# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:26:49 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(3-methylphenyl)-~{N}-[[2-(oxan-4-yl)-7-oxidanyl-pyrazolo[1,5-a]pyrimidin-5-yl]methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(CC(=O)NCc2cc(O)n3nc(cc3n2)C4CCOCC4)c1
#
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
 JPK  JPK  2-(3-methylphenyl)-~{N}-[[2-(oxan-4-yl)-7-oxidanyl-pyrazolo[1,5-a]pyrimidin-5-yl]methyl]ethanamide  ligand  52  28  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JPK
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
 JPK  C4   C  CR16  0  -0.229  -7.6453   0.7383   1.0877
 JPK  C14  C  CH1   0  -0.368   5.1732   0.7662  -0.4023
 JPK  C5   C  CR16  0  -0.329  -6.3818   0.5255   1.6247
 JPK  C6   C  CR6   0   0.162  -5.2491   0.8032   0.8700
 JPK  C11  C  CR16  0  -0.502   0.8125  -3.1245  -0.0269
 JPK  C7   C  CH2   0  -0.681  -3.8748   0.5545   1.4203
 JPK  C8   C  C     0   0.568  -3.3898  -0.8508   1.1040
 JPK  C9   C  CH2   0  -0.291  -1.4449  -2.1932   0.5126
 JPK  C10  C  CR6   0   0.232   0.0213  -1.9898   0.2492
 JPK  C12  C  CR6   0   0.646   2.1490  -2.9484  -0.2664
 JPK  C13  C  CR5   0   0.391   3.9036  -0.0072  -0.2713
 JPK  N1   N  NH1   0  -0.652  -2.0941  -0.9406   0.7801
 JPK  N2   N  N     0  -0.418   2.6302  -1.6843  -0.2205
 JPK  C3   C  CR16  0  -0.312  -7.7849   1.2220  -0.2040
 JPK  N3   N  N     0  -0.328   3.9038  -1.3246  -0.4187
 JPK  C15  C  CH2   0  -0.439   5.5616   1.4391   0.9185
 JPK  C16  C  CH2   0  -0.180   6.8093   2.2865   0.7324
 JPK  O3   O  O2    0  -0.485   6.6499   3.2479  -0.2879
 JPK  C17  C  CH2   0  -0.180   6.3683   2.6537  -1.5361
 JPK  C18  C  CH2   0  -0.440   5.0919   1.8281  -1.5018
 JPK  C19  C  CR15  0  -0.620   2.6266   0.4990   0.0221
 JPK  C20  C  CR56  0   0.602   1.8030  -0.6079   0.0545
 JPK  N4   N  N     0  -0.514   0.4917  -0.7714   0.2879
 JPK  O2   O  OH1   0  -0.566   3.0409  -3.8719  -0.5401
 JPK  O1   O  O     0  -0.494  -4.1273  -1.8238   1.1679
 JPK  C21  C  CR16  0  -0.346  -5.4044   1.2909  -0.4259
 JPK  C2   C  CR6   0   0.116  -6.6618   1.5048  -0.9815
 JPK  C1   C  CH3   0  -0.724  -6.8128   2.0145  -2.3858
 JPK  H1   H  HCR6  0   0.251  -8.5260   0.5279   1.6813
 JPK  H2   H  HCH1  0   0.249   5.9645   0.0554  -0.6661
 JPK  H3   H  HCR6  0   0.246  -6.2796   0.1547   2.6375
 JPK  H4   H  HCR6  0   0.300   0.3804  -4.1157  -0.0478
 JPK  H6   H  HCH2  0   0.275  -3.1695   1.2996   1.0476
 JPK  H7   H  HCH2  0   0.294  -3.8820   0.6504   2.5100
 JPK  H8   H  HCH2  0   0.272  -1.8907  -2.6930  -0.3537
 JPK  H9   H  HCR6  0   0.246  -8.7752   1.3878  -0.6119
