# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 20:13:51 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 3-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC2CCCC2)c3ccn(CCC(=O)N4C[C@@H](C)O[C@H](C)C4)n3
#
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
 D0B  D0B  3-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]propan-1-one  ligand  64  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D0B
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
 D0B  C10  C  CR6   0   0.064   2.7217  -1.9203   0.1156
 D0B  C13  C  CR5   0   0.298   1.4106  -2.5552  -0.0346
 D0B  C15  C  CH2   0  -0.625  -2.4634  -1.1688  -0.4773
 D0B  C17  C  CH2   0  -0.327  -5.6253   0.8688  -1.0938
 D0B  C20  C  CH2   0  -0.310  -3.8631   1.1698   0.5171
 D0B  C21  C  CR15  0   0.044  -0.3303  -3.9011   0.0387
 D0B  C22  C  CR15  0  -0.567   0.9823  -3.8143   0.4354
 D0B  C24  C  CH3   0  -0.686  -4.4896   2.1779   2.7274
 D0B  C01  C  CH3   0  -0.437   7.4952  -0.6462   1.0386
 D0B  C02  C  CR6   0   0.284   5.2120  -0.6659   0.4169
 D0B  C03  C  CR6   0   0.358   4.1030   0.0659  -0.0610
 D0B  O02  O  O2    0  -0.482   4.3498   1.3585  -0.3464
 D0B  C04  C  CR15  0   0.018   3.2845   2.2119  -0.7277
 D0B  C05  C  CH2   0  -0.461   3.8437   3.5375  -1.2225
 D0B  C06  C  CH2   0  -0.456   2.6295   4.4731  -1.1931
 D0B  C07  C  CH2   0  -0.453   1.6633   3.8801  -0.1362
 D0B  C08  C  CH2   0  -0.473   2.3579   2.6279   0.4129
 D0B  C09  C  CR16  0  -0.437   2.8822  -0.5654  -0.2053
 D0B  C11  C  CR16  0  -0.352   3.8167  -2.6288   0.5815
 D0B  C12  C  CR16  0  -0.366   5.0531  -2.0051   0.7309
 D0B  N01  N  N     0  -0.323   0.4234  -1.9387  -0.6690
 D0B  N02  N  NR5   0  -0.269  -0.6153  -2.7619  -0.6164
 D0B  C14  C  CH2   0  -0.261  -1.8774  -2.3698  -1.2059
 D0B  C16  C  C     0   0.582  -3.7774  -0.7325  -1.0951
 D0B  N03  N  NT    0  -0.475  -4.3584   0.3748  -0.5893
 D0B  C18  C  CH1   0   0.010  -6.6545   0.9065   0.0311
 D0B  O03  O  O2    0  -0.496  -6.1538   1.6637   1.1226
 D0B  C19  C  CH1   0   0.041  -4.9062   1.2241   1.6284
 D0B  O04  O  O     0  -0.503  -4.2734  -1.3678  -2.0172
 D0B  C23  C  CH3   0  -0.692  -7.1235  -0.4810   0.4467
 D0B  H01  H  HCH2  0   0.282  -2.6151  -1.4207   0.5764
 D0B  H19  H  HCH2  0   0.285  -1.7438  -0.3468  -0.4963
 D0B  H21  H  HCH2  0   0.268  -5.9732   0.2409  -1.9100
 D0B  H25  H  HCH2  0   0.277  -2.9360   0.7655   0.9150
 D0B  H24  H  HCH2  0   0.245  -3.6489   2.1839   0.1596
 D0B  H26  H  HCR5  0   0.294  -1.0664  -4.6767   0.1761
 D0B  H27  H  HCR5  0   0.264   1.5393  -4.5493   0.9922
 D0B  H30  H  HCH3  0   0.229  -4.3469   3.1883   2.3402
 D0B  H28  H  HCH3  0   0.244  -5.2383   2.2155   3.5186
 D0B  H29  H  HCH3  0   0.235  -3.5502   1.8516   3.1740
 D0B  H02  H  HCH3  0   0.259   8.3001   0.0840   1.0667
 D0B  H03  H  HCH3  0   0.228   7.3284  -1.0252   2.0505
 D0B  H04  H  HCH3  0   0.228   7.7996  -1.4788   0.3986
 D0B  H05  H  HCR5  0   0.225   2.7005   1.7466  -1.5332
