# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:18:05 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-{3-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-1H-pyrazol-5-yl}-N-(3-fluorophenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(NC(=O)Cc2[nH]nc(c2)c3ccc4c([nH]nc4c5[nH]c6ccccc6n5)c3)c1
#
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
 N13  N13  2-{3-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-1H-pyrazol-5-yl}-N-(3-fluorophenyl)acetamide  ligand  52  34  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N13
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
 N13  CA   C  C     0   0.566    5.1818   0.3735   0.3566
 N13  C29  C  CR16  0  -0.487    7.3336  -1.3899  -0.8611
 N13  C30  C  CR6   0   0.554    8.4306  -2.1150  -1.2874
 N13  FA   F  F     0  -0.318    8.3056  -2.8200  -2.4240
 N13  C31  C  CR16  0  -0.430    9.6320  -2.1536  -0.6115
 N13  C32  C  CR16  0  -0.230    9.7250  -1.4168   0.5623
 N13  C33  C  CR16  0  -0.358    8.6530  -0.6773   1.0271
 N13  C28  C  CR6   0   0.399    7.4473  -0.6559   0.3193
 N13  NB   N  NH1   0  -0.751    6.4146   0.1101   0.8597
 N13  OB   O  O     0  -0.448    4.7637  -0.0483  -0.7020
 N13  C26  C  CH2   0  -0.719    4.3555   1.2704   1.2677
 N13  C21  C  CR5   0   0.462    2.9974   1.5272   0.7299
 N13  C25  C  CR15  0  -0.575    1.7996   0.8931   0.9609
 N13  N22  N  NR15  0  -0.466    2.7279   2.5064  -0.1519
 N13  N23  N  N     0  -0.291    1.4557   2.5587  -0.5095
 N13  C24  C  CR5   0   0.270    0.8637   1.5792   0.1591
 N13  C16  C  CR6   0   0.049   -0.5751   1.3352   0.0222
 N13  C17  C  CR16  0  -0.363   -1.3581   2.1880  -0.7345
 N13  C15  C  CR16  0  -0.335   -1.1588   0.2196   0.6742
 N13  C14  C  CR16  0  -0.316   -2.5014  -0.0573   0.5868
 N13  C18  C  CR56  0  -0.103   -3.3062   0.7993  -0.1744
 N13  C19  C  CR56  0   0.470   -2.7200   1.9007  -0.8186
 N13  N11  N  NR15  0  -0.545   -3.7298   2.5346  -1.4654
 N13  N12  N  N     0  -0.250   -4.8990   1.9375  -1.2899
 N13  C13  C  CR5   0   0.153   -4.6833   0.8924  -0.5207
 N13  C02  C  CR5   0   0.443   -5.7682   0.0205  -0.1306
 N13  N03  N  NR15  0  -0.708   -7.0503   0.2379  -0.5259
 N13  C08  C  CR56  0   0.337   -7.8151  -0.7574   0.0163
 N13  C04  C  CR16  0  -0.313   -9.1743  -1.0422  -0.0451
 N13  C05  C  CR16  0  -0.278   -9.6058  -2.1610   0.6462
 N13  C06  C  CR16  0  -0.271   -8.7138  -2.9664   1.3717
 N13  C07  C  CR16  0  -0.343   -7.3627  -2.6765   1.4280
 N13  C09  C  CR56  0   0.152   -6.9068  -1.5528   0.7383
 N13  N01  N  N     0  -0.488   -5.6390  -1.0387   0.6249
 N13  H1   H  HCR6  0   0.300    6.4234  -1.4090  -1.4384
