# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 23:36:48 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-(3-chloro-5-cyanophenoxy)-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: F[S](=O)(=O)Oc1ccc(Oc2cc(Cl)cc(c2)C#N)c(OCCN3C=CC(=O)NC3=O)c1
#
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
 X2S  X2S  '4-(3-chloro-5-cyanophenoxy)-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate'  ligand  45  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X2S
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
 X2S  N    N   NS    0  -0.237  469.9318  -19.7281  127.5077
 X2S  C    C   CSP   0   0.069  469.2656  -19.0799  126.8281
 X2S  O    O   O2    0  -0.494  467.9327  -17.7458  122.4684
 X2S  C1   C   CR6   0  -0.006  468.4342  -18.2755  125.9896
 X2S  C10  C   CR16  0  -0.424  465.2334  -16.5642  120.3190
 X2S  C11  C   CR6   0   0.374  465.9235  -17.3301  121.2496
 X2S  C12  C   CH2   0  -0.200  464.0668  -18.7303  121.6982
 X2S  C13  C   CH2   0  -0.366  463.7638  -19.9214  122.5786
 X2S  C14  C   CR16  0   0.096  463.2702  -18.8517  124.7079
 X2S  C15  C   CR16  0  -0.493  463.4934  -18.5399  125.9947
 X2S  C16  C   CR6   0   0.571  464.6379  -19.1010  126.6677
 X2S  C17  C   CR6   0   0.738  465.2227  -20.2158  124.5272
 X2S  C18  C   CR16  0  -0.314  468.5416  -18.4031  124.6113
 X2S  C2   C   CR16  0  -0.219  467.5378  -17.3880  126.5816
 X2S  C3   C   CR6   0  -0.028  466.7390  -16.6349  125.7436
 X2S  C4   C   CR16  0  -0.280  466.8231  -16.7277  124.3617
 X2S  C5   C   CR6   0   0.406  467.7383  -17.6101  123.8018
 X2S  C6   C   CR6   0   0.228  467.2318  -16.9630  121.5918
 X2S  C7   C   CR16  0  -0.296  467.8400  -15.8689  121.0139
 X2S  C8   C   CR16  0  -0.321  467.1610  -15.1018  120.0744
 X2S  C9   C   CR6   0   0.336  465.8746  -15.4745  119.7541
 X2S  N1   N   NR6   0  -0.521  464.0823  -19.6685  123.9772
 X2S  N2   N   NR16  0  -0.731  465.4207  -19.8993  125.8471
 X2S  O1   O   OC2   0  -0.585  465.1920  -14.7615  118.7608
 X2S  O2   O   OS    0  -0.578  463.5693  -13.8170  120.4042
 X2S  O3   O   OS    0  -0.572  463.5848  -13.1482  117.9772
 X2S  O6   O   O     0  -0.474  465.9848  -20.9326  123.9157
 X2S  S    S   S     0   1.745  464.2434  -13.5618  119.1714
 X2S  CL   CL  CL    0  -0.089  465.5958  -15.5414  126.4319
 X2S  H1   H   HCR6  0   0.321  464.2267  -16.8123  120.0117
 X2S  H2   H   HCH2  0   0.248  463.4410  -17.8742  121.9725
 X2S  H3   H   HCH2  0   0.266  463.8414  -18.9938  120.6603
 X2S  H4   H   HCH2  0   0.297  462.7023  -20.1538  122.4941
 X2S  H5   H   HCH2  0   0.295  464.3157  -20.7970  122.2483
 X2S  H6   H   HCR6  0   0.325  462.4089  -18.4663  124.1798
 X2S  H7   H   HCR6  0   0.292  462.8193  -17.8913  126.5312
 X2S  H8   H   HCR6  0   0.302  469.2480  -19.0938  124.1709
 X2S  H9   H   HCR6  0   0.304  467.4675  -17.3004  127.6555
 X2S  H10  H   HCR6  0   0.309  466.1932  -16.1014  123.7445
