# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:30:25 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CN2C(=O)n3ncnc3c4c5CCN(CC6CCOCC6)Cc5sc24)cc1
#
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
 8HM  8HM  6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one  ligand  60  33  .  2022-07-23  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_8HM
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
 8HM  N1   N  NR6   0  -0.585   2.2076   1.1734   1.3109
 8HM  C4   C  CR56  0   0.548   0.9744   3.1419  -0.2009
 8HM  C6   C  CR6   0   0.754   2.8391   2.3915   1.2412
 8HM  C8   C  CR15  0   0.015   1.6666   5.0883  -0.4810
 8HM  C13  C  CH2   0  -0.301  -2.2825  -0.7125  -0.6840
 8HM  C15  C  CH2   0  -0.294  -2.7913   1.1007  -2.1644
 8HM  C20  C  CR16  0  -0.272   4.4593  -0.6320   0.3354
 8HM  C21  C  CR16  0  -0.367   5.0744  -1.6111  -0.4322
 8HM  C22  C  CR6   0   0.378   4.7094  -2.9477  -0.2736
 8HM  C24  C  CR16  0  -0.286   3.1174  -2.2899   1.4074
 8HM  C26  C  CH3   0  -0.438   6.2528  -3.6825  -1.9187
 8HM  C28  C  CH1   0  -0.296  -5.2401  -1.2264  -0.4692
 8HM  C23  C  CR16  0  -0.330   3.7245  -3.2801   0.6573
 8HM  C3   C  CR56  0   0.009   0.3652   1.8653  -0.1125
 8HM  C12  C  CR5   0   0.206  -0.8509   1.3632  -0.6686
 8HM  C19  C  CR6   0   0.095   3.4729  -0.9518   1.2596
 8HM  C11  C  CR5   0  -0.305  -1.0732   0.0791  -0.3064
 8HM  C2   C  CR56  0   0.083   1.0290   0.9343   0.6486
 8HM  C16  C  CH2   0  -0.506  -1.8145   2.0927  -1.5454
 8HM  C29  C  CH2   0  -0.437  -6.5459  -1.8274  -0.9864
 8HM  C33  C  CH2   0  -0.433  -5.5472  -0.3111   0.7120
 8HM  C30  C  CH2   0  -0.178  -7.3191  -2.4775   0.1498
 8HM  C32  C  CH2   0  -0.179  -6.3795  -1.0471   1.7496
 8HM  C18  C  CH2   0  -0.439   2.8216   0.1071   2.1073
 8HM  N7   N  N     0  -0.467   0.6496   4.2552  -0.8109
 8HM  N9   N  N     0  -0.244   2.5937   4.5785   0.2843
 8HM  N5   N  N     0  -0.470   2.1499   3.3215   0.4689
 8HM  N14  N  NT    0  -0.430  -3.3113   0.1951  -1.1531
 8HM  O17  O  O     0  -0.450   3.8846   2.6565   1.7826
 8HM  O31  O  O2    0  -0.487  -7.5708  -1.5746   1.2045
 8HM  S10  S  S2    0   0.274   0.1899  -0.5649   0.6947
 8HM  H1   H  HCR5  0   0.284   1.7180   6.1107  -0.8232
 8HM  H2   H  HCH2  0   0.229  -2.0203  -1.4693  -1.4444
 8HM  H3   H  HCH2  0   0.263  -2.6469  -1.2626   0.1865
 8HM  H4   H  HCH2  0   0.247  -3.6259   1.6449  -2.6078
 8HM  H5   H  HCH2  0   0.205  -2.2948   0.5557  -2.9844
 8HM  H6   H  HCR6  0   0.257   4.7739   0.3961   0.2024
 8HM  H7   H  HCR6  0   0.282   5.8367  -1.3161  -1.1406
 8HM  H8   H  HCR6  0   0.260   2.3517  -2.5669   2.1228
 8HM  H9   H  HCH3  0   0.261   6.5408  -4.6346  -2.3569
 8HM  H10  H  HCH3  0   0.230   5.8883  -3.0260  -2.7130
 8HM  H11  H  HCH3  0   0.230   7.1334  -3.2255  -1.4603
 8HM  H12  H  HCH1  0   0.228  -4.6275  -2.0613  -0.1040
 8HM  H13  H  HCR6  0   0.265   3.4349  -4.3158   0.7830
