# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 20:14:01 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-[(4-chloro-3-methoxyphenyl)amino]-1-[(3R,4S)-4-cyanooxan-3-yl]-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2nn(cc2C(N)=O)[C@H]3COCC[C@@H]3C#N)ccc1Cl
#
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
 B7V  B7V  3-[(4-chloro-3-methoxyphenyl)amino]-1-[(3R,4S)-4-cyanooxan-3-yl]-1H-pyrazole-4-carboxamide  ligand  44  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B7V
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
 B7V  C1   C   C     0   0.493   1.1765   3.4792   0.5145
 B7V  C2   C   CR15  0   0.081   2.6311   1.4069   0.0182
 B7V  C3   C   CH1   0  -0.111   3.2450  -0.9643  -0.4710
 B7V  C7   C   CH1   0  -0.381   3.9361  -1.3799   0.8383
 B7V  C8   C   CSP   0   0.145   2.9532  -1.7788   1.8376
 B7V  C9   C   CR5   0   0.573   0.4502   1.0683  -0.0211
 B7V  C10  C   CR6   0   0.417  -1.9402   0.3884  -0.0279
 B7V  C11  C   CR16  0  -0.532  -3.2304   0.9224   0.1118
 B7V  C12  C   CR6   0   0.475  -4.3543   0.1128   0.0581
 B7V  C13  C   CH3   0  -0.440  -5.8279   1.9382   0.3911
 B7V  C14  C   CR6   0  -0.179  -4.1849  -1.2630  -0.1420
 B7V  C15  C   CR16  0  -0.195  -2.9186  -1.7906  -0.2814
 B7V  C16  C   CR16  0  -0.369  -1.7893  -0.9844  -0.2287
 B7V  CL   CL  CL    0  -0.126  -5.5796  -2.2868  -0.2126
 B7V  O2   O   O2    0  -0.457  -5.6118   0.5543   0.1850
 B7V  N4   N   NH1   0  -0.801  -0.8956   1.2849   0.0505
 B7V  C    C   CR5   0  -0.386   1.4358   2.0756   0.1906
 B7V  N    N   NH2   0  -0.819   2.2398   4.2699   0.7147
 B7V  O    O   O     0  -0.506   0.0207   3.8994   0.5992
 B7V  N3   N   N     0  -0.344   1.0091  -0.0913  -0.2966
 B7V  N1   N   NR5   0  -0.286   2.3357   0.1390  -0.2701
 B7V  N2   N   NS    0  -0.256   2.1815  -2.0988   2.6281
 B7V  C6   C   CH2   0  -0.447   4.9405  -2.5049   0.5558
 B7V  C5   C   CH2   0  -0.193   5.8752  -2.0749  -0.5606
 B7V  O1   O   O2    0  -0.472   5.1596  -1.7240  -1.7273
 B7V  C4   C   CH2   0  -0.167   4.3065  -0.6319  -1.5237
 B7V  H1   H   HCR5  0   0.318   3.6497   1.7559   0.0878
 B7V  H2   H   HCH1  0   0.310   2.6375  -1.7927  -0.8369
 B7V  H3   H   HCH1  0   0.327   4.4758  -0.5188   1.2476
 B7V  H4   H   HCR6  0   0.292  -3.3366   1.9890   0.2651
 B7V  H5   H   HCH3  0   0.233  -5.4643   2.5348  -0.4491
 B7V  H6   H   HCH3  0   0.265  -6.9030   2.0706   0.4779
 B7V  H7   H   HCH3  0   0.233  -5.3520   2.2901   1.3094
 B7V  H8   H   HCR6  0   0.276  -2.7996  -2.8552  -0.4340
 B7V  H9   H   HCR6  0   0.289  -0.8138  -1.4277  -0.3422
 B7V  H10  H   HNH1  0   0.416  -1.1264   2.2503   0.2455
 B7V  H11  H   HNH2  0   0.411   3.1877   3.9440   0.6474
