# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:08:05 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 4-cyclopentyl-N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-2-[(3S)-tetrahydrofuran-3-ylamino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC12CC3C[C@H](C1)C(NC(=O)c4cnc(N[C@H]5CCOC5)nc4C6CCCC6)[C@@H](C3)C2
#
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
 HD2  HD2  4-cyclopentyl-N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-2-[(3S)-tetrahydrofuran-3-ylamino]pyrimidine-5-carboxamide  ligand  65  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HD2
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
 HD2  C1    C  CR16  0  -0.014   0.9803   0.6833   0.6247
 HD2  C2    C  CR6   0  -0.224   0.5601  -0.6026   0.3089
 HD2  C3    C  CR6   0   0.357   1.5812  -1.5298   0.0322
 HD2  N4    N  N     0  -0.482   2.8484  -1.1684   0.0973
 HD2  C5    C  CR6   0   0.596   3.1405   0.0942   0.4341
 HD2  N6    N  N     0  -0.464   2.2446   1.0531   0.6898
 HD2  N7    N  NH1   0  -0.669   4.4417   0.4065   0.5209
 HD2  C8    C  CH1   0  -0.342   1.3099  -2.9544  -0.3552
 HD2  C9    C  CH2   0  -0.434   1.4529  -3.9282   0.8364
 HD2  C10   C  CH2   0  -0.443   1.8897  -5.2766   0.2215
 HD2  C11   C  CH2   0  -0.461   1.9996  -5.0329  -1.2911
 HD2  C12   C  CH2   0  -0.409   2.2548  -3.5341  -1.4094
 HD2  C13   C  C     0   0.496  -0.8843  -0.9507   0.3728
 HD2  O14   O  O     0  -0.486  -1.2894  -1.9528   0.9491
 HD2  N15   N  NH1   0  -0.660  -1.7068  -0.0641  -0.2161
 HD2  C16   C  CH1   0  -0.016  -3.1523  -0.1500  -0.1418
 HD2  C17   C  CH1   0  -0.286  -3.8019   0.6072  -1.3055
 HD2  C18   C  CH2   0  -0.447  -3.5418   2.1123  -1.1934
 HD2  C19   C  CH1   0  -0.246  -4.0976   2.6300   0.1341
 HD2  C20   C  CH2   0  -0.435  -3.4237   1.8967   1.2945
 HD2  C21   C  CH1   0  -0.265  -3.7019   0.3975   1.1852
 HD2  C22   C  CH2   0  -0.448  -5.2110   0.1485   1.2274
 HD2  C23   C  CT    0   0.256  -5.8912   0.8745   0.0696
 HD2  C24   C  CH2   0  -0.458  -5.6069   2.3748   0.1848
 HD2  C25   C  CH2   0  -0.462  -5.3117   0.3587  -1.2519
 HD2  O26   O  OH1   0  -0.686  -7.2774   0.6034   0.1609
 HD2  C27   C  CH1   0  -0.093   4.9403   1.7128   0.8753
 HD2  C28   C  CH2   0  -0.515   6.4507   1.6909   1.1818
 HD2  C29   C  CH2   0  -0.177   7.0376   2.6858   0.1788
 HD2  O30   O  O2    0  -0.494   5.9749   3.5606  -0.1445
 HD2  C31   C  CH2   0  -0.169   4.8329   2.7464  -0.2643
 HD2  H1    H  HCR6  0   0.267   0.2494   1.4529   0.8574
 HD2  H8    H  HCH1  0   0.250   0.2916  -3.0325  -0.7403
 HD2  H7    H  HNH1  0   0.395   5.0966  -0.3178   0.2739
 HD2  H27   H  HCH1  0   0.266   4.3850   2.0676   1.7447
 HD2  H91C  H  HCH2  0   0.231   2.2111  -3.5611   1.5309
 HD2  H92C  H  HCH2  0   0.242   0.5198  -3.9947   1.3934
 HD2  H121  H  HCH2  0   0.235   2.0594  -3.1399  -2.4085
 HD2  H122  H  HCH2  0   0.225   3.2907  -3.3012  -1.1554
 HD2  H101  H  HCH2  0   0.227   2.8574  -5.5757   0.6268
 HD2  H102  H  HCH2  0   0.230   1.1895  -6.0798   0.4534
