# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 17:24:28 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylamino)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(nc(C)c1F)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)c4sc(cc4)C#N
#
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
 60S  60S  5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylamino)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile  ligand  48  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_60S
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
 60S  C1   C  CR5   0  -0.027   1.1963   0.1266   0.1658
 60S  C2   C  CR15  0  -0.429   1.0119   1.0035  -1.0729
 60S  C4   C  C     0   0.616   2.0545   2.1351   1.3027
 60S  C5   C  C     0   0.599   1.9790   2.1518  -1.1422
 60S  C7   C  CR6   0   0.618  -2.4118   0.2170  -0.1366
 60S  C10  C  CR6   0   0.430  -4.1461  -1.0212   0.6557
 60S  C11  C  CR5   0  -0.081   2.4050  -0.7721   0.1055
 60S  N12  N  N     0  -0.516  -3.1649   1.2018  -0.6160
 60S  C14  C  CR6   0   0.317  -5.0116  -0.0250   0.1648
 60S  C15  C  CH2   0  -0.218  -0.4537   1.4493  -0.9770
 60S  C18  C  CR15  0  -0.232   3.4806  -0.7730   0.9490
 60S  C19  C  CR5   0  -0.260   4.1111  -2.4348  -0.5207
 60S  C24  C  CR15  0  -0.118   4.4615  -1.7241   0.5949
 60S  N3   N  NT    0  -0.542   2.4882   2.5998   0.0507
 60S  N6   N  NH1   0  -0.652   1.2547   1.0274   1.2816
 60S  N8   N  N     0  -0.519  -2.8367  -0.8838   0.4866
 60S  N9   N  NR5   0  -0.513  -1.0740   0.3343  -0.2957
 60S  C13  C  CH2   0  -0.206  -0.1323  -0.6339   0.2108
 60S  S16  S  S2    0   0.317   2.5794  -1.9437  -1.1383
 60S  C17  C  CR6   0   0.118  -4.4908   1.0712  -0.4645
 60S  N20  N  NH1   0  -0.657  -4.6059  -2.1065   1.2900
 60S  N21  N  NS    0  -0.241   5.4589  -4.2944  -1.6580
 60S  N22  N  N     0  -0.682   2.3399   2.6713   2.4192
 60S  C23  C  CSP   0   0.062   4.8537  -3.4570  -1.1453
 60S  O25  O  O     0  -0.440   2.2823   2.6520  -2.2046
 60S  F26  F  F     0  -0.318  -6.3456  -0.1798   0.3258
 60S  C27  C  CH3   0  -0.575   3.4575   3.6858   0.0430
 60S  C28  C  CH3   0  -0.731  -5.3647   2.1495  -1.0221
 60S  C29  C  CH3   0  -0.509  -3.7383  -3.1387   1.8010
 60S  H1   H  HCR5  0   0.312   1.1456   0.4113  -1.9801
 60S  H2   H  HCH2  0   0.246  -0.5656   2.3803  -0.4132
 60S  H3   H  HCH2  0   0.266  -0.8770   1.6132  -1.9680
 60S  H4   H  HCR5  0   0.283   3.5770  -0.1140   1.7991
 60S  H5   H  HCR5  0   0.297   5.3851  -1.8789   1.1327
 60S  H6   H  HCH2  0   0.245  -0.0895  -1.5295  -0.4192
 60S  H7   H  HCH2  0   0.276  -0.3775  -0.9634   1.2217
 60S  H8   H  HNH1  0   0.406  -5.5983  -2.2226   1.3952
 60S  H9   H  H     0   0.358   2.8591   3.5338   2.3352
 60S  H11  H  HCH3  0   0.263   4.2829   3.4482   0.7108
 60S  H12  H  HCH3  0   0.281   3.8537   3.8057  -0.9580
 60S  H13  H  HCH3  0   0.263   3.0037   4.6273   0.3527
 60S  H14  H  HCH3  0   0.261  -5.7572   1.8559  -1.9976
 60S  H15  H  HCH3  0   0.253  -6.2178   2.3659  -0.3810
 60S  H16  H  HCH3  0   0.255  -4.7887   3.0624  -1.1561
