# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:52:51 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccncc1Nc2nn(CCN3CCC(F)(F)CC3)c4ccc(F)cc24
#
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
 6ED  6ED  '3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid'  ligand  50  30  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6ED
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
 6ED  N12  N  N     0  -0.313  -0.5973  -0.0576   0.6700
 6ED  C15  C  CH2   0  -0.277   2.4319   0.4376  -0.2862
 6ED  C17  C  CH2   0  -0.300   4.6815   0.5328  -1.1544
 6ED  C22  C  CH2   0  -0.554   5.5552  -1.2318   0.9541
 6ED  C24  C  CR56  0   0.471  -0.3267   2.1396   0.3979
 6ED  C26  C  CR16  0  -0.491  -2.5568   2.8496  -0.2855
 6ED  O01  O  OH1   0  -0.581  -6.6969  -1.9276  -0.6086
 6ED  O03  O  O     0  -0.460  -5.4880  -0.0651  -0.5374
 6ED  C04  C  CR6   0  -0.112  -4.4375  -2.1480  -0.0371
 6ED  C05  C  CR16  0  -0.324  -4.6250  -3.5241   0.0757
 6ED  C06  C  CR16  0  -0.093  -3.5671  -4.3355   0.4280
 6ED  N07  N  N     0  -0.376  -2.3535  -3.8487   0.6700
 6ED  C08  C  CR16  0  -0.137  -2.1460  -2.5518   0.5711
 6ED  C09  C  CR6   0   0.312  -3.1489  -1.6238   0.2169
 6ED  C11  C  CR5   0   0.512  -1.7523   0.4314   0.2971
 6ED  N13  N  NR5   0  -0.398   0.2642   0.9744   0.7503
 6ED  C25  C  CR56  0  -0.167  -1.6645   1.8424   0.1010
 6ED  C27  C  CR6   0   0.527  -2.0485   4.1180  -0.3609
 6ED  F28  F  F     0  -0.321  -2.8577   5.1278  -0.7305
 6ED  C29  C  CR16  0  -0.415  -0.7111   4.4309  -0.0723
 6ED  C30  C  CR16  0  -0.281   0.1691   3.4464   0.3112
 6ED  C14  C  CH2   0  -0.319   1.6618   0.7333   1.0002
 6ED  N16  N  NT    0  -0.431   3.8382   0.2237  -0.0125
 6ED  C18  C  CH2   0  -0.556   6.1522   0.4945  -0.7575
 6ED  C19  C  CT    0   0.739   6.5012  -0.8435  -0.1547
 6ED  F20  F  F     0  -0.353   7.7941  -0.8380   0.3020
 6ED  F21  F  F     0  -0.357   6.4757  -1.8075  -1.1356
 6ED  C23  C  CH2   0  -0.309   4.1107  -1.1146   0.4839
 6ED  H1   H  HCH2  0   0.216   1.9692  -0.4134  -0.8101
 6ED  H2   H  HCH2  0   0.245   2.3344   1.3024  -0.9470
 6ED  H3   H  HCH2  0   0.208   4.5024  -0.1546  -1.9967
 6ED  H4   H  HCH2  0   0.254   4.4416   1.5357  -1.5104
 6ED  H5   H  HCH2  0   0.269   5.7622  -2.2485   1.2950
 6ED  H6   H  HCH2  0   0.255   5.7165  -0.5557   1.7963
 6ED  H7   H  HCR6  0   0.272  -3.5958   2.6522  -0.5180
 6ED  H8   H  HOH1  0   0.495  -7.4033  -1.3086  -0.8479
 6ED  H9   H  HCR6  0   0.284  -5.5912  -3.9691  -0.1114
 6ED  H10  H  HCR6  0   0.267  -3.6985  -5.4065   0.5183
 6ED  H11  H  HCR6  0   0.291  -1.1457  -2.2016   0.7778
 6ED  H12  H  HNH1  0   0.440  -3.7262   0.2586  -0.1444
 6ED  H13  H  HCR6  0   0.286  -0.3793   5.4577  -0.1551
 6ED  H14  H  HCR6  0   0.286   1.2002   3.6836   0.5354
 6ED  H15  H  HCH2  0   0.272   1.7292  -0.0892   1.7109
 6ED  H16  H  HCH2  0   0.262   2.0838   1.6142   1.4850
 6ED  H18  H  HCH2  0   0.268   6.7854   0.7031  -1.6225
 6ED  H19  H  HCH2  0   0.255   6.3406   1.2669  -0.0088
 6ED  H20  H  HCH2  0   0.212   3.9016  -1.8785  -0.2831
 6ED  H21  H  HCH2  0   0.255   3.4567  -1.3370   1.3274
 6ED  N10  N  NH1   0  -0.813  -2.9110  -0.2839   0.1161
