# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:15:32 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 4-({1-(4-ethylphenyl)-2-methyl-5-[4-(methylsulfanyl)phenyl]-1H-pyrrol-3-yl}methyl)thiomorpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(cc1)n2c(C)c(CN3CCSCC3)cc2c4ccc(SC)cc4
#
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
 JV0  JV0  4-({1-(4-ethylphenyl)-2-methyl-5-[4-(methylsulfanyl)phenyl]-1H-pyrrol-3-yl}methyl)thiomorpholine  ligand  59  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JV0
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
 JV0  C8    C  CH3   0  -0.736  -2.1494   2.1301   0.8247
 JV0  C7    C  CR5   0   0.283  -1.5209   0.7828   0.8502
 JV0  N1    N  NR5   0  -0.610  -0.1881   0.5777   0.5900
 JV0  C6    C  CR6   0   0.232   0.7424   1.6213   0.3596
 JV0  C24   C  CR16  0  -0.236   1.7090   1.9113   1.3133
 JV0  C25   C  CR16  0  -0.305   2.6244   2.9249   1.0798
 JV0  C3    C  CR6   0   0.135   2.5876   3.6730  -0.0950
 JV0  C2    C  CH2   0  -0.504   3.6118   4.7414  -0.3570
 JV0  C1    C  CH3   0  -0.653   4.8816   4.1722  -0.9882
 JV0  C4    C  CR16  0  -0.315   1.6050   3.3742  -1.0355
 JV0  C5    C  CR16  0  -0.247   0.6903   2.3547  -0.8174
 JV0  C9    C  CR5   0  -0.011  -2.0796  -0.4357   1.1617
 JV0  C10   C  CH2   0  -0.367  -3.5146  -0.6846   1.5043
 JV0  N2    N  NT    0  -0.398  -4.4260  -0.2386   0.4625
 JV0  C11   C  CH2   0  -0.258  -5.7960  -0.1918   0.9320
 JV0  C12   C  CH2   0  -0.566  -6.7013   0.5469  -0.0356
 JV0  S1    S  S2    0  -0.047  -6.7876  -0.2819  -1.6452
 JV0  C13   C  CH2   0  -0.564  -5.0000  -0.3865  -1.9270
 JV0  C14   C  CH2   0  -0.256  -4.2767  -1.0148  -0.7515
 JV0  C15   C  CR15  0  -0.440  -1.0457  -1.3989   1.0951
 JV0  C16   C  CR5   0   0.308   0.1199  -0.7573   0.7461
 JV0  C17   C  CR6   0   0.059   1.4426  -1.3374   0.5300
 JV0  C18   C  CR16  0  -0.308   1.8537  -2.4109   1.3281
 JV0  C19   C  CR16  0  -0.250   3.0760  -3.0262   1.1380
 JV0  C23   C  CR16  0  -0.277   2.3181  -0.9087  -0.4684
 JV0  C22   C  CR16  0  -0.247   3.5524  -1.5128  -0.6590
 JV0  C20   C  CR6   0  -0.127   3.9477  -2.5797   0.1422
 JV0  S2    S  S2    0   0.039   5.4862  -3.4202  -0.0082
 JV0  C21   C  CH3   0  -0.795   6.3123  -2.5608  -1.3582
 JV0  H81C  H  HCH3  0   0.243  -2.2502   2.5268  -0.1875
 JV0  H82C  H  HCH3  0   0.261  -3.1522   2.0660   1.2396
 JV0  H83C  H  HCH3  0   0.240  -1.5806   2.8593   1.4046
 JV0  H24   H  HCR6  0   0.264   1.7430   1.3445   2.2350
 JV0  H5    H  HCR6  0   0.267  -0.0565   2.1235  -1.5666
 JV0  H25   H  HCR6  0   0.251   3.3749   3.1438   1.8306
 JV0  H21C  H  HCH2  0   0.242   3.1878   5.5044  -1.0135
 JV0  H22C  H  HCH2  0   0.241   3.8672   5.2417   0.5801
 JV0  H4    H  HCR6  0   0.252   1.5560   3.9432  -1.9565
 JV0  H11C  H  HCH3  0   0.226   5.3364   3.4195  -0.3430
 JV0  H12C  H  HCH3  0   0.225   4.6677   3.7031  -1.9493
 JV0  H13C  H  HCH3  0   0.232   5.6182   4.9585  -1.1569
 JV0  H101  H  HCH2  0   0.211  -3.6455  -1.7554   1.7365
