# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:57:47 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-cyclohexyl-4-methyl-5-phenyl-4H-thieno[3,2-b]pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2cc(sc2c(C3CCCCC3)c1c4ccccc4)C(O)=O
#
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
 VGC  VGC  '6-cyclohexyl-4-methyl-5-phenyl-4H-thieno[3,2-b]pyrrole-2-carboxylic acid'  ligand  44  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VGC
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
 VGC  C15   C  CH2    0  -0.404  -0.7066  -2.3705   1.3555
 VGC  C18   C  CH2    0  -0.435  -1.3798  -3.7383   1.4161
 VGC  C19   C  CH2    0  -0.428  -1.0997  -4.5553   0.1598
 VGC  C17   C  CH2    0  -0.434  -1.5101  -3.7923  -1.0951
 VGC  C16   C  CH2    0  -0.409  -0.8408  -2.4233  -1.1598
 VGC  C14   C  CH1    0  -0.371  -1.1140  -1.5918   0.0990
 VGC  C5    C  CR5    0   0.038  -0.4395  -0.2585   0.0267
 VGC  C2    C  CR55   0  -0.251   0.9532  -0.0006   0.0376
 VGC  S1    S  S2     0   0.144   2.4701  -0.8209   0.0792
 VGC  C3    C  CR5    0  -0.333   3.3314   0.6940   0.0131
 VGC  C6    C  C      0   0.395   4.8305   0.6452   0.0149
 VGC  O1    O  OC    -1  -0.602   5.3263  -0.4983   0.0632
 VGC  O2    O  O      0  -0.589   5.4261   1.7369  -0.0330
 VGC  C4    C  CR15   0  -0.253   2.5029   1.7768  -0.0308
 VGC  C1    C  CR55   0   0.380   1.1449   1.3717  -0.0085
 VGC  N1    N  NR5    0  -0.569  -0.0752   1.9781  -0.0252
 VGC  C20   C  CH3    0  -0.535  -0.2693   3.3809  -0.3122
 VGC  C7    C  CR5    0   0.264  -1.0387   0.9892  -0.0238
 VGC  C8    C  CR6    0   0.029  -2.4741   1.2949  -0.0380
 VGC  C9    C  CR16   0  -0.305  -3.0555   2.0899   0.9527
 VGC  C10   C  CR16   0  -0.244  -4.4172   2.3531   0.9396
 VGC  C11   C  CR16   0  -0.262  -5.2235   1.8173  -0.0570
 VGC  C12   C  CR16   0  -0.243  -4.6579   1.0197  -1.0429
 VGC  C13   C  CR16   0  -0.297  -3.2934   0.7663  -1.0365
 VGC  H151  H  HCH2   0   0.229  -0.9576  -1.7865   2.2445
 VGC  H152  H  HCH2   0   0.205   0.3810  -2.5053   1.3694
 VGC  H181  H  HCH2   0   0.226  -1.0407  -4.2781   2.3038
 VGC  H182  H  HCH2   0   0.209  -2.4613  -3.6054   1.5301
 VGC  H14   H  HCH1   0   0.225  -2.1953  -1.4237   0.1579
 VGC  H191  H  HCH2   0   0.208  -0.0297  -4.7852   0.1091
 VGC  H192  H  HCH2   0   0.226  -1.6215  -5.5143   0.2075
 VGC  H171  H  HCH2   0   0.226  -1.2619  -4.3698  -1.9890
 VGC  H172  H  HCH2   0   0.209  -2.5980  -3.6631  -1.1021
 VGC  H161  H  HCH2   0   0.207   0.2411  -2.5532  -1.2811
 VGC  H162  H  HCH2   0   0.228  -1.1868  -1.8762  -2.0412
 VGC  H4    H  HCR5   0   0.261   2.8613   2.7955  -0.0763
 VGC  H201  H  HCH3   0   0.249  -0.2571   3.5743  -1.3859
 VGC  H202  H  HCH3   0   0.261  -1.2150   3.7286   0.0920
 VGC  H203  H  HCH3   0   0.258   0.5262   3.9578   0.1550
 VGC  H9    H  HCR6   0   0.260  -2.4410   2.4930   1.7489
 VGC  H13   H  HCR6   0   0.255  -2.8533   0.1622  -1.8203
 VGC  H10   H  HCR6   0   0.258  -4.8514   2.9693   1.7162
