# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:13:24 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-pyridin-4-yl-2,4-dihydroindeno[1,2-c]pyrazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1c2ccccc2c3n[nH]c(c13)c4ccncc4
#
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
 LIG  LIG  3-pyridin-4-yl-2,4-dihydroindeno[1,2-c]pyrazole  ligand  29  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIG
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
 LIG  N1    N  NR15  0  -0.534   1.8946   0.4510   0.6965
 LIG  N3    N  N     0  -0.264   2.1348   0.4914  -0.6100
 LIG  C4    C  CR55  0   0.165   0.9543   0.2496  -1.1460
 LIG  C5    C  CR55  0  -0.112  -0.0471   0.0559  -0.1878
 LIG  C6    C  CR5   0   0.394   0.5970   0.1934   1.0217
 LIG  C7    C  CR6   0   0.151   0.1144   0.1020   2.3905
 LIG  C8    C  CR16  0  -0.366   0.9547   0.2088   3.4983
 LIG  C10   C  CR16  0  -0.062   0.4109   0.1093   4.7680
 LIG  N12   N  N     0  -0.407  -0.8805  -0.0870   5.0063
 LIG  C13   C  CR16  0  -0.055  -1.6810  -0.1900   3.9510
 LIG  C15   C  CR16  0  -0.424  -1.2422  -0.1034   2.6412
 LIG  C17   C  CH2   0  -0.571  -1.3598  -0.2206  -0.8434
 LIG  C20   C  CR56  0   0.038  -0.9748  -0.1564  -2.3109
 LIG  C21   C  CR56  0   0.111   0.3926   0.1228  -2.4805
 LIG  C22   C  CR16  0  -0.317   0.9493   0.2282  -3.7459
 LIG  C24   C  CR16  0  -0.261   0.1244   0.0514  -4.8508
 LIG  C26   C  CR16  0  -0.257  -1.2292  -0.2263  -4.6881
 LIG  C28   C  CR16  0  -0.320  -1.7868  -0.3310  -3.4161
 LIG  HN1   H  HNR5  0   0.425   2.6579   0.6219   1.3323
 LIG  HC8   H  HCR6  0   0.262   2.0209   0.3626   3.4016
 LIG  HC10  H  HCR6  0   0.270   1.0584   0.1928   5.6335
 LIG  HC13  H  HCR6  0   0.270  -2.7342  -0.3485   4.1534
 LIG  HC15  H  HCR6  0   0.281  -1.9587  -0.1922   1.8361
 LIG  H171  H  HCH2  0   0.280  -2.1267   0.5203  -0.6001
 LIG  H172  H  HCH2  0   0.281  -1.7718  -1.1982  -0.5779
 LIG  HC22  H  HCR6  0   0.253   2.0026   0.4423  -3.8748
 LIG  HC24  H  HCR6  0   0.258   0.5389   0.1312  -5.8473
 LIG  HC26  H  HCR6  0   0.257  -1.8563  -0.3624  -5.5596
 LIG  HC28  H  HCR6  0   0.255  -2.8425  -0.5438  -3.2993

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
 LIG  N1   N3    aromatic  1.329  0.020  1.329
 LIG  N1   C6    aromatic  1.362  0.020  1.362
 LIG  N1   HN1   single    0.860  0.020  1.020
 LIG  N3   C4    aromatic  1.319  0.020  1.319
 LIG  C4   C5    aromatic  1.399  0.020  1.399
 LIG  C4   C21   aromatic  1.453  0.020  1.453
 LIG  C5   C6    aromatic  1.377  0.020  1.377
 LIG  C5   C17   single    1.493  0.020  1.493
 LIG  C6   C7    single    1.454  0.020  1.454
 LIG  C7   C8    aromatic  1.395  0.020  1.395
 LIG  C7   C15   aromatic  1.395  0.020  1.395
 LIG  C8   C10   aromatic  1.385  0.020  1.385
 LIG  C8   HC8   single    0.930  0.020  1.080
 LIG  C10  N12   aromatic  1.328  0.020  1.328
 LIG  C10  HC10  single    0.930  0.020  1.080
 LIG  N12  C13   aromatic  1.329  0.020  1.329
