# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:41:21 2021
#   Inital geometry file: a 41 line input string
#   Ligand name: (E)-1-(pyrimidin-2-yl)methanimine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=Cc1ncccn1
#
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
 USD  USD  (E)-1-(pyrimidin-2-yl)methanimine  ligand  13  8  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_USD
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
 USD  N1  N  N     0  -0.413  5.5117  -3.4864  21.8819
 USD  C4  C  CR16  0  -0.018  7.3995  -1.7079  22.6521
 USD  N   N  N     0  -0.527  6.1102  -4.9979  19.5630
 USD  C   C  C1    0  -0.084  6.9037  -4.1369  20.0335
 USD  C1  C  CR6   0   0.323  6.6583  -3.3059  21.2403
 USD  N2  N  N     0  -0.410  7.6149  -2.4509  21.5727
 USD  C3  C  CR16  0  -0.340  6.2378  -1.8157  23.3964
 USD  C2  C  CR16  0  -0.008  5.3043  -2.7420  22.9571
 USD  H1  H  HCR6  0   0.286  8.1787  -1.0080  22.9298
 USD  H2  H  H     0   0.347  5.2646  -5.0452  20.1328
 USD  H3  H  H     0   0.261  7.8587  -3.9617  19.5408
 USD  H4  H  HCR6  0   0.293  6.0678  -1.2106  24.2744
 USD  H5  H  HCR6  0   0.288  4.3686  -2.8865  23.4845

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
 USD  N   C   double    1.262  0.020  1.262
 USD  C   C1  single    1.486  0.020  1.486
 USD  C1  N2  aromatic  1.325  0.020  1.325
 USD  C1  N1  aromatic  1.326  0.020  1.326
 USD  N2  C4  aromatic  1.328  0.020  1.328
 USD  N1  C2  aromatic  1.324  0.020  1.324
 USD  C4  C3  aromatic  1.384  0.020  1.384
 USD  C2  C3  aromatic  1.387  0.020  1.387
 USD  C4  H1  single    0.930  0.020  1.080
 USD  N   H2  single    0.890  0.020  1.040
 USD  C   H3  single    0.930  0.020  1.080
 USD  C3  H4  single    0.930  0.020  1.080
 USD  C2  H5  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
 USD  C2  N1  C1  116.86  3.000
 USD  H1  C4  C3  121.07  3.000
 USD  H1  C4  N2  116.94  3.000
 USD  C3  C4  N2  121.99  3.000
 USD  H2  N   C   110.14  3.000
 USD  H3  C   C1  114.99  3.000
 USD  H3  C   N   119.52  3.000
 USD  C1  C   N   125.50  3.000
 USD  N2  C1  C   116.45  3.000
 USD  N2  C1  N1  126.19  3.000
 USD  C   C1  N1  117.37  3.000
 USD  C1  N2  C4  116.60  3.000
 USD  H4  C3  C2  121.74  3.000
 USD  H4  C3  C4  121.72  3.000
 USD  C2  C3  C4  116.54  3.000
 USD  H5  C2  C3  121.07  3.000
 USD  H5  C2  N1  117.10  3.000
 USD  C3  C2  N1  121.83  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
 USD  CONST_01  C4  N2  C1  N1    0.00   0.0  0
 USD  CONST_02  C4  C3  C2  N1    0.00   0.0  0
 USD  CONST_03  C3  C4  N2  C1    0.00   0.0  0
 USD  CONST_04  C3  C2  N1  C1    0.00   0.0  0
 USD  CONST_05  C2  N1  C1  N2    0.00   0.0  0
 USD  CONST_06  C2  C3  C4  N2    0.00   0.0  0
 USD  CONST_07  C   C1  N2  C4  180.00   0.0  0
 USD  CONST_08  C2  N1  C1  C   180.00   0.0  0
 USD  CONST_09  H4  C3  C2  N1  180.00   0.0  0
 USD  CONST_10  H5  C2  C3  C4  180.00   0.0  0
 USD  CONST_11  H1  C4  N2  C1  180.00   0.0  0
 USD  Var_01    N   C   C1  N1    0.29  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
 USD  plan-1  N1  0.020
 USD  plan-1  C4  0.020
 USD  plan-1  C   0.020
 USD  plan-1  C1  0.020
 USD  plan-1  N2  0.020
 USD  plan-1  C3  0.020
 USD  plan-1  C2  0.020
 USD  plan-1  H1  0.020
 USD  plan-1  H4  0.020
 USD  plan-1  H5  0.020
 USD  plan-2  N   0.020
 USD  plan-2  C   0.020
 USD  plan-2  C1  0.020
 USD  plan-2  H2  0.020
 USD  plan-2  H3  0.020

