# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 15:00:33 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(CN)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
 83Q  83Q  "6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine"
  ligand  46  25  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_83Q
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
 83Q  C10   C   CH2   0  -0.344  39.5268  26.0278  46.6082
 83Q  C13   C   CH2   0  -0.257  35.7841  27.0878  46.5248
 83Q  C15   C   CH3   0  -0.657  36.7109  24.9247  45.8084
 83Q  C17   C   CH2   0  -0.335  38.9506  26.5548  44.3307
 83Q  C21   C   CR16  0  -0.247  44.9948  29.8092  44.1777
 83Q  C22   C   CR16  0  -0.239  46.1404  29.5606  43.4402
 83Q  C24   C   CR6   0   0.015  46.6989  31.8829  43.4938
 83Q  C2    C   CR6   0  -0.022  45.5486  32.1435  44.2304
 83Q  C3    C   CR6   0  -0.053  44.6850  31.1042  44.5773
 83Q  C5    C   CR6   0  -0.141  42.2913  30.0345  45.4677
 83Q  C7    C   CR16  0  -0.212  41.4863  28.2053  46.5730
 83Q  C8    C   CR6   0   0.497  40.6845  27.8649  45.4471
 83Q  C11   C   CH2   0  -0.413  38.1681  26.5027  47.1144
 83Q  C12   C   CT    0  -0.099  37.0691  26.3941  46.0445
 83Q  C16   C   CH2   0  -0.408  37.5635  27.0387  44.7415
 83Q  C19   C   CR6   0   0.478  41.5000  29.7109  44.3445
 83Q  C23   C   CR16  0  -0.236  46.9996  30.5909  43.0938
 83Q  N6    N   N     0  -0.307  42.2548  29.2655  46.5452
 83Q  N9    N   NT    0  -0.475  39.9008  26.7637  45.4124
 83Q  N14   N   NH2   0  -0.799  35.9424  28.5069  46.8004
 83Q  N18   N   N     0  -0.483  40.7172  28.6388  44.3649
 83Q  N20   N   NH2   0  -0.825  41.5335  30.4338  43.2068
 83Q  CL2   CL  CL    0  -0.093  47.7614  33.1694  43.0652
 83Q  H102  H   HCH2  0   0.254  39.4980  24.9660  46.3515
 83Q  H101  H   HCH2  0   0.269  40.2812  26.1259  47.3837
 83Q  H132  H   HCH2  0   0.219  35.0366  26.9831  45.7327
 83Q  H131  H   HCH2  0   0.198  35.3977  26.5223  47.3861
 83Q  H153  H   HCH3  0   0.226  36.3627  24.4560  46.7314
 83Q  H151  H   HCH3  0   0.226  35.9108  24.8368  45.0699
 83Q  H152  H   HCH3  0   0.233  37.5498  24.3322  45.4435
 83Q  H171  H   HCH2  0   0.268  39.2916  27.0722  43.4389
 83Q  H172  H   HCH2  0   0.243  38.9416  25.4862  44.0998
 83Q  H211  H   HCR6  0   0.280  44.3412  28.9908  44.4471
 83Q  H221  H   HCR6  0   0.276  46.3705  28.5490  43.1344
 83Q  H071  H   HCR6  0   0.262  41.4986  27.6206  47.4813
 83Q  H112  H   HCH2  0   0.231  38.2795  27.5416  47.4414
 83Q  H111  H   HCH2  0   0.232  37.8855  25.9219  47.9977
 83Q  H161  H   HCH2  0   0.231  37.5930  28.1242  44.8648
 83Q  H162  H   HCH2  0   0.225  36.8545  26.8299  43.9341
 83Q  H231  H   HCR6  0   0.287  47.8951  30.3969  42.5200
 83Q  H1    H   HNH2  0   0.348  35.0305  28.9417  46.8431
 83Q  H142  H   HNH2  0   0.342  36.3492  28.6435  47.7163
 83Q  H201  H   HNH2  0   0.394  40.8100  30.2623  42.5282
 83Q  H202  H   HNH2  0   0.401  41.9084  31.3679  43.2291
 83Q  S4    S   S2    0   0.095  43.2435  31.5115  45.5230
 83Q  CL1   CL  CL    0  -0.085  45.1768  33.7516  44.7211

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
 83Q  N20  C19   single    1.348  0.020  1.348
 83Q  C19  N18   aromatic  1.328  0.020  1.328
