# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 13:33:15 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(NC(=O)N2CCc3n[nH]c(c3C2)c4ccccc4)cc1Cl
#
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
 VXJ  VXJ  N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide  ligand  42  26  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VXJ
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
 VXJ  C10   C   CR16  0  -0.417  -52.3707  -18.2370  27.3421
 VXJ  C11   C   CR16  0  -0.262  -53.6098  -18.6920  26.9235
 VXJ  C17   C   CH2   0  -0.385  -57.8431  -21.3729  26.0855
 VXJ  C16   C   CR5   0  -0.198  -58.5529  -21.1894  24.7796
 VXJ  C15   C   CR5   0   0.237  -59.2346  -20.0110  24.4341
 VXJ  C14   C   CH2   0  -0.501  -59.3373  -18.8367  25.3474
 VXJ  C13   C   CH2   0  -0.334  -58.9642  -19.3074  26.7500
 VXJ  C18   C   CR5   0   0.415  -58.6801  -22.0095  23.6727
 VXJ  C19   C   CR6   0   0.062  -58.1758  -23.3516  23.3953
 VXJ  C20   C   CR16  0  -0.304  -57.8515  -23.7486  22.0953
 VXJ  C21   C   CR16  0  -0.237  -57.3785  -25.0277  21.8467
 VXJ  C22   C   CR16  0  -0.261  -57.2077  -25.9273  22.8909
 VXJ  O01   O   O     0  -0.504  -56.4918  -18.2526  27.2602
 VXJ  C02   C   C     0   0.715  -56.5630  -19.4531  27.0528
 VXJ  N03   N   NH1   0  -0.788  -55.4558  -20.2756  27.1506
 VXJ  C04   C   CR6   0   0.353  -54.2068  -19.7837  27.5520
 VXJ  C05   C   CR16  0  -0.280  -53.5304  -20.4291  28.5829
 VXJ  C06   C   CR6   0  -0.218  -52.2811  -19.9837  28.9826
 VXJ  CL07  CL  CL    0  -0.091  -51.4349  -20.7771  30.2556
 VXJ  C08   C   CR6   0   0.593  -51.7140  -18.8807  28.3717
 VXJ  F09   F   F     0  -0.297  -50.5191  -18.4454  28.7812
 VXJ  N12   N   NT    0  -0.499  -57.7306  -20.0780  26.7403
 VXJ  C23   C   CR16  0  -0.233  -57.5208  -25.5398  24.1868
 VXJ  C24   C   CR16  0  -0.324  -58.0046  -24.2648  24.4374
 VXJ  N25   N   NR15  0  -0.515  -59.3969  -21.2915  22.7803
 VXJ  N26   N   N     0  -0.285  -59.7466  -20.0882  23.2199
 VXJ  H1    H   HCR6  0   0.290  -51.9069  -17.3866  26.8592
 VXJ  H2    H   HCR6  0   0.278  -54.1009  -18.1967  26.0990
 VXJ  H3    H   HCH2  0   0.263  -58.3874  -22.0627  26.7395
 VXJ  H4    H   HCH2  0   0.269  -56.8597  -21.8106  25.9160
 VXJ  H5    H   HCH2  0   0.254  -58.6620  -18.0366  25.0316
 VXJ  H6    H   HCH2  0   0.256  -60.3468  -18.4209  25.3479
 VXJ  H7    H   HCH2  0   0.271  -58.8689  -18.4688  27.4335
 VXJ  H8    H   HCH2  0   0.256  -59.7532  -19.9553  27.1423
 VXJ  H9    H   HCR6  0   0.255  -57.9503  -23.0552  21.2691
 VXJ  H10   H   HCR6  0   0.261  -57.1336  -25.3185  20.8335
 VXJ  H11   H   HCR6  0   0.259  -56.8341  -26.9238  22.6953
 VXJ  H12   H   HNH1  0   0.416  -55.6159  -21.2464  27.3735
 VXJ  H13   H   HCR6  0   0.295  -53.9795  -21.2781  29.0830
 VXJ  H14   H   HCR6  0   0.260  -57.3970  -26.2347  25.0071
 VXJ  H15   H   HCR6  0   0.260  -58.2708  -23.9908  25.4499