 JV0  H102  H  HCH2  0   0.237  -3.7817  -0.1466   2.4196
 JV0  H15   H  HCR5  0   0.244  -1.1550  -2.4629   1.2466
 JV0  H111  H  HCH2  0   0.196  -6.2104  -1.1964   1.1233
 JV0  H112  H  HCH2  0   0.240  -5.8096   0.3448   1.8850
 JV0  H141  H  HCH2  0   0.251  -3.2134  -1.0646  -0.9971
 JV0  H142  H  HCH2  0   0.193  -4.6256  -2.0537  -0.6185
 JV0  H121  H  HCH2  0   0.276  -7.7186   0.5876   0.3540
 JV0  H122  H  HCH2  0   0.260  -6.3481   1.5710  -0.1723
 JV0  H131  H  HCH2  0   0.275  -4.8577  -0.9910  -2.8230
 JV0  H132  H  HCH2  0   0.260  -4.6026   0.6113  -2.1222
 JV0  H18   H  HCR6  0   0.252   1.2081  -2.7663   2.1215
 JV0  H23   H  HCR6  0   0.256   2.0431  -0.0987  -1.1300
 JV0  H19   H  HCR6  0   0.262   3.3569  -3.8538   1.7787
 JV0  H22   H  HCR6  0   0.263   4.1902  -1.1379  -1.4476
 JV0  H211  H  HCH3  0   0.274   5.7655  -2.6576  -2.2944
 JV0  H212  H  HCH3  0   0.274   6.4729  -1.5091  -1.1275
 JV0  H213  H  HCH3  0   0.294   7.2809  -3.0434  -1.4722

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
 JV0  C8   C7    single    1.487  0.020  1.487
 JV0  C7   N1    aromatic  1.373  0.020  1.373
 JV0  C7   C9    aromatic  1.376  0.020  1.376
 JV0  N1   C6    single    1.417  0.020  1.417
 JV0  N1   C16   aromatic  1.379  0.020  1.379
 JV0  C6   C24   aromatic  1.389  0.020  1.389
 JV0  C6   C5    aromatic  1.388  0.020  1.388
 JV0  C24  C25   aromatic  1.386  0.020  1.386
 JV0  C25  C3    aromatic  1.393  0.020  1.393
 JV0  C3   C2    single    1.503  0.020  1.503
 JV0  C3   C4    aromatic  1.393  0.020  1.393
 JV0  C2   C1    single    1.528  0.020  1.528
 JV0  C4   C5    aromatic  1.387  0.020  1.387
 JV0  C9   C10   single    1.496  0.020  1.496
 JV0  C9   C15   aromatic  1.415  0.020  1.415
 JV0  C10  N2    single    1.454  0.020  1.454
 JV0  N2   C11   single    1.449  0.020  1.449
 JV0  N2   C14   single    1.449  0.020  1.449
 JV0  C11  C12   single    1.517  0.020  1.517
 JV0  C12  S1    single    1.812  0.020  1.812
 JV0  S1   C13   single    1.813  0.020  1.813
 JV0  C13  C14   single    1.517  0.020  1.517
 JV0  C15  C16   aromatic  1.375  0.020  1.375
 JV0  C16  C17   single    1.460  0.020  1.460
 JV0  C17  C18   aromatic  1.399  0.020  1.399
 JV0  C17  C23   aromatic  1.395  0.020  1.395
 JV0  C18  C19   aromatic  1.382  0.020  1.382
 JV0  C19  C20   aromatic  1.397  0.020  1.397
 JV0  C23  C22   aromatic  1.387  0.020  1.387
 JV0  C22  C20   aromatic  1.392  0.020  1.392
 JV0  C20  S2    single    1.759  0.020  1.759
 JV0  S2   C21   single    1.801  0.020  1.801
 JV0  C8   H81C  single    0.970  0.020  1.090
 JV0  C8   H82C  single    0.970  0.020  1.090
 JV0  C8   H83C  single    0.970  0.020  1.090
 JV0  C24  H24   single    0.930  0.020  1.080
 JV0  C5   H5    single    0.930  0.020  1.080
 JV0  C25  H25   single    0.930  0.020  1.080
 JV0  C2   H21C  single    0.970  0.020  1.090
 JV0  C2   H22C  single    0.970  0.020  1.090
 JV0  C4   H4    single    0.930  0.020  1.080
