# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:30:19 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)n2ncc(C(=O)NC3[C@H]4CC5C[C@@H]3CC(O)(C5)C4)c2n1
#
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
 4JX  4JX  N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  49  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4JX
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
 4JX  C1    C  CH3   0  -0.738   5.2428   3.0124   0.3948
 4JX  C2    C  CR6   0   0.259   4.7112   1.6319   0.1890
 4JX  C3    C  CR16  0  -0.427   5.6137   0.5381   0.1641
 4JX  C8    C  CR5   0  -0.380   1.6749  -0.2912  -0.3107
 4JX  C9    C  CR15  0  -0.036   1.8916  -1.6741  -0.4293
 4JX  C11   C  C     0   0.516   0.4220   0.4731  -0.3642
 4JX  C14   C  CH1   0  -0.016  -2.0300   0.3197  -0.5292
 4JX  C15   C  CH1   0  -0.283  -3.0037  -0.6690  -1.1829
 4JX  C16   C  CH2   0  -0.448  -3.2336  -1.8889  -0.2852
 4JX  C19   C  CH1   0  -0.262  -2.5947   0.7453   0.8370
 4JX  C20   C  CH2   0  -0.448  -3.9299   1.4584   0.6119
 4JX  C21   C  CT    0   0.256  -4.9194   0.5118  -0.0627
 4JX  C22   C  CH2   0  -0.455  -5.1295  -0.7136   0.8321
 4JX  C4    C  CR6   0   0.436   5.1480  -0.7301  -0.0092
 4JX  N5    N  N     0  -0.413   3.8029  -0.8526  -0.1539
 4JX  C6    C  CR56  0   0.613   2.9572   0.2355  -0.1303
 4JX  N7    N  N     0  -0.438   3.4174   1.4780   0.0443
 4JX  N10   N  N     0  -0.289   3.1609  -2.0125  -0.3364
 4JX  O12   O  O     0  -0.495   0.4100   1.6984  -0.3456
 4JX  N13   N  NH1   0  -0.686  -0.7061  -0.2610  -0.4420
 4JX  C17   C  CH1   0  -0.249  -3.7979  -1.4350   1.0618
 4JX  C18   C  CH2   0  -0.431  -2.8078  -0.4782   1.7285
 4JX  C23   C  CH2   0  -0.463  -4.3361   0.0507  -1.4021
 4JX  O24   O  OH1   0  -0.686  -6.1255   1.2284  -0.2496
 4JX  C25   C  CH3   0  -0.721   5.9794  -1.9574  -0.0486
 4JX  H12   H  HCH3  0   0.260   6.0158   3.2432  -0.3394
 4JX  H13   H  HCH3  0   0.258   4.4489   3.7507   0.3160
 4JX  H11   H  HCH3  0   0.263   5.7051   3.0984   1.3797
 4JX  H3    H  HCR6  0   0.285   6.6751   0.7027   0.2827
 4JX  H9    H  HCR5  0   0.273   1.1621  -2.4547  -0.5899
 4JX  H14   H  HCH1  0   0.248  -1.9593   1.2054  -1.1679
 4JX  H15   H  HCH1  0   0.247  -2.5984  -0.9840  -2.1491
 4JX  H162  H  HCH2  0   0.239  -3.9315  -2.5718  -0.7788
 4JX  H161  H  HCH2  0   0.231  -2.3118  -2.4614  -0.1361
 4JX  H19   H  HCH1  0   0.243  -1.8960   1.4373   1.3139
 4JX  H201  H  HCH2  0   0.234  -4.3356   1.7964   1.5707
 4JX  H202  H  HCH2  0   0.234  -3.7848   2.3509  -0.0061
 4JX  H222  H  HCH2  0   0.231  -5.5670  -0.4030   1.7871
 4JX  H221  H  HCH2  0   0.226  -5.8451  -1.3964   0.3580
 4JX  H1    H  HNH1  0   0.395  -0.6369  -1.2645  -0.4269
 4JX  H17   H  HCH1  0   0.234  -3.9609  -2.3044   1.7042
 4JX  H182  H  HCH2  0   0.230  -1.8571  -0.9846   1.9191
 4JX  H181  H  HCH2  0   0.232  -3.1868  -0.1601   2.7045
 4JX  H232  H  HCH2  0   0.237  -4.1991   0.9107  -2.0657
 4JX  H231  H  HCH2  0   0.232  -5.0404  -0.6266  -1.8987
 4JX  H24   H  HOH1  0   0.439  -6.7548   0.6462  -0.6891
