# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 18:31:59 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CCNC(=O)C2=C(O)C(=O)N=C(N2)c3c(F)cccc3F)ccc1O
#
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
 WTD  WTD  "2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide"
  ligand  47  30  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WTD
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
 WTD  C01  C  CH3   0  -0.432  -34.4851   3.2608  12.8064
 WTD  C03  C  CR6   0   0.286  -32.4615   4.2135  12.0067
 WTD  C04  C  CR16  0  -0.435  -31.7139   3.0673  12.2421
 WTD  C05  C  CR6   0   0.106  -30.3296   3.0604  12.0511
 WTD  C06  C  CH2   0  -0.508  -29.5237   1.8191  12.3146
 WTD  C07  C  CH2   0  -0.311  -28.9555   1.7621  13.7349
 WTD  C09  C  C     0   0.488  -30.6594   2.6522  15.3376
 WTD  C11  C  C     0   0.123  -30.0422   4.0183  15.3290
 WTD  C12  C  C     0   0.184  -28.8387   4.3536  15.8419
 WTD  C14  C  C     0   0.382  -28.4475   5.7626  15.9006
 WTD  C17  C  C     0   0.494  -30.4975   6.3138  15.0018
 WTD  C19  C  CR6   0  -0.420  -31.4515   7.3367  14.5269
 WTD  C20  C  CR6   0   0.591  -31.0658   8.3069  13.6080
 WTD  C22  C  CR16  0  -0.411  -31.9130   9.3070  13.1812
 WTD  C23  C  CR16  0  -0.220  -33.2017   9.3468  13.6908
 WTD  C24  C  CR16  0  -0.419  -33.6376   8.4019  14.6076
 WTD  C25  C  CR6   0   0.580  -32.7544   7.4204  15.0053
 WTD  C27  C  CR16  0  -0.310  -29.7135   4.2316  11.6319
 WTD  C28  C  CR16  0  -0.322  -30.4536   5.3828  11.3910
 WTD  C29  C  CR6   0   0.269  -31.8273   5.3862  11.5657
 WTD  F21  F  F     0  -0.290  -29.8334   8.2516  13.1044
 WTD  F26  F  F     0  -0.295  -33.1571   6.5175  15.9059
 WTD  N08  N  NH1   0  -0.591  -29.9901   1.6586  14.7439
 WTD  N16  N  N     0  -0.461  -29.3459   6.6927  15.4709
 WTD  N18  N  NH1   0  -0.652  -30.8705   5.0342  14.9234
 WTD  O02  O  O2    0  -0.485  -33.7994   4.3183  12.1664
 WTD  O10  O  O     0  -0.456  -31.7277   2.5081  15.9126
 WTD  O13  O  OH1   0  -0.603  -27.9805   3.4492  16.3101
 WTD  O15  O  O     0  -0.478  -27.3403   6.0573  16.3386
 WTD  O30  O  OH1   0  -0.626  -32.5260   6.5089  11.3066
 WTD  H1   H  HCH3  0   0.262  -35.5154   3.5860  12.9261
 WTD  H2   H  HCH3  0   0.231  -34.4719   2.3463  12.2084
 WTD  H3   H  HCH3  0   0.228  -34.0626   3.0457  13.7919
 WTD  H4   H  HCR6  0   0.282  -32.2043   2.1546  12.5583
 WTD  H5   H  HCH2  0   0.253  -30.1279   0.9268  12.1351
 WTD  H6   H  HCH2  0   0.258  -28.6792   1.7717  11.6235
 WTD  H7   H  HCH2  0   0.270  -28.3110   0.8891  13.8362
 WTD  H8   H  HCH2  0   0.265  -28.3315   2.6337  13.9177
 WTD  H9   H  HCR6  0   0.291  -31.5714  10.0362  12.4593
 WTD  H10  H  HCR6  0   0.287  -33.8780  10.1264  13.3682
 WTD  H11  H  HCR6  0   0.292  -34.6384   8.4313  15.0162
