# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:04:43 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1(CC1)c2ccc(cc2)c3cc4nc([nH]c4cc3Cl)O[C@@H]5CO[C@@H]6[C@H](O)CO[C@H]56
#
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
 85V  85V  1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol  ligand  54  31  .  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
;

data_comp_85V
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
 85V  C4   C   CR16  0  -0.299   4.8269   1.0226  -0.9743
 85V  C7   C   CR6   0   0.126   1.5533  -0.5765   0.0000
 85V  C6   C   CR6   0   0.045   2.9593  -0.1165   0.0562
 85V  C9   C   CR56  0   0.179  -0.7764  -0.0430  -0.2550
 85V  C20  C   CH1   0  -0.005  -6.8092   1.4739   0.2243
 85V  C21  C   CH1   0  -0.006  -6.0752   1.3378  -1.1246
 85V  C8   C   CR16  0  -0.384   0.5478   0.3650  -0.2115
 85V  C18  C   CH2   0  -0.197  -4.6462   2.1792   0.5421
 85V  C26  C   CT    0  -0.106   7.0045   1.3507   0.2480
 85V  C1   C   CR16  0  -0.269   3.7294  -0.2797   1.2073
 85V  C2   C   CR16  0  -0.287   5.0242   0.2084   1.2631
 85V  C3   C   CR6   0   0.129   5.5927   0.8681   0.1746
 85V  C5   C   CR16  0  -0.279   3.5244   0.5440  -1.0313
 85V  C10  C   CR56  0   0.330  -1.0885  -1.4020  -0.0869
 85V  C11  C   CR16  0  -0.248  -0.1202  -2.3679   0.1114
 85V  C12  C   CR6   0  -0.143   1.1939  -1.9254   0.1511
 85V  CL   CL  CL    0  -0.133   2.4313  -3.1291   0.3538
 85V  N13  N   NR15  0  -0.733  -2.4570  -1.4603  -0.1723
 85V  C14  C   CR5   0   0.676  -2.8829  -0.1878  -0.3805
 85V  N15  N   N     0  -0.525  -1.9269   0.6927  -0.4347
 85V  O16  O   O2    0  -0.441  -4.1724   0.0192  -0.5091
 85V  C17  C   CH1   0  -0.047  -4.5934   1.3600  -0.7366
 85V  O19  O   O2    0  -0.487  -5.8554   1.8301   1.1906
 85V  O22  O   O2    0  -0.489  -6.5102   0.1528  -1.7308
 85V  C23  C   CH2   0  -0.210  -7.6460  -0.3217  -1.0215
 85V  C24  C   CH1   0  -0.014  -7.4446   0.0932   0.4307
 85V  O25  O   OH1   0  -0.653  -6.5477  -0.7267   1.1270
 85V  C27  C   CH2   0  -0.481   7.3442   2.4361   1.2258
 85V  C28  C   CH2   0  -0.483   7.3357   2.7258  -0.2457
 85V  C29  C   CH2   0  -0.138   8.0382   0.2725   0.0488
 85V  O30  O   OH1   0  -0.664   7.9084  -0.2458  -1.2543
 85V  H1   H   HCR6  0   0.247   5.2471   1.5277  -1.8351
 85V  H2   H   HCH1  0   0.253  -7.6006   2.2285   0.1657
 85V  H3   H   HCH1  0   0.259  -6.2689   2.2007  -1.7715
 85V  H4   H   HCR6  0   0.259   0.8043   1.4107  -0.3251
 85V  H6   H   HCH2  0   0.229  -4.6317   3.2440   0.2766
 85V  H7   H   HCR6  0   0.249   3.3063  -0.7714   2.0742
 85V  H8   H   HCR6  0   0.248   5.6014   0.0865   2.1725
 85V  H9   H   HCR6  0   0.249   2.9440   0.6776  -1.9363
 85V  H10  H   HCR6  0   0.289  -0.3652  -3.4152   0.2244