 4JX  H251  H  HCH3  0   0.268   7.0294  -1.6986   0.0578
 4JX  H252  H  HCH3  0   0.274   5.7036  -2.6399   0.7561
 4JX  H253  H  HCH3  0   0.273   5.8421  -2.4929  -0.9884

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
 4JX  O12  C11   double    1.226  0.020  1.226
 4JX  O24  C21   single    1.415  0.020  1.415
 4JX  C23  C21   single    1.532  0.020  1.532
 4JX  C23  C15   single    1.530  0.020  1.530
 4JX  C20  C21   single    1.527  0.020  1.527
 4JX  C20  C19   single    1.530  0.020  1.530
 4JX  C14  C15   single    1.534  0.020  1.534
 4JX  C14  N13   single    1.448  0.020  1.448
 4JX  C14  C19   single    1.538  0.020  1.538
 4JX  C21  C22   single    1.532  0.020  1.532
 4JX  C15  C16   single    1.532  0.020  1.532
 4JX  C11  N13   single    1.348  0.020  1.348
 4JX  C11  C8    single    1.469  0.020  1.469
 4JX  C19  C18   single    1.529  0.020  1.529
 4JX  C9   C8    aromatic  1.405  0.020  1.405
 4JX  C9   N10   aromatic  1.317  0.020  1.317
 4JX  C8   C6    aromatic  1.398  0.020  1.398
 4JX  C22  C17   single    1.532  0.020  1.532
 4JX  C16  C17   single    1.529  0.020  1.529
 4JX  N10  N5    aromatic  1.338  0.020  1.338
 4JX  C6   N7    aromatic  1.336  0.020  1.336
 4JX  C6   N5    aromatic  1.378  0.020  1.378
 4JX  C18  C17   single    1.530  0.020  1.530
 4JX  N7   C2    aromatic  1.311  0.020  1.311
 4JX  N5   C4    aromatic  1.358  0.020  1.358
 4JX  C2   C1    single    1.494  0.020  1.494
 4JX  C2   C3    aromatic  1.418  0.020  1.418
 4JX  C4   C3    aromatic  1.362  0.020  1.362
 4JX  C4   C25   single    1.483  0.020  1.483
 4JX  C1   H12   single    0.970  0.020  1.090
 4JX  C1   H13   single    0.970  0.020  1.090
 4JX  C1   H11   single    0.970  0.020  1.090
 4JX  C3   H3    single    0.930  0.020  1.080
 4JX  C9   H9    single    0.930  0.020  1.080
 4JX  C14  H14   single    0.970  0.020  1.090
 4JX  C15  H15   single    0.970  0.020  1.090
 4JX  C16  H162  single    0.970  0.020  1.090
 4JX  C16  H161  single    0.970  0.020  1.090
 4JX  C19  H19   single    0.970  0.020  1.090
 4JX  C20  H201  single    0.970  0.020  1.090
 4JX  C20  H202  single    0.970  0.020  1.090
 4JX  C22  H222  single    0.970  0.020  1.090
 4JX  C22  H221  single    0.970  0.020  1.090
 4JX  N13  H1    single    0.860  0.020  1.020
 4JX  C17  H17   single    0.970  0.020  1.090
 4JX  C18  H182  single    0.970  0.020  1.090
 4JX  C18  H181  single    0.970  0.020  1.090
 4JX  C23  H232  single    0.970  0.020  1.090
 4JX  C23  H231  single    0.970  0.020  1.090
 4JX  O24  H24   single    0.850  0.020  0.980
 4JX  C25  H251  single    0.970  0.020  1.090
 4JX  C25  H252  single    0.970  0.020  1.090
 4JX  C25  H253  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
 4JX  H11   C1   H13   108.74  3.000
 4JX  H11   C1   H12   106.89  3.000
 4JX  H13   C1   H12   108.97  3.000
 4JX  H11   C1   C2    110.36  3.000
 4JX  H13   C1   C2    110.97  3.000
 4JX  H12   C1   C2    110.80  3.000
 4JX  N7    C2   C3    122.38  3.000
 4JX  C3    C2   C1    119.26  3.000