 X2S  H11  H   HCR6  0   0.296  468.8538  -15.6151  121.2928
 X2S  H12  H   HCR6  0   0.296  467.6402  -14.2557  119.6027
 X2S  H13  H   HNR6  0   0.418  466.2331  -20.3271  126.2723
 X2S  F1   F   F     0  -0.391  465.3503  -12.4745  119.4891
 X2S  O4   O   O2    0  -0.449  465.4357  -18.4102  121.8649
 X2S  O5   O   O     0  -0.463  464.9378  -18.9334  127.8348

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
 X2S  O3   S    double    1.425  0.020  1.425
 X2S  S    O1   single    1.584  0.020  1.584
 X2S  S    O2   double    1.428  0.020  1.428
 X2S  O1   C9   single    1.400  0.020  1.400
 X2S  C9   C8   aromatic  1.377  0.020  1.377
 X2S  C9   C10  aromatic  1.385  0.020  1.385
 X2S  C8   C7   aromatic  1.390  0.020  1.390
 X2S  C10  C11  aromatic  1.389  0.020  1.389
 X2S  O6   C17  double    1.212  0.020  1.212
 X2S  C7   C6   aromatic  1.379  0.020  1.379
 X2S  C11  O4   single    1.335  0.020  1.335
 X2S  C11  C6   aromatic  1.401  0.020  1.401
 X2S  O4   C12  single    1.416  0.020  1.416
 X2S  C6   O    single    1.368  0.020  1.368
 X2S  C17  N2   single    1.372  0.020  1.372
 X2S  C17  N1   single    1.379  0.020  1.379
 X2S  C13  C12  single    1.512  0.020  1.512
 X2S  C13  N1   single    1.456  0.020  1.456
 X2S  N2   C16  single    1.387  0.020  1.387
 X2S  N1   C14  single    1.364  0.020  1.364
 X2S  O    C5   single    1.354  0.020  1.354
 X2S  C16  O5   double    1.217  0.020  1.217
 X2S  C16  C15  single    1.441  0.020  1.441
 X2S  C14  C15  double    1.343  0.020  1.343
 X2S  C4   C5   aromatic  1.389  0.020  1.389
 X2S  C4   C3   aromatic  1.388  0.020  1.388
 X2S  C5   C18  aromatic  1.389  0.020  1.389
 X2S  C3   CL   single    1.725  0.020  1.725
 X2S  C3   C2   aromatic  1.381  0.020  1.381
 X2S  C18  C1   aromatic  1.388  0.020  1.388
 X2S  C2   C1   aromatic  1.393  0.020  1.393
 X2S  C1   C    single    1.429  0.020  1.429
 X2S  C    N    triple    1.151  0.020  1.151
 X2S  C10  H1   single    0.930  0.020  1.080
 X2S  C12  H2   single    0.970  0.020  1.090
 X2S  C12  H3   single    0.970  0.020  1.090
 X2S  C13  H4   single    0.970  0.020  1.090
 X2S  C13  H5   single    0.970  0.020  1.090
 X2S  C14  H6   single    0.930  0.020  1.080
 X2S  C15  H7   single    0.930  0.020  1.080
 X2S  C18  H8   single    0.930  0.020  1.080
 X2S  C2   H9   single    0.930  0.020  1.080
 X2S  C4   H10  single    0.930  0.020  1.080
 X2S  C7   H11  single    0.930  0.020  1.080
 X2S  C8   H12  single    0.930  0.020  1.080
 X2S  N2   H13  single    0.860  0.020  1.020
 X2S  S    F1   single    1.584  0.020  1.584

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
 X2S  C1   C    N    180.00  3.000
 X2S  C6   O    C5   119.99  3.000
 X2S  C2   C1   C18  122.01  3.000
 X2S  C2   C1   C    118.92  3.000
 X2S  C18  C1   C    119.07  3.000
 X2S  H1   C10  C9   119.71  3.000
 X2S  H1   C10  C11  121.77  3.000
 X2S  C9   C10  C11  118.50  3.000
