# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:18:31 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(5-chloro-1H,3H-benzo[de]isochromen-6-yl)-6-(methylsulfanyl)-1,3,5-triazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(N)nc(n1)c2c(Cl)cc3COCc4cccc2c34
#
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
 B2X  B2X  4-(5-chloro-1H,3H-benzo[de]isochromen-6-yl)-6-(methylsulfanyl)-1,3,5-triazin-2-amine  ligand  36  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B2X
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
 B2X  C1    C   CH2   0  -0.237  -4.4579   1.5550   0.0748
 B2X  O2    O   O2    0  -0.472  -5.3300   0.4700   0.2688
 B2X  C3    C   CH2   0  -0.237  -5.1417  -0.5343  -0.6989
 B2X  C4    C   CR6   0   0.004  -3.7372  -1.0706  -0.6715
 B2X  C5    C   CR16  0  -0.320  -3.4308  -2.3448  -1.0670
 B2X  C6    C   CR16  0  -0.237  -2.0974  -2.7946  -1.0429
 B2X  C7    C   CR16  0  -0.365  -1.0864  -1.9794  -0.6108
 B2X  C8    C   CR66  0   0.137  -1.3647  -0.6588  -0.1866
 B2X  C9    C   CR66  0   0.142  -2.7064  -0.2058  -0.2303
 B2X  C10   C   CR6   0  -0.021  -3.0209   1.1202   0.1558
 B2X  C11   C   CR16  0  -0.275  -2.0308   1.9629   0.5732
 B2X  C12   C   CR6   0  -0.118  -0.6998   1.5091   0.6114
 B2X  CL13  CL  CL    0  -0.114   0.5058   2.6133   1.1825
 B2X  C14   C   CR6   0   0.133  -0.3499   0.2351   0.2521
 B2X  C15   C   CR6   0   0.232   1.0638  -0.2147   0.3302
 B2X  N16   N   N     0  -0.415   1.8981   0.2610  -0.5819
 B2X  N17   N   N     0  -0.435   1.3670  -1.0547   1.2989
 B2X  C18   C   CR6   0   0.582   2.6546  -1.4349   1.3340
 B2X  N19   N   NH2   0  -0.805   3.0249  -2.2903   2.2783
 B2X  N22   N   N     0  -0.442   3.5899  -1.0008   0.4762
 B2X  C23   C   CR6   0   0.239   3.1528  -0.1698  -0.4411
 B2X  S24   S   S2    0   0.072   4.2529   0.4769  -1.6274
 B2X  C25   C   CH3   0  -0.767   5.8212  -0.2771  -1.1564
 B2X  H1    H   HCH2  0   0.236  -4.6399   2.0304  -0.9004
 B2X  H1A   H   HCH2  0   0.263  -4.6783   2.2961   0.8442
 B2X  H3    H   HCH2  0   0.260  -5.8580  -1.3293  -0.4869
 B2X  H3A   H   HCH2  0   0.233  -5.3694  -0.1500  -1.7040
 B2X  H5    H   HCR6  0   0.260  -4.2149  -3.0154  -1.3979
 B2X  H6    H   HCR6  0   0.266  -1.8709  -3.8028  -1.3639
 B2X  H7    H   HCR6  0   0.254  -0.0718  -2.3532  -0.5985
 B2X  H11   H   HCR6  0   0.281  -2.2600   2.9743   0.8839
 B2X  HN19  H   HNH2  0   0.412   2.3524  -2.6465   2.9351
 B2X  HN1A  H   HNH2  0   0.412   3.9746  -2.6159   2.3319
 B2X  H25   H   HCH3  0   0.279   6.1136   0.0207  -0.1531
 B2X  H25A  H   HCH3  0   0.279   5.7720  -1.3606  -1.2233
 B2X  H25B  H   HCH3  0   0.284   6.5556   0.0934  -1.8687

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
 B2X  C1   O2    single    1.405  0.020  1.405
 B2X  C1   C10   single    1.504  0.020  1.504
 B2X  O2   C3    single    1.407  0.020  1.407
 B2X  C3   C4    single    1.504  0.020  1.504
 B2X  C4   C5    aromatic  1.369  0.020  1.369
 B2X  C4   C9    aromatic  1.416  0.020  1.416
 B2X  C5   C6    aromatic  1.407  0.020  1.407
 B2X  C6   C7    aromatic  1.369  0.020  1.369
 B2X  C7   C8    aromatic  1.415  0.020  1.415
 B2X  C8   C9    aromatic  1.417  0.020  1.417
 B2X  C8   C14   aromatic  1.422  0.020  1.422
 B2X  C9   C10   aromatic  1.416  0.020  1.416
 B2X  C10  C11   aromatic  1.366  0.020  1.366
 B2X  C11  C12   aromatic  1.407  0.020  1.407
 B2X  C12  CL13  single    1.732  0.020  1.732
 B2X  C12  C14   aromatic  1.369  0.020  1.369
