# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 01:50:36 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 1H-perimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2cccc3cccc(N1)c23
#
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
 1PK  1PK  '1H-perimidin-2-amine     '  ligand  23  14  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1PK
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
 1PK  N14  N  NH2   0  -0.838   3.6890   0.0132  -0.0855
 1PK  C11  C  CR6   0   0.627   2.3417   0.0638  -0.0235
 1PK  N5   N  NR16  0  -0.764   1.6962  -1.1347  -0.0101
 1PK  N7   N  N     0  -0.540   1.7338   1.2105  -0.0189
 1PK  C3   C  CR66  0   0.289   0.3590   1.2189  -0.0099
 1PK  C8   C  CR16  0  -0.383  -0.3370   2.4160  -0.0146
 1PK  C13  C  CR16  0  -0.240  -1.7395   2.4187   0.0023
 1PK  C10  C  CR16  0  -0.373  -2.4665   1.2532   0.0235
 1PK  C4   C  CR66  0   0.110  -1.8001   0.0069   0.0279
 1PK  C1   C  C     0  -0.060  -0.3849   0.0067   0.0097
 1PK  C9   C  CR16  0  -0.356  -2.4730  -1.2391   0.0493
 1PK  C12  C  CR16  0  -0.251  -1.7598  -2.4099   0.0517
 1PK  C6   C  CR16  0  -0.374  -0.3541  -2.4196   0.0326
 1PK  C2   C  CR66  0   0.431   0.3177  -1.2183   0.0118
 1PK  H1   H  HNH2  0   0.405   4.1716  -0.8214   0.2046
 1PK  H2   H  HNH2  0   0.403   4.1743   0.8740   0.1044
 1PK  H3   H  HNR6  0   0.419   2.2317  -1.9893  -0.0380
 1PK  H4   H  HCR6  0   0.240   0.2132   3.3481  -0.0302
 1PK  H5   H  HCR6  0   0.249  -2.2591   3.3691  -0.0013
 1PK  H6   H  HCR6  0   0.243  -3.5489   1.2782   0.0373
 1PK  H7   H  HCR6  0   0.245  -3.5555  -1.2564   0.0637
 1PK  H8   H  HCR6  0   0.255  -2.2852  -3.3564   0.0687
 1PK  H9   H  HCR6  0   0.262   0.1901  -3.3556   0.0340

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
 1PK  C13  C10  aromatic  1.374  0.020  1.374
 1PK  C13  C8   aromatic  1.403  0.020  1.403
 1PK  C10  C4   aromatic  1.413  0.020  1.413
 1PK  C8   C3   aromatic  1.385  0.020  1.385
 1PK  C4   C9   aromatic  1.416  0.020  1.416
 1PK  C4   C1   aromatic  1.415  0.020  1.415
 1PK  C3   C1   aromatic  1.422  0.020  1.422
 1PK  C3   N7   single    1.375  0.020  1.375
 1PK  C9   C12  aromatic  1.371  0.020  1.371
 1PK  C1   C2   aromatic  1.412  0.020  1.412
 1PK  N7   C11  double    1.298  0.020  1.298
 1PK  C12  C6   aromatic  1.406  0.020  1.406
 1PK  C2   C6   aromatic  1.376  0.020  1.376
 1PK  C2   N5   single    1.381  0.020  1.381
 1PK  C11  N5   single    1.361  0.020  1.361
 1PK  C11  N14  single    1.350  0.020  1.350
 1PK  N14  H1   single    0.890  0.020  1.040
 1PK  N14  H2   single    0.890  0.020  1.040
 1PK  N5   H3   single    0.860  0.020  1.020
 1PK  C8   H4   single    0.930  0.020  1.080
 1PK  C13  H5   single    0.930  0.020  1.080
 1PK  C10  H6   single    0.930  0.020  1.080
 1PK  C9   H7   single    0.930  0.020  1.080
 1PK  C12  H8   single    0.930  0.020  1.080
 1PK  C6   H9   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
 1PK  H2   N14  H1   115.06  3.000
 1PK  H2   N14  C11  116.14  3.000
 1PK  H1   N14  C11  119.76  3.000
 1PK  N7   C11  N5   123.76  3.000
 1PK  N5   C11  N14  116.15  3.000
 1PK  N7   C11  N14  120.06  3.000
 1PK  H3   N5   C2   118.61  3.000
 1PK  H3   N5   C11  119.59  3.000
 1PK  C2   N5   C11  121.78  3.000
