# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:20:44 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-(4-methylpiperidin-1-yl)-N-(2-phenylethyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)c2ccnc(NCCc3ccccc3)n2
#
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
 VUA  VUA  4-(4-methylpiperidin-1-yl)-N-(2-phenylethyl)pyrimidin-2-amine  ligand  46  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VUA
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
 VUA  N1   N  N     0  -0.503   -8.4728  -11.0741  12.8689
 VUA  N3   N  NT    0  -0.487   -8.7065  -11.8833   8.8449
 VUA  C4   C  CR16  0  -0.302   -5.1853  -10.3084  11.6306
 VUA  C5   C  CR16  0  -0.288   -5.3859   -9.4599   9.4027
 VUA  C6   C  CR16  0  -0.465   -8.7994  -12.6973  11.1373
 VUA  C7   C  CR16  0  -0.042   -8.7132  -12.3144  12.4533
 VUA  C8   C  CR6   0   0.131   -5.4757   -9.2484  10.7761
 VUA  C10  C  CR6   0   0.586   -8.3210  -10.1825  11.8828
 VUA  C13  C  CH2   0  -0.312   -9.0103  -13.1608   8.2352
 VUA  C15  C  CH1   0  -0.242  -10.1816  -11.9504   6.3482
 VUA  C17  C  CH2   0  -0.515   -5.9714   -7.9383  11.3166
 VUA  C1   C  CR16  0  -0.267   -4.7791  -11.7599   9.7556
 VUA  C2   C  CR16  0  -0.230   -4.8474  -11.5574  11.1268
 VUA  C3   C  CR16  0  -0.229   -5.0405  -10.7025   8.8937
 VUA  C9   C  CR6   0   0.599   -8.6470  -11.6689  10.1759
 VUA  C11  C  CH2   0  -0.408  -10.2719  -13.0677   7.3842
 VUA  C12  C  CH2   0  -0.411   -9.7800  -10.6437   7.0290
 VUA  C14  C  CH2   0  -0.313   -8.5276  -10.8171   7.8778
 VUA  C16  C  CH3   0  -0.651  -11.4783  -11.8027   5.5654
 VUA  C18  C  CH2   0  -0.296   -7.5046   -7.8987  11.4045
 VUA  N2   N  N     0  -0.519   -8.4380  -10.4183  10.5850
 VUA  N4   N  NH1   0  -0.649   -8.0595   -8.9072  12.2726
 VUA  H2   H  HCR6  0   0.234   -5.6038   -8.6446   8.7220
 VUA  H3   H  HCR6  0   0.257   -8.9753  -13.7316  10.8911
 VUA  H4   H  HCR6  0   0.250   -8.8386  -13.0624  13.2303
 VUA  H5   H  HCH2  0   0.260   -9.1309  -13.9335   8.9887
 VUA  H6   H  HCH2  0   0.231   -8.1610  -13.4647   7.6121
 VUA  H7   H  HCH1  0   0.212   -9.3823  -12.2119   5.6420
 VUA  H8   H  HCH2  0   0.240   -5.5511   -7.7518  12.3085
 VUA  H9   H  HCH2  0   0.241   -5.6492   -7.1129  10.6763
 VUA  H10  H  HCR6  0   0.242   -4.5174  -12.7334   9.3609
 VUA  H11  H  HCR6  0   0.241   -4.6387  -12.3737  11.8071
 VUA  H12  H  HCR6  0   0.241   -4.9829  -10.8493   7.8223
 VUA  H13  H  HCH2  0   0.216  -11.1301  -12.8922   8.0420
 VUA  H14  H  HCH2  0   0.233  -10.4400  -14.0294   6.8924
 VUA  H15  H  HCH2  0   0.229   -9.6002   -9.8691   6.2780
 VUA  H16  H  HCH2  0   0.214  -10.6008  -10.2853   7.6602
 VUA  H17  H  HCH2  0   0.219   -7.6797  -11.0737   7.2314
 VUA  H18  H  HCH2  0   0.280   -8.2675   -9.9021   8.4004
