# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:46:26 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: (7-amino-3,4-dihydroquinolin-1(2H)-yl)(cyclopropyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2CCCN(C(=O)C3CC3)c2c1
#
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
 VYM  VYM  (7-amino-3,4-dihydroquinolin-1(2H)-yl)(cyclopropyl)methanone  ligand  32  16  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VYM
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
 VYM  C01  C  C     0   0.597   -7.7935  -7.1541   -9.0264
 VYM  C02  C  CH1   0  -0.387   -8.6320  -5.9260   -8.9172
 VYM  C03  C  CH2   0  -0.466   -9.4717  -5.7596   -7.6742
 VYM  C04  C  CH2   0  -0.467   -8.2550  -4.9285   -7.8577
 VYM  C05  C  CH2   0  -0.334   -6.7145  -8.7513  -10.5247
 VYM  C06  C  CH2   0  -0.466   -5.9416  -8.1606  -11.6919
 VYM  C07  C  CH2   0  -0.468   -6.8418  -8.0321  -12.9172
 VYM  C13  C  CR16  0  -0.277   -9.2175  -7.5555  -13.5865
 VYM  C08  C  CR6   0  -0.049   -8.2778  -7.7248  -12.5746
 VYM  C09  C  CR6   0   0.324   -8.7381  -7.6630  -11.2562
 VYM  C10  C  CR16  0  -0.417  -10.0967  -7.5055  -10.9851
 VYM  C11  C  CR6   0   0.165  -11.0210  -7.3217  -12.0107
 VYM  C12  C  CR16  0  -0.286  -10.5575  -7.3404  -13.3292
 VYM  N01  N  NT    0  -0.575   -7.8222  -7.8584  -10.2061
 VYM  O01  O  O     0  -0.473   -7.0748  -7.5004   -8.1074
 VYM  H1   H  HCH1  0   0.300   -9.0429  -5.5158   -9.8285
 VYM  H2   H  HCH2  0   0.270  -10.4430  -5.2984   -7.7937
 VYM  H3   H  HCH2  0   0.266   -9.4358  -6.5579   -6.9449
 VYM  H4   H  HCH2  0   0.256   -7.3892  -5.1448   -7.2475
 VYM  H5   H  HCH2  0   0.212   -8.3836  -3.8864   -8.1176
 VYM  H6   H  HCH2  0   0.225   -7.1080  -9.7397  -10.7779
 VYM  H7   H  HCH2  0   0.289   -6.0886  -8.8625   -9.6446
 VYM  H8   H  HCH2  0   0.227   -5.0776  -8.7841  -11.9256
 VYM  H9   H  HCH2  0   0.254   -5.5547  -7.1840  -11.3919
 VYM  H10  H  HCH2  0   0.243   -6.8220  -8.9714  -13.4779
 VYM  H11  H  HCH2  0   0.256   -6.4450  -7.2750  -13.5976
 VYM  H12  H  HCR6  0   0.253   -8.8864  -7.5944  -14.6179
 VYM  H13  H  HCR6  0   0.258  -10.4415  -7.5416   -9.9586
 VYM  H14  H  HCR6  0   0.248  -11.2499  -7.2128  -14.1526
 VYM  H15  H  HNH2  0   0.373  -12.6021  -6.8655  -10.8143
 VYM  H16  H  HNH2  0   0.387  -12.9357  -6.7900  -12.4475
 VYM  N02  N  NH2   0  -0.740  -12.3699  -7.2095  -11.7300

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
 VYM  C13  C12  aromatic  1.381  0.020  1.381
 VYM  C13  C08  aromatic  1.391  0.020  1.391
 VYM  C12  C11  aromatic  1.398  0.020  1.398
 VYM  C07  C08  single    1.508  0.020  1.508
 VYM  C07  C06  single    1.526  0.020  1.526
 VYM  C08  C09  aromatic  1.398  0.020  1.398
