# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:02:39 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: 6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(N)CCN(CC1)c2cnc(Sc3cccc(Cl)c3Cl)c(N)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
 VKP  VKP  6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine  ligand  43  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VKP
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
 VKP  C1   C   CR6   0  -0.147  21.1022  41.7640  5.4693
 VKP  C2   C   CR16  0  -0.217  22.2144  42.9712  3.8810
 VKP  C3   C   CR6   0   0.503  23.0099  41.8348  3.5610
 VKP  C11  C   CR6   0  -0.051  18.5035  40.9913  5.9873
 VKP  C12  C   CR16  0  -0.245  18.4391  40.7132  4.6268
 VKP  C13  C   CR16  0  -0.240  17.3071  40.1268  4.0852
 VKP  C14  C   CR16  0  -0.237  16.2198  39.8110  4.8834
 VKP  C15  C   CR6   0   0.015  16.2751  40.0920  6.2390
 VKP  C16  C   CR6   0  -0.023  17.4078  40.6787  6.7923
 VKP  N1   N   N     0  -0.305  21.2970  42.8971  4.8127
 VKP  N2   N   N     0  -0.484  22.8302  40.7010  4.2334
 VKP  C4   C   CR6   0   0.480  21.8944  40.6333  5.1731
 VKP  N3   N   NH2   0  -0.824  21.7114  39.4463  5.7824
 VKP  N4   N   NT    0  -0.479  23.9363  41.8425  2.5773
 VKP  C5   C   CH2   0  -0.339  24.9055  40.7671  2.4428
 VKP  C6   C   CH2   0  -0.430  26.2458  41.1930  3.0370
 VKP  C7   C   CT    0   0.069  26.7902  42.5035  2.4379
 VKP  C8   C   CH2   0  -0.414  25.6796  43.5614  2.4797
 VKP  C9   C   CH2   0  -0.350  24.3665  43.0516  1.8981
 VKP  C10  C   CH3   0  -0.655  27.2684  42.2790  1.0033
 VKP  N5   N   NH2   0  -0.791  27.9265  43.0265  3.1931
 VKP  S1   S   S2    0   0.097  19.9125  41.7373  6.7625
 VKP  CL1  CL  CL    0  -0.085  17.4701  41.0301  8.4770
 VKP  CL2  CL  CL    0  -0.093  14.9257  39.7056  7.2373
 VKP  H1   H   HCR6  0   0.265  22.3294  43.9254  3.3879
 VKP  H2   H   HCR6  0   0.277  19.2725  40.9587  3.9832
 VKP  H3   H   HCR6  0   0.278  17.2700  39.9159  3.0252
 VKP  H4   H   HCR6  0   0.289  15.3357  39.3543  4.4617
 VKP  H5   H   HNH2  0   0.396  22.4169  38.7403  5.6547
 VKP  H6   H   HNH2  0   0.401  21.1846  39.4057  6.6389
 VKP  H7   H   HCH2  0   0.275  24.5304  39.8734  2.9317
 VKP  H8   H   HCH2  0   0.244  25.0084  40.5380  1.3789
 VKP  H9   H   HCH2  0   0.234  26.9778  40.3911  2.9013
 VKP  H10  H   HCH2  0   0.228  26.1179  41.3264  4.1169
 VKP  H11  H   HCH2  0   0.239  25.9976  44.4559  1.9381
 VKP  H12  H   HCH2  0   0.231  25.5066  43.8636  3.5188
 VKP  H13  H   HCH2  0   0.273  23.6020  43.8218  1.9405
 VKP  H14  H   HCH2  0   0.255  24.4853  42.8097  0.8386
 VKP  H15  H   HCH3  0   0.230  28.0870  41.5558  0.9797
 VKP  H16  H   HCH3  0   0.226  26.4837  41.8959  0.3503
 VKP  H17  H   HCH3  0   0.232  27.6335  43.2117  0.5710
 VKP  H18  H   HNH2  0   0.337  27.6589  43.1388  4.1653
 VKP  H19  H   HNH2  0   0.338  28.6728  42.3392  3.1978

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
 VKP  C10  C7   single    1.529  0.020  1.529
 VKP  C9   C8   single    1.524  0.020  1.524
 VKP  C9   N4   single    1.452  0.020  1.452
 VKP  C8   C7   single    1.534  0.020  1.534
 VKP  C7   N5   single    1.461  0.020  1.461
 VKP  C7   C6   single    1.540  0.020  1.540
 VKP  C5   N4   single    1.454  0.020  1.454
 VKP  C5   C6   single    1.527  0.020  1.527
 VKP  N4   C3   single    1.351  0.020  1.351
 VKP  C3   C2   aromatic  1.424  0.020  1.424
 VKP  C3   N2   aromatic  1.330  0.020  1.330
 VKP  C2   N1   aromatic  1.310  0.020  1.310