 JPK  H10  H  HCH2  0   0.230   4.7395   2.0649   1.2775
 JPK  H11  H  HCH2  0   0.244   5.7476   0.6862   1.6880
 JPK  H12  H  HCH2  0   0.237   7.0439   2.8298   1.6495
 JPK  H13  H  HCH2  0   0.197   7.6649   1.6312   0.5098
 JPK  H14  H  HCH2  0   0.237   6.2780   3.4638  -2.2617
 JPK  H15  H  HCH2  0   0.197   7.2092   2.0203  -1.8564
 JPK  H16  H  HCH2  0   0.245   4.9409   1.3600  -2.4773
 JPK  H17  H  HCH2  0   0.230   4.2364   2.4876  -1.3264
 JPK  H18  H  HCR5  0   0.269   2.3376   1.5225   0.1925
 JPK  H19  H  HCR6  0   0.241  -4.5203   1.5128  -1.0149
 JPK  H20  H  HCH3  0   0.247  -7.2270   1.2441  -3.0391
 JPK  H21  H  HCH3  0   0.245  -7.4904   2.8680  -2.4291
 JPK  H22  H  HCH3  0   0.243  -5.8564   2.3226  -2.8064
 JPK  H5   H  HCH2  0   0.273  -1.5570  -2.8829   1.3548
 JPK  H23  H  HNH1  0   0.408  -1.5167  -0.1138   0.7288
 JPK  H24  H  HOH1  0   0.506   2.6331  -4.7484  -0.5504

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
 JPK  C17  C18  single    1.521  0.020  1.521
 JPK  C17  O3   single    1.411  0.020  1.411
 JPK  C18  C14  single    1.531  0.020  1.531
 JPK  O3   C16  single    1.411  0.020  1.411
 JPK  C16  C15  single    1.520  0.020  1.520
 JPK  C14  C15  single    1.532  0.020  1.532
 JPK  C14  C13  single    1.492  0.020  1.492
 JPK  C19  C13  aromatic  1.405  0.020  1.405
 JPK  C19  C20  aromatic  1.380  0.020  1.380
 JPK  C13  N3   aromatic  1.326  0.020  1.326
 JPK  C20  N4   aromatic  1.342  0.020  1.342
 JPK  C20  N2   aromatic  1.385  0.020  1.385
 JPK  N4   C10  aromatic  1.307  0.020  1.307
 JPK  N3   N2   aromatic  1.338  0.020  1.338
 JPK  O1   C8   double    1.223  0.020  1.223
 JPK  N2   C12  aromatic  1.353  0.020  1.353
 JPK  N1   C8   single    1.339  0.020  1.339
 JPK  N1   C9   single    1.436  0.020  1.436
 JPK  C10  C9   single    1.503  0.020  1.503
 JPK  C10  C11  aromatic  1.411  0.020  1.411
 JPK  C8   C7   single    1.520  0.020  1.520
 JPK  C1   C2   single    1.501  0.020  1.501
 JPK  C12  C11  aromatic  1.369  0.020  1.369
 JPK  C12  O2   single    1.313  0.020  1.313
 JPK  C21  C2   aromatic  1.391  0.020  1.391
 JPK  C21  C6   aromatic  1.393  0.020  1.393
 JPK  C2   C3   aromatic  1.395  0.020  1.395
 JPK  C7   C6   single    1.501  0.020  1.501
 JPK  C6   C5   aromatic  1.389  0.020  1.389
 JPK  C3   C4   aromatic  1.386  0.020  1.386
 JPK  C5   C4   aromatic  1.389  0.020  1.389
 JPK  C4   H1   single    0.930  0.020  1.080
 JPK  C14  H2   single    0.970  0.020  1.090
 JPK  C5   H3   single    0.930  0.020  1.080
 JPK  C11  H4   single    0.930  0.020  1.080
 JPK  C7   H6   single    0.970  0.020  1.090
 JPK  C7   H7   single    0.970  0.020  1.090
