# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:49:38 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC1CCCCC1)NCc2ccccc2O
#
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
 VB3  VB3  2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol  ligand  43  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VB3
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
 VB3  C01   C  CH3   0  -0.653  14.2610  -10.3907  -71.6209
 VB3  C02   C  CH1   0  -0.087  13.7371  -11.4756  -70.6855
 VB3  C04   C  CH2   0  -0.356  11.4689  -12.1437  -69.8765
 VB3  C05   C  CR6   0  -0.027  10.9073  -12.7538  -71.1345
 VB3  C06   C  CR6   0   0.328  10.5336  -11.9282  -72.2075
 VB3  C08   C  CR16  0  -0.344   9.9485  -12.4880  -73.3415
 VB3  C09   C  CR16  0  -0.258   9.7371  -13.8575  -73.4144
 VB3  C10   C  CR16  0  -0.277  10.1189  -14.6862  -72.3680
 VB3  C11   C  CR16  0  -0.304  10.7039  -14.1235  -71.2406
 VB3  C12   C  CH2   0  -0.403  14.7710  -11.7484  -69.5868
 VB3  C13   C  CH1   0  -0.253  14.4575  -12.8423  -68.5694
 VB3  C14   C  CH2   0  -0.453  14.2923  -14.2272  -69.1885
 VB3  C15   C  CH2   0  -0.429  13.7554  -15.2300  -68.1560
 VB3  C16   C  CH2   0  -0.446  14.2010  -14.8837  -66.7285
 VB3  C17   C  CH2   0  -0.446  15.5807  -14.2364  -66.7395
 VB3  C18   C  CH2   0  -0.405  15.5555  -12.8969  -67.4942
 VB3  N03   N  NH1   0  -0.656  12.4178  -11.0741  -70.1812
 VB3  O07   O  OH1   0  -0.660  10.7278  -10.5994  -72.1547
 VB3  H012  H  HCH3  0   0.228  15.2323  -10.6641  -72.0346
 VB3  H013  H  HCH3  0   0.229  13.5778  -10.2249  -72.4537
 VB3  H011  H  HCH3  0   0.219  14.3811   -9.4449  -71.0877
 VB3  H021  H  HCH1  0   0.234  13.5859  -12.3833  -71.2785
 VB3  H042  H  HCH2  0   0.269  10.6578  -11.6881  -69.3007
 VB3  H041  H  HCH2  0   0.241  11.8827  -12.9354  -69.2444
 VB3  H081  H  HCR6  0   0.253   9.6597  -11.8431  -74.1628
 VB3  H091  H  HCR6  0   0.252   9.2797  -14.2770  -74.3013
 VB3  H101  H  HCR6  0   0.247   9.9646  -15.7553  -72.4275
 VB3  H111  H  HCR6  0   0.244  11.0017  -14.7604  -70.4143
 VB3  H121  H  HCH2  0   0.216  15.7220  -11.9929  -70.0731
 VB3  H122  H  HCH2  0   0.218  14.9468  -10.8074  -69.0496
 VB3  H131  H  HCH1  0   0.222  13.5210  -12.5820  -68.0630
 VB3  H141  H  HCH2  0   0.230  13.6249  -14.2016  -70.0537
 VB3  H142  H  HCH2  0   0.223  15.2634  -14.5559  -69.5745
 VB3  H151  H  HCH2  0   0.219  12.6627  -15.2550  -68.2004
 VB3  H152  H  HCH2  0   0.222  14.0925  -16.2359  -68.4170
 VB3  H161  H  HCH2  0   0.216  13.4858  -14.1967  -66.2659
 VB3  H162  H  HCH2  0   0.228  14.2015  -15.7811  -66.1061
 VB3  H171  H  HCH2  0   0.215  16.2879  -14.9227  -67.2152
 VB3  H172  H  HCH2  0   0.228  15.9453  -14.0876  -65.7208
 VB3  H182  H  HCH2  0   0.213  16.5301  -12.7250  -67.9621
 VB3  H181  H  HCH2  0   0.221  15.4046  -12.0722  -66.7923
 VB3  H1    H  HNH1  0   0.371  12.5161  -10.4554  -69.3849
 VB3  H071  H  HOH1  0   0.471  11.3933  -10.4481  -71.4236

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
 VB3  C08  C09   aromatic  1.388  0.020  1.388
 VB3  C08  C06   aromatic  1.393  0.020  1.393
 VB3  C09  C10   aromatic  1.388  0.020  1.388
 VB3  O07  C06   single    1.344  0.020  1.344
 VB3  C06  C05   aromatic  1.404  0.020  1.404
