# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:08:21 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-chloro-4-[(3S,3aS,4S)-4-hydroxy-3-methoxy-3a,4,5,6-tetrahydro-3H-pyrrolo[1,2-b]pyrazol-2-yl]-3-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@@H]2[C@@H](O)CCN2N=C1c3ccc(C#N)c(Cl)c3C
#
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
 JAD  JAD  2-chloro-4-[(3S,3aS,4S)-4-hydroxy-3-methoxy-3a,4,5,6-tetrahydro-3H-pyrrolo[1,2-b]pyrazol-2-yl]-3-methylbenzonitrile  ligand  37  21  .  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_JAD
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
 JAD  CL1  CL  CL    0  -0.081  -3.4464  -1.7555   1.1341
 JAD  C3   C   CR6   0  -0.114  -2.5150  -0.4227   0.5608
 JAD  C2   C   CR6   0   0.100  -3.1897   0.7410   0.1876
 JAD  C7   C   CSP   0   0.052  -4.6093   0.8193   0.2789
 JAD  N1   N   NS    0  -0.235  -5.7557   0.9108   0.3438
 JAD  C4   C   CR6   0   0.171  -1.1300  -0.5258   0.4858
 JAD  C8   C   CH3   0  -0.753  -0.4275  -1.7585   0.9695
 JAD  C5   C   CR6   0   0.015  -0.4262   0.5770  -0.0248
 JAD  C6   C   CR16  0  -0.260  -1.0963   1.7475  -0.3800
 JAD  C1   C   CR16  0  -0.269  -2.4681   1.8379  -0.2735
 JAD  C9   C   CR5   0   0.161   1.0313   0.5299  -0.2070
 JAD  C11  C   CR15  0  -0.057   1.8048  -0.4652  -1.0536
 JAD  O2   O   O2    0  -0.487   1.6054  -0.2063  -2.4232
 JAD  C15  C   CH3   0  -0.413   0.4517  -0.8082  -2.9650
 JAD  C10  C   C     0  -0.155   3.2239  -0.0699  -0.6696
 JAD  C14  C   CR15  0   0.031   3.8684  -0.8718   0.4902
 JAD  O1   O   OH1   0  -0.673   5.1314  -1.3041   0.0349
 JAD  C13  C   CH2   0  -0.494   3.9663   0.1360   1.6419
 JAD  C12  C   CH2   0  -0.322   4.0117   1.4812   0.9228
 JAD  N3   N   N     0  -0.293   3.0697   1.3101  -0.1796
 JAD  N2   N   N     0  -0.205   1.7714   1.4802   0.2181
 JAD  H1   H   HCH3  0   0.270  -0.4877  -2.5694   0.2410
 JAD  H2   H   HCH3  0   0.252   0.6221  -1.5651   1.1783
 JAD  H3   H   HCH3  0   0.272  -0.8707  -2.1227   1.8948
 JAD  H4   H   HCR6  0   0.275  -0.5359   2.5869  -0.7668
 JAD  H5   H   HCR6  0   0.292  -2.9854   2.7429  -0.5594
 JAD  H7   H   HCR5  0   0.255   1.5863  -1.5163  -0.8338
 JAD  H8   H   HCH3  0   0.246   0.4648  -0.6318  -4.0393
 JAD  H9   H   HCH3  0   0.213   0.4405  -1.8903  -2.7917
 JAD  H10  H   HCH3  0   0.214  -0.4757  -0.3897  -2.5626
 JAD  H11  H   H     0   0.287   3.8825  -0.1049  -1.5398
 JAD  H12  H   HCR5  0   0.234   3.2503  -1.7330   0.7746
 JAD  H13  H   HOH1  0   0.453   5.5491  -1.8016   0.7451
 JAD  H14  H   HCH2  0   0.241   3.0727   0.0796   2.2676
 JAD  H15  H   HCH2  0   0.261   4.8276  -0.0466   2.2856
 JAD  H16  H   HCH2  0   0.264   3.7300   2.3354   1.5355
 JAD  H17  H   HCH2  0   0.252   5.0022   1.6728   0.5066

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
 JAD  C13  C14  single    1.534  0.020  1.534
 JAD  C13  C12  single    1.526  0.020  1.526
 JAD  C14  O1   single    1.410  0.020  1.410
 JAD  C14  C10  single    1.550  0.020  1.550
