# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:21:25 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-(6,7-difluoro-5-phenyl-1H-indazol-3-yl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)Nc1n[nH]c2c(F)c(F)c(cc12)c3ccccc3
#
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
 A28  A28  N-(6,7-difluoro-5-phenyl-1H-indazol-3-yl)butanamide  ligand  38  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A28
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
 A28  C1    C  CR6   0  -0.166   1.9311   0.0031  -0.0111
 A28  C2    C  CR6   0   0.386   2.3600  -1.3407  -0.0678
 A28  C3    C  CR6   0   0.416   1.4936  -2.4010  -0.0622
 A28  C4    C  CR16  0  -0.357   0.5750   0.2614   0.0354
 A28  N5    N  NR15  0  -0.558  -0.9570  -2.9206   0.0117
 A28  N6    N  N     0  -0.249  -2.0966  -2.2100   0.0711
 A28  C7    C  CR5   0   0.471  -1.7488  -0.9513   0.0875
 A28  C8    C  CR56  0  -0.167  -0.3268  -0.8058   0.0395
 A28  C9    C  CR56  0   0.294   0.1285  -2.1307  -0.0069
 A28  C10   C  CR6   0   0.094   2.9153   1.1068  -0.0218
 A28  C11   C  CR16  0  -0.293   3.9711   1.1476   0.8895
 A28  C12   C  CR16  0  -0.241   4.8587   2.2134   0.8902
 A28  C13   C  CR16  0  -0.263   4.7074   3.2529  -0.0186
 A28  C14   C  CR16  0  -0.240   3.6594   3.2214  -0.9282
 A28  C15   C  CR16  0  -0.298   2.7717   2.1546  -0.9311
 A28  F16   F  F     0  -0.296   3.6680  -1.6016  -0.1540
 A28  F17   F  F     0  -0.297   1.9342  -3.6595  -0.1193
 A28  N18   N  NH1   0  -0.740  -2.6305   0.1108   0.1519
 A28  C19   C  C     0   0.546  -3.9913   0.0690   0.0231
 A28  C20   C  CH2   0  -0.598  -4.6463   1.4255   0.1608
 A28  O21   O  O     0  -0.446  -4.6028  -0.9590  -0.1751
 A28  C22   C  CH2   0  -0.418  -6.1472   1.4100  -0.0780
 A28  C23   C  CH3   0  -0.678  -6.7548   2.7958   0.0919
 A28  H4    H  HCR6  0   0.267   0.2325   1.2874   0.0852
 A28  H11   H  HCR6  0   0.254   4.0901   0.3607   1.6231
 A28  H12   H  HCR6  0   0.260   5.6687   2.2339   1.6074
 A28  H13   H  HCR6  0   0.259   5.4011   4.0833  -0.0160
 A28  H14   H  HCR6  0   0.259   3.5333   4.0249  -1.6421
 A28  H15   H  HCR6  0   0.257   1.9649   2.1293  -1.6530
 A28  HN18  H  HNH1  0   0.419  -2.2149   1.0167   0.3037
 A28  H20   H  HCH2  0   0.272  -4.4284   1.8077   1.1640
 A28  H20A  H  HCH2  0   0.268  -4.1605   2.1239  -0.5287
 A28  H22   H  HCH2  0   0.225  -6.3557   1.0372  -1.0832
 A28  H22A  H  HCH2  0   0.225  -6.6229   0.7123   0.6141
 A28  H23   H  HCH3  0   0.219  -6.5873   3.1808   1.0997
 A28  H23A  H  HCH3  0   0.230  -6.3194   3.5093  -0.6100
 A28  H23B  H  HCH3  0   0.241  -7.8310   2.7761  -0.0804
 A28  HN5   H  HNR5  0   0.444  -0.9958  -3.9258  -0.0203

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
 A28  C2   C1    aromatic  1.412  0.020  1.412
 A28  C1   C4    aromatic  1.381  0.020  1.381
 A28  C1   C10   single    1.479  0.020  1.479
 A28  C3   C2    aromatic  1.369  0.020  1.369
 A28  F16  C2    single    1.337  0.020  1.337
 A28  F17  C3    single    1.335  0.020  1.335
 A28  C3   C9    aromatic  1.393  0.020  1.393
 A28  C8   C4    aromatic  1.397  0.020  1.397
 A28  C4   H4    single    0.930  0.020  1.080
 A28  N5   N6    aromatic  1.344  0.020  1.344
 A28  N5   C9    aromatic  1.343  0.020  1.343
 A28  N6   C7    aromatic  1.306  0.020  1.306
 A28  C7   C8    aromatic  1.430  0.020  1.430
 A28  C7   N18   single    1.382  0.020  1.382
 A28  C9   C8    aromatic  1.402  0.020  1.402
 A28  C10  C11   aromatic  1.395  0.020  1.395
 A28  C10  C15   aromatic  1.395  0.020  1.395
 A28  C11  C12   aromatic  1.387  0.020  1.387