 8HM  H14  H  HCH2  0   0.252  -1.2826   2.6331  -2.3307
 8HM  H15  H  HCH2  0   0.252  -2.3555   2.8420  -0.9609
 8HM  H16  H  HCH2  0   0.220  -7.1585  -1.0452  -1.4478
 8HM  H17  H  HCH2  0   0.235  -6.3510  -2.5767  -1.7587
 8HM  H18  H  HCH2  0   0.238  -4.6279   0.0497   1.1782
 8HM  H19  H  HCH2  0   0.216  -6.0896   0.5737   0.3603
 8HM  H20  H  HCH2  0   0.233  -8.2889  -2.8386  -0.1973
 8HM  H21  H  HCH2  0   0.193  -6.7573  -3.3490   0.5186
 8HM  H22  H  HCH2  0   0.192  -5.7754  -1.8536   2.1926
 8HM  H23  H  HCH2  0   0.232  -6.6723  -0.3778   2.5609
 8HM  H24  H  HCH2  0   0.311   3.5412   0.5766   2.7737
 8HM  H25  H  HCH2  0   0.298   2.0479  -0.3289   2.7433
 8HM  H26  H  HCH2  0   0.203  -4.2782  -1.2342  -2.3944
 8HM  H27  H  HCH2  0   0.229  -5.1772   0.2341  -2.0273
 8HM  C27  C  CH2   0  -0.242  -4.5008  -0.5081  -1.5926
 8HM  O25  O  O2    0  -0.469   5.2480  -3.9676  -0.9652

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
 8HM  O25  C26  single    1.414  0.020  1.414
 8HM  O25  C22  single    1.345  0.020  1.345
 8HM  C22  C23  aromatic  1.395  0.020  1.395
 8HM  C22  C21  aromatic  1.395  0.020  1.395
 8HM  C23  C24  aromatic  1.383  0.020  1.383
 8HM  C24  C19  aromatic  1.392  0.020  1.392
 8HM  C21  C20  aromatic  1.388  0.020  1.388
 8HM  C20  C19  aromatic  1.389  0.020  1.389
 8HM  C19  C18  single    1.505  0.020  1.505
 8HM  C18  N1   single    1.466  0.020  1.466
 8HM  O17  C6   double    1.207  0.020  1.207
 8HM  C6   N1   single    1.374  0.020  1.374
 8HM  C6   N5   single    1.391  0.020  1.391
 8HM  N1   C2   single    1.373  0.020  1.373
 8HM  N5   N9   aromatic  1.346  0.020  1.346
 8HM  N5   C4   aromatic  1.365  0.020  1.365
 8HM  C2   S10  aromatic  1.719  0.020  1.719
 8HM  C2   C3   aromatic  1.374  0.020  1.374
 8HM  N9   C8   aromatic  1.306  0.020  1.306
 8HM  S10  C11  aromatic  1.736  0.020  1.736
 8HM  C4   C3   aromatic  1.417  0.020  1.417
 8HM  C4   N7   aromatic  1.310  0.020  1.310
 8HM  C3   C12  aromatic  1.428  0.020  1.428
 8HM  C8   N7   aromatic  1.355  0.020  1.355
 8HM  C11  C12  aromatic  1.353  0.020  1.353
 8HM  C11  C13  single    1.494  0.020  1.494
 8HM  C12  C16  single    1.493  0.020  1.493
 8HM  C13  N14  single    1.450  0.020  1.450
 8HM  C32  C33  single    1.520  0.020  1.520
 8HM  C32  O31  single    1.412  0.020  1.412
 8HM  C16  C15  single    1.524  0.020  1.524
 8HM  N14  C15  single    1.454  0.020  1.454
 8HM  N14  C27  single    1.450  0.020  1.450
 8HM  C33  C28  single    1.526  0.020  1.526
 8HM  O31  C30  single    1.411  0.020  1.411
 8HM  C28  C27  single    1.525  0.020  1.525
 8HM  C28  C29  single    1.528  0.020  1.528
 8HM  C30  C29  single    1.520  0.020  1.520
 8HM  C8   H1   single    0.930  0.020  1.080
 8HM  C13  H2   single    0.970  0.020  1.090
 8HM  C13  H3   single    0.970  0.020  1.090
 8HM  C15  H4   single    0.970  0.020  1.090
 8HM  C15  H5   single    0.970  0.020  1.090
 8HM  C20  H6   single    0.930  0.020  1.080
