# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 11:40:15 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: 6-[(Z)-2-{3-[(1S,5S,6S)-3-amino-5-methyl-1-(morpholine-4-carbonyl)-2-thia-4-azabicyclo[4.1.0]hept-3-en-5-yl]-4-fluorophenyl}-1-fluoroethenyl]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(N=C(N)S[C@]2(C[C@@H]12)C(=O)N3CCOCC3)c4cc(ccc4F)\C=C(/F)c5ccc(cn5)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
 U64  U64  6-[(Z)-2-{3-[(1S,5S,6S)-3-amino-5-methyl-1-(morpholine-4-carbonyl)-2-thia-4-azabicyclo[4.1.0]hept-3-en-5-yl]-4-fluorophenyl}-1-fluoroethenyl]pyridine-3-carbonitrile  ligand  58  35  .  2022-07-22  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_U64
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
 U64  C1   C  CR6   0   0.217  70.9455  48.2437   6.9913
 U64  C7   C  C1    0  -0.475  71.1285  47.6455   5.6773
 U64  C15  C  C     0   0.492  72.2436  47.2506   5.0579
 U64  F2   F  F     0  -0.310  73.4493  47.3702   5.6410
 U64  C16  C  CR6   0   0.152  72.3137  46.6671   3.7191
 U64  C20  C  CR16  0  -0.306  73.5379  46.3130   3.1491
 U64  C19  C  CR16  0  -0.124  73.5440  45.7699   1.8797
 U64  C18  C  CR6   0  -0.081  72.3312  45.5956   1.2204
 U64  C25  C  CSP   0   0.054  72.2726  45.0417  -0.0889
 U64  N5   N  NS    0  -0.241  72.2164  44.5934  -1.1486
 U64  C17  C  CR16  0  -0.034  71.1568  45.9799   1.8731
 U64  N4   N  N     0  -0.428  71.1538  46.4974   3.0804
 U64  C6   C  CR16  0  -0.389  69.6373  48.6094   7.3346
 U64  C5   C  CR6   0  -0.020  69.3046  49.1991   8.5456
 U64  C8   C  CR6   0   0.024  67.8736  49.6240   8.8801
 U64  C12  C  CH3   0  -0.653  67.8176  51.1590   8.9276
 U64  N1   N  N     0  -0.397  66.9885  49.2523   7.7949
 U64  C11  C  CR6   0   0.276  66.4020  48.1335   7.7089
 U64  N2   N  NH2   0  -0.797  65.7632  47.7397   6.5816
 U64  S1   S  S2    0   0.076  66.3896  46.8468   8.9416
 U64  C10  C  CR6   0  -0.350  66.6408  47.8297  10.4086
 U64  C14  C  CH2   0  -0.435  68.0274  47.9077  10.9470
 U64  C13  C  C     0   0.589  65.5015  47.7158  11.3998
 U64  O1   O  O     0  -0.481  65.6473  47.0209  12.3944
 U64  N3   N  NT    0  -0.455  64.3574  48.3714  11.1283
 U64  C21  C  CH2   0  -0.339  64.1055  49.2070   9.9694
 U64  C22  C  CH2   0  -0.175  63.4875  50.5241  10.4113
 U64  O2   O  O2    0  -0.480  62.3296  50.3274  11.1872
 U64  C23  C  CH2   0  -0.188  62.6133  49.5615  12.3373
 U64  C24  C  CH2   0  -0.325  63.1844  48.2034  11.9730
 U64  C9   C  CR16  0  -0.221  67.4430  49.0949  10.2599
 U64  C4   C  CR6   0   0.534  70.3606  49.4247   9.4217
 U64  F1   F  F     0  -0.306  70.1240  50.0030  10.6092
 U64  C3   C  CR16  0  -0.379  71.6645  49.0718   9.1347
 U64  C2   C  CR16  0  -0.326  71.9630  48.4813   7.9203
 U64  H1   H  H     0   0.284  70.2257  47.5013   5.0970
 U64  H2   H  HCR6  0   0.292  74.4705  46.4553   3.6737
 U64  H3   H  HCR6  0   0.299  74.4755  45.4881   1.4087