 B7V  H12  H   HNH2  0   0.408   2.1056   5.2462   0.9205
 B7V  H13  H   HCH2  0   0.277   5.5170  -2.7227   1.4554
 B7V  H14  H   HCH2  0   0.261   4.4074  -3.4149   0.2730
 B7V  H15  H   HCH2  0   0.219   6.4975  -1.2347  -0.2232
 B7V  H16  H   HCH2  0   0.258   6.5411  -2.8951  -0.8295
 B7V  H17  H   HCH2  0   0.273   3.8164  -0.4094  -2.4721
 B7V  H18  H   HCH2  0   0.216   4.8763   0.2588  -1.2218

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
 B7V  CL   C14  single    1.732  0.020  1.732
 B7V  C15  C14  aromatic  1.379  0.020  1.379
 B7V  C15  C16  aromatic  1.389  0.020  1.389
 B7V  C14  C12  aromatic  1.401  0.020  1.401
 B7V  C16  C10  aromatic  1.396  0.020  1.396
 B7V  C12  O2   single    1.339  0.020  1.339
 B7V  C12  C11  aromatic  1.386  0.020  1.386
 B7V  O2   C13  single    1.416  0.020  1.416
 B7V  C10  C11  aromatic  1.403  0.020  1.403
 B7V  C10  N4   single    1.379  0.020  1.379
 B7V  N4   C9   single    1.365  0.020  1.365
 B7V  O    C1   double    1.233  0.020  1.233
 B7V  C9   N3   aromatic  1.316  0.020  1.316
 B7V  C9   C    aromatic  1.425  0.020  1.425
 B7V  C4   O1   single    1.401  0.020  1.401
 B7V  C4   C3   single    1.532  0.020  1.532
 B7V  N3   N1   aromatic  1.347  0.020  1.347
 B7V  O1   C5   single    1.413  0.020  1.413
 B7V  C1   C    single    1.464  0.020  1.464
 B7V  C1   N    single    1.340  0.020  1.340
 B7V  C    C2   aromatic  1.380  0.020  1.380
 B7V  N1   C2   aromatic  1.333  0.020  1.333
 B7V  N1   C3   single    1.444  0.020  1.444
 B7V  C3   C7   single    1.538  0.020  1.538
 B7V  C5   C6   single    1.518  0.020  1.518
 B7V  C7   C6   single    1.534  0.020  1.534
 B7V  C7   C8   single    1.457  0.020  1.457
 B7V  C8   N2   triple    1.150  0.020  1.150
 B7V  C2   H1   single    0.930  0.020  1.080
 B7V  C3   H2   single    0.970  0.020  1.090
 B7V  C7   H3   single    0.970  0.020  1.090
 B7V  C11  H4   single    0.930  0.020  1.080
 B7V  C13  H5   single    0.970  0.020  1.090
 B7V  C13  H6   single    0.970  0.020  1.090
 B7V  C13  H7   single    0.970  0.020  1.090
 B7V  C15  H8   single    0.930  0.020  1.080
 B7V  C16  H9   single    0.930  0.020  1.080
 B7V  N4   H10  single    0.860  0.020  1.020
 B7V  N    H11  single    0.860  0.020  1.020
 B7V  N    H12  single    0.860  0.020  1.020
 B7V  C6   H13  single    0.970  0.020  1.090
 B7V  C6   H14  single    0.970  0.020  1.090
 B7V  C5   H15  single    0.970  0.020  1.090
 B7V  C5   H16  single    0.970  0.020  1.090
 B7V  C4   H17  single    0.970  0.020  1.090
 B7V  C4   H18  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
 B7V  O    C1   N    122.18  3.000
 B7V  N    C1   C    117.28  3.000
 B7V  O    C1   C    120.55  3.000
