# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 11:16:30 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(Nc1nccc(n1)c2cccnc2)c3ccccc3
#
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
 1QO  1QO  N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine  ligand  34  20  .  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_1QO
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
 1QO  N1   N  NH1   0  -0.661  -1.3200  -0.3827  -0.2168
 1QO  C2   C  CR6   0   0.606  -0.1162  -0.9687  -0.0896
 1QO  N3   N  N     0  -0.495   0.9468  -0.1558  -0.0869
 1QO  C4   C  CR16  0  -0.406   2.2899  -2.0842   0.2261
 1QO  N4   N  N     0  -0.399   5.6570   0.5567  -0.1700
 1QO  C5   C  CR6   0   0.290   2.1410  -0.7060   0.0668
 1QO  C6   C  CR6   0  -0.044   3.2946   0.2154   0.0770
 1QO  C11  C  CR6   0   0.064  -3.7342  -0.1862  -0.1812
 1QO  C12  C  CR16  0  -0.306  -4.6527  -0.0194  -1.2112
 1QO  C13  C  CR16  0  -0.240  -5.7424   0.8306  -1.0584
 1QO  C1   C  CH2   0  -0.310  -2.5605  -1.1146  -0.3408
 1QO  N2   N  N     0  -0.468  -0.0761  -2.2999   0.0285
 1QO  C3   C  CR16  0  -0.008   1.1260  -2.8295   0.1901
 1QO  C7   C  CR16  0  -0.164   3.1240   1.5742   0.3337
 1QO  C8   C  CR16  0  -0.314   4.2322   2.4015   0.3464
 1QO  C9   C  CR16  0  -0.062   5.4782   1.8461   0.0922
 1QO  C10  C  CR16  0  -0.097   4.5911  -0.2310  -0.1751
 1QO  C14  C  CR16  0  -0.266  -5.9204   1.5261   0.1286
 1QO  C15  C  CR16  0  -0.240  -5.0044   1.3680   1.1629
 1QO  C16  C  CR16  0  -0.283  -3.9200   0.5174   1.0084
 1QO  H3   H  HNH1  0   0.395  -1.3229   0.6065  -0.4058
 1QO  H5   H  HCR6  0   0.270   3.2460  -2.5593   0.3833
 1QO  H10  H  HCR6  0   0.254  -4.5169  -0.5565  -2.1425
 1QO  H11  H  HCR6  0   0.257  -6.4480   0.9511  -1.8703
 1QO  H2   H  HCH2  0   0.246  -2.6210  -1.6305  -1.3049
 1QO  H1   H  HCH2  0   0.256  -2.5946  -1.8893   0.4280
 1QO  H4   H  HCR6  0   0.272   1.1666  -3.9081   0.2978
 1QO  H6   H  HCR6  0   0.273   2.1362   1.9690   0.5296
 1QO  H7   H  HCR6  0   0.276   4.1382   3.4592   0.5500
 1QO  H8   H  HCR6  0   0.271   6.3661   2.4683   0.1002
 1QO  H9   H  HCR6  0   0.264   4.7779  -1.2736  -0.4080
 1QO  H12  H  HCR6  0   0.257  -6.7672   2.1893   0.2492
 1QO  H13  H  HCR6  0   0.257  -5.1385   1.9054   2.0931
 1QO  H14  H  HCR6  0   0.254  -3.2136   0.3963   1.8213

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
 1QO  C3   N2   aromatic  1.323  0.020  1.323
 1QO  C3   C4   aromatic  1.383  0.020  1.383
 1QO  N2   C2   aromatic  1.337  0.020  1.337
 1QO  C4   C5   aromatic  1.395  0.020  1.395
 1QO  C2   N1   single    1.345  0.020  1.345
 1QO  C2   N3   aromatic  1.338  0.020  1.338
 1QO  N1   C1   single    1.446  0.020  1.446
 1QO  C5   N3   aromatic  1.324  0.020  1.324
 1QO  C5   C6   single    1.476  0.020  1.476
 1QO  C16  C15  aromatic  1.387  0.020  1.387
 1QO  C16  C11  aromatic  1.395  0.020  1.395
 1QO  C1   C11  single    1.505  0.020  1.505
 1QO  C15  C14  aromatic  1.391  0.020  1.391
 1QO  C7   C6   aromatic  1.393  0.020  1.393
 1QO  C7   C8   aromatic  1.383  0.020  1.383