 83Q  C19  C5    aromatic  1.412  0.020  1.412
 83Q  N18  C8    aromatic  1.331  0.020  1.331
 83Q  C22  C21   aromatic  1.385  0.020  1.385
 83Q  C22  C23   aromatic  1.386  0.020  1.386
 83Q  C21  C3    aromatic  1.390  0.020  1.390
 83Q  C17  N9    single    1.455  0.020  1.455
 83Q  C17  C16   single    1.525  0.020  1.525
 83Q  C23  C24   aromatic  1.386  0.020  1.386
 83Q  C3   S4    single    1.771  0.020  1.771
 83Q  C3   C2    aromatic  1.395  0.020  1.395
 83Q  S4   C5    single    1.758  0.020  1.758
 83Q  C5   N6    aromatic  1.324  0.020  1.324
 83Q  C24  C2    aromatic  1.391  0.020  1.391
 83Q  C24  CL2   single    1.723  0.020  1.723
 83Q  C2   CL1   single    1.722  0.020  1.722
 83Q  C8   N9    single    1.352  0.020  1.352
 83Q  C8   C7    aromatic  1.424  0.020  1.424
 83Q  N9   C10   single    1.453  0.020  1.453
 83Q  C16  C12   single    1.536  0.020  1.536
 83Q  N6   C7    aromatic  1.310  0.020  1.310
 83Q  C15  C12   single    1.531  0.020  1.531
 83Q  C12  C13   single    1.537  0.020  1.537
 83Q  C12  C11   single    1.538  0.020  1.538
 83Q  C10  C11   single    1.526  0.020  1.526
 83Q  C13  N14   single    1.454  0.020  1.454
 83Q  C10  H102  single    0.970  0.020  1.090
 83Q  C10  H101  single    0.970  0.020  1.090
 83Q  C13  H132  single    0.970  0.020  1.090
 83Q  C13  H131  single    0.970  0.020  1.090
 83Q  C15  H153  single    0.970  0.020  1.090
 83Q  C15  H151  single    0.970  0.020  1.090
 83Q  C15  H152  single    0.970  0.020  1.090
 83Q  C17  H171  single    0.970  0.020  1.090
 83Q  C17  H172  single    0.970  0.020  1.090
 83Q  C21  H211  single    0.930  0.020  1.080
 83Q  C22  H221  single    0.930  0.020  1.080
 83Q  C7   H071  single    0.930  0.020  1.080
 83Q  C11  H112  single    0.970  0.020  1.090
 83Q  C11  H111  single    0.970  0.020  1.090
 83Q  C16  H161  single    0.970  0.020  1.090
 83Q  C16  H162  single    0.970  0.020  1.090
 83Q  C23  H231  single    0.930  0.020  1.080
 83Q  N14  H1    single    0.890  0.020  1.040
 83Q  N14  H142  single    0.890  0.020  1.040
 83Q  N20  H201  single    0.890  0.020  1.040
 83Q  N20  H202  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
 83Q  H101  C10  H102  105.89  3.000
 83Q  H101  C10  N9    111.29  3.000
 83Q  H102  C10  N9    107.80  3.000
 83Q  H101  C10  C11   110.70  3.000
 83Q  H102  C10  C11   110.91  3.000
 83Q  N9    C10  C11   110.16  3.000
 83Q  H131  C13  H132  106.11  3.000
 83Q  H131  C13  N14   113.04  3.000
 83Q  H132  C13  N14   107.76  3.000
 83Q  H131  C13  C12   107.83  3.000
 83Q  H132  C13  C12   107.56  3.000
 83Q  N14   C13  C12   114.12  3.000
 83Q  H152  C15  H151  107.08  3.000
 83Q  H152  C15  H153  107.16  3.000
 83Q  H151  C15  H153  107.66  3.000
 83Q  H152  C15  C12   113.16  3.000
 83Q  H151  C15  C12   110.67  3.000
 83Q  H153  C15  C12   110.86  3.000
 83Q  H172  C17  H171  107.15  3.000
 83Q  H172  C17  N9    107.62  3.000
 83Q  H171  C17  N9    109.70  3.000
 83Q  H172  C17  C16   111.07  3.000
 83Q  H171  C17  C16   110.83  3.000
 83Q  N9    C17  C16   110.37  3.000
 83Q  H211  C21  C3    119.91  3.000
 83Q  H211  C21  C22   119.78  3.000
 83Q  C3    C21  C22   120.31  3.000
 83Q  H221  C22  C23   119.53  3.000
 83Q  H221  C22  C21   119.63  3.000
