# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 20:23:47 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: N-(piperidin-4-yl)-6-(trifluoromethyl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc(NC2CCNCC2)ncn1
#
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
 8VD  8VD  "N-(piperidin-4-yl)-6-(trifluoromethyl)pyrimidin-4-amine"
  ligand  30  17  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8VD
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
 8VD  C3   C  CR6   0   0.552  22.8336  33.5073   8.7915
 8VD  N1   N  NH1   0  -0.593  20.0416  30.4569  12.0866
 8VD  C8   C  CH2   0  -0.440  21.0891  30.4318   9.8839
 8VD  C5   C  CH2   0  -0.429  21.4535  32.3368  11.4630
 8VD  N    N  NH1   0  -0.649  22.5320  32.2836   9.2315
 8VD  C    C  CT    0   1.050  21.6047  37.0673   8.5559
 8VD  C1   C  CR6   0   0.008  22.4192  35.8039   8.4461
 8VD  C2   C  CR16  0  -0.409  21.9714  34.6178   8.9572
 8VD  C4   C  CH1   0  -0.082  21.3508  31.9296   9.9927
 8VD  C6   C  CH2   0  -0.296  20.2062  31.8932  12.2139
 8VD  C7   C  CH2   0  -0.295  19.8623  30.0563  10.7031
 8VD  C9   C  CR16  0   0.054  24.3085  34.8612   7.7124
 8VD  F    F  F     0  -0.307  22.2926  38.0337   9.1684
 8VD  F1   F  F     0  -0.309  21.2733  37.5226   7.3439
 8VD  F2   F  F     0  -0.298  20.4747  36.8894   9.2414
 8VD  N2   N  N     0  -0.452  24.0066  33.6594   8.1617
 8VD  N3   N  N     0  -0.454  23.5828  35.9617   7.8152
 8VD  H11  H  HCH2  0   0.246  20.9393  30.1502   8.8396
 8VD  H10  H  HCH2  0   0.229  21.9588  29.8797  10.2547
 8VD  H3   H  HCH2  0   0.226  22.3369  31.8672  11.9045
 8VD  H4   H  HCH2  0   0.241  21.5771  33.4183  11.5573
 8VD  H1   H  HNH1  0   0.394  23.2501  31.5835   9.1126
 8VD  H    H  HCR6  0   0.297  21.0207  34.5348   9.4609
 8VD  H2   H  HCH1  0   0.243  20.4923  32.4445   9.5467
 8VD  H6   H  HCH2  0   0.237  20.2998  32.1487  13.2708
 8VD  H5   H  HCH2  0   0.192  19.3399  32.4552  11.8263
 8VD  H8   H  HCH2  0   0.192  18.9756  30.5188  10.2384
 8VD  H9   H  HCH2  0   0.238  19.7126  28.9759  10.6627
 8VD  H12  H  HCR6  0   0.262  25.2619  34.9561   7.2031
 8VD  H7   H  HNH1  0   0.352  19.2435  30.1568  12.6308

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
 8VD  F1  C    single    1.336  0.020  1.336
 8VD  N3  C9   aromatic  1.322  0.020  1.322
 8VD  N3  C1   aromatic  1.333  0.020  1.333
 8VD  C9  N2   aromatic  1.318  0.020  1.318
 8VD  N2  C3   aromatic  1.340  0.020  1.340
 8VD  C1  C    single    1.507  0.020  1.507
 8VD  C1  C2   aromatic  1.367  0.020  1.367
 8VD  C   F    single    1.335  0.020  1.335
 8VD  C   F2   single    1.334  0.020  1.334
 8VD  C3  C2   aromatic  1.416  0.020  1.416
 8VD  C3  N    single    1.335  0.020  1.335