 VGC  H11   H  HCR6   0   0.258  -6.2865   2.0206  -0.0642
 VGC  H12   H  HCR6   0   0.258  -5.2774   0.5994  -1.8246

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
 VGC  C15  C18   single    1.526  0.020  1.526
 VGC  C15  C14   single    1.533  0.020  1.533
 VGC  C18  C19   single    1.525  0.020  1.525
 VGC  C19  C17   single    1.525  0.020  1.525
 VGC  C17  C16   single    1.525  0.020  1.525
 VGC  C16  C14   single    1.533  0.020  1.533
 VGC  C14  C5    single    1.496  0.020  1.496
 VGC  C5   C2    aromatic  1.416  0.020  1.416
 VGC  C5   C7    aromatic  1.385  0.020  1.385
 VGC  C2   S1    aromatic  1.725  0.020  1.725
 VGC  C2   C1    aromatic  1.386  0.020  1.386
 VGC  S1   C3    aromatic  1.744  0.020  1.744
 VGC  C3   C6    single    1.500  0.020  1.500
 VGC  C3   C4    aromatic  1.364  0.020  1.364
 VGC  C6   O1    deloc     1.247  0.020  1.247
 VGC  C6   O2    deloc     1.244  0.020  1.244
 VGC  C4   C1    aromatic  1.417  0.020  1.417
 VGC  C1   N1    aromatic  1.363  0.020  1.363
 VGC  N1   C20   single    1.445  0.020  1.445
 VGC  N1   C7    aromatic  1.381  0.020  1.381
 VGC  C7   C8    single    1.468  0.020  1.468
 VGC  C8   C9    aromatic  1.397  0.020  1.397
 VGC  C8   C13   aromatic  1.396  0.020  1.396
 VGC  C9   C10   aromatic  1.387  0.020  1.387
 VGC  C10  C11   aromatic  1.389  0.020  1.389
 VGC  C11  C12   aromatic  1.389  0.020  1.389
 VGC  C12  C13   aromatic  1.388  0.020  1.388
 VGC  C15  H151  single    0.970  0.020  1.090
 VGC  C15  H152  single    0.970  0.020  1.090
 VGC  C18  H181  single    0.970  0.020  1.090
 VGC  C18  H182  single    0.970  0.020  1.090
 VGC  C14  H14   single    0.970  0.020  1.090
 VGC  C19  H191  single    0.970  0.020  1.090
 VGC  C19  H192  single    0.970  0.020  1.090
 VGC  C17  H171  single    0.970  0.020  1.090
 VGC  C17  H172  single    0.970  0.020  1.090
 VGC  C16  H161  single    0.970  0.020  1.090
 VGC  C16  H162  single    0.970  0.020  1.090
 VGC  C4   H4    single    0.930  0.020  1.080
 VGC  C20  H201  single    0.970  0.020  1.090
 VGC  C20  H202  single    0.970  0.020  1.090
 VGC  C20  H203  single    0.970  0.020  1.090
 VGC  C9   H9    single    0.930  0.020  1.080
 VGC  C13  H13   single    0.930  0.020  1.080
 VGC  C10  H10   single    0.930  0.020  1.080
 VGC  C11  H11   single    0.930  0.020  1.080
 VGC  C12  H12   single    0.930  0.020  1.080

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
 VGC  H152  C15  H151  106.46  3.000
 VGC  H152  C15  C14   109.66  3.000
 VGC  H151  C15  C14   109.52  3.000
 VGC  H152  C15  C18   109.09  3.000
 VGC  H151  C15  C18   110.21  3.000
 VGC  C14   C15  C18   111.75  3.000
 VGC  H182  C18  H181  106.36  3.000
 VGC  H182  C18  C19   109.39  3.000
 VGC  H181  C18  C19   110.35  3.000
 VGC  H182  C18  C15   109.33  3.000
 VGC  H181  C18  C15   109.76  3.000
 VGC  C19   C18  C15   111.51  3.000
 VGC  H192  C19  H191  106.51  3.000
 VGC  H192  C19  C17   110.28  3.000
 VGC  H191  C19  C17   109.26  3.000
 VGC  H192  C19  C18   110.28  3.000