 HD2  H111  H  HCH2  0   0.232   2.7797  -5.6343  -1.7598
 HD2  H112  H  HCH2  0   0.220   1.0580  -5.2866  -1.7851
 HD2  H15   H  HNH1  0   0.399  -1.2973   0.6758  -0.7631
 HD2  H16   H  HCH1  0   0.251  -3.4239  -1.2069  -0.2243
 HD2  H17   H  HCH1  0   0.249  -3.4042   0.2247  -2.2502
 HD2  H21   H  HCH1  0   0.245  -3.2283  -0.1327   2.0154
 HD2  H181  H  HCH2  0   0.231  -2.4752   2.3453  -1.2788
 HD2  H182  H  HCH2  0   0.239  -4.0251   2.6235  -2.0314
 HD2  H251  H  HCH2  0   0.234  -5.7943   0.8712  -2.0921
 HD2  H252  H  HCH2  0   0.237  -5.5271  -0.7091  -1.3614
 HD2  H19   H  HCH1  0   0.234  -3.9091   3.7038   0.2169
 HD2  H201  H  HCH2  0   0.232  -2.3467   2.0909   1.2966
 HD2  H202  H  HCH2  0   0.234  -3.8050   2.2722   2.2492
 HD2  H241  H  HCH2  0   0.231  -6.0255   2.7561   1.1223
 HD2  H242  H  HCH2  0   0.227  -6.1035   2.9090  -0.6342
 HD2  H221  H  HCH2  0   0.234  -5.4195  -0.9250   1.1683
 HD2  H222  H  HCH2  0   0.235  -5.6192   0.5032   2.1797
 HD2  H26   H  HOH1  0   0.439  -7.7194   1.0507  -0.5690
 HD2  H281  H  HCH2  0   0.261   6.6351   2.0078   2.2072
 HD2  H282  H  HCH2  0   0.256   6.8838   0.6964   1.0673
 HD2  H311  H  HCH2  0   0.205   4.8154   2.2192  -1.2293
 HD2  H312  H  HCH2  0   0.239   3.9425   3.3708  -0.1956
 HD2  H291  H  HCH2  0   0.237   7.8649   3.2713   0.5804
 HD2  H292  H  HCH2  0   0.210   7.3932   2.1610  -0.7175

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
 HD2  C1   C2    aromatic  1.389  0.020  1.389
 HD2  C1   N6    aromatic  1.319  0.020  1.319
 HD2  C2   C3    aromatic  1.407  0.020  1.407
 HD2  C2   C13   single    1.487  0.020  1.487
 HD2  C3   N4    aromatic  1.319  0.020  1.319
 HD2  C3   C8    single    1.501  0.020  1.501
 HD2  N4   C5    aromatic  1.339  0.020  1.339
 HD2  C5   N6    aromatic  1.337  0.020  1.337
 HD2  C5   N7    single    1.341  0.020  1.341
 HD2  N7   C27   single    1.442  0.020  1.442
 HD2  C8   C9    single    1.545  0.020  1.545
 HD2  C8   C12   single    1.530  0.020  1.530
 HD2  C9   C10   single    1.545  0.020  1.545
 HD2  C10  C11   single    1.536  0.020  1.536
 HD2  C11  C12   single    1.525  0.020  1.525
 HD2  C13  O14   double    1.225  0.020  1.225
 HD2  C13  N15   single    1.345  0.020  1.345
 HD2  N15  C16   single    1.450  0.020  1.450
 HD2  C16  C17   single    1.533  0.020  1.533
 HD2  C16  C21   single    1.537  0.020  1.537
 HD2  C17  C18   single    1.532  0.020  1.532
 HD2  C17  C25   single    1.531  0.020  1.531
 HD2  C18  C19   single    1.530  0.020  1.530
 HD2  C19  C20   single    1.529  0.020  1.529
 HD2  C19  C24   single    1.532  0.020  1.532
 HD2  C20  C21   single    1.529  0.020  1.529
 HD2  C21  C22   single    1.530  0.020  1.530
 HD2  C22  C23   single    1.527  0.020  1.527
 HD2  C23  C24   single    1.531  0.020  1.531
 HD2  C23  C25   single    1.532  0.020  1.532
 HD2  C23  O26   single    1.415  0.020  1.415
 HD2  C27  C28   single    1.541  0.020  1.541
 HD2  C27  C31   single    1.542  0.020  1.542
 HD2  C28  C29   single    1.530  0.020  1.530
 HD2  C29  O30   single    1.414  0.020  1.414
