# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 17:31:13 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: [4-[5-[5-(dimethylcarbamoyl)pyridin-3-yl]-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-2-methanoyl-5-methoxy-phenyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(B(O)O)c(C=O)cc1c2c[nH]c3ncc(cc23)c4cncc(c4)C(=O)N(C)C
#
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
 HJ9  HJ9  '[4-[5-[5-(dimethylcarbamoyl)pyridin-3-yl]-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-2-methanoyl-5-methoxy-phenyl]boronic acid'  ligand  54  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJ9
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
 HJ9  B33  B  B     0   0.499  123.2212  19.7407   7.4389
 HJ9  C04  C  CH3   0  -0.532  115.3299  10.8940   1.2552
 HJ9  C05  C  CH3   0  -0.524  113.6712  12.0845  -0.0854
 HJ9  C06  C  CR6   0  -0.143  115.5304  13.2163   2.9977
 HJ9  C07  C  CR16  0  -0.069  115.1429  13.4984   4.3033
 HJ9  C09  C  CR16  0  -0.095  117.3007  13.6143   5.0133
 HJ9  C10  C  CR6   0   0.001  117.8102  13.3670   3.7386
 HJ9  C11  C  CR6   0  -0.028  119.2599  13.3208   3.4931
 HJ9  C12  C  CR16  0  -0.118  119.7984  12.3130   2.6723
 HJ9  C14  C  CR56  0   0.474  121.8746  13.0919   2.9376
 HJ9  C16  C  CR15  0  -0.027  123.6887  14.2502   3.4707
 HJ9  C17  C  CR5   0  -0.021  122.6617  14.8788   4.1255
 HJ9  C18  C  CR6   0  -0.065  122.7994  16.0961   4.9248
 HJ9  C19  C  CR16  0  -0.328  123.5359  17.1677   4.4543
 HJ9  C20  C  CR6   0  -0.073  123.7316  18.3440   5.1847
 HJ9  C21  C  C1    0   0.116  124.5611  19.3201   4.4846
 HJ9  C32  C  CR6   0  -0.088  123.1385  18.4834   6.4613
 HJ9  C36  C  CR16  0  -0.470  122.3962  17.4038   6.9302
 HJ9  C37  C  CR6   0   0.395  122.2303  16.2232   6.2020
 HJ9  C39  C  CH3   0  -0.446  120.9659  15.1983   7.9401
 HJ9  C40  C  CR56  0   0.027  121.4771  14.1430   3.7937
 HJ9  C41  C  CR16  0  -0.300  120.1181  14.2527   4.0636
 HJ9  C42  C  CR16  0  -0.201  116.8880  13.1619   2.7174
 HJ9  N03  N  NT    0  -0.441  114.5744  12.1137   1.0472
 HJ9  N08  N  N     0  -0.392  116.0067  13.6806   5.2913
 HJ9  N13  N  N     0  -0.414  121.0818  12.1885   2.3866
 HJ9  N15  N  NR15  0  -0.666  123.2207  13.1816   2.7668
 HJ9  O01  O  O     0  -0.477  113.6195  13.9887   1.8744
 HJ9  O34  O  OH1   0  -0.647  123.9309  20.8602   7.2075
 HJ9  O35  O  OH1   0  -0.635  122.5067  19.6279   8.5936
 HJ9  O38  O  O2    0  -0.450  121.5612  15.1629   6.6539
 HJ9  H1   H  HCH3  0   0.264  115.7783  10.8618   2.2429
 HJ9  H2   H  HCH3  0   0.256  114.6611  10.0360   1.1693
 HJ9  H3   H  HCH3  0   0.247  116.1190  10.7857   0.5093
 HJ9  H4   H  HCH3  0   0.254  113.4221  13.0907  -0.4094
 HJ9  H5   H  HCH3  0   0.248  114.1596  11.5684  -0.9107
 HJ9  H6   H  HCH3  0   0.241  112.7460  11.5533   0.1506
 HJ9  H7   H  HCR6  0   0.270  114.0911  13.5675   4.5584
