# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:31:23 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-{5-chloro-4-[(2,4-difluorobenzyl)oxy]-6-oxopyrimidin-1(6H)-yl}-N-(2-hydroxyethyl)-4-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1N2C=NC(=C(Cl)C2=O)OCc3ccc(F)cc3F)C(=O)NCCO
#
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
 29A  29A  3-{5-chloro-4-[(2,4-difluorobenzyl)oxy]-6-oxopyrimidin-1(6H)-yl}-N-(2-hydroxyethyl)-4-methylbenzamide  ligand  49  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_29A
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
 29A  C1    C   CR6   0  -0.189    5.1712   0.6833   0.0682
 29A  C2    C   CR6   0   0.560    6.1319   1.6402  -0.2241
 29A  C3    C   CR16  0  -0.553    7.4752   1.4793   0.0430
 29A  C4    C   CR6   0   0.535    7.8617   0.2919   0.6353
 29A  C5    C   CR16  0  -0.410    6.9564  -0.6990   0.9527
 29A  C6    C   CR16  0  -0.264    5.6135  -0.4923   0.6647
 29A  C7    C   CH2   0  -0.167    3.7357   0.9651  -0.2764
 29A  O8    O   O2    0  -0.461    2.9705  -0.1561   0.1422
 29A  C9    C   CR6   0   0.659    1.6777  -0.1942  -0.1045
 29A  C10   C   CR6   0  -0.367    0.9677  -1.2987   0.2899
 29A  C11   C   CR6   0   0.616   -0.4350  -1.3949   0.0446
 29A  N12   N   NR6   0  -0.621   -0.9452  -0.2668  -0.6282
 29A  C13   C   CR16  0   0.192   -0.1656   0.7739  -0.9690
 29A  N14   N   N     0  -0.483    1.1018   0.8480  -0.7334
 29A  C15   C   CR6   0   0.255   -2.3413  -0.2387  -0.9432
 29A  C16   C   CR6   0   0.117   -2.8006  -0.9112  -2.0754
 29A  C17   C   CR16  0  -0.305   -4.1642  -0.8384  -2.3405
 29A  C18   C   CR16  0  -0.262   -5.0295  -0.1448  -1.5092
 29A  C19   C   CR6   0  -0.058   -4.5504   0.5139  -0.3815
 29A  C20   C   CR16  0  -0.260   -3.1871   0.4700  -0.1123
 29A  F21   F   F     0  -0.304    5.7310   2.7835  -0.8002
 29A  F22   F   F     0  -0.308    9.1605   0.1061   0.9032
 29A  CL23  CL  CL    0  -0.079    1.7281  -2.6101   1.0928
 29A  O24   O   O     0  -0.453   -1.1659  -2.3157   0.3520
 29A  C25   C   CH3   0  -0.741   -1.8797  -1.6840  -2.9670
 29A  C26   C   C     0   0.538   -5.4268   1.2990   0.5415
 29A  O27   O   O     0  -0.489   -4.9768   2.2281   1.1990
 29A  N28   N   NH1   0  -0.649   -6.7116   0.9198   0.5919
 29A  C29   C   CH2   0  -0.289   -7.6830   1.5592   1.4528
 29A  C30   C   CH2   0  -0.186   -9.0873   1.2249   1.0027
 29A  O31   O   OH1   0  -0.673   -9.2545  -0.1753   1.0575
 29A  HN28  H   HNH1  0   0.403   -6.9791   0.0363   0.1870
 29A  HO31  H   HOH1  0   0.461  -10.0731  -0.4030   0.6080
 29A  H3    H   HCR6  0   0.306    8.1919   2.2515  -0.2039
 29A  H5    H   HCR6  0   0.287    7.2857  -1.6191   1.4155
 29A  H6    H   HCR6  0   0.275    4.9077  -1.2719   0.9130
 29A  H7    H   HCH2  0   0.267    3.3854   1.8696   0.2277
 29A  H7A   H   HCH2  0   0.267    3.6212   1.1219  -1.3519
 29A  H13   H   HCR6  0   0.320   -0.6595   1.5927  -1.4770
 29A  H17   H   HCR6  0   0.269   -4.5568  -1.3299  -3.2213
 29A  H18   H   HCR6  0   0.266   -6.0787  -0.1036  -1.7726
 29A  H20   H   HCR6  0   0.274   -2.7842   0.9790   0.7538
 29A  H25   H   HCH3  0   0.264   -1.5632  -2.6113  -2.4864
 29A  H25A  H   HCH3  0   0.265   -2.3776  -1.9492  -3.8973