 D0B  H07  H  HCH2  0   0.231   4.6119   3.8822  -0.5244
 D0B  H06  H  HCH2  0   0.244   4.3022   3.4628  -2.2094
 D0B  H08  H  HCH2  0   0.238   2.9231   5.4950  -0.9552
 D0B  H09  H  HCH2  0   0.233   2.1476   4.5044  -2.1711
 D0B  H10  H  HCH2  0   0.238   1.4356   4.5891   0.6594
 D0B  H11  H  HCH2  0   0.234   0.7133   3.6127  -0.6006
 D0B  H12  H  HCH2  0   0.245   1.6515   1.8534   0.7120
 D0B  H13  H  HCH2  0   0.233   2.9684   2.8736   1.2865
 D0B  H14  H  HCR6  0   0.273   2.0202  -0.0189  -0.5616
 D0B  H15  H  HCR6  0   0.248   3.7300  -3.6783   0.8312
 D0B  H16  H  HCR6  0   0.281   5.8873  -2.5879   1.0974
 D0B  H17  H  HCH2  0   0.266  -2.5421  -3.2289  -1.1479
 D0B  H18  H  HCH2  0   0.267  -1.7139  -2.1479  -2.2601
 D0B  H22  H  HCH1  0   0.243  -7.5199   1.4676  -0.3316
 D0B  H23  H  HCH1  0   0.215  -5.0006   0.2125   2.0479
 D0B  H32  H  HCH3  0   0.228  -6.3070  -1.1299   0.7660
 D0B  H33  H  HCH3  0   0.241  -7.8404  -0.4141   1.2652
 D0B  H31  H  HCH3  0   0.237  -7.6200  -0.9700  -0.3920
 D0B  O01  O  O2    0  -0.462   6.3605   0.0257   0.5320
 D0B  H20  H  HCH2  0   0.255  -5.4763   1.8793  -1.4893

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
 D0B  C01  O01  single    1.413  0.020  1.413
 D0B  C12  C11  aromatic  1.393  0.020  1.393
 D0B  C12  C02  aromatic  1.385  0.020  1.385
 D0B  C11  C10  aromatic  1.385  0.020  1.385
 D0B  O01  C02  single    1.346  0.020  1.346
 D0B  C15  C14  single    1.522  0.020  1.522
 D0B  C15  C16  single    1.516  0.020  1.516
 D0B  C02  C03  aromatic  1.412  0.020  1.412
 D0B  N01  N02  aromatic  1.326  0.020  1.326
 D0B  N01  C13  aromatic  1.326  0.020  1.326
 D0B  C14  N02  single    1.447  0.020  1.447
 D0B  C10  C13  single    1.464  0.020  1.464
 D0B  C10  C09  aromatic  1.402  0.020  1.402
 D0B  N02  C21  aromatic  1.345  0.020  1.345
 D0B  C13  C22  aromatic  1.411  0.020  1.411
 D0B  C03  C09  aromatic  1.382  0.020  1.382
 D0B  C03  O02  single    1.347  0.020  1.347
 D0B  C16  O04  double    1.225  0.020  1.225
 D0B  C16  N03  single    1.349  0.020  1.349
 D0B  C17  N03  single    1.450  0.020  1.450
 D0B  C17  C18  single    1.525  0.020  1.525
 D0B  C23  C18  single    1.522  0.020  1.522
 D0B  N03  C20  single    1.450  0.020  1.450
 D0B  C21  C22  aromatic  1.374  0.020  1.374
 D0B  O02  C04  single    1.417  0.020  1.417
 D0B  C18  O03  single    1.420  0.020  1.420
 D0B  C20  C19  single    1.525  0.020  1.525
 D0B  O03  C19  single    1.416  0.020  1.416
 D0B  C04  C05  single    1.521  0.020  1.521
 D0B  C04  C08  single    1.527  0.020  1.527
 D0B  C19  C24  single    1.514  0.020  1.514
 D0B  C05  C06  single    1.533  0.020  1.533
 D0B  C08  C07  single    1.534  0.020  1.534
 D0B  C07  C06  single    1.550  0.020  1.550
 D0B  C15  H01  single    0.970  0.020  1.090
 D0B  C15  H19  single    0.970  0.020  1.090
 D0B  C17  H20  single    0.970  0.020  1.090
 D0B  C17  H21  single    0.970  0.020  1.090
 D0B  C20  H25  single    0.970  0.020  1.090