 U64  H4   H  HCR6  0   0.294  70.1963  45.8568   1.3865
 U64  H5   H  HCR6  0   0.268  68.8523  48.4312   6.6128
 U64  H6   H  HCH3  0   0.237  68.4565  51.5733   9.7044
 U64  H7   H  HCH3  0   0.243  68.1200  51.5756   7.9674
 U64  H8   H  HCH3  0   0.235  66.7944  51.4819   9.1290
 U64  H9   H  HNH2  0   0.396  65.7007  48.4209   5.8407
 U64  H10  H  HNH2  0   0.401  64.9767  47.1155   6.6577
 U64  H11  H  HCH2  0   0.277  68.1454  47.9580  12.0214
 U64  H12  H  HCH2  0   0.271  68.7862  47.3240  10.4403
 U64  H13  H  HCH2  0   0.254  63.4346  48.6850   9.2787
 U64  H14  H  HCH2  0   0.273  65.0240  49.4263   9.4358
 U64  H15  H  HCH2  0   0.207  64.2367  51.1007  10.9736
 U64  H16  H  HCH2  0   0.250  63.2019  51.1053   9.5337
 U64  H17  H  HCH2  0   0.211  63.3214  50.0912  12.9899
 U64  H18  H  HCH2  0   0.246  61.6789  49.4331  12.8850
 U64  H19  H  HCH2  0   0.250  62.4360  47.6154  11.4308
 U64  H20  H  HCH2  0   0.272  63.4514  47.6587  12.8745
 U64  H21  H  HCR6  0   0.289  67.1160  49.8858  10.9281
 U64  H22  H  HCR6  0   0.283  72.4436  49.2624   9.8612
 U64  H23  H  HCR6  0   0.267  72.9885  48.2153   7.7197

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
 U64  N5   C25  triple    1.152  0.020  1.152
 U64  C25  C18  single    1.423  0.020  1.423
 U64  C18  C17  aromatic  1.397  0.020  1.397
 U64  C18  C19  aromatic  1.391  0.020  1.391
 U64  C17  N4   aromatic  1.314  0.020  1.314
 U64  C19  C20  aromatic  1.381  0.020  1.381
 U64  N4   C16  aromatic  1.335  0.020  1.335
 U64  C20  C16  aromatic  1.396  0.020  1.396
 U64  C16  C15  single    1.462  0.020  1.462
 U64  C15  C7   double    1.335  0.020  1.335
 U64  C15  F2   single    1.345  0.020  1.345
 U64  C7   C1   single    1.455  0.020  1.455
 U64  N2   C11  single    1.354  0.020  1.354
 U64  C1   C6   aromatic  1.401  0.020  1.401
 U64  C1   C2   aromatic  1.398  0.020  1.398
 U64  C6   C5   aromatic  1.387  0.020  1.387
 U64  C11  N1   double    1.266  0.020  1.266
 U64  C11  S1   single    1.782  0.020  1.782
 U64  N1   C8   single    1.449  0.020  1.449
 U64  C2   C3   aromatic  1.383  0.020  1.383
 U64  S1   C10  single    1.784  0.020  1.784
 U64  C5   C8   single    1.530  0.020  1.530
 U64  C5   C4   aromatic  1.391  0.020  1.391
 U64  C8   C12  single    1.537  0.020  1.537
 U64  C8   C9   single    1.539  0.020  1.539
 U64  C3   C4   aromatic  1.381  0.020  1.381
 U64  C4   F1   single    1.342  0.020  1.342
 U64  C21  C22  single    1.520  0.020  1.520
 U64  C21  N3   single    1.451  0.020  1.451
 U64  C10  C9   single    1.505  0.020  1.505
 U64  C10  C14  single    1.490  0.020  1.490
 U64  C10  C13  single    1.514  0.020  1.514
 U64  C9   C14  single    1.491  0.020  1.491
 U64  C22  O2   single    1.408  0.020  1.408
 U64  N3   C13  single    1.346  0.020  1.346
 U64  N3   C24  single    1.455  0.020  1.455
 U64  C13  O1   double    1.222  0.020  1.222
 U64  O2   C23  single    1.411  0.020  1.411
 U64  C24  C23  single    1.518  0.020  1.518