 N13  H2   H  HCR6  0   0.279   10.4637  -2.7363  -0.9832
 N13  H3   H  HCR6  0   0.273   10.6505  -1.4182   1.1225
 N13  H4   H  HCR6  0   0.276    8.7482  -0.1100   1.9445
 N13  H5   H  HNH1  0   0.426    6.6317   0.5409   1.7466
 N13  H6   H  HCH2  0   0.319    4.2733   0.8012   2.2508
 N13  H7   H  HCH2  0   0.315    4.8944   2.2092   1.4263
 N13  H8   H  HCR5  0   0.269    1.6390   0.0569   1.6212
 N13  H9   H  HNR5  0   0.420    3.3794   3.1705  -0.5410
 N13  H10  H  HCR6  0   0.268   -0.9320   3.0468  -1.2354
 N13  H11  H  HCR6  0   0.254   -0.5289  -0.4384   1.2579
 N13  H12  H  HCR6  0   0.258   -2.9270  -0.9143   1.0895
 N13  H13  H  HNR5  0   0.424   -3.6761   3.3669  -2.0309
 N13  H14  H  HNR5  0   0.421   -7.3679   1.0013  -1.1028
 N13  H15  H  HCR6  0   0.267   -9.8626  -0.4233  -0.6053
 N13  H16  H  HCR6  0   0.256  -10.6557  -2.4220   0.6269
 N13  H17  H  HCR6  0   0.253   -9.0959  -3.8325   1.8959
 N13  H18  H  HCR6  0   0.254   -6.6776  -3.2986   1.9895

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
 N13  OB   CA   double    1.214  0.020  1.214
 N13  C32  C33  aromatic  1.383  0.020  1.383
 N13  C32  C31  aromatic  1.389  0.020  1.389
 N13  C33  C28  aromatic  1.398  0.020  1.398
 N13  C31  C30  aromatic  1.379  0.020  1.379
 N13  CA   C26  single    1.522  0.020  1.522
 N13  CA   NB   single    1.357  0.020  1.357
 N13  C28  NB   single    1.395  0.020  1.395
 N13  C28  C29  aromatic  1.395  0.020  1.395
 N13  C26  C21  single    1.483  0.020  1.483
 N13  C30  C29  aromatic  1.382  0.020  1.382
 N13  C30  FA   single    1.343  0.020  1.343
 N13  C21  C25  aromatic  1.375  0.020  1.375
 N13  C21  N22  aromatic  1.345  0.020  1.345
 N13  C25  C24  aromatic  1.411  0.020  1.411
 N13  N22  N23  aromatic  1.323  0.020  1.323
 N13  N23  C24  aromatic  1.325  0.020  1.325
 N13  C24  C16  single    1.466  0.020  1.466
 N13  C16  C15  aromatic  1.418  0.020  1.418
 N13  C16  C17  aromatic  1.383  0.020  1.383
 N13  C15  C14  aromatic  1.374  0.020  1.374
 N13  C17  C19  aromatic  1.394  0.020  1.394
 N13  C14  C18  aromatic  1.400  0.020  1.400
 N13  C19  C18  aromatic  1.404  0.020  1.404
 N13  C19  N11  aromatic  1.356  0.020  1.356
 N13  C18  C13  aromatic  1.423  0.020  1.423
 N13  N11  N12  aromatic  1.325  0.020  1.325
 N13  C13  N12  aromatic  1.315  0.020  1.315
 N13  C13  C02  single    1.445  0.020  1.445
 N13  N01  C02  aromatic  1.307  0.020  1.307
 N13  N01  C09  aromatic  1.373  0.020  1.373
 N13  C02  N03  aromatic  1.359  0.020  1.359
 N13  C09  C07  aromatic  1.395  0.020  1.395
 N13  C09  C08  aromatic  1.407  0.020  1.407
 N13  C07  C06  aromatic  1.383  0.020  1.383
