# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:39:57 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 4-methoxy-N-phenyl-3-({3-[(1H-pyrrolo[2,3-b]pyridin-5-ylmethyl)sulfanyl]propanoyl}amino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1NC(=O)CCSCc2cnc3[nH]ccc3c2)C(=O)Nc4ccccc4
#
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
 AK6  AK6  4-methoxy-N-phenyl-3-({3-[(1H-pyrrolo[2,3-b]pyridin-5-ylmethyl)sulfanyl]propanoyl}amino)benzamide  ligand  57  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AK6
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
 AK6  C30   C  CR16  0  -0.252   -7.1058   1.1801   0.4632
 AK6  C28   C  CR56  0   0.460   -9.0829  -0.0731  -0.0240
 AK6  C26   C  CR16  0  -0.106   -7.2597  -0.5090  -1.2397
 AK6  C23   C  CH3   0  -0.439    2.7173  -5.0910  -0.2138
 AK6  C22   C  CR16  0  -0.310    7.3371   3.0710  -0.5012
 AK6  C17   C  CR6   0   0.380    7.4777   1.8388   0.1390
 AK6  C20   C  CR16  0  -0.273    9.5365   3.7308   0.2635
 AK6  C12   C  CR6   0   0.351    2.9479  -2.7295  -0.1385
 AK6  C11   C  CR16  0  -0.372    4.3165  -2.7782  -0.3689
 AK6  C10   C  CR16  0  -0.296    5.0628  -1.6095  -0.3924
 AK6  C9    C  CR6   0  -0.065    4.4556  -0.3791  -0.1772
 AK6  C8    C  CR16  0  -0.311    3.0787  -0.3295   0.0458
 AK6  C7    C  CR6   0   0.293    2.3195  -1.4850   0.0688
 AK6  C3    C  C     0   0.559    0.0407  -0.5695  -0.1229
 AK6  C2    C  CH2   0  -0.547   -2.3988  -0.0372  -0.4559
 AK6  C1    C  CH2   0  -0.591   -1.3824  -0.8751   0.2983
 AK6  O15   O  O     0  -0.464    4.6382   1.9603  -0.4838
 AK6  N16   N  NH1   0  -0.762    6.5156   0.8233   0.1094
 AK6  C21   C  CR16  0  -0.246    8.3661   4.0011  -0.4303
 AK6  C19   C  CR16  0  -0.243    9.6769   2.5009   0.8934
 AK6  C18   C  CR16  0  -0.351    8.6590   1.5646   0.8332
 AK6  N5    N  NH1   0  -0.739    0.9413  -1.4869   0.3162
 AK6  O6    O  O     0  -0.465    0.3408   0.4106  -0.7770
 AK6  S4    S  S2    0  -0.018   -4.0629  -0.4855   0.1156
 AK6  C25   C  CR6   0   0.004   -6.5036   0.4551  -0.5541
 AK6  C29   C  CR56  0   0.020   -8.4434   0.9243   0.7497
 AK6  C33   C  CR15  0  -0.447   -9.4160   1.4203   1.6695
 AK6  C32   C  CR15  0  -0.000  -10.5659   0.7270   1.4245
 AK6  N31   N  NR15  0  -0.661  -10.3687  -0.1679   0.4090
 AK6  N27   N  N     0  -0.423   -8.5308  -0.7825  -0.9950
 AK6  H30   H  HCR6  0   0.260   -6.5457   1.9278   1.0129
 AK6  H26   H  HCR6  0   0.253   -6.7903  -1.0806  -2.0347
 AK6  H24   H  HCH2  0   0.283   -4.7456   1.6772  -0.6990
 AK6  H24A  H  HCH2  0   0.283   -4.8761   0.4417  -1.9543
 AK6  H23   H  HCH3  0   0.237    3.1803  -5.2356  -1.1924
 AK6  H23A  H  HCH3  0   0.236    3.4597  -5.2781   0.5650
 AK6  H23B  H  HCH3  0   0.267    1.9008  -5.7988  -0.1017
 AK6  H20   H  HCR6  0   0.256   10.3287   4.4657   0.3110
 AK6  H11   H  HCR6  0   0.292    4.8156  -3.7191  -0.5539
 AK6  H10   H  HCR6  0   0.267    6.1206  -1.6898  -0.6083
 AK6  H8    H  HCR6  0   0.272    2.6078   0.6247   0.2269
 AK6  H2    H  HCH2  0   0.271   -2.2363   1.0256  -0.2761
