# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:33:28 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-[3-hydroxy-2-(hydroxymethyl)propyl]-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(CC(CO)CO)NC(=O)NC1=O
#
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
 CCV  CCV  6-[3-hydroxy-2-(hydroxymethyl)propyl]-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  29  15  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CCV
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
 CCV  N1    N  NR16  0  -0.714   1.0741   0.5663   0.7444
 CCV  O1    O  OC    0  -0.485   2.6876   0.1728   2.2943
 CCV  O2    O  OC    0  -0.469  -1.6298  -0.5929   3.4116
 CCV  N2    N  NR16  0  -0.715   0.5046  -0.1786   2.8260
 CCV  C1    C  CR6   0   0.658   1.5141   0.1851   1.9771
 CCV  C2    C  CR6   0   0.562  -0.8513  -0.2302   2.5450
 CCV  C3    C  CR6   0  -0.215  -1.2213   0.1702   1.2003
 CCV  C4    C  CH3   0  -0.746  -2.6684   0.1484   0.8081
 CCV  C5    C  CR6   0   0.426  -0.2386   0.5580   0.3529
 CCV  C11   C  CH2   0  -0.535  -0.4832   1.0027  -1.0536
 CCV  C12   C  CH1   0  -0.302  -0.3679  -0.1235  -2.0980
 CCV  C13   C  CH2   0  -0.132  -0.5684   0.4951  -3.4765
 CCV  C14   C  CH2   0  -0.178   0.9291  -0.9097  -1.9843
 CCV  O3    O  OH1   0  -0.672  -0.6003  -0.5251  -4.4469
 CCV  O4    O  OH1   0  -0.669   2.0231  -0.0133  -2.0257
 CCV  H1    H  HNR6  0   0.424   1.7782   0.7757   0.0452
 CCV  H2    H  HNR6  0   0.422   0.7866  -0.4603   3.7564
 CCV  H43   H  HCH3  0   0.261  -3.2799  -0.2241   1.6263
 CCV  H42   H  HCH3  0   0.249  -3.0376   1.1432   0.5537
 CCV  H41   H  HCH3  0   0.247  -2.8493  -0.4969  -0.0522
 CCV  H112  H  HCH2  0   0.280  -1.4811   1.4365  -1.1194
 CCV  H111  H  HCH2  0   0.277   0.2144   1.8076  -1.2964
 CCV  H12   H  HCH1  0   0.257  -1.1805  -0.8373  -1.9215
 CCV  H132  H  HCH2  0   0.203  -1.5064   1.0669  -3.4699
 CCV  H131  H  HCH2  0   0.201   0.2374   1.2139  -3.6716
 CCV  H142  H  HCH2  0   0.214   0.9209  -1.4874  -1.0509
 CCV  H141  H  HCH2  0   0.232   0.9820  -1.6399  -2.7979
 CCV  H3    H  HOH1  0   0.456  -0.6013  -0.1134  -5.3155
 CCV  H4    H  HOH1  0   0.464   2.8363  -0.5270  -2.0126

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
 CCV  N1   C1    aromatic  1.363  0.020  1.363
 CCV  N1   C5    aromatic  1.370  0.020  1.370
 CCV  N1   H1    single    0.860  0.020  1.020
 CCV  O1   C1    double    1.216  0.020  1.216
 CCV  O2   C2    double    1.220  0.020  1.220
 CCV  N2   C1    aromatic  1.368  0.020  1.368
 CCV  N2   C2    aromatic  1.386  0.020  1.386
 CCV  N2   H2    single    0.860  0.020  1.020
 CCV  C2   C3    aromatic  1.451  0.020  1.451
 CCV  C3   C4    single    1.499  0.020  1.499
 CCV  C3   C5    aromatic  1.354  0.020  1.354
 CCV  C4   H43   single    0.970  0.020  1.090
 CCV  C4   H42   single    0.970  0.020  1.090
 CCV  C4   H41   single    0.970  0.020  1.090
 CCV  C5   C11   single    1.495  0.020  1.495
 CCV  C11  C12   single    1.540  0.020  1.540
 CCV  C11  H112  single    0.970  0.020  1.090
 CCV  C11  H111  single    0.970  0.020  1.090
 CCV  C12  C13   single    1.524  0.020  1.524
 CCV  C12  C14   single    1.521  0.020  1.521
 CCV  C12  H12   single    0.970  0.020  1.090
 CCV  C13  O3    single    1.408  0.020  1.408
 CCV  C13  H132  single    0.970  0.020  1.090
 CCV  C13  H131  single    0.970  0.020  1.090
 CCV  C14  O4    single    1.415  0.020  1.415
 CCV  C14  H142  single    0.970  0.020  1.090
 CCV  C14  H141  single    0.970  0.020  1.090