 N13  N03  C08  aromatic  1.367  0.020  1.367
 N13  C08  C04  aromatic  1.390  0.020  1.390
 N13  C06  C05  aromatic  1.404  0.020  1.404
 N13  C04  C05  aromatic  1.384  0.020  1.384
 N13  C29  H1   single    0.930  0.020  1.080
 N13  C31  H2   single    0.930  0.020  1.080
 N13  C32  H3   single    0.930  0.020  1.080
 N13  C33  H4   single    0.930  0.020  1.080
 N13  NB   H5   single    0.860  0.020  1.020
 N13  C26  H6   single    0.970  0.020  1.090
 N13  C26  H7   single    0.970  0.020  1.090
 N13  C25  H8   single    0.930  0.020  1.080
 N13  N22  H9   single    0.860  0.020  1.020
 N13  C17  H10  single    0.930  0.020  1.080
 N13  C15  H11  single    0.930  0.020  1.080
 N13  C14  H12  single    0.930  0.020  1.080
 N13  N11  H13  single    0.860  0.020  1.020
 N13  N03  H14  single    0.860  0.020  1.020
 N13  C04  H15  single    0.930  0.020  1.080
 N13  C05  H16  single    0.930  0.020  1.080
 N13  C06  H17  single    0.930  0.020  1.080
 N13  C07  H18  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
 N13  C26  CA   OB   122.67  3.000
 N13  C26  CA   NB   112.68  3.000
 N13  OB   CA   NB   124.66  3.000
 N13  H1   C29  C28  122.10  3.000
 N13  H1   C29  C30  119.71  3.000
 N13  C28  C29  C30  118.19  3.000
 N13  C31  C30  FA   118.76  3.000
 N13  FA   C30  C29  117.54  3.000
 N13  C31  C30  C29  123.70  3.000
 N13  H2   C31  C32  121.65  3.000
 N13  H2   C31  C30  121.11  3.000
 N13  C32  C31  C30  117.24  3.000
 N13  H3   C32  C33  119.34  3.000
 N13  H3   C32  C31  119.61  3.000
 N13  C33  C32  C31  121.05  3.000
 N13  H4   C33  C28  119.78  3.000
 N13  H4   C33  C32  119.78  3.000
 N13  C28  C33  C32  120.44  3.000
 N13  NB   C28  C33  116.79  3.000
 N13  NB   C28  C29  123.82  3.000
 N13  C33  C28  C29  119.38  3.000
 N13  H5   NB   C28  114.55  3.000
 N13  H5   NB   CA   115.98  3.000
 N13  C28  NB   CA   129.45  3.000
 N13  H7   C26  H6   105.97  3.000
 N13  H7   C26  C21  110.80  3.000
 N13  H6   C26  C21  109.38  3.000
 N13  H7   C26  CA   108.96  3.000
 N13  H6   C26  CA   109.05  3.000
 N13  C21  C26  CA   112.46  3.000
 N13  N22  C21  C25  105.74  3.000
 N13  N22  C21  C26  123.18  3.000
 N13  C25  C21  C26  131.07  3.000
 N13  H8   C25  C24  128.82  3.000
 N13  H8   C25  C21  126.21  3.000
 N13  C24  C25  C21  104.96  3.000
 N13  H9   N22  N23  119.41  3.000
 N13  H9   N22  C21  127.08  3.000
 N13  N23  N22  C21  113.50  3.000
 N13  C24  N23  N22  105.31  3.000
 N13  C16  C24  N23  120.96  3.000
 N13  C16  C24  C25  128.57  3.000
 N13  N23  C24  C25  110.48  3.000
 N13  C15  C16  C17  120.24  3.000
 N13  C17  C16  C24  120.27  3.000
 N13  C15  C16  C24  119.48  3.000