 6ED  C02  C  C     0   0.584  -5.5689  -1.2718  -0.4144

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
 6ED  F20  C19  single    1.371  0.020  1.371
 6ED  C18  C17  single    1.524  0.020  1.524
 6ED  C18  C19  single    1.508  0.020  1.508
 6ED  C17  N16  single    1.453  0.020  1.453
 6ED  C19  C22  single    1.508  0.020  1.508
 6ED  C19  F21  single    1.376  0.020  1.376
 6ED  C22  C23  single    1.524  0.020  1.524
 6ED  N16  C23  single    1.453  0.020  1.453
 6ED  N16  C15  single    1.449  0.020  1.449
 6ED  C15  C14  single    1.528  0.020  1.528
 6ED  C14  N13  single    1.440  0.020  1.440
 6ED  N13  N12  aromatic  1.347  0.020  1.347
 6ED  N13  C24  aromatic  1.353  0.020  1.353
 6ED  N07  C08  aromatic  1.317  0.020  1.317
 6ED  N07  C06  aromatic  1.330  0.020  1.330
 6ED  N12  C11  aromatic  1.309  0.020  1.309
 6ED  C08  C09  aromatic  1.412  0.020  1.412
 6ED  C24  C30  aromatic  1.400  0.020  1.400
 6ED  C24  C25  aromatic  1.402  0.020  1.402
 6ED  C30  C29  aromatic  1.375  0.020  1.375
 6ED  C06  C05  aromatic  1.379  0.020  1.379
 6ED  C11  C25  aromatic  1.427  0.020  1.427
 6ED  C11  N10  single    1.374  0.020  1.374
 6ED  C25  C26  aromatic  1.400  0.020  1.400
 6ED  C09  N10  single    1.365  0.020  1.365
 6ED  C09  C04  aromatic  1.414  0.020  1.414
 6ED  C29  C27  aromatic  1.404  0.020  1.404
 6ED  C05  C04  aromatic  1.393  0.020  1.393
 6ED  C04  C02  single    1.480  0.020  1.480
 6ED  C27  C26  aromatic  1.369  0.020  1.369
 6ED  C27  F28  single    1.346  0.020  1.346
 6ED  C02  O03  double    1.216  0.020  1.216
 6ED  C02  O01  single    1.319  0.020  1.319
 6ED  C15  H1   single    0.970  0.020  1.090
 6ED  C15  H2   single    0.970  0.020  1.090
 6ED  C17  H3   single    0.970  0.020  1.090
 6ED  C17  H4   single    0.970  0.020  1.090
 6ED  C22  H5   single    0.970  0.020  1.090
 6ED  C22  H6   single    0.970  0.020  1.090
 6ED  C26  H7   single    0.930  0.020  1.080
 6ED  O01  H8   single    0.850  0.020  0.980
 6ED  C05  H9   single    0.930  0.020  1.080
 6ED  C06  H10  single    0.930  0.020  1.080
 6ED  C08  H11  single    0.930  0.020  1.080
 6ED  N10  H12  single    0.860  0.020  1.020
 6ED  C29  H13  single    0.930  0.020  1.080
 6ED  C30  H14  single    0.930  0.020  1.080
 6ED  C14  H15  single    0.970  0.020  1.090
 6ED  C14  H16  single    0.970  0.020  1.090
 6ED  C18  H18  single    0.970  0.020  1.090
 6ED  C18  H19  single    0.970  0.020  1.090
 6ED  C23  H20  single    0.970  0.020  1.090
 6ED  C23  H21  single    0.970  0.020  1.090

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
 6ED  N13  N12  C11  107.17  3.000
 6ED  H2   C15  H1   106.64  3.000
 6ED  H2   C15  N16  108.53  3.000
 6ED  H1   C15  N16  112.56  3.000
 6ED  H2   C15  C14  108.12  3.000
 6ED  H1   C15  C14  109.77  3.000
 6ED  N16  C15  C14  111.03  3.000
 6ED  H4   C17  H3   106.76  3.000
 6ED  H4   C17  C18  108.68  3.000
 6ED  H3   C17  C18  109.89  3.000
 6ED  H4   C17  N16  108.94  3.000
 6ED  H3   C17  N16  111.95  3.000
 6ED  C18  C17  N16  110.50  3.000
 6ED  H6   C22  H5   107.92  3.000
 6ED  H6   C22  C23  109.29  3.000
 6ED  H5   C22  C23  110.34  3.000
 6ED  H6   C22  C19  108.36  3.000
