# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 14:10:37 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: ~{N}-methyl-1,6-naphthyridin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ccnc2ccncc12
#
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
 M0Q  M0Q  ~{N}-methyl-1,6-naphthyridin-4-amine  ligand  21  12  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M0Q
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
 M0Q  C01  C  CH3   0  -0.533   3.5047  -1.0482  -0.0057
 M0Q  C03  C  CR6   0   0.466   1.2357  -0.1254   0.0094
 M0Q  C04  C  CR16  0  -0.445   1.6970   1.1891  -0.0063
 M0Q  C05  C  CR16  0  -0.078   0.7818   2.2398  -0.0110
 M0Q  C07  C  CR66  0   0.279  -1.0099   0.8611   0.0124
 M0Q  C08  C  CR16  0  -0.363  -2.4071   0.6578   0.0214
 M0Q  C09  C  CR16  0  -0.083  -2.9049  -0.6141   0.0397
 M0Q  C11  C  CR16  0  -0.099  -0.8335  -1.5501   0.0427
 M0Q  C12  C  CR66  0  -0.081  -0.1924  -0.2953   0.0210
 M0Q  N02  N  NH1   0  -0.676   2.0687  -1.1728   0.0165
 M0Q  N06  N  N     0  -0.470  -0.5281   2.1218  -0.0031
 M0Q  N10  N  N     0  -0.407  -2.1315  -1.7186   0.0516
 M0Q  H1   H  HCH3  0   0.242   3.8569  -0.5526  -0.9133
 M0Q  H2   H  HCH3  0   0.243   3.8723  -0.4860   0.8551
 M0Q  H3   H  HCH3  0   0.268   3.9365  -2.0437   0.0296
 M0Q  H4   H  HCR6  0   0.280   2.7536   1.4152  -0.0196
 M0Q  H5   H  HCR6  0   0.261   1.1696   3.2538  -0.0244
 M0Q  H6   H  HCR6  0   0.268  -3.0687   1.5136   0.0139
 M0Q  H7   H  HCR6  0   0.267  -3.9755  -0.7824   0.0462
 M0Q  H8   H  HCR6  0   0.253  -0.2492  -2.4658   0.0551
 M0Q  H9   H  HNH1  0   0.409   1.6953  -2.1042  -0.0144

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
 M0Q  N10  C11  aromatic  1.309  0.020  1.309
 M0Q  N10  C09  aromatic  1.348  0.020  1.348
 M0Q  C11  C12  aromatic  1.409  0.020  1.409
 M0Q  C09  C08  aromatic  1.366  0.020  1.366
 M0Q  N02  C01  single    1.442  0.020  1.442
 M0Q  N02  C03  single    1.338  0.020  1.338
 M0Q  C12  C03  aromatic  1.438  0.020  1.438
 M0Q  C12  C07  aromatic  1.416  0.020  1.416
 M0Q  C08  C07  aromatic  1.412  0.020  1.412
 M0Q  C03  C04  aromatic  1.393  0.020  1.393
 M0Q  C07  N06  aromatic  1.350  0.020  1.350
 M0Q  C04  C05  aromatic  1.393  0.020  1.393
 M0Q  N06  C05  aromatic  1.315  0.020  1.315
 M0Q  C01  H1   single    0.970  0.020  1.090
 M0Q  C01  H2   single    0.970  0.020  1.090
 M0Q  C01  H3   single    0.970  0.020  1.090
 M0Q  C04  H4   single    0.930  0.020  1.080
 M0Q  C05  H5   single    0.930  0.020  1.080
 M0Q  C08  H6   single    0.930  0.020  1.080
 M0Q  C09  H7   single    0.930  0.020  1.080
 M0Q  C11  H8   single    0.930  0.020  1.080
 M0Q  N02  H9   single    0.860  0.020  1.020