 CCV  O3   H3    single    0.850  0.020  0.980
 CCV  O4   H4    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
 CCV  H1    N1   C5    118.01  3.000
 CCV  H1    N1   C1    117.20  3.000
 CCV  C5    N1   C1    124.47  3.000
 CCV  H2    N2   C2    116.66  3.000
 CCV  H2    N2   C1    116.02  3.000
 CCV  C2    N2   C1    127.30  3.000
 CCV  N2    C1   O1    123.20  3.000
 CCV  N2    C1   N1    113.41  3.000
 CCV  O1    C1   N1    123.39  3.000
 CCV  C3    C2   N2    115.29  3.000
 CCV  C3    C2   O2    125.28  3.000
 CCV  N2    C2   O2    119.43  3.000
 CCV  C5    C3   C4    122.74  3.000
 CCV  C5    C3   C2    118.29  3.000
 CCV  C4    C3   C2    118.98  3.000
 CCV  H41   C4   H42   107.42  3.000
 CCV  H41   C4   H43   107.31  3.000
 CCV  H42   C4   H43   107.31  3.000
 CCV  H41   C4   C3    112.02  3.000
 CCV  H42   C4   C3    111.98  3.000
 CCV  H43   C4   C3    110.55  3.000
 CCV  C11   C5   C3    123.71  3.000
 CCV  C11   C5   N1    115.07  3.000
 CCV  C3    C5   N1    121.22  3.000
 CCV  H111  C11  H112  106.14  3.000
 CCV  H111  C11  C12   109.89  3.000
 CCV  H112  C11  C12   108.58  3.000
 CCV  H111  C11  C5    108.89  3.000
 CCV  H112  C11  C5    108.95  3.000
 CCV  C12   C11  C5    114.09  3.000
 CCV  H12   C12  C14   106.47  3.000
 CCV  H12   C12  C13   108.21  3.000
 CCV  C14   C12  C13   112.93  3.000
 CCV  H12   C12  C11   108.15  3.000
 CCV  C14   C12  C11   113.02  3.000
 CCV  C13   C12  C11   107.86  3.000
 CCV  H131  C13  H132  106.68  3.000
 CCV  H131  C13  O3    111.63  3.000
 CCV  H132  C13  O3    111.22  3.000
 CCV  H131  C13  C12   109.27  3.000
 CCV  H132  C13  C12   108.55  3.000
 CCV  O3    C13  C12   109.40  3.000
 CCV  H141  C14  H142  106.34  3.000
 CCV  H141  C14  O4    111.31  3.000
 CCV  H142  C14  O4    111.35  3.000
 CCV  H141  C14  C12   109.30  3.000
 CCV  H142  C14  C12   109.22  3.000
 CCV  O4    C14  C12   109.25  3.000
 CCV  H3    O3   C13   108.20  3.000
 CCV  H4    O4   C14   108.36  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
 CCV  CONST_01  C2   N2   C1   N1      0.00   0.0  0
 CCV  CONST_02  C2   C3   C5   N1      0.00   0.0  0
 CCV  CONST_03  C5   N1   C1   N2      0.00   0.0  0
 CCV  CONST_04  C5   C3   C2   N2      0.00   0.0  0
 CCV  CONST_05  C3   C5   N1   C1      0.00   0.0  0
 CCV  CONST_06  C3   C2   N2   C1      0.00   0.0  0
 CCV  CONST_07  C4   C3   C5   N1    180.00   0.0  0
 CCV  CONST_08  C5   N1   C1   O1    180.00   0.0  0
 CCV  CONST_09  C2   N2   C1   O1    180.00   0.0  0
 CCV  CONST_10  C1   N2   C2   O2    180.00   0.0  0
 CCV  CONST_11  C5   C3   C2   O2    180.00   0.0  0
 CCV  CONST_12  C4   C3   C2   N2    180.00   0.0  0
 CCV  CONST_13  C11  C5   N1   C1    180.00   0.0  0
 CCV  CONST_14  C11  C5   C3   C2    180.00   0.0  0
 CCV  CONST_15  H2   N2   C1   N1    180.00   0.0  0
 CCV  CONST_16  H1   N1   C1   N2    180.00   0.0  0
 CCV  Var_01    C12  C11  C5   N1     86.77  30.0  2
 CCV  Var_02    H43  C4   C3   C2     -2.25  30.0  2
 CCV  Var_03    C13  C12  C11  C5   -177.06  30.0  3
 CCV  Var_04    O3   C13  C12  C11  -174.28  30.0  3
 CCV  Var_05    O4   C14  C12  C11   -53.70  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
 CCV  plan-1  N1   0.020
 CCV  plan-1  O1   0.020
 CCV  plan-1  O2   0.020
 CCV  plan-1  N2   0.020
 CCV  plan-1  C1   0.020
 CCV  plan-1  C2   0.020
 CCV  plan-1  C3   0.020
 CCV  plan-1  C4   0.020
 CCV  plan-1  C5   0.020
 CCV  plan-1  C11  0.020
 CCV  plan-1  H1   0.020
 CCV  plan-1  H2   0.020