 83Q  C23   C22  C21   120.84  3.000
 83Q  CL2   C24  C23   119.39  3.000
 83Q  CL2   C24  C2    120.13  3.000
 83Q  C23   C24  C2    120.48  3.000
 83Q  CL1   C2   C3    119.42  3.000
 83Q  CL1   C2   C24   120.30  3.000
 83Q  C3    C2   C24   120.28  3.000
 83Q  S4    C3   C2    117.72  3.000
 83Q  C2    C3   C21   118.98  3.000
 83Q  S4    C3   C21   123.30  3.000
 83Q  S4    C5   N6    118.50  3.000
 83Q  N6    C5   C19   119.92  3.000
 83Q  S4    C5   C19   121.41  3.000
 83Q  H071  C7   N6    116.70  3.000
 83Q  H071  C7   C8    122.82  3.000
 83Q  N6    C7   C8    120.49  3.000
 83Q  N18   C8   N9    117.84  3.000
 83Q  N9    C8   C7    122.79  3.000
 83Q  N18   C8   C7    119.36  3.000
 83Q  H111  C11  H112  106.79  3.000
 83Q  H111  C11  C12   109.85  3.000
 83Q  H112  C11  C12   110.34  3.000
 83Q  H111  C11  C10   109.42  3.000
 83Q  H112  C11  C10   107.69  3.000
 83Q  C12   C11  C10   112.56  3.000
 83Q  C16   C12  C11   109.31  3.000
 83Q  C11   C12  C15   110.03  3.000
 83Q  C16   C12  C15   110.33  3.000
 83Q  C11   C12  C13   110.38  3.000
 83Q  C15   C12  C13   106.60  3.000
 83Q  C16   C12  C13   110.17  3.000
 83Q  H162  C16  H161  106.86  3.000
 83Q  H162  C16  C12   109.72  3.000
 83Q  H161  C16  C12   109.26  3.000
 83Q  H162  C16  C17   109.26  3.000
 83Q  H161  C16  C17   108.72  3.000
 83Q  C12   C16  C17   112.84  3.000
 83Q  N20   C19  N18   117.43  3.000
 83Q  N18   C19  C5    120.23  3.000
 83Q  N20   C19  C5    122.31  3.000
 83Q  H231  C23  C24   120.02  3.000
 83Q  H231  C23  C22   120.86  3.000
 83Q  C24   C23  C22   119.12  3.000
 83Q  C7    N6   C5    120.23  3.000
 83Q  C8    N9   C17   120.97  3.000
 83Q  C8    N9   C10   122.73  3.000
 83Q  C17   N9   C10   111.78  3.000
 83Q  H142  N14  H1    105.45  3.000
 83Q  H142  N14  C13   110.32  3.000
 83Q  H1    N14  C13   109.24  3.000
 83Q  C19   N18  C8    119.78  3.000
 83Q  H202  N20  H201  116.14  3.000
 83Q  H202  N20  C19   119.21  3.000
 83Q  H201  N20  C19   117.36  3.000
 83Q  C5    S4   C3    103.34  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
 83Q  CONST_01  C24   C23  C22  C21     0.00   0.0  0
 83Q  CONST_02  C24   C2   C3   C21     0.00   0.0  0
 83Q  CONST_03  C2    C3   C21  C22     0.00   0.0  0
 83Q  CONST_04  C2    C24  C23  C22     0.00   0.0  0
 83Q  CONST_05  C23   C22  C21  C3      0.00   0.0  0
 83Q  CONST_06  C23   C24  C2   C3      0.00   0.0  0
 83Q  CONST_07  C8    N18  C19  C5      0.00   0.0  0
 83Q  CONST_08  C8    C7   N6   C5      0.00   0.0  0
 83Q  CONST_09  C19   N18  C8   C7      0.00   0.0  0
 83Q  CONST_10  C19   C5   N6   C7      0.00   0.0  0
 83Q  CONST_11  N18   C19  C5   N6      0.00   0.0  0
 83Q  CONST_12  N18   C8   C7   N6      0.00   0.0  0
 83Q  CONST_13  N9    C8   N18  C19   180.00   0.0  0
 83Q  CONST_14  N9    C8   C7   N6    180.00   0.0  0
 83Q  CONST_15  CL1   C2   C3   C21   180.00   0.0  0
 83Q  CONST_16  S4    C3   C21  C22   180.00   0.0  0
 83Q  CONST_17  CL2   C24  C23  C22   180.00   0.0  0
 83Q  CONST_18  S4    C3   C2   C24   180.00   0.0  0
 83Q  CONST_19  CL2   C24  C2   C3    180.00   0.0  0
 83Q  CONST_20  S4    C5   N6   C7    180.00   0.0  0
 83Q  CONST_21  N20   C19  N18  C8    180.00   0.0  0
 83Q  CONST_22  CL1   C2   C24  C23   180.00   0.0  0
