# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 12:07:01 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2~{S})-1-[[(4~{R})-4-(2-chloranyl-4-fluoranyl-phenyl)-5-methoxycarbonyl-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-4,4-bis(fluoranyl)pyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C1=C(CN2CC(F)(F)C[C@H]2C(O)=O)NC(=N[C@H]1c3ccc(F)cc3Cl)c4sccn4
#
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
 7TL  7TL  '(2~{S})-1-[[(4~{R})-4-(2-chloranyl-4-fluoranyl-phenyl)-5-methoxycarbonyl-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-4,4-bis(fluoranyl)pyrrolidine-2-carboxylic acid'  ligand  52  34  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7TL
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
 7TL  C01  C   CH3   0  -0.436  -0.5459   3.5997  -3.6873
 7TL  O02  O   O2    0  -0.416  -0.7913   2.4857  -2.8347
 7TL  C03  C   C     0   0.491   0.2637   1.8456  -2.3343
 7TL  O04  O   O     0  -0.565   1.4051   2.1833  -2.5754
 7TL  C05  C   CR6   0  -0.020  -0.1435   0.7280  -1.4923
 7TL  C06  C   CR6   0   0.212   0.7579   0.0222  -0.7664
 7TL  N07  N   NR16  0  -0.666   0.3245  -1.0527  -0.0528
 7TL  C08  C   CR6   0   0.407  -0.9199  -1.5737  -0.2906
 7TL  N09  N   N     0  -0.414  -1.8362  -1.0038  -0.9546
 7TL  C10  C   CR16  0  -0.245  -1.6115   0.3620  -1.4027
 7TL  C11  C   CR6   0   0.145  -2.3983   1.2754  -0.4743
 7TL  C12  C   CR16  0  -0.276  -1.7779   1.9683   0.5593
 7TL  C13  C   CR16  0  -0.385  -2.4829   2.7739   1.4405
 7TL  C14  C   CR6   0   0.460  -3.8475   2.8840   1.2726
 7TL  C15  C   CR16  0  -0.371  -4.5186   2.2172   0.2670
 7TL  C16  C   CR6   0   0.002  -3.7800   1.4160  -0.5900
 7TL  CL1  CL  CL    0  -0.089  -4.6442   0.5860  -1.8419
 7TL  F18  F   F     0  -0.259  -4.5531   3.6615   2.1050
 7TL  C19  C   CR5   0   0.001  -1.1569  -2.9050   0.2687
 7TL  N20  N   N     0  -0.299  -0.2820  -3.5740   0.9504
 7TL  C21  C   CR15  0  -0.097  -0.7921  -4.7707   1.3487
 7TL  C22  C   CR15  0  -0.433  -2.0753  -5.0095   0.9617
 7TL  S23  S   S2    0   0.289  -2.6755  -3.6840   0.0648
 7TL  C24  C   CH2   0  -0.387   2.2451   0.2807  -0.6460
 7TL  N25  N   NT    0  -0.406   2.8151  -0.4449   0.4601
 7TL  C26  C   CH2   0  -0.383   2.7513   0.2045   1.7641
 7TL  C27  C   CT    0   0.726   4.1332  -0.0203   2.3537
 7TL  C28  C   CH2   0  -0.588   4.6550  -1.2590   1.6652
 7TL  C29  C   CH1   0  -0.177   4.1080  -1.0613   0.2495
 7TL  C30  C   C     0   0.514   3.9847  -2.3747  -0.4944
 7TL  O31  O   OH1   0  -0.390   5.1815  -2.8862  -0.7415
 7TL  O32  O   O     0  -0.632   2.9471  -2.8907  -0.8156
 7TL  F33  F   F     0  -0.333   4.1245  -0.1187   3.7068
 7TL  F34  F   F     0  -0.346   4.9446   1.0435   2.0648
 7TL  H1   H   HCH3  0   0.257  -0.0057   4.3907  -3.1674
 7TL  H2   H   HCH3  0   0.278   0.0139   3.3102  -4.5768
 7TL  H3   H   HCH3  0   0.288  -1.5236   3.9688  -3.9832
 7TL  H4   H   HCR6  0   0.267  -0.7057   1.8880   0.6820
 7TL  H5   H   HCR6  0   0.284  -1.9773   3.3021   2.2375
 7TL  H6   H   HCR6  0   0.281  -5.5894   2.3214   0.1545
 7TL  H7   H   HCR5  0   0.246  -0.1849  -5.4495   1.9292
 7TL  H8   H   HCR5  0   0.327  -2.6790  -5.8810   1.1599
 7TL  H9   H   HCH2  0   0.296   2.7201  -0.0343  -1.5774