 AK6  H2A   H  HCH2  0   0.271   -2.3273  -0.2150  -1.5299
 AK6  H1    H  HCH2  0   0.277   -1.5852  -1.9401   0.1569
 AK6  H1A   H  HCH2  0   0.292   -1.4624  -0.6890   1.3741
 AK6  HN16  H  HNH1  0   0.420    6.8310  -0.0593   0.4808
 AK6  H21   H  HCR6  0   0.258    8.2437   4.9520  -0.9332
 AK6  H19   H  HCR6  0   0.260   10.5815   2.2658   1.4393
 AK6  H18   H  HCR6  0   0.269    8.7787   0.6086   1.3306
 AK6  HN5   H  HNH1  0   0.412    0.5706  -2.3103   0.7662
 AK6  H33   H  HCR5  0   0.255   -9.2840   2.1877   2.4147
 AK6  H32   H  HCR5  0   0.289  -11.5287   0.8041   1.9029
 AK6  HN31  H  HNR5  0   0.412  -11.0631  -0.7998   0.0453
 AK6  C24   C  CH2   0  -0.622   -5.0604   0.6518  -0.8994
 AK6  O13   O  O2    0  -0.465    2.1455  -3.8002  -0.0914
 AK6  C14   C  C     0   0.531    5.1976   0.9123  -0.2070
 AK6  H22   H  HCR6  0   0.275    6.4448   3.3122  -1.0552

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
 AK6  C25  C30   aromatic  1.387  0.020  1.387
 AK6  C30  C29   aromatic  1.392  0.020  1.392
 AK6  C30  H30   single    0.930  0.020  1.080
 AK6  N27  C28   aromatic  1.323  0.020  1.323
 AK6  C29  C28   aromatic  1.415  0.020  1.415
 AK6  C28  N31   aromatic  1.360  0.020  1.360
 AK6  C25  C26   aromatic  1.404  0.020  1.404
 AK6  C26  N27   aromatic  1.323  0.020  1.323
 AK6  C26  H26   single    0.930  0.020  1.080
 AK6  C24  S4    single    1.822  0.020  1.822
 AK6  C24  C25   single    1.497  0.020  1.497
 AK6  C24  H24   single    0.970  0.020  1.090
 AK6  C24  H24A  single    0.970  0.020  1.090
 AK6  C23  O13   single    1.417  0.020  1.417
 AK6  C23  H23   single    0.970  0.020  1.090
 AK6  C23  H23A  single    0.970  0.020  1.090
 AK6  C23  H23B  single    0.970  0.020  1.090
 AK6  C21  C22   aromatic  1.389  0.020  1.389
 AK6  C22  C17   aromatic  1.396  0.020  1.396
 AK6  C22  H22   single    0.930  0.020  1.080
 AK6  C18  C17   aromatic  1.397  0.020  1.397
 AK6  C17  N16   single    1.399  0.020  1.399
 AK6  C20  C19   aromatic  1.389  0.020  1.389
 AK6  C20  C21   aromatic  1.387  0.020  1.387
 AK6  C20  H20   single    0.930  0.020  1.080
 AK6  C11  C12   aromatic  1.389  0.020  1.389
 AK6  C12  C7    aromatic  1.409  0.020  1.409
 AK6  C12  O13   single    1.339  0.020  1.339
 AK6  N16  C14   single    1.358  0.020  1.358
 AK6  C14  O15   double    1.220  0.020  1.220
 AK6  C14  C9    single    1.490  0.020  1.490
 AK6  C10  C11   aromatic  1.387  0.020  1.387
 AK6  C11  H11   single    0.930  0.020  1.080
 AK6  C10  C9    aromatic  1.389  0.020  1.389
 AK6  C10  H10   single    0.930  0.020  1.080
 AK6  C9   C8    aromatic  1.396  0.020  1.396
 AK6  C8   C7    aromatic  1.383  0.020  1.383
 AK6  C8   H8    single    0.930  0.020  1.080
 AK6  C7   N5    single    1.400  0.020  1.400
 AK6  O6   C3    double    1.216  0.020  1.216
 AK6  N5   C3    single    1.359  0.020  1.359
 AK6  C3   C1    single    1.515  0.020  1.515
 AK6  S4   C2    single    1.816  0.020  1.816
 AK6  C2   C1    single    1.518  0.020  1.518
 AK6  C2   H2    single    0.970  0.020  1.090
 AK6  C2   H2A   single    0.970  0.020  1.090