 HD2  O30  C31   single    1.408  0.020  1.408
 HD2  C1   H1    single    0.930  0.020  1.080
 HD2  C8   H8    single    0.970  0.020  1.090
 HD2  N7   H7    single    0.860  0.020  1.020
 HD2  C27  H27   single    0.970  0.020  1.090
 HD2  C9   H91C  single    0.970  0.020  1.090
 HD2  C9   H92C  single    0.970  0.020  1.090
 HD2  C12  H121  single    0.970  0.020  1.090
 HD2  C12  H122  single    0.970  0.020  1.090
 HD2  C10  H101  single    0.970  0.020  1.090
 HD2  C10  H102  single    0.970  0.020  1.090
 HD2  C11  H111  single    0.970  0.020  1.090
 HD2  C11  H112  single    0.970  0.020  1.090
 HD2  N15  H15   single    0.860  0.020  1.020
 HD2  C16  H16   single    0.970  0.020  1.090
 HD2  C17  H17   single    0.970  0.020  1.090
 HD2  C21  H21   single    0.970  0.020  1.090
 HD2  C18  H181  single    0.970  0.020  1.090
 HD2  C18  H182  single    0.970  0.020  1.090
 HD2  C25  H251  single    0.970  0.020  1.090
 HD2  C25  H252  single    0.970  0.020  1.090
 HD2  C19  H19   single    0.970  0.020  1.090
 HD2  C20  H201  single    0.970  0.020  1.090
 HD2  C20  H202  single    0.970  0.020  1.090
 HD2  C24  H241  single    0.970  0.020  1.090
 HD2  C24  H242  single    0.970  0.020  1.090
 HD2  C22  H221  single    0.970  0.020  1.090
 HD2  C22  H222  single    0.970  0.020  1.090
 HD2  O26  H26   single    0.850  0.020  0.980
 HD2  C28  H281  single    0.970  0.020  1.090
 HD2  C28  H282  single    0.970  0.020  1.090
 HD2  C31  H311  single    0.970  0.020  1.090
 HD2  C31  H312  single    0.970  0.020  1.090
 HD2  C29  H291  single    0.970  0.020  1.090
 HD2  C29  H292  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
 HD2  H1    C1   N6    115.82  3.000
 HD2  H1    C1   C2    120.06  3.000
 HD2  N6    C1   C2    124.11  3.000
 HD2  C13   C2   C3    124.00  3.000
 HD2  C13   C2   C1    120.05  3.000
 HD2  C3    C2   C1    115.80  3.000
 HD2  C8    C3   N4    116.51  3.000
 HD2  C8    C3   C2    123.03  3.000
 HD2  N4    C3   C2    120.46  3.000
 HD2  C5    N4   C3    118.70  3.000
 HD2  N7    C5   N6    118.08  3.000
 HD2  N7    C5   N4    116.59  3.000
 HD2  N6    C5   N4    125.33  3.000
 HD2  C5    N6   C1    115.58  3.000
 HD2  H7    N7   C27   119.13  3.000
 HD2  H7    N7   C5    116.58  3.000
 HD2  C27   N7   C5    124.21  3.000
 HD2  H8    C8   C12   107.82  3.000
 HD2  H8    C8   C9    108.26  3.000
 HD2  C12   C8   C9    103.62  3.000
 HD2  H8    C8   C3    109.12  3.000
 HD2  C12   C8   C3    115.20  3.000
 HD2  C9    C8   C3    112.48  3.000
 HD2  H92C  C9   H91C  106.88  3.000
 HD2  H92C  C9   C10   113.12  3.000
 HD2  H91C  C9   C10   110.51  3.000
 HD2  H92C  C9   C8    110.70  3.000
 HD2  H91C  C9   C8    110.05  3.000
 HD2  C10   C9   C8    105.62  3.000
 HD2  H102  C10  H101  106.78  3.000
 HD2  H102  C10  C11   111.85  3.000
 HD2  H101  C10  C11   110.24  3.000
 HD2  H102  C10  C9    112.13  3.000
 HD2  H101  C10  C9    110.01  3.000
 HD2  C11   C10  C9    105.88  3.000
 HD2  H112  C11  H111  107.09  3.000
 HD2  H112  C11  C12   109.71  3.000