 B7V  H1   C2   N1   122.05  3.000
 B7V  H1   C2   C    130.75  3.000
 B7V  N1   C2   C    107.20  3.000
 B7V  H2   C3   C4   108.68  3.000
 B7V  H2   C3   N1   106.05  3.000
 B7V  C4   C3   N1   111.49  3.000
 B7V  H2   C3   C7   109.32  3.000
 B7V  N1   C3   C7   111.79  3.000
 B7V  C4   C3   C7   109.42  3.000
 B7V  H3   C7   C6   108.82  3.000
 B7V  H3   C7   C8   106.94  3.000
 B7V  C6   C7   C8   111.53  3.000
 B7V  H3   C7   C3   109.09  3.000
 B7V  C8   C7   C3   110.77  3.000
 B7V  C6   C7   C3   109.61  3.000
 B7V  N2   C8   C7   180.00  3.000
 B7V  N3   C9   C    111.10  3.000
 B7V  C    C9   N4   124.19  3.000
 B7V  N3   C9   N4   124.71  3.000
 B7V  N4   C10  C16  124.46  3.000
 B7V  N4   C10  C11  116.32  3.000
 B7V  C16  C10  C11  119.21  3.000
 B7V  H4   C11  C12  120.09  3.000
 B7V  H4   C11  C10  118.63  3.000
 B7V  C12  C11  C10  121.29  3.000
 B7V  O2   C12  C14  116.81  3.000
 B7V  O2   C12  C11  124.42  3.000
 B7V  C14  C12  C11  118.77  3.000
 B7V  H7   C13  H6   108.94  3.000
 B7V  H7   C13  H5   108.99  3.000
 B7V  H6   C13  H5   108.91  3.000
 B7V  H7   C13  O2   111.76  3.000
 B7V  H6   C13  O2   106.36  3.000
 B7V  H5   C13  O2   111.77  3.000
 B7V  CL   C14  C15  120.62  3.000
 B7V  C15  C14  C12  120.09  3.000
 B7V  CL   C14  C12  119.29  3.000
 B7V  H8   C15  C16  119.15  3.000
 B7V  H8   C15  C14  119.45  3.000
 B7V  C16  C15  C14  121.39  3.000
 B7V  H9   C16  C15  119.56  3.000
 B7V  H9   C16  C10  121.19  3.000
 B7V  C15  C16  C10  119.25  3.000
 B7V  C13  O2   C12  118.65  3.000
 B7V  H10  N4   C10  117.30  3.000
 B7V  H10  N4   C9   112.74  3.000
 B7V  C10  N4   C9   129.85  3.000
 B7V  C9   C    C2   103.76  3.000
 B7V  C2   C    C1   130.21  3.000
 B7V  C9   C    C1   126.03  3.000
 B7V  H12  N    H11  117.00  3.000
 B7V  H12  N    C1   119.80  3.000
 B7V  H11  N    C1   123.18  3.000
 B7V  N1   N3   C9   105.28  3.000
 B7V  N3   N1   C3   119.14  3.000
 B7V  C3   N1   C2   128.11  3.000
 B7V  N3   N1   C2   112.65  3.000
 B7V  H14  C6   H13  107.77  3.000
 B7V  H14  C6   C5   110.26  3.000
 B7V  H13  C6   C5   109.74  3.000
 B7V  H14  C6   C7   109.83  3.000
 B7V  H13  C6   C7   109.91  3.000
 B7V  C5   C6   C7   109.32  3.000
 B7V  H16  C5   H15  107.77  3.000
 B7V  H16  C5   O1   107.01  3.000
 B7V  H15  C5   O1   110.52  3.000
 B7V  H16  C5   C6   110.15  3.000
 B7V  H15  C5   C6   109.85  3.000
 B7V  O1   C5   C6   111.45  3.000
 B7V  C4   O1   C5   112.46  3.000
 B7V  H18  C4   H17  107.84  3.000
 B7V  H18  C4   O1   110.85  3.000
 B7V  H17  C4   O1   107.84  3.000
 B7V  H18  C4   C3   110.26  3.000
 B7V  H17  C4   C3   109.30  3.000
 B7V  O1   C4   C3   110.66  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