 U64  C7   H1   single    0.930  0.020  1.080
 U64  C20  H2   single    0.930  0.020  1.080
 U64  C19  H3   single    0.930  0.020  1.080
 U64  C17  H4   single    0.930  0.020  1.080
 U64  C6   H5   single    0.930  0.020  1.080
 U64  C12  H6   single    0.970  0.020  1.090
 U64  C12  H7   single    0.970  0.020  1.090
 U64  C12  H8   single    0.970  0.020  1.090
 U64  N2   H9   single    0.890  0.020  1.040
 U64  N2   H10  single    0.890  0.020  1.040
 U64  C14  H11  single    0.970  0.020  1.090
 U64  C14  H12  single    0.970  0.020  1.090
 U64  C21  H13  single    0.970  0.020  1.090
 U64  C21  H14  single    0.970  0.020  1.090
 U64  C22  H15  single    0.970  0.020  1.090
 U64  C22  H16  single    0.970  0.020  1.090
 U64  C23  H17  single    0.970  0.020  1.090
 U64  C23  H18  single    0.970  0.020  1.090
 U64  C24  H19  single    0.970  0.020  1.090
 U64  C24  H20  single    0.970  0.020  1.090
 U64  C9   H21  single    0.970  0.020  1.090
 U64  C3   H22  single    0.930  0.020  1.080
 U64  C2   H23  single    0.930  0.020  1.080

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
 U64  C2   C1   C6   118.18  3.000
 U64  C2   C1   C7   125.33  3.000
 U64  C6   C1   C7   116.49  3.000
 U64  H1   C7   C15  114.10  3.000
 U64  H1   C7   C1   115.70  3.000
 U64  C15  C7   C1   130.20  3.000
 U64  C16  C15  F2   112.93  3.000
 U64  F2   C15  C7   121.42  3.000
 U64  C16  C15  C7   125.65  3.000
 U64  N4   C16  C20  122.29  3.000
 U64  C20  C16  C15  121.14  3.000
 U64  N4   C16  C15  116.56  3.000
 U64  H2   C20  C19  119.66  3.000
 U64  H2   C20  C16  121.71  3.000
 U64  C19  C20  C16  118.63  3.000
 U64  H3   C19  C18  120.79  3.000
 U64  H3   C19  C20  120.46  3.000
 U64  C18  C19  C20  118.75  3.000
 U64  C17  C18  C25  120.15  3.000
 U64  C17  C18  C19  118.47  3.000
 U64  C25  C18  C19  121.38  3.000
 U64  N5   C25  C18  180.00  3.000
 U64  H4   C17  N4   117.09  3.000
 U64  H4   C17  C18  120.25  3.000
 U64  N4   C17  C18  122.65  3.000
 U64  C17  N4   C16  119.20  3.000
 U64  H5   C6   C5   118.60  3.000
 U64  H5   C6   C1   118.12  3.000
 U64  C5   C6   C1   123.28  3.000
 U64  C4   C5   C8   121.84  3.000
 U64  C4   C5   C6   115.90  3.000
 U64  C8   C5   C6   122.22  3.000
 U64  C9   C8   N1   114.35  3.000
 U64  C9   C8   C12  107.79  3.000
 U64  N1   C8   C12  104.90  3.000
 U64  C9   C8   C5   111.24  3.000
 U64  C12  C8   C5   108.56  3.000
 U64  N1   C8   C5   109.66  3.000
 U64  H8   C12  H7   108.04  3.000
 U64  H8   C12  H6   107.82  3.000
 U64  H7   C12  H6   108.70  3.000
 U64  H8   C12  C8   109.59  3.000
 U64  H7   C12  C8   110.16  3.000
 U64  H6   C12  C8   112.40  3.000
 U64  C11  N1   C8   124.09  3.000
 U64  S1   C11  N2   111.26  3.000
 U64  S1   C11  N1   126.46  3.000
 U64  N2   C11  N1   122.13  3.000
 U64  H10  N2   H9   115.20  3.000
 U64  H10  N2   C11  119.06  3.000
 U64  H9   N2   C11  116.40  3.000
 U64  C10  S1   C11   99.79  3.000