 JPK  C9   H8   single    0.970  0.020  1.090
 JPK  C3   H9   single    0.930  0.020  1.080
 JPK  C15  H10  single    0.970  0.020  1.090
 JPK  C15  H11  single    0.970  0.020  1.090
 JPK  C16  H12  single    0.970  0.020  1.090
 JPK  C16  H13  single    0.970  0.020  1.090
 JPK  C17  H14  single    0.970  0.020  1.090
 JPK  C17  H15  single    0.970  0.020  1.090
 JPK  C18  H16  single    0.970  0.020  1.090
 JPK  C18  H17  single    0.970  0.020  1.090
 JPK  C19  H18  single    0.930  0.020  1.080
 JPK  C21  H19  single    0.930  0.020  1.080
 JPK  C1   H20  single    0.970  0.020  1.090
 JPK  C1   H21  single    0.970  0.020  1.090
 JPK  C1   H22  single    0.970  0.020  1.090
 JPK  C9   H5   single    0.970  0.020  1.090
 JPK  N1   H23  single    0.860  0.020  1.020
 JPK  O2   H24  single    0.850  0.020  0.980

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
 JPK  H1   C4   C3   119.78  3.000
 JPK  H1   C4   C5   119.88  3.000
 JPK  C3   C4   C5   120.34  3.000
 JPK  H2   C14  C18  108.39  3.000
 JPK  H2   C14  C15  108.01  3.000
 JPK  C18  C14  C15  109.14  3.000
 JPK  H2   C14  C13  107.42  3.000
 JPK  C15  C14  C13  111.56  3.000
 JPK  C18  C14  C13  112.18  3.000
 JPK  H3   C5   C6   119.96  3.000
 JPK  H3   C5   C4   119.98  3.000
 JPK  C6   C5   C4   120.06  3.000
 JPK  C21  C6   C7   120.07  3.000
 JPK  C7   C6   C5   120.94  3.000
 JPK  C21  C6   C5   118.97  3.000
 JPK  H4   C11  C12  120.30  3.000
 JPK  H4   C11  C10  121.13  3.000
 JPK  C12  C11  C10  118.58  3.000
 JPK  H7   C7   H6   106.53  3.000
 JPK  H7   C7   C8   106.88  3.000
 JPK  H6   C7   C8   110.73  3.000
 JPK  H7   C7   C6   110.16  3.000
 JPK  H6   C7   C6   110.69  3.000
 JPK  C8   C7   C6   111.66  3.000
 JPK  O1   C8   N1   122.90  3.000
 JPK  N1   C8   C7   114.91  3.000
 JPK  O1   C8   C7   122.17  3.000
 JPK  H5   C9   H8   106.23  3.000
 JPK  H5   C9   N1   111.10  3.000
 JPK  H8   C9   N1   111.19  3.000
 JPK  H5   C9   C10  108.66  3.000
 JPK  H8   C9   C10  108.67  3.000
 JPK  N1   C9   C10  110.83  3.000
 JPK  N4   C10  C9   118.17  3.000
 JPK  C9   C10  C11  118.20  3.000
 JPK  N4   C10  C11  123.64  3.000
 JPK  O2   C12  N2   115.00  3.000
 JPK  O2   C12  C11  127.53  3.000
 JPK  N2   C12  C11  117.47  3.000
 JPK  C19  C13  N3   112.43  3.000
 JPK  N3   C13  C14  120.34  3.000
 JPK  C19  C13  C14  127.23  3.000
 JPK  H23  N1   C9   116.50  3.000
 JPK  H23  N1   C8   120.73  3.000
 JPK  C9   N1   C8   122.76  3.000
 JPK  C20  N2   N3   112.88  3.000
 JPK  N3   N2   C12  125.77  3.000
 JPK  C20  N2   C12  121.35  3.000
 JPK  H9   C3   C2   119.66  3.000
 JPK  H9   C3   C4   119.74  3.000
 JPK  C2   C3   C4   120.60  3.000