 A28  C11  H11   single    0.930  0.020  1.080
 A28  C12  C13   aromatic  1.389  0.020  1.389
 A28  C12  H12   single    0.930  0.020  1.080
 A28  C14  C13   aromatic  1.388  0.020  1.388
 A28  C13  H13   single    0.930  0.020  1.080
 A28  C15  C14   aromatic  1.388  0.020  1.388
 A28  C14  H14   single    0.930  0.020  1.080
 A28  C15  H15   single    0.930  0.020  1.080
 A28  N18  C19   single    1.368  0.020  1.368
 A28  N18  HN18  single    0.860  0.020  1.020
 A28  C19  C20   single    1.513  0.020  1.513
 A28  C19  O21   double    1.212  0.020  1.212
 A28  C20  C22   single    1.520  0.020  1.520
 A28  C20  H20   single    0.970  0.020  1.090
 A28  C20  H20A  single    0.970  0.020  1.090
 A28  C22  C23   single    1.523  0.020  1.523
 A28  C22  H22   single    0.970  0.020  1.090
 A28  C22  H22A  single    0.970  0.020  1.090
 A28  C23  H23   single    0.970  0.020  1.090
 A28  C23  H23A  single    0.970  0.020  1.090
 A28  C23  H23B  single    0.970  0.020  1.090
 A28  N5   HN5   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
 A28  C10   C1   C4    120.93  3.000
 A28  C10   C1   C2    120.53  3.000
 A28  C4    C1   C2    118.53  3.000
 A28  F16   C2   C3    117.93  3.000
 A28  F16   C2   C1    119.06  3.000
 A28  C3    C2   C1    123.00  3.000
 A28  F17   C3   C9    120.55  3.000
 A28  C9    C3   C2    118.04  3.000
 A28  F17   C3   C2    121.40  3.000
 A28  H4    C4   C8    121.30  3.000
 A28  H4    C4   C1    119.29  3.000
 A28  C8    C4   C1    119.40  3.000
 A28  HN5   N5   C9    128.20  3.000
 A28  HN5   N5   N6    119.78  3.000
 A28  C9    N5   N6    112.02  3.000
 A28  C7    N6   N5    106.52  3.000
 A28  N18   C7   C8    123.90  3.000
 A28  N18   C7   N6    124.85  3.000
 A28  C8    C7   N6    111.25  3.000
 A28  C9    C8   C7    103.17  3.000
 A28  C9    C8   C4    120.81  3.000
 A28  C7    C8   C4    136.02  3.000
 A28  C8    C9   N5    107.04  3.000
 A28  C8    C9   C3    120.21  3.000
 A28  N5    C9   C3    132.75  3.000
 A28  C15   C10  C11   118.80  3.000
 A28  C15   C10  C1    119.80  3.000
 A28  C11   C10  C1    121.37  3.000
 A28  H11   C11  C12   119.21  3.000
 A28  H11   C11  C10   120.31  3.000
 A28  C12   C11  C10   120.46  3.000
 A28  H12   C12  C13   120.06  3.000
 A28  H12   C12  C11   119.60  3.000
 A28  C13   C12  C11   120.33  3.000
 A28  H13   C13  C14   120.20  3.000
 A28  H13   C13  C12   120.19  3.000
 A28  C14   C13  C12   119.61  3.000
 A28  H14   C14  C15   119.66  3.000
 A28  H14   C14  C13   120.23  3.000
 A28  C15   C14  C13   120.11  3.000
 A28  H15   C15  C14   119.73  3.000
 A28  H15   C15  C10   119.59  3.000
 A28  C14   C15  C10   120.68  3.000
 A28  HN18  N18  C19   116.86  3.000
 A28  HN18  N18  C7    115.76  3.000
 A28  C19   N18  C7    127.37  3.000
 A28  O21   C19  C20   123.84  3.000
 A28  O21   C19  N18   122.90  3.000
 A28  C20   C19  N18   113.26  3.000
 A28  H20A  C20  H20   105.42  3.000
 A28  H20A  C20  C22   110.22  3.000
 A28  H20   C20  C22   110.11  3.000
 A28  H20A  C20  C19   108.81  3.000
 A28  H20   C20  C19   108.07  3.000
 A28  C22   C20  C19   113.84  3.000
 A28  H22A  C22  H22   106.39  3.000
 A28  H22A  C22  C23   109.69  3.000
 A28  H22   C22  C23   109.70  3.000
 A28  H22A  C22  C20   109.70  3.000
 A28  H22   C22  C20   109.67  3.000
 A28  C23   C22  C20   111.55  3.000
 A28  H23B  C23  H23A  107.70  3.000
 A28  H23B  C23  H23   107.68  3.000
 A28  H23A  C23  H23   107.57  3.000
 A28  H23B  C23  C22   111.10  3.000
 A28  H23A  C23  C22   111.35  3.000
 A28  H23   C23  C22   111.27  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