 X2S  O4   C11  C6   116.14  3.000
 X2S  C6   C11  C10  118.89  3.000
 X2S  O4   C11  C10  124.98  3.000
 X2S  H3   C12  H2   107.94  3.000
 X2S  H3   C12  O4   111.42  3.000
 X2S  H2   C12  O4   110.25  3.000
 X2S  H3   C12  C13  108.75  3.000
 X2S  H2   C12  C13  110.82  3.000
 X2S  O4   C12  C13  107.66  3.000
 X2S  H5   C13  H4   107.42  3.000
 X2S  H5   C13  N1   108.71  3.000
 X2S  H4   C13  N1   108.93  3.000
 X2S  H5   C13  C12  110.86  3.000
 X2S  H4   C13  C12  108.54  3.000
 X2S  N1   C13  C12  112.24  3.000
 X2S  H6   C14  N1   115.21  3.000
 X2S  H6   C14  C15  121.17  3.000
 X2S  N1   C14  C15  123.61  3.000
 X2S  H7   C15  C16  119.88  3.000
 X2S  H7   C15  C14  120.83  3.000
 X2S  C16  C15  C14  119.28  3.000
 X2S  O5   C16  N2   120.51  3.000
 X2S  O5   C16  C15  126.16  3.000
 X2S  N2   C16  C15  113.33  3.000
 X2S  O6   C17  N2   122.09  3.000
 X2S  N2   C17  N1   114.30  3.000
 X2S  O6   C17  N1   123.60  3.000
 X2S  H8   C18  C5   120.33  3.000
 X2S  H8   C18  C1   120.89  3.000
 X2S  C5   C18  C1   118.78  3.000
 X2S  H9   C2   C3   121.44  3.000
 X2S  H9   C2   C1   121.07  3.000
 X2S  C3   C2   C1   117.50  3.000
 X2S  CL   C3   C4   118.68  3.000
 X2S  CL   C3   C2   119.13  3.000
 X2S  C4   C3   C2   122.19  3.000
 X2S  H10  C4   C5   121.43  3.000
 X2S  H10  C4   C3   119.62  3.000
 X2S  C5   C4   C3   118.94  3.000
 X2S  C4   C5   C18  120.58  3.000
 X2S  C18  C5   O    115.69  3.000
 X2S  C4   C5   O    123.72  3.000
 X2S  C7   C6   C11  121.16  3.000
 X2S  C11  C6   O    119.00  3.000
 X2S  C7   C6   O    119.77  3.000
 X2S  H11  C7   C8   120.17  3.000
 X2S  H11  C7   C6   119.44  3.000
 X2S  C8   C7   C6   120.38  3.000
 X2S  H12  C8   C9   121.64  3.000
 X2S  H12  C8   C7   120.69  3.000
 X2S  C9   C8   C7   117.66  3.000
 X2S  O1   C9   C8   118.86  3.000
 X2S  C8   C9   C10  123.41  3.000
 X2S  O1   C9   C10  117.66  3.000
 X2S  C17  N1   C14  121.07  3.000
 X2S  C14  N1   C13  119.23  3.000
 X2S  C17  N1   C13  119.66  3.000
 X2S  H13  N2   C17  115.01  3.000
 X2S  H13  N2   C16  116.61  3.000
 X2S  C17  N2   C16  128.36  3.000
 X2S  S    O1   C9   119.59  3.000
 X2S  F1   S    O3   106.97  3.000
 X2S  F1   S    O2   106.23  3.000
 X2S  O3   S    O2   123.86  3.000
 X2S  F1   S    O1    98.83  3.000
 X2S  O2   S    O1   111.79  3.000
 X2S  O3   S    O1   106.23  3.000
 X2S  C12  O4   C11  118.81  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
 X2S  CONST_01  C4   C5   C18  C1      0.00   0.0  0
 X2S  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 X2S  CONST_03  C7   C8   C9   C10     0.00   0.0  0
 X2S  CONST_04  C7   C6   C11  C10     0.00   0.0  0
 X2S  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 X2S  CONST_06  C8   C7   C6   C11     0.00   0.0  0
 X2S  CONST_07  C3   C4   C5   C18     0.00   0.0  0
 X2S  CONST_08  C3   C2   C1   C18     0.00   0.0  0