 VKP  C13  C12  aromatic  1.385  0.020  1.385
 VKP  C13  C14  aromatic  1.385  0.020  1.385
 VKP  N2   C4   aromatic  1.328  0.020  1.328
 VKP  C12  C11  aromatic  1.390  0.020  1.390
 VKP  N1   C1   aromatic  1.324  0.020  1.324
 VKP  C14  C15  aromatic  1.386  0.020  1.386
 VKP  C4   C1   aromatic  1.412  0.020  1.412
 VKP  C4   N3   single    1.347  0.020  1.347
 VKP  C1   S1   single    1.757  0.020  1.757
 VKP  C11  S1   single    1.773  0.020  1.773
 VKP  C11  C16  aromatic  1.395  0.020  1.395
 VKP  C15  C16  aromatic  1.390  0.020  1.390
 VKP  C15  CL2  single    1.722  0.020  1.722
 VKP  C16  CL1  single    1.722  0.020  1.722
 VKP  C2   H1   single    0.930  0.020  1.080
 VKP  C12  H2   single    0.930  0.020  1.080
 VKP  C13  H3   single    0.930  0.020  1.080
 VKP  C14  H4   single    0.930  0.020  1.080
 VKP  N3   H5   single    0.890  0.020  1.040
 VKP  N3   H6   single    0.890  0.020  1.040
 VKP  C5   H7   single    0.970  0.020  1.090
 VKP  C5   H8   single    0.970  0.020  1.090
 VKP  C6   H9   single    0.970  0.020  1.090
 VKP  C6   H10  single    0.970  0.020  1.090
 VKP  C8   H11  single    0.970  0.020  1.090
 VKP  C8   H12  single    0.970  0.020  1.090
 VKP  C9   H13  single    0.970  0.020  1.090
 VKP  C9   H14  single    0.970  0.020  1.090
 VKP  C10  H15  single    0.970  0.020  1.090
 VKP  C10  H16  single    0.970  0.020  1.090
 VKP  C10  H17  single    0.970  0.020  1.090
 VKP  N5   H18  single    0.890  0.020  1.040
 VKP  N5   H19  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
 VKP  S1   C1   C4   121.46  3.000
 VKP  S1   C1   N1   118.52  3.000
 VKP  C4   C1   N1   119.92  3.000
 VKP  H1   C2   N1   116.70  3.000
 VKP  H1   C2   C3   122.89  3.000
 VKP  N1   C2   C3   120.41  3.000
 VKP  N4   C3   N2   117.74  3.000
 VKP  N2   C3   C2   119.42  3.000
 VKP  N4   C3   C2   122.83  3.000
 VKP  S1   C11  C16  117.79  3.000
 VKP  C16  C11  C12  118.91  3.000
 VKP  S1   C11  C12  123.30  3.000
 VKP  H2   C12  C13  119.56  3.000
 VKP  H2   C12  C11  120.09  3.000
 VKP  C13  C12  C11  120.35  3.000
 VKP  H3   C13  C14  119.56  3.000
 VKP  H3   C13  C12  119.59  3.000
 VKP  C14  C13  C12  120.85  3.000
 VKP  H4   C14  C15  120.01  3.000
 VKP  H4   C14  C13  120.90  3.000
 VKP  C15  C14  C13  119.08  3.000
 VKP  CL2  C15  C16  120.15  3.000
 VKP  CL2  C15  C14  119.36  3.000
 VKP  C16  C15  C14  120.49  3.000
 VKP  CL1  C16  C15  120.32  3.000
 VKP  CL1  C16  C11  119.36  3.000
 VKP  C15  C16  C11  120.32  3.000
 VKP  C2   N1   C1   120.29  3.000
 VKP  C4   N2   C3   119.76  3.000
 VKP  N3   C4   N2   117.44  3.000
 VKP  N3   C4   C1   122.32  3.000
 VKP  N2   C4   C1   120.19  3.000
 VKP  H6   N3   H5   116.53  3.000
 VKP  H6   N3   C4   119.46  3.000
 VKP  H5   N3   C4   117.76  3.000
 VKP  C9   N4   C5   112.04  3.000
 VKP  C5   N4   C3   121.34  3.000
 VKP  C9   N4   C3   123.26  3.000
 VKP  H8   C5   H7   107.36  3.000
 VKP  H8   C5   C6   110.77  3.000
 VKP  H7   C5   C6   110.95  3.000
 VKP  H8   C5   N4   107.93  3.000
 VKP  H7   C5   N4   109.69  3.000
 VKP  C6   C5   N4   110.05  3.000
 VKP  H10  C6   H9   106.83  3.000
 VKP  H10  C6   C7   108.73  3.000
 VKP  H9   C6   C7   109.81  3.000
 VKP  H10  C6   C5   108.37  3.000
 VKP  H9   C6   C5   109.55  3.000
 VKP  C7   C6   C5   113.34  3.000
 VKP  N5   C7   C10  107.12  3.000
 VKP  N5   C7   C8   107.58  3.000
 VKP  C10  C7   C8   110.68  3.000
 VKP  N5   C7   C6   112.23  3.000
 VKP  C8   C7   C6   108.67  3.000
 VKP  C10  C7   C6   110.52  3.000
 VKP  H12  C8   H11  106.86  3.000