 6ED  H5   C22  C19  110.50  3.000
 6ED  C23  C22  C19  110.36  3.000
 6ED  C30  C24  C25  121.50  3.000
 6ED  C25  C24  N13  106.81  3.000
 6ED  C30  C24  N13  131.69  3.000
 6ED  H7   C26  C27  120.89  3.000
 6ED  H7   C26  C25  122.67  3.000
 6ED  C27  C26  C25  116.44  3.000
 6ED  H8   O01  C02  110.01  3.000
 6ED  C09  C04  C05  118.30  3.000
 6ED  C05  C04  C02  120.17  3.000
 6ED  C09  C04  C02  121.53  3.000
 6ED  H9   C05  C06  119.22  3.000
 6ED  H9   C05  C04  120.88  3.000
 6ED  C06  C05  C04  119.91  3.000
 6ED  H10  C06  N07  117.23  3.000
 6ED  H10  C06  C05  120.68  3.000
 6ED  N07  C06  C05  122.09  3.000
 6ED  C08  N07  C06  119.37  3.000
 6ED  H11  C08  C09  119.54  3.000
 6ED  H11  C08  N07  116.80  3.000
 6ED  C09  C08  N07  123.66  3.000
 6ED  N10  C09  C08  122.69  3.000
 6ED  N10  C09  C04  120.64  3.000
 6ED  C08  C09  C04  116.67  3.000
 6ED  C25  C11  N10  123.27  3.000
 6ED  N10  C11  N12  125.98  3.000
 6ED  C25  C11  N12  110.75  3.000
 6ED  C14  N13  C24  127.82  3.000
 6ED  C24  N13  N12  111.41  3.000
 6ED  C14  N13  N12  120.19  3.000
 6ED  C11  C25  C26  135.23  3.000
 6ED  C26  C25  C24  120.94  3.000
 6ED  C11  C25  C24  103.83  3.000
 6ED  C29  C27  F28  117.53  3.000
 6ED  F28  C27  C26  119.16  3.000
 6ED  C29  C27  C26  123.31  3.000
 6ED  H13  C29  C30  120.28  3.000
 6ED  H13  C29  C27  119.21  3.000
 6ED  C30  C29  C27  120.51  3.000
 6ED  H14  C30  C29  120.73  3.000
 6ED  H14  C30  C24  121.96  3.000
 6ED  C29  C30  C24  117.31  3.000
 6ED  H16  C14  H15  107.21  3.000
 6ED  H16  C14  N13  108.51  3.000
 6ED  H15  C14  N13  107.44  3.000
 6ED  H16  C14  C15  109.60  3.000
 6ED  H15  C14  C15  111.84  3.000
 6ED  N13  C14  C15  112.05  3.000
 6ED  C23  N16  C17  110.83  3.000
 6ED  C23  N16  C15  112.49  3.000
 6ED  C17  N16  C15  112.56  3.000
 6ED  H19  C18  H18  107.93  3.000
 6ED  H19  C18  C19  108.27  3.000
 6ED  H18  C18  C19  110.60  3.000
 6ED  H19  C18  C17  109.10  3.000
 6ED  H18  C18  C17  110.40  3.000
 6ED  C19  C18  C17  110.46  3.000
 6ED  F21  C19  F20  104.94  3.000
 6ED  F21  C19  C18  109.41  3.000
 6ED  F20  C19  C18  110.35  3.000
 6ED  F21  C19  C22  109.40  3.000
 6ED  C18  C19  C22  112.15  3.000
 6ED  F20  C19  C22  110.34  3.000
 6ED  H21  C23  H20  106.45  3.000
 6ED  H21  C23  N16  109.86  3.000
 6ED  H20  C23  N16  111.40  3.000
 6ED  H21  C23  C22  108.32  3.000
 6ED  H20  C23  C22  109.95  3.000
 6ED  N16  C23  C22  110.73  3.000
 6ED  H12  N10  C11  115.70  3.000
 6ED  H12  N10  C09  113.85  3.000
 6ED  C11  N10  C09  130.44  3.000
 6ED  C04  C02  O03  124.24  3.000
 6ED  O03  C02  O01  122.38  3.000
 6ED  C04  C02  O01  113.39  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
 6ED  CONST_01  C30  C24  N13  N12   180.00   0.0  0
 6ED  CONST_02  C25  C24  N13  N12     0.00   0.0  0
 6ED  CONST_03  C24  C25  C11  N12     0.00   0.0  0
 6ED  CONST_04  C26  C25  C11  N12   180.00   0.0  0
 6ED  CONST_05  C11  N12  N13  C24     0.00   0.0  0
 6ED  CONST_06  C27  C29  C30  C24     0.00   0.0  0
 6ED  CONST_07  C27  C26  C25  C24     0.00   0.0  0
 6ED  CONST_08  N13  C24  C25  C26   180.00   0.0  0
 6ED  CONST_09  C30  C24  C25  C26     0.00   0.0  0