 LIG  C13  C15   aromatic  1.384  0.020  1.384
 LIG  C13  HC13  single    0.930  0.020  1.080
 LIG  C15  HC15  single    0.930  0.020  1.080
 LIG  C17  C20   single    1.518  0.020  1.518
 LIG  C17  H171  single    0.970  0.020  1.090
 LIG  C17  H172  single    0.970  0.020  1.090
 LIG  C20  C21   aromatic  1.406  0.020  1.406
 LIG  C20  C28   aromatic  1.382  0.020  1.382
 LIG  C21  C22   aromatic  1.387  0.020  1.387
 LIG  C22  C24   aromatic  1.390  0.020  1.390
 LIG  C22  HC22  single    0.930  0.020  1.080
 LIG  C24  C26   aromatic  1.391  0.020  1.391
 LIG  C24  HC24  single    0.930  0.020  1.080
 LIG  C26  C28   aromatic  1.393  0.020  1.393
 LIG  C26  HC26  single    0.930  0.020  1.080
 LIG  C28  HC28  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
 LIG  HN1   N1   C6    127.06  3.000
 LIG  HN1   N1   N3    118.56  3.000
 LIG  C6    N1   N3    114.37  3.000
 LIG  C4    N3   N1    103.43  3.000
 LIG  C21   C4   C5    109.88  3.000
 LIG  C21   C4   N3    137.32  3.000
 LIG  C5    C4   N3    112.80  3.000
 LIG  C17   C5   C6    144.62  3.000
 LIG  C17   C5   C4    110.74  3.000
 LIG  C6    C5   C4    104.65  3.000
 LIG  C7    C6   C5    131.69  3.000
 LIG  C7    C6   N1    123.55  3.000
 LIG  C5    C6   N1    104.75  3.000
 LIG  C15   C7   C8    117.03  3.000
 LIG  C15   C7   C6    120.08  3.000
 LIG  C8    C7   C6    122.88  3.000
 LIG  HC8   C8   C10   118.64  3.000
 LIG  HC8   C8   C7    122.26  3.000
 LIG  C10   C8   C7    119.09  3.000
 LIG  HC10  C10  N12   116.68  3.000
 LIG  HC10  C10  C8    119.47  3.000
 LIG  N12   C10  C8    123.85  3.000
 LIG  C13   N12  C10   117.06  3.000
 LIG  HC13  C13  C15   119.59  3.000
 LIG  HC13  C13  N12   116.64  3.000
 LIG  C15   C13  N12   123.77  3.000
 LIG  HC15  C15  C13   119.30  3.000
 LIG  HC15  C15  C7    121.51  3.000
 LIG  C13   C15  C7    119.19  3.000
 LIG  H172  C17  H171  106.70  3.000
 LIG  H172  C17  C20   111.59  3.000
 LIG  H171  C17  C20   111.36  3.000
 LIG  H172  C17  C5    112.96  3.000
 LIG  H171  C17  C5    113.16  3.000
 LIG  C20   C17  C5    101.17  3.000
 LIG  C28   C20  C21   119.99  3.000
 LIG  C28   C20  C17   128.20  3.000
 LIG  C21   C20  C17   111.81  3.000
 LIG  C22   C21  C20   121.04  3.000
 LIG  C22   C21  C4    132.55  3.000
 LIG  C20   C21  C4    106.41  3.000
 LIG  HC22  C22  C24   120.53  3.000
 LIG  HC22  C22  C21   120.95  3.000
 LIG  C24   C22  C21   118.52  3.000
 LIG  HC24  C24  C26   119.67  3.000
 LIG  HC24  C24  C22   119.68  3.000
 LIG  C26   C24  C22   120.65  3.000
 LIG  HC26  C26  C28   119.60  3.000
 LIG  HC26  C26  C24   119.65  3.000
 LIG  C28   C26  C24   120.75  3.000
 LIG  HC28  C28  C26   120.22  3.000
 LIG  HC28  C28  C20   120.73  3.000
 LIG  C26   C28  C20   119.04  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
 LIG  CONST_01  C5    C4   N3   N1      0.00   0.0  0
 LIG  CONST_02  C21   C4   N3   N1    180.00   0.0  0
 LIG  CONST_03  C4    C5   C6   N1      0.00   0.0  0
 LIG  CONST_04  C8    C7   C6   N1      0.00   0.0  0