 7TL  H10  H   HCH2  0   0.256   2.4250   1.3556  -0.5594
 7TL  H12  H   HCH2  0   0.265   2.5240   1.2719   1.6811
 7TL  H13  H   HCH2  0   0.248   1.9909  -0.2478   2.4072
 7TL  H14  H   HCH2  0   0.261   5.7392  -1.3471   1.7041
 7TL  H15  H   HCH2  0   0.302   4.2128  -2.1405   2.1347
 7TL  H16  H   HCH1  0   0.320   4.7951  -0.4188  -0.3206
 7TL  H17  H   HOH1  0   0.512   5.0997  -3.7338  -1.2045
 7TL  H18  H   HNR6  0   0.403   1.0387  -1.6236   0.3885
 7TL  H19  H   HCR6  0   0.272  -2.0568   0.4429  -2.3959

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
 7TL  F33  C27  single    1.357  0.020  1.357
 7TL  C21  C22  aromatic  1.361  0.020  1.361
 7TL  C21  N20  aromatic  1.360  0.020  1.360
 7TL  C28  C27  single    1.510  0.020  1.510
 7TL  C28  C29  single    1.530  0.020  1.530
 7TL  O32  C30  double    1.203  0.020  1.203
 7TL  F34  C27  single    1.369  0.020  1.369
 7TL  C27  C26  single    1.519  0.020  1.519
 7TL  C22  S23  aromatic  1.709  0.020  1.709
 7TL  N20  C19  aromatic  1.295  0.020  1.295
 7TL  C30  O31  single    1.325  0.020  1.325
 7TL  C30  C29  single    1.515  0.020  1.515
 7TL  C29  N25  single    1.448  0.020  1.448
 7TL  N25  C26  single    1.458  0.020  1.458
 7TL  N25  C24  single    1.440  0.020  1.440
 7TL  C19  S23  aromatic  1.719  0.020  1.719
 7TL  C19  C08  single    1.463  0.020  1.463
 7TL  N07  C08  single    1.370  0.020  1.370
 7TL  N07  C06  single    1.361  0.020  1.361
 7TL  C08  N09  double    1.267  0.020  1.267
 7TL  C24  C06  single    1.514  0.020  1.514
 7TL  C06  C05  double    1.356  0.020  1.356
 7TL  N09  C10  single    1.455  0.020  1.455
 7TL  C05  C10  single    1.516  0.020  1.516
 7TL  C05  C03  single    1.457  0.020  1.457
 7TL  C10  C11  single    1.522  0.020  1.522
 7TL  C12  C13  aromatic  1.387  0.020  1.387
 7TL  C12  C11  aromatic  1.390  0.020  1.390
 7TL  O04  C03  double    1.214  0.020  1.214
 7TL  C13  C14  aromatic  1.379  0.020  1.379
 7TL  C03  O02  single    1.332  0.020  1.332
 7TL  C11  C16  aromatic  1.394  0.020  1.394
 7TL  C14  F18  single    1.340  0.020  1.340
 7TL  C14  C15  aromatic  1.381  0.020  1.381
 7TL  C16  C15  aromatic  1.386  0.020  1.386
 7TL  C16  CL1  single    1.733  0.020  1.733
 7TL  O02  C01  single    1.424  0.020  1.424
 7TL  C01  H1   single    0.970  0.020  1.090
 7TL  C01  H2   single    0.970  0.020  1.090
 7TL  C01  H3   single    0.970  0.020  1.090
 7TL  C12  H4   single    0.930  0.020  1.080
 7TL  C13  H5   single    0.930  0.020  1.080
 7TL  C15  H6   single    0.930  0.020  1.080
 7TL  C21  H7   single    0.930  0.020  1.080
 7TL  C22  H8   single    0.930  0.020  1.080
 7TL  C24  H9   single    0.970  0.020  1.090
 7TL  C24  H10  single    0.970  0.020  1.090
 7TL  C26  H12  single    0.970  0.020  1.090
 7TL  C26  H13  single    0.970  0.020  1.090
 7TL  C28  H14  single    0.970  0.020  1.090
 7TL  C28  H15  single    0.970  0.020  1.090
 7TL  C29  H16  single    0.970  0.020  1.090
 7TL  O31  H17  single    0.850  0.020  0.980
 7TL  N07  H18  single    0.890  0.020  1.040
 7TL  C10  H19  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
 7TL  H3   C01  H2   109.28  3.000
 7TL  H3   C01  H1   109.24  3.000
 7TL  H2   C01  H1   109.11  3.000
 7TL  H3   C01  O02  105.89  3.000
