# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:58:33 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc(N)c2[nH]cnc12
#
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
 54K  54K  7-methyl-3H-imidazo[4,5-c]pyridin-4-amine  ligand  19  11  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_54K
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
 54K  N1   N  N     0  -0.463  -0.5825   1.9338  -0.1225
 54K  C2   C  CR16  0  -0.148   0.7601   1.8239  -0.1064
 54K  C3   C  CR6   0  -0.068   1.4748   0.6491  -0.0442
 54K  C3M  C  CH3   0  -0.725   2.9684   0.5948  -0.0213
 54K  C4   C  CR56  0   0.208   0.6786  -0.5099  -0.0039
 54K  C5   C  CR56  0   0.199  -0.7102  -0.4006  -0.0318
 54K  C6   C  CR6   0   0.392  -1.3385   0.8544  -0.0873
 54K  N6   N  NH2   0  -0.836  -2.6995   0.9893  -0.1629
 54K  N7   N  NR15  0  -0.652  -1.1706  -1.6923   0.0092
 54K  C8   C  CR15  0   0.107  -0.0842  -2.4887   0.0596
 54K  N9   N  N     0  -0.460   1.0445  -1.8285   0.0546
 54K  H1   H  HCR6  0   0.242   1.2974   2.7673  -0.1433
 54K  H2   H  HCH3  0   0.239   3.3388   0.1286   0.8935
 54K  H3   H  HCH3  0   0.238   3.3606   0.0117  -0.8566
 54K  H4   H  HCH3  0   0.240   3.3961   1.5951  -0.0830
 54K  H5   H  HNH2  0   0.384  -3.0396   1.9158   0.0426
 54K  H6   H  HNH2  0   0.386  -3.2604   0.2706   0.2658
 54K  H7   H  HNR5  0   0.424  -2.1267  -2.0103  -0.0070
 54K  H8   H  HCR5  0   0.290  -0.1776  -3.5636   0.0979

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
 54K  C3M  C3  single    1.495  0.020  1.495
 54K  C2   C3  aromatic  1.377  0.020  1.377
 54K  C2   N1  aromatic  1.347  0.020  1.347
 54K  C3   C4  aromatic  1.407  0.020  1.407
 54K  N1   C6  aromatic  1.318  0.020  1.318
 54K  C4   N9  aromatic  1.370  0.020  1.370
 54K  C4   C5  aromatic  1.393  0.020  1.393
 54K  C6   C5  aromatic  1.405  0.020  1.405
 54K  C6   N6  single    1.370  0.020  1.370
 54K  N9   C8  aromatic  1.308  0.020  1.308
 54K  C5   N7  aromatic  1.372  0.020  1.372
 54K  C8   N7  aromatic  1.348  0.020  1.348
 54K  C2   H1  single    0.930  0.020  1.080
 54K  C3M  H2  single    0.970  0.020  1.090
 54K  C3M  H3  single    0.970  0.020  1.090
 54K  C3M  H4  single    0.970  0.020  1.090
 54K  N6   H5  single    0.890  0.020  1.040
 54K  N6   H6  single    0.890  0.020  1.040
 54K  N7   H7  single    0.860  0.020  1.020
 54K  C8   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
 54K  C6   N1   C2   120.29  3.000
 54K  H1   C2   C3   119.07  3.000
 54K  H1   C2   N1   114.94  3.000
 54K  C3   C2   N1   125.99  3.000
 54K  C4   C3   C3M  122.36  3.000
 54K  C4   C3   C2   114.24  3.000
 54K  C3M  C3   C2   123.40  3.000
 54K  H4   C3M  H3   107.82  3.000
 54K  H4   C3M  H2   107.84  3.000
