# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 23:19:43 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 3-[4-[6-chloranyl-5-[[(3~{R})-pyrrolidin-3-yl]amino]-1~{H}-indazol-3-yl]pyrazol-1-yl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc2[nH]nc(c3cnn(c3)c4cccc(c4)C#N)c2cc1N[C@@H]5CCNC5
#
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
 E56  E56  "3-[4-[6-chloranyl-5-[[(3R)-pyrrolidin-3-yl]amino]-1H-indazol-3-yl]pyrazol-1-yl]benzenecarbonitrile"
  ligand  47  29  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E56
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
 E56  C16  C   CR16  0  -0.248  23.0748   -8.6238  -21.9878
 E56  C19  C   CSP   0   0.059  24.0046   -7.4227  -20.0784
 E56  C02  C   CR6   0  -0.146  12.5738  -10.2605  -17.2466
 E56  C03  C   CR16  0  -0.258  13.0190  -11.3911  -17.8818
 E56  C04  C   CR56  0   0.384  14.3110  -11.3504  -18.4073
 E56  C07  C   CR5   0   0.200  16.3260  -10.5727  -18.9566
 E56  C08  C   CR5   0  -0.176  17.5247   -9.7852  -19.1719
 E56  C09  C   CR15  0  -0.104  17.9627   -8.6208  -18.5000
 E56  C12  C   CR15  0   0.049  18.5264  -10.0379  -20.0798
 E56  C13  C   CR6   0   0.407  20.6656   -8.9145  -20.6155
 E56  C14  C   CR16  0  -0.293  20.8077   -9.4287  -21.9002
 E56  C15  C   CR16  0  -0.235  22.0109   -9.2870  -22.5738
 E56  C17  C   CR6   0   0.022  22.9157   -8.1031  -20.7049
 E56  C18  C   CR16  0  -0.298  21.7191   -8.2456  -20.0091
 E56  C21  C   CR56  0  -0.070  15.1150  -10.2102  -18.2927
 E56  C22  C   CR16  0  -0.493  14.6227   -9.0628  -17.6574
 E56  C23  C   CR6   0   0.456  13.3455   -9.0652  -17.1151
 E56  C25  C   CR15  0  -0.105  13.4545   -6.6995  -16.4356
 E56  C26  C   CH2   0  -0.488  12.7890   -5.7296  -15.4494
 E56  C27  C   CH2   0  -0.308  12.9308   -4.3432  -16.1198
 E56  C29  C   CH2   0  -0.319  13.4028   -5.9113  -17.7576
 E56  N05  N   NR15  0  -0.545  15.0395  -12.2655  -19.0918
 E56  N06  N   N     0  -0.256  16.2409  -11.8046  -19.4164
 E56  N10  N   N     0  -0.265  19.1213   -8.2045  -18.9569
 E56  N11  N   NR5   0  -0.413  19.4558   -9.0689  -19.9176
 E56  N20  N   NS    0  -0.241  24.8848   -6.8767  -19.5747
 E56  N24  N   NH1   0  -0.697  12.8234   -7.9950  -16.4263
 E56  N28  N   NR15  0  -0.583  13.6460   -4.5294  -17.3856
 E56  H1   H   HCR6  0   0.286  24.0120   -8.5080  -22.5140
 E56  H2   H   HCR6  0   0.291  12.3924  -12.2688  -17.9652
 E56  H3   H   HCR5  0   0.268  17.4803   -8.0825  -17.6988
 E56  H4   H   HCR5  0   0.302  18.6379  -10.8347  -20.7962
 E56  H5   H   HCR6  0   0.296  19.9827   -9.9277  -22.3909
 E56  H6   H   HCR6  0   0.283  22.1117   -9.6904  -23.5718
 E56  H7   H   HCR6  0   0.299  21.6145   -7.8471  -19.0100
 E56  H8   H   HCR6  0   0.270  15.2324   -8.1733  -17.5982
 E56  H9   H   HCR5  0   0.243  14.5036   -6.8250  -16.1487
 E56  H10  H   HCH2  0   0.237  11.7359   -5.9888  -15.3149
 E56  H11  H   HCH2  0   0.249  13.2569   -5.7710  -14.4665