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
 M0Q  H3   C01  H2   108.21  3.000
 M0Q  H3   C01  H1   108.35  3.000
 M0Q  H2   C01  H1   108.23  3.000
 M0Q  H3   C01  N02  108.45  3.000
 M0Q  H2   C01  N02  111.58  3.000
 M0Q  H1   C01  N02  111.91  3.000
 M0Q  N02  C03  C12  121.70  3.000
 M0Q  C12  C03  C04  116.13  3.000
 M0Q  N02  C03  C04  122.17  3.000
 M0Q  H4   C04  C05  118.97  3.000
 M0Q  H4   C04  C03  121.42  3.000
 M0Q  C05  C04  C03  119.61  3.000
 M0Q  H5   C05  N06  116.08  3.000
 M0Q  H5   C05  C04  118.01  3.000
 M0Q  N06  C05  C04  125.90  3.000
 M0Q  N06  C07  C12  123.83  3.000
 M0Q  N06  C07  C08  119.20  3.000
 M0Q  C12  C07  C08  116.97  3.000
 M0Q  H6   C08  C09  120.92  3.000
 M0Q  H6   C08  C07  119.42  3.000
 M0Q  C09  C08  C07  119.66  3.000
 M0Q  H7   C09  N10  116.06  3.000
 M0Q  H7   C09  C08  120.31  3.000
 M0Q  N10  C09  C08  123.63  3.000
 M0Q  H8   C11  N10  115.13  3.000
 M0Q  H8   C11  C12  120.40  3.000
 M0Q  N10  C11  C12  124.46  3.000
 M0Q  C11  C12  C07  117.69  3.000
 M0Q  C07  C12  C03  118.46  3.000
 M0Q  C11  C12  C03  123.85  3.000
 M0Q  H9   N02  C03  119.63  3.000
 M0Q  H9   N02  C01  116.76  3.000
 M0Q  C03  N02  C01  123.52  3.000
 M0Q  C07  N06  C05  116.07  3.000
 M0Q  C11  N10  C09  117.60  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
 M0Q  CONST_01  N10  C11  C12  C03  180.00   0.0  0
 M0Q  CONST_02  C08  C07  C12  C03  180.00   0.0  0
 M0Q  CONST_03  N06  C07  C12  C03    0.00   0.0  0
 M0Q  CONST_04  N06  C05  C04  C03    0.00   0.0  0
 M0Q  CONST_05  C11  C12  C03  C04  180.00   0.0  0
 M0Q  CONST_06  C07  C12  C03  C04    0.00   0.0  0
 M0Q  CONST_07  C07  N06  C05  C04    0.00   0.0  0
 M0Q  CONST_08  C12  C03  C04  C05    0.00   0.0  0
 M0Q  CONST_09  C12  C07  N06  C05    0.00   0.0  0
 M0Q  CONST_10  C08  C07  N06  C05  180.00   0.0  0
 M0Q  CONST_11  N10  C11  C12  C07    0.00   0.0  0
 M0Q  CONST_12  N10  C09  C08  C07    0.00   0.0  0
 M0Q  CONST_13  C11  N10  C09  C08    0.00   0.0  0
 M0Q  CONST_14  C11  C12  C07  C08    0.00   0.0  0
 M0Q  CONST_15  C12  C11  N10  C09    0.00   0.0  0
 M0Q  CONST_16  C12  C07  C08  C09    0.00   0.0  0
 M0Q  CONST_17  N06  C07  C08  C09  180.00   0.0  0
 M0Q  CONST_18  N06  C07  C12  C11  180.00   0.0  0
 M0Q  CONST_19  N02  C03  C04  C05  180.00   0.0  0
 M0Q  CONST_20  N02  C03  C12  C07  180.00   0.0  0
 M0Q  CONST_21  N02  C03  C12  C11    0.00   0.0  0
 M0Q  CONST_22  H8   C11  C12  C03    0.00   0.0  0
 M0Q  CONST_23  H5   C05  C04  C03  180.00   0.0  0
 M0Q  CONST_24  H7   C09  C08  C07  180.00   0.0  0
 M0Q  CONST_25  H4   C04  C03  C12  180.00   0.0  0
 M0Q  CONST_26  H6   C08  C07  C12  180.00   0.0  0
 M0Q  CONST_27  C12  C03  N02  C01  180.00   0.0  0
 M0Q  CONST_28  C04  C03  N02  C01    0.00   0.0  0
 M0Q  CONST_29  H9   N02  C03  C04  180.00   0.0  0
 M0Q  Var_01    H1   C01  N02  C03  -61.85  30.0  3

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
 M0Q  plan-1  C03  0.020
 M0Q  plan-1  C04  0.020
 M0Q  plan-1  C05  0.020
 M0Q  plan-1  C07  0.020
 M0Q  plan-1  C08  0.020
 M0Q  plan-1  C09  0.020
 M0Q  plan-1  C11  0.020
 M0Q  plan-1  C12  0.020
 M0Q  plan-1  N02  0.020
 M0Q  plan-1  N06  0.020
 M0Q  plan-1  N10  0.020
 M0Q  plan-1  H4   0.020
 M0Q  plan-1  H5   0.020
 M0Q  plan-1  H6   0.020
 M0Q  plan-1  H7   0.020
 M0Q  plan-1  H8   0.020
 M0Q  plan-2  C01  0.020
 M0Q  plan-2  C03  0.020
 M0Q  plan-2  N02  0.020
 M0Q  plan-2  H9   0.020