 WTD  H12  H  HCR6  0   0.248  -28.6410   4.2523  11.4803
 WTD  H13  H  HCR6  0   0.263  -29.9634   6.2868  11.0524
 WTD  H14  H  HNH1  0   0.403  -30.4492   0.7589  14.8019
 WTD  H15  H  HNH1  0   0.447  -31.7578   4.7863  14.5059
 WTD  H16  H  HOH1  0   0.473  -27.1866   3.9261  16.6027
 WTD  H17  H  HOH1  0   0.468  -33.4498   6.3930  11.5603

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
 WTD  C28  C27  aromatic  1.390  0.020  1.390
 WTD  C28  C29  aromatic  1.385  0.020  1.385
 WTD  C27  C05  aromatic  1.388  0.020  1.388
 WTD  O30  C29  single    1.347  0.020  1.347
 WTD  C29  C03  aromatic  1.404  0.020  1.404
 WTD  C05  C06  single    1.503  0.020  1.503
 WTD  C05  C04  aromatic  1.397  0.020  1.397
 WTD  C06  C07  single    1.531  0.020  1.531
 WTD  C03  C04  aromatic  1.389  0.020  1.389
 WTD  C03  O02  single    1.351  0.020  1.351
 WTD  O02  C01  single    1.414  0.020  1.414
 WTD  C07  N08  single    1.449  0.020  1.449
 WTD  C22  C23  aromatic  1.386  0.020  1.386
 WTD  C22  C20  aromatic  1.378  0.020  1.378
 WTD  C23  C24  aromatic  1.387  0.020  1.387
 WTD  N08  C09  single    1.337  0.020  1.337
 WTD  F21  C20  single    1.332  0.020  1.332
 WTD  C20  C19  aromatic  1.391  0.020  1.391
 WTD  C24  C25  aromatic  1.379  0.020  1.379
 WTD  C19  C25  aromatic  1.391  0.020  1.391
 WTD  C19  C17  single    1.477  0.020  1.477
 WTD  C25  F26  single    1.337  0.020  1.337
 WTD  N18  C17  single    1.335  0.020  1.335
 WTD  N18  C11  single    1.372  0.020  1.372
 WTD  C09  C11  single    1.499  0.020  1.499
 WTD  C09  O10  double    1.222  0.020  1.222
 WTD  C17  N16  double    1.300  0.020  1.300
 WTD  C11  C12  double    1.351  0.020  1.351
 WTD  N16  C14  single    1.363  0.020  1.363
 WTD  C12  C14  single    1.463  0.020  1.463
 WTD  C12  O13  single    1.332  0.020  1.332
 WTD  C14  O15  double    1.227  0.020  1.227
 WTD  C01  H1   single    0.970  0.020  1.090
 WTD  C01  H2   single    0.970  0.020  1.090
 WTD  C01  H3   single    0.970  0.020  1.090
 WTD  C04  H4   single    0.930  0.020  1.080
 WTD  C06  H5   single    0.970  0.020  1.090
 WTD  C06  H6   single    0.970  0.020  1.090
 WTD  C07  H7   single    0.970  0.020  1.090
 WTD  C07  H8   single    0.970  0.020  1.090
 WTD  C22  H9   single    0.930  0.020  1.080
 WTD  C23  H10  single    0.930  0.020  1.080
 WTD  C24  H11  single    0.930  0.020  1.080
 WTD  C27  H12  single    0.930  0.020  1.080
 WTD  C28  H13  single    0.930  0.020  1.080
 WTD  N08  H14  single    0.890  0.020  1.040
 WTD  N18  H15  single    0.860  0.020  1.020
 WTD  O13  H16  single    0.850  0.020  0.980
 WTD  O30  H17  single    0.850  0.020  0.980

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
 WTD  H3   C01  H2   108.90  3.000
 WTD  H3   C01  H1   109.01  3.000
 WTD  H2   C01  H1   108.79  3.000