 7TL  H2   C01  O02  111.67  3.000
 7TL  H1   C01  O02  111.56  3.000
 7TL  C03  O02  C01  117.67  3.000
 7TL  C05  C03  O04  126.19  3.000
 7TL  O04  C03  O02  122.44  3.000
 7TL  C05  C03  O02  111.37  3.000
 7TL  C10  C05  C06  119.12  3.000
 7TL  C10  C05  C03  119.34  3.000
 7TL  C06  C05  C03  121.53  3.000
 7TL  C24  C06  N07  113.95  3.000
 7TL  C24  C06  C05  127.35  3.000
 7TL  N07  C06  C05  118.70  3.000
 7TL  H18  N07  C08  120.04  3.000
 7TL  H18  N07  C06  116.61  3.000
 7TL  C08  N07  C06  119.91  3.000
 7TL  C19  C08  N09  119.50  3.000
 7TL  N09  C08  N07  125.23  3.000
 7TL  C19  C08  N07  115.26  3.000
 7TL  C10  N09  C08  118.16  3.000
 7TL  H19  C10  C11  107.44  3.000
 7TL  H19  C10  N09  106.67  3.000
 7TL  C11  C10  N09  107.20  3.000
 7TL  H19  C10  C05  108.87  3.000
 7TL  C11  C10  C05  113.08  3.000
 7TL  N09  C10  C05  113.24  3.000
 7TL  C16  C11  C12  116.99  3.000
 7TL  C16  C11  C10  121.51  3.000
 7TL  C12  C11  C10  121.47  3.000
 7TL  H4   C12  C13  118.35  3.000
 7TL  H4   C12  C11  119.30  3.000
 7TL  C13  C12  C11  122.35  3.000
 7TL  H5   C13  C14  120.88  3.000
 7TL  H5   C13  C12  120.95  3.000
 7TL  C14  C13  C12  118.16  3.000
 7TL  F18  C14  C15  118.48  3.000
 7TL  C15  C14  C13  122.08  3.000
 7TL  F18  C14  C13  119.45  3.000
 7TL  H6   C15  C16  121.25  3.000
 7TL  H6   C15  C14  120.69  3.000
 7TL  C16  C15  C14  118.06  3.000
 7TL  CL1  C16  C15  117.24  3.000
 7TL  CL1  C16  C11  120.40  3.000
 7TL  C15  C16  C11  122.36  3.000
 7TL  S23  C19  N20  115.16  3.000
 7TL  S23  C19  C08  120.67  3.000
 7TL  N20  C19  C08  124.17  3.000
 7TL  C21  N20  C19  110.80  3.000
 7TL  H7   C21  C22  124.92  3.000
 7TL  H7   C21  N20  119.96  3.000
 7TL  C22  C21  N20  115.12  3.000
 7TL  H8   C22  S23  121.77  3.000
 7TL  H8   C22  C21  128.11  3.000
 7TL  S23  C22  C21  110.12  3.000
 7TL  C22  S23  C19   88.80  3.000
 7TL  H10  C24  H9   106.24  3.000
 7TL  H10  C24  N25  111.68  3.000
 7TL  H9   C24  N25  109.73  3.000
 7TL  H10  C24  C06  109.62  3.000
 7TL  H9   C24  C06  108.06  3.000
 7TL  N25  C24  C06  111.33  3.000
 7TL  C29  N25  C26  111.03  3.000
 7TL  C26  N25  C24  116.43  3.000
 7TL  C29  N25  C24  117.14  3.000
 7TL  H13  C26  H12  107.66  3.000
 7TL  H13  C26  C27  110.06  3.000
 7TL  H12  C26  C27  111.27  3.000
 7TL  H13  C26  N25  111.85  3.000
 7TL  H12  C26  N25  112.06  3.000
 7TL  C27  C26  N25  103.97  3.000
 7TL  F34  C27  F33  105.70  3.000
 7TL  F34  C27  C28  109.66  3.000
 7TL  F33  C27  C28  113.42  3.000
 7TL  F34  C27  C26  110.02  3.000
 7TL  C28  C27  C26  105.00  3.000
 7TL  F33  C27  C26  113.08  3.000
 7TL  H15  C28  H14  108.82  3.000
 7TL  H15  C28  C29  110.93  3.000
 7TL  H14  C28  C29  113.54  3.000
 7TL  H15  C28  C27  109.03  3.000
 7TL  H14  C28  C27  113.22  3.000
 7TL  C29  C28  C27  101.09  3.000
 7TL  H16  C29  C30  107.63  3.000
 7TL  H16  C29  C28  109.37  3.000
 7TL  C30  C29  C28  111.80  3.000
 7TL  H16  C29  N25  112.61  3.000
 7TL  C30  C29  N25  111.59  3.000
 7TL  C28  C29  N25  103.86  3.000
 7TL  O32  C30  O31  124.34  3.000
 7TL  O31  C30  C29  110.66  3.000
 7TL  O32  C30  C29  125.00  3.000
 7TL  H17  O31  C30  110.51  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
