# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 13:59:56 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: [(3R)-3-benzylmorpholin-4-yl][5-(4-methylpyridin-2-yl)-1H-pyrazol-3-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(c1)c2[nH]nc(c2)C(=O)N3CCOC[C@H]3Cc4ccccc4
#
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
 O5P  O5P  '[(3R)-3-benzylmorpholin-4-yl][5-(4-methylpyridin-2-yl)-1H-pyrazol-3-yl]methanone'  ligand  49  27  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O5P
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
 O5P  C1   C  CR6   0   0.195   6.9739   0.0977  -0.3850
 O5P  C2   C  CR16  0  -0.367   7.2801   0.7046   0.8275
 O5P  C3   C  CR16  0  -0.066   6.2481   1.0551   1.6854
 O5P  C11  C  CR15  0  -0.478   2.1518   0.4124   0.8043
 O5P  C15  C  CH2   0  -0.364  -1.0539  -2.1186  -0.0496
 O5P  C16  C  CH2   0  -0.173  -1.5643  -2.7583   1.2330
 O5P  C18  C  CH2   0  -0.151  -3.2134  -1.1038   1.4634
 O5P  C19  C  CH1   0  -0.106  -2.7554  -0.4493   0.1645
 O5P  C20  C  CH2   0  -0.543  -3.2365   0.9958   0.0031
 O5P  C21  C  CR6   0   0.128  -4.7077   1.0352  -0.3198
 O5P  C22  C  CR16  0  -0.317  -5.6492   1.3211   0.6653
 O5P  C23  C  CR16  0  -0.240  -7.0070   1.3415   0.3712
 O5P  C24  C  CR16  0  -0.271  -7.4432   1.0789  -0.9201
 O5P  C25  C  CR16  0  -0.240  -6.5129   0.7981  -1.9138
 O5P  C26  C  CR16  0  -0.302  -5.1583   0.7764  -1.6134
 O5P  C27  C  CH3   0  -0.724   8.0370  -0.2817  -1.3671
 O5P  C10  C  CR5   0   0.111   1.0357  -0.0420   0.0855
 O5P  C5   C  CR6   0   0.217   4.6629   0.2585   0.2628
 O5P  C6   C  CR16  0  -0.359   5.6288  -0.1262  -0.6611
 O5P  C7   C  CR5   0   0.404   3.2344   0.0525   0.0306
 O5P  N13  N  NT    0  -0.479  -1.3137  -0.6801   0.0014
 O5P  N4   N  N     0  -0.436   4.9692   0.8422   1.4211
 O5P  N8   N  NR15  0  -0.514   2.7157  -0.5571  -1.0594
 O5P  N9   N  N     0  -0.252   1.4010  -0.6241  -1.0481
 O5P  O14  O  O     0  -0.469  -0.6417   1.1931   1.1152
 O5P  O17  O  O2    0  -0.481  -2.9290  -2.4860   1.4583
 O5P  H28  H  HCR6  0   0.268   8.3062   0.9020   1.1086
 O5P  H29  H  HCR6  0   0.265   6.4714   1.5299   2.6344
 O5P  H32  H  HCR5  0   0.272   2.1708   0.9248   1.7506
 O5P  H33  H  HCH2  0   0.283   0.0049  -2.3269  -0.1638
 O5P  H34  H  HCH2  0   0.256  -1.5651  -2.5366  -0.9198
 O5P  H35  H  HCH2  0   0.246  -1.4550  -3.8424   1.1762
 O5P  H36  H  HCH2  0   0.207  -0.9539  -2.4017   2.0759
 O5P  H38  H  HCH2  0   0.211  -2.7327  -0.6014   2.3152
 O5P  H37  H  HCH2  0   0.243  -4.2936  -1.0061   1.5820
 O5P  H39  H  HCH1  0   0.265  -3.2067  -1.0180  -0.6573
 O5P  H40  H  HCH2  0   0.262  -3.0427   1.5799   0.9004
 O5P  H41  H  HCH2  0   0.262  -2.6768   1.4619  -0.8110
 O5P  H42  H  HCR6  0   0.251  -5.3163   1.5343   1.6748
 O5P  H43  H  HCR6  0   0.254  -7.7233   1.5645   1.1518
 O5P  H44  H  HCR6  0   0.254  -8.5002   1.0966  -1.1523
 O5P  H45  H  HCR6  0   0.254  -6.8429   0.5979  -2.9252
 O5P  H46  H  HCR6  0   0.249  -4.4393   0.5639  -2.3969
 O5P  H49  H  HCH3  0   0.262   8.1133   0.4719  -2.1531
 O5P  H47  H  HCH3  0   0.254   9.0120  -0.3597  -0.8892
 O5P  H48  H  HCH3  0   0.254   7.8121  -1.2319  -1.8501
