# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:41:37 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-[(2R)-3-fluoro-2-(hydroxymethyl)propyl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NC(=O)C(=C1C[C@H](CO)CF)C
#
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
 NMF  NMF  6-[(2R)-3-fluoro-2-(hydroxymethyl)propyl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione  ligand  31  16  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NMF
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
 NMF  F     F  F     0  -0.373  -0.9164  -0.4807  -1.8543
 NMF  C1    C  CR6   0   0.709   2.0805   1.2776  -0.3367
 NMF  N1    N  NR6   0  -0.570   0.8139   1.2134   0.1932
 NMF  O1    O  O     0  -0.491   2.5517   2.3015  -0.7944
 NMF  C2    C  CR6   0   0.551   2.3566  -1.1129   0.1681
 NMF  N2    N  NR16  0  -0.721   2.7827   0.1086  -0.3087
 NMF  O2    O  O     0  -0.472   3.1133  -2.0710   0.1335
 NMF  C3    C  CR6   0  -0.206   0.9976  -1.1265   0.6633
 NMF  O3    O  OH1   0  -0.668  -4.5918   0.4078  -0.2421
 NMF  C4    C  CH3   0  -0.756   0.4541  -2.4413   1.1473
 NMF  C5    C  CR6   0   0.460   0.2722   0.0233   0.6392
 NMF  C11   C  CH2   0  -0.587  -1.1514   0.0401   1.1116
 NMF  C12   C  CH1   0  -0.344  -2.2222   0.2213   0.0217
 NMF  C13   C  CH2   0  -0.139  -3.5884   0.0531   0.6792
 NMF  C14   C  CH2   0   0.008  -2.0701  -0.7596  -1.1224
 NMF  HN2   H  HNR6  0   0.422   3.7197   0.1520  -0.6894
 NMF  HO3   H  HOH1  0   0.459  -5.4459   0.2033   0.1490
 NMF  H4    H  HCH3  0   0.265   1.2314  -3.2000   1.1173
 NMF  H4A   H  HCH3  0   0.249   0.0941  -2.3895   2.1753
 NMF  H4B   H  HCH3  0   0.246  -0.3679  -2.8045   0.5287
 NMF  H6    H  HCH3  0   0.275   0.7400   3.2725   0.5620
 NMF  H6A   H  HCH3  0   0.261  -0.2616   2.7394  -0.7951
 NMF  H6B   H  HCH3  0   0.271  -0.7612   2.4292   0.8691
 NMF  H11   H  HCH2  0   0.288  -1.3509  -0.8973   1.6280
 NMF  H11A  H  HCH2  0   0.294  -1.2793   0.8163   1.8707
 NMF  H12   H  HCH1  0   0.262  -2.1759   1.2344  -0.3883
 NMF  H13   H  HCH2  0   0.214  -3.6240   0.6866   1.5748
 NMF  H13A  H  HCH2  0   0.203  -3.6995  -0.9855   1.0211
 NMF  H14   H  HCH2  0   0.229  -2.9174  -0.6922  -1.8037
 NMF  H14A  H  HCH2  0   0.203  -1.9997  -1.7852  -0.7512
 NMF  C6    C  CH3   0  -0.543   0.0897   2.4804   0.2025

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
 NMF  F    C14   single  1.395  0.020  1.395
 NMF  C1   N1    single  1.374  0.020  1.374
 NMF  C1   O1    double  1.216  0.020  1.216
 NMF  C1   N2    single  1.364  0.020  1.364
 NMF  N1   C5    single  1.382  0.020  1.382
 NMF  N1   C6    single  1.459  0.020  1.459
 NMF  C2   N2    single  1.379  0.020  1.379
 NMF  C2   O2    double  1.221  0.020  1.221
 NMF  C2   C3    single  1.446  0.020  1.446
 NMF  C3   C4    single  1.503  0.020  1.503
 NMF  C3   C5    double  1.360  0.020  1.360
 NMF  O3   C13   single  1.408  0.020  1.408
 NMF  C5   C11   single  1.500  0.020  1.500
 NMF  C11  C12   single  1.539  0.020  1.539
 NMF  C12  C13   single  1.525  0.020  1.525
 NMF  C12  C14   single  1.515  0.020  1.515
 NMF  N2   HN2   single  0.860  0.020  1.020
 NMF  O3   HO3   single  0.850  0.020  0.980
 NMF  C4   H4    single  0.970  0.020  1.090
 NMF  C4   H4A   single  0.970  0.020  1.090
 NMF  C4   H4B   single  0.970  0.020  1.090
 NMF  C6   H6    single  0.970  0.020  1.090
 NMF  C6   H6A   single  0.970  0.020  1.090
 NMF  C6   H6B   single  0.970  0.020  1.090