 VYM  C11  N02  single    1.382  0.020  1.382
 VYM  C11  C10  aromatic  1.393  0.020  1.393
 VYM  C06  C05  single    1.520  0.020  1.520
 VYM  C09  C10  aromatic  1.394  0.020  1.394
 VYM  C09  N01  single    1.407  0.020  1.407
 VYM  C05  N01  single    1.458  0.020  1.458
 VYM  N01  C01  single    1.374  0.020  1.374
 VYM  C01  C02  single    1.491  0.020  1.491
 VYM  C01  O01  double    1.217  0.020  1.217
 VYM  C02  C03  single    1.509  0.020  1.509
 VYM  C02  C04  single    1.503  0.020  1.503
 VYM  C03  C04  single    1.485  0.020  1.485
 VYM  C02  H1   single    0.970  0.020  1.090
 VYM  C03  H2   single    0.970  0.020  1.090
 VYM  C03  H3   single    0.970  0.020  1.090
 VYM  C04  H4   single    0.970  0.020  1.090
 VYM  C04  H5   single    0.970  0.020  1.090
 VYM  C05  H6   single    0.970  0.020  1.090
 VYM  C05  H7   single    0.970  0.020  1.090
 VYM  C06  H8   single    0.970  0.020  1.090
 VYM  C06  H9   single    0.970  0.020  1.090
 VYM  C07  H10  single    0.970  0.020  1.090
 VYM  C07  H11  single    0.970  0.020  1.090
 VYM  C13  H12  single    0.930  0.020  1.080
 VYM  C10  H13  single    0.930  0.020  1.080
 VYM  C12  H14  single    0.930  0.020  1.080
 VYM  N02  H15  single    0.890  0.020  1.040
 VYM  N02  H16  single    0.890  0.020  1.040

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
 VYM  O01  C01  N01  120.98  3.000
 VYM  O01  C01  C02  120.74  3.000
 VYM  N01  C01  C02  118.25  3.000
 VYM  H1   C02  C04  115.97  3.000
 VYM  H1   C02  C03  116.17  3.000
 VYM  C04  C02  C03   59.06  3.000
 VYM  H1   C02  C01  117.70  3.000
 VYM  C04  C02  C01  117.20  3.000
 VYM  C03  C02  C01  117.65  3.000
 VYM  H3   C03  H2   114.76  3.000
 VYM  H3   C03  C04  117.98  3.000
 VYM  H2   C03  C04  118.91  3.000
 VYM  H3   C03  C02  117.09  3.000
 VYM  H2   C03  C02  117.10  3.000
 VYM  C04  C03  C02   60.27  3.000
 VYM  H5   C04  H4   115.06  3.000
 VYM  H5   C04  C03  118.13  3.000
 VYM  H4   C04  C03  118.33  3.000
 VYM  H5   C04  C02  116.11  3.000
 VYM  H4   C04  C02  117.77  3.000
 VYM  C03  C04  C02   60.67  3.000
 VYM  H7   C05  H6   107.61  3.000
 VYM  H7   C05  N01  108.89  3.000
 VYM  H6   C05  N01  109.32  3.000
 VYM  H7   C05  C06  111.67  3.000
 VYM  H6   C05  C06  110.89  3.000
 VYM  N01  C05  C06  108.44  3.000
 VYM  H9   C06  H8   106.82  3.000
 VYM  H9   C06  C07  110.75  3.000
 VYM  H8   C06  C07  110.08  3.000
 VYM  H9   C06  C05  108.46  3.000
 VYM  H8   C06  C05  110.20  3.000
 VYM  C07  C06  C05  110.46  3.000
 VYM  H11  C07  H10  105.62  3.000
 VYM  H11  C07  C08  110.25  3.000
 VYM  H10  C07  C08  107.98  3.000
 VYM  H11  C07  C06  110.13  3.000
 VYM  H10  C07  C06  109.18  3.000
 VYM  C08  C07  C06  113.36  3.000