 O5P  H30  H  HCR6  0   0.257   5.3519  -0.5985  -1.5957
 O5P  H31  H  HNR5  0   0.429   3.2124  -0.9457  -1.8462
 O5P  C12  C  C     0   0.522  -0.3823   0.1939   0.4610

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
 O5P  C2   C3   aromatic  1.387  0.020  1.387
 O5P  C2   C1   aromatic  1.390  0.020  1.390
 O5P  C3   N4   aromatic  1.323  0.020  1.323
 O5P  C27  C1   single    1.496  0.020  1.496
 O5P  C1   C6   aromatic  1.391  0.020  1.391
 O5P  N4   C5   aromatic  1.333  0.020  1.333
 O5P  C6   C5   aromatic  1.391  0.020  1.391
 O5P  C5   C7   single    1.462  0.020  1.462
 O5P  C7   C11  aromatic  1.378  0.020  1.378
 O5P  C7   N8   aromatic  1.352  0.020  1.352
 O5P  C11  C10  aromatic  1.403  0.020  1.403
 O5P  N8   N9   aromatic  1.316  0.020  1.316
 O5P  C10  N9   aromatic  1.326  0.020  1.326
 O5P  C10  C12  single    1.486  0.020  1.486
 O5P  O14  C12  double    1.222  0.020  1.222
 O5P  C24  C25  aromatic  1.390  0.020  1.390
 O5P  C24  C23  aromatic  1.388  0.020  1.388
 O5P  C12  N13  single    1.357  0.020  1.357
 O5P  C25  C26  aromatic  1.388  0.020  1.388
 O5P  C23  C22  aromatic  1.389  0.020  1.389
 O5P  C26  C21  aromatic  1.394  0.020  1.394
 O5P  N13  C19  single    1.469  0.020  1.469
 O5P  N13  C15  single    1.463  0.020  1.463
 O5P  C22  C21  aromatic  1.392  0.020  1.392
 O5P  C21  C20  single    1.507  0.020  1.507
 O5P  C19  C20  single    1.532  0.020  1.532
 O5P  C19  C18  single    1.525  0.020  1.525
 O5P  C15  C16  single    1.521  0.020  1.521
 O5P  C16  O17  single    1.410  0.020  1.410
 O5P  C18  O17  single    1.411  0.020  1.411
 O5P  C2   H28  single    0.930  0.020  1.080
 O5P  C3   H29  single    0.930  0.020  1.080
 O5P  C11  H32  single    0.930  0.020  1.080
 O5P  C15  H33  single    0.970  0.020  1.090
 O5P  C15  H34  single    0.970  0.020  1.090
 O5P  C16  H35  single    0.970  0.020  1.090
 O5P  C16  H36  single    0.970  0.020  1.090
 O5P  C18  H38  single    0.970  0.020  1.090
 O5P  C18  H37  single    0.970  0.020  1.090
 O5P  C19  H39  single    0.970  0.020  1.090
 O5P  C20  H40  single    0.970  0.020  1.090
 O5P  C20  H41  single    0.970  0.020  1.090
 O5P  C22  H42  single    0.930  0.020  1.080
 O5P  C23  H43  single    0.930  0.020  1.080
 O5P  C24  H44  single    0.930  0.020  1.080
 O5P  C25  H45  single    0.930  0.020  1.080
 O5P  C26  H46  single    0.930  0.020  1.080
 O5P  C27  H49  single    0.970  0.020  1.090
 O5P  C27  H47  single    0.970  0.020  1.090
 O5P  C27  H48  single    0.970  0.020  1.090
 O5P  C6   H30  single    0.930  0.020  1.080
 O5P  N8   H31  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
 O5P  C6   C1   C27  121.06  3.000
 O5P  C6   C1   C2   117.15  3.000
 O5P  C27  C1   C2   121.78  3.000
 O5P  H28  C2   C3   119.92  3.000
 O5P  H28  C2   C1   121.01  3.000
 O5P  C3   C2   C1   119.07  3.000
 O5P  H29  C3   N4   116.38  3.000
 O5P  H29  C3   C2   119.91  3.000
 O5P  N4   C3   C2   123.71  3.000
 O5P  H32  C11  C7   127.15  3.000
 O5P  H32  C11  C10  128.22  3.000
 O5P  C7   C11  C10  104.63  3.000
 O5P  H34  C15  H33  107.42  3.000
 O5P  H34  C15  N13  108.72  3.000
 O5P  H33  C15  N13  111.45  3.000
 O5P  H34  C15  C16  110.71  3.000
