# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:05:21 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (2R)-hydroxy(phenyl)ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C#N)c1ccccc1
#
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
 MXN  MXN  (2R)-hydroxy(phenyl)ethanenitrile  ligand  17  10  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MXN
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
 MXN  C1    C  CR6   0   0.070   0.0647  -0.0663   0.2226
 MXN  C2    C  CR16  0  -0.327   0.9537  -0.8282   0.9711
 MXN  C3    C  CR16  0  -0.129   2.3120  -0.8007   0.6851
 MXN  C4    C  CR16  0  -0.321   2.7888  -0.0029  -0.3442
 MXN  C5    C  CR16  0  -0.214   1.9039   0.7627  -1.0939
 MXN  C6    C  CR16  0  -0.241   0.5464   0.7307  -0.8130
 MXN  C7    C  CH1   0  -0.082  -1.4007  -0.0536   0.5904
 MXN  C8    C  CSP   0   0.127  -2.2358  -0.2193  -0.6181
 MXN  N9    N  NS    0  -0.292  -2.9048  -0.3420  -1.5456
 MXN  O10   O  OH1   0  -0.615  -1.7968   1.0789   1.3086
 MXN  H2    H  HCR6  0   0.238   0.5847  -1.4509   1.7769
 MXN  H3    H  HCR6  0   0.267   2.9949  -1.4072   1.2656
 MXN  H4    H  HCR6  0   0.243   3.8476   0.0202  -0.5664
 MXN  H5    H  HCR6  0   0.266   2.2698   1.3849  -1.9002
 MXN  H6    H  HCR6  0   0.205  -0.1336   1.3221  -1.4153
 MXN  H7    H  HCH1  0   0.346  -1.6136  -0.9162   1.2273
 MXN  HO10  H  HOH1  0   0.459  -1.5011   1.8729   0.8468

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
 MXN  C7   C1    single    1.511  0.020  1.511
 MXN  C1   C2    aromatic  1.390  0.020  1.390
 MXN  C1   C6    aromatic  1.393  0.020  1.393
 MXN  C2   C3    aromatic  1.388  0.020  1.388
 MXN  C2   H2    single    0.930  0.020  1.080
 MXN  C3   C4    aromatic  1.387  0.020  1.387
 MXN  C3   H3    single    0.930  0.020  1.080
 MXN  C5   C4    aromatic  1.390  0.020  1.390
 MXN  C4   H4    single    0.930  0.020  1.080
 MXN  C6   C5    aromatic  1.387  0.020  1.387
 MXN  C5   H5    single    0.930  0.020  1.080
 MXN  C6   H6    single    0.930  0.020  1.080
 MXN  O10  C7    single    1.398  0.020  1.398
 MXN  C7   C8    single    1.478  0.020  1.478
 MXN  C7   H7    single    0.970  0.020  1.090
 MXN  C8   N9    triple    1.150  0.020  1.150
 MXN  O10  HO10  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
 MXN  C7    C1   C6   120.77  3.000
 MXN  C6    C1   C2   119.54  3.000
 MXN  C7    C1   C2   119.60  3.000
 MXN  H2    C2   C3   119.86  3.000
 MXN  H2    C2   C1   119.87  3.000
 MXN  C3    C2   C1   120.27  3.000
 MXN  H3    C3   C4   120.23  3.000
 MXN  H3    C3   C2   119.72  3.000
 MXN  C4    C3   C2   120.04  3.000
 MXN  H4    C4   C5   120.03  3.000
 MXN  H4    C4   C3   120.07  3.000
 MXN  C5    C4   C3   119.90  3.000
 MXN  H5    C5   C6   119.68  3.000
 MXN  H5    C5   C4   120.23  3.000
 MXN  C6    C5   C4   120.09  3.000
 MXN  H6    C6   C5   119.28  3.000
 MXN  H6    C6   C1   120.56  3.000
 MXN  C5    C6   C1   120.16  3.000
 MXN  H7    C7   O10  106.54  3.000
 MXN  H7    C7   C8   106.13  3.000
 MXN  O10   C7   C8   110.53  3.000
 MXN  H7    C7   C1   108.91  3.000
 MXN  C8    C7   C1   110.36  3.000
 MXN  O10   C7   C1   113.99  3.000
 MXN  N9    C8   C7   180.00  3.000
 MXN  HO10  O10  C7   109.50  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
 MXN  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 MXN  CONST_02  C4  C5  C6  C1    0.00  0.0  0
 MXN  CONST_03  C5  C6  C1  C2    0.00  0.0  0
 MXN  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 MXN  CONST_05  C6  C1  C2  C3    0.00  0.0  0
 MXN  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 MXN  CONST_07  C7  C1  C2  C3  180.00  0.0  0
 MXN  CONST_08  C7  C1  C6  C5  180.00  0.0  0
 MXN  CONST_09  H3  C3  C2  C1  180.00  0.0  0
 MXN  CONST_10  H5  C5  C6  C1  180.00  0.0  0
 MXN  CONST_11  H6  C6  C1  C2  180.00  0.0  0
 MXN  CONST_12  H4  C4  C3  C2  180.00  0.0  0
 MXN  CONST_13  H2  C2  C3  C4  180.00  0.0  0

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
 MXN  chir_01  C7  C1  O10  C8  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
 MXN  plan-1  C1  0.020
 MXN  plan-1  C2  0.020
 MXN  plan-1  C3  0.020
 MXN  plan-1  C4  0.020
 MXN  plan-1  C5  0.020
 MXN  plan-1  C6  0.020
 MXN  plan-1  C7  0.020
 MXN  plan-1  H2  0.020
 MXN  plan-1  H3  0.020
 MXN  plan-1  H4  0.020
 MXN  plan-1  H5  0.020
 MXN  plan-1  H6  0.020