 1PK  C3   N7   C11  118.28  3.000
 1PK  C1   C3   C8   118.29  3.000
 1PK  C1   C3   N7   121.18  3.000
 1PK  C8   C3   N7   120.52  3.000
 1PK  H4   C8   C13  120.45  3.000
 1PK  H4   C8   C3   119.27  3.000
 1PK  C13  C8   C3   120.28  3.000
 1PK  H5   C13  C10  119.38  3.000
 1PK  H5   C13  C8   118.77  3.000
 1PK  C10  C13  C8   121.85  3.000
 1PK  H6   C10  C4   119.45  3.000
 1PK  H6   C10  C13  120.64  3.000
 1PK  C4   C10  C13  119.91  3.000
 1PK  C9   C4   C1   118.37  3.000
 1PK  C1   C4   C10  118.14  3.000
 1PK  C9   C4   C10  123.50  3.000
 1PK  C2   C1   C4   119.84  3.000
 1PK  C2   C1   C3   118.63  3.000
 1PK  C4   C1   C3   121.53  3.000
 1PK  H7   C9   C12  120.43  3.000
 1PK  H7   C9   C4   119.29  3.000
 1PK  C12  C9   C4   120.28  3.000
 1PK  H8   C12  C6   118.65  3.000
 1PK  H8   C12  C9   119.61  3.000
 1PK  C6   C12  C9   121.74  3.000
 1PK  H9   C6   C2   120.61  3.000
 1PK  H9   C6   C12  120.56  3.000
 1PK  C2   C6   C12  118.83  3.000
 1PK  C6   C2   C1   120.95  3.000
 1PK  C6   C2   N5   122.69  3.000
 1PK  C1   C2   N5   116.36  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
 1PK  CONST_01  C10  C13  C8   C3     0.00  0.0  0
 1PK  CONST_02  C10  C4   C1   C3     0.00  0.0  0
 1PK  CONST_03  C9   C4   C1   C3   180.00  0.0  0
 1PK  CONST_04  C6   C2   C1   C3   180.00  0.0  0
 1PK  CONST_05  C4   C10  C13  C8     0.00  0.0  0
 1PK  CONST_06  C4   C1   C3   C8     0.00  0.0  0
 1PK  CONST_07  C2   C1   C3   C8   180.00  0.0  0
 1PK  CONST_08  C9   C4   C10  C13  180.00  0.0  0
 1PK  CONST_09  C1   C4   C10  C13    0.00  0.0  0
 1PK  CONST_10  C1   C3   C8   C13    0.00  0.0  0
 1PK  CONST_11  C12  C9   C4   C10  180.00  0.0  0
 1PK  CONST_12  C2   C1   C4   C10  180.00  0.0  0
 1PK  CONST_13  C6   C12  C9   C4     0.00  0.0  0
 1PK  CONST_14  C6   C2   C1   C4     0.00  0.0  0
 1PK  CONST_15  C12  C9   C4   C1     0.00  0.0  0
 1PK  CONST_16  C12  C6   C2   C1     0.00  0.0  0
 1PK  CONST_17  C2   C1   C4   C9     0.00  0.0  0
 1PK  CONST_18  C2   C6   C12  C9     0.00  0.0  0
 1PK  CONST_19  C3   N7   C11  N5     0.00  0.0  0
 1PK  CONST_20  C2   N5   C11  N7     0.00  0.0  0
 1PK  CONST_21  C3   N7   C11  N14  180.00  0.0  0
 1PK  CONST_22  C2   N5   C11  N14  180.00  0.0  0
 1PK  CONST_23  H9   C6   C2   N5     0.00  0.0  0
 1PK  CONST_24  H4   C8   C3   N7     0.00  0.0  0
 1PK  CONST_25  H5   C13  C8   C3   180.00  0.0  0
 1PK  CONST_26  H6   C10  C13  C8   180.00  0.0  0
 1PK  CONST_27  H7   C9   C4   C10    0.00  0.0  0
 1PK  CONST_28  H8   C12  C9   C4   180.00  0.0  0
 1PK  CONST_29  H3   N5   C11  N7   180.00  0.0  0
 1PK  CONST_31  H2   N14  C11  N5   180.00  0.0  0

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
 1PK  plan-1  N14  0.020
 1PK  plan-1  C11  0.020
 1PK  plan-1  N5   0.020
 1PK  plan-1  N7   0.020
 1PK  plan-1  C3   0.020
 1PK  plan-1  C8   0.020
 1PK  plan-1  C13  0.020
 1PK  plan-1  C10  0.020
 1PK  plan-1  C4   0.020
 1PK  plan-1  C1   0.020
 1PK  plan-1  C9   0.020
 1PK  plan-1  C12  0.020
 1PK  plan-1  C6   0.020
 1PK  plan-1  C2   0.020
 1PK  plan-1  H1   0.020
 1PK  plan-1  H2   0.020
 1PK  plan-1  H3   0.020
 1PK  plan-1  H4   0.020
 1PK  plan-1  H5   0.020
 1PK  plan-1  H6   0.020
 1PK  plan-1  H7   0.020
 1PK  plan-1  H8   0.020
 1PK  plan-1  H9   0.020