 29A  H25B  H   HCH3  0   0.254   -0.9786  -1.1240  -3.2184
 29A  H29   H   HCH2  0   0.242   -7.5385   1.2580   2.4957
 29A  H29A  H   HCH2  0   0.252   -7.5533   2.6405   1.4097
 29A  H30   H   HCH2  0   0.217   -9.7909   1.7472   1.6614
 29A  H30A  H   HCH2  0   0.212   -9.2432   1.6096  -0.0118

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
 29A  C6    C1    aromatic  1.391  0.020  1.391
 29A  C2    C1    aromatic  1.387  0.020  1.387
 29A  C1    C7    single    1.503  0.020  1.503
 29A  C3    C2    aromatic  1.379  0.020  1.379
 29A  C2    F21   single    1.342  0.020  1.342
 29A  C4    C3    aromatic  1.382  0.020  1.382
 29A  C3    H3    single    0.930  0.020  1.080
 29A  F22   C4    single    1.339  0.020  1.339
 29A  C4    C5    aromatic  1.379  0.020  1.379
 29A  C5    C6    aromatic  1.389  0.020  1.389
 29A  C5    H5    single    0.930  0.020  1.080
 29A  C6    H6    single    0.930  0.020  1.080
 29A  C7    O8    single    1.421  0.020  1.421
 29A  C7    H7    single    0.970  0.020  1.090
 29A  C7    H7A   single    0.970  0.020  1.090
 29A  O8    C9    single    1.317  0.020  1.317
 29A  C9    C10   double    1.371  0.020  1.371
 29A  C9    N14   single    1.347  0.020  1.347
 29A  CL23  C10   single    1.715  0.020  1.715
 29A  C10   C11   single    1.427  0.020  1.427
 29A  C11   O24   double    1.215  0.020  1.215
 29A  C11   N12   single    1.409  0.020  1.409
 29A  C13   N12   single    1.344  0.020  1.344
 29A  N12   C15   single    1.432  0.020  1.432
 29A  N14   C13   double    1.291  0.020  1.291
 29A  C13   H13   single    0.930  0.020  1.080
 29A  C15   C16   aromatic  1.395  0.020  1.395
 29A  C15   C20   aromatic  1.381  0.020  1.381
 29A  C25   C16   single    1.497  0.020  1.497
 29A  C16   C17   aromatic  1.391  0.020  1.391
 29A  C17   C18   aromatic  1.386  0.020  1.386
 29A  C17   H17   single    0.930  0.020  1.080
 29A  C19   C18   aromatic  1.391  0.020  1.391
 29A  C18   H18   single    0.930  0.020  1.080
 29A  C20   C19   aromatic  1.390  0.020  1.390
 29A  C19   C26   single    1.495  0.020  1.495
 29A  C20   H20   single    0.930  0.020  1.080
 29A  C25   H25   single    0.970  0.020  1.090
 29A  C25   H25A  single    0.970  0.020  1.090
 29A  C25   H25B  single    0.970  0.020  1.090
 29A  O27   C26   double    1.224  0.020  1.224
 29A  C26   N28   single    1.341  0.020  1.341
 29A  N28   HN28  single    0.890  0.020  1.040
 29A  N28   C29   single    1.447  0.020  1.447
 29A  C29   C30   single    1.512  0.020  1.512
 29A  C29   H29   single    0.970  0.020  1.090
 29A  C29   H29A  single    0.970  0.020  1.090
 29A  C30   O31   single    1.411  0.020  1.411
 29A  C30   H30   single    0.970  0.020  1.090
 29A  C30   H30A  single    0.970  0.020  1.090
 29A  HO31  O31   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
 29A  C7    C1   C6    124.11  3.000
 29A  C7    C1   C2    118.94  3.000
 29A  C6    C1   C2    116.96  3.000
 29A  F21   C2   C3    118.28  3.000
 29A  F21   C2   C1    118.13  3.000
 29A  C3    C2   C1    123.60  3.000
 29A  H3    C3   C4    121.71  3.000
 29A  H3    C3   C2    121.18  3.000
 29A  C4    C3   C2    117.11  3.000
 29A  F22   C4   C5    119.40  3.000
 29A  C5    C4   C3    122.16  3.000
 29A  F22   C4   C3    118.44  3.000
