# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:51:01 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-(2,6-dimethylphenyl)-4-(methylsulfanyl)-6-(piperazin-1-yl)-1,3,5-triazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(nc(n1)c2c(C)cccc2C)N3CCNCC3
#
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
 DXO  DXO  2-(2,6-dimethylphenyl)-4-(methylsulfanyl)-6-(piperazin-1-yl)-1,3,5-triazine  ligand  43  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DXO
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
 DXO  C11   C  CH3   0  -0.743   1.5538  -1.9370  -2.3168
 DXO  C10   C  CR6   0   0.103   2.4267  -1.7745  -1.1041
 DXO  C9    C  CR16  0  -0.327   3.5917  -2.5270  -0.9817
 DXO  C8    C  CR16  0  -0.226   4.4093  -2.3943   0.1292
 DXO  C7    C  CR16  0  -0.328   4.0759  -1.4981   1.1327
 DXO  C5    C  CR6   0   0.105   2.9275  -0.7174   1.0381
 DXO  C6    C  CH3   0  -0.746   2.5846   0.2507   2.1348
 DXO  C4    C  CR6   0   0.018   2.1083  -0.8698  -0.0857
 DXO  C3    C  CR6   0   0.243   0.8759  -0.0479  -0.2043
 DXO  N2    N  N     0  -0.419   1.0403   1.2610  -0.3931
 DXO  C1    C  CR6   0   0.236  -0.0981   1.9330  -0.4911
 DXO  S     S  S2    0   0.060  -0.0534   3.6651  -0.7107
 DXO  C     C  CH3   0  -0.766   1.7153   4.0174  -0.6840
 DXO  N1    N  N     0  -0.453  -0.2779  -0.6709  -0.1187
 DXO  C2    C  CR6   0   0.663  -1.3728   0.1012  -0.2578
 DXO  N     N  N     0  -0.482  -1.3129   1.4267  -0.4440
 DXO  N3    N  NT    0  -0.497  -2.5727  -0.4849  -0.2051
 DXO  C15   C  CH2   0  -0.305  -3.8165   0.2440  -0.3919
 DXO  C14   C  CH2   0  -0.295  -4.7822  -0.0748   0.7368
 DXO  N4    N  NH1   0  -0.602  -4.9801  -1.5091   0.8177
 DXO  C13   C  CH2   0  -0.296  -3.7290  -2.1895   1.0903
 DXO  C12   C  CH2   0  -0.304  -2.7449  -1.9186  -0.0348
 DXO  H111  H  HCH3  0   0.254   0.6115  -2.4249  -2.0658
 DXO  H112  H  HCH3  0   0.242   1.3048  -0.9772  -2.7726
 DXO  H113  H  HCH3  0   0.250   2.0523  -2.5426  -3.0722
 DXO  H9    H  HCR6  0   0.249   3.8585  -3.2223  -1.7684
 DXO  H8    H  HCR6  0   0.254   5.3093  -2.9900   0.2122
 DXO  H7    H  HCR6  0   0.250   4.7157  -1.4002   2.0013
 DXO  H61C  H  HCH3  0   0.255   2.6502   1.2828   1.7892
 DXO  H62C  H  HCH3  0   0.243   1.5687   0.1019   2.5049
 DXO  H63C  H  HCH3  0   0.250   3.2636   0.1353   2.9782
 DXO  HC1   H  HCH3  0   0.278   2.1575   3.7364   0.2682
 DXO  HC2   H  HCH3  0   0.277   2.2304   3.5105  -1.4951
 DXO  HC3   H  HCH3  0   0.282   1.8060   5.0934  -0.8176
 DXO  H151  H  HCH2  0   0.274  -3.6155   1.3099  -0.4300
 DXO  H152  H  HCH2  0   0.240  -4.2584  -0.0539  -1.3488
 DXO  H121  H  HCH2  0   0.239  -3.1272  -2.3430  -0.9692
 DXO  H122  H  HCH2  0   0.275  -1.7855  -2.3792   0.1784
