# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 17:53:15 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(1,3-benzodioxol-5-yl)-5-[(3-fluoro-4-methoxybenzyl)sulfanyl]-1,3,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CSc2oc(nn2)c3ccc4OCOc4c3)cc1F
#
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
 34O  34O  2-(1,3-benzodioxol-5-yl)-5-[(3-fluoro-4-methoxybenzyl)sulfanyl]-1,3,4-oxadiazole  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_34O
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
 34O  C8    C  CH2   0   0.070  -8.3029   0.2183   0.1474
 34O  C10   C  CR5   0   0.483  -2.4190   0.4671  -0.1807
 34O  C6    C  CR56  0   0.314  -6.3622  -0.8525   0.3427
 34O  C5    C  CR56  0   0.329  -6.1007   0.4442  -0.0836
 34O  C4    C  CR16  0  -0.367  -4.8279   0.9071  -0.2650
 34O  C1    C  CR16  0  -0.327  -5.3536  -1.7454   0.6064
 34O  C2    C  CR16  0  -0.296  -4.0436  -1.2940   0.4286
 34O  C3    C  CR6   0  -0.043  -3.7799   0.0035   0.0025
 34O  C19   C  CR6   0   0.478   5.7138   0.3423   0.9215
 34O  C20   C  CR6   0   0.236   6.3719  -0.2859  -0.1397
 34O  O23   O  O2    0  -0.461   7.6349  -0.6716   0.0840
 34O  C24   C  CH3   0  -0.440   8.3296  -1.3195  -0.9667
 34O  C21   C  CR16  0  -0.365   5.6671  -0.4522  -1.3265
 34O  C22   C  CR16  0  -0.275   4.3564  -0.0023  -1.4357
 34O  C18   C  CR16  0  -0.429   4.4184   0.7862   0.8236
 34O  C17   C  CR6   0   0.075   3.7208   0.6223  -0.3736
 34O  C16   C  CH2   0  -0.631   2.3014   1.0825  -0.4888
 34O  C12   C  CR5   0   0.322  -0.3116   0.3951  -0.2011
 34O  N13   N  N     0  -0.308  -0.6351   1.5765  -0.5930
 34O  N14   N  N     0  -0.311  -2.0068   1.6194  -0.5785
 34O  O11   O  O     0  -0.418  -1.3835  -0.3600   0.0771
 34O  O7    O  O     0  -0.476  -7.6929  -1.0389   0.4238
 34O  O9    O  O     0  -0.483  -7.2685   1.0950  -0.2804
 34O  H8    H  HCH2  0   0.249  -9.0420   0.1013  -0.6454
 34O  H8A   H  HCH2  0   0.242  -8.7711   0.6083   1.0552
 34O  H4    H  HCR6  0   0.282  -4.6295   1.9168  -0.5978
 34O  H1    H  HCR6  0   0.285  -5.5567  -2.7550   0.9351
 34O  H2    H  HCR6  0   0.269  -3.2339  -1.9812   0.6317
 34O  H24   H  HCH3  0   0.234   8.4274  -0.6769  -1.8448
 34O  H24A  H  HCH3  0   0.265   9.3207  -1.5468  -0.5839
 34O  H24B  H  HCH3  0   0.234   7.8412  -2.2514  -1.2610
 34O  H21   H  HCR6  0   0.295   6.1270  -0.9316  -2.1793
 34O  H22   H  HCR6  0   0.267   3.8315  -0.1432  -2.3723
 34O  H18   H  HCR6  0   0.284   3.9543   1.2669   1.6764
 34O  H16   H  HCH2  0   0.313   2.0914   1.9225   0.1714
 34O  H16A  H  HCH2  0   0.314   2.0483   1.3614  -1.5103
 34O  S15   S  S2    0   0.101   1.2429  -0.3263   0.0072
 34O  F25   F  F     0  -0.311   6.3886   0.5127   2.0676

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
 34O  C8   O7    single    1.424  0.020  1.424
 34O  C8   O9    single    1.422  0.020  1.422
 34O  C10  C3    single    1.449  0.020  1.449
 34O  C10  N14   aromatic  1.287  0.020  1.287
 34O  C10  O11   aromatic  1.350  0.020  1.350
 34O  C6   C5    aromatic  1.390  0.020  1.390
 34O  C6   C1    aromatic  1.373  0.020  1.373
 34O  C6   O7    single    1.346  0.020  1.346
 34O  C5   C4    aromatic  1.366  0.020  1.366
 34O  C5   O9    single    1.351  0.020  1.351
 34O  C4   C3    aromatic  1.409  0.020  1.409
 34O  C1   C2    aromatic  1.397  0.020  1.397
 34O  C2   C3    aromatic  1.391  0.020  1.391
 34O  F25  C19   single    1.341  0.020  1.341
 34O  C19  C20   aromatic  1.398  0.020  1.398
 34O  C19  C18   aromatic  1.373  0.020  1.373