 VXJ  H16   H   HNR5  0   0.417  -59.7220  -21.6005  21.8772

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
 VXJ  C21  C20   aromatic  1.386  0.020  1.386
 VXJ  C21  C22   aromatic  1.389  0.020  1.389
 VXJ  C20  C19   aromatic  1.397  0.020  1.397
 VXJ  N25  N26   aromatic  1.328  0.020  1.328
 VXJ  N25  C18   aromatic  1.351  0.020  1.351
 VXJ  N26  C15   aromatic  1.320  0.020  1.320
 VXJ  C22  C23   aromatic  1.388  0.020  1.388
 VXJ  C19  C18   single    1.460  0.020  1.460
 VXJ  C19  C24   aromatic  1.396  0.020  1.396
 VXJ  C18  C16   aromatic  1.383  0.020  1.383
 VXJ  C15  C16   aromatic  1.405  0.020  1.405
 VXJ  C15  C14   single    1.491  0.020  1.491
 VXJ  C23  C24   aromatic  1.387  0.020  1.387
 VXJ  C16  C17   single    1.498  0.020  1.498
 VXJ  C14  C13   single    1.526  0.020  1.526
 VXJ  C17  N12   single    1.455  0.020  1.455
 VXJ  N12  C13   single    1.455  0.020  1.455
 VXJ  N12  C02   single    1.361  0.020  1.361
 VXJ  C11  C10   aromatic  1.385  0.020  1.385
 VXJ  C11  C04   aromatic  1.394  0.020  1.394
 VXJ  C10  C08   aromatic  1.380  0.020  1.380
 VXJ  C02  O01   double    1.220  0.020  1.220
 VXJ  C02  N03   single    1.383  0.020  1.383
 VXJ  N03  C04   single    1.401  0.020  1.401
 VXJ  C04  C05   aromatic  1.392  0.020  1.392
 VXJ  C08  F09   single    1.336  0.020  1.336
 VXJ  C08  C06   aromatic  1.383  0.020  1.383
 VXJ  C05  C06   aromatic  1.385  0.020  1.385
 VXJ  C06  CL07  single    1.722  0.020  1.722
 VXJ  C10  H1    single    0.930  0.020  1.080
 VXJ  C11  H2    single    0.930  0.020  1.080
 VXJ  C17  H3    single    0.970  0.020  1.090
 VXJ  C17  H4    single    0.970  0.020  1.090
 VXJ  C14  H5    single    0.970  0.020  1.090
 VXJ  C14  H6    single    0.970  0.020  1.090
 VXJ  C13  H7    single    0.970  0.020  1.090
 VXJ  C13  H8    single    0.970  0.020  1.090
 VXJ  C20  H9    single    0.930  0.020  1.080
 VXJ  C21  H10   single    0.930  0.020  1.080
 VXJ  C22  H11   single    0.930  0.020  1.080
 VXJ  N03  H12   single    0.890  0.020  1.040
 VXJ  C05  H13   single    0.930  0.020  1.080
 VXJ  C23  H14   single    0.930  0.020  1.080
 VXJ  C24  H15   single    0.930  0.020  1.080
 VXJ  N25  H16   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
 VXJ  H1    C10  C08   119.69  3.000
 VXJ  H1    C10  C11   120.45  3.000
 VXJ  C08   C10  C11   119.86  3.000
 VXJ  H2    C11  C04   120.58  3.000
 VXJ  H2    C11  C10   119.14  3.000
 VXJ  C04   C11  C10   120.28  3.000
 VXJ  H4    C17  H3    106.76  3.000
 VXJ  H4    C17  N12   110.95  3.000
 VXJ  H3    C17  N12   109.28  3.000
 VXJ  H4    C17  C16   109.95  3.000
 VXJ  H3    C17  C16   111.24  3.000
 VXJ  N12   C17  C16   108.66  3.000
 VXJ  C18   C16  C15   104.83  3.000
 VXJ  C15   C16  C17   123.18  3.000
 VXJ  C18   C16  C17   131.96  3.000
 VXJ  N26   C15  C14   125.64  3.000
 VXJ  C14   C15  C16   122.92  3.000