 JV0  C1   H11C  single    0.970  0.020  1.090
 JV0  C1   H12C  single    0.970  0.020  1.090
 JV0  C1   H13C  single    0.970  0.020  1.090
 JV0  C10  H101  single    0.970  0.020  1.090
 JV0  C10  H102  single    0.970  0.020  1.090
 JV0  C15  H15   single    0.930  0.020  1.080
 JV0  C11  H111  single    0.970  0.020  1.090
 JV0  C11  H112  single    0.970  0.020  1.090
 JV0  C14  H141  single    0.970  0.020  1.090
 JV0  C14  H142  single    0.970  0.020  1.090
 JV0  C12  H121  single    0.970  0.020  1.090
 JV0  C12  H122  single    0.970  0.020  1.090
 JV0  C13  H131  single    0.970  0.020  1.090
 JV0  C13  H132  single    0.970  0.020  1.090
 JV0  C18  H18   single    0.930  0.020  1.080
 JV0  C23  H23   single    0.930  0.020  1.080
 JV0  C19  H19   single    0.930  0.020  1.080
 JV0  C22  H22   single    0.930  0.020  1.080
 JV0  C21  H211  single    0.970  0.020  1.090
 JV0  C21  H212  single    0.970  0.020  1.090
 JV0  C21  H213  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
 JV0  H83C  C8   H82C  108.50  3.000
 JV0  H83C  C8   H81C  107.33  3.000
 JV0  H82C  C8   H81C  106.86  3.000
 JV0  H83C  C8   C7    112.08  3.000
 JV0  H82C  C8   C7    109.27  3.000
 JV0  H81C  C8   C7    112.59  3.000
 JV0  C9    C7   N1    107.74  3.000
 JV0  C9    C7   C8    129.38  3.000
 JV0  N1    C7   C8    122.84  3.000
 JV0  C16   N1   C6    125.79  3.000
 JV0  C16   N1   C7    109.87  3.000
 JV0  C6    N1   C7    123.92  3.000
 JV0  C5    C6   C24   119.89  3.000
 JV0  C5    C6   N1    120.16  3.000
 JV0  C24   C6   N1    119.95  3.000
 JV0  H24   C24  C25   120.37  3.000
 JV0  H24   C24  C6    119.82  3.000
 JV0  C25   C24  C6    119.80  3.000
 JV0  H25   C25  C3    119.60  3.000
 JV0  H25   C25  C24   119.25  3.000
 JV0  C3    C25  C24   121.16  3.000
 JV0  C4    C3   C2    121.04  3.000
 JV0  C4    C3   C25   118.22  3.000
 JV0  C2    C3   C25   120.71  3.000
 JV0  H22C  C2   H21C  106.65  3.000
 JV0  H22C  C2   C1    109.31  3.000
 JV0  H21C  C2   C1    109.55  3.000
 JV0  H22C  C2   C3    109.59  3.000
 JV0  H21C  C2   C3    109.68  3.000
 JV0  C1    C2   C3    111.93  3.000
 JV0  H13C  C1   H12C  107.84  3.000
 JV0  H13C  C1   H11C  107.90  3.000
 JV0  H12C  C1   H11C  107.83  3.000
 JV0  H13C  C1   C2    110.89  3.000
 JV0  H12C  C1   C2    111.18  3.000
 JV0  H11C  C1   C2    111.05  3.000
 JV0  H4    C4   C5    119.32  3.000
 JV0  H4    C4   C3    119.55  3.000
 JV0  C5    C4   C3    121.12  3.000
 JV0  H5    C5   C4    120.20  3.000
 JV0  H5    C5   C6    119.99  3.000
 JV0  C4    C5   C6    119.81  3.000
 JV0  C15   C9   C10   126.76  3.000
 JV0  C15   C9   C7    107.19  3.000
 JV0  C10   C9   C7    126.05  3.000
 JV0  H102  C10  H101  105.78  3.000
 JV0  H102  C10  N2    107.17  3.000
 JV0  H101  C10  N2    111.97  3.000
 JV0  H102  C10  C9    110.10  3.000
 JV0  H101  C10  C9    108.87  3.000
 JV0  N2    C10  C9    112.71  3.000
 JV0  C14   N2   C11   112.72  3.000
 JV0  C14   N2   C10   111.80  3.000
 JV0  C11   N2   C10   111.74  3.000