 34O  C20  O23   single    1.339  0.020  1.339
 34O  C20  C21   aromatic  1.390  0.020  1.390
 34O  O23  C24   single    1.416  0.020  1.416
 34O  C21  C22   aromatic  1.390  0.020  1.390
 34O  C22  C17   aromatic  1.386  0.020  1.386
 34O  C18  C17   aromatic  1.395  0.020  1.395
 34O  C17  C16   single    1.497  0.020  1.497
 34O  C16  S15   single    1.831  0.020  1.831
 34O  S15  C12   single    1.726  0.020  1.726
 34O  C12  N13   aromatic  1.286  0.020  1.286
 34O  C12  O11   aromatic  1.340  0.020  1.340
 34O  N13  N14   aromatic  1.372  0.020  1.372
 34O  C8   H8    single    0.970  0.020  1.090
 34O  C8   H8A   single    0.970  0.020  1.090
 34O  C4   H4    single    0.930  0.020  1.080
 34O  C1   H1    single    0.930  0.020  1.080
 34O  C2   H2    single    0.930  0.020  1.080
 34O  C24  H24   single    0.970  0.020  1.090
 34O  C24  H24A  single    0.970  0.020  1.090
 34O  C24  H24B  single    0.970  0.020  1.090
 34O  C21  H21   single    0.930  0.020  1.080
 34O  C22  H22   single    0.930  0.020  1.080
 34O  C18  H18   single    0.930  0.020  1.080
 34O  C16  H16   single    0.970  0.020  1.090
 34O  C16  H16A  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
 34O  H8A   C8   H8    110.59  3.000
 34O  H8A   C8   O9    109.97  3.000
 34O  H8    C8   O9    109.91  3.000
 34O  H8A   C8   O7    109.70  3.000
 34O  H8    C8   O7    109.67  3.000
 34O  O9    C8   O7    106.92  3.000
 34O  O11   C10  N14   111.22  3.000
 34O  O11   C10  C3    120.00  3.000
 34O  N14   C10  C3    128.78  3.000
 34O  O7    C6   C1    128.66  3.000
 34O  O7    C6   C5    109.49  3.000
 34O  C1    C6   C5    121.85  3.000
 34O  O9    C5   C4    128.50  3.000
 34O  O9    C5   C6    109.36  3.000
 34O  C4    C5   C6    122.14  3.000
 34O  H4    C4   C3    121.37  3.000
 34O  H4    C4   C5    121.87  3.000
 34O  C3    C4   C5    116.76  3.000
 34O  H1    C1   C2    121.11  3.000
 34O  H1    C1   C6    121.87  3.000
 34O  C2    C1   C6    117.02  3.000
 34O  H2    C2   C3    120.56  3.000
 34O  H2    C2   C1    118.23  3.000
 34O  C3    C2   C1    121.21  3.000
 34O  C2    C3   C4    121.02  3.000
 34O  C2    C3   C10   121.01  3.000
 34O  C4    C3   C10   117.98  3.000
 34O  C18   C19  C20   122.38  3.000
 34O  C18   C19  F25   119.65  3.000
 34O  C20   C19  F25   117.97  3.000
 34O  C21   C20  O23   125.88  3.000
 34O  C21   C20  C19   117.59  3.000
 34O  O23   C20  C19   116.53  3.000
 34O  C24   O23  C20   118.05  3.000
 34O  H24B  C24  H24A  108.92  3.000
 34O  H24B  C24  H24   108.98  3.000
 34O  H24A  C24  H24   108.93  3.000
 34O  H24B  C24  O23   111.76  3.000
 34O  H24A  C24  O23   106.36  3.000
 34O  H24   C24  O23   111.78  3.000
 34O  H21   C21  C22   118.87  3.000
 34O  H21   C21  C20   120.72  3.000
 34O  C22   C21  C20   120.42  3.000
 34O  H22   C22  C17   119.93  3.000
 34O  H22   C22  C21   118.87  3.000
 34O  C17   C22  C21   121.20  3.000
 34O  H18   C18  C17   120.89  3.000
 34O  H18   C18  C19   119.45  3.000
 34O  C17   C18  C19   119.66  3.000
 34O  C16   C17  C18   120.27  3.000
 34O  C16   C17  C22   120.96  3.000
 34O  C18   C17  C22   118.75  3.000
 34O  H16A  C16  H16   109.05  3.000
 34O  H16A  C16  S15   108.48  3.000
 34O  H16   C16  S15   108.53  3.000
 34O  H16A  C16  C17   111.81  3.000
 34O  H16   C16  C17   111.93  3.000
 34O  S15   C16  C17   106.91  3.000
 34O  O11   C12  N13   112.30  3.000
 34O  O11   C12  S15   117.37  3.000
 34O  N13   C12  S15   130.33  3.000
 34O  N14   N13  C12   106.07  3.000