 8VD  N   C4   single    1.449  0.020  1.449
 8VD  C8  C4   single    1.524  0.020  1.524
 8VD  C8  C7   single    1.522  0.020  1.522
 8VD  C4  C5   single    1.529  0.020  1.529
 8VD  C7  N1   single    1.451  0.020  1.451
 8VD  C5  C6   single    1.522  0.020  1.522
 8VD  N1  C6   single    1.451  0.020  1.451
 8VD  N1  H7   single    0.890  0.020  1.040
 8VD  C8  H11  single    0.970  0.020  1.090
 8VD  C8  H10  single    0.970  0.020  1.090
 8VD  C5  H3   single    0.970  0.020  1.090
 8VD  C5  H4   single    0.970  0.020  1.090
 8VD  N   H1   single    0.860  0.020  1.020
 8VD  C2  H    single    0.930  0.020  1.080
 8VD  C4  H2   single    0.970  0.020  1.090
 8VD  C6  H6   single    0.970  0.020  1.090
 8VD  C6  H5   single    0.970  0.020  1.090
 8VD  C7  H8   single    0.970  0.020  1.090
 8VD  C7  H9   single    0.970  0.020  1.090
 8VD  C9  H12  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
 8VD  N2   C3  C2   119.94  3.000
 8VD  C2   C3  N    122.88  3.000
 8VD  N2   C3  N    117.18  3.000
 8VD  H7   N1  C7   109.48  3.000
 8VD  H7   N1  C6   109.63  3.000
 8VD  C7   N1  C6   111.76  3.000
 8VD  H10  C8  H11  107.63  3.000
 8VD  H10  C8  C7   109.48  3.000
 8VD  H11  C8  C7   109.90  3.000
 8VD  H10  C8  C4   109.57  3.000
 8VD  H11  C8  C4   110.20  3.000
 8VD  C7   C8  C4   110.02  3.000
 8VD  H4   C5  H3   107.39  3.000
 8VD  H4   C5  C6   109.80  3.000
 8VD  H3   C5  C6   109.73  3.000
 8VD  H4   C5  C4   110.75  3.000
 8VD  H3   C5  C4   109.15  3.000
 8VD  C6   C5  C4   109.98  3.000
 8VD  H1   N   C4   118.17  3.000
 8VD  H1   N   C3   115.85  3.000
 8VD  C4   N   C3   125.54  3.000
 8VD  F2   C   F1   107.55  3.000
 8VD  F2   C   F    107.29  3.000
 8VD  F1   C   F    107.29  3.000
 8VD  F2   C   C1   112.56  3.000
 8VD  F    C   C1   111.21  3.000
 8VD  F1   C   C1   110.70  3.000
 8VD  N3   C1  C2   124.45  3.000
 8VD  C2   C1  C    121.54  3.000
 8VD  N3   C1  C    114.02  3.000
 8VD  H    C2  C1   122.00  3.000
 8VD  H    C2  C3   122.07  3.000
 8VD  C1   C2  C3   115.93  3.000
 8VD  H2   C4  N    108.06  3.000
 8VD  H2   C4  C5   108.59  3.000
 8VD  N    C4  C5   112.66  3.000
 8VD  H2   C4  C8   107.34  3.000
 8VD  C5   C4  C8   109.99  3.000
 8VD  N    C4  C8   110.03  3.000
 8VD  H5   C6  H6   106.76  3.000
 8VD  H5   C6  C5   108.77  3.000
 8VD  H6   C6  C5   109.84  3.000
 8VD  H5   C6  N1   112.60  3.000
 8VD  H6   C6  N1   109.05  3.000
 8VD  C5   C6  N1   109.77  3.000
 8VD  H9   C7  H8   106.82  3.000
 8VD  H9   C7  C8   109.56  3.000
 8VD  H8   C7  C8   108.53  3.000
 8VD  H9   C7  N1   108.99  3.000
 8VD  H8   C7  N1   112.66  3.000
 8VD  C8   C7  N1   110.20  3.000
 8VD  H12  C9  N3   116.49  3.000
 8VD  H12  C9  N2   116.16  3.000
