# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:31:36 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (4Z)-2-methyl-5-methylidenepyrimidin-4(5H)-imine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC(=N)C(=C)C=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
 ICP  ICP  (4Z)-2-methyl-5-methylidenepyrimidin-4(5H)-imine  ligand  16  9  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ICP
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
 ICP  N1A   N  N     0  -0.421   1.2753   0.1485   1.0433
 ICP  C2A   C  CR6   0   0.369  -0.0720   0.0195   1.4055
 ICP  CM2   C  CH3   0  -0.727  -0.2918   0.0185   2.8774
 ICP  N3A   N  N     0  -0.439  -1.0721  -0.0918   0.6116
 ICP  C4A   C  CR6   0   0.328  -0.8668  -0.0932  -0.7671
 ICP  N4A   N  N     0  -0.594  -1.8323  -0.1882  -1.5865
 ICP  C5A   C  CR6   0   0.007   0.5277   0.0215  -1.2429
 ICP  C6A   C  CR16  0   0.001   1.5344   0.1448  -0.2085
 ICP  C7A   C  C2    0  -0.504   0.8900   0.0173  -2.5319
 ICP  HM21  H  HCH3  0   0.263   0.2866  -0.7836   3.3388
 ICP  HM22  H  HCH3  0   0.263   0.0713   0.9536   3.3083
 ICP  HM23  H  HCH3  0   0.254  -1.3427  -0.1060   3.1233
 ICP  HN4   H  H     0   0.339  -2.7076  -0.2571  -1.0731
 ICP  H6A1  H  HCR6  0   0.287   2.5733   0.2395  -0.5157
 ICP  H7A1  H  H     0   0.287   1.9302   0.1079  -2.8178
 ICP  H7A2  H  H     0   0.288   0.1625  -0.0758  -3.3261

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
 ICP  N1A  C2A   single  1.401  0.020  1.401
 ICP  N1A  C6A   double  1.278  0.020  1.278
 ICP  C2A  CM2   single  1.488  0.020  1.488
 ICP  C2A  N3A   double  1.282  0.020  1.282
 ICP  CM2  HM21  single  0.970  0.020  1.090
 ICP  CM2  HM22  single  0.970  0.020  1.090
 ICP  CM2  HM23  single  0.970  0.020  1.090
 ICP  N3A  C4A   single  1.394  0.020  1.394
 ICP  C4A  N4A   double  1.270  0.020  1.270
 ICP  C4A  C5A   single  1.478  0.020  1.478
 ICP  N4A  HN4   single  0.890  0.020  1.040
 ICP  C5A  C6A   single  1.449  0.020  1.449
 ICP  C5A  C7A   double  1.339  0.020  1.339
 ICP  C6A  H6A1  single  0.930  0.020  1.080
 ICP  C7A  H7A1  single  0.930  0.020  1.080
 ICP  C7A  H7A2  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
 ICP  C6A   N1A  C2A   116.60  3.000
 ICP  N3A   C2A  CM2   119.82  3.000
 ICP  N3A   C2A  N1A   126.74  3.000
 ICP  CM2   C2A  N1A   113.44  3.000
 ICP  HM23  CM2  HM22  109.30  3.000
 ICP  HM23  CM2  HM21  109.44  3.000
 ICP  HM22  CM2  HM21  106.64  3.000
 ICP  HM23  CM2  C2A   111.52  3.000
 ICP  HM22  CM2  C2A   109.92  3.000
 ICP  HM21  CM2  C2A   109.90  3.000
 ICP  C4A   N3A  C2A   119.86  3.000
 ICP  C5A   C4A  N4A   121.03  3.000
 ICP  C5A   C4A  N3A   117.22  3.000
 ICP  N4A   C4A  N3A   121.76  3.000
 ICP  HN4   N4A  C4A   109.50  3.000
 ICP  C7A   C5A  C6A   119.97  3.000
 ICP  C7A   C5A  C4A   124.40  3.000
 ICP  C6A   C5A  C4A   115.62  3.000
 ICP  H6A1  C6A  C5A   118.01  3.000
 ICP  H6A1  C6A  N1A   118.04  3.000
 ICP  C5A   C6A  N1A   123.96  3.000
 ICP  H7A2  C7A  H7A1  117.38  3.000
 ICP  H7A2  C7A  C5A   121.69  3.000
 ICP  H7A1  C7A  C5A   120.93  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
 ICP  CONST_01  C4A   N3A  C2A  N1A    0.00   0.0  0
 ICP  CONST_02  C5A   C4A  N3A  C2A    0.00   0.0  0
 ICP  CONST_03  C6A   N1A  C2A  N3A    0.00   0.0  0
 ICP  CONST_04  N4A   C4A  N3A  C2A  180.00   0.0  0
 ICP  CONST_05  C6A   N1A  C2A  CM2  180.00   0.0  0
 ICP  CONST_06  C4A   N3A  C2A  CM2  180.00   0.0  0
 ICP  CONST_07  HN4   N4A  C4A  N3A    0.00   0.0  0
 ICP  Var_01    H7A1  C7A  C5A  C4A  179.81   0.0  2
 ICP  Var_02    HM21  CM2  C2A  N1A  -57.14  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
 ICP  plan-1  N1A   0.020
 ICP  plan-1  C2A   0.020
 ICP  plan-1  CM2   0.020
 ICP  plan-1  N3A   0.020
 ICP  plan-1  C4A   0.020
 ICP  plan-1  N4A   0.020
 ICP  plan-1  C5A   0.020
 ICP  plan-1  C6A   0.020
 ICP  plan-1  C7A   0.020
 ICP  plan-1  HN4   0.020
 ICP  plan-1  H6A1  0.020
 ICP  plan-1  H7A1  0.020
 ICP  plan-1  H7A2  0.020