 34O  N13   N14  C10   107.19  3.000
 34O  C12   O11  C10   103.22  3.000
 34O  C6    O7   C8    106.82  3.000
 34O  C5    O9   C8    106.73  3.000
 34O  C12   S15  C16    99.58  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
 34O  CONST_01  C5   C4   C3   C10  180.00   0.0  0
 34O  CONST_02  C1   C2   C3   C10  180.00   0.0  0
 34O  CONST_03  C12  N13  N14  C10    0.00   0.0  0
 34O  CONST_04  N13  C12  O11  C10    0.00   0.0  0
 34O  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 34O  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 34O  CONST_07  C2   C1   C6   C5     0.00   0.0  0
 34O  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 34O  CONST_09  C1   C6   C5   C4     0.00   0.0  0
 34O  CONST_10  N14  C10  C3   C4     0.00   0.0  0
 34O  CONST_11  O11  C10  C3   C4   180.00   0.0  0
 34O  CONST_12  C1   C2   C3   C4     0.00   0.0  0
 34O  CONST_13  N14  C10  C3   C2   180.00   0.0  0
 34O  CONST_14  O11  C10  C3   C2     0.00   0.0  0
 34O  CONST_15  N13  N14  C10  C3   180.00   0.0  0
 34O  CONST_16  C12  O11  C10  C3   180.00   0.0  0
 34O  CONST_17  C22  C21  C20  C19    0.00   0.0  0
 34O  CONST_18  C22  C17  C18  C19    0.00   0.0  0
 34O  CONST_19  C17  C18  C19  C20    0.00   0.0  0
 34O  CONST_20  C17  C22  C21  C20    0.00   0.0  0
 34O  CONST_21  C18  C19  C20  C21    0.00   0.0  0
 34O  CONST_22  C18  C17  C22  C21    0.00   0.0  0
 34O  CONST_23  N14  C10  O11  C12    0.00   0.0  0
 34O  CONST_24  O11  C10  N14  N13    0.00   0.0  0
 34O  CONST_25  O11  C12  N13  N14    0.00   0.0  0
 34O  CONST_26  S15  C12  O11  C10  180.00   0.0  0
 34O  CONST_27  C21  C20  C19  F25  180.00   0.0  0
 34O  CONST_28  C17  C18  C19  F25  180.00   0.0  0
 34O  CONST_29  C16  C17  C18  C19  180.00   0.0  0
 34O  CONST_30  C18  C19  C20  O23  180.00   0.0  0
 34O  CONST_31  C22  C21  C20  O23  180.00   0.0  0
 34O  CONST_32  C16  C17  C22  C21  180.00   0.0  0
 34O  CONST_33  N14  N13  C12  S15  180.00   0.0  0
 34O  CONST_34  H4   C4   C3   C10    0.00   0.0  0
 34O  CONST_35  H2   C2   C3   C10    0.00   0.0  0
 34O  CONST_36  H1   C1   C6   C5   180.00   0.0  0
 34O  CONST_37  H21  C21  C20  C19  180.00   0.0  0
 34O  CONST_38  H18  C18  C19  C20  180.00   0.0  0
 34O  CONST_39  H22  C22  C21  C20  180.00   0.0  0
 34O  Var_01    C5   C6   O7   C8    -4.95  30.0  1
 34O  Var_02    C6   C5   O9   C8     5.14  30.0  1
 34O  Var_03    O9   C8   O7   C6     7.98  30.0  1
 34O  Var_04    O7   C8   O9   C5    -8.04  30.0  1
 34O  Var_05    C21  C20  O23  C24   -0.58  30.0  2
 34O  Var_06    S15  C16  C17  C22   88.34  30.0  2
 34O  Var_07    N13  C12  S15  C16    0.12  30.0  2
 34O  Var_08    H24  C24  O23  C20   61.29  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
 34O  plan-1  C10  0.020
 34O  plan-1  C3   0.020
 34O  plan-1  C12  0.020
 34O  plan-1  N13  0.020
 34O  plan-1  N14  0.020
 34O  plan-1  O11  0.020
 34O  plan-1  S15  0.020
 34O  plan-2  C19  0.020
 34O  plan-2  C20  0.020
 34O  plan-2  O23  0.020
 34O  plan-2  C21  0.020
 34O  plan-2  C22  0.020
 34O  plan-2  C18  0.020
 34O  plan-2  C17  0.020
 34O  plan-2  C16  0.020
 34O  plan-2  H21  0.020
 34O  plan-2  H22  0.020
 34O  plan-2  H18  0.020
 34O  plan-2  F25  0.020
 34O  plan-3  C10  0.020
 34O  plan-3  C6   0.020
 34O  plan-3  C5   0.020
 34O  plan-3  C4   0.020
 34O  plan-3  C1   0.020
 34O  plan-3  C2   0.020
 34O  plan-3  C3   0.020
 34O  plan-3  O7   0.020
 34O  plan-3  O9   0.020
 34O  plan-3  H4   0.020
 34O  plan-3  H1   0.020
 34O  plan-3  H2   0.020

