  0
 MVW  Var_01    C16  C17  C18  C1    53.74  30.0  1
 MVW  Var_02    C16  N12  C15  C1   -58.81  30.0  1
 MVW  Var_03    C17  C18  C1   C15  -54.62  30.0  1
 MVW  Var_04    N12  C15  C1   C18   58.26  30.0  1
 MVW  Var_05    N12  C11  C9   C3   109.20  30.0  2
 MVW  Var_06    C9   C11  N12  C15  -59.31  30.0  2
 MVW  Var_07    H8   C14  C10  C2    57.18  30.0  2
 MVW  Var_08    H5   C13  C8   C7   118.94  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
 MVW  chir_01  C16  C19  C17  N12  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
 MVW  plan-1  C16  0.020
 MVW  plan-1  C19  0.020
 MVW  plan-1  C20  0.020
 MVW  plan-1  C21  0.020
 MVW  plan-1  C22  0.020
 MVW  plan-1  C23  0.020
 MVW  plan-1  C24  0.020
 MVW  plan-1  H18  0.020
 MVW  plan-1  H19  0.020
 MVW  plan-1  H20  0.020
 MVW  plan-1  H21  0.020
 MVW  plan-1  H22  0.020
 MVW  plan-2  C2   0.020
 MVW  plan-2  C3   0.020
 MVW  plan-2  C11  0.020
 MVW  plan-2  C4   0.020
 MVW  plan-2  C5   0.020
 MVW  plan-2  N6   0.020
 MVW  plan-2  C7   0.020
 MVW  plan-2  C8   0.020
 MVW  plan-2  C9   0.020
 MVW  plan-2  C10  0.020
 MVW  plan-2  H23  0.020
 MVW  plan-2  H24  0.020
 MVW  plan-2  H25  0.020
 MVW  plan-2  H26  0.020
 MVW  plan-2  C13  0.020
 MVW  plan-2  C14  0.020