 8HM  C21  H7   single    0.930  0.020  1.080
 8HM  C24  H8   single    0.930  0.020  1.080
 8HM  C26  H9   single    0.970  0.020  1.090
 8HM  C26  H10  single    0.970  0.020  1.090
 8HM  C26  H11  single    0.970  0.020  1.090
 8HM  C28  H12  single    0.970  0.020  1.090
 8HM  C23  H13  single    0.930  0.020  1.080
 8HM  C16  H14  single    0.970  0.020  1.090
 8HM  C16  H15  single    0.970  0.020  1.090
 8HM  C29  H16  single    0.970  0.020  1.090
 8HM  C29  H17  single    0.970  0.020  1.090
 8HM  C33  H18  single    0.970  0.020  1.090
 8HM  C33  H19  single    0.970  0.020  1.090
 8HM  C30  H20  single    0.970  0.020  1.090
 8HM  C30  H21  single    0.970  0.020  1.090
 8HM  C32  H22  single    0.970  0.020  1.090
 8HM  C32  H23  single    0.970  0.020  1.090
 8HM  C18  H24  single    0.970  0.020  1.090
 8HM  C18  H25  single    0.970  0.020  1.090
 8HM  C27  H26  single    0.970  0.020  1.090
 8HM  C27  H27  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
 8HM  C18  N1   C2   119.67  3.000
 8HM  C2   N1   C6   121.63  3.000
 8HM  C18  N1   C6   118.69  3.000
 8HM  N5   C4   N7   109.28  3.000
 8HM  N7   C4   C3   133.45  3.000
 8HM  N5   C4   C3   117.27  3.000
 8HM  O17  C6   N5   122.10  3.000
 8HM  N5   C6   N1   113.15  3.000
 8HM  O17  C6   N1   124.75  3.000
 8HM  H1   C8   N9   121.45  3.000
 8HM  H1   C8   N7   122.74  3.000
 8HM  N9   C8   N7   115.81  3.000
 8HM  H3   C13  H2   106.42  3.000
 8HM  H3   C13  N14  109.66  3.000
 8HM  H2   C13  N14  112.00  3.000
 8HM  H3   C13  C11  109.60  3.000
 8HM  H2   C13  C11  110.18  3.000
 8HM  N14  C13  C11  108.94  3.000
 8HM  H5   C15  H4   106.79  3.000
 8HM  H5   C15  N14  111.75  3.000
 8HM  H4   C15  N14  108.66  3.000
 8HM  H5   C15  C16  109.58  3.000
 8HM  H4   C15  C16  109.33  3.000
 8HM  N14  C15  C16  110.63  3.000
 8HM  H6   C20  C19  120.42  3.000
 8HM  H6   C20  C21  118.22  3.000
 8HM  C19  C20  C21  121.35  3.000
 8HM  H7   C21  C22  121.35  3.000
 8HM  H7   C21  C20  118.83  3.000
 8HM  C22  C21  C20  119.82  3.000
 8HM  O25  C22  C23  116.43  3.000
 8HM  C23  C22  C21  119.27  3.000
 8HM  O25  C22  C21  124.30  3.000
 8HM  H8   C24  C19  119.74  3.000
 8HM  H8   C24  C23  119.03  3.000
 8HM  C19  C24  C23  121.24  3.000
 8HM  H11  C26  H10  108.81  3.000
 8HM  H11  C26  H9   108.78  3.000
 8HM  H10  C26  H9   108.76  3.000
 8HM  H11  C26  O25  111.96  3.000
 8HM  H10  C26  O25  111.96  3.000
 8HM  H9   C26  O25  106.47  3.000
 8HM  H12  C28  C27  109.44  3.000
 8HM  H12  C28  C33  108.12  3.000
 8HM  C27  C28  C33  112.67  3.000
 8HM  H12  C28  C29  106.88  3.000
 8HM  C27  C28  C29  110.51  3.000
 8HM  C33  C28  C29  109.03  3.000
 8HM  H13  C23  C24  120.31  3.000
 8HM  H13  C23  C22  119.61  3.000
 8HM  C24  C23  C22  120.08  3.000
 8HM  C2   C3   C12  112.89  3.000
 8HM  C12  C3   C4   131.17  3.000
 8HM  C2   C3   C4   115.94  3.000
 8HM  C16  C12  C11  121.00  3.000
 8HM  C16  C12  C3   127.33  3.000
