# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:30:27 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: ethyl 2-({N-[2-(1H-indol-3-yl)ethyl]glycyl}amino)-4-phenylthiophene-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1c(NC(=O)CNCCc2c[nH]c3ccccc23)scc1c4ccccc4
#
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
 RB4  RB4  'ethyl 2-({N-[2-(1H-indol-3-yl)ethyl]glycyl}amino)-4-phenylthiophene-3-carboxylate'  ligand  57  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RB4
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
 RB4  C1    C  CR5   0  -0.139    3.1991   0.0080  -0.1017
 RB4  N1    N  NH1   0  -0.726    0.7664   0.2647  -0.1694
 RB4  O1    O  O     0  -0.484    2.1194  -2.0969  -0.0050
 RB4  S1    S  S2    0   0.284    2.3713   2.4485  -0.2393
 RB4  C2    C  C     0   0.580    3.1450  -1.4549  -0.1446
 RB4  N2    N  NH1   0  -0.593   -2.7890   1.0616  -0.4474
 RB4  O2    O  O2    0  -0.441    4.3173  -2.0025  -0.3769
 RB4  C3    C  CH2   0  -0.176    4.4287  -3.4319  -0.4064
 RB4  N3    N  NR15  0  -0.680   -8.3656  -0.5024  -1.5195
 RB4  O3    O  O     0  -0.440   -0.3129   2.2346  -0.3240
 RB4  C4    C  CH3   0  -0.673    5.8709  -3.7620  -0.7050
 RB4  C5    C  CR5   0   0.208    4.3779   0.8334  -0.1030
 RB4  C6    C  CR6   0   0.078    5.7765   0.3792   0.0333
 RB4  C7    C  CR15  0  -0.553    4.0659   2.1508  -0.1814
 RB4  C8    C  CR5   0   0.124    2.0411   0.7629  -0.1541
 RB4  C9    C  C     0   0.536   -0.3613   1.0237  -0.2533
 RB4  C10   C  CH2   0  -0.387   -1.6434   0.2237  -0.2212
 RB4  C11   C  CH2   0  -0.236   -4.0352   0.3215  -0.4602
 RB4  C12   C  CH2   0  -0.540   -5.2050   1.2496  -0.7744
 RB4  C13   C  CR5   0   0.019   -6.5169   0.5399  -0.7966
 RB4  C14   C  CR16  0  -0.267    6.1997  -0.2848   1.1835
 RB4  C15   C  CR16  0  -0.221    7.5231  -0.6644   1.3308
 RB4  C16   C  CR16  0  -0.247    8.4451  -0.3884   0.3280
 RB4  C17   C  CR16  0  -0.222    8.0341   0.2771  -0.8167
 RB4  C18   C  CR16  0  -0.282    6.7070   0.6602  -0.9616
 RB4  C19   C  CR56  0   0.030   -7.2797   0.1042   0.3365
 RB4  C20   C  CR56  0   0.367   -8.4342  -0.5424  -0.1582
 RB4  C21   C  CR15  0  -0.061   -7.2222   0.1465  -1.8968
 RB4  C22   C  CR16  0  -0.356   -7.1015   0.2100   1.7202
 RB4  C23   C  CR16  0  -0.250   -8.0593  -0.3187   2.5625
 RB4  C24   C  CR16  0  -0.267   -9.1993  -0.9584   2.0490
 RB4  C25   C  CR16  0  -0.282   -9.4028  -1.0790   0.6881
 RB4  HN1   H  HNH1  0   0.441    0.7048  -0.7468  -0.0924
 RB4  HN2   H  HNH1  0   0.339   -2.8309   1.7762   0.2688
 RB4  H3    H  HCH2  0   0.231    4.1223  -3.8438   0.5575
 RB4  H3A   H  HCH2  0   0.233    3.7655  -3.8393  -1.1721
 RB4  H4    H  HCH3  0   0.233    6.1731  -3.3792  -1.6792
 RB4  H4A   H  HCH3  0   0.240    6.5384  -3.3468   0.0495
 RB4  H4B   H  HCH3  0   0.230    5.9965  -4.8443  -0.7142
 RB4  H7    H  HCR5  0   0.279    4.7538   2.9819  -0.1689
 RB4  H10   H  HCH2  0   0.246   -1.6678  -0.3320   0.7313
 RB4  H10A  H  HCH2  0   0.264   -1.5937  -0.5378  -1.0064