 E56  H12  H   HCH2  0   0.236  13.4607   -3.6263  -15.4934
 E56  H13  H   HCH2  0   0.224  11.9425   -3.9219  -16.3180
 E56  H14  H   HCH2  0   0.220  12.4017   -6.0109  -18.1929
 E56  H15  H   HCH2  0   0.244  14.1233   -6.2489  -18.5031
 E56  H16  H   HNR5  0   0.417  14.7769  -13.2040  -19.3456
 E56  H17  H   HNH1  0   0.370  11.8159   -7.9561  -16.3922
 E56  H18  H   HNR5  0   0.345  14.6385   -4.4132  -17.2200
 E56  CL1  CL  CL    0  -0.117  10.9757  -10.2876  -16.5672

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
 E56  C15  C16  aromatic  1.384  0.020  1.384
 E56  C15  C14  aromatic  1.386  0.020  1.386
 E56  C16  C17  aromatic  1.394  0.020  1.394
 E56  C14  C13  aromatic  1.391  0.020  1.391
 E56  C17  C19  single    1.429  0.020  1.429
 E56  C17  C18  aromatic  1.391  0.020  1.391
 E56  C13  C18  aromatic  1.387  0.020  1.387
 E56  C13  N11  single    1.405  0.020  1.405
 E56  C12  N11  aromatic  1.352  0.020  1.352
 E56  C12  C08  aromatic  1.375  0.020  1.375
 E56  C19  N20  triple    1.152  0.020  1.152
 E56  N11  N10  aromatic  1.335  0.020  1.335
 E56  N06  N05  aromatic  1.327  0.020  1.327
 E56  N06  C07  aromatic  1.318  0.020  1.318
 E56  C08  C07  single    1.450  0.020  1.450
 E56  C08  C09  aromatic  1.414  0.020  1.414
 E56  N05  C04  aromatic  1.355  0.020  1.355
 E56  C07  C21  aromatic  1.428  0.020  1.428
 E56  N10  C09  aromatic  1.313  0.020  1.313
 E56  C04  C21  aromatic  1.400  0.020  1.400
 E56  C04  C03  aromatic  1.395  0.020  1.395
 E56  C21  C22  aromatic  1.401  0.020  1.401
 E56  C03  C02  aromatic  1.371  0.020  1.371
 E56  C29  N28  single    1.452  0.020  1.452
 E56  C29  C25  single    1.540  0.020  1.540
 E56  C22  C23  aromatic  1.388  0.020  1.388
 E56  C02  C23  aromatic  1.429  0.020  1.429
 E56  C02  CL1  single    1.737  0.020  1.737
 E56  N28  C27  single    1.466  0.020  1.466
 E56  C23  N24  single    1.376  0.020  1.376
 E56  C25  N24  single    1.441  0.020  1.441
 E56  C25  C26  single    1.535  0.020  1.535
 E56  C27  C26  single    1.547  0.020  1.547
 E56  C16  H1   single    0.930  0.020  1.080
 E56  C03  H2   single    0.930  0.020  1.080
 E56  C09  H3   single    0.930  0.020  1.080
 E56  C12  H4   single    0.930  0.020  1.080
 E56  C14  H5   single    0.930  0.020  1.080
 E56  C15  H6   single    0.930  0.020  1.080
 E56  C18  H7   single    0.930  0.020  1.080
 E56  C22  H8   single    0.930  0.020  1.080
 E56  C25  H9   single    0.970  0.020  1.090
 E56  C26  H10  single    0.970  0.020  1.090
 E56  C26  H11  single    0.970  0.020  1.090
 E56  C27  H12  single    0.970  0.020  1.090
 E56  C27  H13  single    0.970  0.020  1.090
 E56  C29  H14  single    0.970  0.020  1.090
 E56  C29  H15  single    0.970  0.020  1.090
 E56  N05  H16  single    0.860  0.020  1.020
 E56  N24  H17  single    0.890  0.020  1.040
 E56  N28  H18  single    0.890  0.020  1.040