 85V  H11  H   HNR5  0   0.424  -3.0401  -2.2801  -0.1047
 85V  H13  H   HCH1  0   0.275  -3.9594   1.8233  -1.4940
 85V  H14  H   HCH2  0   0.217  -8.5658   0.1310  -1.4134
 85V  H15  H   HCH2  0   0.247  -7.7214  -1.4030  -1.1537
 85V  H16  H   HCH1  0   0.229  -8.4115   0.1654   0.9439
 85V  H17  H   HOH1  0   0.451  -6.9344  -1.6060   1.1817
 85V  H18  H   HCH2  0   0.252   6.5409   2.8417   1.8277
 85V  H19  H   HCH2  0   0.251   8.2991   2.3833   1.7354
 85V  H20  H   HCH2  0   0.251   8.2846   2.8731  -0.7471
 85V  H21  H   HCH2  0   0.251   6.5309   3.3370  -0.6354
 85V  H22  H   HCH2  0   0.192   9.0365   0.6989   0.2174
 85V  H23  H   HCH2  0   0.203   7.8938  -0.5076   0.8082
 85V  H24  H   HOH1  0   0.453   8.4898  -1.0074  -1.3324
 85V  H5   H   HCH2  0   0.255  -3.8094   1.9936   1.2160

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
 85V  C28  C27  single    1.500  0.020  1.500
 85V  C28  C26  single    1.498  0.020  1.498
 85V  C5   C4   aromatic  1.389  0.020  1.389
 85V  C5   C6   aromatic  1.392  0.020  1.392
 85V  C4   C3   aromatic  1.389  0.020  1.389
 85V  C18  C17  single    1.519  0.020  1.519
 85V  C18  O19  single    1.416  0.020  1.416
 85V  C14  O16  single    1.312  0.020  1.312
 85V  C14  N13  aromatic  1.358  0.020  1.358
 85V  C14  N15  aromatic  1.301  0.020  1.301
 85V  O16  C17  single    1.424  0.020  1.424
 85V  N13  C10  aromatic  1.372  0.020  1.372
 85V  C17  C21  single    1.532  0.020  1.532
 85V  N15  C9   aromatic  1.377  0.020  1.377
 85V  C9   C10  aromatic  1.404  0.020  1.404
 85V  C9   C8   aromatic  1.386  0.020  1.386
 85V  C10  C11  aromatic  1.382  0.020  1.382
 85V  C8   C7   aromatic  1.394  0.020  1.394
 85V  C11  C12  aromatic  1.387  0.020  1.387
 85V  C7   C12  aromatic  1.404  0.020  1.404
 85V  C7   C6   single    1.480  0.020  1.480
 85V  C12  CL   single    1.738  0.020  1.738
 85V  C27  C26  single    1.500  0.020  1.500
 85V  C6   C1   aromatic  1.395  0.020  1.395
 85V  C3   C26  single    1.494  0.020  1.494
 85V  C3   C2   aromatic  1.394  0.020  1.394
 85V  C26  C29  single    1.507  0.020  1.507
 85V  O19  C20  single    1.404  0.020  1.404
 85V  C1   C2   aromatic  1.385  0.020  1.385
 85V  C29  O30  single    1.408  0.020  1.408
 85V  C21  C20  single    1.542  0.020  1.542
 85V  C21  O22  single    1.400  0.020  1.400
 85V  C20  C24  single    1.534  0.020  1.534
 85V  O22  C23  single    1.421  0.020  1.421
 85V  C23  C24  single    1.524  0.020  1.524
 85V  C24  O25  single    1.401  0.020  1.401
 85V  C4   H1   single    0.930  0.020  1.080
 85V  C20  H2   single    0.970  0.020  1.090
 85V  C21  H3   single    0.970  0.020  1.090
 85V  C8   H4   single    0.930  0.020  1.080