 VB3  C10  C11   aromatic  1.389  0.020  1.389
 VB3  C01  C02   single    1.525  0.020  1.525
 VB3  C05  C11   aromatic  1.389  0.020  1.389
 VB3  C05  C04   single    1.507  0.020  1.507
 VB3  C02  N03   single    1.468  0.020  1.468
 VB3  C02  C12   single    1.533  0.020  1.533
 VB3  N03  C04   single    1.462  0.020  1.462
 VB3  C12  C13   single    1.526  0.020  1.526
 VB3  C14  C13   single    1.526  0.020  1.526
 VB3  C14  C15   single    1.536  0.020  1.536
 VB3  C13  C18   single    1.538  0.020  1.538
 VB3  C15  C16   single    1.535  0.020  1.535
 VB3  C18  C17   single    1.538  0.020  1.538
 VB3  C16  C17   single    1.524  0.020  1.524
 VB3  C01  H012  single    0.970  0.020  1.090
 VB3  C01  H013  single    0.970  0.020  1.090
 VB3  C01  H011  single    0.970  0.020  1.090
 VB3  C02  H021  single    0.970  0.020  1.090
 VB3  C04  H042  single    0.970  0.020  1.090
 VB3  C04  H041  single    0.970  0.020  1.090
 VB3  C08  H081  single    0.930  0.020  1.080
 VB3  C09  H091  single    0.930  0.020  1.080
 VB3  C10  H101  single    0.930  0.020  1.080
 VB3  C11  H111  single    0.930  0.020  1.080
 VB3  C12  H121  single    0.970  0.020  1.090
 VB3  C12  H122  single    0.970  0.020  1.090
 VB3  C13  H131  single    0.970  0.020  1.090
 VB3  C14  H141  single    0.970  0.020  1.090
 VB3  C14  H142  single    0.970  0.020  1.090
 VB3  C15  H151  single    0.970  0.020  1.090
 VB3  C15  H152  single    0.970  0.020  1.090
 VB3  C16  H161  single    0.970  0.020  1.090
 VB3  C16  H162  single    0.970  0.020  1.090
 VB3  C17  H171  single    0.970  0.020  1.090
 VB3  C17  H172  single    0.970  0.020  1.090
 VB3  C18  H182  single    0.970  0.020  1.090
 VB3  C18  H181  single    0.970  0.020  1.090
 VB3  N03  H1    single    0.890  0.020  1.040
 VB3  O07  H071  single    0.850  0.020  0.980

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
 VB3  H011  C01  H013  108.07  3.000
 VB3  H011  C01  H012  107.71  3.000
 VB3  H013  C01  H012  107.85  3.000
 VB3  H011  C01  C02   110.76  3.000
 VB3  H013  C01  C02   111.19  3.000
 VB3  H012  C01  C02   111.11  3.000
 VB3  H021  C02  N03   106.78  3.000
 VB3  H021  C02  C12   109.50  3.000
 VB3  N03   C02  C12   114.11  3.000
 VB3  H021  C02  C01   107.76  3.000
 VB3  C12   C02  C01   109.54  3.000
 VB3  N03   C02  C01   108.95  3.000
 VB3  H041  C04  H042  106.12  3.000
 VB3  H041  C04  N03   113.85  3.000
 VB3  H042  C04  N03   106.63  3.000
 VB3  H041  C04  C05   109.28  3.000
 VB3  H042  C04  C05   109.37  3.000
 VB3  N03   C04  C05   111.36  3.000
 VB3  C11   C05  C06   118.85  3.000
 VB3  C11   C05  C04   121.18  3.000
 VB3  C06   C05  C04   119.93  3.000
 VB3  O07   C06  C08   119.33  3.000
 VB3  O07   C06  C05   120.85  3.000
 VB3  C08   C06  C05   119.82  3.000
 VB3  H081  C08  C09   120.46  3.000
 VB3  H081  C08  C06   119.33  3.000
 VB3  C09   C08  C06   120.21  3.000
 VB3  H091  C09  C10   120.16  3.000
 VB3  H091  C09  C08   119.34  3.000
 VB3  C10   C09  C08   120.50  3.000
 VB3  H101  C10  C11   120.33  3.000
 VB3  H101  C10  C09   120.61  3.000
 VB3  C11   C10  C09   119.06  3.000
 VB3  H111  C11  C10   119.72  3.000
 VB3  H111  C11  C05   118.73  3.000
 VB3  C10   C11  C05   121.54  3.000
 VB3  H122  C12  H121  105.63  3.000