 O5P  H33  C15  C16  109.59  3.000
 O5P  N13  C15  C16  108.94  3.000
 O5P  H36  C16  H35  107.84  3.000
 O5P  H36  C16  O17  110.62  3.000
 O5P  H35  C16  O17  107.29  3.000
 O5P  H36  C16  C15  108.87  3.000
 O5P  H35  C16  C15  109.89  3.000
 O5P  O17  C16  C15  112.22  3.000
 O5P  H37  C18  H38  107.92  3.000
 O5P  H37  C18  O17  106.71  3.000
 O5P  H38  C18  O17  111.24  3.000
 O5P  H37  C18  C19  110.58  3.000
 O5P  H38  C18  C19  109.42  3.000
 O5P  O17  C18  C19  110.91  3.000
 O5P  H39  C19  N13  103.84  3.000
 O5P  H39  C19  C20  106.33  3.000
 O5P  N13  C19  C20  116.41  3.000
 O5P  H39  C19  C18  106.98  3.000
 O5P  C20  C19  C18  113.61  3.000
 O5P  N13  C19  C18  108.77  3.000
 O5P  H41  C20  H40  107.11  3.000
 O5P  H41  C20  C21  109.24  3.000
 O5P  H40  C20  C21  109.67  3.000
 O5P  H41  C20  C19  108.68  3.000
 O5P  H40  C20  C19  111.33  3.000
 O5P  C21  C20  C19  110.73  3.000
 O5P  C26  C21  C22  118.43  3.000
 O5P  C22  C21  C20  120.93  3.000
 O5P  C26  C21  C20  120.64  3.000
 O5P  H42  C22  C23  119.62  3.000
 O5P  H42  C22  C21  119.44  3.000
 O5P  C23  C22  C21  120.93  3.000
 O5P  H43  C23  C24  120.12  3.000
 O5P  H43  C23  C22  119.80  3.000
 O5P  C24  C23  C22  120.08  3.000
 O5P  H44  C24  C25  120.24  3.000
 O5P  H44  C24  C23  120.22  3.000
 O5P  C25  C24  C23  119.54  3.000
 O5P  H45  C25  C26  119.80  3.000
 O5P  H45  C25  C24  120.09  3.000
 O5P  C26  C25  C24  120.12  3.000
 O5P  H46  C26  C25  119.59  3.000
 O5P  H46  C26  C21  119.51  3.000
 O5P  C25  C26  C21  120.90  3.000
 O5P  H48  C27  H47  108.49  3.000
 O5P  H48  C27  H49  107.30  3.000
 O5P  H47  C27  H49  107.64  3.000
 O5P  H48  C27  C1   111.43  3.000
 O5P  H47  C27  C1   111.49  3.000
 O5P  H49  C27  C1   110.32  3.000
 O5P  N9   C10  C12  123.29  3.000
 O5P  C12  C10  C11  125.33  3.000
 O5P  N9   C10  C11  111.17  3.000
 O5P  N4   C5   C7   115.11  3.000
 O5P  C7   C5   C6   122.29  3.000
 O5P  N4   C5   C6   122.60  3.000
 O5P  H30  C6   C5   121.08  3.000
 O5P  H30  C6   C1   119.25  3.000
 O5P  C5   C6   C1   119.68  3.000
 O5P  N8   C7   C5   124.50  3.000
 O5P  N8   C7   C11  105.60  3.000
 O5P  C5   C7   C11  129.91  3.000
 O5P  C19  N13  C15  109.43  3.000
 O5P  C15  N13  C12  121.55  3.000
 O5P  C19  N13  C12  122.31  3.000
 O5P  C5   N4   C3   117.79  3.000
 O5P  H31  N8   N9   118.62  3.000
 O5P  H31  N8   C7   127.86  3.000
 O5P  N9   N8   C7   113.52  3.000
 O5P  N8   N9   C10  105.08  3.000
 O5P  C18  O17  C16  112.63  3.000
 O5P  O14  C12  N13  124.20  3.000
 O5P  N13  C12  C10  117.84  3.000
 O5P  O14  C12  C10  117.89  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
 O5P  CONST_01  N4   C3   C2   C1      0.00   0.0  0
 O5P  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 O5P  CONST_03  C7   C5   C6   C1    180.00   0.0  0
 O5P  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 O5P  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 O5P  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 O5P  CONST_07  C6   C5   N4   C3      0.00   0.0  0
 O5P  CONST_08  C7   C5   N4   C3    180.00   0.0  0
 O5P  CONST_09  N4   C5   C7   C11     0.00   0.0  0
 O5P  CONST_10  C6   C5   C7   C11   180.00   0.0  0