 D0B  C20  H24  single    0.970  0.020  1.090
 D0B  C21  H26  single    0.930  0.020  1.080
 D0B  C22  H27  single    0.930  0.020  1.080
 D0B  C24  H30  single    0.970  0.020  1.090
 D0B  C24  H28  single    0.970  0.020  1.090
 D0B  C24  H29  single    0.970  0.020  1.090
 D0B  C01  H02  single    0.970  0.020  1.090
 D0B  C01  H03  single    0.970  0.020  1.090
 D0B  C01  H04  single    0.970  0.020  1.090
 D0B  C04  H05  single    0.970  0.020  1.090
 D0B  C05  H07  single    0.970  0.020  1.090
 D0B  C05  H06  single    0.970  0.020  1.090
 D0B  C06  H08  single    0.970  0.020  1.090
 D0B  C06  H09  single    0.970  0.020  1.090
 D0B  C07  H10  single    0.970  0.020  1.090
 D0B  C07  H11  single    0.970  0.020  1.090
 D0B  C08  H12  single    0.970  0.020  1.090
 D0B  C08  H13  single    0.970  0.020  1.090
 D0B  C09  H14  single    0.930  0.020  1.080
 D0B  C11  H15  single    0.930  0.020  1.080
 D0B  C12  H16  single    0.930  0.020  1.080
 D0B  C14  H17  single    0.970  0.020  1.090
 D0B  C14  H18  single    0.970  0.020  1.090
 D0B  C18  H22  single    0.970  0.020  1.090
 D0B  C19  H23  single    0.970  0.020  1.090
 D0B  C23  H32  single    0.970  0.020  1.090
 D0B  C23  H33  single    0.970  0.020  1.090
 D0B  C23  H31  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
 D0B  C11  C10  C09  118.75  3.000
 D0B  C09  C10  C13  119.88  3.000
 D0B  C11  C10  C13  121.37  3.000
 D0B  N01  C13  C22  110.39  3.000
 D0B  C22  C13  C10  128.66  3.000
 D0B  N01  C13  C10  120.94  3.000
 D0B  H19  C15  H01  106.33  3.000
 D0B  H19  C15  C16  110.32  3.000
 D0B  H01  C15  C16  109.79  3.000
 D0B  H19  C15  C14  109.37  3.000
 D0B  H01  C15  C14  109.43  3.000
 D0B  C16  C15  C14  111.45  3.000
 D0B  H21  C17  H20  107.78  3.000
 D0B  H21  C17  C18  110.62  3.000
 D0B  H20  C17  C18  109.59  3.000
 D0B  H21  C17  N03  110.12  3.000
 D0B  H20  C17  N03  108.72  3.000
 D0B  C18  C17  N03  109.96  3.000
 D0B  H24  C20  H25  107.26  3.000
 D0B  H24  C20  C19  109.77  3.000
 D0B  H25  C20  C19  109.26  3.000
 D0B  H24  C20  N03  108.97  3.000
 D0B  H25  C20  N03  111.53  3.000
 D0B  C19  C20  N03  110.00  3.000
 D0B  H26  C21  N02  121.80  3.000
 D0B  H26  C21  C22  131.37  3.000
 D0B  N02  C21  C22  106.83  3.000
 D0B  H27  C22  C21  126.88  3.000
 D0B  H27  C22  C13  128.62  3.000
 D0B  C21  C22  C13  104.49  3.000
 D0B  H29  C24  H28  107.75  3.000
 D0B  H29  C24  H30  108.04  3.000
 D0B  H28  C24  H30  108.39  3.000
 D0B  H29  C24  C19  110.24  3.000
 D0B  H28  C24  C19  111.09  3.000
 D0B  H30  C24  C19  111.21  3.000
 D0B  H04  C01  H03  108.67  3.000
 D0B  H04  C01  H02  108.69  3.000
 D0B  H03  C01  H02  108.78  3.000
 D0B  H04  C01  O01  112.08  3.000
 D0B  H03  C01  O01  111.98  3.000
 D0B  H02  C01  O01  106.53  3.000
 D0B  C12  C02  C03  119.20  3.000
 D0B  C03  C02  O01  115.65  3.000
 D0B  C12  C02  O01  125.15  3.000
 D0B  C09  C03  O02  125.33  3.000
 D0B  O02  C03  C02  115.17  3.000
 D0B  C09  C03  C02  119.50  3.000