 AK6  C1   H1    single    0.970  0.020  1.090
 AK6  C1   H1A   single    0.970  0.020  1.090
 AK6  N16  HN16  single    0.860  0.020  1.020
 AK6  C21  H21   single    0.930  0.020  1.080
 AK6  C19  C18   aromatic  1.384  0.020  1.384
 AK6  C19  H19   single    0.930  0.020  1.080
 AK6  C18  H18   single    0.930  0.020  1.080
 AK6  N5   HN5   single    0.860  0.020  1.020
 AK6  C29  C33   aromatic  1.428  0.020  1.428
 AK6  C33  C32   aromatic  1.365  0.020  1.365
 AK6  C33  H33   single    0.930  0.020  1.080
 AK6  N31  C32   aromatic  1.368  0.020  1.368
 AK6  C32  H32   single    0.930  0.020  1.080
 AK6  N31  HN31  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
 AK6  H30   C30  C29   121.27  3.000
 AK6  H30   C30  C25   120.54  3.000
 AK6  C29   C30  C25   118.19  3.000
 AK6  N27   C28  N31   126.20  3.000
 AK6  N31   C28  C29   107.60  3.000
 AK6  N27   C28  C29   126.20  3.000
 AK6  H26   C26  N27   116.23  3.000
 AK6  H26   C26  C25   119.09  3.000
 AK6  N27   C26  C25   124.68  3.000
 AK6  H23B  C23  H23A  109.01  3.000
 AK6  H23B  C23  H23   108.96  3.000
 AK6  H23A  C23  H23   109.15  3.000
 AK6  H23B  C23  O13   106.33  3.000
 AK6  H23A  C23  O13   111.64  3.000
 AK6  H23   C23  O13   111.66  3.000
 AK6  H22   C22  C21   119.33  3.000
 AK6  H22   C22  C17   121.12  3.000
 AK6  C21   C22  C17   119.55  3.000
 AK6  C18   C17  N16   116.71  3.000
 AK6  N16   C17  C22   124.18  3.000
 AK6  C18   C17  C22   119.10  3.000
 AK6  H20   C20  C19   120.51  3.000
 AK6  H20   C20  C21   120.50  3.000
 AK6  C19   C20  C21   118.99  3.000
 AK6  O13   C12  C7    115.70  3.000
 AK6  O13   C12  C11   124.64  3.000
 AK6  C7    C12  C11   119.65  3.000
 AK6  H11   C11  C10   118.82  3.000
 AK6  H11   C11  C12   120.93  3.000
 AK6  C10   C11  C12   120.24  3.000
 AK6  H10   C10  C9    121.58  3.000
 AK6  H10   C10  C11   117.82  3.000
 AK6  C9    C10  C11   120.58  3.000
 AK6  C8    C9   C10   119.17  3.000
 AK6  C8    C9   C14   117.63  3.000
 AK6  C10   C9   C14   123.18  3.000
 AK6  H8    C8   C7    119.76  3.000
 AK6  H8    C8   C9    119.25  3.000
 AK6  C7    C8   C9    120.97  3.000
 AK6  N5    C7   C8    122.99  3.000
 AK6  N5    C7   C12   117.62  3.000
 AK6  C8    C7   C12   119.38  3.000
 AK6  O6    C3   N5    123.68  3.000
 AK6  N5    C3   C1    113.37  3.000
 AK6  O6    C3   C1    122.95  3.000
 AK6  H2A   C2   H2    108.15  3.000
 AK6  H2A   C2   S4    109.25  3.000
 AK6  H2    C2   S4    109.00  3.000
 AK6  H2A   C2   C1    110.81  3.000
 AK6  H2    C2   C1    110.88  3.000
 AK6  S4    C2   C1    108.72  3.000
 AK6  H1A   C1   H1    106.21  3.000
 AK6  H1A   C1   C2    110.22  3.000
 AK6  H1    C1   C2    110.44  3.000
 AK6  H1A   C1   C3    107.91  3.000
 AK6  H1    C1   C3    109.55  3.000
 AK6  C2    C1   C3    112.30  3.000
 AK6  HN16  N16  C14   116.53  3.000
 AK6  HN16  N16  C17   114.36  3.000
 AK6  C14   N16  C17   128.65  3.000
 AK6  H21   C21  C20   119.93  3.000
 AK6  H21   C21  C22   118.73  3.000
 AK6  C20   C21  C22   121.34  3.000
 AK6  H19   C19  C18   119.31  3.000
 AK6  H19   C19  C20   120.37  3.000