 60S  H17  H  HCH3  0   0.251  -4.3519  -3.8705   2.3185
 60S  H18  H  HCH3  0   0.235  -3.1919  -3.6466   1.0048
 60S  H19  H  HCH3  0   0.237  -3.0096  -2.7372   2.5055
 60S  H20  H  HNH1  0   0.401   1.0519   0.6553   2.1975

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
 60S  C24  C18  aromatic  1.411  0.020  1.411
 60S  C24  C19  aromatic  1.368  0.020  1.368
 60S  C18  C11  aromatic  1.367  0.020  1.367
 60S  N21  C23  triple    1.153  0.020  1.153
 60S  C23  C19  single    1.409  0.020  1.409
 60S  C19  S16  aromatic  1.723  0.020  1.723
 60S  C28  C17  single    1.496  0.020  1.496
 60S  C11  S16  aromatic  1.718  0.020  1.718
 60S  C11  C1   single    1.507  0.020  1.507
 60S  N12  C17  aromatic  1.341  0.020  1.341
 60S  N12  C7   aromatic  1.329  0.020  1.329
 60S  C17  C14  aromatic  1.367  0.020  1.367
 60S  C13  C1   single    1.532  0.020  1.532
 60S  C13  N9   single    1.442  0.020  1.442
 60S  C1   C2   single    1.529  0.020  1.529
 60S  C1   N6   single    1.435  0.020  1.435
 60S  C14  F26  single    1.353  0.020  1.353
 60S  C14  C10  aromatic  1.408  0.020  1.408
 60S  C7   N9   single    1.352  0.020  1.352
 60S  C7   N8   aromatic  1.334  0.020  1.334
 60S  N9   C15  single    1.446  0.020  1.446
 60S  C2   C15  single    1.535  0.020  1.535
 60S  C2   C5   single    1.503  0.020  1.503
 60S  C10  N8   aromatic  1.327  0.020  1.327
 60S  C10  N20  single    1.338  0.020  1.338
 60S  N6   C4   single    1.366  0.020  1.366
 60S  C5   O25  double    1.213  0.020  1.213
 60S  C5   N3   single    1.372  0.020  1.372
 60S  N20  C29  single    1.442  0.020  1.442
 60S  C4   N3   single    1.404  0.020  1.404
 60S  C4   N22  double    1.271  0.020  1.271
 60S  N3   C27  single    1.456  0.020  1.456
 60S  C2   H1   single    0.970  0.020  1.090
 60S  C15  H2   single    0.970  0.020  1.090
 60S  C15  H3   single    0.970  0.020  1.090
 60S  C18  H4   single    0.930  0.020  1.080
 60S  C24  H5   single    0.930  0.020  1.080
 60S  C13  H6   single    0.970  0.020  1.090
 60S  C13  H7   single    0.970  0.020  1.090
 60S  N20  H8   single    0.860  0.020  1.020
 60S  N22  H9   single    0.890  0.020  1.040
 60S  C27  H11  single    0.970  0.020  1.090
 60S  C27  H12  single    0.970  0.020  1.090
 60S  C27  H13  single    0.970  0.020  1.090
 60S  C28  H14  single    0.970  0.020  1.090
 60S  C28  H15  single    0.970  0.020  1.090
 60S  C28  H16  single    0.970  0.020  1.090
 60S  C29  H17  single    0.970  0.020  1.090
 60S  C29  H18  single    0.970  0.020  1.090
 60S  C29  H19  single    0.970  0.020  1.090
 60S  N6   H20  single    0.890  0.020  1.040

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
 60S  C13  C1   N6   108.91  3.000
 60S  N6   C1   C11  111.88  3.000
 60S  C13  C1   C11  113.63  3.000
 60S  N6   C1   C2   105.95  3.000
 60S  C13  C1   C2   101.77  3.000
 60S  C11  C1   C2   113.97  3.000
 60S  H1   C2   C15  109.05  3.000
 60S  H1   C2   C5   107.30  3.000
 60S  C15  C2   C5   113.29  3.000
 60S  H1   C2   C1   110.33  3.000