 85V  C18  H5   single    0.970  0.020  1.090
 85V  C18  H6   single    0.970  0.020  1.090
 85V  C1   H7   single    0.930  0.020  1.080
 85V  C2   H8   single    0.930  0.020  1.080
 85V  C5   H9   single    0.930  0.020  1.080
 85V  C11  H10  single    0.930  0.020  1.080
 85V  N13  H11  single    0.860  0.020  1.020
 85V  C17  H13  single    0.970  0.020  1.090
 85V  C23  H14  single    0.970  0.020  1.090
 85V  C23  H15  single    0.970  0.020  1.090
 85V  C24  H16  single    0.970  0.020  1.090
 85V  O25  H17  single    0.850  0.020  0.980
 85V  C27  H18  single    0.970  0.020  1.090
 85V  C27  H19  single    0.970  0.020  1.090
 85V  C28  H20  single    0.970  0.020  1.090
 85V  C28  H21  single    0.970  0.020  1.090
 85V  C29  H22  single    0.970  0.020  1.090
 85V  C29  H23  single    0.970  0.020  1.090
 85V  O30  H24  single    0.850  0.020  0.980

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
 85V  H1   C4   C5   119.47  3.000
 85V  H1   C4   C3   119.69  3.000
 85V  C5   C4   C3   120.84  3.000
 85V  C12  C7   C8   118.73  3.000
 85V  C12  C7   C6   122.52  3.000
 85V  C8   C7   C6   118.76  3.000
 85V  C5   C6   C1   118.44  3.000
 85V  C1   C6   C7   121.29  3.000
 85V  C5   C6   C7   120.21  3.000
 85V  N15  C9   C10  110.29  3.000
 85V  C10  C9   C8   119.56  3.000
 85V  N15  C9   C8   130.15  3.000
 85V  H2   C20  C24  109.15  3.000
 85V  H2   C20  O19  110.67  3.000
 85V  C24  C20  O19  114.66  3.000
 85V  H2   C20  C21  110.98  3.000
 85V  C24  C20  C21  103.63  3.000
 85V  O19  C20  C21  107.53  3.000
 85V  H3   C21  O22  110.85  3.000
 85V  H3   C21  C17  108.01  3.000
 85V  O22  C21  C17  114.99  3.000
 85V  H3   C21  C20  111.28  3.000
 85V  O22  C21  C20  107.79  3.000
 85V  C17  C21  C20  103.75  3.000
 85V  H4   C8   C9   120.49  3.000
 85V  H4   C8   C7   119.83  3.000
 85V  C9   C8   C7   119.68  3.000
 85V  H6   C18  H5   107.73  3.000
 85V  H6   C18  O19  111.18  3.000
 85V  H5   C18  O19  109.29  3.000
 85V  H6   C18  C17  108.60  3.000
 85V  H5   C18  C17  113.68  3.000
 85V  O19  C18  C17  106.39  3.000
 85V  C29  C26  C28  117.49  3.000
 85V  C29  C26  C27  116.66  3.000
 85V  C28  C26  C27   60.03  3.000
 85V  C29  C26  C3   114.25  3.000
 85V  C27  C26  C3   118.68  3.000
 85V  C28  C26  C3   119.29  3.000
 85V  H7   C1   C2   119.55  3.000
 85V  H7   C1   C6   119.89  3.000
 85V  C2   C1   C6   120.55  3.000
 85V  H8   C2   C3   119.42  3.000
 85V  H8   C2   C1   119.47  3.000
 85V  C3   C2   C1   121.11  3.000
 85V  C2   C3   C26  119.99  3.000
 85V  C2   C3   C4   118.26  3.000
 85V  C26  C3   C4   121.72  3.000
 85V  H9   C5   C6   119.58  3.000
 85V  H9   C5   C4   119.62  3.000
 85V  C6   C5   C4   120.80  3.000
 85V  N13  C10  C11  132.68  3.000
 85V  C11  C10  C9   122.53  3.000