 VUA  H19  H  HCH3  0   0.225  -11.7345  -12.7255   5.0415
 VUA  H20  H  HCH3  0   0.214  -12.3102  -11.5573   6.2299
 VUA  H21  H  HCH3  0   0.225  -11.4018  -11.0077   4.8220
 VUA  H22  H  HCH2  0   0.247   -7.8147   -6.9196  11.7736
 VUA  H23  H  HCH2  0   0.249   -7.9307   -8.0202  10.4105
 VUA  H24  H  HNH1  0   0.374   -7.8755   -8.8046  13.2579
 VUA  H1   H  HCR6  0   0.238   -5.2418  -10.1605  12.7031

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
 VUA  C16  C15  single    1.522  0.020  1.522
 VUA  C15  C12  single    1.527  0.020  1.527
 VUA  C15  C11  single    1.526  0.020  1.526
 VUA  C12  C14  single    1.523  0.020  1.523
 VUA  C11  C13  single    1.525  0.020  1.525
 VUA  C14  N3   single    1.451  0.020  1.451
 VUA  C13  N3   single    1.448  0.020  1.448
 VUA  C3   C5   aromatic  1.387  0.020  1.387
 VUA  C3   C1   aromatic  1.389  0.020  1.389
 VUA  N3   C9   single    1.349  0.020  1.349
 VUA  C5   C8   aromatic  1.393  0.020  1.393
 VUA  C1   C2   aromatic  1.388  0.020  1.388
 VUA  C9   N2   aromatic  1.332  0.020  1.332
 VUA  C9   C6   aromatic  1.416  0.020  1.416
 VUA  N2   C10  aromatic  1.324  0.020  1.324
 VUA  C8   C17  single    1.501  0.020  1.501
 VUA  C8   C4   aromatic  1.392  0.020  1.392
 VUA  C2   C4   aromatic  1.389  0.020  1.389
 VUA  C6   C7   aromatic  1.373  0.020  1.373
 VUA  C18  C17  single    1.536  0.020  1.536
 VUA  C18  N4   single    1.442  0.020  1.442
 VUA  C10  N4   single    1.359  0.020  1.359
 VUA  C10  N1   aromatic  1.338  0.020  1.338
 VUA  C7   N1   aromatic  1.330  0.020  1.330
 VUA  C4   H1   single    0.930  0.020  1.080
 VUA  C5   H2   single    0.930  0.020  1.080
 VUA  C6   H3   single    0.930  0.020  1.080
 VUA  C7   H4   single    0.930  0.020  1.080
 VUA  C13  H5   single    0.970  0.020  1.090
 VUA  C13  H6   single    0.970  0.020  1.090
 VUA  C15  H7   single    0.970  0.020  1.090
 VUA  C17  H8   single    0.970  0.020  1.090
 VUA  C17  H9   single    0.970  0.020  1.090
 VUA  C1   H10  single    0.930  0.020  1.080
 VUA  C2   H11  single    0.930  0.020  1.080
 VUA  C3   H12  single    0.930  0.020  1.080
 VUA  C11  H13  single    0.970  0.020  1.090
 VUA  C11  H14  single    0.970  0.020  1.090
 VUA  C12  H15  single    0.970  0.020  1.090
 VUA  C12  H16  single    0.970  0.020  1.090
 VUA  C14  H17  single    0.970  0.020  1.090
 VUA  C14  H18  single    0.970  0.020  1.090
 VUA  C16  H19  single    0.970  0.020  1.090
 VUA  C16  H20  single    0.970  0.020  1.090
 VUA  C16  H21  single    0.970  0.020  1.090
 VUA  C18  H22  single    0.970  0.020  1.090
 VUA  C18  H23  single    0.970  0.020  1.090
 VUA  N4   H24  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
 VUA  C10  N1   C7   114.31  3.000
 VUA  C14  N3   C9   122.37  3.000