 B7V  CONST_01  N3   C9   C    C2     0.00   0.0  0
 B7V  CONST_02  C9   N3   N1   C2     0.00   0.0  0
 B7V  CONST_03  N1   C2   C    C9     0.00   0.0  0
 B7V  CONST_04  C14  C15  C16  C10    0.00   0.0  0
 B7V  CONST_05  C14  C12  C11  C10    0.00   0.0  0
 B7V  CONST_06  C15  C14  C12  C11    0.00   0.0  0
 B7V  CONST_07  C15  C16  C10  C11    0.00   0.0  0
 B7V  CONST_08  C16  C15  C14  C12    0.00   0.0  0
 B7V  CONST_09  C16  C10  C11  C12    0.00   0.0  0
 B7V  CONST_10  N1   N3   C9   C      0.00   0.0  0
 B7V  CONST_11  N3   N1   C2   C      0.00   0.0  0
 B7V  CONST_12  C9   N3   N1   C3   180.00   0.0  0
 B7V  CONST_13  C    C2   N1   C3   180.00   0.0  0
 B7V  CONST_14  N3   C9   C    C1   180.00   0.0  0
 B7V  CONST_15  N1   C2   C    C1   180.00   0.0  0
 B7V  CONST_16  N4   C9   C    C2   180.00   0.0  0
 B7V  CONST_17  O2   C12  C11  C10  180.00   0.0  0
 B7V  CONST_18  CL   C14  C12  C11  180.00   0.0  0
 B7V  CONST_19  N4   C10  C11  C12  180.00   0.0  0
 B7V  CONST_20  O2   C12  C14  C15  180.00   0.0  0
 B7V  CONST_21  N4   C10  C16  C15  180.00   0.0  0
 B7V  CONST_22  CL   C14  C15  C16  180.00   0.0  0
 B7V  CONST_23  N1   N3   C9   N4   180.00   0.0  0
 B7V  CONST_24  H1   C2   N1   C3     0.00   0.0  0
 B7V  CONST_25  H8   C15  C16  C10  180.00   0.0  0
 B7V  CONST_26  H9   C16  C10  C11  180.00   0.0  0
 B7V  CONST_27  H4   C11  C12  C14  180.00   0.0  0
 B7V  CONST_28  H11  N    C1   C      0.00   0.0  0
 B7V  CONST_29  H12  N    C1   C    180.00   0.0  0
 B7V  Var_01    O1   C5   C6   C7   -56.67  30.0  1
 B7V  Var_02    C16  C10  N4   C9    -1.14  30.0  2
 B7V  Var_03    N3   C9   N4   C10    5.85  30.0  2
 B7V  Var_04    H17  C4   O1   C5   178.44  30.0  1
 B7V  Var_05    O    C1   C    C2   178.40  30.0  2
 B7V  Var_06    C14  C12  O2   C13  179.89  30.0  2
 B7V  Var_07    H5   C13  O2   C12   61.94  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
 B7V  chir_01  C3  C4  N1  C7  positiv
 B7V  chir_02  C7  C3  C6  C8  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
 B7V  plan-1  C1   0.020
 B7V  plan-1  C2   0.020
 B7V  plan-1  C3   0.020
 B7V  plan-1  C9   0.020
 B7V  plan-1  N4   0.020
 B7V  plan-1  C    0.020
 B7V  plan-1  N3   0.020
 B7V  plan-1  N1   0.020
 B7V  plan-1  H1   0.020
 B7V  plan-2  C10  0.020
 B7V  plan-2  C11  0.020
 B7V  plan-2  C12  0.020
 B7V  plan-2  C14  0.020
 B7V  plan-2  C15  0.020
 B7V  plan-2  C16  0.020
 B7V  plan-2  CL   0.020
 B7V  plan-2  O2   0.020
 B7V  plan-2  N4   0.020
 B7V  plan-2  H4   0.020
 B7V  plan-2  H8   0.020
 B7V  plan-2  H9   0.020
 B7V  plan-3  C1   0.020
 B7V  plan-3  C    0.020
 B7V  plan-3  N    0.020
 B7V  plan-3  O    0.020
 B7V  plan-3  H11  0.020
 B7V  plan-3  H12  0.020