 29A  H5    C5   C6    120.66  3.000
 29A  H5    C5   C4    120.66  3.000
 29A  C6    C5   C4    118.68  3.000
 29A  H6    C6   C5    118.46  3.000
 29A  H6    C6   C1    120.05  3.000
 29A  C5    C6   C1    121.49  3.000
 29A  H7A   C7   H7    107.55  3.000
 29A  H7A   C7   O8    110.29  3.000
 29A  H7    C7   O8    110.16  3.000
 29A  H7A   C7   C1    110.65  3.000
 29A  H7    C7   C1    110.82  3.000
 29A  O8    C7   C1    107.40  3.000
 29A  C9    O8   C7    119.77  3.000
 29A  N14   C9   C10   122.44  3.000
 29A  N14   C9   O8    119.02  3.000
 29A  C10   C9   O8    118.54  3.000
 29A  CL23  C10  C11   117.68  3.000
 29A  C11   C10  C9    120.92  3.000
 29A  CL23  C10  C9    121.40  3.000
 29A  O24   C11  N12   120.64  3.000
 29A  N12   C11  C10   112.58  3.000
 29A  O24   C11  C10   126.78  3.000
 29A  C15   N12  C13   119.64  3.000
 29A  C15   N12  C11   118.29  3.000
 29A  C13   N12  C11   122.07  3.000
 29A  H13   C13  N14   119.33  3.000
 29A  H13   C13  N12   116.09  3.000
 29A  N14   C13  N12   124.57  3.000
 29A  C13   N14  C9    117.42  3.000
 29A  C20   C15  C16   122.29  3.000
 29A  C20   C15  N12   118.35  3.000
 29A  C16   C15  N12   119.36  3.000
 29A  C25   C16  C17   121.10  3.000
 29A  C17   C16  C15   116.89  3.000
 29A  C25   C16  C15   122.01  3.000
 29A  H17   C17  C18   119.27  3.000
 29A  H17   C17  C16   119.13  3.000
 29A  C18   C17  C16   121.59  3.000
 29A  H18   C18  C19   120.86  3.000
 29A  H18   C18  C17   118.57  3.000
 29A  C19   C18  C17   120.55  3.000
 29A  C26   C19  C20   118.15  3.000
 29A  C26   C19  C18   123.17  3.000
 29A  C20   C19  C18   118.67  3.000
 29A  H20   C20  C19   120.33  3.000
 29A  H20   C20  C15   119.65  3.000
 29A  C19   C20  C15   120.01  3.000
 29A  H25B  C25  H25A  107.83  3.000
 29A  H25B  C25  H25   107.35  3.000
 29A  H25A  C25  H25   107.59  3.000
 29A  H25B  C25  C16   112.37  3.000
 29A  H25A  C25  C16   110.72  3.000
 29A  H25   C25  C16   110.78  3.000
 29A  N28   C26  O27   123.15  3.000
 29A  N28   C26  C19   115.88  3.000
 29A  O27   C26  C19   120.97  3.000
 29A  HN28  N28  C29   116.63  3.000
 29A  C29   N28  C26   122.74  3.000
 29A  HN28  N28  C26   119.15  3.000
 29A  H29A  C29  H29   107.15  3.000
 29A  H29A  C29  C30   108.55  3.000
 29A  H29   C29  C30   110.20  3.000
 29A  H29A  C29  N28   109.57  3.000
 29A  H29   C29  N28   110.89  3.000
 29A  C30   C29  N28   110.41  3.000
 29A  H30A  C30  H30   107.31  3.000
 29A  H30A  C30  O31   111.55  3.000
 29A  H30   C30  O31   111.92  3.000
 29A  H30A  C30  C29   109.27  3.000
 29A  H30   C30  C29   108.18  3.000
 29A  O31   C30  C29   108.54  3.000
 29A  HO31  O31  C30   108.53  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
 29A  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 29A  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 29A  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 29A  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 29A  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 29A  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 29A  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 29A  CONST_08  C18   C19  C20  C15     0.00   0.0  0
 29A  CONST_09  C19   C20  C15  C16     0.00   0.0  0