 HJ9  H8   H  HCR6  0   0.267  117.9802  13.7560   5.8480
 HJ9  H9   H  HCR6  0   0.259  119.1385  11.5671   2.2410
 HJ9  H10  H  HCR5  0   0.298  124.7403  14.4910   3.4711
 HJ9  H11  H  HCR6  0   0.268  123.9728  17.0884   3.4652
 HJ9  H12  H  H     0   0.229  124.8887  18.9856   3.4878
 HJ9  H15  H  HCR6  0   0.293  121.9392  17.4804   7.9065
 HJ9  H16  H  HCH3  0   0.266  120.4948  14.2292   8.0808
 HJ9  H17  H  HCH3  0   0.239  121.7097  15.3497   8.7252
 HJ9  H18  H  HCH3  0   0.238  120.2031  15.9764   8.0140
 HJ9  H19  H  HCR6  0   0.259  119.7278  15.0549   4.6769
 HJ9  H20  H  HCR6  0   0.282  117.2320  12.9888   1.7041
 HJ9  H21  H  HNR5  0   0.415  123.7834  12.5532   2.2153
 HJ9  H22  H  HOH1  0   0.483  122.5835  20.4004   9.1628
 HJ9  O1   O  O     0  -0.435  124.9229  20.4193   4.8694
 HJ9  H13  H  HOH1  0   0.488  124.3899  20.8333   6.3385
 HJ9  C02  C  C     0   0.511  114.4865  13.1263   1.9301

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
 HJ9  C05  N03  single    1.449  0.020  1.449
 HJ9  N03  C04  single    1.450  0.020  1.450
 HJ9  N03  C02  single    1.346  0.020  1.346
 HJ9  O01  C02  double    1.224  0.020  1.224
 HJ9  C02  C06  single    1.496  0.020  1.496
 HJ9  N13  C12  aromatic  1.321  0.020  1.321
 HJ9  N13  C14  aromatic  1.322  0.020  1.322
 HJ9  N15  C14  aromatic  1.360  0.020  1.360
 HJ9  N15  C16  aromatic  1.363  0.020  1.363
 HJ9  C12  C11  aromatic  1.407  0.020  1.407
 HJ9  C42  C06  aromatic  1.387  0.020  1.387
 HJ9  C42  C10  aromatic  1.391  0.020  1.391
 HJ9  C14  C40  aromatic  1.413  0.020  1.413
 HJ9  C06  C07  aromatic  1.391  0.020  1.391
 HJ9  C16  C17  aromatic  1.371  0.020  1.371
 HJ9  C11  C10  single    1.471  0.020  1.471
 HJ9  C11  C41  aromatic  1.389  0.020  1.389
 HJ9  C40  C17  aromatic  1.433  0.020  1.433
 HJ9  C40  C41  aromatic  1.390  0.020  1.390
 HJ9  C10  C09  aromatic  1.395  0.020  1.395
 HJ9  C17  C18  single    1.463  0.020  1.463
 HJ9  C07  N08  aromatic  1.325  0.020  1.325
 HJ9  C19  C18  aromatic  1.383  0.020  1.383
 HJ9  C19  C20  aromatic  1.398  0.020  1.398
 HJ9  C21  C20  single    1.460  0.020  1.460
 HJ9  C18  C37  aromatic  1.404  0.020  1.404
 HJ9  C09  N08  aromatic  1.325  0.020  1.325
 HJ9  C20  C32  aromatic  1.415  0.020  1.415
 HJ9  C37  O38  single    1.333  0.020  1.333
 HJ9  C37  C36  aromatic  1.397  0.020  1.397
 HJ9  C32  C36  aromatic  1.392  0.020  1.392
 HJ9  C32  B33  single    1.595  0.020  1.595
 HJ9  O38  C39  single    1.418  0.020  1.418
 HJ9  B33  O34  single    1.346  0.020  1.346
 HJ9  B33  O35  single    1.363  0.020  1.363
 HJ9  C04  H1   single    0.970  0.020  1.090
 HJ9  C04  H2   single    0.970  0.020  1.090
 HJ9  C04  H3   single    0.970  0.020  1.090
 HJ9  C05  H4   single    0.970  0.020  1.090
 HJ9  C05  H5   single    0.970  0.020  1.090
 HJ9  C05  H6   single    0.970  0.020  1.090
 HJ9  C07  H7   single    0.930  0.020  1.080