 85V  N13  C10  C9   104.79  3.000
 85V  H10  C11  C12  121.37  3.000
 85V  H10  C11  C10  122.21  3.000
 85V  C12  C11  C10  116.42  3.000
 85V  CL   C12  C11  117.18  3.000
 85V  CL   C12  C7   119.71  3.000
 85V  C11  C12  C7   123.08  3.000
 85V  H11  N13  C14  126.21  3.000
 85V  H11  N13  C10  127.38  3.000
 85V  C14  N13  C10  106.41  3.000
 85V  O16  C14  N15  127.68  3.000
 85V  N15  C14  N13  114.22  3.000
 85V  O16  C14  N13  118.10  3.000
 85V  C14  N15  C9   104.29  3.000
 85V  C17  O16  C14  117.05  3.000
 85V  H13  C17  O16  109.82  3.000
 85V  H13  C17  C18  112.05  3.000
 85V  O16  C17  C18  112.55  3.000
 85V  H13  C17  C21  113.11  3.000
 85V  O16  C17  C21  108.23  3.000
 85V  C18  C17  C21  100.80  3.000
 85V  C18  O19  C20  109.12  3.000
 85V  C23  O22  C21  108.36  3.000
 85V  H15  C23  H14  107.90  3.000
 85V  H15  C23  C24  113.21  3.000
 85V  H14  C23  C24  109.80  3.000
 85V  H15  C23  O22  109.00  3.000
 85V  H14  C23  O22  110.73  3.000
 85V  C24  C23  O22  106.22  3.000
 85V  H16  C24  O25  111.74  3.000
 85V  H16  C24  C23  110.32  3.000
 85V  O25  C24  C23  113.51  3.000
 85V  H16  C24  C20  111.65  3.000
 85V  O25  C24  C20  109.18  3.000
 85V  C23  C24  C20   99.88  3.000
 85V  H17  O25  C24  107.81  3.000
 85V  H19  C27  H18  114.24  3.000
 85V  H19  C27  C28  118.41  3.000
 85V  H18  C27  C28  117.97  3.000
 85V  H19  C27  C26  118.09  3.000
 85V  H18  C27  C26  117.75  3.000
 85V  C28  C27  C26   59.93  3.000
 85V  H21  C28  H20  114.05  3.000
 85V  H21  C28  C27  117.79  3.000
 85V  H20  C28  C27  118.39  3.000
 85V  H21  C28  C26  118.18  3.000
 85V  H20  C28  C26  118.09  3.000
 85V  C27  C28  C26   60.04  3.000
 85V  H23  C29  H22  106.80  3.000
 85V  H23  C29  O30  111.49  3.000
 85V  H22  C29  O30  111.63  3.000
 85V  H23  C29  C26  109.06  3.000
 85V  H22  C29  C26  108.99  3.000
 85V  O30  C29  C26  108.81  3.000
 85V  H24  O30  C29  108.11  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
 85V  CONST_01  C7   C6   C5   C4    180.00   0.0  0
 85V  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 85V  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 85V  CONST_04  N15  C9   C8   C7    180.00   0.0  0
 85V  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 85V  CONST_06  C10  C11  C12  C7      0.00   0.0  0
 85V  CONST_07  C2   C1   C6   C7    180.00   0.0  0
 85V  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 85V  CONST_09  C9   C8   C7   C6    180.00   0.0  0
 85V  CONST_10  C11  C12  C7   C6    180.00   0.0  0
 85V  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 85V  CONST_12  N13  C14  N15  C9      0.00   0.0  0
 85V  CONST_13  C14  N13  C10  C9      0.00   0.0  0