 WTD  H3   C01  O02  111.57  3.000
 WTD  H2   C01  O02  111.87  3.000
 WTD  H1   C01  O02  106.61  3.000
 WTD  O02  C03  C29  114.80  3.000
 WTD  O02  C03  C04  125.24  3.000
 WTD  C29  C03  C04  119.96  3.000
 WTD  H4   C04  C05  118.96  3.000
 WTD  H4   C04  C03  120.08  3.000
 WTD  C05  C04  C03  120.95  3.000
 WTD  C27  C05  C06  120.78  3.000
 WTD  C06  C05  C04  120.74  3.000
 WTD  C27  C05  C04  118.47  3.000
 WTD  H6   C06  H5   106.75  3.000
 WTD  H6   C06  C07  107.36  3.000
 WTD  H5   C06  C07  109.11  3.000
 WTD  H6   C06  C05  109.84  3.000
 WTD  H5   C06  C05  110.44  3.000
 WTD  C07  C06  C05  113.10  3.000
 WTD  H8   C07  H7   106.68  3.000
 WTD  H8   C07  N08  110.49  3.000
 WTD  H7   C07  N08  107.48  3.000
 WTD  H8   C07  C06  109.83  3.000
 WTD  H7   C07  C06  109.61  3.000
 WTD  N08  C07  C06  112.57  3.000
 WTD  O10  C09  N08  123.99  3.000
 WTD  O10  C09  C11  118.05  3.000
 WTD  N08  C09  C11  117.94  3.000
 WTD  N18  C11  C12  117.80  3.000
 WTD  C12  C11  C09  126.23  3.000
 WTD  N18  C11  C09  115.34  3.000
 WTD  O13  C12  C14  117.87  3.000
 WTD  O13  C12  C11  122.62  3.000
 WTD  C14  C12  C11  119.50  3.000
 WTD  O15  C14  N16  122.94  3.000
 WTD  O15  C14  C12  119.14  3.000
 WTD  N16  C14  C12  117.92  3.000
 WTD  N18  C17  N16  123.23  3.000
 WTD  N16  C17  C19  119.10  3.000
 WTD  N18  C17  C19  117.67  3.000
 WTD  C25  C19  C20  116.43  3.000
 WTD  C25  C19  C17  122.43  3.000
 WTD  C20  C19  C17  121.09  3.000
 WTD  F21  C20  C22  118.78  3.000
 WTD  F21  C20  C19  118.51  3.000
 WTD  C22  C20  C19  122.70  3.000
 WTD  H9   C22  C23  121.30  3.000
 WTD  H9   C22  C20  120.12  3.000
 WTD  C23  C22  C20  118.58  3.000
 WTD  H10  C23  C24  119.46  3.000
 WTD  H10  C23  C22  119.51  3.000
 WTD  C24  C23  C22  121.04  3.000
 WTD  H11  C24  C25  120.20  3.000
 WTD  H11  C24  C23  121.48  3.000
 WTD  C25  C24  C23  118.31  3.000
 WTD  F26  C25  C24  118.81  3.000
 WTD  F26  C25  C19  118.24  3.000
 WTD  C24  C25  C19  122.94  3.000
 WTD  H12  C27  C28  119.15  3.000
 WTD  H12  C27  C05  119.85  3.000
 WTD  C28  C27  C05  121.00  3.000
 WTD  H13  C28  C29  119.11  3.000
 WTD  H13  C28  C27  120.32  3.000
 WTD  C29  C28  C27  120.56  3.000
 WTD  O30  C29  C28  119.48  3.000
 WTD  O30  C29  C03  121.47  3.000
 WTD  C28  C29  C03  119.05  3.000
 WTD  H14  N08  C09  114.10  3.000
 WTD  H14  N08  C07  115.31  3.000
 WTD  C09  N08  C07  127.85  3.000
 WTD  C17  N16  C14  119.93  3.000
 WTD  H15  N18  C17  120.28  3.000
 WTD  H15  N18  C11  118.04  3.000
 WTD  C17  N18  C11  121.57  3.000
 WTD  C03  O02  C01  118.40  3.000
 WTD  H16  O13  C12  107.40  3.000
 WTD  H17  O30  C29  110.23  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
 WTD  CONST_01  C27  C28  C29  C03     0.00   0.0  0
 WTD  CONST_02  C27  C05  C04  C03     0.00   0.0  0
