# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:16:47 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-(2-methylpropyl)-2-oxidanylidene-1~{H}-pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC1=NC(=O)NC(=C1)C(O)=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
 S6Y  S6Y  '4-(2-methylpropyl)-2-oxidanylidene-1~{H}-pyrimidine-6-carboxylic acid'  ligand  26  14  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S6Y
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
 S6Y  N1   N  N     0  -0.466  4.0972   5.5977  14.3818
 S6Y  C2   C  CR6   0   0.327  6.7316   4.8435  14.4886
 S6Y  C3   C  CR16  0  -0.393  6.3916   6.1014  14.8535
 S6Y  C4   C  CR6   0   0.313  5.0075   6.4373  14.7822
 S6Y  C5   C  CH2   0  -0.497  4.5825   7.8053  15.2096
 S6Y  C7   C  CH3   0  -0.651  4.3650   9.4574  17.0776
 S6Y  C8   C  CH3   0  -0.651  3.8888   7.0341  17.5226
 S6Y  C9   C  CR6   0   0.556  4.4344   4.3223  14.0079
 S6Y  O3   O  O     0  -0.486  3.6142   3.5066  13.6275
 S6Y  N2   N  NR16  0  -0.692  5.7742   3.9863  14.0824
 S6Y  C1   C  C     0   0.532  8.1224   4.2930  14.4875
 S6Y  O2   O  OH1   0  -0.570  9.0057   5.1734  14.8960
 S6Y  O1   O  O     0  -0.415  8.3571   3.1642  14.1440
 S6Y  C6   C  CH1   0  -0.254  4.7338   8.0209  16.7249
 S6Y  H1   H  HCR6  0   0.296  7.1232   6.8251  15.1773
 S6Y  H3   H  HCH2  0   0.266  5.1969   8.5425  14.6840
 S6Y  H4   H  HCH2  0   0.254  3.5439   7.9645  14.9126
 S6Y  H5   H  HCH3  0   0.232  4.4956   9.6399  18.1450
 S6Y  H6   H  HCH3  0   0.230  4.9838  10.1760  16.5383
 S6Y  H7   H  HCH3  0   0.219  3.3209   9.6616  16.8306
 S6Y  H8   H  HCH3  0   0.233  4.0151   7.1998  18.5935
 S6Y  H9   H  HCH3  0   0.220  2.8277   7.1511  17.2905
 S6Y  H10  H  HCH3  0   0.230  4.1586   5.9966  17.3203
 S6Y  H11  H  HOH1  0   0.504  9.8990   4.7950  14.8859
 S6Y  H12  H  HCH1  0   0.235  5.7857   7.8662  16.9899
 S6Y  H2   H  HNR6  0   0.429  6.0412   3.0475  13.8093

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
 S6Y  O3  C9   double  1.218  0.020  1.218
 S6Y  C9  N2   single  1.383  0.020  1.383
 S6Y  C9  N1   single  1.371  0.020  1.371
 S6Y  N2  C2   single  1.348  0.020  1.348
 S6Y  N1  C4   double  1.301  0.020  1.301
 S6Y  O1  C1   double  1.203  0.020  1.203
 S6Y  C2  C1   single  1.496  0.020  1.496
 S6Y  C2  C3   double  1.353  0.020  1.353
 S6Y  C1  O2   single  1.312  0.020  1.312
 S6Y  C4  C3   single  1.426  0.020  1.426
 S6Y  C4  C5   single  1.495  0.020  1.495
 S6Y  C5  C6   single  1.538  0.020  1.538
 S6Y  C6  C7   single  1.524  0.020  1.524
 S6Y  C6  C8   single  1.525  0.020  1.525
 S6Y  C3  H1   single  0.930  0.020  1.080
 S6Y  C5  H3   single  0.970  0.020  1.090
 S6Y  C5  H4   single  0.970  0.020  1.090
 S6Y  C7  H5   single  0.970  0.020  1.090
 S6Y  C7  H6   single  0.970  0.020  1.090