 HJ9  C09  H8   single    0.930  0.020  1.080
 HJ9  C12  H9   single    0.930  0.020  1.080
 HJ9  C16  H10  single    0.930  0.020  1.080
 HJ9  C19  H11  single    0.930  0.020  1.080
 HJ9  C21  H12  single    0.930  0.020  1.080
 HJ9  C36  H15  single    0.930  0.020  1.080
 HJ9  C39  H16  single    0.970  0.020  1.090
 HJ9  C39  H17  single    0.970  0.020  1.090
 HJ9  C39  H18  single    0.970  0.020  1.090
 HJ9  C41  H19  single    0.930  0.020  1.080
 HJ9  C42  H20  single    0.930  0.020  1.080
 HJ9  N15  H21  single    0.860  0.020  1.020
 HJ9  O35  H22  single    0.850  0.020  0.980
 HJ9  C21  O1   double    1.219  0.020  1.219
 HJ9  O34  H13  single    0.850  0.020  0.980

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
 HJ9  O35  B33  O34  119.42  3.000
 HJ9  O35  B33  C32  115.28  3.000
 HJ9  O34  B33  C32  125.30  3.000
 HJ9  H3   C04  H2   108.14  3.000
 HJ9  H3   C04  H1   108.68  3.000
 HJ9  H2   C04  H1   107.55  3.000
 HJ9  H3   C04  N03  111.24  3.000
 HJ9  H2   C04  N03  109.32  3.000
 HJ9  H1   C04  N03  111.77  3.000
 HJ9  H6   C05  H5   108.24  3.000
 HJ9  H6   C05  H4   108.70  3.000
 HJ9  H5   C05  H4   108.41  3.000
 HJ9  H6   C05  N03  111.64  3.000
 HJ9  H5   C05  N03  108.81  3.000
 HJ9  H4   C05  N03  110.95  3.000
 HJ9  C42  C06  C07  118.05  3.000
 HJ9  C07  C06  C02  119.19  3.000
 HJ9  C42  C06  C02  122.44  3.000
 HJ9  H7   C07  N08  116.62  3.000
 HJ9  H7   C07  C06  120.27  3.000
 HJ9  N08  C07  C06  123.11  3.000
 HJ9  H8   C09  N08  116.32  3.000
 HJ9  H8   C09  C10  119.81  3.000
 HJ9  N08  C09  C10  123.87  3.000
 HJ9  C42  C10  C11  121.75  3.000
 HJ9  C11  C10  C09  121.20  3.000
 HJ9  C42  C10  C09  117.05  3.000
 HJ9  C41  C11  C12  118.92  3.000
 HJ9  C41  C11  C10  121.28  3.000
 HJ9  C12  C11  C10  119.81  3.000
 HJ9  H9   C12  N13  116.11  3.000
 HJ9  H9   C12  C11  119.43  3.000
 HJ9  N13  C12  C11  124.45  3.000
 HJ9  N15  C14  N13  125.89  3.000
 HJ9  N15  C14  C40  107.79  3.000
 HJ9  N13  C14  C40  126.31  3.000
 HJ9  H10  C16  N15  120.67  3.000
 HJ9  H10  C16  C17  128.89  3.000
 HJ9  N15  C16  C17  110.44  3.000
 HJ9  C40  C17  C18  129.15  3.000
 HJ9  C18  C17  C16  124.91  3.000
 HJ9  C40  C17  C16  105.85  3.000
 HJ9  C37  C18  C19  117.08  3.000
 HJ9  C37  C18  C17  122.30  3.000
 HJ9  C19  C18  C17  120.61  3.000
 HJ9  H11  C19  C20  118.79  3.000
 HJ9  H11  C19  C18  117.92  3.000
 HJ9  C20  C19  C18  123.28  3.000
 HJ9  C32  C20  C21  127.24  3.000
 HJ9  C32  C20  C19  119.71  3.000
 HJ9  C21  C20  C19  113.05  3.000
 HJ9  O1   C21  H12  118.11  3.000
 HJ9  O1   C21  C20  128.31  3.000
 HJ9  H12  C21  C20  113.58  3.000
 HJ9  C36  C32  C20  116.83  3.000
 HJ9  C36  C32  B33  115.64  3.000
 HJ9  C20  C32  B33  127.53  3.000
 HJ9  H15  C36  C37  118.73  3.000
 HJ9  H15  C36  C32  118.35  3.000
 HJ9  C37  C36  C32  122.91  3.000
 HJ9  O38  C37  C36  123.72  3.000
