# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:56:39 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: N-benzyl-2-[(E)-iminomethyl]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=Cc1ncc(cn1)C(=O)NCc2ccccc2
#
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
 2UQ  2UQ  N-benzyl-2-[(E)-iminomethyl]pyrimidine-5-carboxamide  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2UQ
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
 2UQ  C1   C  CR6   0  -0.171   1.4976   0.7577   0.1179
 2UQ  C2   C  CR16  0   0.000   2.7050   1.4435   0.0970
 2UQ  C11  C  CR6   0   0.082  -3.2160   0.3569  -0.2017
 2UQ  C12  C  C1    0  -0.102   5.1683  -1.1721   0.1452
 2UQ  C14  C  CR16  0  -0.284  -3.2892  -0.3276   1.0105
 2UQ  C15  C  CR16  0  -0.241  -4.2355  -1.3226   1.2015
 2UQ  C16  C  CR16  0  -0.265  -5.1215  -1.6480   0.1799
 2UQ  C17  C  CR16  0  -0.240  -5.0537  -0.9730  -1.0299
 2UQ  C18  C  CR16  0  -0.303  -4.1029   0.0238  -1.2185
 2UQ  N3   N  N     0  -0.411   3.8699   0.8163   0.0999
 2UQ  C4   C  CR6   0   0.362   3.8423  -0.5110   0.1430
 2UQ  N5   N  N     0  -0.388   2.7500  -1.2617   0.1894
 2UQ  C6   C  CR16  0  -0.024   1.5902  -0.6287   0.1763
 2UQ  C7   C  C     0   0.549   0.2138   1.5180   0.1375
 2UQ  O8   O  O     0  -0.478   0.1731   2.6495   0.5969
 2UQ  N9   N  NH1   0  -0.643  -0.8486   0.8712  -0.3635
 2UQ  C10  C  CH2   0  -0.338  -2.1836   1.4340  -0.4013
 2UQ  N13  N  N     0  -0.510   5.2771  -2.4277   0.2041
 2UQ  H1   H  HCR6  0   0.289   2.7290   2.5266   0.0693
 2UQ  H2   H  H     0   0.248   6.0079  -0.4778   0.0934
 2UQ  H3   H  HCR6  0   0.253  -2.6032  -0.0781   1.8118
 2UQ  H4   H  HCR6  0   0.257  -4.2851  -1.8443   2.1486
 2UQ  H5   H  HCR6  0   0.258  -5.8609  -2.4242   0.3282
 2UQ  H6   H  HCR6  0   0.257  -5.7380  -1.2220  -1.8306
 2UQ  H7   H  HCR6  0   0.255  -4.0529   0.5469  -2.1661
 2UQ  H8   H  HCR6  0   0.281   0.7041  -1.2522   0.2348
 2UQ  H9   H  HNH1  0   0.412  -0.7078   0.0096  -0.8670
 2UQ  H10  H  HCH2  0   0.263  -2.3536   1.9500  -1.3500
 2UQ  H11  H  HCH2  0   0.271  -2.2592   2.1814   0.3882
 2UQ  H12  H  H     0   0.362   6.2580  -2.6941   0.1960

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
 2UQ  N5   C6   aromatic  1.321  0.020  1.321
 2UQ  N5   C4   aromatic  1.326  0.020  1.326
 2UQ  C6   C1   aromatic  1.391  0.020  1.391
 2UQ  C18  C17  aromatic  1.390  0.020  1.390
 2UQ  C18  C11  aromatic  1.390  0.020  1.390
 2UQ  C17  C16  aromatic  1.387  0.020  1.387
 2UQ  N9   C10  single    1.449  0.020  1.449
 2UQ  N9   C7   single    1.341  0.020  1.341
 2UQ  C10  C11  single    1.505  0.020  1.505
 2UQ  C11  C14  aromatic  1.394  0.020  1.394