 8HM  C11  C12  C3   111.68  3.000
 8HM  C18  C19  C24  120.40  3.000
 8HM  C18  C19  C20  121.35  3.000
 8HM  C24  C19  C20  118.24  3.000
 8HM  S10  C11  C12  112.78  3.000
 8HM  C12  C11  C13  124.64  3.000
 8HM  S10  C11  C13  122.57  3.000
 8HM  S10  C2   C3   111.73  3.000
 8HM  C3   C2   N1   124.34  3.000
 8HM  S10  C2   N1   123.92  3.000
 8HM  H15  C16  H14  106.64  3.000
 8HM  H15  C16  C12  109.88  3.000
 8HM  H14  C16  C12  110.48  3.000
 8HM  H15  C16  C15  110.25  3.000
 8HM  H14  C16  C15  110.02  3.000
 8HM  C12  C16  C15  109.53  3.000
 8HM  H17  C29  H16  106.95  3.000
 8HM  H17  C29  C30  108.99  3.000
 8HM  H16  C29  C30  109.61  3.000
 8HM  H17  C29  C28  110.88  3.000
 8HM  H16  C29  C28  109.86  3.000
 8HM  C30  C29  C28  110.48  3.000
 8HM  H19  C33  H18  106.67  3.000
 8HM  H19  C33  C32  109.82  3.000
 8HM  H18  C33  C32  109.23  3.000
 8HM  H19  C33  C28  109.61  3.000
 8HM  H18  C33  C28  111.05  3.000
 8HM  C32  C33  C28  110.38  3.000
 8HM  H21  C30  H20  107.35  3.000
 8HM  H21  C30  O31  110.32  3.000
 8HM  H20  C30  O31  106.91  3.000
 8HM  H21  C30  C29  109.23  3.000
 8HM  H20  C30  C29  110.84  3.000
 8HM  O31  C30  C29  112.07  3.000
 8HM  H23  C32  H22  107.30  3.000
 8HM  H23  C32  O31  106.83  3.000
 8HM  H22  C32  O31  110.16  3.000
 8HM  H23  C32  C33  110.93  3.000
 8HM  H22  C32  C33  109.20  3.000
 8HM  O31  C32  C33  112.28  3.000
 8HM  H25  C18  H24  106.52  3.000
 8HM  H25  C18  C19  110.71  3.000
 8HM  H24  C18  C19  111.26  3.000
 8HM  H25  C18  N1   108.06  3.000
 8HM  H24  C18  N1   107.22  3.000
 8HM  C19  C18  N1   112.78  3.000
 8HM  C8   N7   C4   102.88  3.000
 8HM  N5   N9   C8   102.18  3.000
 8HM  N9   N5   C6   122.49  3.000
 8HM  N9   N5   C4   109.85  3.000
 8HM  C6   N5   C4   127.66  3.000
 8HM  C27  N14  C15  112.63  3.000
 8HM  C27  N14  C13  112.12  3.000
 8HM  C15  N14  C13  111.17  3.000
 8HM  C32  O31  C30  112.15  3.000
 8HM  C2   S10  C11   90.93  3.000
 8HM  H27  C27  H26  106.39  3.000
 8HM  H27  C27  N14  107.37  3.000
 8HM  H26  C27  N14  111.93  3.000
 8HM  H27  C27  C28  108.22  3.000
 8HM  H26  C27  C28  108.84  3.000
 8HM  N14  C27  C28  113.76  3.000
 8HM  C26  O25  C22  118.58  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
 8HM  CONST_01  C8   N9   N5   C4      0.00   0.0  0
 8HM  CONST_02  S10  C2   C3   C4    180.00   0.0  0
 8HM  CONST_03  C11  C12  C3   C4    180.00   0.0  0
 8HM  CONST_04  N9   C8   N7   C4      0.00   0.0  0
 8HM  CONST_05  N5   C4   N7   C8      0.00   0.0  0
 8HM  CONST_06  C3   C4   N7   C8    180.00   0.0  0
 8HM  CONST_07  C23  C22  C21  C20     0.00   0.0  0
 8HM  CONST_08  C23  C24  C19  C20     0.00   0.0  0
 8HM  CONST_09  C24  C23  C22  C21     0.00   0.0  0
 8HM  CONST_10  C24  C19  C20  C21     0.00   0.0  0
 8HM  CONST_11  C19  C24  C23  C22     0.00   0.0  0
 8HM  CONST_12  C19  C20  C21  C22     0.00   0.0  0
 8HM  CONST_13  C11  S10  C2   C3      0.00   0.0  0