 X2S  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 X2S  CONST_10  C5   C18  C1   C2      0.00   0.0  0
 X2S  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 X2S  CONST_12  C9   C10  C11  C6      0.00   0.0  0
 X2S  CONST_13  N2   C17  N1   C14     0.00   0.0  0
 X2S  CONST_14  C17  N2   C16  C15     0.00   0.0  0
 X2S  CONST_15  N1   C17  N2   C16     0.00   0.0  0
 X2S  CONST_16  C5   C18  C1   C     180.00   0.0  0
 X2S  CONST_17  C3   C2   C1   C     180.00   0.0  0
 X2S  CONST_18  C8   C7   C6   O     180.00   0.0  0
 X2S  CONST_19  C10  C11  C6   O     180.00   0.0  0
 X2S  CONST_20  C3   C4   C5   O     180.00   0.0  0
 X2S  CONST_21  C1   C18  C5   O     180.00   0.0  0
 X2S  CONST_22  CL   C3   C2   C1    180.00   0.0  0
 X2S  CONST_23  O1   C9   C10  C11   180.00   0.0  0
 X2S  CONST_24  CL   C3   C4   C5    180.00   0.0  0
 X2S  CONST_25  O1   C9   C8   C7    180.00   0.0  0
 X2S  CONST_26  O4   C11  C6   C7    180.00   0.0  0
 X2S  CONST_27  O4   C11  C10  C9    180.00   0.0  0
 X2S  CONST_28  N2   C17  N1   C13   180.00   0.0  0
 X2S  CONST_29  O6   C17  N1   C14   180.00   0.0  0
 X2S  CONST_30  O6   C17  N2   C16   180.00   0.0  0
 X2S  CONST_31  O5   C16  N2   C17   180.00   0.0  0
 X2S  CONST_32  H12  C8   C9   C10   180.00   0.0  0
 X2S  CONST_33  H11  C7   C6   C11   180.00   0.0  0
 X2S  CONST_34  H10  C4   C5   C18   180.00   0.0  0
 X2S  CONST_35  H9   C2   C1   C18   180.00   0.0  0
 X2S  CONST_36  H8   C18  C1   C2    180.00   0.0  0
 X2S  CONST_37  H1   C10  C11  C6    180.00   0.0  0
 X2S  CONST_38  H13  N2   C16  C15   180.00   0.0  0
 X2S  CONST_39  O6   C17  N1   C13     0.00   0.0  0
 X2S  Var_01    C7   C6   O    C5    101.38  30.0  1
 X2S  Var_02    C6   C11  O4   C12   171.76  30.0  1
 X2S  Var_03    C17  N1   C13  C12  -103.80  30.0  3
 X2S  Var_04    C13  C12  O4   C11  -175.71  30.0  3
 X2S  Var_05    O3   S    O1   C9   -173.44  30.0  2
 X2S  Var_06    O4   C12  C13  N1     57.14  30.0  3

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
 X2S  plan-1  C13  0.020
 X2S  plan-1  C14  0.020
 X2S  plan-1  C15  0.020
 X2S  plan-1  C16  0.020
 X2S  plan-1  C17  0.020
 X2S  plan-1  N1   0.020
 X2S  plan-1  N2   0.020
 X2S  plan-1  O6   0.020
 X2S  plan-1  H6   0.020
 X2S  plan-1  H7   0.020
 X2S  plan-1  H13  0.020
 X2S  plan-1  O5   0.020
 X2S  plan-2  N    0.020
 X2S  plan-2  C    0.020
 X2S  plan-2  O    0.020
 X2S  plan-2  C1   0.020
 X2S  plan-2  C18  0.020
 X2S  plan-2  C2   0.020
 X2S  plan-2  C3   0.020
 X2S  plan-2  C4   0.020
 X2S  plan-2  C5   0.020
 X2S  plan-2  CL   0.020
 X2S  plan-2  H8   0.020
 X2S  plan-2  H9   0.020
 X2S  plan-2  H10  0.020
 X2S  plan-3  O    0.020
 X2S  plan-3  C10  0.020
 X2S  plan-3  C11  0.020
 X2S  plan-3  C6   0.020
 X2S  plan-3  C7   0.020
 X2S  plan-3  C8   0.020
 X2S  plan-3  C9   0.020
 X2S  plan-3  O1   0.020
 X2S  plan-3  H1   0.020
 X2S  plan-3  H11  0.020
 X2S  plan-3  H12  0.020
 X2S  plan-3  O4   0.020

