# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:35:59 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 1-(6-methoxypyridin-2-yl)-N-methylmethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cccc(OC)n1
#
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
 X1M  X1M  1-(6-methoxypyridin-2-yl)-N-methylmethanamine  ligand  23  11  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X1M
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
 X1M  C4   C  CR6   0   0.254  30.8728  32.0849  3.5719
 X1M  C5   C  CR16  0  -0.373  31.5081  32.6703  2.4932
 X1M  C6   C  CH2   0  -0.314  29.5803  31.3306  3.4238
 X1M  C7   C  CH3   0  -0.516  27.3815  30.9944  4.3381
 X1M  C8   C  CH3   0  -0.415  32.3094  32.2143  7.3008
 X1M  N1   N  N     0  -0.493  31.3768  32.1399  4.8089
 X1M  N2   N  NH1   0  -0.589  28.6041  31.7679  4.4010
 X1M  C3   C  CR6   0   0.519  32.5077  32.7766  5.0123
 X1M  C1   C  CR16  0  -0.139  32.7130  33.3364  2.7167
 X1M  C2   C  CR16  0  -0.399  33.2334  33.4007  3.9891
 X1M  O1   O  O2    0  -0.470  33.0154  32.8466  6.2447
 X1M  H3   H  HCR6  0   0.259  31.0744  32.6168  1.5040
 X1M  H4   H  HCH2  0   0.238  29.1804  31.4937  2.4201
 X1M  H5   H  HCH2  0   0.210  29.7972  30.2508  3.4956
 X1M  H7   H  HCH3  0   0.232  26.7063  31.3084  5.1338
 X1M  H8   H  HCH3  0   0.221  26.8753  31.1737  3.3877
 X1M  H9   H  HCH3  0   0.193  27.5309  29.9091  4.4293
 X1M  H12  H  HCH3  0   0.244  32.9002  32.3842  8.1975
 X1M  H10  H  HCH3  0   0.227  31.3150  32.6413  7.4402
 X1M  H11  H  HCH3  0   0.227  32.2065  31.1406  7.1367
 X1M  H6   H  HNH1  0   0.345  29.0126  31.6723  5.3222
 X1M  H1   H  HCR6  0   0.271  33.2366  33.8067  1.8944
 X1M  H2   H  HCR6  0   0.268  34.1632  33.9103  4.2022

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
 X1M  C5  C1   aromatic  1.395  0.020  1.395
 X1M  C5  C4   aromatic  1.382  0.020  1.382
 X1M  C1  C2   aromatic  1.376  0.020  1.376
 X1M  C6  C4   single    1.504  0.020  1.504
 X1M  C6  N2   single    1.449  0.020  1.449
 X1M  C4  N1   aromatic  1.337  0.020  1.337
 X1M  C2  C3   aromatic  1.401  0.020  1.401
 X1M  C7  N2   single    1.448  0.020  1.448
 X1M  N1  C3   aromatic  1.314  0.020  1.314
 X1M  C3  O1   single    1.335  0.020  1.335
 X1M  O1  C8   single    1.419  0.020  1.419
 X1M  C5  H3   single    0.930  0.020  1.080
 X1M  C6  H4   single    0.970  0.020  1.090
 X1M  C6  H5   single    0.970  0.020  1.090
 X1M  C7  H7   single    0.970  0.020  1.090
 X1M  C7  H8   single    0.970  0.020  1.090
 X1M  C7  H9   single    0.970  0.020  1.090
 X1M  C8  H12  single    0.970  0.020  1.090
 X1M  C8  H10  single    0.970  0.020  1.090
 X1M  C8  H11  single    0.970  0.020  1.090