 6ED  CONST_10  C30  C29  C27  C26     0.00   0.0  0
 6ED  CONST_11  N07  C08  C09  C04     0.00   0.0  0
 6ED  CONST_12  N07  C06  C05  C04     0.00   0.0  0
 6ED  CONST_13  C08  N07  C06  C05     0.00   0.0  0
 6ED  CONST_14  C08  C09  C04  C05     0.00   0.0  0
 6ED  CONST_15  C09  C08  N07  C06     0.00   0.0  0
 6ED  CONST_16  C09  C04  C05  C06     0.00   0.0  0
 6ED  CONST_17  N13  C24  C25  C11     0.00   0.0  0
 6ED  CONST_18  C30  C24  C25  C11   180.00   0.0  0
 6ED  CONST_19  C27  C26  C25  C11   180.00   0.0  0
 6ED  CONST_20  C25  C11  N12  N13     0.00   0.0  0
 6ED  CONST_21  C29  C30  C24  N13   180.00   0.0  0
 6ED  CONST_22  C29  C30  C24  C25     0.00   0.0  0
 6ED  CONST_23  C29  C27  C26  C25     0.00   0.0  0
 6ED  CONST_24  N10  C11  C25  C24   180.00   0.0  0
 6ED  CONST_25  N10  C11  C25  C26     0.00   0.0  0
 6ED  CONST_26  C08  C09  C04  C02   180.00   0.0  0
 6ED  CONST_27  C06  C05  C04  C02   180.00   0.0  0
 6ED  CONST_28  N10  C09  C04  C05   180.00   0.0  0
 6ED  CONST_29  N10  C09  C08  N07   180.00   0.0  0
 6ED  CONST_30  N13  N12  C11  N10   180.00   0.0  0
 6ED  CONST_31  C14  N13  N12  C11   180.00   0.0  0
 6ED  CONST_32  C14  N13  C24  C25   180.00   0.0  0
 6ED  CONST_33  F28  C27  C26  C25   180.00   0.0  0
 6ED  CONST_34  C30  C29  C27  F28   180.00   0.0  0
 6ED  CONST_35  C14  N13  C24  C30     0.00   0.0  0
 6ED  CONST_36  H13  C29  C30  C24   180.00   0.0  0
 6ED  CONST_37  H7   C26  C25  C24   180.00   0.0  0
 6ED  CONST_38  H11  C08  C09  C04   180.00   0.0  0
 6ED  CONST_39  H10  C06  C05  C04   180.00   0.0  0
 6ED  CONST_40  H9   C05  C06  N07   180.00   0.0  0
 6ED  CONST_41  H14  C30  C24  N13     0.00   0.0  0
 6ED  CONST_42  H8   O01  C02  C04   180.00   0.0  0
 6ED  Var_01    C22  C19  C18  C17   -51.58  30.0  1
 6ED  Var_02    C22  C23  N16  C17    61.49  30.0  1
 6ED  Var_03    C19  C18  C17  N16    55.98  30.0  1
 6ED  Var_04    C19  C22  C23  N16   -55.73  30.0  1
 6ED  Var_05    C23  N16  C17  C18   -61.51  30.0  1
 6ED  Var_06    C23  C22  C19  C18    51.37  30.0  1
 6ED  Var_07    C09  N10  C11  N12    -2.80  30.0  2
 6ED  Var_08    C11  N10  C09  C04  -179.03  30.0  2
 6ED  Var_09    C15  C14  N13  N12    85.36  30.0  2
 6ED  Var_10    C14  C15  N16  C17  -154.09  30.0  3
 6ED  Var_11    C09  C04  C02  O01  -179.75  30.0  1
 6ED  Var_12    N16  C15  C14  N13   178.92  30.0  1

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
 6ED  plan-1  C04  0.020
 6ED  plan-1  C05  0.020
 6ED  plan-1  C06  0.020
 6ED  plan-1  N07  0.020
 6ED  plan-1  C08  0.020
 6ED  plan-1  C09  0.020
 6ED  plan-1  H9   0.020
 6ED  plan-1  H10  0.020
 6ED  plan-1  H11  0.020
 6ED  plan-1  N10  0.020
 6ED  plan-1  C02  0.020
 6ED  plan-2  N12  0.020
 6ED  plan-2  C24  0.020
 6ED  plan-2  C26  0.020
 6ED  plan-2  C11  0.020
 6ED  plan-2  N13  0.020
 6ED  plan-2  C25  0.020
 6ED  plan-2  C27  0.020
 6ED  plan-2  F28  0.020
 6ED  plan-2  C29  0.020
 6ED  plan-2  C30  0.020
 6ED  plan-2  C14  0.020
 6ED  plan-2  H7   0.020
 6ED  plan-2  H13  0.020
 6ED  plan-2  H14  0.020
 6ED  plan-2  N10  0.020
 6ED  plan-3  O01  0.020
 6ED  plan-3  O03  0.020
 6ED  plan-3  C04  0.020
 6ED  plan-3  H8   0.020
 6ED  plan-3  C02  0.020