 2UQ  C12  C4   single    1.482  0.020  1.482
 2UQ  C12  N13  double    1.262  0.020  1.262
 2UQ  C16  C15  aromatic  1.391  0.020  1.391
 2UQ  C4   N3   aromatic  1.328  0.020  1.328
 2UQ  C1   C7   single    1.492  0.020  1.492
 2UQ  C1   C2   aromatic  1.389  0.020  1.389
 2UQ  C14  C15  aromatic  1.386  0.020  1.386
 2UQ  C7   O8   double    1.222  0.020  1.222
 2UQ  N3   C2   aromatic  1.323  0.020  1.323
 2UQ  C2   H1   single    0.930  0.020  1.080
 2UQ  C12  H2   single    0.930  0.020  1.080
 2UQ  C14  H3   single    0.930  0.020  1.080
 2UQ  C15  H4   single    0.930  0.020  1.080
 2UQ  C16  H5   single    0.930  0.020  1.080
 2UQ  C17  H6   single    0.930  0.020  1.080
 2UQ  C18  H7   single    0.930  0.020  1.080
 2UQ  C6   H8   single    0.930  0.020  1.080
 2UQ  N9   H9   single    0.860  0.020  1.020
 2UQ  C10  H10  single    0.970  0.020  1.090
 2UQ  C10  H11  single    0.970  0.020  1.090
 2UQ  N13  H12  single    0.890  0.020  1.040

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
 2UQ  C7   C1   C6   124.37  3.000
 2UQ  C7   C1   C2   119.78  3.000
 2UQ  C6   C1   C2   115.79  3.000
 2UQ  H1   C2   N3   117.02  3.000
 2UQ  H1   C2   C1   120.88  3.000
 2UQ  N3   C2   C1   122.10  3.000
 2UQ  C10  C11  C18  120.81  3.000
 2UQ  C10  C11  C14  120.18  3.000
 2UQ  C18  C11  C14  119.01  3.000
 2UQ  H2   C12  N13  124.70  3.000
 2UQ  H2   C12  C4   113.88  3.000
 2UQ  N13  C12  C4   121.42  3.000
 2UQ  H3   C14  C15  119.70  3.000
 2UQ  H3   C14  C11  119.77  3.000
 2UQ  C15  C14  C11  120.54  3.000
 2UQ  H4   C15  C16  120.05  3.000
 2UQ  H4   C15  C14  119.85  3.000
 2UQ  C16  C15  C14  120.10  3.000
 2UQ  H5   C16  C17  120.13  3.000
 2UQ  H5   C16  C15  120.16  3.000
 2UQ  C17  C16  C15  119.71  3.000
 2UQ  H6   C17  C18  119.80  3.000
 2UQ  H6   C17  C16  120.16  3.000
 2UQ  C18  C17  C16  120.04  3.000
 2UQ  H7   C18  C17  119.75  3.000
 2UQ  H7   C18  C11  119.65  3.000
 2UQ  C17  C18  C11  120.60  3.000
 2UQ  C4   N3   C2   117.09  3.000
 2UQ  N5   C4   N3   125.73  3.000
 2UQ  N3   C4   C12  115.29  3.000
 2UQ  N5   C4   C12  118.98  3.000
 2UQ  C6   N5   C4   116.83  3.000
 2UQ  H8   C6   N5   116.17  3.000
 2UQ  H8   C6   C1   121.39  3.000
 2UQ  N5   C6   C1   122.44  3.000
 2UQ  N9   C7   O8   124.11  3.000
 2UQ  O8   C7   C1   120.36  3.000
 2UQ  N9   C7   C1   115.53  3.000
 2UQ  H9   N9   C10  116.59  3.000
 2UQ  H9   N9   C7   119.23  3.000
 2UQ  C10  N9   C7   123.52  3.000
 2UQ  H11  C10  H10  107.11  3.000
 2UQ  H11  C10  N9   108.14  3.000
 2UQ  H10  C10  N9   110.44  3.000
 2UQ  H11  C10  C11  110.31  3.000
 2UQ  H10  C10  C11  110.25  3.000
 2UQ  N9   C10  C11  110.51  3.000