 S6Y  C7  H7   single  0.970  0.020  1.090
 S6Y  C8  H8   single  0.970  0.020  1.090
 S6Y  C8  H9   single  0.970  0.020  1.090
 S6Y  C8  H10  single  0.970  0.020  1.090
 S6Y  O2  H11  single  0.850  0.020  0.980
 S6Y  C6  H12  single  0.970  0.020  1.090
 S6Y  N2  H2   single  0.860  0.020  1.020

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
 S6Y  C9   N1  C4  120.80  3.000
 S6Y  C1   C2  N2  115.23  3.000
 S6Y  C1   C2  C3  125.16  3.000
 S6Y  N2   C2  C3  119.61  3.000
 S6Y  H1   C3  C4  121.01  3.000
 S6Y  H1   C3  C2  122.29  3.000
 S6Y  C4   C3  C2  116.70  3.000
 S6Y  C5   C4  C3  118.50  3.000
 S6Y  C5   C4  N1  118.65  3.000
 S6Y  C3   C4  N1  122.84  3.000
 S6Y  H4   C5  H3  107.77  3.000
 S6Y  H4   C5  C6  109.94  3.000
 S6Y  H3   C5  C6  108.88  3.000
 S6Y  H4   C5  C4  109.03  3.000
 S6Y  H3   C5  C4  108.64  3.000
 S6Y  C6   C5  C4  112.46  3.000
 S6Y  H7   C7  H6  107.90  3.000
 S6Y  H7   C7  H5  107.73  3.000
 S6Y  H6   C7  H5  107.80  3.000
 S6Y  H7   C7  C6  110.80  3.000
 S6Y  H6   C7  C6  111.66  3.000
 S6Y  H5   C7  C6  110.80  3.000
 S6Y  H10  C8  H9  107.62  3.000
 S6Y  H10  C8  H8  107.33  3.000
 S6Y  H9   C8  H8  107.74  3.000
 S6Y  H10  C8  C6  112.43  3.000
 S6Y  H9   C8  C6  110.96  3.000
 S6Y  H8   C8  C6  110.56  3.000
 S6Y  N2   C9  O3  120.43  3.000
 S6Y  N2   C9  N1  116.71  3.000
 S6Y  O3   C9  N1  122.87  3.000
 S6Y  H2   N2  C9  117.75  3.000
 S6Y  H2   N2  C2  118.90  3.000
 S6Y  C9   N2  C2  123.35  3.000
 S6Y  O1   C1  O2  125.95  3.000
 S6Y  O2   C1  C2  112.26  3.000
 S6Y  O1   C1  C2  121.80  3.000
 S6Y  H11  O2  C1  110.79  3.000
 S6Y  H12  C6  C8  108.31  3.000
 S6Y  H12  C6  C7  108.02  3.000
 S6Y  C8   C6  C7  110.78  3.000
 S6Y  H12  C6  C5  108.24  3.000
 S6Y  C8   C6  C5  111.73  3.000
 S6Y  C7   C6  C5  109.65  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
 S6Y  CONST_01  C2   N2  C9  N1     0.00   0.0  0
 S6Y  CONST_02  N2   C9  N1  C4     0.00   0.0  0
 S6Y  CONST_03  O3   C9  N2  C2   180.00   0.0  0
 S6Y  CONST_04  O3   C9  N1  C4   180.00   0.0  0
 S6Y  CONST_05  H2   N2  C9  N1   180.00   0.0  0
 S6Y  CONST_06  H11  O2  C1  C2   180.00   0.0  0
 S6Y  Var_01    C6   C5  C4  N1   110.13  30.0  3
 S6Y  Var_02    O1   C1  C2  C3  -179.63  30.0  2
 S6Y  Var_03    C7   C6  C5  C4   176.58  30.0  3
 S6Y  Var_04    H5   C7  C6  C5  -178.24  30.0  3
 S6Y  Var_05    H8   C8  C6  C5   179.65  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
 S6Y  plan-1  N1   0.020
 S6Y  plan-1  C2   0.020
 S6Y  plan-1  C3   0.020
 S6Y  plan-1  C4   0.020
 S6Y  plan-1  C5   0.020
 S6Y  plan-1  C9   0.020
 S6Y  plan-1  O3   0.020
 S6Y  plan-1  N2   0.020
 S6Y  plan-1  C1   0.020
 S6Y  plan-1  H1   0.020
 S6Y  plan-1  H2   0.020
 S6Y  plan-2  C2   0.020
 S6Y  plan-2  C1   0.020
 S6Y  plan-2  O2   0.020
 S6Y  plan-2  O1   0.020
 S6Y  plan-2  H11  0.020