 JV0  H112  C11  H111  106.92  3.000
 JV0  H112  C11  C12   108.03  3.000
 JV0  H111  C11  C12   109.26  3.000
 JV0  H112  C11  N2    108.05  3.000
 JV0  H111  C11  N2    112.45  3.000
 JV0  C12   C11  N2    111.92  3.000
 JV0  H122  C12  H121  108.15  3.000
 JV0  H122  C12  S1    109.46  3.000
 JV0  H121  C12  S1    106.86  3.000
 JV0  H122  C12  C11   110.09  3.000
 JV0  H121  C12  C11   110.31  3.000
 JV0  S1    C12  C11   111.85  3.000
 JV0  C13   S1   C12    96.75  3.000
 JV0  H132  C13  H131  108.20  3.000
 JV0  H132  C13  C14   110.09  3.000
 JV0  H131  C13  C14   110.19  3.000
 JV0  H132  C13  S1    109.52  3.000
 JV0  H131  C13  S1    106.77  3.000
 JV0  C14   C13  S1    111.95  3.000
 JV0  H142  C14  H141  106.96  3.000
 JV0  H142  C14  C13   109.42  3.000
 JV0  H141  C14  C13   107.99  3.000
 JV0  H142  C14  N2    111.76  3.000
 JV0  H141  C14  N2    108.25  3.000
 JV0  C13   C14  N2    112.24  3.000
 JV0  H15   C15  C16   125.51  3.000
 JV0  H15   C15  C9    126.16  3.000
 JV0  C16   C15  C9    108.28  3.000
 JV0  C17   C16  C15   128.30  3.000
 JV0  C17   C16  N1    124.76  3.000
 JV0  C15   C16  N1    106.92  3.000
 JV0  C23   C17  C18   117.35  3.000
 JV0  C23   C17  C16   123.51  3.000
 JV0  C18   C17  C16   119.10  3.000
 JV0  H18   C18  C19   118.83  3.000
 JV0  H18   C18  C17   119.63  3.000
 JV0  C19   C18  C17   121.54  3.000
 JV0  H19   C19  C20   120.26  3.000
 JV0  H19   C19  C18   119.21  3.000
 JV0  C20   C19  C18   120.52  3.000
 JV0  H23   C23  C22   117.93  3.000
 JV0  H23   C23  C17   120.56  3.000
 JV0  C22   C23  C17   121.51  3.000
 JV0  H22   C22  C20   121.21  3.000
 JV0  H22   C22  C23   118.29  3.000
 JV0  C20   C22  C23   120.50  3.000
 JV0  S2    C20  C22   124.43  3.000
 JV0  S2    C20  C19   117.00  3.000
 JV0  C22   C20  C19   118.57  3.000
 JV0  C21   S2   C20   103.72  3.000
 JV0  H213  C21  H212  108.62  3.000
 JV0  H213  C21  H211  108.51  3.000
 JV0  H212  C21  H211  110.02  3.000
 JV0  H213  C21  S2    105.98  3.000
 JV0  H212  C21  S2    111.71  3.000
 JV0  H211  C21  S2    111.83  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
 JV0  CONST_03  C15   C16  N1   C7      0.00   0.0  0
 JV0  CONST_04  C17   C16  N1   C7    180.00   0.0  0
 JV0  CONST_05  C16   C15  C9   C7      0.00   0.0  0
 JV0  CONST_06  C15   C9   C7   N1      0.00   0.0  0
 JV0  CONST_07  C25   C24  C6   N1    180.00   0.0  0
 JV0  CONST_08  C4    C5   C6   N1    180.00   0.0  0
 JV0  CONST_09  C9    C15  C16  N1      0.00   0.0  0
 JV0  CONST_12  C9    C7   N1   C6    180.00   0.0  0
 JV0  CONST_13  C15   C16  N1   C6    180.00   0.0  0
 JV0  CONST_14  C17   C16  N1   C6      0.00   0.0  0
 JV0  CONST_15  C3    C25  C24  C6      0.00   0.0  0
 JV0  CONST_16  C3    C4   C5   C6      0.00   0.0  0
 JV0  CONST_18  C4    C5   C6   C24     0.00   0.0  0
 JV0  CONST_19  C4    C3   C25  C24     0.00   0.0  0
 JV0  CONST_20  C5    C6   C24  C25     0.00   0.0  0
 JV0  CONST_21  C5    C4   C3   C25     0.00   0.0  0