 JAD  C12  N3   single    1.460  0.020  1.460
 JAD  N1   C7   triple    1.152  0.020  1.152
 JAD  C7   C2   single    1.425  0.020  1.425
 JAD  C1   C2   aromatic  1.392  0.020  1.392
 JAD  C1   C6   aromatic  1.379  0.020  1.379
 JAD  C2   C3   aromatic  1.396  0.020  1.396
 JAD  C6   C5   aromatic  1.395  0.020  1.395
 JAD  N2   C9   double    1.277  0.020  1.277
 JAD  N2   N3   single    1.368  0.020  1.368
 JAD  C3   CL1  single    1.724  0.020  1.724
 JAD  C3   C4   aromatic  1.391  0.020  1.391
 JAD  C5   C4   aromatic  1.404  0.020  1.404
 JAD  C5   C9   single    1.470  0.020  1.470
 JAD  C4   C8   single    1.499  0.020  1.499
 JAD  C9   C11  single    1.518  0.020  1.518
 JAD  N3   C10  single    1.472  0.020  1.472
 JAD  C10  C11  single    1.522  0.020  1.522
 JAD  C11  O2   single    1.408  0.020  1.408
 JAD  O2   C15  single    1.410  0.020  1.410
 JAD  C8   H1   single    0.970  0.020  1.090
 JAD  C8   H2   single    0.970  0.020  1.090
 JAD  C8   H3   single    0.970  0.020  1.090
 JAD  C6   H4   single    0.930  0.020  1.080
 JAD  C1   H5   single    0.930  0.020  1.080
 JAD  C11  H7   single    0.970  0.020  1.090
 JAD  C15  H8   single    0.970  0.020  1.090
 JAD  C15  H9   single    0.970  0.020  1.090
 JAD  C15  H10  single    0.970  0.020  1.090
 JAD  C10  H11  single    0.970  0.020  1.090
 JAD  C14  H12  single    0.970  0.020  1.090
 JAD  O1   H13  single    0.850  0.020  0.980
 JAD  C13  H14  single    0.970  0.020  1.090
 JAD  C13  H15  single    0.970  0.020  1.090
 JAD  C12  H16  single    0.970  0.020  1.090
 JAD  C12  H17  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
 JAD  C4   C3   C2   121.91  3.000
 JAD  C4   C3   CL1  119.91  3.000
 JAD  C2   C3   CL1  118.18  3.000
 JAD  C1   C2   C7   119.65  3.000
 JAD  C1   C2   C3   119.67  3.000
 JAD  C7   C2   C3   120.68  3.000
 JAD  N1   C7   C2   180.00  3.000
 JAD  C5   C4   C8   121.89  3.000
 JAD  C8   C4   C3   120.68  3.000
 JAD  C5   C4   C3   117.42  3.000
 JAD  H3   C8   H2   106.81  3.000
 JAD  H3   C8   H1   107.24  3.000
 JAD  H2   C8   H1   108.27  3.000
 JAD  H3   C8   C4   111.01  3.000
 JAD  H2   C8   C4   111.59  3.000
 JAD  H1   C8   C4   111.70  3.000
 JAD  C9   C5   C6   118.15  3.000
 JAD  C9   C5   C4   121.13  3.000
 JAD  C6   C5   C4   120.72  3.000
 JAD  H4   C6   C1   119.51  3.000
 JAD  H4   C6   C5   119.59  3.000
 JAD  C1   C6   C5   120.89  3.000
 JAD  H5   C1   C6   120.70  3.000
 JAD  H5   C1   C2   119.96  3.000
 JAD  C6   C1   C2   119.33  3.000
 JAD  N2   C9   C11  112.21  3.000
 JAD  C11  C9   C5   126.54  3.000
 JAD  N2   C9   C5   120.63  3.000
 JAD  H7   C11  C10  112.60  3.000
 JAD  H7   C11  O2   110.08  3.000
 JAD  C10  C11  O2   109.24  3.000
 JAD  H7   C11  C9   114.54  3.000
 JAD  O2   C11  C9   110.47  3.000
 JAD  C10  C11  C9    99.44  3.000
 JAD  C15  O2   C11  114.28  3.000
 JAD  H10  C15  H9   108.11  3.000
 JAD  H10  C15  H8   108.12  3.000
 JAD  H9   C15  H8   108.43  3.000
 JAD  H10  C15  O2   112.90  3.000
 JAD  H9   C15  O2   111.67  3.000