 4JX  N7    C2   C1    118.36  3.000
 4JX  H3    C3   C4    119.44  3.000
 4JX  H3    C3   C2    120.37  3.000
 4JX  C4    C3   C2    120.18  3.000
 4JX  C6    C8   C11   126.24  3.000
 4JX  C6    C8   C9    103.90  3.000
 4JX  C11   C8   C9    129.86  3.000
 4JX  H9    C9   N10   118.40  3.000
 4JX  H9    C9   C8    128.29  3.000
 4JX  N10   C9   C8    113.31  3.000
 4JX  N13   C11  O12   122.49  3.000
 4JX  N13   C11  C8    115.63  3.000
 4JX  O12   C11  C8    121.88  3.000
 4JX  H14   C14  N13   107.49  3.000
 4JX  H14   C14  C19   108.56  3.000
 4JX  N13   C14  C19   113.14  3.000
 4JX  H14   C14  C15   108.30  3.000
 4JX  C19   C14  C15   108.89  3.000
 4JX  N13   C14  C15   110.33  3.000
 4JX  H15   C15  C23   109.36  3.000
 4JX  H15   C15  C16   110.11  3.000
 4JX  C23   C15  C16   109.13  3.000
 4JX  H15   C15  C14   109.07  3.000
 4JX  C16   C15  C14   111.03  3.000
 4JX  C23   C15  C14   108.10  3.000
 4JX  H161  C16  H162  105.78  3.000
 4JX  H161  C16  C17   110.23  3.000
 4JX  H162  C16  C17   110.31  3.000
 4JX  H161  C16  C15   111.70  3.000
 4JX  H162  C16  C15   109.17  3.000
 4JX  C17   C16  C15   109.58  3.000
 4JX  H19   C19  C18   109.96  3.000
 4JX  H19   C19  C20   109.08  3.000
 4JX  C18   C19  C20   109.70  3.000
 4JX  H19   C19  C14   109.15  3.000
 4JX  C18   C19  C14   110.35  3.000
 4JX  C20   C19  C14   108.57  3.000
 4JX  H202  C20  H201  106.96  3.000
 4JX  H202  C20  C21   109.99  3.000
 4JX  H201  C20  C21   109.77  3.000
 4JX  H202  C20  C19   110.31  3.000
 4JX  H201  C20  C19   109.78  3.000
 4JX  C21   C20  C19   109.97  3.000
 4JX  O24   C21  C23   111.18  3.000
 4JX  C23   C21  C22   108.79  3.000
 4JX  O24   C21  C22   111.42  3.000
 4JX  C22   C21  C20   109.08  3.000
 4JX  C23   C21  C20   109.04  3.000
 4JX  O24   C21  C20   107.26  3.000
 4JX  H221  C22  H222  107.02  3.000
 4JX  H221  C22  C17   109.80  3.000
 4JX  H222  C22  C17   110.49  3.000
 4JX  H221  C22  C21   109.57  3.000
 4JX  H222  C22  C21   109.71  3.000
 4JX  C17   C22  C21   110.19  3.000
 4JX  C25   C4   N5    118.54  3.000
 4JX  C25   C4   C3    125.61  3.000
 4JX  N5    C4   C3    115.85  3.000
 4JX  N10   N5   C6    113.09  3.000
 4JX  C6    N5   C4    122.32  3.000
 4JX  N10   N5   C4    124.59  3.000
 4JX  N7    C6   N5    121.66  3.000
 4JX  N5    C6   C8    105.26  3.000
 4JX  N7    C6   C8    133.08  3.000
 4JX  C6    N7   C2    117.61  3.000
 4JX  N5    N10  C9    104.43  3.000
 4JX  H1    N13  C14   117.63  3.000
 4JX  H1    N13  C11   119.00  3.000
 4JX  C14   N13  C11   123.37  3.000
 4JX  H17   C17  C18   109.75  3.000
 4JX  H17   C17  C22   109.46  3.000
 4JX  C18   C17  C22   109.47  3.000
 4JX  H17   C17  C16   109.66  3.000
 4JX  C18   C17  C16   109.31  3.000
 4JX  C22   C17  C16   109.18  3.000
 4JX  H181  C18  H182  106.27  3.000
 4JX  H181  C18  C17   110.27  3.000
 4JX  H182  C18  C17   110.42  3.000
 4JX  H181  C18  C19   109.62  3.000
 4JX  H182  C18  C19   110.54  3.000
 4JX  C17   C18  C19   109.67  3.000
 4JX  H231  C23  H232  106.93  3.000
 4JX  H231  C23  C21   109.73  3.000