 HJ9  C36  C37  C18  120.17  3.000
 HJ9  O38  C37  C18  116.10  3.000
 HJ9  H18  C39  H17  109.16  3.000
 HJ9  H18  C39  H16  108.90  3.000
 HJ9  H17  C39  H16  109.01  3.000
 HJ9  H18  C39  O38  111.87  3.000
 HJ9  H17  C39  O38  111.69  3.000
 HJ9  H16  C39  O38  106.10  3.000
 HJ9  C41  C40  C17  136.27  3.000
 HJ9  C41  C40  C14  116.84  3.000
 HJ9  C17  C40  C14  106.84  3.000
 HJ9  H19  C41  C40  121.41  3.000
 HJ9  H19  C41  C11  120.45  3.000
 HJ9  C40  C41  C11  118.12  3.000
 HJ9  H20  C42  C10  119.96  3.000
 HJ9  H20  C42  C06  120.37  3.000
 HJ9  C10  C42  C06  119.65  3.000
 HJ9  C05  N03  C04  114.84  3.000
 HJ9  C04  N03  C02  124.94  3.000
 HJ9  C05  N03  C02  119.15  3.000
 HJ9  C09  N08  C07  118.25  3.000
 HJ9  C14  N13  C12  115.34  3.000
 HJ9  H21  N15  C16  125.45  3.000
 HJ9  H21  N15  C14  125.47  3.000
 HJ9  C16  N15  C14  109.07  3.000
 HJ9  H13  O34  B33  112.06  3.000
 HJ9  H22  O35  B33  113.13  3.000
 HJ9  C39  O38  C37  119.91  3.000
 HJ9  O01  C02  N03  123.11  3.000
 HJ9  O01  C02  C06  118.97  3.000
 HJ9  N03  C02  C06  117.89  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
 HJ9  CONST_01  C11  C10  C42  C06   180.00   0.0  0
 HJ9  CONST_02  C09  C10  C42  C06     0.00   0.0  0
 HJ9  CONST_03  C09  N08  C07  C06     0.00   0.0  0
 HJ9  CONST_04  C10  C42  C06  C07     0.00   0.0  0
 HJ9  CONST_05  C10  C09  N08  C07     0.00   0.0  0
 HJ9  CONST_08  N13  C12  C11  C10   180.00   0.0  0
 HJ9  CONST_09  C40  C41  C11  C10   180.00   0.0  0
 HJ9  CONST_10  C14  N13  C12  C11     0.00   0.0  0
 HJ9  CONST_11  N08  C09  C10  C11   180.00   0.0  0
 HJ9  CONST_12  C14  C40  C41  C11     0.00   0.0  0
 HJ9  CONST_13  C17  C40  C41  C11   180.00   0.0  0
 HJ9  CONST_14  N15  C14  N13  C12   180.00   0.0  0
 HJ9  CONST_15  C40  C14  N13  C12     0.00   0.0  0
 HJ9  CONST_17  C40  C41  C11  C12     0.00   0.0  0
 HJ9  CONST_18  C17  C16  N15  C14     0.00   0.0  0
 HJ9  CONST_19  C16  C17  C40  C14     0.00   0.0  0
 HJ9  CONST_20  C18  C17  C40  C14   180.00   0.0  0
 HJ9  CONST_21  N13  C14  N15  C16   180.00   0.0  0
 HJ9  CONST_22  C40  C14  N15  C16     0.00   0.0  0
 HJ9  CONST_23  C41  C40  C17  C16   180.00   0.0  0
 HJ9  CONST_26  N13  C14  C40  C17   180.00   0.0  0
 HJ9  CONST_27  N15  C14  C40  C17     0.00   0.0  0
 HJ9  CONST_28  C20  C19  C18  C17   180.00   0.0  0
 HJ9  CONST_29  C36  C37  C18  C17   180.00   0.0  0
 HJ9  CONST_30  N15  C16  C17  C18   180.00   0.0  0
 HJ9  CONST_31  C41  C40  C17  C18     0.00   0.0  0
 HJ9  CONST_32  C32  C20  C19  C18     0.00   0.0  0
 HJ9  CONST_33  C32  C36  C37  C18     0.00   0.0  0
 HJ9  CONST_35  C36  C37  C18  C19     0.00   0.0  0
 HJ9  CONST_36  C36  C32  C20  C19     0.00   0.0  0
 HJ9  CONST_37  C37  C18  C19  C20     0.00   0.0  0
 HJ9  CONST_38  C37  C36  C32  C20     0.00   0.0  0
 HJ9  CONST_40  N15  C16  C17  C40     0.00   0.0  0