 U64  C9   C10  C13  121.92  3.000
 U64  C13  C10  C14  117.89  3.000
 U64  C9   C10  C14   59.71  3.000
 U64  C13  C10  S1   113.01  3.000
 U64  C14  C10  S1   117.21  3.000
 U64  C9   C10  S1   117.19  3.000
 U64  H12  C14  H11  114.41  3.000
 U64  H12  C14  C9   119.22  3.000
 U64  H11  C14  C9   117.61  3.000
 U64  H12  C14  C10  117.05  3.000
 U64  H11  C14  C10  117.57  3.000
 U64  C9   C14  C10   60.67  3.000
 U64  N3   C13  O1   122.85  3.000
 U64  O1   C13  C10  119.05  3.000
 U64  N3   C13  C10  118.08  3.000
 U64  C24  N3   C21  112.97  3.000
 U64  C24  N3   C13  120.78  3.000
 U64  C21  N3   C13  126.10  3.000
 U64  H14  C21  H13  107.74  3.000
 U64  H14  C21  C22  108.18  3.000
 U64  H13  C21  C22  110.32  3.000
 U64  H14  C21  N3   111.25  3.000
 U64  H13  C21  N3   109.61  3.000
 U64  C22  C21  N3   109.72  3.000
 U64  H16  C22  H15  108.08  3.000
 U64  H16  C22  O2   107.61  3.000
 U64  H15  C22  O2   110.60  3.000
 U64  H16  C22  C21  109.52  3.000
 U64  H15  C22  C21  109.01  3.000
 U64  O2   C22  C21  111.93  3.000
 U64  C23  O2   C22  111.09  3.000
 U64  H18  C23  H17  108.09  3.000
 U64  H18  C23  C24  109.73  3.000
 U64  H17  C23  C24  109.35  3.000
 U64  H18  C23  O2   107.52  3.000
 U64  H17  C23  O2   110.61  3.000
 U64  C24  C23  O2   111.46  3.000
 U64  H20  C24  H19  108.03  3.000
 U64  H20  C24  C23  109.99  3.000
 U64  H19  C24  C23  110.01  3.000
 U64  H20  C24  N3   109.96  3.000
 U64  H19  C24  N3   108.99  3.000
 U64  C23  C24  N3   109.84  3.000
 U64  H21  C9   C14  114.48  3.000
 U64  H21  C9   C10  113.01  3.000
 U64  C14  C9   C10   59.62  3.000
 U64  H21  C9   C8   112.67  3.000
 U64  C14  C9   C8   125.25  3.000
 U64  C10  C9   C8   121.77  3.000
 U64  C3   C4   F1   117.43  3.000
 U64  F1   C4   C5   119.57  3.000
 U64  C3   C4   C5   123.00  3.000
 U64  H22  C3   C2   120.62  3.000
 U64  H22  C3   C4   119.68  3.000
 U64  C2   C3   C4   119.70  3.000
 U64  H23  C2   C3   118.29  3.000
 U64  H23  C2   C1   121.78  3.000
 U64  C3   C2   C1   119.93  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
 U64  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 U64  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 U64  CONST_03  C18  C17  N4   C16     0.00   0.0  0
 U64  CONST_04  C18  C19  C20  C16     0.00   0.0  0
 U64  CONST_05  C17  C18  C19  C20     0.00   0.0  0
 U64  CONST_06  C17  N4   C16  C20     0.00   0.0  0
 U64  CONST_07  N4   C17  C18  C19     0.00   0.0  0
 U64  CONST_08  N4   C16  C20  C19     0.00   0.0  0
 U64  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 U64  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 U64  CONST_11  C2   C1   C6   C5      0.00   0.0  0
 U64  CONST_12  C2   C3   C4   C5      0.00   0.0  0
 U64  CONST_13  C8   C5   C6   C1    180.00   0.0  0
 U64  CONST_14  C3   C4   C5   C8    180.00   0.0  0
 U64  CONST_15  S1   C11  N1   C8      0.00   0.0  0
 U64  CONST_16  C5   C6   C1   C7    180.00   0.0  0