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
 E56  H1   C16  C17  120.46  3.000
 E56  H1   C16  C15  120.78  3.000
 E56  C17  C16  C15  118.76  3.000
 E56  N20  C19  C17  180.00  3.000
 E56  CL1  C02  C23  118.29  3.000
 E56  CL1  C02  C03  117.85  3.000
 E56  C23  C02  C03  123.86  3.000
 E56  H2   C03  C04  122.07  3.000
 E56  H2   C03  C02  121.12  3.000
 E56  C04  C03  C02  116.81  3.000
 E56  N05  C04  C21  106.42  3.000
 E56  C21  C04  C03  121.65  3.000
 E56  N05  C04  C03  131.93  3.000
 E56  N06  C07  C21  110.17  3.000
 E56  C21  C07  C08  129.21  3.000
 E56  N06  C07  C08  120.61  3.000
 E56  C12  C08  C09  103.85  3.000
 E56  C09  C08  C07  129.25  3.000
 E56  C12  C08  C07  126.88  3.000
 E56  H3   C09  N10  119.65  3.000
 E56  H3   C09  C08  128.69  3.000
 E56  N10  C09  C08  111.66  3.000
 E56  H4   C12  N11  122.59  3.000
 E56  H4   C12  C08  130.56  3.000
 E56  N11  C12  C08  106.84  3.000
 E56  N11  C13  C18  119.32  3.000
 E56  N11  C13  C14  120.40  3.000
 E56  C18  C13  C14  120.28  3.000
 E56  H5   C14  C15  119.25  3.000
 E56  H5   C14  C13  120.76  3.000
 E56  C15  C14  C13  119.98  3.000
 E56  H6   C15  C14  119.43  3.000
 E56  H6   C15  C16  119.87  3.000
 E56  C14  C15  C16  120.69  3.000
 E56  C18  C17  C19  119.01  3.000
 E56  C18  C17  C16  121.34  3.000
 E56  C19  C17  C16  119.65  3.000
 E56  H7   C18  C17  120.51  3.000
 E56  H7   C18  C13  120.55  3.000
 E56  C17  C18  C13  118.94  3.000
 E56  C22  C21  C07  135.79  3.000
 E56  C22  C21  C04  120.16  3.000
 E56  C07  C21  C04  104.02  3.000
 E56  H8   C22  C23  119.97  3.000
 E56  H8   C22  C21  120.07  3.000
 E56  C23  C22  C21  119.95  3.000
 E56  N24  C23  C22  122.93  3.000
 E56  N24  C23  C02  119.47  3.000
 E56  C22  C23  C02  117.56  3.000
 E56  H9   C25  N24  108.36  3.000
 E56  H9   C25  C29  108.41  3.000
 E56  N24  C25  C29  116.80  3.000
 E56  H9   C25  C26  108.63  3.000
 E56  N24  C25  C26  111.96  3.000
 E56  C29  C25  C26  102.33  3.000
 E56  H11  C26  H10  107.08  3.000
 E56  H11  C26  C27  112.69  3.000
 E56  H10  C26  C27  110.75  3.000
 E56  H11  C26  C25  111.68  3.000
 E56  H10  C26  C25  110.31  3.000
 E56  C27  C26  C25  104.37  3.000
 E56  H13  C27  H12  106.90  3.000
 E56  H13  C27  N28  109.50  3.000
 E56  H12  C27  N28  110.04  3.000
 E56  H13  C27  C26  109.96  3.000
 E56  H12  C27  C26  112.66  3.000
 E56  N28  C27  C26  107.77  3.000
 E56  H15  C29  H14  107.69  3.000
 E56  H15  C29  N28  111.05  3.000
 E56  H14  C29  N28  109.95  3.000
 E56  H15  C29  C25  113.97  3.000
 E56  H14  C29  C25  108.97  3.000
 E56  N28  C29  C25  105.17  3.000
 E56  H16  N05  N06  119.87  3.000
 E56  H16  N05  C04  128.05  3.000
 E56  N06  N05  C04  112.07  3.000
 E56  N05  N06  C07  107.32  3.000
 E56  N11  N10  C09  105.44  3.000
 E56  N10  N11  C13  120.13  3.000
 E56  N10  N11  C12  112.21  3.000
 E56  C13  N11  C12  127.65  3.000
 E56  H17  N24  C25  113.76  3.000