 JAD  H8   C15  O2   107.47  3.000
 JAD  H11  C10  N3   111.01  3.000
 JAD  H11  C10  C14  109.20  3.000
 JAD  N3   C10  C14  106.22  3.000
 JAD  H11  C10  C11  110.66  3.000
 JAD  N3   C10  C11  103.28  3.000
 JAD  C14  C10  C11  116.22  3.000
 JAD  H12  C14  C13  110.92  3.000
 JAD  H12  C14  O1   110.33  3.000
 JAD  C13  C14  O1   112.74  3.000
 JAD  H12  C14  C10  111.45  3.000
 JAD  O1   C14  C10  106.82  3.000
 JAD  C13  C14  C10  104.39  3.000
 JAD  H13  O1   C14  107.99  3.000
 JAD  H15  C13  H14  107.42  3.000
 JAD  H15  C13  C12  113.71  3.000
 JAD  H14  C13  C12  109.86  3.000
 JAD  H15  C13  C14  112.56  3.000
 JAD  H14  C13  C14  110.13  3.000
 JAD  C12  C13  C14  103.14  3.000
 JAD  H17  C12  H16  108.17  3.000
 JAD  H17  C12  N3   108.55  3.000
 JAD  H16  C12  N3   110.49  3.000
 JAD  H17  C12  C13  111.19  3.000
 JAD  H16  C12  C13  114.77  3.000
 JAD  N3   C12  C13  103.49  3.000
 JAD  N2   N3   C12  112.21  3.000
 JAD  N2   N3   C10  108.22  3.000
 JAD  C12  N3   C10  107.07  3.000
 JAD  N3   N2   C9   111.13  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
 JAD  CONST_01  C6   C1   C2   C3      0.00   0.0  0
 JAD  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 JAD  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 JAD  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 JAD  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 JAD  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 JAD  CONST_07  C9   C5   C4   C3    180.00   0.0  0
 JAD  CONST_08  C9   C5   C6   C1    180.00   0.0  0
 JAD  CONST_09  C1   C2   C3   CL1   180.00   0.0  0
 JAD  CONST_10  C5   C4   C3   CL1   180.00   0.0  0
 JAD  CONST_11  C8   C4   C3   C2    180.00   0.0  0
 JAD  CONST_12  C6   C1   C2   C7    180.00   0.0  0
 JAD  CONST_13  C4   C3   C2   C7    180.00   0.0  0
 JAD  CONST_14  C6   C5   C4   C8    180.00   0.0  0
 JAD  CONST_15  C9   C5   C4   C8      0.00   0.0  0
 JAD  CONST_16  H5   C1   C2   C3    180.00   0.0  0
 JAD  CONST_17  H4   C6   C1   C2    180.00   0.0  0
 JAD  Var_01    N2   C9   C5   C4   -131.72  30.0  2
 JAD  Var_02    C12  N3   N2   C9   -131.84  30.0  1
 JAD  Var_03    C13  C12  N3   C10   -37.79  30.0  1
 JAD  Var_04    N3   C12  C13  C14    38.77  30.0  1
 JAD  Var_05    H1   C8   C4   C3     79.00  30.0  2
 JAD  Var_06    H8   C15  O2   C11  -173.81  30.0  3

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
 JAD  chir_01  C11  C9  C10  O2   positiv
 JAD  chir_02  C10  N3  C14  C11  negativ
 JAD  chir_03  C14  O1  C10  C13  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
 JAD  plan-1  CL1  0.020
 JAD  plan-1  C3   0.020
 JAD  plan-1  C2   0.020
 JAD  plan-1  C7   0.020
 JAD  plan-1  N1   0.020
 JAD  plan-1  C4   0.020
 JAD  plan-1  C8   0.020
 JAD  plan-1  C5   0.020
 JAD  plan-1  C6   0.020
 JAD  plan-1  C1   0.020
 JAD  plan-1  C9   0.020
 JAD  plan-1  H4   0.020
 JAD  plan-1  H5   0.020
 JAD  plan-2  C10  0.020
 JAD  plan-2  C12  0.020
 JAD  plan-2  N3   0.020
 JAD  plan-2  N2   0.020