 WTD  CONST_03  C28  C27  C05  C04     0.00   0.0  0
 WTD  CONST_04  C28  C29  C03  C04     0.00   0.0  0
 WTD  CONST_05  C29  C28  C27  C05     0.00   0.0  0
 WTD  CONST_06  C29  C03  C04  C05     0.00   0.0  0
 WTD  CONST_07  C23  C22  C20  C19     0.00   0.0  0
 WTD  CONST_08  C23  C24  C25  C19     0.00   0.0  0
 WTD  CONST_09  C24  C23  C22  C20     0.00   0.0  0
 WTD  CONST_10  C24  C25  C19  C20     0.00   0.0  0
 WTD  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 WTD  CONST_12  C25  C19  C20  C22     0.00   0.0  0
 WTD  CONST_13  C22  C20  C19  C17   180.00   0.0  0
 WTD  CONST_14  C24  C25  C19  C17   180.00   0.0  0
 WTD  CONST_15  C19  C17  N18  C11   180.00   0.0  0
 WTD  CONST_16  N16  C17  N18  C11     0.00   0.0  0
 WTD  CONST_17  C19  C17  N16  C14   180.00   0.0  0
 WTD  CONST_18  N18  C17  N16  C14     0.00   0.0  0
 WTD  CONST_19  C06  C05  C04  C03   180.00   0.0  0
 WTD  CONST_20  O30  C29  C03  C04   180.00   0.0  0
 WTD  CONST_21  O02  C03  C04  C05   180.00   0.0  0
 WTD  CONST_22  C28  C27  C05  C06   180.00   0.0  0
 WTD  CONST_23  F21  C20  C19  C17     0.00   0.0  0
 WTD  CONST_24  F26  C25  C19  C17     0.00   0.0  0
 WTD  CONST_25  F26  C25  C19  C20   180.00   0.0  0
 WTD  CONST_26  F21  C20  C22  C23   180.00   0.0  0
 WTD  CONST_27  F26  C25  C24  C23   180.00   0.0  0
 WTD  CONST_28  F21  C20  C19  C25   180.00   0.0  0
 WTD  CONST_29  O30  C29  C28  C27   180.00   0.0  0
 WTD  CONST_30  O02  C03  C29  C28   180.00   0.0  0
 WTD  CONST_31  H13  C28  C29  C03   180.00   0.0  0
 WTD  CONST_32  H12  C27  C05  C04   180.00   0.0  0
 WTD  CONST_33  H13  C28  C27  C05   180.00   0.0  0
 WTD  CONST_34  H9   C22  C20  C19   180.00   0.0  0
 WTD  CONST_35  H11  C24  C25  C19   180.00   0.0  0
 WTD  CONST_36  H10  C23  C22  C20   180.00   0.0  0
 WTD  CONST_37  H11  C24  C23  C22   180.00   0.0  0
 WTD  CONST_38  H9   C22  C23  C24   180.00   0.0  0
 WTD  CONST_39  H10  C23  C24  C25   180.00   0.0  0
 WTD  CONST_40  H4   C04  C05  C27   180.00   0.0  0
 WTD  CONST_41  H12  C27  C28  C29   180.00   0.0  0
 WTD  CONST_42  H4   C04  C03  C29   180.00   0.0  0
 WTD  CONST_43  H15  N18  C17  C19     0.00   0.0  0
 WTD  CONST_44  H15  N18  C17  N16   180.00   0.0  0
 WTD  CONST_46  H14  N08  C09  C11   180.00   0.0  0
 WTD  CONST_48  H14  N08  C09  O10     0.00   0.0  0
 WTD  Var_01    N16  C14  C12  C11     2.22  30.0  1
 WTD  Var_02    C17  N18  C11  C12     1.43  30.0  1
 WTD  Var_03    C17  N16  C14  C12    -1.39  30.0  1
 WTD  Var_04    N18  C11  C12  C14    -2.19  30.0  1
 WTD  Var_05    N18  C17  C19  C20  -128.04  30.0  2
 WTD  Var_06    N16  C17  C19  C20    51.91  30.0  2
 WTD  Var_07    N18  C17  C19  C25    54.61  30.0  2
 WTD  Var_08    N16  C17  C19  C25  -125.44  30.0  2
 WTD  Var_09    C17  N18  C11  C09   172.83  30.0  1