 VXJ  N26   C15  C16   111.44  3.000
 VXJ  H6    C14  H5    107.01  3.000
 VXJ  H6    C14  C13   110.07  3.000
 VXJ  H5    C14  C13   109.89  3.000
 VXJ  H6    C14  C15   111.34  3.000
 VXJ  H5    C14  C15   110.90  3.000
 VXJ  C13   C14  C15   107.65  3.000
 VXJ  H8    C13  H7    107.16  3.000
 VXJ  H8    C13  N12   107.48  3.000
 VXJ  H7    C13  N12   109.81  3.000
 VXJ  H8    C13  C14   109.64  3.000
 VXJ  H7    C13  C14   111.21  3.000
 VXJ  N12   C13  C14   111.39  3.000
 VXJ  N25   C18  C19   123.10  3.000
 VXJ  C19   C18  C16   131.69  3.000
 VXJ  N25   C18  C16   105.20  3.000
 VXJ  C24   C19  C20   118.69  3.000
 VXJ  C24   C19  C18   120.11  3.000
 VXJ  C20   C19  C18   121.20  3.000
 VXJ  H9    C20  C21   119.02  3.000
 VXJ  H9    C20  C19   120.43  3.000
 VXJ  C21   C20  C19   120.54  3.000
 VXJ  H10   C21  C22   120.14  3.000
 VXJ  H10   C21  C20   119.54  3.000
 VXJ  C22   C21  C20   120.32  3.000
 VXJ  H11   C22  C23   120.24  3.000
 VXJ  H11   C22  C21   120.20  3.000
 VXJ  C23   C22  C21   119.56  3.000
 VXJ  N12   C02  N03   115.48  3.000
 VXJ  N03   C02  O01   121.76  3.000
 VXJ  N12   C02  O01   122.74  3.000
 VXJ  H12   N03  C04   114.58  3.000
 VXJ  H12   N03  C02   117.45  3.000
 VXJ  C04   N03  C02   121.69  3.000
 VXJ  C05   C04  N03   118.86  3.000
 VXJ  C05   C04  C11   119.28  3.000
 VXJ  N03   C04  C11   121.83  3.000
 VXJ  H13   C05  C06   119.53  3.000
 VXJ  H13   C05  C04   120.28  3.000
 VXJ  C06   C05  C04   120.20  3.000
 VXJ  C08   C06  CL07  119.51  3.000
 VXJ  CL07  C06  C05   120.55  3.000
 VXJ  C08   C06  C05   119.93  3.000
 VXJ  F09   C08  C06   119.43  3.000
 VXJ  C06   C08  C10   120.43  3.000
 VXJ  F09   C08  C10   120.14  3.000
 VXJ  C02   N12  C13   118.88  3.000
 VXJ  C02   N12  C17   125.33  3.000
 VXJ  C13   N12  C17   114.13  3.000
 VXJ  H14   C23  C24   119.56  3.000
 VXJ  H14   C23  C22   120.17  3.000
 VXJ  C24   C23  C22   120.26  3.000
 VXJ  H15   C24  C23   119.19  3.000
 VXJ  H15   C24  C19   120.17  3.000
 VXJ  C23   C24  C19   120.62  3.000
 VXJ  H16   N25  N26   119.29  3.000
 VXJ  H16   N25  C18   126.85  3.000
 VXJ  N26   N25  C18   113.74  3.000
 VXJ  N25   N26  C15   104.79  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
 VXJ  CONST_01  C05   C04  C11  C10    0.00   0.0  0
 VXJ  CONST_02  C05   C06  C08  C10    0.00   0.0  0
 VXJ  CONST_03  C06   C08  C10  C11    0.00   0.0  0
 VXJ  CONST_04  C06   C05  C04  C11    0.00   0.0  0
 VXJ  CONST_05  N26   N25  C18  C16    0.00   0.0  0
 VXJ  CONST_08  N25   N26  C15  C16    0.00   0.0  0
 VXJ  CONST_09  C18   N25  N26  C15    0.00   0.0  0
 VXJ  CONST_10  N25   C18  C16  C15    0.00   0.0  0
 VXJ  CONST_11  C19   C18  C16  C15  180.00   0.0  0
 VXJ  CONST_12  C21   C20  C19  C18  180.00   0.0  0
 VXJ  CONST_13  C23   C24  C19  C18  180.00   0.0  0
 VXJ  CONST_14  N26   C15  C16  C18    0.00   0.0  0