 VYM  H12  C13  C12  118.63  3.000
 VYM  H12  C13  C08  118.78  3.000
 VYM  C12  C13  C08  122.59  3.000
 VYM  C09  C08  C13  117.27  3.000
 VYM  C09  C08  C07  122.48  3.000
 VYM  C13  C08  C07  120.18  3.000
 VYM  N01  C09  C10  120.32  3.000
 VYM  N01  C09  C08  118.90  3.000
 VYM  C10  C09  C08  120.62  3.000
 VYM  H13  C10  C11  119.39  3.000
 VYM  H13  C10  C09  119.38  3.000
 VYM  C11  C10  C09  121.22  3.000
 VYM  N02  C11  C12  121.07  3.000
 VYM  N02  C11  C10  120.58  3.000
 VYM  C12  C11  C10  118.22  3.000
 VYM  H14  C12  C11  120.23  3.000
 VYM  H14  C12  C13  119.78  3.000
 VYM  C11  C12  C13  119.96  3.000
 VYM  C09  N01  C05  114.62  3.000
 VYM  C05  N01  C01  119.05  3.000
 VYM  C09  N01  C01  125.66  3.000
 VYM  H16  N02  H15  112.16  3.000
 VYM  H16  N02  C11  115.99  3.000
 VYM  H15  N02  C11  115.98  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
 VYM  CONST_01  C10  C11  C12  C13     0.00   0.0  0
 VYM  CONST_02  C10  C09  C08  C13     0.00   0.0  0
 VYM  CONST_03  C11  C12  C13  C08     0.00   0.0  0
 VYM  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 VYM  CONST_05  C12  C13  C08  C09     0.00   0.0  0
 VYM  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 VYM  CONST_07  N02  C11  C12  C13   180.00   0.0  0
 VYM  CONST_08  N02  C11  C10  C09   180.00   0.0  0
 VYM  CONST_09  C09  N01  C01  C02     0.00   0.0  0
 VYM  CONST_11  H12  C13  C08  C07     0.00   0.0  0
 VYM  CONST_12  H14  C12  C13  C08   180.00   0.0  0
 VYM  CONST_13  H13  C10  C09  C08   180.00   0.0  0
 VYM  CONST_15  O01  C01  N01  C09   180.00   0.0  0
 VYM  Var_01    C08  C07  C06  C05    33.37  30.0  1
 VYM  Var_02    C08  C09  N01  C05   -30.64  30.0  1
 VYM  Var_03    C13  C08  C07  C06   178.92  30.0  1
 VYM  Var_04    C09  N01  C05  C06    60.26  30.0  1
 VYM  Var_05    N01  C05  C06  C07   -60.71  30.0  1
 VYM  Var_06    C04  C03  C02  C01   106.72  30.0  1
 VYM  Var_07    N01  C01  C02  C03   133.01  30.0  2
 VYM  Var_08    H4   C04  C03  C02  -107.71  30.0  1

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
 VYM  chir_01  C02  C01  C03  C04  both

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
 VYM  plan-1  C01  0.020
 VYM  plan-1  C02  0.020
 VYM  plan-1  C05  0.020
 VYM  plan-1  C09  0.020
 VYM  plan-1  N01  0.020
 VYM  plan-1  O01  0.020
 VYM  plan-2  C07  0.020
 VYM  plan-2  C13  0.020
 VYM  plan-2  C08  0.020
 VYM  plan-2  C09  0.020
 VYM  plan-2  C10  0.020
 VYM  plan-2  C11  0.020
 VYM  plan-2  C12  0.020
 VYM  plan-2  N01  0.020
 VYM  plan-2  H12  0.020
 VYM  plan-2  H13  0.020
 VYM  plan-2  H14  0.020
 VYM  plan-2  N02  0.020
 VYM  plan-3  C11  0.020
 VYM  plan-3  H15  0.020
 VYM  plan-3  H16  0.020
 VYM  plan-3  N02  0.020