 B2X  C14  C15   single    1.486  0.020  1.486
 B2X  C15  N16   aromatic  1.324  0.020  1.324
 B2X  C15  N17   aromatic  1.318  0.020  1.318
 B2X  N16  C23   aromatic  1.334  0.020  1.334
 B2X  N17  C18   aromatic  1.343  0.020  1.343
 B2X  C18  N19   single    1.327  0.020  1.327
 B2X  C18  N22   aromatic  1.341  0.020  1.341
 B2X  N22  C23   aromatic  1.313  0.020  1.313
 B2X  C23  S24   single    1.742  0.020  1.742
 B2X  S24  C25   single    1.803  0.020  1.803
 B2X  C1   H1    single    0.970  0.020  1.090
 B2X  C1   H1A   single    0.970  0.020  1.090
 B2X  C3   H3    single    0.970  0.020  1.090
 B2X  C3   H3A   single    0.970  0.020  1.090
 B2X  C5   H5    single    0.930  0.020  1.080
 B2X  C6   H6    single    0.930  0.020  1.080
 B2X  C7   H7    single    0.930  0.020  1.080
 B2X  C11  H11   single    0.930  0.020  1.080
 B2X  N19  HN19  single    0.860  0.020  1.020
 B2X  N19  HN1A  single    0.860  0.020  1.020
 B2X  C25  H25   single    0.970  0.020  1.090
 B2X  C25  H25A  single    0.970  0.020  1.090
 B2X  C25  H25B  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
 B2X  H1A   C1   H1    107.35  3.000
 B2X  H1A   C1   C10   110.58  3.000
 B2X  H1    C1   C10   109.32  3.000
 B2X  H1A   C1   O2    107.57  3.000
 B2X  H1    C1   O2    110.70  3.000
 B2X  C10   C1   O2    111.25  3.000
 B2X  C3    O2   C1    111.90  3.000
 B2X  H3A   C3   H3    107.23  3.000
 B2X  H3A   C3   C4    109.55  3.000
 B2X  H3    C3   C4    110.48  3.000
 B2X  H3A   C3   O2    110.57  3.000
 B2X  H3    C3   O2    107.37  3.000
 B2X  C4    C3   O2    111.53  3.000
 B2X  C9    C4   C5    119.71  3.000
 B2X  C9    C4   C3    117.89  3.000
 B2X  C5    C4   C3    122.40  3.000
 B2X  H5    C5   C6    119.54  3.000
 B2X  H5    C5   C4    120.16  3.000
 B2X  C6    C5   C4    120.31  3.000
 B2X  H6    C6   C7    119.60  3.000
 B2X  H6    C6   C5    119.41  3.000
 B2X  C7    C6   C5    120.99  3.000
 B2X  H7    C7   C8    120.26  3.000
 B2X  H7    C7   C6    119.39  3.000
 B2X  C8    C7   C6    120.35  3.000
 B2X  C14   C8   C9    118.97  3.000
 B2X  C14   C8   C7    122.62  3.000
 B2X  C9    C8   C7    118.39  3.000
 B2X  C10   C9   C8    120.08  3.000
 B2X  C10   C9   C4    119.67  3.000
 B2X  C8    C9   C4    120.25  3.000
 B2X  C11   C10  C9    120.00  3.000
 B2X  C11   C10  C1    122.08  3.000
 B2X  C9    C10  C1    117.92  3.000
 B2X  H11   C11  C12   119.60  3.000
 B2X  H11   C11  C10   120.71  3.000
 B2X  C12   C11  C10   119.69  3.000
 B2X  C14   C12  CL13  120.13  3.000
 B2X  C14   C12  C11   122.33  3.000
 B2X  CL13  C12  C11   117.51  3.000
 B2X  C15   C14  C12   120.74  3.000
 B2X  C15   C14  C8    120.33  3.000
 B2X  C12   C14  C8    118.93  3.000
 B2X  N17   C15  N16   126.18  3.000
 B2X  N17   C15  C14   116.78  3.000
 B2X  N16   C15  C14   117.03  3.000
 B2X  C23   N16  C15   113.82  3.000
 B2X  C18   N17  C15   114.86  3.000
 B2X  N22   C18  N19   117.98  3.000
 B2X  N22   C18  N17   124.07  3.000
 B2X  N19   C18  N17   117.95  3.000
 B2X  HN1A  N19  HN19  118.84  3.000
 B2X  HN1A  N19  C18   120.68  3.000
 B2X  HN19  N19  C18   120.45  3.000
 B2X  C23   N22  C18   114.81  3.000
 B2X  S24   C23  N22   120.04  3.000
 B2X  S24   C23  N16   113.71  3.000
 B2X  N22   C23  N16   126.25  3.000
 B2X  C25   S24  C23   102.48  3.000
 B2X  H25B  C25  H25A  109.25  3.000
 B2X  H25B  C25  H25   109.24  3.000
 B2X  H25A  C25  H25   110.01  3.000
 B2X  H25B  C25  S24   105.88  3.000
 B2X  H25A  C25  S24   111.20  3.000