 N13  H10  C17  C19  121.35  3.000
 N13  H10  C17  C16  121.33  3.000
 N13  C19  C17  C16  117.32  3.000
 N13  H11  C15  C14  118.74  3.000
 N13  H11  C15  C16  119.14  3.000
 N13  C14  C15  C16  122.12  3.000
 N13  H12  C14  C18  120.77  3.000
 N13  H12  C14  C15  121.00  3.000
 N13  C18  C14  C15  118.23  3.000
 N13  C13  C18  C19  103.95  3.000
 N13  C13  C18  C14  136.76  3.000
 N13  C19  C18  C14  119.30  3.000
 N13  N11  C19  C18  105.93  3.000
 N13  N11  C19  C17  131.27  3.000
 N13  C18  C19  C17  122.79  3.000
 N13  H13  N11  N12  119.58  3.000
 N13  H13  N11  C19  127.87  3.000
 N13  N12  N11  C19  112.54  3.000
 N13  C13  N12  N11  106.91  3.000
 N13  C02  C13  N12  120.93  3.000
 N13  C02  C13  C18  128.40  3.000
 N13  N12  C13  C18  110.67  3.000
 N13  N01  C02  N03  113.01  3.000
 N13  N03  C02  C13  122.21  3.000
 N13  N01  C02  C13  124.78  3.000
 N13  H14  N03  C08  127.01  3.000
 N13  H14  N03  C02  125.78  3.000
 N13  C08  N03  C02  107.21  3.000
 N13  C09  C08  C04  122.56  3.000
 N13  C04  C08  N03  132.73  3.000
 N13  C09  C08  N03  104.71  3.000
 N13  H15  C04  C05  121.51  3.000
 N13  H15  C04  C08  121.85  3.000
 N13  C05  C04  C08  116.64  3.000
 N13  H16  C05  C06  119.17  3.000
 N13  H16  C05  C04  119.24  3.000
 N13  C06  C05  C04  121.59  3.000
 N13  H17  C06  C07  119.54  3.000
 N13  H17  C06  C05  119.03  3.000
 N13  C07  C06  C05  121.43  3.000
 N13  H18  C07  C09  120.84  3.000
 N13  H18  C07  C06  121.26  3.000
 N13  C09  C07  C06  117.90  3.000
 N13  N01  C09  C07  130.11  3.000
 N13  C07  C09  C08  119.88  3.000
 N13  N01  C09  C08  110.01  3.000
 N13  C09  N01  C02  105.06  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
 N13  CONST_01  C32  C33  C28  C29     0.00   0.0  0
 N13  CONST_02  C32  C31  C30  C29     0.00   0.0  0
 N13  CONST_03  C33  C32  C31  C30     0.00   0.0  0
 N13  CONST_04  C33  C28  C29  C30     0.00   0.0  0
 N13  CONST_05  C28  C33  C32  C31     0.00   0.0  0
 N13  CONST_06  C28  C29  C30  C31     0.00   0.0  0
 N13  CONST_07  N23  C24  C25  C21     0.00   0.0  0
 N13  CONST_08  C16  C24  C25  C21   180.00   0.0  0
 N13  CONST_09  C24  N23  N22  C21     0.00   0.0  0
 N13  CONST_10  N23  N22  C21  C25     0.00   0.0  0
 N13  CONST_11  N22  N23  C24  C25     0.00   0.0  0
 N13  CONST_12  C15  C16  C24  C25     0.00   0.0  0
 N13  CONST_13  C17  C16  C24  C25   180.00   0.0  0
 N13  CONST_14  C24  C25  C21  N22     0.00   0.0  0
 N13  CONST_15  C16  C24  N23  N22   180.00   0.0  0
 N13  CONST_16  C15  C16  C24  N23   180.00   0.0  0
 N13  CONST_17  C17  C16  C24  N23     0.00   0.0  0
 N13  CONST_18  C14  C15  C16  C24   180.00   0.0  0