 1QO  C6   C10  aromatic  1.394  0.020  1.394
 1QO  C11  C12  aromatic  1.390  0.020  1.390
 1QO  C8   C9   aromatic  1.388  0.020  1.388
 1QO  C10  N4   aromatic  1.325  0.020  1.325
 1QO  C14  C13  aromatic  1.387  0.020  1.387
 1QO  C12  C13  aromatic  1.390  0.020  1.390
 1QO  C9   N4   aromatic  1.328  0.020  1.328
 1QO  N1   H3   single    0.860  0.020  1.020
 1QO  C4   H5   single    0.930  0.020  1.080
 1QO  C12  H10  single    0.930  0.020  1.080
 1QO  C13  H11  single    0.930  0.020  1.080
 1QO  C1   H2   single    0.970  0.020  1.090
 1QO  C1   H1   single    0.970  0.020  1.090
 1QO  C3   H4   single    0.930  0.020  1.080
 1QO  C7   H6   single    0.930  0.020  1.080
 1QO  C8   H7   single    0.930  0.020  1.080
 1QO  C9   H8   single    0.930  0.020  1.080
 1QO  C10  H9   single    0.930  0.020  1.080
 1QO  C14  H12  single    0.930  0.020  1.080
 1QO  C15  H13  single    0.930  0.020  1.080
 1QO  C16  H14  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
 1QO  H3   N1   C1   118.60  3.000
 1QO  H3   N1   C2   116.64  3.000
 1QO  C1   N1   C2   123.75  3.000
 1QO  N2   C2   N3   125.51  3.000
 1QO  N3   C2   N1   116.52  3.000
 1QO  N2   C2   N1   117.97  3.000
 1QO  C5   N3   C2   117.67  3.000
 1QO  H5   C4   C3   120.82  3.000
 1QO  H5   C4   C5   123.09  3.000
 1QO  C3   C4   C5   116.08  3.000
 1QO  C10  N4   C9   118.00  3.000
 1QO  C6   C5   C4   122.16  3.000
 1QO  C6   C5   N3   116.51  3.000
 1QO  C4   C5   N3   121.33  3.000
 1QO  C10  C6   C7   117.35  3.000
 1QO  C10  C6   C5   121.71  3.000
 1QO  C7   C6   C5   120.94  3.000
 1QO  C16  C11  C1   120.37  3.000
 1QO  C1   C11  C12  120.72  3.000
 1QO  C16  C11  C12  118.91  3.000
 1QO  H10  C12  C13  119.72  3.000
 1QO  H10  C12  C11  119.63  3.000
 1QO  C13  C12  C11  120.65  3.000
 1QO  H11  C13  C14  120.15  3.000
 1QO  H11  C13  C12  119.78  3.000
 1QO  C14  C13  C12  120.07  3.000
 1QO  H1   C1   H2   106.49  3.000
 1QO  H1   C1   C11  109.80  3.000
 1QO  H2   C1   C11  109.93  3.000
 1QO  H1   C1   N1   109.00  3.000
 1QO  H2   C1   N1   111.19  3.000
 1QO  C11  C1   N1   110.35  3.000
 1QO  C3   N2   C2   115.88  3.000
 1QO  H4   C3   N2   116.36  3.000
 1QO  H4   C3   C4   120.13  3.000
 1QO  N2   C3   C4   123.51  3.000
 1QO  H6   C7   C8   120.78  3.000
 1QO  H6   C7   C6   120.08  3.000
 1QO  C8   C7   C6   119.14  3.000
 1QO  H7   C8   C9   120.27  3.000
 1QO  H7   C8   C7   121.15  3.000
 1QO  C9   C8   C7   118.58  3.000
 1QO  H8   C9   C8   120.29  3.000
 1QO  H8   C9   N4   116.64  3.000
 1QO  C8   C9   N4   123.07  3.000
 1QO  H9   C10  C6   120.45  3.000
 1QO  H9   C10  N4   115.70  3.000
 1QO  C6   C10  N4   123.84  3.000
 1QO  H12  C14  C15  120.14  3.000
 1QO  H12  C14  C13  120.19  3.000
 1QO  C15  C14  C13  119.66  3.000
 1QO  H13  C15  C16  119.80  3.000
 1QO  H13  C15  C14  120.07  3.000
 1QO  C16  C15  C14  120.13  3.000
 1QO  H14  C16  C15  119.65  3.000
 1QO  H14  C16  C11  119.78  3.000
 1QO  C15  C16  C11  120.58  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
 1QO  CONST_01  C4   C3   N2   C2     0.00   0.0  0