 HD2  H111  C11  C12   112.88  3.000
 HD2  H112  C11  C10   110.28  3.000
 HD2  H111  C11  C10   112.75  3.000
 HD2  C12   C11  C10   104.15  3.000
 HD2  H122  C12  H121  107.81  3.000
 HD2  H122  C12  C11   110.51  3.000
 HD2  H121  C12  C11   113.33  3.000
 HD2  H122  C12  C8    110.17  3.000
 HD2  H121  C12  C8    112.54  3.000
 HD2  C11   C12  C8    102.44  3.000
 HD2  N15   C13  O14   122.88  3.000
 HD2  N15   C13  C2    114.88  3.000
 HD2  O14   C13  C2    122.21  3.000
 HD2  H15   N15  C16   118.47  3.000
 HD2  H15   N15  C13   118.25  3.000
 HD2  C16   N15  C13   123.24  3.000
 HD2  H16   C16  C21   108.68  3.000
 HD2  H16   C16  C17   108.34  3.000
 HD2  C21   C16  C17   109.14  3.000
 HD2  H16   C16  N15   107.51  3.000
 HD2  C21   C16  N15   112.30  3.000
 HD2  C17   C16  N15   110.75  3.000
 HD2  H17   C17  C25   109.38  3.000
 HD2  H17   C17  C18   110.18  3.000
 HD2  C25   C17  C18   108.93  3.000
 HD2  H17   C17  C16   109.20  3.000
 HD2  C25   C17  C16   108.13  3.000
 HD2  C18   C17  C16   110.98  3.000
 HD2  H182  C18  H181  105.73  3.000
 HD2  H182  C18  C19   110.25  3.000
 HD2  H181  C18  C19   110.46  3.000
 HD2  H182  C18  C17   109.16  3.000
 HD2  H181  C18  C17   111.65  3.000
 HD2  C19   C18  C17   109.54  3.000
 HD2  H19   C19  C24   109.33  3.000
 HD2  H19   C19  C20   109.72  3.000
 HD2  C24   C19  C20   109.22  3.000
 HD2  H19   C19  C18   109.61  3.000
 HD2  C24   C19  C18   109.29  3.000
 HD2  C20   C19  C18   109.64  3.000
 HD2  H202  C20  H201  106.28  3.000
 HD2  H202  C20  C21   109.60  3.000
 HD2  H201  C20  C21   110.69  3.000
 HD2  H202  C20  C19   110.11  3.000
 HD2  H201  C20  C19   110.49  3.000
 HD2  C21   C20  C19   109.62  3.000
 HD2  H21   C21  C22   109.12  3.000
 HD2  H21   C21  C20   110.03  3.000
 HD2  C22   C21  C20   109.70  3.000
 HD2  H21   C21  C16   109.14  3.000
 HD2  C22   C21  C16   108.57  3.000
 HD2  C20   C21  C16   110.24  3.000
 HD2  H222  C22  H221  107.07  3.000
 HD2  H222  C22  C23   109.84  3.000
 HD2  H221  C22  C23   109.90  3.000
 HD2  H222  C22  C21   109.81  3.000
 HD2  H221  C22  C21   110.23  3.000
 HD2  C23   C22  C21   109.95  3.000
 HD2  O26   C23  C25   111.20  3.000
 HD2  O26   C23  C24   111.39  3.000
 HD2  C25   C23  C24   108.93  3.000
 HD2  O26   C23  C22   107.24  3.000
 HD2  C25   C23  C22   109.00  3.000
 HD2  C24   C23  C22   109.03  3.000
 HD2  H242  C24  H241  107.25  3.000
 HD2  H242  C24  C23   109.69  3.000
 HD2  H241  C24  C23   109.54  3.000
 HD2  H242  C24  C19   109.90  3.000
 HD2  H241  C24  C19   110.30  3.000
 HD2  C23   C24  C19   110.11  3.000
 HD2  H252  C25  H251  107.02  3.000
 HD2  H252  C25  C23   109.88  3.000
 HD2  H251  C25  C23   109.70  3.000
 HD2  H252  C25  C17   110.42  3.000
 HD2  H251  C25  C17   109.36  3.000
 HD2  C23   C25  C17   110.40  3.000
 HD2  H26   O26  C23   108.15  3.000
 HD2  H27   C27  C31   109.60  3.000
 HD2  H27   C27  C28   110.18  3.000
 HD2  C31   C27  C28   102.99  3.000
 HD2  H27   C27  N7    108.33  3.000
 HD2  C31   C27  N7    113.66  3.000
 HD2  C28   C27  N7    112.01  3.000