 4JX  H232  C23  C21   109.95  3.000
 4JX  H231  C23  C15   109.50  3.000
 4JX  H232  C23  C15   110.32  3.000
 4JX  C21   C23  C15   110.36  3.000
 4JX  H24   O24  C21   108.12  3.000
 4JX  H253  C25  H252  107.26  3.000
 4JX  H253  C25  H251  108.85  3.000
 4JX  H252  C25  H251  108.74  3.000
 4JX  H253  C25  C4    111.02  3.000
 4JX  H252  C25  C4    110.89  3.000
 4JX  H251  C25  C4    110.00  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
 4JX  CONST_01  C8    C6   N7   C2    180.00   0.0  0
 4JX  CONST_02  N5    C6   N7   C2      0.00   0.0  0
 4JX  CONST_03  N5    C4   C3   C2      0.00   0.0  0
 4JX  CONST_04  C6    N7   C2   C3      0.00   0.0  0
 4JX  CONST_05  N10   N5   C4   C3    180.00   0.0  0
 4JX  CONST_06  C6    N5   C4   C3      0.00   0.0  0
 4JX  CONST_07  N5    N10  C9   C8      0.00   0.0  0
 4JX  CONST_08  N10   N5   C6   C8      0.00   0.0  0
 4JX  CONST_09  C4    N5   C6   C8    180.00   0.0  0
 4JX  CONST_10  N7    C6   C8   C9    180.00   0.0  0
 4JX  CONST_11  N5    C6   C8   C9      0.00   0.0  0
 4JX  CONST_12  C6    N5   N10  C9      0.00   0.0  0
 4JX  CONST_13  C4    N5   N10  C9    180.00   0.0  0
 4JX  CONST_14  N7    C6   N5   C4      0.00   0.0  0
 4JX  CONST_15  N7    C2   C3   C4      0.00   0.0  0
 4JX  CONST_16  N10   C9   C8   C6      0.00   0.0  0
 4JX  CONST_17  N10   N5   C6   N7    180.00   0.0  0
 4JX  CONST_18  C6    N7   C2   C1    180.00   0.0  0
 4JX  CONST_19  C4    C3   C2   C1    180.00   0.0  0
 4JX  CONST_20  C25   C4   C3   C2    180.00   0.0  0
 4JX  CONST_21  N10   C9   C8   C11   180.00   0.0  0
 4JX  CONST_22  N7    C6   C8   C11     0.00   0.0  0
 4JX  CONST_23  N5    C6   C8   C11   180.00   0.0  0
 4JX  CONST_24  C25   C4   N5   C6    180.00   0.0  0
 4JX  CONST_25  C25   C4   N5   N10     0.00   0.0  0
 4JX  CONST_26  H9    C9   N10  N5    180.00   0.0  0
 4JX  CONST_27  H3    C3   C4   N5    180.00   0.0  0
 4JX  CONST_28  C14   N13  C11  C8    180.00   0.0  0
 4JX  CONST_29  O12   C11  N13  C14     0.00   0.0  0
 4JX  CONST_30  H1    N13  C11  C8      0.00   0.0  0
 4JX  Var_01    O12   C11  C8   C9   -174.24  30.0  2
 4JX  Var_02    H12   C1   C2   C3     54.54  30.0  2
 4JX  Var_03    H251  C25  C4   C3     -1.37  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
 4JX  chir_01  C14  C15  N13  C19  positiv
 4JX  chir_02  C15  C23  C14  C16  negativ
 4JX  chir_03  C19  C20  C14  C18  positiv
 4JX  chir_04  C21  C23  C20  C22  positiv
 4JX  chir_05  C17  C22  C16  C18  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
 4JX  plan-1  C1   0.020
 4JX  plan-1  C2   0.020
 4JX  plan-1  C3   0.020
 4JX  plan-1  C8   0.020
 4JX  plan-1  C9   0.020
 4JX  plan-1  C11  0.020
 4JX  plan-1  C4   0.020
 4JX  plan-1  N5   0.020
 4JX  plan-1  C6   0.020
 4JX  plan-1  N7   0.020
 4JX  plan-1  N10  0.020
 4JX  plan-1  C25  0.020
 4JX  plan-1  H3   0.020
 4JX  plan-1  H9   0.020
 4JX  plan-2  C8   0.020
 4JX  plan-2  C11  0.020
 4JX  plan-2  C14  0.020
 4JX  plan-2  O12  0.020
 4JX  plan-2  N13  0.020
 4JX  plan-2  H1   0.020