 HJ9  CONST_41  N13  C12  C11  C41     0.00   0.0  0
 HJ9  CONST_43  N13  C14  C40  C41     0.00   0.0  0
 HJ9  CONST_44  N15  C14  C40  C41   180.00   0.0  0
 HJ9  CONST_45  N08  C07  C06  C42     0.00   0.0  0
 HJ9  CONST_46  N08  C09  C10  C42     0.00   0.0  0
 HJ9  CONST_47  C19  C20  C32  B33   180.00   0.0  0
 HJ9  CONST_48  C37  C36  C32  B33   180.00   0.0  0
 HJ9  CONST_49  C10  C42  C06  C02   180.00   0.0  0
 HJ9  CONST_50  N08  C07  C06  C02   180.00   0.0  0
 HJ9  CONST_51  O38  C37  C18  C17     0.00   0.0  0
 HJ9  CONST_52  C21  C20  C19  C18   180.00   0.0  0
 HJ9  CONST_53  O38  C37  C18  C19   180.00   0.0  0
 HJ9  CONST_54  C36  C32  C20  C21   180.00   0.0  0
 HJ9  CONST_55  O38  C37  C36  C32   180.00   0.0  0
 HJ9  CONST_56  H20  C42  C06  C07   180.00   0.0  0
 HJ9  CONST_57  H8   C09  N08  C07   180.00   0.0  0
 HJ9  CONST_58  H7   C07  N08  C09   180.00   0.0  0
 HJ9  CONST_59  H9   C12  C11  C10     0.00   0.0  0
 HJ9  CONST_60  H19  C41  C11  C10     0.00   0.0  0
 HJ9  CONST_61  H10  C16  N15  C14   180.00   0.0  0
 HJ9  CONST_62  H21  N15  C16  C17   180.00   0.0  0
 HJ9  CONST_63  H11  C19  C18  C17     0.00   0.0  0
 HJ9  CONST_64  H15  C36  C37  C18   180.00   0.0  0
 HJ9  CONST_66  C06  C02  N03  C05   180.00   0.0  0
 HJ9  CONST_68  O01  C02  N03  C05     0.00   0.0  0
 HJ9  Var_01    N03  C02  C06  C07  -136.34  30.0  2
 HJ9  Var_02    O1   C21  C20  C19  -178.68  30.0  2
 HJ9  Var_03    O34  B33  C32  C20    -2.91  30.0  2
 HJ9  Var_04    H16  C39  O38  C37  -179.48  30.0  3
 HJ9  Var_05    H4   C05  N03  C02    32.18  30.0  3
 HJ9  Var_06    H1   C04  N03  C02     3.36  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
 HJ9  plan-1  B33  0.020
 HJ9  plan-1  C17  0.020
 HJ9  plan-1  C18  0.020
 HJ9  plan-1  C19  0.020
 HJ9  plan-1  C20  0.020
 HJ9  plan-1  C21  0.020
 HJ9  plan-1  C32  0.020
 HJ9  plan-1  C36  0.020
 HJ9  plan-1  C37  0.020
 HJ9  plan-1  O38  0.020
 HJ9  plan-1  H11  0.020
 HJ9  plan-1  H15  0.020
 HJ9  plan-2  C06  0.020
 HJ9  plan-2  C07  0.020
 HJ9  plan-2  C09  0.020
 HJ9  plan-2  C10  0.020
 HJ9  plan-2  C11  0.020
 HJ9  plan-2  C42  0.020
 HJ9  plan-2  N08  0.020
 HJ9  plan-2  H7   0.020
 HJ9  plan-2  H8   0.020
 HJ9  plan-2  H20  0.020
 HJ9  plan-2  C02  0.020
 HJ9  plan-3  C10  0.020
 HJ9  plan-3  C11  0.020
 HJ9  plan-3  C12  0.020
 HJ9  plan-3  C14  0.020
 HJ9  plan-3  C16  0.020
 HJ9  plan-3  C17  0.020
 HJ9  plan-3  C18  0.020
 HJ9  plan-3  C40  0.020
 HJ9  plan-3  C41  0.020
 HJ9  plan-3  N13  0.020
 HJ9  plan-3  N15  0.020
 HJ9  plan-3  H9   0.020
 HJ9  plan-3  H10  0.020
 HJ9  plan-3  H19  0.020
 HJ9  plan-3  H21  0.020
 HJ9  plan-4  C04  0.020
 HJ9  plan-4  C05  0.020
 HJ9  plan-4  C06  0.020
 HJ9  plan-4  N03  0.020
 HJ9  plan-4  O01  0.020
 HJ9  plan-4  C02  0.020
 HJ9  plan-5  C20  0.020
 HJ9  plan-5  C21  0.020
 HJ9  plan-5  H12  0.020
 HJ9  plan-5  O1   0.020