 JPK  N2   N3   C13  104.51  3.000
 JPK  H11  C15  H10  106.92  3.000
 JPK  H11  C15  C16  109.31  3.000
 JPK  H10  C15  C16  109.77  3.000
 JPK  H11  C15  C14  110.34  3.000
 JPK  H10  C15  C14  110.10  3.000
 JPK  C16  C15  C14  110.33  3.000
 JPK  H13  C16  H12  107.42  3.000
 JPK  H13  C16  O3   110.32  3.000
 JPK  H12  C16  O3   107.02  3.000
 JPK  H13  C16  C15  109.33  3.000
 JPK  H12  C16  C15  110.56  3.000
 JPK  O3   C16  C15  112.06  3.000
 JPK  C17  O3   C16  112.05  3.000
 JPK  H15  C17  H14  107.28  3.000
 JPK  H15  C17  C18  109.60  3.000
 JPK  H14  C17  C18  110.40  3.000
 JPK  H15  C17  O3   110.33  3.000
 JPK  H14  C17  O3   106.99  3.000
 JPK  C18  C17  O3   112.10  3.000
 JPK  H17  C18  H16  107.05  3.000
 JPK  H17  C18  C17  109.43  3.000
 JPK  H16  C18  C17  109.18  3.000
 JPK  H17  C18  C14  110.15  3.000
 JPK  H16  C18  C14  110.57  3.000
 JPK  C17  C18  C14  110.39  3.000
 JPK  H18  C19  C20  126.75  3.000
 JPK  H18  C19  C13  128.28  3.000
 JPK  C20  C19  C13  104.98  3.000
 JPK  N4   C20  C19  133.24  3.000
 JPK  N4   C20  N2   121.56  3.000
 JPK  C19  C20  N2   105.20  3.000
 JPK  C20  N4   C10  117.41  3.000
 JPK  H24  O2   C12  110.70  3.000
 JPK  H19  C21  C2   119.21  3.000
 JPK  H19  C21  C6   119.05  3.000
 JPK  C2   C21  C6   121.74  3.000
 JPK  C1   C2   C21  121.11  3.000
 JPK  C21  C2   C3   118.29  3.000
 JPK  C1   C2   C3   120.61  3.000
 JPK  H22  C1   H21  107.98  3.000
 JPK  H22  C1   H20  107.56  3.000
 JPK  H21  C1   H20  107.02  3.000
 JPK  H22  C1   C2   111.65  3.000
 JPK  H21  C1   C2   111.43  3.000
 JPK  H20  C1   C2   111.00  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
 JPK  CONST_01  C21  C2   C3   C4      0.00   0.0  0
 JPK  CONST_02  C21  C6   C5   C4      0.00   0.0  0
 JPK  CONST_03  C2   C21  C6   C5      0.00   0.0  0
 JPK  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 JPK  CONST_05  C3   C2   C21  C6      0.00   0.0  0
 JPK  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 JPK  CONST_07  C20  N4   C10  C11     0.00   0.0  0
 JPK  CONST_08  C20  N2   C12  C11     0.00   0.0  0
 JPK  CONST_09  N3   N2   C12  C11   180.00   0.0  0
 JPK  CONST_10  C19  C20  N4   C10   180.00   0.0  0
 JPK  CONST_11  N2   C20  N4   C10     0.00   0.0  0
 JPK  CONST_12  N2   C12  C11  C10     0.00   0.0  0
 JPK  CONST_13  C19  C20  N2   C12   180.00   0.0  0
 JPK  CONST_14  N4   C20  N2   C12     0.00   0.0  0
 JPK  CONST_15  C13  N3   N2   C12   180.00   0.0  0
 JPK  CONST_16  N4   C10  C11  C12     0.00   0.0  0
 JPK  CONST_17  N4   C20  C19  C13   180.00   0.0  0
 JPK  CONST_18  N2   C20  C19  C13     0.00   0.0  0
 JPK  CONST_19  C20  N2   N3   C13     0.00   0.0  0