 DXO  H141  H  HCH2  0   0.201  -4.3899   0.3589   1.6703
 DXO  H142  H  HCH2  0   0.243  -5.7361   0.4122   0.5269
 DXO  H4    H  HNH1  0   0.359  -5.6523  -1.7228   1.5423
 DXO  H131  H  HCH2  0   0.201  -3.2692  -1.8780   2.0419
 DXO  H132  H  HCH2  0   0.244  -3.9057  -3.2645   1.1501

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
 DXO  C11  C10   single    1.503  0.020  1.503
 DXO  C10  C9    aromatic  1.392  0.020  1.392
 DXO  C10  C4    aromatic  1.399  0.020  1.399
 DXO  C9   C8    aromatic  1.386  0.020  1.386
 DXO  C8   C7    aromatic  1.386  0.020  1.386
 DXO  C7   C5    aromatic  1.392  0.020  1.392
 DXO  C5   C6    single    1.503  0.020  1.503
 DXO  C5   C4    aromatic  1.399  0.020  1.399
 DXO  C4   C3    single    1.486  0.020  1.486
 DXO  C3   N2    aromatic  1.333  0.020  1.333
 DXO  C3   N1    aromatic  1.314  0.020  1.314
 DXO  N2   C1    aromatic  1.326  0.020  1.326
 DXO  C1   S     single    1.747  0.020  1.747
 DXO  C1   N     aromatic  1.317  0.020  1.317
 DXO  S    C     single    1.804  0.020  1.804
 DXO  N1   C2    aromatic  1.347  0.020  1.347
 DXO  C2   N     aromatic  1.340  0.020  1.340
 DXO  C2   N3    single    1.336  0.020  1.336
 DXO  N3   C15   single    1.454  0.020  1.454
 DXO  N3   C12   single    1.454  0.020  1.454
 DXO  C15  C14   single    1.519  0.020  1.519
 DXO  C14  N4    single    1.450  0.020  1.450
 DXO  N4   C13   single    1.450  0.020  1.450
 DXO  C13  C12   single    1.519  0.020  1.519
 DXO  C11  H111  single    0.970  0.020  1.090
 DXO  C11  H112  single    0.970  0.020  1.090
 DXO  C11  H113  single    0.970  0.020  1.090
 DXO  C9   H9    single    0.930  0.020  1.080
 DXO  C8   H8    single    0.930  0.020  1.080
 DXO  C7   H7    single    0.930  0.020  1.080
 DXO  C6   H61C  single    0.970  0.020  1.090
 DXO  C6   H62C  single    0.970  0.020  1.090
 DXO  C6   H63C  single    0.970  0.020  1.090
 DXO  C    HC1   single    0.970  0.020  1.090
 DXO  C    HC2   single    0.970  0.020  1.090
 DXO  C    HC3   single    0.970  0.020  1.090
 DXO  C15  H151  single    0.970  0.020  1.090
 DXO  C15  H152  single    0.970  0.020  1.090
 DXO  C12  H121  single    0.970  0.020  1.090
 DXO  C12  H122  single    0.970  0.020  1.090
 DXO  C14  H141  single    0.970  0.020  1.090
 DXO  C14  H142  single    0.970  0.020  1.090
 DXO  N4   H4    single    0.890  0.020  1.040
 DXO  C13  H131  single    0.970  0.020  1.090
 DXO  C13  H132  single    0.970  0.020  1.090

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
 DXO  H113  C11  H112  107.68  3.000
 DXO  H113  C11  H111  107.84  3.000
 DXO  H112  C11  H111  107.01  3.000
 DXO  H113  C11  C10   110.73  3.000
 DXO  H112  C11  C10   111.99  3.000
 DXO  H111  C11  C10   111.38  3.000