 RB4  H11   H  HCH2  0   0.217   -3.9750  -0.4464  -1.2365
 RB4  H11A  H  HCH2  0   0.194   -4.2269  -0.2129   0.4835
 RB4  H12   H  HCH2  0   0.218   -5.2345   2.0558  -0.0323
 RB4  H12A  H  HCH2  0   0.236   -5.0210   1.7307  -1.7374
 RB4  H14   H  HCR6  0   0.224    5.4893  -0.4954   1.9728
 RB4  H15   H  HCR6  0   0.233    7.8395  -1.1731   2.2317
 RB4  H16   H  HCR6  0   0.235    9.4784  -0.6877   0.4428
 RB4  H17   H  HCR6  0   0.234    8.7454   0.4977  -1.6017
 RB4  H18   H  HCR6  0   0.229    6.3885   1.1726  -1.8607
 RB4  H21   H  HCR5  0   0.254   -6.9928   0.2823  -2.9417
 RB4  H22   H  HCR6  0   0.217   -6.2271   0.7018   2.1284
 RB4  H23   H  HCR6  0   0.228   -7.9335  -0.2416   3.6343
 RB4  H24   H  HCR6  0   0.231   -9.9341  -1.3633   2.7322
 RB4  H25   H  HCR6  0   0.231  -10.2850  -1.5704   0.2989
 RB4  HN3   H  HNR5  0   0.378   -9.0526  -0.8619  -2.1567

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
 RB4  C8   C1    aromatic  1.383  0.020  1.383
 RB4  C5   C1    aromatic  1.439  0.020  1.439
 RB4  C1   C2    single    1.464  0.020  1.464
 RB4  C9   N1    single    1.362  0.020  1.362
 RB4  N1   C8    single    1.369  0.020  1.369
 RB4  N1   HN1   single    0.860  0.020  1.020
 RB4  C2   O1    double    1.218  0.020  1.218
 RB4  S1   C7    aromatic  1.722  0.020  1.722
 RB4  S1   C8    aromatic  1.720  0.020  1.720
 RB4  C2   O2    single    1.315  0.020  1.315
 RB4  N2   C10   single    1.437  0.020  1.437
 RB4  N2   C11   single    1.449  0.020  1.449
 RB4  N2   HN2   single    0.890  0.020  1.040
 RB4  O2   C3    single    1.434  0.020  1.434
 RB4  C4   C3    single    1.509  0.020  1.509
 RB4  C3   H3    single    0.970  0.020  1.090
 RB4  C3   H3A   single    0.970  0.020  1.090
 RB4  C21  N3    aromatic  1.368  0.020  1.368
 RB4  N3   C20   aromatic  1.364  0.020  1.364
 RB4  O3   C9    double    1.214  0.020  1.214
 RB4  C4   H4    single    0.970  0.020  1.090
 RB4  C4   H4A   single    0.970  0.020  1.090
 RB4  C4   H4B   single    0.970  0.020  1.090
 RB4  C7   C5    aromatic  1.356  0.020  1.356
 RB4  C5   C6    single    1.477  0.020  1.477
 RB4  C14  C6    aromatic  1.394  0.020  1.394
 RB4  C6   C18   aromatic  1.391  0.020  1.391
 RB4  C7   H7    single    0.930  0.020  1.080
 RB4  C9   C10   single    1.512  0.020  1.512
 RB4  C10  H10   single    0.970  0.020  1.090
 RB4  C10  H10A  single    0.970  0.020  1.090
 RB4  C12  C11   single    1.526  0.020  1.526
 RB4  C11  H11   single    0.970  0.020  1.090
 RB4  C11  H11A  single    0.970  0.020  1.090
 RB4  C12  C13   single    1.492  0.020  1.492
 RB4  C12  H12   single    0.970  0.020  1.090
 RB4  C12  H12A  single    0.970  0.020  1.090
 RB4  C21  C13   aromatic  1.365  0.020  1.365
 RB4  C13  C19   aromatic  1.434  0.020  1.434
 RB4  C14  C15   aromatic  1.385  0.020  1.385
 RB4  C14  H14   single    0.930  0.020  1.080
 RB4  C15  C16   aromatic  1.390  0.020  1.390
 RB4  C15  H15   single    0.930  0.020  1.080
 RB4  C16  C17   aromatic  1.386  0.020  1.386
 RB4  C16  H16   single    0.930  0.020  1.080