 7TL  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 7TL  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 7TL  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 7TL  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 7TL  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 7TL  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 7TL  CONST_07  C22  C21  N20  C19     0.00   0.0  0
 7TL  CONST_08  C21  C22  S23  C19     0.00   0.0  0
 7TL  CONST_09  S23  C22  C21  N20     0.00   0.0  0
 7TL  CONST_10  C22  S23  C19  N20     0.00   0.0  0
 7TL  CONST_11  S23  C19  N20  C21     0.00   0.0  0
 7TL  CONST_12  C21  N20  C19  C08   180.00   0.0  0
 7TL  CONST_13  C22  S23  C19  C08   180.00   0.0  0
 7TL  CONST_14  C13  C12  C11  C10   180.00   0.0  0
 7TL  CONST_15  C15  C16  C11  C10   180.00   0.0  0
 7TL  CONST_16  C19  C08  N07  C06   180.00   0.0  0
 7TL  CONST_17  N09  C08  N07  C06     0.00   0.0  0
 7TL  CONST_18  C10  N09  C08  N07     0.00   0.0  0
 7TL  CONST_19  C19  C08  N09  C10   180.00   0.0  0
 7TL  CONST_20  CL1  C16  C11  C10     0.00   0.0  0
 7TL  CONST_21  F18  C14  C13  C12   180.00   0.0  0
 7TL  CONST_22  CL1  C16  C11  C12   180.00   0.0  0
 7TL  CONST_23  CL1  C16  C15  C14   180.00   0.0  0
 7TL  CONST_24  F18  C14  C15  C16   180.00   0.0  0
 7TL  CONST_25  H4   C12  C11  C10     0.00   0.0  0
 7TL  CONST_26  H5   C13  C12  C11   180.00   0.0  0
 7TL  CONST_27  H6   C15  C16  C11   180.00   0.0  0
 7TL  CONST_28  H7   C21  N20  C19   180.00   0.0  0
 7TL  CONST_29  H8   C22  S23  C19   180.00   0.0  0
 7TL  CONST_30  H18  N07  C08  N09   180.00   0.0  0
 7TL  CONST_31  H17  O31  C30  C29   180.00   0.0  0
 7TL  Var_01    C08  N07  C06  C05    13.78  30.0  1
 7TL  Var_02    N20  C19  C08  N07     0.30  30.0  3
 7TL  Var_03    C10  C05  C06  N07     4.55  30.0  1
 7TL  Var_04    C28  C27  C26  N25   -24.85  30.0  1
 7TL  Var_05    C29  C28  C27  C26    37.41  30.0  1
 7TL  Var_06    C29  N25  C26  C27     1.46  30.0  1
 7TL  Var_07    N25  C24  C06  C05   165.22  30.0  3
 7TL  Var_08    C06  C05  C03  O02  -172.95  30.0  2
 7TL  Var_09    C05  C03  O02  C01  -179.59  30.0  3
 7TL  Var_10    H1   C01  O02  C03   -61.44  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
 7TL  chir_01  C10  N09  C05  C11  positiv
 7TL  chir_02  C29  N25  C28  C30  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
 7TL  plan-1  C08  0.020
 7TL  plan-1  C19  0.020
 7TL  plan-1  N20  0.020
 7TL  plan-1  C21  0.020
 7TL  plan-1  C22  0.020
 7TL  plan-1  S23  0.020
 7TL  plan-1  H7   0.020
 7TL  plan-1  H8   0.020
 7TL  plan-2  C06  0.020
 7TL  plan-2  N07  0.020
 7TL  plan-2  C08  0.020
 7TL  plan-2  N09  0.020
 7TL  plan-2  C10  0.020
 7TL  plan-2  C19  0.020
 7TL  plan-2  H18  0.020
 7TL  plan-3  C10  0.020
 7TL  plan-3  C11  0.020
 7TL  plan-3  C12  0.020
 7TL  plan-3  C13  0.020
 7TL  plan-3  C14  0.020
 7TL  plan-3  C15  0.020
 7TL  plan-3  C16  0.020
 7TL  plan-3  CL1  0.020
 7TL  plan-3  F18  0.020
 7TL  plan-3  H4   0.020
 7TL  plan-3  H5   0.020
 7TL  plan-3  H6   0.020
 7TL  plan-4  C29  0.020
 7TL  plan-4  C30  0.020
 7TL  plan-4  O31  0.020
 7TL  plan-4  O32  0.020
 7TL  plan-4  H17  0.020
 7TL  plan-5  O02  0.020
 7TL  plan-5  C03  0.020
 7TL  plan-5  O04  0.020
 7TL  plan-5  C05  0.020