 D0B  C04  O02  C03  119.82  3.000
 D0B  H05  C04  C08  109.90  3.000
 D0B  H05  C04  C05  109.03  3.000
 D0B  C08  C04  C05  103.21  3.000
 D0B  H05  C04  O02  109.99  3.000
 D0B  C08  C04  O02  114.78  3.000
 D0B  C05  C04  O02  109.63  3.000
 D0B  H06  C05  H07  107.69  3.000
 D0B  H06  C05  C06  113.08  3.000
 D0B  H07  C05  C06  110.59  3.000
 D0B  H06  C05  C04  112.90  3.000
 D0B  H07  C05  C04  108.97  3.000
 D0B  C06  C05  C04  103.55  3.000
 D0B  H09  C06  H08  106.73  3.000
 D0B  H09  C06  C07  110.30  3.000
 D0B  H08  C06  C07  112.21  3.000
 D0B  H09  C06  C05  110.50  3.000
 D0B  H08  C06  C05  111.30  3.000
 D0B  C07  C06  C05  105.86  3.000
 D0B  H11  C07  H10  106.76  3.000
 D0B  H11  C07  C08  110.29  3.000
 D0B  H10  C07  C08  111.38  3.000
 D0B  H11  C07  C06  110.27  3.000
 D0B  H10  C07  C06  112.28  3.000
 D0B  C08  C07  C06  105.91  3.000
 D0B  H13  C08  H12  107.59  3.000
 D0B  H13  C08  C07  110.82  3.000
 D0B  H12  C08  C07  112.63  3.000
 D0B  H13  C08  C04  108.60  3.000
 D0B  H12  C08  C04  113.86  3.000
 D0B  C07  C08  C04  103.29  3.000
 D0B  H14  C09  C03  120.52  3.000
 D0B  H14  C09  C10  118.22  3.000
 D0B  C03  C09  C10  121.26  3.000
 D0B  H15  C11  C12  118.72  3.000
 D0B  H15  C11  C10  120.69  3.000
 D0B  C12  C11  C10  120.59  3.000
 D0B  H16  C12  C11  118.67  3.000
 D0B  H16  C12  C02  120.63  3.000
 D0B  C11  C12  C02  120.71  3.000
 D0B  N02  N01  C13  106.00  3.000
 D0B  C14  N02  N01  119.91  3.000
 D0B  C14  N02  C21  127.80  3.000
 D0B  N01  N02  C21  112.28  3.000
 D0B  H18  C14  H17  107.70  3.000
 D0B  H18  C14  N02  108.57  3.000
 D0B  H17  C14  N02  107.29  3.000
 D0B  H18  C14  C15  111.11  3.000
 D0B  H17  C14  C15  111.25  3.000
 D0B  N02  C14  C15  110.77  3.000
 D0B  O04  C16  N03  122.26  3.000
 D0B  N03  C16  C15  117.18  3.000
 D0B  O04  C16  C15  120.56  3.000
 D0B  C16  N03  C20  126.10  3.000
 D0B  C20  N03  C17  112.16  3.000
 D0B  C16  N03  C17  121.70  3.000
 D0B  H22  C18  C23  108.33  3.000
 D0B  H22  C18  O03  105.10  3.000
 D0B  C23  C18  O03  112.64  3.000
 D0B  H22  C18  C17  107.58  3.000
 D0B  O03  C18  C17  110.02  3.000
 D0B  C23  C18  C17  112.74  3.000
 D0B  C19  O03  C18  114.82  3.000
 D0B  H23  C19  O03  110.26  3.000
 D0B  H23  C19  C24  109.06  3.000
 D0B  O03  C19  C24  107.83  3.000
 D0B  H23  C19  C20  107.70  3.000
 D0B  C24  C19  C20  111.30  3.000
 D0B  O03  C19  C20  110.69  3.000
 D0B  H31  C23  H33  107.79  3.000
 D0B  H31  C23  H32  107.42  3.000
 D0B  H33  C23  H32  108.00  3.000
 D0B  H31  C23  C18  109.82  3.000
 D0B  H33  C23  C18  110.58  3.000
 D0B  H32  C23  C18  113.05  3.000
 D0B  C02  O01  C01  118.15  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
 D0B  CONST_01  C02  C12  C11  C10     0.00   0.0  0
 D0B  CONST_02  N02  N01  C13  C10   180.00   0.0  0
 D0B  CONST_03  C21  C22  C13  C10   180.00   0.0  0
 D0B  CONST_04  C02  C03  C09  C10     0.00   0.0  0
 D0B  CONST_05  C21  N02  N01  C13     0.00   0.0  0
 D0B  CONST_06  C12  C11  C10  C13   180.00   0.0  0