 RB4  C18  C17   aromatic  1.389  0.020  1.389
 RB4  C17  H17   single    0.930  0.020  1.080
 RB4  C18  H18   single    0.930  0.020  1.080
 RB4  C19  C20   aromatic  1.413  0.020  1.413
 RB4  C19  C22   aromatic  1.399  0.020  1.399
 RB4  C20  C25   aromatic  1.394  0.020  1.394
 RB4  C21  H21   single    0.930  0.020  1.080
 RB4  C22  C23   aromatic  1.381  0.020  1.381
 RB4  C22  H22   single    0.930  0.020  1.080
 RB4  C23  C24   aromatic  1.404  0.020  1.404
 RB4  C23  H23   single    0.930  0.020  1.080
 RB4  C25  C24   aromatic  1.381  0.020  1.381
 RB4  C24  H24   single    0.930  0.020  1.080
 RB4  C25  H25   single    0.930  0.020  1.080
 RB4  N3   HN3   single    0.860  0.020  1.020

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
 RB4  C8    C1   C5   111.88  3.000
 RB4  C5    C1   C2   127.10  3.000
 RB4  C8    C1   C2   120.87  3.000
 RB4  HN1   N1   C9   120.61  3.000
 RB4  HN1   N1   C8   114.70  3.000
 RB4  C9    N1   C8   124.68  3.000
 RB4  C8    S1   C7    91.02  3.000
 RB4  O2    C2   O1   123.47  3.000
 RB4  O2    C2   C1   112.85  3.000
 RB4  O1    C2   C1   123.66  3.000
 RB4  HN2   N2   C11  109.33  3.000
 RB4  HN2   N2   C10  109.45  3.000
 RB4  C11   N2   C10  112.89  3.000
 RB4  C3    O2   C2   119.22  3.000
 RB4  H3A   C3   H3   107.93  3.000
 RB4  H3A   C3   C4   111.10  3.000
 RB4  H3    C3   C4   111.11  3.000
 RB4  H3A   C3   O2   109.83  3.000
 RB4  H3    C3   O2   109.63  3.000
 RB4  C4    C3   O2   107.23  3.000
 RB4  HN3   N3   C21  124.54  3.000
 RB4  HN3   N3   C20  126.08  3.000
 RB4  C21   N3   C20  109.35  3.000
 RB4  H4B   C4   H4A  108.28  3.000
 RB4  H4B   C4   H4   108.03  3.000
 RB4  H4A   C4   H4   108.38  3.000
 RB4  H4B   C4   C3   109.21  3.000
 RB4  H4A   C4   C3   111.41  3.000
 RB4  H4    C4   C3   111.42  3.000
 RB4  C7    C5   C6   121.47  3.000
 RB4  C6    C5   C1   126.82  3.000
 RB4  C7    C5   C1   111.64  3.000
 RB4  C18   C6   C14  118.91  3.000
 RB4  C18   C6   C5   120.36  3.000
 RB4  C14   C6   C5   120.68  3.000
 RB4  H7    C7   C5   126.94  3.000
 RB4  H7    C7   S1   119.65  3.000
 RB4  C5    C7   S1   113.36  3.000
 RB4  S1    C8   N1   122.34  3.000
 RB4  S1    C8   C1   112.09  3.000
 RB4  N1    C8   C1   125.55  3.000
 RB4  C10   C9   O3   124.26  3.000
 RB4  C10   C9   N1   113.96  3.000
 RB4  O3    C9   N1   121.77  3.000
 RB4  H10A  C10  H10  105.66  3.000
 RB4  H10A  C10  C9   108.32  3.000
 RB4  H10   C10  C9   107.68  3.000
 RB4  H10A  C10  N2   109.19  3.000
 RB4  H10   C10  N2   114.33  3.000
 RB4  C9    C10  N2   111.36  3.000
 RB4  H11A  C11  H11  106.09  3.000
 RB4  H11A  C11  C12  109.76  3.000
 RB4  H11   C11  C12  108.85  3.000
 RB4  H11A  C11  N2   112.95  3.000
 RB4  H11   C11  N2   108.52  3.000
 RB4  C12   C11  N2   110.51  3.000
 RB4  H12A  C12  H12  106.11  3.000
 RB4  H12A  C12  C13  110.16  3.000
 RB4  H12   C12  C13  109.65  3.000
 RB4  H12A  C12  C11  108.68  3.000
 RB4  H12   C12  C11  109.19  3.000
 RB4  C13   C12  C11  112.83  3.000
 RB4  C21   C13  C19  105.93  3.000