 E56  H17  N24  C23  115.21  3.000
 E56  C25  N24  C23  122.00  3.000
 E56  H18  N28  C29  108.38  3.000
 E56  H18  N28  C27  108.81  3.000
 E56  C29  N28  C27  105.10  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
 E56  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 E56  CONST_02  C13  C18  C17  C16     0.00   0.0  0
 E56  CONST_03  N05  C04  C03  C02   180.00   0.0  0
 E56  CONST_04  C21  C04  C03  C02     0.00   0.0  0
 E56  CONST_05  C21  C22  C23  C02     0.00   0.0  0
 E56  CONST_06  N06  N05  C04  C03   180.00   0.0  0
 E56  CONST_07  C07  C21  C04  C03   180.00   0.0  0
 E56  CONST_08  C22  C21  C04  C03     0.00   0.0  0
 E56  CONST_09  C22  C23  C02  C03     0.00   0.0  0
 E56  CONST_10  C07  N06  N05  C04     0.00   0.0  0
 E56  CONST_11  N06  C07  C21  C04     0.00   0.0  0
 E56  CONST_12  C08  C07  C21  C04   180.00   0.0  0
 E56  CONST_13  C23  C22  C21  C04     0.00   0.0  0
 E56  CONST_14  C23  C02  C03  C04     0.00   0.0  0
 E56  CONST_15  N11  C12  C08  C07   180.00   0.0  0
 E56  CONST_16  N10  C09  C08  C07   180.00   0.0  0
 E56  CONST_17  N05  C04  C21  C07     0.00   0.0  0
 E56  CONST_18  C23  C22  C21  C07   180.00   0.0  0
 E56  CONST_19  C13  N11  C12  C08   180.00   0.0  0
 E56  CONST_20  N10  N11  C12  C08     0.00   0.0  0
 E56  CONST_21  N05  N06  C07  C08   180.00   0.0  0
 E56  CONST_22  C22  C21  C07  C08     0.00   0.0  0
 E56  CONST_23  N11  N10  C09  C08     0.00   0.0  0
 E56  CONST_24  N11  C12  C08  C09     0.00   0.0  0
 E56  CONST_27  C13  N11  N10  C09   180.00   0.0  0
 E56  CONST_28  C12  N11  N10  C09     0.00   0.0  0
 E56  CONST_33  N10  C09  C08  C12     0.00   0.0  0
 E56  CONST_34  C17  C16  C15  C14     0.00   0.0  0
 E56  CONST_35  C17  C18  C13  C14     0.00   0.0  0
 E56  CONST_37  C18  C17  C16  C15     0.00   0.0  0
 E56  CONST_38  C18  C13  C14  C15     0.00   0.0  0
 E56  CONST_39  N11  C13  C14  C15   180.00   0.0  0
 E56  CONST_40  N11  C13  C18  C17   180.00   0.0  0
 E56  CONST_42  N05  N06  C07  C21     0.00   0.0  0
 E56  CONST_43  N06  N05  C04  C21     0.00   0.0  0
 E56  CONST_44  N06  C07  C21  C22   180.00   0.0  0
 E56  CONST_45  N05  C04  C21  C22   180.00   0.0  0
 E56  CONST_46  C15  C16  C17  C19   180.00   0.0  0
 E56  CONST_47  C13  C18  C17  C19   180.00   0.0  0
 E56  CONST_48  N24  C23  C02  C03   180.00   0.0  0
 E56  CONST_49  CL1  C02  C03  C04   180.00   0.0  0
 E56  CONST_50  N24  C23  C22  C21   180.00   0.0  0
 E56  CONST_51  CL1  C02  C23  C22   180.00   0.0  0
 E56  CONST_52  C25  N24  C23  C02   180.00   0.0  0
 E56  CONST_53  C25  N24  C23  C22     0.00   0.0  0
 E56  CONST_54  H5   C14  C15  C16   180.00   0.0  0
 E56  CONST_55  H7   C18  C17  C16   180.00   0.0  0
 E56  CONST_56  H8   C22  C23  C02   180.00   0.0  0
 E56  CONST_57  H16  N05  C04  C03     0.00   0.0  0
 E56  CONST_58  H8   C22  C21  C04   180.00   0.0  0
 E56  CONST_59  H16  N05  N06  C07   180.00   0.0  0