 VXJ  CONST_15  C22   C21  C20  C19    0.00   0.0  0
 VXJ  CONST_16  N26   N25  C18  C19  180.00   0.0  0
 VXJ  CONST_17  C22   C23  C24  C19    0.00   0.0  0
 VXJ  CONST_18  C23   C22  C21  C20    0.00   0.0  0
 VXJ  CONST_20  C23   C24  C19  C20    0.00   0.0  0
 VXJ  CONST_21  C24   C19  C20  C21    0.00   0.0  0
 VXJ  CONST_22  C24   C23  C22  C21    0.00   0.0  0
 VXJ  CONST_23  C08   C10  C11  C04    0.00   0.0  0
 VXJ  CONST_24  C08   C06  C05  C04    0.00   0.0  0
 VXJ  CONST_26  C19   C18  C16  C17    0.00   0.0  0
 VXJ  CONST_27  N03   C04  C11  C10  180.00   0.0  0
 VXJ  CONST_28  CL07  C06  C08  C10  180.00   0.0  0
 VXJ  CONST_29  F09   C08  C10  C11  180.00   0.0  0
 VXJ  CONST_30  C06   C05  C04  N03  180.00   0.0  0
 VXJ  CONST_31  CL07  C06  C05  C04  180.00   0.0  0
 VXJ  CONST_32  F09   C08  C06  C05  180.00   0.0  0
 VXJ  CONST_33  H13   C05  C04  C11  180.00   0.0  0
 VXJ  CONST_34  H16   N25  C18  C16  180.00   0.0  0
 VXJ  CONST_35  H9    C20  C19  C18    0.00   0.0  0
 VXJ  CONST_36  H15   C24  C19  C18    0.00   0.0  0
 VXJ  CONST_37  H10   C21  C20  C19  180.00   0.0  0
 VXJ  CONST_38  H14   C23  C24  C19  180.00   0.0  0
 VXJ  CONST_39  H11   C22  C21  C20  180.00   0.0  0
 VXJ  CONST_40  H1    C10  C11  C04  180.00   0.0  0
 VXJ  CONST_41  H2    C11  C04  C05  180.00   0.0  0
 VXJ  CONST_43  O01   C02  N12  C13    0.00   0.0  0
 VXJ  CONST_46  N12   C02  N03  C04  180.00   0.0  0
 VXJ  CONST_48  N03   C02  N12  C13  180.00   0.0  0
 VXJ  CONST_50  C04   N03  C02  O01    0.00   0.0  0
 VXJ  Var_01    C14   C13  N12  C17  -68.82  30.0  1
 VXJ  Var_02    C13   C14  C15  C16  -16.12  30.0  1
 VXJ  Var_03    C13   N12  C17  C16   46.81  30.0  1
 VXJ  Var_04    N12   C17  C16  C15  -12.74  30.0  1
 VXJ  Var_05    N12   C13  C14  C15   48.30  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
 VXJ  plan-1  C10   0.020
 VXJ  plan-1  C11   0.020
 VXJ  plan-1  N03   0.020
 VXJ  plan-1  C04   0.020
 VXJ  plan-1  C05   0.020
 VXJ  plan-1  C06   0.020
 VXJ  plan-1  CL07  0.020
 VXJ  plan-1  C08   0.020
 VXJ  plan-1  F09   0.020
 VXJ  plan-1  H1    0.020
 VXJ  plan-1  H2    0.020
 VXJ  plan-1  H13   0.020
 VXJ  plan-2  C18   0.020
 VXJ  plan-2  C19   0.020
 VXJ  plan-2  C20   0.020
 VXJ  plan-2  C21   0.020
 VXJ  plan-2  C22   0.020
 VXJ  plan-2  C23   0.020
 VXJ  plan-2  C24   0.020
 VXJ  plan-2  H9    0.020
 VXJ  plan-2  H10   0.020
 VXJ  plan-2  H11   0.020
 VXJ  plan-2  H14   0.020
 VXJ  plan-2  H15   0.020
 VXJ  plan-3  C17   0.020
 VXJ  plan-3  C16   0.020
 VXJ  plan-3  C15   0.020
 VXJ  plan-3  C14   0.020
 VXJ  plan-3  C18   0.020
 VXJ  plan-3  C19   0.020
 VXJ  plan-3  N25   0.020
 VXJ  plan-3  N26   0.020
 VXJ  plan-3  H16   0.020
 VXJ  plan-4  C17   0.020
 VXJ  plan-4  C13   0.020
 VXJ  plan-4  O01   0.020
 VXJ  plan-4  C02   0.020
 VXJ  plan-4  N03   0.020
 VXJ  plan-4  C04   0.020
 VXJ  plan-4  N12   0.020
 VXJ  plan-4  H12   0.020