 U64  CONST_17  C3   C2   C1   C7    180.00   0.0  0
 U64  CONST_18  C17  N4   C16  C15   180.00   0.0  0
 U64  CONST_19  C19  C20  C16  C15   180.00   0.0  0
 U64  CONST_20  C25  C18  C19  C20   180.00   0.0  0
 U64  CONST_21  N4   C17  C18  C25   180.00   0.0  0
 U64  CONST_22  F1   C4   C5   C6    180.00   0.0  0
 U64  CONST_23  F1   C4   C5   C8      0.00   0.0  0
 U64  CONST_24  C2   C3   C4   F1    180.00   0.0  0
 U64  CONST_25  C21  N3   C13  C10     0.00   0.0  0
 U64  CONST_26  C24  N3   C13  C10   180.00   0.0  0
 U64  CONST_27  N2   C11  N1   C8    180.00   0.0  0
 U64  CONST_28  H22  C3   C2   C1    180.00   0.0  0
 U64  CONST_29  H4   C17  N4   C16   180.00   0.0  0
 U64  CONST_30  H3   C19  C20  C16   180.00   0.0  0
 U64  CONST_31  H2   C20  C19  C18   180.00   0.0  0
 U64  CONST_32  H23  C2   C1   C6    180.00   0.0  0
 U64  CONST_33  H5   C6   C5   C8      0.00   0.0  0
 U64  CONST_34  C21  N3   C13  O1    180.00   0.0  0
 U64  CONST_35  C24  N3   C13  O1      0.00   0.0  0
 U64  CONST_36  H9   N2   C11  N1      0.00   0.0  0
 U64  Var_01    S1   C10  C9   C8      7.90  30.0  1
 U64  Var_02    C9   C10  S1   C11   -30.33  30.0  1
 U64  Var_03    O2   C22  C21  N3    -54.75  30.0  1
 U64  Var_04    O2   C23  C24  N3     55.33  30.0  1
 U64  Var_05    C23  C24  N3   C21   -52.98  30.0  1
 U64  Var_06    C24  N3   C21  C22    52.48  30.0  1
 U64  Var_07    C24  C23  O2   C22   -58.90  30.0  1
 U64  Var_08    N3   C13  C10  S1    -75.65  30.0  3
 U64  Var_09    C16  C15  C7   C1   -179.42   0.0  2
 U64  Var_10    N4   C16  C15  C7     -1.28  30.0  2
 U64  Var_11    C6   C1   C7   C15   177.04  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
 U64  chir_01  C8   C5  N1   C9   negativ
 U64  chir_02  C10  C9  C14  C13  both
 U64  chir_03  C9   C8  C10  C14  both

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
 U64  plan-1  C1   0.020
 U64  plan-1  C7   0.020
 U64  plan-1  C6   0.020
 U64  plan-1  C5   0.020
 U64  plan-1  C8   0.020
 U64  plan-1  C4   0.020
 U64  plan-1  F1   0.020
 U64  plan-1  C3   0.020
 U64  plan-1  C2   0.020
 U64  plan-1  H5   0.020
 U64  plan-1  H22  0.020
 U64  plan-1  H23  0.020
 U64  plan-2  C15  0.020
 U64  plan-2  C16  0.020
 U64  plan-2  C20  0.020
 U64  plan-2  C19  0.020
 U64  plan-2  C18  0.020
 U64  plan-2  C25  0.020
 U64  plan-2  N5   0.020
 U64  plan-2  C17  0.020
 U64  plan-2  N4   0.020
 U64  plan-2  H2   0.020
 U64  plan-2  H3   0.020
 U64  plan-2  H4   0.020
 U64  plan-3  C10  0.020
 U64  plan-3  C13  0.020
 U64  plan-3  O1   0.020
 U64  plan-3  N3   0.020
 U64  plan-3  C21  0.020
 U64  plan-3  C24  0.020
 U64  plan-4  C8   0.020
 U64  plan-4  N1   0.020
 U64  plan-4  C11  0.020
 U64  plan-4  N2   0.020
 U64  plan-4  S1   0.020
 U64  plan-4  H9   0.020
 U64  plan-4  H10  0.020
 U64  plan-5  C1   0.020
 U64  plan-5  C7   0.020
 U64  plan-5  C15  0.020
 U64  plan-5  F2   0.020
 U64  plan-5  C16  0.020
 U64  plan-5  H1   0.020