 N13  CONST_19  C19  C17  C16  C24   180.00   0.0  0
 N13  CONST_20  C18  C14  C15  C16     0.00   0.0  0
 N13  CONST_21  C18  C19  C17  C16     0.00   0.0  0
 N13  CONST_22  N11  C19  C17  C16   180.00   0.0  0
 N13  CONST_23  C14  C15  C16  C17     0.00   0.0  0
 N13  CONST_24  C14  C18  C19  C17     0.00   0.0  0
 N13  CONST_25  C13  C18  C19  C17   180.00   0.0  0
 N13  CONST_26  N12  N11  C19  C17   180.00   0.0  0
 N13  CONST_27  C19  C17  C16  C15     0.00   0.0  0
 N13  CONST_28  C19  C18  C14  C15     0.00   0.0  0
 N13  CONST_29  C13  C18  C14  C15   180.00   0.0  0
 N13  CONST_30  N11  C19  C18  C14   180.00   0.0  0
 N13  CONST_31  N12  C13  C18  C14   180.00   0.0  0
 N13  CONST_32  C02  C13  C18  C14     0.00   0.0  0
 N13  CONST_33  N12  N11  C19  C18     0.00   0.0  0
 N13  CONST_34  N11  N12  C13  C18     0.00   0.0  0
 N13  CONST_35  N01  C02  C13  C18     0.00   0.0  0
 N13  CONST_36  N03  C02  C13  C18   180.00   0.0  0
 N13  CONST_37  N12  C13  C18  C19     0.00   0.0  0
 N13  CONST_38  C02  C13  C18  C19   180.00   0.0  0
 N13  CONST_39  C13  N12  N11  C19     0.00   0.0  0
 N13  CONST_40  C13  C18  C19  N11     0.00   0.0  0
 N13  CONST_41  C02  C13  N12  N11   180.00   0.0  0
 N13  CONST_42  N01  C02  C13  N12   180.00   0.0  0
 N13  CONST_43  N03  C02  C13  N12     0.00   0.0  0
 N13  CONST_44  C09  N01  C02  C13   180.00   0.0  0
 N13  CONST_45  C08  N03  C02  C13   180.00   0.0  0
 N13  CONST_46  C07  C09  N01  C02   180.00   0.0  0
 N13  CONST_47  C08  C09  N01  C02     0.00   0.0  0
 N13  CONST_48  C09  C08  N03  C02     0.00   0.0  0
 N13  CONST_49  C04  C08  N03  C02   180.00   0.0  0
 N13  CONST_50  C09  N01  C02  N03     0.00   0.0  0
 N13  CONST_51  N01  C09  C08  N03     0.00   0.0  0
 N13  CONST_52  C07  C09  C08  N03   180.00   0.0  0
 N13  CONST_53  C05  C04  C08  N03   180.00   0.0  0
 N13  CONST_54  C06  C07  C09  C08     0.00   0.0  0
 N13  CONST_55  N01  C02  N03  C08     0.00   0.0  0
 N13  CONST_56  C06  C05  C04  C08     0.00   0.0  0
 N13  CONST_57  N01  C09  C08  C04   180.00   0.0  0
 N13  CONST_58  C07  C09  C08  C04     0.00   0.0  0
 N13  CONST_59  C07  C06  C05  C04     0.00   0.0  0
 N13  CONST_60  C09  C07  C06  C05     0.00   0.0  0
 N13  CONST_61  C09  C08  C04  C05     0.00   0.0  0
 N13  CONST_62  N01  C09  C07  C06   180.00   0.0  0
 N13  CONST_63  NB   C28  C29  C30   180.00   0.0  0
 N13  CONST_64  C32  C31  C30  FA    180.00   0.0  0
 N13  CONST_65  C28  C29  C30  FA    180.00   0.0  0
 N13  CONST_66  NB   C28  C33  C32   180.00   0.0  0
 N13  CONST_67  C24  C25  C21  C26   180.00   0.0  0
 N13  CONST_68  N23  N22  C21  C26   180.00   0.0  0