 JV0  CONST_23  C16   N1   C7   C9      0.00   0.0  0
 JV0  CONST_24  C17   C16  C15  C9    180.00   0.0  0
 JV0  CONST_27  C19   C18  C17  C16   180.00   0.0  0
 JV0  CONST_28  C22   C23  C17  C16   180.00   0.0  0
 JV0  CONST_29  C20   C19  C18  C17     0.00   0.0  0
 JV0  CONST_30  C20   C22  C23  C17     0.00   0.0  0
 JV0  CONST_31  C22   C23  C17  C18     0.00   0.0  0
 JV0  CONST_32  C22   C20  C19  C18     0.00   0.0  0
 JV0  CONST_33  C23   C17  C18  C19     0.00   0.0  0
 JV0  CONST_34  C23   C22  C20  C19     0.00   0.0  0
 JV0  CONST_35  C6    N1   C7   C8      0.00   0.0  0
 JV0  CONST_36  C16   N1   C7   C8    180.00   0.0  0
 JV0  CONST_37  C15   C9   C7   C8    180.00   0.0  0
 JV0  CONST_38  C10   C9   C7   N1    180.00   0.0  0
 JV0  CONST_39  C2    C3   C25  C24   180.00   0.0  0
 JV0  CONST_40  C5    C4   C3   C2    180.00   0.0  0
 JV0  CONST_41  C16   C15  C9   C10   180.00   0.0  0
 JV0  CONST_42  S2    C20  C19  C18   180.00   0.0  0
 JV0  CONST_43  S2    C20  C22  C23   180.00   0.0  0
 JV0  CONST_44  H15   C15  C9   C7    180.00   0.0  0
 JV0  CONST_45  H24   C24  C6   N1      0.00   0.0  0
 JV0  CONST_46  H5    C5   C6   N1      0.00   0.0  0
 JV0  CONST_47  H25   C25  C24  C6    180.00   0.0  0
 JV0  CONST_48  H4    C4   C5   C6    180.00   0.0  0
 JV0  CONST_49  H18   C18  C17  C16     0.00   0.0  0
 JV0  CONST_50  H23   C23  C17  C16     0.00   0.0  0
 JV0  CONST_51  H19   C19  C18  C17   180.00   0.0  0
 JV0  CONST_52  H22   C22  C23  C17   180.00   0.0  0
 JV0  Var_01    S1    C12  C11  N2     62.59  30.0  1
 JV0  Var_02    S1    C13  C14  N2    -61.91  30.0  1
 JV0  Var_03    C13   C14  N2   C11    65.10  30.0  1
 JV0  Var_04    C14   N2   C11  C12   -65.39  30.0  1
 JV0  Var_05    C14   C13  S1   C12    52.12  30.0  1
 JV0  Var_06    N2    C10  C9   C7     56.98  30.0  2
 JV0  Var_07    C11   N2   C10  C9   -166.35  30.0  3
 JV0  Var_08    C1    C2   C3   C25    85.38  30.0  2
 JV0  Var_09    H81C  C8   C7   N1     71.97  30.0  2
 JV0  Var_10    H11C  C1   C2   C3    -59.17  30.0  3
 JV0  Var_11    H211  C21  S2   C20   -62.85  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
 JV0  plan-1  C8   0.020
 JV0  plan-1  C7   0.020
 JV0  plan-1  N1   0.020
 JV0  plan-1  C6   0.020
 JV0  plan-1  C9   0.020
 JV0  plan-1  C10  0.020
 JV0  plan-1  C15  0.020
 JV0  plan-1  C16  0.020
 JV0  plan-1  C17  0.020
 JV0  plan-1  H15  0.020
 JV0  plan-2  N1   0.020
 JV0  plan-2  C6   0.020
 JV0  plan-2  C24  0.020
 JV0  plan-2  C25  0.020
 JV0  plan-2  C3   0.020
 JV0  plan-2  C2   0.020
 JV0  plan-2  C4   0.020
 JV0  plan-2  C5   0.020
 JV0  plan-2  H24  0.020
 JV0  plan-2  H5   0.020
 JV0  plan-2  H25  0.020
 JV0  plan-2  H4   0.020
 JV0  plan-3  C16  0.020
 JV0  plan-3  C17  0.020
 JV0  plan-3  C18  0.020
 JV0  plan-3  C19  0.020
 JV0  plan-3  C23  0.020
 JV0  plan-3  C22  0.020
 JV0  plan-3  C20  0.020
 JV0  plan-3  S2   0.020
 JV0  plan-3  H18  0.020
 JV0  plan-3  H23  0.020
 JV0  plan-3  H19  0.020
 JV0  plan-3  H22  0.020