 8HM  CONST_14  N9   N5   C4   C3    180.00   0.0  0
 8HM  CONST_15  S10  C11  C12  C3      0.00   0.0  0
 8HM  CONST_16  S10  C2   C3   C12     0.00   0.0  0
 8HM  CONST_17  N5   C4   C3   C12   180.00   0.0  0
 8HM  CONST_18  N7   C4   C3   C12     0.00   0.0  0
 8HM  CONST_19  C2   S10  C11  C12     0.00   0.0  0
 8HM  CONST_20  C2   C3   C12  C11     0.00   0.0  0
 8HM  CONST_21  N5   C4   C3   C2      0.00   0.0  0
 8HM  CONST_22  N7   C4   C3   C2    180.00   0.0  0
 8HM  CONST_23  N9   N5   C4   N7      0.00   0.0  0
 8HM  CONST_24  N5   N9   C8   N7      0.00   0.0  0
 8HM  CONST_25  N9   N5   C6   N1    180.00   0.0  0
 8HM  CONST_26  C4   N5   C6   N1      0.00   0.0  0
 8HM  CONST_27  N5   C6   N1   C2      0.00   0.0  0
 8HM  CONST_28  O25  C22  C21  C20   180.00   0.0  0
 8HM  CONST_29  C18  C19  C20  C21   180.00   0.0  0
 8HM  CONST_30  O25  C22  C23  C24   180.00   0.0  0
 8HM  CONST_31  C18  C19  C24  C23   180.00   0.0  0
 8HM  CONST_32  O17  C6   N5   C4    180.00   0.0  0
 8HM  CONST_33  O17  C6   N1   C2    180.00   0.0  0
 8HM  CONST_34  N5   C6   N1   C18   180.00   0.0  0
 8HM  CONST_35  O17  C6   N5   N9      0.00   0.0  0
 8HM  CONST_36  H1   C8   N7   C4    180.00   0.0  0
 8HM  CONST_37  H8   C24  C19  C20   180.00   0.0  0
 8HM  CONST_38  H13  C23  C22  C21   180.00   0.0  0
 8HM  CONST_39  H6   C20  C21  C22   180.00   0.0  0
 8HM  CONST_40  H7   C21  C22  C23   180.00   0.0  0
 8HM  CONST_41  O17  C6   N1   C18     0.00   0.0  0
 8HM  Var_01    C16  C15  N14  C13   -69.47  30.0  1
 8HM  Var_02    C3   C12  C16  C15   166.98  30.0  1
 8HM  Var_03    C11  C13  N14  C15    50.50  30.0  1
 8HM  Var_04    O31  C32  C33  C28   -56.00  30.0  1
 8HM  Var_05    O31  C30  C29  C28    56.13  30.0  1
 8HM  Var_06    N14  C13  C11  C12   -15.82  30.0  1
 8HM  Var_07    N14  C15  C16  C12    47.16  30.0  1
 8HM  Var_08    C24  C19  C18  N1   -124.81  30.0  1
 8HM  Var_09    C19  C18  N1   C6   -105.09  30.0  2
 8HM  Var_10    C28  C27  N14  C13    66.28  30.0  3
 8HM  Var_11    C23  C22  O25  C26  -179.86  30.0  2
 8HM  Var_12    H9   C26  O25  C22  -179.78  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
 8HM  chir_01  C28  C33  C27  C29  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
 8HM  plan-1  C20  0.020
 8HM  plan-1  C21  0.020
 8HM  plan-1  C22  0.020
 8HM  plan-1  C24  0.020
 8HM  plan-1  C23  0.020
 8HM  plan-1  C19  0.020
 8HM  plan-1  C18  0.020
 8HM  plan-1  H6   0.020
 8HM  plan-1  H7   0.020
 8HM  plan-1  H8   0.020
 8HM  plan-1  H13  0.020
 8HM  plan-1  O25  0.020
 8HM  plan-2  N1   0.020
 8HM  plan-2  C4   0.020
 8HM  plan-2  C6   0.020
 8HM  plan-2  C8   0.020
 8HM  plan-2  C13  0.020
 8HM  plan-2  C3   0.020
 8HM  plan-2  C12  0.020
 8HM  plan-2  C11  0.020
 8HM  plan-2  C2   0.020
 8HM  plan-2  C16  0.020
 8HM  plan-2  C18  0.020
 8HM  plan-2  N7   0.020
 8HM  plan-2  N9   0.020
 8HM  plan-2  N5   0.020
 8HM  plan-2  O17  0.020
 8HM  plan-2  S10  0.020
 8HM  plan-2  H1   0.020