 JPK  CONST_20  C19  C13  N3   N2      0.00   0.0  0
 JPK  CONST_21  C20  C19  C13  N3      0.00   0.0  0
 JPK  CONST_22  C19  C20  N2   N3      0.00   0.0  0
 JPK  CONST_23  N4   C20  N2   N3    180.00   0.0  0
 JPK  CONST_24  C20  C19  C13  C14   180.00   0.0  0
 JPK  CONST_25  N2   N3   C13  C14   180.00   0.0  0
 JPK  CONST_26  C1   C2   C3   C4    180.00   0.0  0
 JPK  CONST_27  C7   C6   C5   C4    180.00   0.0  0
 JPK  CONST_28  C1   C2   C21  C6    180.00   0.0  0
 JPK  CONST_29  C2   C21  C6   C7    180.00   0.0  0
 JPK  CONST_30  C20  N4   C10  C9    180.00   0.0  0
 JPK  CONST_31  C12  C11  C10  C9    180.00   0.0  0
 JPK  CONST_32  O2   C12  C11  C10   180.00   0.0  0
 JPK  CONST_33  O2   C12  N2   N3      0.00   0.0  0
 JPK  CONST_34  O2   C12  N2   C20   180.00   0.0  0
 JPK  CONST_35  H18  C19  C13  C14     0.00   0.0  0
 JPK  CONST_36  H19  C21  C6   C5    180.00   0.0  0
 JPK  CONST_37  H9   C3   C4   C5    180.00   0.0  0
 JPK  CONST_38  H1   C4   C5   C6    180.00   0.0  0
 JPK  CONST_39  H4   C11  C12  N2    180.00   0.0  0
 JPK  CONST_40  H3   C5   C4   C3    180.00   0.0  0
 JPK  CONST_41  C9   N1   C8   C7    180.00   0.0  0
 JPK  CONST_42  O1   C8   N1   C9      0.00   0.0  0
 JPK  CONST_43  H23  N1   C8   C7      0.00   0.0  0
 JPK  Var_01    O3   C17  C18  C14   -56.06  30.0  1
 JPK  Var_02    O3   C16  C15  C14    56.21  30.0  1
 JPK  Var_03    C18  C17  O3   C16    59.75  30.0  1
 JPK  Var_04    C8   C7   C6   C5     89.90  30.0  2
 JPK  Var_05    N1   C9   C10  C11   179.73  30.0  2
 JPK  Var_06    H20  C1   C2   C3    -68.28  30.0  2
 JPK  Var_07    O1   C8   C7   C6    -40.55  30.0  1
 JPK  Var_08    C10  C9   N1   C8   -176.98  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
 JPK  chir_01  C14  C18  C15  C13  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
 JPK  plan-1  C4   0.020
 JPK  plan-1  C5   0.020
 JPK  plan-1  C6   0.020
 JPK  plan-1  C7   0.020
 JPK  plan-1  C3   0.020
 JPK  plan-1  C21  0.020
 JPK  plan-1  C2   0.020
 JPK  plan-1  C1   0.020
 JPK  plan-1  H1   0.020
 JPK  plan-1  H3   0.020
 JPK  plan-1  H9   0.020
 JPK  plan-1  H19  0.020
 JPK  plan-2  C14  0.020
 JPK  plan-2  C11  0.020
 JPK  plan-2  C9   0.020
 JPK  plan-2  C10  0.020
 JPK  plan-2  C12  0.020
 JPK  plan-2  C13  0.020
 JPK  plan-2  N2   0.020
 JPK  plan-2  N3   0.020
 JPK  plan-2  C19  0.020
 JPK  plan-2  C20  0.020
 JPK  plan-2  N4   0.020
 JPK  plan-2  O2   0.020
 JPK  plan-2  H4   0.020
 JPK  plan-2  H18  0.020
 JPK  plan-3  C7   0.020
 JPK  plan-3  C8   0.020
 JPK  plan-3  C9   0.020
 JPK  plan-3  N1   0.020
 JPK  plan-3  O1   0.020
 JPK  plan-3  H23  0.020