 D0B  CONST_07  C03  C09  C10  C13   180.00   0.0  0
 D0B  CONST_08  N02  C21  C22  C13     0.00   0.0  0
 D0B  CONST_09  N01  C13  C22  C21     0.00   0.0  0
 D0B  CONST_10  N02  N01  C13  C22     0.00   0.0  0
 D0B  CONST_11  C11  C10  C13  C22     0.00   0.0  0
 D0B  CONST_12  C09  C10  C13  C22   180.00   0.0  0
 D0B  CONST_13  N01  N02  C21  C22     0.00   0.0  0
 D0B  CONST_14  C11  C12  C02  C03     0.00   0.0  0
 D0B  CONST_15  C11  C10  C09  C03     0.00   0.0  0
 D0B  CONST_16  C12  C11  C10  C09     0.00   0.0  0
 D0B  CONST_17  N01  C13  C10  C09     0.00   0.0  0
 D0B  CONST_18  C12  C02  C03  C09     0.00   0.0  0
 D0B  CONST_19  N01  C13  C10  C11   180.00   0.0  0
 D0B  CONST_20  O02  C03  C09  C10   180.00   0.0  0
 D0B  CONST_21  C14  N02  N01  C13   180.00   0.0  0
 D0B  CONST_22  C14  N02  C21  C22   180.00   0.0  0
 D0B  CONST_23  C11  C12  C02  O01   180.00   0.0  0
 D0B  CONST_24  C09  C03  C02  O01   180.00   0.0  0
 D0B  CONST_25  C12  C02  C03  O02   180.00   0.0  0
 D0B  CONST_26  H16  C12  C11  C10   180.00   0.0  0
 D0B  CONST_27  H27  C22  C13  C10     0.00   0.0  0
 D0B  CONST_28  H15  C11  C10  C13     0.00   0.0  0
 D0B  CONST_29  H14  C09  C10  C13     0.00   0.0  0
 D0B  CONST_30  H26  C21  C22  C13   180.00   0.0  0
 D0B  CONST_31  C17  N03  C16  C15   180.00   0.0  0
 D0B  CONST_32  C20  N03  C16  C15     0.00   0.0  0
 D0B  CONST_33  O04  C16  N03  C17     0.00   0.0  0
 D0B  CONST_34  O04  C16  N03  C20   180.00   0.0  0
 D0B  Var_01    C19  C20  N03  C17    56.13  30.0  1
 D0B  Var_02    C18  C17  N03  C20   -56.95  30.0  1
 D0B  Var_03    C07  C06  C05  C04    24.88  30.0  1
 D0B  Var_04    C06  C07  C08  C04   -25.29  30.0  1
 D0B  Var_05    C08  C07  C06  C05     0.33  30.0  1
 D0B  Var_06    C09  C03  O02  C04     5.41  30.0  2
 D0B  Var_07    N01  N02  C14  C15   -64.72  30.0  2
 D0B  Var_08    C12  C02  O01  C01    -1.43  30.0  2
 D0B  Var_09    C16  C15  C14  N02   179.20  30.0  2
 D0B  Var_10    N03  C16  C15  C14  -176.08  30.0  3
 D0B  Var_11    H02  C01  O01  C02  -179.05  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
 D0B  chir_01  C04  O02  C05  C08  positiv
 D0B  chir_02  C18  C17  C23  O03  negativ
 D0B  chir_03  C19  O03  C20  C24  negativ

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
 D0B  plan-1  C10  0.020
 D0B  plan-1  C13  0.020
 D0B  plan-1  C21  0.020
 D0B  plan-1  C22  0.020
 D0B  plan-1  N01  0.020
 D0B  plan-1  N02  0.020
 D0B  plan-1  C14  0.020
 D0B  plan-1  H26  0.020
 D0B  plan-1  H27  0.020
 D0B  plan-2  C15  0.020
 D0B  plan-2  C17  0.020
 D0B  plan-2  C20  0.020
 D0B  plan-2  C16  0.020
 D0B  plan-2  N03  0.020
 D0B  plan-2  O04  0.020
 D0B  plan-3  C10  0.020
 D0B  plan-3  C13  0.020
 D0B  plan-3  C02  0.020
 D0B  plan-3  C03  0.020
 D0B  plan-3  O02  0.020
 D0B  plan-3  C09  0.020
 D0B  plan-3  C11  0.020
 D0B  plan-3  C12  0.020
 D0B  plan-3  H14  0.020
 D0B  plan-3  H15  0.020
 D0B  plan-3  H16  0.020
 D0B  plan-3  O01  0.020