 60S  C5   C2   C1   113.45  3.000
 60S  C15  C2   C1   103.37  3.000
 60S  N22  C4   N6   119.14  3.000
 60S  N22  C4   N3   125.05  3.000
 60S  N6   C4   N3   115.80  3.000
 60S  O25  C5   N3   122.28  3.000
 60S  N3   C5   C2   116.63  3.000
 60S  O25  C5   C2   121.10  3.000
 60S  N9   C7   N8   116.20  3.000
 60S  N8   C7   N12  126.81  3.000
 60S  N9   C7   N12  116.99  3.000
 60S  N20  C10  N8   118.90  3.000
 60S  N20  C10  C14  121.85  3.000
 60S  N8   C10  C14  119.25  3.000
 60S  S16  C11  C18  111.50  3.000
 60S  S16  C11  C1   121.14  3.000
 60S  C18  C11  C1   127.35  3.000
 60S  C17  N12  C7   116.58  3.000
 60S  F26  C14  C17  121.48  3.000
 60S  F26  C14  C10  118.93  3.000
 60S  C17  C14  C10  119.58  3.000
 60S  H3   C15  H2   107.51  3.000
 60S  H3   C15  N9   112.19  3.000
 60S  H2   C15  N9   111.68  3.000
 60S  H3   C15  C2   110.96  3.000
 60S  H2   C15  C2   112.15  3.000
 60S  N9   C15  C2   102.42  3.000
 60S  H4   C18  C24  123.13  3.000
 60S  H4   C18  C11  123.75  3.000
 60S  C24  C18  C11  113.11  3.000
 60S  C23  C19  S16  121.08  3.000
 60S  S16  C19  C24  111.83  3.000
 60S  C23  C19  C24  127.10  3.000
 60S  H5   C24  C19  123.40  3.000
 60S  H5   C24  C18  124.48  3.000
 60S  C19  C24  C18  112.12  3.000
 60S  C27  N3   C5   119.09  3.000
 60S  C27  N3   C4   117.21  3.000
 60S  C5   N3   C4   123.54  3.000
 60S  H20  N6   C4   113.73  3.000
 60S  H20  N6   C1   117.78  3.000
 60S  C4   N6   C1   123.00  3.000
 60S  C10  N8   C7   117.33  3.000
 60S  C13  N9   C15  113.75  3.000
 60S  C15  N9   C7   123.13  3.000
 60S  C13  N9   C7   123.12  3.000
 60S  H7   C13  H6   107.13  3.000
 60S  H7   C13  N9   112.41  3.000
 60S  H6   C13  N9   111.85  3.000
 60S  H7   C13  C1   111.85  3.000
 60S  H6   C13  C1   110.80  3.000
 60S  N9   C13  C1   102.87  3.000
 60S  C19  S16  C11   91.44  3.000
 60S  C28  C17  C14  121.81  3.000
 60S  C14  C17  N12  120.45  3.000
 60S  C28  C17  N12  117.74  3.000
 60S  H8   N20  C29  118.32  3.000
 60S  H8   N20  C10  118.86  3.000
 60S  C29  N20  C10  122.80  3.000
 60S  H9   N22  C4   113.74  3.000
 60S  N21  C23  C19  180.00  3.000
 60S  H13  C27  H12  108.61  3.000
 60S  H13  C27  H11  109.27  3.000
 60S  H12  C27  H11  108.29  3.000
 60S  H13  C27  N3   111.45  3.000
 60S  H12  C27  N3   109.33  3.000
 60S  H11  C27  N3   109.82  3.000
 60S  H16  C28  H15  108.70  3.000
 60S  H16  C28  H14  107.82  3.000
 60S  H15  C28  H14  107.33  3.000
 60S  H16  C28  C17  109.97  3.000
 60S  H15  C28  C17  112.43  3.000
 60S  H14  C28  C17  110.44  3.000
 60S  H19  C29  H18  107.95  3.000
 60S  H19  C29  H17  108.53  3.000
 60S  H18  C29  H17  108.48  3.000
 60S  H19  C29  N20  111.56  3.000
 60S  H18  C29  N20  112.09  3.000
 60S  H17  C29  N20  108.13  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
 60S  CONST_01  C14  C17  N12  C7      0.00   0.0  0
 60S  CONST_02  C14  C10  N8   C7      0.00   0.0  0
 60S  CONST_03  N12  C17  C14  C10     0.00   0.0  0
 60S  CONST_04  N12  C7   N8   C10     0.00   0.0  0
 60S  CONST_05  C19  C24  C18  C11     0.00   0.0  0