 B2X  H25   C25  S24   111.14  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
 B2X  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 B2X  CONST_02  C7    C8   C9   C4      0.00   0.0  0
 B2X  CONST_03  C14   C8   C9   C4    180.00   0.0  0
 B2X  CONST_04  C11   C10  C9   C4    180.00   0.0  0
 B2X  CONST_05  C8    C9   C4   C5      0.00   0.0  0
 B2X  CONST_06  C10   C9   C4   C5    180.00   0.0  0
 B2X  CONST_07  C8    C7   C6   C5      0.00   0.0  0
 B2X  CONST_08  C9    C4   C5   C6      0.00   0.0  0
 B2X  CONST_09  C9    C8   C7   C6      0.00   0.0  0
 B2X  CONST_10  C14   C8   C7   C6    180.00   0.0  0
 B2X  CONST_11  C10   C9   C8   C7    180.00   0.0  0
 B2X  CONST_12  C12   C14  C8   C7    180.00   0.0  0
 B2X  CONST_13  C15   C14  C8   C7      0.00   0.0  0
 B2X  CONST_14  C11   C10  C9   C8      0.00   0.0  0
 B2X  CONST_15  C11   C12  C14  C8      0.00   0.0  0
 B2X  CONST_18  C12   C14  C8   C9      0.00   0.0  0
 B2X  CONST_19  C15   C14  C8   C9    180.00   0.0  0
 B2X  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 B2X  CONST_21  C14   C8   C9   C10     0.00   0.0  0
 B2X  CONST_22  C14   C12  C11  C10     0.00   0.0  0
 B2X  CONST_23  C15   C14  C12  C11   180.00   0.0  0
 B2X  CONST_26  C23   N16  C15  C14   180.00   0.0  0
 B2X  CONST_27  C18   N17  C15  C14   180.00   0.0  0
 B2X  CONST_28  N22   C23  N16  C15     0.00   0.0  0
 B2X  CONST_29  N22   C18  N17  C15     0.00   0.0  0
 B2X  CONST_30  C18   N17  C15  N16     0.00   0.0  0
 B2X  CONST_31  C18   N22  C23  N16     0.00   0.0  0
 B2X  CONST_32  C23   N16  C15  N17     0.00   0.0  0
 B2X  CONST_33  C23   N22  C18  N17     0.00   0.0  0
 B2X  CONST_34  CL13  C12  C14  C8    180.00   0.0  0
 B2X  CONST_35  CL13  C12  C11  C10   180.00   0.0  0
 B2X  CONST_36  C15   C14  C12  CL13    0.00   0.0  0
 B2X  CONST_37  S24   C23  N16  C15   180.00   0.0  0
 B2X  CONST_38  N19   C18  N17  C15   180.00   0.0  0
 B2X  CONST_39  S24   C23  N22  C18   180.00   0.0  0
 B2X  CONST_40  C23   N22  C18  N19   180.00   0.0  0
 B2X  CONST_41  H11   C11  C10  C1      0.00   0.0  0
 B2X  CONST_42  H5    C5   C4   C3      0.00   0.0  0
 B2X  CONST_43  H6    C6   C5   C4    180.00   0.0  0
 B2X  CONST_44  H7    C7   C6   C5    180.00   0.0  0
 B2X  CONST_45  HN19  N19  C18  N17     0.00   0.0  0
 B2X  CONST_46  HN1A  N19  C18  N17   180.00   0.0  0
 B2X  Var_01    C4    C3   O2   C1     59.46  30.0  1
 B2X  Var_02    C9    C10  C1   O2     29.48  30.0  1
 B2X  Var_03    C5    C4   C3   O2    152.44  30.0  1
 B2X  Var_04    C10   C1   O2   C3    -60.01  30.0  1
 B2X  Var_05    H25   C25  S24  C23   -61.47  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
 B2X  plan-1  C14   0.020
 B2X  plan-1  C15   0.020
 B2X  plan-1  N16   0.020
 B2X  plan-1  N17   0.020
 B2X  plan-1  C18   0.020
 B2X  plan-1  N19   0.020
 B2X  plan-1  N22   0.020
 B2X  plan-1  C23   0.020
 B2X  plan-1  S24   0.020
 B2X  plan-2  C1    0.020
 B2X  plan-2  C3    0.020
 B2X  plan-2  C4    0.020
 B2X  plan-2  C5    0.020
 B2X  plan-2  C6    0.020
 B2X  plan-2  C7    0.020
 B2X  plan-2  C8    0.020
 B2X  plan-2  C9    0.020
 B2X  plan-2  C10   0.020
 B2X  plan-2  C11   0.020
 B2X  plan-2  C12   0.020
 B2X  plan-2  CL13  0.020
 B2X  plan-2  C14   0.020
 B2X  plan-2  C15   0.020
 B2X  plan-2  H5    0.020
 B2X  plan-2  H6    0.020
 B2X  plan-2  H7    0.020
 B2X  plan-2  H11   0.020
 B2X  plan-3  C18   0.020
 B2X  plan-3  N19   0.020
 B2X  plan-3  HN19  0.020
 B2X  plan-3  HN1A  0.020