 VGC  H191  C19  C18   109.27  3.000
 VGC  C17   C19  C18   111.14  3.000
 VGC  H172  C17  H171  106.41  3.000
 VGC  H172  C17  C16   109.25  3.000
 VGC  H171  C17  C16   109.88  3.000
 VGC  H172  C17  C19   109.36  3.000
 VGC  H171  C17  C19   110.34  3.000
 VGC  C16   C17  C19   111.46  3.000
 VGC  H162  C16  H161  106.40  3.000
 VGC  H162  C16  C14   109.52  3.000
 VGC  H161  C16  C14   109.33  3.000
 VGC  H162  C16  C17   110.14  3.000
 VGC  H161  C16  C17   109.35  3.000
 VGC  C14   C16  C17   111.95  3.000
 VGC  H14   C14  C5    108.11  3.000
 VGC  H14   C14  C16   107.65  3.000
 VGC  C5    C14  C16   111.31  3.000
 VGC  H14   C14  C15   107.22  3.000
 VGC  C5    C14  C15   111.87  3.000
 VGC  C16   C14  C15   110.49  3.000
 VGC  C7    C5   C2    105.17  3.000
 VGC  C7    C5   C14   127.56  3.000
 VGC  C2    C5   C14   127.25  3.000
 VGC  C1    C2   S1    110.48  3.000
 VGC  C1    C2   C5    108.42  3.000
 VGC  S1    C2   C5    141.10  3.000
 VGC  C3    S1   C2     91.17  3.000
 VGC  C4    C3   C6    129.26  3.000
 VGC  C4    C3   S1    113.00  3.000
 VGC  C6    C3   S1    117.74  3.000
 VGC  O2    C6   O1    127.99  3.000
 VGC  O2    C6   C3    116.73  3.000
 VGC  O1    C6   C3    115.28  3.000
 VGC  H4    C4   C1    126.00  3.000
 VGC  H4    C4   C3    123.24  3.000
 VGC  C1    C4   C3    110.77  3.000
 VGC  N1    C1   C4    136.94  3.000
 VGC  N1    C1   C2    108.48  3.000
 VGC  C4    C1   C2    114.58  3.000
 VGC  C7    N1   C20   127.00  3.000
 VGC  C7    N1   C1    107.83  3.000
 VGC  C20   N1   C1    123.69  3.000
 VGC  H203  C20  H202  107.89  3.000
 VGC  H203  C20  H201  108.69  3.000
 VGC  H202  C20  H201  108.62  3.000
 VGC  H203  C20  N1    109.34  3.000
 VGC  H202  C20  N1    110.73  3.000
 VGC  H201  C20  N1    111.47  3.000
 VGC  C8    C7   N1    122.23  3.000
 VGC  C8    C7   C5    127.67  3.000
 VGC  N1    C7   C5    110.08  3.000
 VGC  C13   C8   C9    118.59  3.000
 VGC  C13   C8   C7    120.14  3.000
 VGC  C9    C8   C7    121.25  3.000
 VGC  H9    C9   C10   119.55  3.000
 VGC  H9    C9   C8    119.79  3.000
 VGC  C10   C9   C8    120.66  3.000
 VGC  H10   C10  C11   120.09  3.000
 VGC  H10   C10  C9    119.68  3.000
 VGC  C11   C10  C9    120.22  3.000
 VGC  H11   C11  C12   120.22  3.000
 VGC  H11   C11  C10   120.15  3.000
 VGC  C12   C11  C10   119.63  3.000
 VGC  H12   C12  C13   119.68  3.000
 VGC  H12   C12  C11   120.18  3.000
 VGC  C13   C12  C11   120.14  3.000
 VGC  H13   C13  C12   119.87  3.000
 VGC  H13   C13  C8    119.37  3.000
 VGC  C12   C13  C8    120.75  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
 VGC  CONST_01  C3    S1   C2   C5   180.00   0.0  0
 VGC  CONST_02  C4    C1   C2   C5   180.00   0.0  0
 VGC  CONST_03  N1    C1   C2   C5     0.00   0.0  0
 VGC  CONST_04  C1    N1   C7   C5     0.00   0.0  0
 VGC  CONST_07  N1    C7   C5   C2     0.00   0.0  0
 VGC  CONST_08  C8    C7   C5   C2   180.00   0.0  0
 VGC  CONST_09  C4    C3   S1   C2     0.00   0.0  0
 VGC  CONST_10  C3    C4   C1   C2     0.00   0.0  0