 N13  CONST_69  H4   C33  C28  C29   180.00   0.0  0
 N13  CONST_70  H2   C31  C30  C29   180.00   0.0  0
 N13  CONST_71  H3   C32  C31  C30   180.00   0.0  0
 N13  CONST_72  H1   C29  C30  C31   180.00   0.0  0
 N13  CONST_73  H9   N22  C21  C25   180.00   0.0  0
 N13  CONST_74  H8   C25  C21  N22   180.00   0.0  0
 N13  CONST_75  H11  C15  C16  C24     0.00   0.0  0
 N13  CONST_76  H10  C17  C16  C24     0.00   0.0  0
 N13  CONST_77  H12  C14  C15  C16   180.00   0.0  0
 N13  CONST_78  H13  N11  C19  C17     0.00   0.0  0
 N13  CONST_79  H14  N03  C02  C13     0.00   0.0  0
 N13  CONST_80  H15  C04  C08  N03     0.00   0.0  0
 N13  CONST_81  H18  C07  C09  C08   180.00   0.0  0
 N13  CONST_82  H16  C05  C04  C08   180.00   0.0  0
 N13  CONST_83  H17  C06  C05  C04   180.00   0.0  0
 N13  CONST_84  C33  C28  NB   CA    180.00   0.0  0
 N13  CONST_85  C29  C28  NB   CA      0.00   0.0  0
 N13  CONST_86  H5   NB   C28  C29   180.00   0.0  0
 N13  CONST_87  OB   CA   NB   C28     0.00   0.0  0
 N13  CONST_88  C26  CA   NB   C28   180.00   0.0  0
 N13  Var_01    C25  C21  C26  CA     94.17  30.0  2
 N13  Var_02    C21  C26  CA   NB   -178.55  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
 N13  plan-1  C26  0.020
 N13  plan-1  C21  0.020
 N13  plan-1  C25  0.020
 N13  plan-1  N22  0.020
 N13  plan-1  N23  0.020
 N13  plan-1  C24  0.020
 N13  plan-1  C16  0.020
 N13  plan-1  H8   0.020
 N13  plan-1  H9   0.020
 N13  plan-2  C29  0.020
 N13  plan-2  C30  0.020
 N13  plan-2  FA   0.020
 N13  plan-2  C31  0.020
 N13  plan-2  C32  0.020
 N13  plan-2  C33  0.020
 N13  plan-2  C28  0.020
 N13  plan-2  NB   0.020
 N13  plan-2  H1   0.020
 N13  plan-2  H2   0.020
 N13  plan-2  H3   0.020
 N13  plan-2  H4   0.020
 N13  plan-3  C24  0.020
 N13  plan-3  C16  0.020
 N13  plan-3  C17  0.020
 N13  plan-3  C15  0.020
 N13  plan-3  C14  0.020
 N13  plan-3  C18  0.020
 N13  plan-3  C19  0.020
 N13  plan-3  N11  0.020
 N13  plan-3  N12  0.020
 N13  plan-3  C13  0.020
 N13  plan-3  C02  0.020
 N13  plan-3  H10  0.020
 N13  plan-3  H11  0.020
 N13  plan-3  H12  0.020
 N13  plan-3  H13  0.020
 N13  plan-4  C13  0.020
 N13  plan-4  C02  0.020
 N13  plan-4  N03  0.020
 N13  plan-4  C08  0.020
 N13  plan-4  C04  0.020
 N13  plan-4  C05  0.020
 N13  plan-4  C06  0.020
 N13  plan-4  C07  0.020
 N13  plan-4  C09  0.020
 N13  plan-4  N01  0.020
 N13  plan-4  H14  0.020
 N13  plan-4  H15  0.020
 N13  plan-4  H16  0.020
 N13  plan-4  H17  0.020
 N13  plan-4  H18  0.020
 N13  plan-5  CA   0.020
 N13  plan-5  C28  0.020
 N13  plan-5  NB   0.020
 N13  plan-5  OB   0.020
 N13  plan-5  C26  0.020
 N13  plan-5  H5   0.020