 DXO  C4    C10  C9    118.42  3.000
 DXO  C4    C10  C11   121.68  3.000
 DXO  C9    C10  C11   119.90  3.000
 DXO  H9    C9   C8    119.90  3.000
 DXO  H9    C9   C10   119.28  3.000
 DXO  C8    C9   C10   120.83  3.000
 DXO  H8    C8   C7    120.02  3.000
 DXO  H8    C8   C9    119.95  3.000
 DXO  C7    C8   C9    120.03  3.000
 DXO  H7    C7   C5    119.41  3.000
 DXO  H7    C7   C8    119.80  3.000
 DXO  C5    C7   C8    120.79  3.000
 DXO  C4    C5   C6    121.52  3.000
 DXO  C4    C5   C7    118.47  3.000
 DXO  C6    C5   C7    120.00  3.000
 DXO  H63C  C6   H62C  107.66  3.000
 DXO  H63C  C6   H61C  107.96  3.000
 DXO  H62C  C6   H61C  107.01  3.000
 DXO  H63C  C6   C5    110.77  3.000
 DXO  H62C  C6   C5    111.85  3.000
 DXO  H61C  C6   C5    111.39  3.000
 DXO  C3    C4   C5    119.31  3.000
 DXO  C3    C4   C10   119.23  3.000
 DXO  C5    C4   C10   121.46  3.000
 DXO  N1    C3   N2    125.68  3.000
 DXO  N1    C3   C4    117.43  3.000
 DXO  N2    C3   C4    116.89  3.000
 DXO  C1    N2   C3    113.73  3.000
 DXO  N     C1   S     114.17  3.000
 DXO  N     C1   N2    126.49  3.000
 DXO  S     C1   N2    119.34  3.000
 DXO  C     S    C1    102.53  3.000
 DXO  HC3   C    HC2   109.28  3.000
 DXO  HC3   C    HC1   109.22  3.000
 DXO  HC2   C    HC1   109.91  3.000
 DXO  HC3   C    S     105.85  3.000
 DXO  HC2   C    S     111.28  3.000
 DXO  HC1   C    S     111.19  3.000
 DXO  C2    N1   C3    115.80  3.000
 DXO  N3    C2   N     118.65  3.000
 DXO  N3    C2   N1    118.32  3.000
 DXO  N     C2   N1    123.03  3.000
 DXO  C2    N    C1    115.25  3.000
 DXO  C12   N3   C15   114.08  3.000
 DXO  C12   N3   C2    122.92  3.000
 DXO  C15   N3   C2    122.91  3.000
 DXO  H152  C15  H151  108.13  3.000
 DXO  H152  C15  C14   109.61  3.000
 DXO  H151  C15  C14   110.48  3.000
 DXO  H152  C15  N3    108.72  3.000
 DXO  H151  C15  N3    109.78  3.000
 DXO  C14   C15  N3    110.07  3.000
 DXO  H142  C14  H141  107.37  3.000
 DXO  H142  C14  N4    109.44  3.000
 DXO  H141  C14  N4    113.01  3.000
 DXO  H142  C14  C15   108.60  3.000
 DXO  H141  C14  C15   108.70  3.000
 DXO  N4    C14  C15   109.62  3.000
 DXO  H4    N4   C13   109.86  3.000
 DXO  H4    N4   C14   109.86  3.000
 DXO  C13   N4   C14   110.90  3.000
 DXO  H132  C13  H131  107.39  3.000
 DXO  H132  C13  C12   108.73  3.000
 DXO  H131  C13  C12   108.59  3.000
 DXO  H132  C13  N4    109.45  3.000
 DXO  H131  C13  N4    112.94  3.000
 DXO  C12   C13  N4    109.64  3.000
 DXO  H122  C12  H121  108.16  3.000
 DXO  H122  C12  C13   110.58  3.000
 DXO  H121  C12  C13   109.67  3.000
 DXO  H122  C12  N3    109.68  3.000
 DXO  H121  C12  N3    108.88  3.000
 DXO  C13   C12  N3    109.84  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