 WTD  Var_10    C14  C12  C11  C09  -172.55  30.0  1
 WTD  Var_11    O15  C14  C12  C11  -178.29  30.0  1
 WTD  Var_12    O15  C14  N16  C17   179.14  30.0  1
 WTD  Var_13    O13  C12  C14  N16  -177.45  30.0  1
 WTD  Var_14    O13  C12  C11  N18   177.47  30.0  1
 WTD  Var_15    H15  N18  C11  C12   177.68  30.0  1
 WTD  Var_16    C29  C03  O02  C01  -170.06  30.0  1
 WTD  Var_17    C04  C03  O02  C01     9.96  30.0  1
 WTD  Var_18    C07  C06  C05  C04   -92.94  30.0  2
 WTD  Var_19    C27  C05  C06  C07    86.09  30.0  2
 WTD  Var_20    O13  C12  C11  C09     7.11  30.0  1
 WTD  Var_21    N08  C09  C11  C12   -58.74  30.0  2
 WTD  Var_22    O10  C09  C11  C12   119.62  30.0  2
 WTD  Var_23    N18  C11  C09  N08   130.70  30.0  2
 WTD  Var_24    O10  C09  C11  N18   -50.95  30.0  2
 WTD  Var_25    O15  C14  C12  O13     2.03  30.0  1
 WTD  Var_26    H5   C06  C05  C04    29.66  30.0  2
 WTD  Var_27    H6   C06  C05  C04   147.14  30.0  2
 WTD  Var_28    H15  N18  C11  C09   -10.91  30.0  1
 WTD  Var_29    H5   C06  C05  C27  -151.32  30.0  2
 WTD  Var_30    H6   C06  C05  C27   -33.84  30.0  2
 WTD  Var_31    N08  C07  C06  C05    65.49  30.0  3
 WTD  Var_32    H1   C01  O02  C03   174.17  30.0  3
 WTD  Var_33    H2   C01  O02  C03   -67.02  30.0  3
 WTD  Var_34    H3   C01  O02  C03    55.26  30.0  3
 WTD  Var_35    H7   C07  C06  C05  -174.95  30.0  3
 WTD  Var_36    H8   C07  C06  C05   -58.06  30.0  3
 WTD  Var_37    C09  N08  C07  C06   -87.10  30.0  3
 WTD  Var_38    H14  N08  C07  C06    72.85  30.0  3
 WTD  Var_39    H7   C07  N08  C09   152.12  30.0  1
 WTD  Var_40    H8   C07  N08  C09    36.09  30.0  1
 WTD  Var_41    H5   C06  C07  N08   -57.84  30.0  2
 WTD  Var_42    H6   C06  C07  N08  -173.18  30.0  2

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
 WTD  plan-1  C17  0.020
 WTD  plan-1  C19  0.020
 WTD  plan-1  C20  0.020
 WTD  plan-1  C22  0.020
 WTD  plan-1  C23  0.020
 WTD  plan-1  C24  0.020
 WTD  plan-1  C25  0.020
 WTD  plan-1  F21  0.020
 WTD  plan-1  F26  0.020
 WTD  plan-1  H9   0.020
 WTD  plan-1  H10  0.020
 WTD  plan-1  H11  0.020
 WTD  plan-2  C03  0.020
 WTD  plan-2  C04  0.020
 WTD  plan-2  C05  0.020
 WTD  plan-2  C06  0.020
 WTD  plan-2  C27  0.020
 WTD  plan-2  C28  0.020
 WTD  plan-2  C29  0.020
 WTD  plan-2  O02  0.020
 WTD  plan-2  O30  0.020
 WTD  plan-2  H4   0.020
 WTD  plan-2  H12  0.020
 WTD  plan-2  H13  0.020
 WTD  plan-3  C07  0.020
 WTD  plan-3  C09  0.020
 WTD  plan-3  C11  0.020
 WTD  plan-3  N08  0.020
 WTD  plan-3  O10  0.020
 WTD  plan-3  H14  0.020
 WTD  plan-4  C12  0.020
 WTD  plan-4  C14  0.020
 WTD  plan-4  N16  0.020
 WTD  plan-4  O15  0.020
 WTD  plan-5  C11  0.020
 WTD  plan-5  C14  0.020
 WTD  plan-5  C17  0.020
 WTD  plan-5  C19  0.020
 WTD  plan-5  N16  0.020
 WTD  plan-5  N18  0.020
 WTD  plan-5  H15  0.020