 8VD  N3   C9  N2   127.35  3.000
 8VD  C9   N2  C3   117.66  3.000
 8VD  C9   N3  C1   114.67  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
 8VD  CONST_01  N3   C9  N2  C3     0.00   0.0  0
 8VD  CONST_02  N3   C1  C2  C3     0.00   0.0  0
 8VD  CONST_03  N2   C9  N3  C1     0.00   0.0  0
 8VD  CONST_04  N2   C3  C2  C1     0.00   0.0  0
 8VD  CONST_05  C9   N3  C1  C2     0.00   0.0  0
 8VD  CONST_06  C9   N2  C3  C2     0.00   0.0  0
 8VD  CONST_07  C    C1  C2  C3   180.00   0.0  0
 8VD  CONST_08  C9   N2  C3  N    180.00   0.0  0
 8VD  CONST_09  C1   C2  C3  N    180.00   0.0  0
 8VD  CONST_10  C9   N3  C1  C    180.00   0.0  0
 8VD  CONST_11  C4   N   C3  C2     0.00   0.0  0
 8VD  CONST_12  N2   C3  N   C4   180.00   0.0  0
 8VD  CONST_13  H12  C9  N2  C3   180.00   0.0  0
 8VD  CONST_14  H12  C9  N3  C1   180.00   0.0  0
 8VD  CONST_15  H    C2  C3  N2   180.00   0.0  0
 8VD  CONST_16  H    C2  C1  N3   180.00   0.0  0
 8VD  CONST_17  H1   N   C3  C2   180.00   0.0  0
 8VD  CONST_18  H1   N   C3  N2     0.00   0.0  0
 8VD  Var_01    C4   C8  C7  N1   -57.12  30.0  1
 8VD  Var_02    C4   C5  C6  N1    57.81  30.0  1
 8VD  Var_03    C6   N1  C7  C8    61.46  30.0  1
 8VD  Var_04    C7   N1  C6  C5   -61.72  30.0  1
 8VD  Var_05    H11  C8  C7  N1  -178.64  30.0  1
 8VD  Var_06    H10  C8  C7  N1    63.35  30.0  1
 8VD  Var_07    H3   C5  C6  N1   -62.27  30.0  1
 8VD  Var_08    H4   C5  C6  N1   179.92  30.0  1
 8VD  Var_09    H7   N1  C7  C8  -176.87  30.0  1
 8VD  Var_10    H7   N1  C6  C5   176.70  30.0  1
 8VD  Var_11    H8   C7  C8  C4    66.67  30.0  1
 8VD  Var_12    H9   C7  C8  C4  -177.04  30.0  1
 8VD  Var_13    H6   C6  C5  C4   177.70  30.0  1
 8VD  Var_14    H5   C6  C5  C4   -65.79  30.0  1
 8VD  Var_15    H8   C7  N1  C6   -59.91  30.0  1
 8VD  Var_16    H9   C7  N1  C6  -178.28  30.0  1
 8VD  Var_17    H6   C6  N1  C7   177.91  30.0  1
 8VD  Var_18    H5   C6  N1  C7    59.60  30.0  1
 8VD  Var_19    F1   C   C1  C2  -117.53  30.0  2
 8VD  Var_20    F    C   C1  C2   123.30  30.0  2
 8VD  Var_21    F2   C   C1  C2     2.87  30.0  2
 8VD  Var_22    N3   C1  C   F    -56.86  30.0  3
 8VD  Var_23    N3   C1  C   F1    62.31  30.0  3
 8VD  Var_24    N3   C1  C   F2  -177.29  30.0  3

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
 8VD  chir_01  C4  N  C8  C5  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
 8VD  plan-1  C3   0.020
 8VD  plan-1  N    0.020
 8VD  plan-1  C    0.020
 8VD  plan-1  C1   0.020
 8VD  plan-1  C2   0.020
 8VD  plan-1  C9   0.020
 8VD  plan-1  N2   0.020
 8VD  plan-1  N3   0.020
 8VD  plan-1  H    0.020
 8VD  plan-1  H12  0.020
 8VD  plan-2  C3   0.020
 8VD  plan-2  N    0.020
 8VD  plan-2  C4   0.020
 8VD  plan-2  H1   0.020

