# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 10:23:06 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 3-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccnc1N
#
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
 93Q  93Q  '3-methylpyridin-2-amine  '  ligand  16  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_93Q
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
 93Q  C1  C  CR6   0  -0.019   0.5683   0.7041   0.0372
 93Q  C3  C  CR16  0  -0.354  -1.8435   0.7166   0.0111
 93Q  C4  C  CR16  0  -0.076  -1.7994  -0.6619  -0.0121
 93Q  C5  C  CR6   0   0.398   0.4885  -0.7076   0.0076
 93Q  N1  N  NH2   0  -0.832   1.6254  -1.4662   0.0562
 93Q  C   C  CH3   0  -0.747   1.8942   1.3986   0.0834
 93Q  N   N  N     0  -0.456  -0.6681  -1.3621  -0.0171
 93Q  C2  C  CR16  0  -0.197  -0.6259   1.3955   0.0349
 93Q  H1  H  HCR6  0   0.255  -2.7865   1.2448   0.0105
 93Q  H2  H  HCR6  0   0.252  -2.7167  -1.2412  -0.0309
 93Q  H3  H  HNH2  0   0.391   2.4794  -1.0626  -0.2909
 93Q  H4  H  HNH2  0   0.381   1.5102  -2.4353  -0.1923
 93Q  H5  H  HCH3  0   0.244   2.5067   1.1740  -0.7940
 93Q  H6  H  HCH3  0   0.256   1.7654   2.4791   0.1208
 93Q  H7  H  HCH3  0   0.248   2.4732   1.1015   0.9609
 93Q  H8  H  HCR6  0   0.257  -0.6090   2.4791   0.0561

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
 93Q  C3  C4  aromatic  1.379  0.020  1.379
 93Q  C3  C2  aromatic  1.394  0.020  1.394
 93Q  C4  N   aromatic  1.330  0.020  1.330
 93Q  C2  C1  aromatic  1.380  0.020  1.380
 93Q  N   C5  aromatic  1.329  0.020  1.329
 93Q  C1  C5  aromatic  1.414  0.020  1.414
 93Q  C1  C   single    1.497  0.020  1.497
 93Q  C5  N1  single    1.368  0.020  1.368
 93Q  C3  H1  single    0.930  0.020  1.080
 93Q  C4  H2  single    0.930  0.020  1.080
 93Q  N1  H3  single    0.890  0.020  1.040
 93Q  N1  H4  single    0.890  0.020  1.040
 93Q  C   H5  single    0.970  0.020  1.090
 93Q  C   H6  single    0.970  0.020  1.090
 93Q  C   H7  single    0.970  0.020  1.090
 93Q  C2  H8  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
 93Q  C2  C1  C   122.27  3.000
 93Q  C   C1  C5  120.90  3.000
 93Q  C2  C1  C5  116.83  3.000
 93Q  H1  C3  C2  121.60  3.000
 93Q  H1  C3  C4  121.08  3.000
 93Q  C2  C3  C4  117.32  3.000
 93Q  H2  C4  N   115.96  3.000
 93Q  H2  C4  C3  120.45  3.000
 93Q  N   C4  C3  123.59  3.000
 93Q  N   C5  N1  116.80  3.000
 93Q  N1  C5  C1  120.40  3.000
 93Q  N   C5  C1  122.75  3.000
 93Q  H4  N1  H3  113.45  3.000
 93Q  H4  N1  C5  115.46  3.000
 93Q  H3  N1  C5  118.09  3.000
 93Q  H7  C   H6  107.75  3.000
 93Q  H7  C   H5  106.97  3.000
 93Q  H6  C   H5  107.32  3.000
 93Q  H7  C   C1  111.58  3.000
 93Q  H6  C   C1  110.89  3.000
 93Q  H5  C   C1  112.09  3.000
 93Q  C5  N   C4  118.73  3.000
 93Q  H8  C2  C3  120.05  3.000
 93Q  H8  C2  C1  119.17  3.000
 93Q  C3  C2  C1  120.78  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
 93Q  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 93Q  CONST_02  C4  N   C5  C1    0.00   0.0  0
 93Q  CONST_03  C5  N   C4  C3    0.00   0.0  0
 93Q  CONST_04  C5  C1  C2  C3    0.00   0.0  0
 93Q  CONST_05  C2  C3  C4  N     0.00   0.0  0
 93Q  CONST_06  C2  C1  C5  N     0.00   0.0  0
 93Q  CONST_07  C   C1  C2  C3  180.00   0.0  0
 93Q  CONST_08  N1  C5  N   C4  180.00   0.0  0
 93Q  CONST_09  C2  C1  C5  N1  180.00   0.0  0
 93Q  CONST_10  N   C5  C1  C   180.00   0.0  0
 93Q  CONST_11  H1  C3  C2  C1  180.00   0.0  0
 93Q  CONST_12  H8  C2  C3  C4  180.00   0.0  0
 93Q  CONST_13  H2  C4  N   C5  180.00   0.0  0
 93Q  CONST_15  H4  N1  C5  C1  180.00   0.0  0
 93Q  Var_01    H5  C   C1  C5   61.18  30.0  2

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
 93Q  plan-1  C1  0.020
 93Q  plan-1  C3  0.020
 93Q  plan-1  C4  0.020
 93Q  plan-1  C5  0.020
 93Q  plan-1  N1  0.020
 93Q  plan-1  C   0.020
 93Q  plan-1  N   0.020
 93Q  plan-1  C2  0.020
 93Q  plan-1  H1  0.020
 93Q  plan-1  H2  0.020
 93Q  plan-1  H8  0.020
 93Q  plan-2  C5  0.020
 93Q  plan-2  N1  0.020
 93Q  plan-2  H3  0.020
 93Q  plan-2  H4  0.020