 LIG  CONST_05  C15   C7   C6   N1    180.00   0.0  0
 LIG  CONST_06  C5    C6   N1   N3      0.00   0.0  0
 LIG  CONST_07  C7    C6   N1   N3    180.00   0.0  0
 LIG  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 LIG  CONST_09  C20   C21  C4   N3    180.00   0.0  0
 LIG  CONST_10  C22   C21  C4   N3      0.00   0.0  0
 LIG  CONST_11  C6    N1   N3   C4      0.00   0.0  0
 LIG  CONST_12  C7    C6   C5   C4    180.00   0.0  0
 LIG  CONST_13  C28   C20  C21  C4    180.00   0.0  0
 LIG  CONST_14  C24   C22  C21  C4    180.00   0.0  0
 LIG  CONST_15  C20   C21  C4   C5      0.00   0.0  0
 LIG  CONST_16  C22   C21  C4   C5    180.00   0.0  0
 LIG  CONST_17  C8    C7   C6   C5    180.00   0.0  0
 LIG  CONST_18  C15   C7   C6   C5      0.00   0.0  0
 LIG  CONST_19  C21   C4   C5   C6    180.00   0.0  0
 LIG  CONST_20  C10   C8   C7   C6    180.00   0.0  0
 LIG  CONST_21  C13   C15  C7   C6    180.00   0.0  0
 LIG  CONST_22  N12   C10  C8   C7      0.00   0.0  0
 LIG  CONST_23  N12   C13  C15  C7      0.00   0.0  0
 LIG  CONST_24  C13   C15  C7   C8      0.00   0.0  0
 LIG  CONST_25  C13   N12  C10  C8      0.00   0.0  0
 LIG  CONST_26  C15   C7   C8   C10     0.00   0.0  0
 LIG  CONST_27  C15   C13  N12  C10     0.00   0.0  0
 LIG  CONST_28  C24   C22  C21  C20     0.00   0.0  0
 LIG  CONST_29  C24   C26  C28  C20     0.00   0.0  0
 LIG  CONST_30  C26   C28  C20  C21     0.00   0.0  0
 LIG  CONST_31  C26   C24  C22  C21     0.00   0.0  0
 LIG  CONST_32  C28   C20  C21  C22     0.00   0.0  0
 LIG  CONST_33  C28   C26  C24  C22     0.00   0.0  0
 LIG  CONST_34  C17   C5   C6   C7      0.00   0.0  0
 LIG  CONST_35  HN1   N1   N3   C4    180.00   0.0  0
 LIG  CONST_36  HC22  C22  C21  C4      0.00   0.0  0
 LIG  CONST_37  HC8   C8   C7   C6      0.00   0.0  0
 LIG  CONST_38  HC15  C15  C7   C6      0.00   0.0  0
 LIG  CONST_39  HC10  C10  C8   C7    180.00   0.0  0
 LIG  CONST_40  HC13  C13  C15  C7    180.00   0.0  0
 LIG  CONST_41  HC28  C28  C20  C17     0.00   0.0  0
 LIG  CONST_42  HC26  C26  C28  C20   180.00   0.0  0
 LIG  CONST_43  HC24  C24  C22  C21   180.00   0.0  0
 LIG  Var_01    H171  C17  C5   C4   -119.32  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
 LIG  plan-1  C6    0.020
 LIG  plan-1  C7    0.020
 LIG  plan-1  C8    0.020
 LIG  plan-1  C10   0.020
 LIG  plan-1  N12   0.020
 LIG  plan-1  C13   0.020
 LIG  plan-1  C15   0.020
 LIG  plan-1  HC8   0.020
 LIG  plan-1  HC10  0.020
 LIG  plan-1  HC13  0.020
 LIG  plan-1  HC15  0.020
 LIG  plan-2  N1    0.020
 LIG  plan-2  N3    0.020
 LIG  plan-2  C4    0.020
 LIG  plan-2  C5    0.020
 LIG  plan-2  C6    0.020
 LIG  plan-2  C7    0.020
 LIG  plan-2  C17   0.020
 LIG  plan-2  C20   0.020
 LIG  plan-2  C21   0.020
 LIG  plan-2  C22   0.020
 LIG  plan-2  C24   0.020
 LIG  plan-2  C26   0.020
 LIG  plan-2  C28   0.020
 LIG  plan-2  HN1   0.020
 LIG  plan-2  HC22  0.020
 LIG  plan-2  HC24  0.020
 LIG  plan-2  HC26  0.020
 LIG  plan-2  HC28  0.020