 NMF  C11  H11   single  0.970  0.020  1.090
 NMF  C11  H11A  single  0.970  0.020  1.090
 NMF  C12  H12   single  0.970  0.020  1.090
 NMF  C13  H13   single  0.970  0.020  1.090
 NMF  C13  H13A  single  0.970  0.020  1.090
 NMF  C14  H14   single  0.970  0.020  1.090
 NMF  C14  H14A  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
 NMF  N2    C1   O1   121.98  3.000
 NMF  N2    C1   N1   115.24  3.000
 NMF  O1    C1   N1   122.77  3.000
 NMF  C6    N1   C5   123.45  3.000
 NMF  C6    N1   C1   114.78  3.000
 NMF  C5    N1   C1   121.74  3.000
 NMF  C3    C2   O2   125.77  3.000
 NMF  C3    C2   N2   114.64  3.000
 NMF  O2    C2   N2   119.59  3.000
 NMF  HN2   N2   C2   117.00  3.000
 NMF  HN2   N2   C1   115.60  3.000
 NMF  C2    N2   C1   127.40  3.000
 NMF  C5    C3   C4   123.54  3.000
 NMF  C5    C3   C2   119.16  3.000
 NMF  C4    C3   C2   117.27  3.000
 NMF  HO3   O3   C13  108.27  3.000
 NMF  H4B   C4   H4A  107.56  3.000
 NMF  H4B   C4   H4   106.90  3.000
 NMF  H4A   C4   H4   107.18  3.000
 NMF  H4B   C4   C3   112.40  3.000
 NMF  H4A   C4   C3   112.43  3.000
 NMF  H4    C4   C3   110.08  3.000
 NMF  C11   C5   C3   120.68  3.000
 NMF  C11   C5   N1   117.65  3.000
 NMF  C3    C5   N1   121.66  3.000
 NMF  H11A  C11  H11  105.11  3.000
 NMF  H11A  C11  C12  109.08  3.000
 NMF  H11   C11  C12  108.05  3.000
 NMF  H11A  C11  C5   109.73  3.000
 NMF  H11   C11  C5   108.28  3.000
 NMF  C12   C11  C5   116.02  3.000
 NMF  H12   C12  C14  108.21  3.000
 NMF  H12   C12  C13  107.55  3.000
 NMF  C14   C12  C13  110.13  3.000
 NMF  H12   C12  C11  110.19  3.000
 NMF  C14   C12  C11  112.89  3.000
 NMF  C13   C12  C11  107.75  3.000
 NMF  H13A  C13  H13  106.76  3.000
 NMF  H13A  C13  C12  109.20  3.000
 NMF  H13   C13  C12  108.49  3.000
 NMF  H13A  C13  O3   111.69  3.000
 NMF  H13   C13  O3   111.44  3.000
 NMF  C12   C13  O3   109.18  3.000
 NMF  H14A  C14  H14  108.70  3.000
 NMF  H14A  C14  C12  110.96  3.000
 NMF  H14   C14  C12  110.74  3.000
 NMF  H14A  C14  F    108.22  3.000
 NMF  H14   C14  F    107.63  3.000
 NMF  C12   C14  F    110.49  3.000
 NMF  H6B   C6   H6A  108.78  3.000
 NMF  H6B   C6   H6   107.55  3.000
 NMF  H6A   C6   H6   108.85  3.000
 NMF  H6B   C6   N1   110.67  3.000
 NMF  H6A   C6   N1   111.14  3.000
 NMF  H6    C6   N1   109.77  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
 NMF  CONST_01  C3   C2   N2  C1    0.00   0.0  0
 NMF  CONST_02  C2   N2   C1  N1    0.00   0.0  0
 NMF  CONST_03  C5   N1   C1  N2    0.00   0.0  0
 NMF  CONST_04  O2   C2   N2  C1  180.00   0.0  0
 NMF  CONST_05  C5   N1   C1  O1  180.00   0.0  0
 NMF  CONST_06  C2   N2   C1  O1  180.00   0.0  0
 NMF  CONST_07  C6   N1   C1  N2  180.00   0.0  0
 NMF  CONST_08  HN2  N2   C1  N1  180.00   0.0  0
 NMF  CONST_09  C6   N1   C1  O1    0.00   0.0  0
 NMF  Var_01    C12  C11  C5  N1   70.86  30.0  3
 NMF  Var_02    H6   C6   N1  C1  -45.39  30.0  3
 NMF  Var_03    H4   C4   C3  C2    4.44  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
 NMF  chir_01  C12  C11  C13  C14  positiv

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
 NMF  plan-1  C1   0.020
 NMF  plan-1  N1   0.020
 NMF  plan-1  O1   0.020
 NMF  plan-1  C2   0.020
 NMF  plan-1  N2   0.020
 NMF  plan-1  O2   0.020
 NMF  plan-1  C3   0.020
 NMF  plan-1  C4   0.020
 NMF  plan-1  C5   0.020
 NMF  plan-1  C11  0.020
 NMF  plan-1  HN2  0.020
 NMF  plan-1  C6   0.020