 1QO  CONST_02  C4   C5   N3   C2     0.00   0.0  0
 1QO  CONST_03  C6   C5   N3   C2   180.00   0.0  0
 1QO  CONST_04  C3   N2   C2   N3     0.00   0.0  0
 1QO  CONST_05  C3   C4   C5   N3     0.00   0.0  0
 1QO  CONST_10  C5   C6   C10  N4   180.00   0.0  0
 1QO  CONST_11  C7   C6   C10  N4     0.00   0.0  0
 1QO  CONST_12  C7   C8   C9   N4     0.00   0.0  0
 1QO  CONST_13  N2   C3   C4   C5     0.00   0.0  0
 1QO  CONST_14  N2   C2   N3   C5     0.00   0.0  0
 1QO  CONST_15  C8   C7   C6   C5   180.00   0.0  0
 1QO  CONST_16  C3   C4   C5   C6   180.00   0.0  0
 1QO  CONST_17  C9   C8   C7   C6     0.00   0.0  0
 1QO  CONST_18  C9   N4   C10  C6     0.00   0.0  0
 1QO  CONST_19  C14  C15  C16  C11    0.00   0.0  0
 1QO  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 1QO  CONST_21  C15  C16  C11  C12    0.00   0.0  0
 1QO  CONST_22  C15  C14  C13  C12    0.00   0.0  0
 1QO  CONST_23  C16  C15  C14  C13    0.00   0.0  0
 1QO  CONST_24  C16  C11  C12  C13    0.00   0.0  0
 1QO  CONST_25  C10  C6   C7   C8     0.00   0.0  0
 1QO  CONST_26  C10  N4   C9   C8     0.00   0.0  0
 1QO  CONST_27  C3   N2   C2   N1   180.00   0.0  0
 1QO  CONST_28  C5   N3   C2   N1   180.00   0.0  0
 1QO  CONST_29  C1   C11  C12  C13  180.00   0.0  0
 1QO  CONST_30  C15  C16  C11  C1   180.00   0.0  0
 1QO  CONST_31  H4   C3   N2   C2   180.00   0.0  0
 1QO  CONST_32  H5   C4   C5   N3   180.00   0.0  0
 1QO  CONST_33  H7   C8   C9   N4   180.00   0.0  0
 1QO  CONST_34  H6   C7   C6   C5     0.00   0.0  0
 1QO  CONST_35  H9   C10  C6   C5     0.00   0.0  0
 1QO  CONST_36  H13  C15  C16  C11  180.00   0.0  0
 1QO  CONST_37  H11  C13  C12  C11  180.00   0.0  0
 1QO  CONST_38  H14  C16  C11  C12  180.00   0.0  0
 1QO  CONST_39  H12  C14  C13  C12  180.00   0.0  0
 1QO  CONST_40  H8   C9   C8   C7   180.00   0.0  0
 1QO  CONST_41  H10  C12  C13  C14  180.00   0.0  0
 1QO  CONST_42  C1   N1   C2   N3   180.00   0.0  0
 1QO  CONST_43  N2   C2   N1   C1     0.00   0.0  0
 1QO  CONST_44  H3   N1   C2   N3     0.00   0.0  0
 1QO  Var_01    C16  C11  C1   N1   -61.17  30.0  2
 1QO  Var_02    C11  C1   N1   C2   168.39  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
 1QO  plan-1  N1   0.020
 1QO  plan-1  C2   0.020
 1QO  plan-1  N3   0.020
 1QO  plan-1  C4   0.020
 1QO  plan-1  C5   0.020
 1QO  plan-1  C6   0.020
 1QO  plan-1  N2   0.020
 1QO  plan-1  C3   0.020
 1QO  plan-1  H5   0.020
 1QO  plan-1  H4   0.020
 1QO  plan-2  N4   0.020
 1QO  plan-2  C5   0.020
 1QO  plan-2  C6   0.020
 1QO  plan-2  C7   0.020
 1QO  plan-2  C8   0.020
 1QO  plan-2  C9   0.020
 1QO  plan-2  C10  0.020
 1QO  plan-2  H6   0.020
 1QO  plan-2  H7   0.020
 1QO  plan-2  H8   0.020
 1QO  plan-2  H9   0.020
 1QO  plan-3  C11  0.020
 1QO  plan-3  C12  0.020
 1QO  plan-3  C13  0.020
 1QO  plan-3  C1   0.020
 1QO  plan-3  C14  0.020
 1QO  plan-3  C15  0.020
 1QO  plan-3  C16  0.020
 1QO  plan-3  H10  0.020
 1QO  plan-3  H11  0.020
 1QO  plan-3  H12  0.020
 1QO  plan-3  H13  0.020
 1QO  plan-3  H14  0.020
 1QO  plan-4  N1   0.020
 1QO  plan-4  C2   0.020
 1QO  plan-4  C1   0.020
 1QO  plan-4  H3   0.020