 HD2  H282  C28  H281  107.28  3.000
 HD2  H282  C28  C29   111.82  3.000
 HD2  H281  C28  C29   111.29  3.000
 HD2  H282  C28  C27   112.41  3.000
 HD2  H281  C28  C27   110.43  3.000
 HD2  C29   C28  C27   103.67  3.000
 HD2  H292  C29  H291  108.16  3.000
 HD2  H292  C29  O30   110.64  3.000
 HD2  H291  C29  O30   108.80  3.000
 HD2  H292  C29  C28   110.41  3.000
 HD2  H291  C29  C28   113.51  3.000
 HD2  O30   C29  C28   105.31  3.000
 HD2  C31   O30  C29   105.74  3.000
 HD2  H312  C31  H311  108.48  3.000
 HD2  H312  C31  O30   109.03  3.000
 HD2  H311  C31  O30   111.40  3.000
 HD2  H312  C31  C27   113.22  3.000
 HD2  H311  C31  C27   109.17  3.000
 HD2  O30   C31  C27   105.56  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
 HD2  CONST_01  N4    C3   C2   C1      0.00   0.0  0
 HD2  CONST_02  N4    C5   N6   C1      0.00   0.0  0
 HD2  CONST_03  C5    N6   C1   C2      0.00   0.0  0
 HD2  CONST_04  C5    N4   C3   C2      0.00   0.0  0
 HD2  CONST_05  N6    C1   C2   C3      0.00   0.0  0
 HD2  CONST_06  N6    C5   N4   C3      0.00   0.0  0
 HD2  CONST_07  C8    C3   C2   C1    180.00   0.0  0
 HD2  CONST_08  C8    C3   N4   C5    180.00   0.0  0
 HD2  CONST_09  N7    C5   N6   C1    180.00   0.0  0
 HD2  CONST_10  N7    C5   N4   C3    180.00   0.0  0
 HD2  CONST_11  C13   C2   C3   N4    180.00   0.0  0
 HD2  CONST_12  C13   C2   C1   N6    180.00   0.0  0
 HD2  CONST_13  C13   C2   C3   C8      0.00   0.0  0
 HD2  CONST_14  C27   N7   C5   N4    180.00   0.0  0
 HD2  CONST_15  C27   N7   C5   N6      0.00   0.0  0
 HD2  CONST_16  H1    C1   C2   C3    180.00   0.0  0
 HD2  CONST_17  C16   N15  C13  C2    180.00   0.0  0
 HD2  CONST_18  H7    N7   C5   N4      0.00   0.0  0
 HD2  CONST_19  C16   N15  C13  O14     0.00   0.0  0
 HD2  CONST_20  H15   N15  C13  C2      0.00   0.0  0
 HD2  Var_01    C11   C10  C9   C8      0.66  30.0  1
 HD2  Var_02    C10   C11  C12  C8    -40.94  30.0  1
 HD2  Var_03    C12   C11  C10  C9     24.84  30.0  1
 HD2  Var_04    O30   C29  C28  C27    24.45  30.0  1
 HD2  Var_05    H311  C31  O30  C29   -78.22  30.0  1
 HD2  Var_06    O14   C13  C2   C1   -131.30  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
 HD2  chir_01  C8   C3   C9   C12  positiv
 HD2  chir_02  C16  N15  C17  C21  positiv
 HD2  chir_03  C17  C25  C18  C16  negativ
 HD2  chir_04  C19  C24  C20  C18  negativ
 HD2  chir_05  C21  C22  C20  C16  positiv
 HD2  chir_06  C23  C22  C24  C25  negativ
 HD2  chir_07  C27  N7   C28  C31  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
 HD2  plan-1  C2   0.020
 HD2  plan-1  C13  0.020
 HD2  plan-1  O14  0.020
 HD2  plan-1  N15  0.020
 HD2  plan-1  C16  0.020
 HD2  plan-1  H15  0.020
 HD2  plan-2  C5   0.020
 HD2  plan-2  N7   0.020
 HD2  plan-2  C27  0.020
 HD2  plan-2  H7   0.020
 HD2  plan-3  C1   0.020
 HD2  plan-3  C2   0.020
 HD2  plan-3  C3   0.020
 HD2  plan-3  N4   0.020
 HD2  plan-3  C5   0.020
 HD2  plan-3  N6   0.020
 HD2  plan-3  N7   0.020
 HD2  plan-3  C8   0.020
 HD2  plan-3  C13  0.020
 HD2  plan-3  H1   0.020