 54K  H3   C3M  H2   106.94  3.000
 54K  H4   C3M  C3   110.97  3.000
 54K  H3   C3M  C3   111.51  3.000
 54K  H2   C3M  C3   111.55  3.000
 54K  N9   C4   C5   110.04  3.000
 54K  C5   C4   C3   119.93  3.000
 54K  N9   C4   C3   130.03  3.000
 54K  N7   C5   C6   133.81  3.000
 54K  N7   C5   C4   105.08  3.000
 54K  C6   C5   C4   121.11  3.000
 54K  N6   C6   C5   122.32  3.000
 54K  N6   C6   N1   119.19  3.000
 54K  C5   C6   N1   118.44  3.000
 54K  H6   N6   H5   112.40  3.000
 54K  H6   N6   C6   117.35  3.000
 54K  H5   N6   C6   114.49  3.000
 54K  H7   N7   C8   125.37  3.000
 54K  H7   N7   C5   127.95  3.000
 54K  C8   N7   C5   106.67  3.000
 54K  H8   C8   N9   125.27  3.000
 54K  H8   C8   N7   121.32  3.000
 54K  N9   C8   N7   113.41  3.000
 54K  C8   N9   C4   104.81  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
 54K  CONST_01  C4   C3   C2  N1     0.00   0.0  0
 54K  CONST_02  C4   C5   C6  N1     0.00   0.0  0
 54K  CONST_03  N7   C5   C6  N1   180.00   0.0  0
 54K  CONST_04  N9   C4   C3  C2   180.00   0.0  0
 54K  CONST_05  C5   C4   C3  C2     0.00   0.0  0
 54K  CONST_06  C5   C6   N1  C2     0.00   0.0  0
 54K  CONST_07  C6   N1   C2  C3     0.00   0.0  0
 54K  CONST_08  C8   N9   C4  C3   180.00   0.0  0
 54K  CONST_09  C6   C5   C4  C3     0.00   0.0  0
 54K  CONST_10  N7   C5   C4  C3   180.00   0.0  0
 54K  CONST_11  N7   C8   N9  C4     0.00   0.0  0
 54K  CONST_12  C8   N7   C5  C4     0.00   0.0  0
 54K  CONST_13  C8   N9   C4  C5     0.00   0.0  0
 54K  CONST_14  N9   C8   N7  C5     0.00   0.0  0
 54K  CONST_15  N9   C4   C5  C6   180.00   0.0  0
 54K  CONST_16  C8   N7   C5  C6   180.00   0.0  0
 54K  CONST_17  N9   C4   C5  N7     0.00   0.0  0
 54K  CONST_18  C3M  C3   C2  N1   180.00   0.0  0
 54K  CONST_19  N6   C6   N1  C2   180.00   0.0  0
 54K  CONST_20  N9   C4   C3  C3M    0.00   0.0  0
 54K  CONST_21  C5   C4   C3  C3M  180.00   0.0  0
 54K  CONST_22  N6   C6   C5  C4   180.00   0.0  0
 54K  CONST_23  N7   C5   C6  N6     0.00   0.0  0
 54K  CONST_24  H1   C2   C3  C4   180.00   0.0  0
 54K  CONST_25  H8   C8   N9  C4   180.00   0.0  0
 54K  CONST_26  H7   N7   C5  C4   180.00   0.0  0
 54K  Var_01    H2   C3M  C3  C2   118.99  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
 54K  plan-1  N1   0.020
 54K  plan-1  C2   0.020
 54K  plan-1  C3   0.020
 54K  plan-1  C3M  0.020
 54K  plan-1  C4   0.020
 54K  plan-1  C5   0.020
 54K  plan-1  C6   0.020
 54K  plan-1  N6   0.020
 54K  plan-1  N7   0.020
 54K  plan-1  C8   0.020
 54K  plan-1  N9   0.020
 54K  plan-1  H1   0.020
 54K  plan-1  H7   0.020
 54K  plan-1  H8   0.020
 54K  plan-2  C6   0.020
 54K  plan-2  N6   0.020
 54K  plan-2  H5   0.020
 54K  plan-2  H6   0.020