 VUA  C9   N3   C13  124.39  3.000
 VUA  C14  N3   C13  113.19  3.000
 VUA  H1   C4   C2   119.62  3.000
 VUA  H1   C4   C8   119.50  3.000
 VUA  C2   C4   C8   120.86  3.000
 VUA  H2   C5   C3   119.57  3.000
 VUA  H2   C5   C8   119.47  3.000
 VUA  C3   C5   C8   120.95  3.000
 VUA  H3   C6   C9   124.02  3.000
 VUA  H3   C6   C7   119.79  3.000
 VUA  C9   C6   C7   116.19  3.000
 VUA  H4   C7   C6   119.10  3.000
 VUA  H4   C7   N1   116.08  3.000
 VUA  C6   C7   N1   124.81  3.000
 VUA  C17  C8   C5   120.59  3.000
 VUA  C17  C8   C4   120.82  3.000
 VUA  C5   C8   C4   118.44  3.000
 VUA  N4   C10  N2   117.73  3.000
 VUA  N4   C10  N1   115.83  3.000
 VUA  N2   C10  N1   126.41  3.000
 VUA  H6   C13  H5   106.45  3.000
 VUA  H6   C13  C11  109.92  3.000
 VUA  H5   C13  C11  109.81  3.000
 VUA  H6   C13  N3   108.75  3.000
 VUA  H5   C13  N3   111.04  3.000
 VUA  C11  C13  N3   110.78  3.000
 VUA  H7   C15  C16  108.21  3.000
 VUA  H7   C15  C12  107.40  3.000
 VUA  C16  C15  C12  111.74  3.000
 VUA  H7   C15  C11  107.78  3.000
 VUA  C12  C15  C11  109.83  3.000
 VUA  C16  C15  C11  111.70  3.000
 VUA  H9   C17  H8   106.81  3.000
 VUA  H9   C17  C18  107.95  3.000
 VUA  H8   C17  C18  109.11  3.000
 VUA  H9   C17  C8   110.53  3.000
 VUA  H8   C17  C8   110.40  3.000
 VUA  C18  C17  C8   111.87  3.000
 VUA  H10  C1   C3   120.25  3.000
 VUA  H10  C1   C2   120.22  3.000
 VUA  C3   C1   C2   119.52  3.000
 VUA  H11  C2   C1   120.08  3.000
 VUA  H11  C2   C4   119.81  3.000
 VUA  C1   C2   C4   120.11  3.000
 VUA  H12  C3   C1   120.05  3.000
 VUA  H12  C3   C5   119.86  3.000
 VUA  C1   C3   C5   120.09  3.000
 VUA  N2   C9   C6   119.35  3.000
 VUA  C6   C9   N3   123.33  3.000
 VUA  N2   C9   N3   117.31  3.000
 VUA  H14  C11  H13  106.89  3.000
 VUA  H14  C11  C15  110.34  3.000
 VUA  H13  C11  C15  109.68  3.000
 VUA  H14  C11  C13  108.94  3.000
 VUA  H13  C11  C13  108.84  3.000
 VUA  C15  C11  C13  112.00  3.000
 VUA  H16  C12  H15  106.68  3.000
 VUA  H16  C12  C14  109.41  3.000
 VUA  H15  C12  C14  109.16  3.000
 VUA  H16  C12  C15  109.86  3.000
 VUA  H15  C12  C15  110.06  3.000
 VUA  C14  C12  C15  111.55  3.000
 VUA  H18  C14  H17  107.21  3.000
 VUA  H18  C14  C12  111.68  3.000
 VUA  H17  C14  C12  109.51  3.000
 VUA  H18  C14  N3   109.16  3.000
 VUA  H17  C14  N3   108.44  3.000
 VUA  C12  C14  N3   110.72  3.000
 VUA  H21  C16  H20  107.70  3.000
 VUA  H21  C16  H19  107.78  3.000
 VUA  H20  C16  H19  107.64  3.000
 VUA  H21  C16  C15  111.19  3.000
 VUA  H20  C16  C15  110.96  3.000
 VUA  H19  C16  C15  111.39  3.000
 VUA  H23  C18  H22  107.32  3.000
 VUA  H23  C18  N4   108.73  3.000
 VUA  H22  C18  N4   108.33  3.000
 VUA  H23  C18  C17  109.61  3.000
 VUA  H22  C18  C17  109.03  3.000
 VUA  N4   C18  C17  113.61  3.000