 83Q  CONST_23  N20   C19  C5   N6    180.00   0.0  0
 83Q  CONST_24  S4    C5   C19  N18   180.00   0.0  0
 83Q  CONST_25  H231  C23  C22  C21   180.00   0.0  0
 83Q  CONST_26  H221  C22  C23  C24   180.00   0.0  0
 83Q  CONST_27  H211  C21  C3   C2    180.00   0.0  0
 83Q  CONST_28  H231  C23  C24  C2    180.00   0.0  0
 83Q  CONST_29  H221  C22  C21  C3    180.00   0.0  0
 83Q  CONST_30  H071  C7   N6   C5    180.00   0.0  0
 83Q  CONST_31  H211  C21  C22  C23   180.00   0.0  0
 83Q  CONST_32  H071  C7   C8   N9      0.00   0.0  0
 83Q  CONST_33  H071  C7   C8   N18   180.00   0.0  0
 83Q  CONST_34  H201  N20  C19  C5    180.00   0.0  0
 83Q  CONST_36  H201  N20  C19  N18     0.00   0.0  0
 83Q  Var_01    C16   C17  N9   C10    60.84  30.0  1
 83Q  Var_02    N18   C8   N9   C10  -164.71  30.0  1
 83Q  Var_03    C7    C8   N9   C10    16.66  30.0  1
 83Q  Var_04    N18   C8   N9   C17   -10.55  30.0  1
 83Q  Var_05    C7    C8   N9   C17   170.82  30.0  1
 83Q  Var_06    C11   C10  N9   C17   -61.34  30.0  1
 83Q  Var_07    C16   C17  N9   C8    -95.91  30.0  1
 83Q  Var_08    C11   C10  N9   C8     94.93  30.0  1
 83Q  Var_09    N9    C17  C16  C12   -55.00  30.0  1
 83Q  Var_10    N9    C10  C11  C12    55.98  30.0  1
 83Q  Var_11    C5    S4   C3   C21   -11.29  30.0  2
 83Q  Var_12    C5    S4   C3   C2    169.14  30.0  2
 83Q  Var_13    C19   C5   S4   C3    -80.18  30.0  2
 83Q  Var_14    N6    C5   S4   C3    104.44  30.0  2
 83Q  Var_15    H171  C17  N9   C10  -176.76  30.0  1
 83Q  Var_16    H172  C17  N9   C10   -60.51  30.0  1
 83Q  Var_17    H102  C10  N9   C17    59.80  30.0  1
 83Q  Var_18    H101  C10  N9   C17   175.50  30.0  1
 83Q  Var_19    H171  C17  N9   C8     26.50  30.0  1
 83Q  Var_20    H172  C17  N9   C8    142.75  30.0  1
 83Q  Var_21    H102  C10  N9   C8   -143.93  30.0  1
 83Q  Var_22    H101  C10  N9   C8    -28.23  30.0  1
 83Q  Var_23    H171  C17  C16  C12  -176.74  30.0  1
 83Q  Var_24    H172  C17  C16  C12    64.27  30.0  1
 83Q  Var_25    H102  C10  C11  C12   -63.28  30.0  1
 83Q  Var_26    H101  C10  C11  C12   179.48  30.0  1
 83Q  Var_27    H161  C16  C17  N9     66.38  30.0  1
 83Q  Var_28    H162  C16  C17  N9   -177.34  30.0  1
 83Q  Var_29    H112  C11  C10  N9    -65.86  30.0  1
 83Q  Var_30    H111  C11  C10  N9    178.42  30.0  1
 83Q  Var_31    H1    N14  C13  C12   163.55  30.0  3
 83Q  Var_32    H142  N14  C13  C12   -80.98  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
 83Q  chir_01  C12  C16  C13  C11  positiv

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
 83Q  plan-1  C21   0.020
 83Q  plan-1  C22   0.020
 83Q  plan-1  C24   0.020
 83Q  plan-1  C2    0.020
 83Q  plan-1  C3    0.020
 83Q  plan-1  C23   0.020
 83Q  plan-1  CL2   0.020
 83Q  plan-1  H211  0.020
 83Q  plan-1  H221  0.020
 83Q  plan-1  H231  0.020
 83Q  plan-1  S4    0.020
 83Q  plan-1  CL1   0.020
 83Q  plan-2  C5    0.020
 83Q  plan-2  C7    0.020
 83Q  plan-2  C8    0.020
 83Q  plan-2  C19   0.020
 83Q  plan-2  N6    0.020
 83Q  plan-2  N9    0.020
 83Q  plan-2  N18   0.020
 83Q  plan-2  N20   0.020
 83Q  plan-2  H071  0.020
 83Q  plan-2  S4    0.020
 83Q  plan-3  C19   0.020
 83Q  plan-3  N20   0.020
 83Q  plan-3  H201  0.020
 83Q  plan-3  H202  0.020