 2UQ  H12  N13  C12  110.10  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
 2UQ  CONST_01  C4   N5   C6   C1      0.00   0.0  0
 2UQ  CONST_02  C4   N3   C2   C1      0.00   0.0  0
 2UQ  CONST_03  N5   C6   C1   C2      0.00   0.0  0
 2UQ  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 2UQ  CONST_05  C16  C17  C18  C11     0.00   0.0  0
 2UQ  CONST_06  C16  C15  C14  C11     0.00   0.0  0
 2UQ  CONST_07  C17  C18  C11  C14     0.00   0.0  0
 2UQ  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 2UQ  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 2UQ  CONST_10  C18  C11  C14  C15     0.00   0.0  0
 2UQ  CONST_11  C6   N5   C4   N3      0.00   0.0  0
 2UQ  CONST_12  C6   C1   C2   N3      0.00   0.0  0
 2UQ  CONST_13  C12  C4   N3   C2    180.00   0.0  0
 2UQ  CONST_14  C6   N5   C4   C12   180.00   0.0  0
 2UQ  CONST_15  C10  C11  C14  C15   180.00   0.0  0
 2UQ  CONST_16  C10  C11  C18  C17   180.00   0.0  0
 2UQ  CONST_17  C7   C1   C2   N3    180.00   0.0  0
 2UQ  CONST_18  C7   C1   C6   N5    180.00   0.0  0
 2UQ  CONST_19  H8   C6   C1   C2    180.00   0.0  0
 2UQ  CONST_20  H6   C17  C18  C11   180.00   0.0  0
 2UQ  CONST_21  H4   C15  C14  C11   180.00   0.0  0
 2UQ  CONST_22  H7   C18  C11  C14   180.00   0.0  0
 2UQ  CONST_23  H5   C16  C15  C14   180.00   0.0  0
 2UQ  CONST_24  H3   C14  C15  C16   180.00   0.0  0
 2UQ  CONST_25  H1   C2   N3   C4    180.00   0.0  0
 2UQ  CONST_26  C10  N9   C7   C1    180.00   0.0  0
 2UQ  CONST_27  H9   N9   C7   C1      0.00   0.0  0
 2UQ  CONST_28  C10  N9   C7   O8      0.00   0.0  0
 2UQ  Var_01    N9   C7   C1   C2    154.57  30.0  2
 2UQ  Var_02    N9   C10  C11  C14    65.08  30.0  2
 2UQ  Var_03    N13  C12  C4   N3    178.93  30.0  3
 2UQ  Var_04    C7   N9   C10  C11  -145.75  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
 2UQ  plan-1  C11  0.020
 2UQ  plan-1  C14  0.020
 2UQ  plan-1  C15  0.020
 2UQ  plan-1  C16  0.020
 2UQ  plan-1  C17  0.020
 2UQ  plan-1  C18  0.020
 2UQ  plan-1  C10  0.020
 2UQ  plan-1  H3   0.020
 2UQ  plan-1  H4   0.020
 2UQ  plan-1  H5   0.020
 2UQ  plan-1  H6   0.020
 2UQ  plan-1  H7   0.020
 2UQ  plan-2  C1   0.020
 2UQ  plan-2  C2   0.020
 2UQ  plan-2  C12  0.020
 2UQ  plan-2  N3   0.020
 2UQ  plan-2  C4   0.020
 2UQ  plan-2  N5   0.020
 2UQ  plan-2  C6   0.020
 2UQ  plan-2  C7   0.020
 2UQ  plan-2  H1   0.020
 2UQ  plan-2  H8   0.020
 2UQ  plan-3  C1   0.020
 2UQ  plan-3  C7   0.020
 2UQ  plan-3  O8   0.020
 2UQ  plan-3  N9   0.020
 2UQ  plan-3  C10  0.020
 2UQ  plan-3  H9   0.020
 2UQ  plan-4  C12  0.020
 2UQ  plan-4  C4   0.020
 2UQ  plan-4  N13  0.020
 2UQ  plan-4  H2   0.020
 2UQ  plan-4  H12  0.020