 AK6  C18   C19  C20   120.32  3.000
 AK6  H18   C18  C19   119.69  3.000
 AK6  H18   C18  C17   119.61  3.000
 AK6  C19   C18  C17   120.70  3.000
 AK6  HN5   N5   C3    116.85  3.000
 AK6  HN5   N5   C7    116.20  3.000
 AK6  C3    N5   C7    126.48  3.000
 AK6  C2    S4   C24    99.92  3.000
 AK6  C24   C25  C26   119.78  3.000
 AK6  C24   C25  C30   121.29  3.000
 AK6  C26   C25  C30   118.90  3.000
 AK6  C33   C29  C28   106.81  3.000
 AK6  C33   C29  C30   136.35  3.000
 AK6  C28   C29  C30   116.83  3.000
 AK6  H33   C33  C32   126.08  3.000
 AK6  H33   C33  C29   127.54  3.000
 AK6  C32   C33  C29   106.37  3.000
 AK6  H32   C32  N31   120.33  3.000
 AK6  H32   C32  C33   129.54  3.000
 AK6  N31   C32  C33   110.13  3.000
 AK6  HN31  N31  C32   125.40  3.000
 AK6  HN31  N31  C28   125.51  3.000
 AK6  C32   N31  C28   109.09  3.000
 AK6  C26   N27  C28   115.20  3.000
 AK6  H24A  C24  H24   108.04  3.000
 AK6  H24A  C24  C25   111.14  3.000
 AK6  H24   C24  C25   111.05  3.000
 AK6  H24A  C24  S4    109.02  3.000
 AK6  H24   C24  S4    109.05  3.000
 AK6  C25   C24  S4    108.50  3.000
 AK6  C12   O13  C23   118.92  3.000
 AK6  N16   C14  O15   123.65  3.000
 AK6  O15   C14  C9    121.40  3.000
 AK6  N16   C14  C9    114.95  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
 AK6  CONST_01  N27   C26  C25  C30     0.00   0.0  0
 AK6  CONST_02  N27   C28  C29  C30     0.00   0.0  0
 AK6  CONST_03  N31   C28  C29  C30   180.00   0.0  0
 AK6  CONST_04  C32   C33  C29  C30   180.00   0.0  0
 AK6  CONST_05  C25   C26  N27  C28     0.00   0.0  0
 AK6  CONST_06  C25   C30  C29  C28     0.00   0.0  0
 AK6  CONST_07  C32   C33  C29  C28     0.00   0.0  0
 AK6  CONST_08  C33   C32  N31  C28     0.00   0.0  0
 AK6  CONST_09  C29   C30  C25  C26     0.00   0.0  0
 AK6  CONST_10  C29   C28  N27  C26     0.00   0.0  0
 AK6  CONST_11  N31   C28  N27  C26   180.00   0.0  0
 AK6  CONST_12  C19   C20  C21  C22     0.00   0.0  0
 AK6  CONST_13  C19   C18  C17  C22     0.00   0.0  0
 AK6  CONST_14  C20   C21  C22  C17     0.00   0.0  0
 AK6  CONST_15  C20   C19  C18  C17     0.00   0.0  0
 AK6  CONST_16  C9    C10  C11  C12     0.00   0.0  0
 AK6  CONST_17  C9    C8   C7   C12     0.00   0.0  0
 AK6  CONST_18  C8    C7   C12  C11     0.00   0.0  0
 AK6  CONST_19  C8    C9   C10  C11     0.00   0.0  0
 AK6  CONST_20  C7    C12  C11  C10     0.00   0.0  0
 AK6  CONST_21  C7    C8   C9   C10     0.00   0.0  0
 AK6  CONST_22  C18   C17  C22  C21     0.00   0.0  0
 AK6  CONST_23  C18   C19  C20  C21     0.00   0.0  0
 AK6  CONST_24  C33   C29  C30  C25   180.00   0.0  0
 AK6  CONST_25  C32   N31  C28  C29     0.00   0.0  0
 AK6  CONST_26  N31   C32  C33  C29     0.00   0.0  0
 AK6  CONST_27  N27   C28  C29  C33   180.00   0.0  0
 AK6  CONST_28  N31   C28  C29  C33     0.00   0.0  0
 AK6  CONST_29  N27   C28  N31  C32   180.00   0.0  0
 AK6  CONST_30  C29   C30  C25  C24   180.00   0.0  0
 AK6  CONST_31  N27   C26  C25  C24   180.00   0.0  0
 AK6  CONST_32  C11   C10  C9   C14   180.00   0.0  0
 AK6  CONST_33  C7    C8   C9   C14   180.00   0.0  0