 VB3  H122  C12  C13   108.72  3.000
 VB3  H121  C12  C13   108.31  3.000
 VB3  H122  C12  C02   107.83  3.000
 VB3  H121  C12  C02   107.88  3.000
 VB3  C13   C12  C02   117.82  3.000
 VB3  H131  C13  C18   107.19  3.000
 VB3  H131  C13  C14   108.09  3.000
 VB3  C18   C13  C14   109.19  3.000
 VB3  H131  C13  C12   108.26  3.000
 VB3  C18   C13  C12   110.18  3.000
 VB3  C14   C13  C12   113.72  3.000
 VB3  H142  C14  H141  105.63  3.000
 VB3  H142  C14  C15   110.54  3.000
 VB3  H141  C14  C15   109.50  3.000
 VB3  H142  C14  C13   108.62  3.000
 VB3  H141  C14  C13   111.47  3.000
 VB3  C15   C14  C13   110.95  3.000
 VB3  H152  C15  H151  106.11  3.000
 VB3  H152  C15  C16   109.90  3.000
 VB3  H151  C15  C16   109.45  3.000
 VB3  H152  C15  C14   109.42  3.000
 VB3  H151  C15  C14   109.68  3.000
 VB3  C16   C15  C14   112.10  3.000
 VB3  H162  C16  H161  105.97  3.000
 VB3  H162  C16  C17   110.65  3.000
 VB3  H161  C16  C17   109.15  3.000
 VB3  H162  C16  C15   110.16  3.000
 VB3  H161  C16  C15   110.18  3.000
 VB3  C17   C16  C15   110.61  3.000
 VB3  H172  C17  H171  105.97  3.000
 VB3  H172  C17  C18   110.16  3.000
 VB3  H171  C17  C18   110.10  3.000
 VB3  H172  C17  C16   110.69  3.000
 VB3  H171  C17  C16   108.78  3.000
 VB3  C18   C17  C16   111.02  3.000
 VB3  H181  C18  H182  106.19  3.000
 VB3  H181  C18  C17   110.14  3.000
 VB3  H182  C18  C17   109.39  3.000
 VB3  H181  C18  C13   108.87  3.000
 VB3  H182  C18  C13   109.34  3.000
 VB3  C17   C18  C13   112.70  3.000
 VB3  H1    N03  C04   110.24  3.000
 VB3  H1    N03  C02   110.47  3.000
 VB3  C04   N03  C02   117.05  3.000
 VB3  H071  O07  C06   105.93  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
 VB3  CONST_01  C09   C08  C06  C05    0.00   0.0  0
 VB3  CONST_02  C09   C10  C11  C05    0.00   0.0  0
 VB3  CONST_03  C10   C09  C08  C06    0.00   0.0  0
 VB3  CONST_04  C10   C11  C05  C06    0.00   0.0  0
 VB3  CONST_05  C11   C10  C09  C08    0.00   0.0  0
 VB3  CONST_06  C11   C05  C06  C08    0.00   0.0  0
 VB3  CONST_07  C08   C06  C05  C04  180.00   0.0  0
 VB3  CONST_08  C10   C11  C05  C04  180.00   0.0  0
 VB3  CONST_09  O07   C06  C08  C09  180.00   0.0  0
 VB3  CONST_10  O07   C06  C05  C11  180.00   0.0  0
 VB3  CONST_11  H081  C08  C06  C05  180.00   0.0  0
 VB3  CONST_12  H101  C10  C11  C05  180.00   0.0  0
 VB3  CONST_13  H091  C09  C08  C06  180.00   0.0  0
 VB3  CONST_14  H111  C11  C05  C06  180.00   0.0  0
 VB3  Var_01    C16   C15  C14  C13  -30.17  30.0  1
 VB3  Var_02    C16   C17  C18  C13  -27.39  30.0  1
 VB3  Var_03    C17   C16  C15  C14  -32.56  30.0  1
 VB3  Var_04    C18   C17  C16  C15   63.43  30.0  1
 VB3  Var_05    N03   C04  C05  C06  -42.15  30.0  2
 VB3  Var_06    C05   C04  N03  C02  -74.03  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
 VB3  chir_01  C02  C01  N03  C12  positiv
 VB3  chir_02  C13  C12  C14  C18  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
 VB3  plan-1  C04   0.020
 VB3  plan-1  C05   0.020
 VB3  plan-1  C06   0.020
 VB3  plan-1  C08   0.020
 VB3  plan-1  C09   0.020
 VB3  plan-1  C10   0.020
 VB3  plan-1  C11   0.020
 VB3  plan-1  O07   0.020
 VB3  plan-1  H081  0.020
 VB3  plan-1  H091  0.020
 VB3  plan-1  H101  0.020
 VB3  plan-1  H111  0.020