 DXO  CONST_01  C7    C8   C9   C10     0.00   0.0  0
 DXO  CONST_02  C7    C5   C4   C10     0.00   0.0  0
 DXO  CONST_05  C5    C4   C10  C9      0.00   0.0  0
 DXO  CONST_06  C3    C4   C10  C9    180.00   0.0  0
 DXO  CONST_07  C5    C7   C8   C9      0.00   0.0  0
 DXO  CONST_08  C4    C10  C9   C8      0.00   0.0  0
 DXO  CONST_09  C4    C5   C7   C8      0.00   0.0  0
 DXO  CONST_10  C3    C4   C5   C7    180.00   0.0  0
 DXO  CONST_13  C1    N2   C3   C4    180.00   0.0  0
 DXO  CONST_14  C2    N1   C3   C4    180.00   0.0  0
 DXO  CONST_15  N     C1   N2   C3      0.00   0.0  0
 DXO  CONST_16  N     C2   N1   C3      0.00   0.0  0
 DXO  CONST_17  C2    N1   C3   N2      0.00   0.0  0
 DXO  CONST_18  C2    N    C1   N2      0.00   0.0  0
 DXO  CONST_19  N1    C3   N2   C1      0.00   0.0  0
 DXO  CONST_20  N1    C2   N    C1      0.00   0.0  0
 DXO  CONST_21  N3    C2   N1   C3    180.00   0.0  0
 DXO  CONST_22  N3    C2   N    C1    180.00   0.0  0
 DXO  CONST_23  C8    C9   C10  C11   180.00   0.0  0
 DXO  CONST_24  C5    C4   C10  C11   180.00   0.0  0
 DXO  CONST_25  C3    C4   C10  C11     0.00   0.0  0
 DXO  CONST_26  C6    C5   C4   C10   180.00   0.0  0
 DXO  CONST_27  C6    C5   C7   C8    180.00   0.0  0
 DXO  CONST_28  C3    C4   C5   C6      0.00   0.0  0
 DXO  CONST_29  S     C1   N2   C3    180.00   0.0  0
 DXO  CONST_30  C2    N    C1   S     180.00   0.0  0
 DXO  CONST_31  H8    C8   C9   C10   180.00   0.0  0
 DXO  CONST_32  H7    C7   C8   C9    180.00   0.0  0
 DXO  CONST_33  H9    C9   C8   C7    180.00   0.0  0
 DXO  Var_01    C15   N3   C2   N1   -177.68  30.0  2
 DXO  Var_02    C14   C15  N3   C2   -129.87  30.0  1
 DXO  Var_03    C13   C12  N3   C2    129.72  30.0  1
 DXO  Var_04    N4    C14  C15  N3    -55.47  30.0  1
 DXO  Var_05    N4    C13  C12  N3     55.91  30.0  1
 DXO  Var_06    C13   N4   C14  C15    60.74  30.0  1
 DXO  Var_07    C12   C13  N4   C14   -61.04  30.0  1
 DXO  Var_08    N     C1   S    C     178.50  30.0  2
 DXO  Var_09    H111  C11  C10  C9    110.24  30.0  2
 DXO  Var_10    H61C  C6   C5   C7    113.41  30.0  2
 DXO  Var_11    HC1   C    S    C1    -61.48  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
 DXO  plan-1  C11  0.020
 DXO  plan-1  C10  0.020
 DXO  plan-1  C9   0.020
 DXO  plan-1  C8   0.020
 DXO  plan-1  C7   0.020
 DXO  plan-1  C5   0.020
 DXO  plan-1  C6   0.020
 DXO  plan-1  C4   0.020
 DXO  plan-1  C3   0.020
 DXO  plan-1  H9   0.020
 DXO  plan-1  H8   0.020
 DXO  plan-1  H7   0.020
 DXO  plan-2  C4   0.020
 DXO  plan-2  C3   0.020
 DXO  plan-2  N2   0.020
 DXO  plan-2  C1   0.020
 DXO  plan-2  S    0.020
 DXO  plan-2  N1   0.020
 DXO  plan-2  C2   0.020
 DXO  plan-2  N    0.020
 DXO  plan-2  N3   0.020