 O5P  CONST_11  N9   N8   C7   C11     0.00   0.0  0
 O5P  CONST_12  N8   N9   C10  C11     0.00   0.0  0
 O5P  CONST_13  C24  C25  C26  C21     0.00   0.0  0
 O5P  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 O5P  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 O5P  CONST_16  C25  C26  C21  C22     0.00   0.0  0
 O5P  CONST_17  C26  C25  C24  C23     0.00   0.0  0
 O5P  CONST_18  C26  C21  C22  C23     0.00   0.0  0
 O5P  CONST_19  C5   C7   C11  C10   180.00   0.0  0
 O5P  CONST_20  N8   C7   C11  C10     0.00   0.0  0
 O5P  CONST_21  C7   N8   N9   C10     0.00   0.0  0
 O5P  CONST_22  N9   N8   C7   C5    180.00   0.0  0
 O5P  CONST_23  N8   C7   C5   C6      0.00   0.0  0
 O5P  CONST_24  N9   C10  C11  C7      0.00   0.0  0
 O5P  CONST_25  N8   C7   C5   N4    180.00   0.0  0
 O5P  CONST_26  C27  C1   C2   C3    180.00   0.0  0
 O5P  CONST_27  C7   C11  C10  C12   180.00   0.0  0
 O5P  CONST_28  N8   N9   C10  C12   180.00   0.0  0
 O5P  CONST_29  C25  C26  C21  C20   180.00   0.0  0
 O5P  CONST_30  C23  C22  C21  C20   180.00   0.0  0
 O5P  CONST_31  C5   C6   C1   C27   180.00   0.0  0
 O5P  CONST_33  C10  C12  N13  C19   180.00   0.0  0
 O5P  CONST_34  H29  C3   C2   C1    180.00   0.0  0
 O5P  CONST_35  H30  C6   C1   C2    180.00   0.0  0
 O5P  CONST_36  H31  N8   C7   C11   180.00   0.0  0
 O5P  CONST_37  H45  C25  C26  C21   180.00   0.0  0
 O5P  CONST_38  H43  C23  C22  C21   180.00   0.0  0
 O5P  CONST_39  H44  C24  C23  C22   180.00   0.0  0
 O5P  CONST_40  H46  C26  C21  C22   180.00   0.0  0
 O5P  CONST_41  H42  C22  C23  C24   180.00   0.0  0
 O5P  CONST_42  H32  C11  C7   C5      0.00   0.0  0
 O5P  CONST_43  H28  C2   C1   C6    180.00   0.0  0
 O5P  CONST_45  O14  C12  N13  C19     0.00   0.0  0
 O5P  Var_01    C19  N13  C15  C16   -58.60  30.0  1
 O5P  Var_02    C19  C18  O17  C16    56.07  30.0  1
 O5P  Var_03    O17  C16  C15  N13    55.96  30.0  1
 O5P  Var_04    N13  C12  C10  C11  -155.74  30.0  2
 O5P  Var_05    C26  C21  C20  C19   -78.81  30.0  2
 O5P  Var_06    H35  C16  O17  C18  -176.08  30.0  1
 O5P  Var_07    H49  C27  C1   C2    -99.26  30.0  2

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
 O5P  chir_01  C19  N13  C20  C18  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
 O5P  plan-1  C11  0.020
 O5P  plan-1  C10  0.020
 O5P  plan-1  C5   0.020
 O5P  plan-1  C7   0.020
 O5P  plan-1  N8   0.020
 O5P  plan-1  N9   0.020
 O5P  plan-1  H32  0.020
 O5P  plan-1  H31  0.020
 O5P  plan-1  C12  0.020
 O5P  plan-2  C1   0.020
 O5P  plan-2  C2   0.020
 O5P  plan-2  C3   0.020
 O5P  plan-2  C27  0.020
 O5P  plan-2  C5   0.020
 O5P  plan-2  C6   0.020
 O5P  plan-2  C7   0.020
 O5P  plan-2  N4   0.020
 O5P  plan-2  H28  0.020
 O5P  plan-2  H29  0.020
 O5P  plan-2  H30  0.020
 O5P  plan-3  C20  0.020
 O5P  plan-3  C21  0.020
 O5P  plan-3  C22  0.020
 O5P  plan-3  C23  0.020
 O5P  plan-3  C24  0.020
 O5P  plan-3  C25  0.020
 O5P  plan-3  C26  0.020
 O5P  plan-3  H42  0.020
 O5P  plan-3  H43  0.020
 O5P  plan-3  H44  0.020
 O5P  plan-3  H45  0.020
 O5P  plan-3  H46  0.020
 O5P  plan-4  C15  0.020
 O5P  plan-4  C19  0.020
 O5P  plan-4  C10  0.020
 O5P  plan-4  N13  0.020
 O5P  plan-4  O14  0.020
 O5P  plan-4  C12  0.020