 AK6  CONST_34  N5    C7   C12  C11   180.00   0.0  0
 AK6  CONST_35  O13   C12  C11  C10   180.00   0.0  0
 AK6  CONST_36  N5    C7   C8   C9    180.00   0.0  0
 AK6  CONST_37  O13   C12  C7   C8    180.00   0.0  0
 AK6  CONST_38  C21   C22  C17  N16   180.00   0.0  0
 AK6  CONST_39  C19   C18  C17  N16   180.00   0.0  0
 AK6  CONST_40  H26   C26  C25  C30   180.00   0.0  0
 AK6  CONST_41  H33   C33  C29  C30     0.00   0.0  0
 AK6  CONST_42  H30   C30  C29  C28   180.00   0.0  0
 AK6  CONST_43  H32   C32  N31  C28   180.00   0.0  0
 AK6  CONST_44  H20   C20  C21  C22   180.00   0.0  0
 AK6  CONST_45  H18   C18  C17  C22   180.00   0.0  0
 AK6  CONST_46  H21   C21  C22  C17   180.00   0.0  0
 AK6  CONST_47  H19   C19  C18  C17   180.00   0.0  0
 AK6  CONST_48  H22   C22  C21  C20   180.00   0.0  0
 AK6  CONST_49  H10   C10  C11  C12   180.00   0.0  0
 AK6  CONST_50  H8    C8   C7   C12   180.00   0.0  0
 AK6  CONST_51  H11   C11  C10  C9    180.00   0.0  0
 AK6  CONST_52  HN31  N31  C28  C29   180.00   0.0  0
 AK6  CONST_53  C9    C14  N16  C17   180.00   0.0  0
 AK6  CONST_58  HN16  N16  C17  C22   180.00   0.0  0
 AK6  CONST_60  O15   C14  N16  C17     0.00   0.0  0
 AK6  CONST_61  O6    C3   N5   C7      0.00   0.0  0
 AK6  CONST_62  C1    C3   N5   C7    180.00   0.0  0
 AK6  Var_01    S4    C24  C25  C30    89.33  30.0  2
 AK6  Var_02    C11   C12  O13  C23     3.43  30.0  2
 AK6  Var_03    N16   C14  C9   C10   -26.87  30.0  2
 AK6  Var_04    C25   C24  S4   C2   -178.97  30.0  1
 AK6  Var_05    H23   C23  O13  C12   -63.88  30.0  3
 AK6  Var_06    C1    C2   S4   C24   179.15  30.0  3
 AK6  Var_07    S4    C2   C1   C3    179.72  30.0  1
 AK6  Var_08    O6    C3   C1   C2     14.00  30.0  2

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
 AK6  plan-1  C12   0.020
 AK6  plan-1  C11   0.020
 AK6  plan-1  C10   0.020
 AK6  plan-1  C9    0.020
 AK6  plan-1  C8    0.020
 AK6  plan-1  C7    0.020
 AK6  plan-1  N5    0.020
 AK6  plan-1  H11   0.020
 AK6  plan-1  H10   0.020
 AK6  plan-1  H8    0.020
 AK6  plan-1  O13   0.020
 AK6  plan-1  C14   0.020
 AK6  plan-2  C22   0.020
 AK6  plan-2  C17   0.020
 AK6  plan-2  C20   0.020
 AK6  plan-2  N16   0.020
 AK6  plan-2  C21   0.020
 AK6  plan-2  C19   0.020
 AK6  plan-2  C18   0.020
 AK6  plan-2  H20   0.020
 AK6  plan-2  H21   0.020
 AK6  plan-2  H19   0.020
 AK6  plan-2  H18   0.020
 AK6  plan-2  H22   0.020
 AK6  plan-3  C30   0.020
 AK6  plan-3  C28   0.020
 AK6  plan-3  C26   0.020
 AK6  plan-3  C25   0.020
 AK6  plan-3  C29   0.020
 AK6  plan-3  C33   0.020
 AK6  plan-3  C32   0.020
 AK6  plan-3  N31   0.020
 AK6  plan-3  N27   0.020
 AK6  plan-3  H30   0.020
 AK6  plan-3  H26   0.020
 AK6  plan-3  H33   0.020
 AK6  plan-3  H32   0.020
 AK6  plan-3  HN31  0.020
 AK6  plan-3  C24   0.020
 AK6  plan-4  C7    0.020
 AK6  plan-4  C3    0.020
 AK6  plan-4  C1    0.020
 AK6  plan-4  N5    0.020
 AK6  plan-4  O6    0.020
 AK6  plan-4  HN5   0.020
 AK6  plan-5  C17   0.020
 AK6  plan-5  C9    0.020
 AK6  plan-5  O15   0.020
 AK6  plan-5  N16   0.020
 AK6  plan-5  HN16  0.020
 AK6  plan-5  C14   0.020