 VGC  CONST_11  C7    N1   C1   C2     0.00   0.0  0
 VGC  CONST_12  C7    C5   C2   S1   180.00   0.0  0
 VGC  CONST_13  C4    C1   C2   S1     0.00   0.0  0
 VGC  CONST_14  N1    C1   C2   S1   180.00   0.0  0
 VGC  CONST_15  C1    C4   C3   S1     0.00   0.0  0
 VGC  CONST_16  C1    C2   S1   C3     0.00   0.0  0
 VGC  CONST_17  N1    C1   C4   C3   180.00   0.0  0
 VGC  CONST_18  C7    N1   C1   C4   180.00   0.0  0
 VGC  CONST_19  C7    C5   C2   C1     0.00   0.0  0
 VGC  CONST_20  C8    C7   N1   C1   180.00   0.0  0
 VGC  CONST_23  C10   C9   C8   C7   180.00   0.0  0
 VGC  CONST_24  C12   C13  C8   C7   180.00   0.0  0
 VGC  CONST_25  C11   C10  C9   C8     0.00   0.0  0
 VGC  CONST_26  C11   C12  C13  C8     0.00   0.0  0
 VGC  CONST_27  C12   C13  C8   C9     0.00   0.0  0
 VGC  CONST_28  C12   C11  C10  C9     0.00   0.0  0
 VGC  CONST_29  C13   C8   C9   C10    0.00   0.0  0
 VGC  CONST_30  C13   C12  C11  C10    0.00   0.0  0
 VGC  CONST_31  S1    C2   C5   C14    0.00   0.0  0
 VGC  CONST_32  C1    C2   C5   C14  180.00   0.0  0
 VGC  CONST_33  N1    C7   C5   C14  180.00   0.0  0
 VGC  CONST_34  C8    C7   C5   C14    0.00   0.0  0
 VGC  CONST_35  C20   N1   C7   C5   180.00   0.0  0
 VGC  CONST_36  C6    C3   S1   C2   180.00   0.0  0
 VGC  CONST_37  C20   N1   C1   C2   180.00   0.0  0
 VGC  CONST_38  C1    C4   C3   C6   180.00   0.0  0
 VGC  CONST_39  C20   N1   C1   C4     0.00   0.0  0
 VGC  CONST_40  C8    C7   N1   C20    0.00   0.0  0
 VGC  CONST_41  H4    C4   C1   C2   180.00   0.0  0
 VGC  CONST_42  H9    C9   C8   C7     0.00   0.0  0
 VGC  CONST_43  H13   C13  C8   C7     0.00   0.0  0
 VGC  CONST_44  H10   C10  C9   C8   180.00   0.0  0
 VGC  CONST_45  H12   C12  C13  C8   180.00   0.0  0
 VGC  CONST_46  H11   C11  C10  C9   180.00   0.0  0
 VGC  Var_01    C17   C19  C18  C15  -55.24  30.0  1
 VGC  Var_02    C16   C17  C19  C18   55.04  30.0  1
 VGC  Var_03    C14   C15  C18  C19   55.44  30.0  1
 VGC  Var_04    C14   C16  C17  C19  -55.16  30.0  1
 VGC  Var_05    O1    C6   C3   S1     0.07  30.0  2
 VGC  Var_06    H201  C20  N1   C1    80.93  30.0  2

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
 VGC  chir_01  C14  C15  C16  C5  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
 VGC  plan-1  C7   0.020
 VGC  plan-1  C8   0.020
 VGC  plan-1  C9   0.020
 VGC  plan-1  C10  0.020
 VGC  plan-1  C11  0.020
 VGC  plan-1  C12  0.020
 VGC  plan-1  C13  0.020
 VGC  plan-1  H9   0.020
 VGC  plan-1  H13  0.020
 VGC  plan-1  H10  0.020
 VGC  plan-1  H11  0.020
 VGC  plan-1  H12  0.020
 VGC  plan-2  C14  0.020
 VGC  plan-2  C5   0.020
 VGC  plan-2  C2   0.020
 VGC  plan-2  S1   0.020
 VGC  plan-2  C3   0.020
 VGC  plan-2  C6   0.020
 VGC  plan-2  C4   0.020
 VGC  plan-2  C1   0.020
 VGC  plan-2  N1   0.020
 VGC  plan-2  C20  0.020
 VGC  plan-2  C7   0.020
 VGC  plan-2  C8   0.020
 VGC  plan-2  H4   0.020
 VGC  plan-3  C3   0.020
 VGC  plan-3  C6   0.020
 VGC  plan-3  O1   0.020
 VGC  plan-3  O2   0.020