 A28  CONST_01  C9    C3   C2   C1     0.00   0.0  0
 A28  CONST_02  C7    C8   C4   C1   180.00   0.0  0
 A28  CONST_03  C9    C8   C4   C1     0.00   0.0  0
 A28  CONST_04  C12   C11  C10  C1   180.00   0.0  0
 A28  CONST_05  C14   C15  C10  C1   180.00   0.0  0
 A28  CONST_06  C8    C4   C1   C2     0.00   0.0  0
 A28  CONST_09  N5    C9   C3   C2   180.00   0.0  0
 A28  CONST_10  C8    C9   C3   C2     0.00   0.0  0
 A28  CONST_11  C4    C1   C2   C3     0.00   0.0  0
 A28  CONST_12  C10   C1   C2   C3   180.00   0.0  0
 A28  CONST_13  N6    N5   C9   C3   180.00   0.0  0
 A28  CONST_14  C4    C8   C9   C3     0.00   0.0  0
 A28  CONST_15  C7    C8   C9   C3   180.00   0.0  0
 A28  CONST_18  N6    C7   C8   C4   180.00   0.0  0
 A28  CONST_19  N5    C9   C8   C4   180.00   0.0  0
 A28  CONST_20  C8    C7   N6   N5     0.00   0.0  0
 A28  CONST_21  C7    C8   C9   N5     0.00   0.0  0
 A28  CONST_22  C8    C9   N5   N6     0.00   0.0  0
 A28  CONST_23  C9    C8   C7   N6     0.00   0.0  0
 A28  CONST_24  C9    N5   N6   C7     0.00   0.0  0
 A28  CONST_25  C10   C1   C4   C8   180.00   0.0  0
 A28  CONST_26  C13   C12  C11  C10    0.00   0.0  0
 A28  CONST_27  C13   C14  C15  C10    0.00   0.0  0
 A28  CONST_28  C14   C15  C10  C11    0.00   0.0  0
 A28  CONST_29  C14   C13  C12  C11    0.00   0.0  0
 A28  CONST_30  C15   C10  C11  C12    0.00   0.0  0
 A28  CONST_31  C15   C14  C13  C12    0.00   0.0  0
 A28  CONST_32  F17   C3   C2   C1   180.00   0.0  0
 A28  CONST_33  F16   C2   C1   C4   180.00   0.0  0
 A28  CONST_34  N18   C7   C8   C4     0.00   0.0  0
 A28  CONST_35  N18   C7   N6   N5   180.00   0.0  0
 A28  CONST_36  F17   C3   C9   N5     0.00   0.0  0
 A28  CONST_37  F17   C3   C9   C8   180.00   0.0  0
 A28  CONST_38  F16   C2   C3   C9   180.00   0.0  0
 A28  CONST_39  N18   C7   C8   C9   180.00   0.0  0
 A28  CONST_40  F16   C2   C1   C10    0.00   0.0  0
 A28  CONST_41  H11   C11  C10  C1     0.00   0.0  0
 A28  CONST_42  H15   C15  C10  C1     0.00   0.0  0
 A28  CONST_43  H4    C4   C1   C2   180.00   0.0  0
 A28  CONST_44  HN5   N5   C9   C3     0.00   0.0  0
 A28  CONST_45  H12   C12  C11  C10  180.00   0.0  0
 A28  CONST_46  H14   C14  C15  C10  180.00   0.0  0
 A28  CONST_47  H13   C13  C12  C11  180.00   0.0  0
 A28  CONST_48  C19   N18  C7   N6     0.00   0.0  0
 A28  CONST_49  C19   N18  C7   C8   180.00   0.0  0
 A28  CONST_50  HN18  N18  C7   N6   180.00   0.0  0
 A28  CONST_51  C20   C19  N18  C7   180.00   0.0  0
 A28  CONST_52  O21   C19  N18  C7     0.00   0.0  0
 A28  Var_01    C22   C20  C19  N18  175.89  30.0  3
 A28  Var_02    C23   C22  C20  C19  179.23  30.0  3
 A28  Var_03    H23   C23  C22  C20  -60.00  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
 A28  plan-1  C1    0.020
 A28  plan-1  C10   0.020
 A28  plan-1  C11   0.020
 A28  plan-1  C12   0.020
 A28  plan-1  C13   0.020
 A28  plan-1  C14   0.020
 A28  plan-1  C15   0.020
 A28  plan-1  H11   0.020
 A28  plan-1  H12   0.020
 A28  plan-1  H13   0.020
 A28  plan-1  H14   0.020
 A28  plan-1  H15   0.020
 A28  plan-2  C1    0.020
 A28  plan-2  C2    0.020
 A28  plan-2  C3    0.020
 A28  plan-2  C4    0.020
 A28  plan-2  N5    0.020
 A28  plan-2  N6    0.020
 A28  plan-2  C7    0.020
 A28  plan-2  C8    0.020
 A28  plan-2  C9    0.020
 A28  plan-2  C10   0.020
 A28  plan-2  F16   0.020
 A28  plan-2  F17   0.020
 A28  plan-2  N18   0.020
 A28  plan-2  H4    0.020
 A28  plan-2  HN5   0.020
 A28  plan-3  C7    0.020
 A28  plan-3  N18   0.020
 A28  plan-3  C19   0.020
 A28  plan-3  C20   0.020
 A28  plan-3  O21   0.020
 A28  plan-3  HN18  0.020