 X1M  N2  H6   single    0.890  0.020  1.040
 X1M  C1  H1   single    0.930  0.020  1.080
 X1M  C2  H2   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
 X1M  N1   C4  C6   115.84  3.000
 X1M  N1   C4  C5   122.11  3.000
 X1M  C6   C4  C5   122.05  3.000
 X1M  H3   C5  C1   121.11  3.000
 X1M  H3   C5  C4   120.58  3.000
 X1M  C1   C5  C4   118.31  3.000
 X1M  H5   C6  H4   106.12  3.000
 X1M  H5   C6  N2   112.57  3.000
 X1M  H4   C6  N2   109.14  3.000
 X1M  H5   C6  C4   108.38  3.000
 X1M  H4   C6  C4   109.28  3.000
 X1M  N2   C6  C4   111.18  3.000
 X1M  H9   C7  H8   107.30  3.000
 X1M  H9   C7  H7   107.95  3.000
 X1M  H8   C7  H7   107.52  3.000
 X1M  H9   C7  N2   114.15  3.000
 X1M  H8   C7  N2   109.97  3.000
 X1M  H7   C7  N2   109.72  3.000
 X1M  H11  C8  H10  108.57  3.000
 X1M  H11  C8  H12  109.21  3.000
 X1M  H10  C8  H12  109.19  3.000
 X1M  H11  C8  O1   111.93  3.000
 X1M  H10  C8  O1   111.97  3.000
 X1M  H12  C8  O1   105.89  3.000
 X1M  C3   N1  C4   119.19  3.000
 X1M  H6   N2  C7   109.26  3.000
 X1M  H6   N2  C6   108.26  3.000
 X1M  C7   N2  C6   112.23  3.000
 X1M  O1   C3  C2   116.99  3.000
 X1M  O1   C3  N1   119.72  3.000
 X1M  C2   C3  N1   123.28  3.000
 X1M  H1   C1  C2   119.94  3.000
 X1M  H1   C1  C5   120.24  3.000
 X1M  C2   C1  C5   119.81  3.000
 X1M  H2   C2  C1   121.96  3.000
 X1M  H2   C2  C3   120.75  3.000
 X1M  C1   C2  C3   117.29  3.000
 X1M  C3   O1  C8   118.33  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
 X1M  CONST_01  C2   C1  C5  C4     0.00   0.0  0
 X1M  CONST_02  C2   C3  N1  C4     0.00   0.0  0
 X1M  CONST_03  C3   C2  C1  C5     0.00   0.0  0
 X1M  CONST_04  C3   N1  C4  C5     0.00   0.0  0
 X1M  CONST_05  C1   C5  C4  N1     0.00   0.0  0
 X1M  CONST_06  C1   C2  C3  N1     0.00   0.0  0
 X1M  CONST_07  O1   C3  N1  C4   180.00   0.0  0
 X1M  CONST_08  C1   C5  C4  C6   180.00   0.0  0
 X1M  CONST_09  C3   N1  C4  C6   180.00   0.0  0
 X1M  CONST_10  O1   C3  C2  C1   180.00   0.0  0
 X1M  CONST_11  H1   C1  C5  C4   180.00   0.0  0
 X1M  CONST_12  H2   C2  C1  C5   180.00   0.0  0
 X1M  CONST_13  H3   C5  C4  N1   180.00   0.0  0
 X1M  Var_01    N2   C6  C4  C5  -130.82  30.0  2
 X1M  Var_02    C2   C3  O1  C8  -179.46  30.0  2
 X1M  Var_03    C7   N2  C6  C4  -176.10  30.0  3
 X1M  Var_04    H12  C8  O1  C3   179.29  30.0  3
 X1M  Var_05    H7   C7  N2  C6   175.97  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
 X1M  plan-1  C4  0.020
 X1M  plan-1  C5  0.020
 X1M  plan-1  C6  0.020
 X1M  plan-1  N1  0.020
 X1M  plan-1  C3  0.020
 X1M  plan-1  C1  0.020
 X1M  plan-1  C2  0.020
 X1M  plan-1  O1  0.020
 X1M  plan-1  H3  0.020
 X1M  plan-1  H1  0.020
 X1M  plan-1  H2  0.020