 VKP  H12  C8   C9   108.55  3.000
 VKP  H11  C8   C9   109.60  3.000
 VKP  H12  C8   C7   109.28  3.000
 VKP  H11  C8   C7   109.89  3.000
 VKP  C9   C8   C7   112.50  3.000
 VKP  H14  C9   H13  105.75  3.000
 VKP  H14  C9   C8   110.50  3.000
 VKP  H13  C9   C8   110.76  3.000
 VKP  H14  C9   N4   107.53  3.000
 VKP  H13  C9   N4   111.33  3.000
 VKP  C8   C9   N4   110.81  3.000
 VKP  H17  C10  H16  107.70  3.000
 VKP  H17  C10  H15  107.85  3.000
 VKP  H16  C10  H15  107.08  3.000
 VKP  H17  C10  C7   110.55  3.000
 VKP  H16  C10  C7   112.86  3.000
 VKP  H15  C10  C7   110.60  3.000
 VKP  H19  N5   H18  105.34  3.000
 VKP  H19  N5   C7   109.38  3.000
 VKP  H18  N5   C7   109.26  3.000
 VKP  C11  S1   C1   102.86  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
 VKP  CONST_01  C3   C2   N1   C1      0.00   0.0  0
 VKP  CONST_02  C3   N2   C4   C1      0.00   0.0  0
 VKP  CONST_03  C4   N2   C3   C2      0.00   0.0  0
 VKP  CONST_04  C4   C1   N1   C2      0.00   0.0  0
 VKP  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 VKP  CONST_06  C14  C15  C16  C11     0.00   0.0  0
 VKP  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 VKP  CONST_08  C15  C16  C11  C12     0.00   0.0  0
 VKP  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 VKP  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 VKP  CONST_11  N2   C3   C2   N1      0.00   0.0  0
 VKP  CONST_12  N2   C4   C1   N1      0.00   0.0  0
 VKP  CONST_13  N4   C3   C2   N1    180.00   0.0  0
 VKP  CONST_14  N4   C3   N2   C4    180.00   0.0  0
 VKP  CONST_15  S1   C1   N1   C2    180.00   0.0  0
 VKP  CONST_16  N3   C4   N2   C3    180.00   0.0  0
 VKP  CONST_17  CL2  C15  C16  C11   180.00   0.0  0
 VKP  CONST_18  CL1  C16  C11  C12   180.00   0.0  0
 VKP  CONST_19  S1   C11  C12  C13   180.00   0.0  0
 VKP  CONST_20  CL2  C15  C14  C13   180.00   0.0  0
 VKP  CONST_21  CL1  C16  C15  C14   180.00   0.0  0
 VKP  CONST_22  S1   C11  C16  C15   180.00   0.0  0
 VKP  CONST_23  N3   C4   C1   N1    180.00   0.0  0
 VKP  CONST_24  S1   C1   C4   N2    180.00   0.0  0
 VKP  CONST_25  H1   C2   N1   C1    180.00   0.0  0
 VKP  CONST_26  H3   C13  C12  C11   180.00   0.0  0
 VKP  CONST_27  H4   C14  C13  C12   180.00   0.0  0
 VKP  CONST_28  H2   C12  C13  C14   180.00   0.0  0
 VKP  CONST_29  H5   N3   C4   C1    180.00   0.0  0
 VKP  Var_01    C9   N4   C3   C2     10.29  30.0  1
 VKP  Var_02    C8   C9   N4   C3     98.83  30.0  1
 VKP  Var_03    C6   C5   N4   C3   -100.18  30.0  1
 VKP  Var_04    C7   C8   C9   N4     56.00  30.0  1
 VKP  Var_05    C7   C6   C5   N4    -55.09  30.0  1
 VKP  Var_06    C12  C11  S1   C1     -7.43  30.0  2
 VKP  Var_07    N1   C1   S1   C11   100.35  30.0  2

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
 VKP  chir_01  C7  C8  N5  C6  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
 VKP  plan-1  C1   0.020
 VKP  plan-1  C2   0.020
 VKP  plan-1  C3   0.020
 VKP  plan-1  N1   0.020
 VKP  plan-1  N2   0.020
 VKP  plan-1  C4   0.020
 VKP  plan-1  N3   0.020
 VKP  plan-1  N4   0.020
 VKP  plan-1  S1   0.020
 VKP  plan-1  H1   0.020
 VKP  plan-2  C11  0.020
 VKP  plan-2  C12  0.020
 VKP  plan-2  C13  0.020
 VKP  plan-2  C14  0.020
 VKP  plan-2  C15  0.020
 VKP  plan-2  C16  0.020
 VKP  plan-2  S1   0.020
 VKP  plan-2  CL1  0.020
 VKP  plan-2  CL2  0.020
 VKP  plan-2  H2   0.020
 VKP  plan-2  H3   0.020
 VKP  plan-2  H4   0.020
 VKP  plan-3  C4   0.020
 VKP  plan-3  N3   0.020
 VKP  plan-3  H5   0.020
 VKP  plan-3  H6   0.020