 RB4  C19   C13  C12  126.93  3.000
 RB4  C21   C13  C12  127.13  3.000
 RB4  H14   C14  C15  119.76  3.000
 RB4  H14   C14  C6   119.67  3.000
 RB4  C15   C14  C6   120.57  3.000
 RB4  H15   C15  C16  120.01  3.000
 RB4  H15   C15  C14  119.80  3.000
 RB4  C16   C15  C14  120.19  3.000
 RB4  H16   C16  C17  120.23  3.000
 RB4  H16   C16  C15  120.14  3.000
 RB4  C17   C16  C15  119.63  3.000
 RB4  H17   C17  C18  119.75  3.000
 RB4  H17   C17  C16  120.13  3.000
 RB4  C18   C17  C16  120.12  3.000
 RB4  H18   C18  C17  119.89  3.000
 RB4  H18   C18  C6   119.52  3.000
 RB4  C17   C18  C6   120.59  3.000
 RB4  C22   C19  C20  119.01  3.000
 RB4  C22   C19  C13  133.69  3.000
 RB4  C20   C19  C13  107.29  3.000
 RB4  C25   C20  C19  122.11  3.000
 RB4  C25   C20  N3   130.73  3.000
 RB4  C19   C20  N3   107.16  3.000
 RB4  H21   C21  C13  129.41  3.000
 RB4  H21   C21  N3   120.32  3.000
 RB4  C13   C21  N3   110.26  3.000
 RB4  H22   C22  C23  120.27  3.000
 RB4  H22   C22  C19  120.66  3.000
 RB4  C23   C22  C19  119.08  3.000
 RB4  H23   C23  C24  119.28  3.000
 RB4  H23   C23  C22  119.76  3.000
 RB4  C24   C23  C22  120.96  3.000
 RB4  H24   C24  C25  119.29  3.000
 RB4  H24   C24  C23  119.40  3.000
 RB4  C25   C24  C23  121.30  3.000
 RB4  H25   C25  C24  120.94  3.000
 RB4  H25   C25  C20  121.53  3.000
 RB4  C24   C25  C20  117.53  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
 RB4  CONST_01  C7   S1   C8   C1      0.00   0.0  0
 RB4  CONST_02  S1   C7   C5   C1      0.00   0.0  0
 RB4  CONST_05  C6   C5   C7   S1    180.00   0.0  0
 RB4  CONST_06  C5   C1   C8   S1      0.00   0.0  0
 RB4  CONST_07  C19  C13  C21  N3      0.00   0.0  0
 RB4  CONST_08  C13  C19  C20  N3      0.00   0.0  0
 RB4  CONST_09  C22  C19  C20  N3    180.00   0.0  0
 RB4  CONST_10  C24  C25  C20  N3    180.00   0.0  0
 RB4  CONST_11  C8   S1   C7   C5      0.00   0.0  0
 RB4  CONST_12  C15  C14  C6   C5    180.00   0.0  0
 RB4  CONST_13  C17  C18  C6   C5    180.00   0.0  0
 RB4  CONST_14  C8   C1   C5   C6    180.00   0.0  0
 RB4  CONST_15  C16  C15  C14  C6      0.00   0.0  0
 RB4  CONST_16  C16  C17  C18  C6      0.00   0.0  0
 RB4  CONST_17  C8   C1   C5   C7      0.00   0.0  0
 RB4  CONST_20  C20  N3   C21  C13     0.00   0.0  0
 RB4  CONST_21  C25  C20  C19  C13   180.00   0.0  0
 RB4  CONST_22  C23  C22  C19  C13   180.00   0.0  0
 RB4  CONST_23  C17  C18  C6   C14     0.00   0.0  0
 RB4  CONST_24  C17  C16  C15  C14     0.00   0.0  0
 RB4  CONST_25  C18  C6   C14  C15     0.00   0.0  0
 RB4  CONST_26  C18  C17  C16  C15     0.00   0.0  0
 RB4  CONST_27  C21  N3   C20  C19     0.00   0.0  0
 RB4  CONST_28  C24  C25  C20  C19     0.00   0.0  0
 RB4  CONST_29  C24  C23  C22  C19     0.00   0.0  0
 RB4  CONST_30  C21  C13  C19  C20     0.00   0.0  0
 RB4  CONST_31  C23  C22  C19  C20     0.00   0.0  0
 RB4  CONST_32  C23  C24  C25  C20     0.00   0.0  0
 RB4  CONST_33  C25  C20  N3   C21   180.00   0.0  0
 RB4  CONST_34  C22  C19  C13  C21   180.00   0.0  0
 RB4  CONST_35  C25  C20  C19  C22     0.00   0.0  0