 29A  CONST_10  C19   C18  C17  C16     0.00   0.0  0
 29A  CONST_11  C20   C15  C16  C17     0.00   0.0  0
 29A  CONST_12  C20   C19  C18  C17     0.00   0.0  0
 29A  CONST_13  C17   C16  C15  N12   180.00   0.0  0
 29A  CONST_14  C19   C20  C15  N12   180.00   0.0  0
 29A  CONST_15  N12   C13  N14  C9      0.00   0.0  0
 29A  CONST_16  C13   N12  C11  C10     0.00   0.0  0
 29A  CONST_17  C15   N12  C11  C10   180.00   0.0  0
 29A  CONST_18  N14   C13  N12  C11     0.00   0.0  0
 29A  CONST_19  C15   N12  C13  N14   180.00   0.0  0
 29A  CONST_20  F22   C4   C3   C2    180.00   0.0  0
 29A  CONST_21  C7    C1   C2   C3    180.00   0.0  0
 29A  CONST_22  F21   C2   C3   C4    180.00   0.0  0
 29A  CONST_23  C7    C1   C6   C5    180.00   0.0  0
 29A  CONST_24  F21   C2   C1   C6    180.00   0.0  0
 29A  CONST_25  F22   C4   C5   C6    180.00   0.0  0
 29A  CONST_26  C25   C16  C15  N12     0.00   0.0  0
 29A  CONST_27  C26   C19  C20  C15   180.00   0.0  0
 29A  CONST_28  C26   C19  C18  C17   180.00   0.0  0
 29A  CONST_29  C25   C16  C17  C18   180.00   0.0  0
 29A  CONST_30  C25   C16  C15  C20   180.00   0.0  0
 29A  CONST_31  O24   C11  N12  C13   180.00   0.0  0
 29A  CONST_32  O24   C11  N12  C15     0.00   0.0  0
 29A  CONST_33  H5    C5   C6   C1    180.00   0.0  0
 29A  CONST_34  H3    C3   C2   C1    180.00   0.0  0
 29A  CONST_35  H6    C6   C1   C2    180.00   0.0  0
 29A  CONST_36  H20   C20  C15  N12     0.00   0.0  0
 29A  CONST_37  H17   C17  C16  C15   180.00   0.0  0
 29A  CONST_38  H18   C18  C17  C16   180.00   0.0  0
 29A  CONST_39  H13   C13  N14  C9    180.00   0.0  0
 29A  CONST_40  C29   N28  C26  C19   180.00   0.0  0
 29A  CONST_41  HN28  N28  C26  C19     0.00   0.0  0
 29A  CONST_42  C29   N28  C26  O27     0.00   0.0  0
 29A  Var_01    C16   C15  N12  C11   -81.64  30.0  2
 29A  Var_02    O8    C7   C1   C2   -179.17  30.0  2
 29A  Var_03    C10   C9   O8   C7    178.88  30.0  3
 29A  Var_04    O27   C26  C19  C18  -153.09  30.0  2
 29A  Var_05    H25   C25  C16  C15    73.04  30.0  2
 29A  Var_06    C30   C29  N28  C26   162.74  30.0  3
 29A  Var_07    O31   C30  C29  N28    59.83  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
 29A  plan-1  C1    0.020
 29A  plan-1  C2    0.020
 29A  plan-1  C3    0.020
 29A  plan-1  C4    0.020
 29A  plan-1  C5    0.020
 29A  plan-1  C6    0.020
 29A  plan-1  C7    0.020
 29A  plan-1  F21   0.020
 29A  plan-1  F22   0.020
 29A  plan-1  H3    0.020
 29A  plan-1  H5    0.020
 29A  plan-1  H6    0.020
 29A  plan-2  O8    0.020
 29A  plan-2  C9    0.020
 29A  plan-2  C10   0.020
 29A  plan-2  C11   0.020
 29A  plan-2  N12   0.020
 29A  plan-2  C13   0.020
 29A  plan-2  N14   0.020
 29A  plan-2  C15   0.020
 29A  plan-2  CL23  0.020
 29A  plan-2  O24   0.020
 29A  plan-2  H13   0.020
 29A  plan-3  N12   0.020
 29A  plan-3  C15   0.020
 29A  plan-3  C16   0.020
 29A  plan-3  C17   0.020
 29A  plan-3  C18   0.020
 29A  plan-3  C19   0.020
 29A  plan-3  C20   0.020
 29A  plan-3  C25   0.020
 29A  plan-3  C26   0.020
 29A  plan-3  H17   0.020
 29A  plan-3  H18   0.020
 29A  plan-3  H20   0.020
 29A  plan-4  C19   0.020
 29A  plan-4  C26   0.020
 29A  plan-4  O27   0.020
 29A  plan-4  N28   0.020
 29A  plan-4  C29   0.020
 29A  plan-4  HN28  0.020