 85V  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 85V  CONST_15  C12  C7   C8   C9      0.00   0.0  0
 85V  CONST_16  C14  N15  C9   C8    180.00   0.0  0
 85V  CONST_17  N13  C10  C9   C8    180.00   0.0  0
 85V  CONST_18  C11  C10  C9   C8      0.00   0.0  0
 85V  CONST_19  C11  C12  C7   C8      0.00   0.0  0
 85V  CONST_23  C5   C4   C3   C2      0.00   0.0  0
 85V  CONST_24  C5   C6   C1   C2      0.00   0.0  0
 85V  CONST_26  N15  C14  N13  C10     0.00   0.0  0
 85V  CONST_27  C14  N15  C9   C10     0.00   0.0  0
 85V  CONST_28  C14  N13  C10  C11   180.00   0.0  0
 85V  CONST_29  N15  C9   C10  C11   180.00   0.0  0
 85V  CONST_30  N13  C10  C11  C12   180.00   0.0  0
 85V  CONST_31  N15  C9   C10  N13     0.00   0.0  0
 85V  CONST_32  C5   C4   C3   C26   180.00   0.0  0
 85V  CONST_33  C1   C2   C3   C26   180.00   0.0  0
 85V  CONST_34  CL   C12  C7   C6      0.00   0.0  0
 85V  CONST_35  O16  C14  N15  C9    180.00   0.0  0
 85V  CONST_36  CL   C12  C7   C8    180.00   0.0  0
 85V  CONST_37  O16  C14  N13  C10   180.00   0.0  0
 85V  CONST_38  CL   C12  C11  C10   180.00   0.0  0
 85V  CONST_39  H8   C2   C3   C4    180.00   0.0  0
 85V  CONST_40  H10  C11  C12  C7    180.00   0.0  0
 85V  CONST_41  H9   C5   C6   C7      0.00   0.0  0
 85V  CONST_42  H7   C1   C6   C7      0.00   0.0  0
 85V  CONST_43  H1   C4   C5   C6    180.00   0.0  0
 85V  CONST_44  H4   C8   C7   C6      0.00   0.0  0
 85V  CONST_45  H11  N13  C10  C9    180.00   0.0  0
 85V  Var_01    C28  C26  C3   C4     46.59  30.0  2
 85V  Var_02    C17  C18  O19  C20   -30.00  30.0  1
 85V  Var_03    C24  C23  O22  C21   -32.10  30.0  1
 85V  Var_04    C27  C28  C26  C3    108.16  30.0  1
 85V  Var_05    H18  C27  C28  C26  -107.56  30.0  1
 85V  Var_06    O30  C29  C26  C3     63.59  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
 85V  chir_01  C20  O19  C21  C24  negativ
 85V  chir_02  C21  O22  C20  C17  negativ
 85V  chir_04  C17  O16  C21  C18  negativ
 85V  chir_05  C24  O25  C20  C23  negativ
 85V  chir_06  C26  C27  C3   C29  both

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
 85V  plan-1  C4   0.020
 85V  plan-1  C7   0.020
 85V  plan-1  C6   0.020
 85V  plan-1  C26  0.020
 85V  plan-1  C1   0.020
 85V  plan-1  C2   0.020
 85V  plan-1  C3   0.020
 85V  plan-1  C5   0.020
 85V  plan-1  H1   0.020
 85V  plan-1  H7   0.020
 85V  plan-1  H8   0.020
 85V  plan-1  H9   0.020
 85V  plan-2  C7   0.020
 85V  plan-2  C6   0.020
 85V  plan-2  C9   0.020
 85V  plan-2  C8   0.020
 85V  plan-2  C10  0.020
 85V  plan-2  C11  0.020
 85V  plan-2  C12  0.020
 85V  plan-2  CL   0.020
 85V  plan-2  N13  0.020
 85V  plan-2  C14  0.020
 85V  plan-2  N15  0.020
 85V  plan-2  O16  0.020
 85V  plan-2  H4   0.020
 85V  plan-2  H10  0.020
 85V  plan-2  H11  0.020