 RB4  CONST_36  C25  C24  C23  C22     0.00   0.0  0
 RB4  CONST_37  C5   C1   C8   N1    180.00   0.0  0
 RB4  CONST_38  C7   S1   C8   N1    180.00   0.0  0
 RB4  CONST_39  C2   C1   C8   S1    180.00   0.0  0
 RB4  CONST_40  C7   C5   C1   C2    180.00   0.0  0
 RB4  CONST_41  C6   C5   C1   C2      0.00   0.0  0
 RB4  CONST_42  C12  C13  C21  N3    180.00   0.0  0
 RB4  CONST_43  C20  C19  C13  C12   180.00   0.0  0
 RB4  CONST_44  C22  C19  C13  C12     0.00   0.0  0
 RB4  CONST_45  H7   C7   C5   C1    180.00   0.0  0
 RB4  CONST_46  H25  C25  C20  N3      0.00   0.0  0
 RB4  CONST_47  H14  C14  C6   C5      0.00   0.0  0
 RB4  CONST_48  H18  C18  C6   C5      0.00   0.0  0
 RB4  CONST_49  H15  C15  C14  C6    180.00   0.0  0
 RB4  CONST_50  H17  C17  C18  C6    180.00   0.0  0
 RB4  CONST_51  HN3  N3   C21  C13   180.00   0.0  0
 RB4  CONST_52  H22  C22  C19  C13     0.00   0.0  0
 RB4  CONST_53  H16  C16  C15  C14   180.00   0.0  0
 RB4  CONST_54  H21  C21  C13  C19   180.00   0.0  0
 RB4  CONST_55  H23  C23  C22  C19   180.00   0.0  0
 RB4  CONST_56  H24  C24  C25  C20   180.00   0.0  0
 RB4  CONST_57  C9   N1   C8   C1    180.00   0.0  0
 RB4  CONST_58  C9   N1   C8   S1      0.00   0.0  0
 RB4  CONST_59  HN1  N1   C8   C1      0.00   0.0  0
 RB4  CONST_60  C8   N1   C9   O3      0.00   0.0  0
 RB4  CONST_61  C10  C9   N1   C8    180.00   0.0  0
 RB4  Var_01    C8   C1   C2   O1    -12.59  30.0  2
 RB4  Var_02    C21  C13  C12  C11  -101.99  30.0  2
 RB4  Var_03    C13  C12  C11  N2   -179.83  30.0  1
 RB4  Var_04    N2   C10  C9   N1   -174.19  30.0  3
 RB4  Var_05    C4   C3   O2   C2    179.43  30.0  3
 RB4  Var_06    C11  N2   C10  C9    178.40  30.0  1
 RB4  Var_07    C12  C11  N2   C10  -177.12  30.0  3
 RB4  Var_08    H4   C4   C3   O2    -61.92  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
 RB4  plan-1  C1   0.020
 RB4  plan-1  N1   0.020
 RB4  plan-1  S1   0.020
 RB4  plan-1  C2   0.020
 RB4  plan-1  C5   0.020
 RB4  plan-1  C6   0.020
 RB4  plan-1  C7   0.020
 RB4  plan-1  C8   0.020
 RB4  plan-1  H7   0.020
 RB4  plan-2  C5   0.020
 RB4  plan-2  C6   0.020
 RB4  plan-2  C14  0.020
 RB4  plan-2  C15  0.020
 RB4  plan-2  C16  0.020
 RB4  plan-2  C17  0.020
 RB4  plan-2  C18  0.020
 RB4  plan-2  H14  0.020
 RB4  plan-2  H15  0.020
 RB4  plan-2  H16  0.020
 RB4  plan-2  H17  0.020
 RB4  plan-2  H18  0.020
 RB4  plan-3  N3   0.020
 RB4  plan-3  C12  0.020
 RB4  plan-3  C13  0.020
 RB4  plan-3  C19  0.020
 RB4  plan-3  C20  0.020
 RB4  plan-3  C21  0.020
 RB4  plan-3  C22  0.020
 RB4  plan-3  C23  0.020
 RB4  plan-3  C24  0.020
 RB4  plan-3  C25  0.020
 RB4  plan-3  H21  0.020
 RB4  plan-3  H22  0.020
 RB4  plan-3  H23  0.020
 RB4  plan-3  H24  0.020
 RB4  plan-3  H25  0.020
 RB4  plan-3  HN3  0.020
 RB4  plan-4  N1   0.020
 RB4  plan-4  O3   0.020
 RB4  plan-4  C8   0.020
 RB4  plan-4  C9   0.020
 RB4  plan-4  C10  0.020
 RB4  plan-4  HN1  0.020
 RB4  plan-5  C1   0.020
 RB4  plan-5  O1   0.020
 RB4  plan-5  C2   0.020
 RB4  plan-5  O2   0.020