 60S  CONST_06  C24  C19  S16  C11     0.00   0.0  0
 60S  CONST_07  S16  C19  C24  C18     0.00   0.0  0
 60S  CONST_08  C19  S16  C11  C18     0.00   0.0  0
 60S  CONST_09  S16  C11  C18  C24     0.00   0.0  0
 60S  CONST_10  C17  N12  C7   N8      0.00   0.0  0
 60S  CONST_11  C17  C14  C10  N8      0.00   0.0  0
 60S  CONST_12  C24  C18  C11  C1    180.00   0.0  0
 60S  CONST_13  C19  S16  C11  C1    180.00   0.0  0
 60S  CONST_14  N9   C7   N8   C10   180.00   0.0  0
 60S  CONST_15  C17  N12  C7   N9    180.00   0.0  0
 60S  CONST_17  C4   N3   C5   C2      0.00   0.0  0
 60S  CONST_18  N6   C4   N3   C5      0.00   0.0  0
 60S  CONST_19  C28  C17  N12  C7    180.00   0.0  0
 60S  CONST_20  N20  C10  N8   C7    180.00   0.0  0
 60S  CONST_21  C28  C17  C14  C10   180.00   0.0  0
 60S  CONST_22  C23  C19  S16  C11   180.00   0.0  0
 60S  CONST_23  F26  C14  C17  N12   180.00   0.0  0
 60S  CONST_24  C23  C19  C24  C18   180.00   0.0  0
 60S  CONST_25  F26  C14  C10  N8    180.00   0.0  0
 60S  CONST_26  N20  C10  C14  C17   180.00   0.0  0
 60S  CONST_28  C27  N3   C5   C2    180.00   0.0  0
 60S  CONST_29  O25  C5   N3   C4    180.00   0.0  0
 60S  CONST_30  N22  C4   N3   C5    180.00   0.0  0
 60S  CONST_31  C27  N3   C4   N6    180.00   0.0  0
 60S  CONST_32  H4   C18  C11  C1      0.00   0.0  0
 60S  CONST_33  H5   C24  C18  C11   180.00   0.0  0
 60S  CONST_34  H20  N6   C4   N3    180.00   0.0  0
 60S  CONST_35  C29  N20  C10  C14   180.00   0.0  0
 60S  CONST_36  C29  N20  C10  N8      0.00   0.0  0
 60S  CONST_37  C27  N3   C4   N22     0.00   0.0  0
 60S  CONST_38  C27  N3   C5   O25     0.00   0.0  0
 60S  CONST_39  H8   N20  C10  C14     0.00   0.0  0
 60S  CONST_40  H9   N22  C4   N3      0.00   0.0  0
 60S  Var_01    C7   N9   C13  C1   -163.53  30.0  1
 60S  Var_02    C13  N9   C15  C2      8.95  30.0  1
 60S  Var_03    H11  C27  N3   C4     49.78  30.0  3
 60S  Var_04    H14  C28  C17  N12    98.19  30.0  2
 60S  Var_05    H17  C29  N20  C10   176.69  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
 60S  chir_01  C1  C13  C2   N6  negativ
 60S  chir_02  C2  C1   C15  C5  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
 60S  plan-1  C1   0.020
 60S  plan-1  C11  0.020
 60S  plan-1  C18  0.020
 60S  plan-1  C19  0.020
 60S  plan-1  C24  0.020
 60S  plan-1  S16  0.020
 60S  plan-1  N21  0.020
 60S  plan-1  C23  0.020
 60S  plan-1  H4   0.020
 60S  plan-1  H5   0.020
 60S  plan-2  C7   0.020
 60S  plan-2  C10  0.020
 60S  plan-2  N12  0.020
 60S  plan-2  C14  0.020
 60S  plan-2  N8   0.020
 60S  plan-2  N9   0.020
 60S  plan-2  C17  0.020
 60S  plan-2  N20  0.020
 60S  plan-2  F26  0.020
 60S  plan-2  C28  0.020
 60S  plan-3  C10  0.020
 60S  plan-3  N20  0.020
 60S  plan-3  C29  0.020
 60S  plan-3  H8   0.020
 60S  plan-4  C1   0.020
 60S  plan-4  C2   0.020
 60S  plan-4  C4   0.020
 60S  plan-4  C5   0.020
 60S  plan-4  N3   0.020
 60S  plan-4  N6   0.020
 60S  plan-4  N22  0.020
 60S  plan-4  O25  0.020
 60S  plan-4  C27  0.020
 60S  plan-4  H9   0.020
 60S  plan-4  H20  0.020