 E56  CONST_60  H4   C12  C08  C07     0.00   0.0  0
 E56  CONST_61  H3   C09  C08  C07     0.00   0.0  0
 E56  CONST_62  H8   C22  C21  C07     0.00   0.0  0
 E56  CONST_63  H4   C12  C08  C09   180.00   0.0  0
 E56  CONST_64  H3   C09  C08  C12   180.00   0.0  0
 E56  CONST_65  H6   C15  C14  C13   180.00   0.0  0
 E56  CONST_66  H4   C12  N11  C13     0.00   0.0  0
 E56  CONST_67  H1   C16  C15  C14   180.00   0.0  0
 E56  CONST_68  H7   C18  C13  C14   180.00   0.0  0
 E56  CONST_69  H6   C15  C16  C17   180.00   0.0  0
 E56  CONST_70  H1   C16  C17  C18   180.00   0.0  0
 E56  CONST_71  H5   C14  C13  C18   180.00   0.0  0
 E56  CONST_72  H16  N05  C04  C21   180.00   0.0  0
 E56  CONST_73  H2   C03  C04  C21   180.00   0.0  0
 E56  CONST_74  H2   C03  C02  C23   180.00   0.0  0
 E56  CONST_75  H2   C03  C04  N05     0.00   0.0  0
 E56  CONST_76  H4   C12  N11  N10   180.00   0.0  0
 E56  CONST_77  H5   C14  C13  N11     0.00   0.0  0
 E56  CONST_78  H7   C18  C13  N11     0.00   0.0  0
 E56  CONST_79  H3   C09  N10  N11   180.00   0.0  0
 E56  Var_01    C27  N28  C29  C25   -38.62  30.0  1
 E56  Var_02    N28  C27  C26  C25    -0.78  30.0  1
 E56  Var_03    C29  N28  C27  C26    24.41  30.0  1
 E56  Var_04    H18  N28  C29  C25    77.58  30.0  1
 E56  Var_05    H12  C27  C26  C25  -122.37  30.0  1
 E56  Var_06    H13  C27  C26  C25   118.51  30.0  1
 E56  Var_07    H18  N28  C27  C26   -91.49  30.0  1
 E56  Var_08    H14  C29  N28  C27    78.56  30.0  1
 E56  Var_09    H15  C29  N28  C27  -162.36  30.0  1
 E56  Var_10    H12  C27  N28  C29   147.61  30.0  1
 E56  Var_11    H13  C27  N28  C29   -95.18  30.0  1
 E56  Var_12    H10  C26  C27  N28  -119.48  30.0  1
 E56  Var_13    H11  C26  C27  N28   120.59  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E56  chir_01  C25  C29  N24  C26  positiv

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
 E56  plan-1  C07  0.020
 E56  plan-1  C08  0.020
 E56  plan-1  C09  0.020
 E56  plan-1  C12  0.020
 E56  plan-1  C13  0.020
 E56  plan-1  N10  0.020
 E56  plan-1  N11  0.020
 E56  plan-1  H3   0.020
 E56  plan-1  H4   0.020
 E56  plan-2  C16  0.020
 E56  plan-2  C19  0.020
 E56  plan-2  C13  0.020
 E56  plan-2  C14  0.020
 E56  plan-2  C15  0.020
 E56  plan-2  C17  0.020
 E56  plan-2  C18  0.020
 E56  plan-2  N11  0.020
 E56  plan-2  N20  0.020
 E56  plan-2  H1   0.020
 E56  plan-2  H5   0.020
 E56  plan-2  H6   0.020
 E56  plan-2  H7   0.020
 E56  plan-3  C02  0.020
 E56  plan-3  C03  0.020
 E56  plan-3  C04  0.020
 E56  plan-3  C07  0.020
 E56  plan-3  C08  0.020
 E56  plan-3  C21  0.020
 E56  plan-3  C22  0.020
 E56  plan-3  C23  0.020
 E56  plan-3  N05  0.020
 E56  plan-3  N06  0.020
 E56  plan-3  N24  0.020
 E56  plan-3  H2   0.020
 E56  plan-3  H8   0.020
 E56  plan-3  H16  0.020
 E56  plan-3  CL1  0.020
 E56  plan-4  C23  0.020
 E56  plan-4  C25  0.020
 E56  plan-4  N24  0.020
 E56  plan-4  H17  0.020