 VUA  C9   N2   C10  118.81  3.000
 VUA  H24  N4   C18  116.57  3.000
 VUA  H24  N4   C10  114.28  3.000
 VUA  C18  N4   C10  123.91  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
 VUA  CONST_01  C9   N2   C10  N1      0.00   0.0  0
 VUA  CONST_02  C9   C6   C7   N1      0.00   0.0  0
 VUA  CONST_03  C3   C5   C8   C4      0.00   0.0  0
 VUA  CONST_04  C3   C1   C2   C4      0.00   0.0  0
 VUA  CONST_05  C2   C1   C3   C5      0.00   0.0  0
 VUA  CONST_06  C2   C4   C8   C5      0.00   0.0  0
 VUA  CONST_07  C10  N2   C9   C6      0.00   0.0  0
 VUA  CONST_08  C10  N1   C7   C6      0.00   0.0  0
 VUA  CONST_09  N2   C9   C6   C7      0.00   0.0  0
 VUA  CONST_10  N2   C10  N1   C7      0.00   0.0  0
 VUA  CONST_11  C1   C3   C5   C8      0.00   0.0  0
 VUA  CONST_12  C1   C2   C4   C8      0.00   0.0  0
 VUA  CONST_13  C10  N2   C9   N3    180.00   0.0  0
 VUA  CONST_14  C7   C6   C9   N3    180.00   0.0  0
 VUA  CONST_15  N4   C10  N1   C7    180.00   0.0  0
 VUA  CONST_16  C3   C5   C8   C17   180.00   0.0  0
 VUA  CONST_17  C2   C4   C8   C17   180.00   0.0  0
 VUA  CONST_18  N4   C10  N2   C9    180.00   0.0  0
 VUA  CONST_19  H3   C6   C7   N1    180.00   0.0  0
 VUA  CONST_20  H2   C5   C8   C4    180.00   0.0  0
 VUA  CONST_21  H10  C1   C2   C4    180.00   0.0  0
 VUA  CONST_22  H1   C4   C8   C5    180.00   0.0  0
 VUA  CONST_23  H12  C3   C5   C8    180.00   0.0  0
 VUA  CONST_24  H11  C2   C4   C8    180.00   0.0  0
 VUA  CONST_25  H4   C7   N1   C10   180.00   0.0  0
 VUA  CONST_28  H24  N4   C10  N1      0.00   0.0  0
 VUA  Var_01    C15  C12  C14  N3    -55.39  30.0  1
 VUA  Var_02    C15  C11  C13  N3     54.34  30.0  1
 VUA  Var_03    C14  N3   C9   C6   -179.06  30.0  1
 VUA  Var_04    C12  C14  N3   C13    58.74  30.0  1
 VUA  Var_05    C11  C13  N3   C9    119.24  30.0  1
 VUA  Var_06    C18  C17  C8   C4    -90.14  30.0  2
 VUA  Var_07    N4   C18  C17  C8     60.72  30.0  1
 VUA  Var_08    C17  C18  N4   C10   -84.57  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VUA  chir_01  C15  C16  C12  C11  negativ

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
 VUA  plan-1  C4   0.020
 VUA  plan-1  C5   0.020
 VUA  plan-1  C8   0.020
 VUA  plan-1  C17  0.020
 VUA  plan-1  C1   0.020
 VUA  plan-1  C2   0.020
 VUA  plan-1  C3   0.020
 VUA  plan-1  H2   0.020
 VUA  plan-1  H10  0.020
 VUA  plan-1  H11  0.020
 VUA  plan-1  H12  0.020
 VUA  plan-1  H1   0.020
 VUA  plan-2  N1   0.020
 VUA  plan-2  N3   0.020
 VUA  plan-2  C6   0.020
 VUA  plan-2  C7   0.020
 VUA  plan-2  C10  0.020
 VUA  plan-2  C9   0.020
 VUA  plan-2  N2   0.020
 VUA  plan-2  N4   0.020
 VUA  plan-2  H3   0.020
 VUA  plan-2  H4   0.020
 VUA  plan-3  C10  0.020
 VUA  plan-3  C18  0.020
 VUA  plan-3  N4   0.020
 VUA  plan-3  H24  0.020

