# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 05:27:04 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (2~{R},3~{S})-3-methanoyl-4-methyl-2-oxidanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C=O)[C@@H](O)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
 V08  V08  "(2 {R},3 {S})-3-methanoyl-4-methyl-2-hydroxy-pentanoic acid"  ligand  22  11  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V08
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
 V08  C4   C  CH1    0  -0.106  62.3405  -138.4338  41.3422
 V08  C7   C  CH1    0  -0.338  62.4803  -136.9728  41.8212
 V08  C8   C  CH1    0  -0.232  63.3331  -136.0931  40.8897
 V08  C3   C  C      0   0.397  61.4562  -139.2466  42.3214
 V08  O13  O  OC    -1  -0.578  60.2729  -138.9036  42.4499
 V08  O5   O  OH1    0  -0.688  63.5933  -139.0527  41.2201
 V08  C37  C  CH3    0  -0.662  62.7905  -136.0755  39.4642
 V08  C9   C  CH3    0  -0.659  63.4108  -134.6670  41.4336
 V08  C16  C  C1     0   0.182  63.0856  -136.9853  43.1974
 V08  O17  O  O      0  -0.377  62.4831  -136.7838  44.2239
 V08  H1   H  HCH1   0   0.226  61.8309  -138.4133  40.3700
 V08  H2   H  HCH1   0   0.240  61.4735  -136.5494  41.8907
 V08  H3   H  HCH1   0   0.226  64.3487  -136.5026  40.8651
 V08  H5   H  HOH1   0   0.427  63.5260  -139.7719  41.8785
 V08  H6   H  HCH3   0   0.233  62.8401  -137.0523  38.9839
 V08  H7   H  HCH3   0   0.216  61.7492  -135.7453  39.4448
 V08  H8   H  HCH3   0   0.231  63.3663  -135.3835  38.8480
 V08  H9   H  HCH3   0   0.229  63.8732  -134.6202  42.4218
 V08  H10  H  HCH3   0   0.233  64.0025  -134.0319  40.7730
 V08  H11  H  HCH3   0   0.219  62.4141  -134.2270  41.5149
 V08  H12  H  H      0   0.180  64.1679  -137.2143  43.2225
 V08  O8   O  O      0  -0.600  62.0576  -140.1827  42.8966

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
 V08  C37  C8   single  1.525  0.020  1.525
 V08  C8   C9   single  1.528  0.020  1.528
 V08  C8   C7   single  1.539  0.020  1.539
 V08  C4   O5   single  1.403  0.020  1.403
 V08  C4   C7   single  1.544  0.020  1.544
 V08  C4   C3   single  1.550  0.020  1.550
 V08  O8   C3   deloc   1.253  0.020  1.253
 V08  C7   C16  single  1.503  0.020  1.503
 V08  C3   O13  deloc   1.239  0.020  1.239
 V08  C16  O17  double  1.207  0.020  1.207
 V08  C4   H1   single  0.970  0.020  1.090
 V08  C7   H2   single  0.970  0.020  1.090
 V08  C8   H3   single  0.970  0.020  1.090
 V08  O5   H5   single  0.850  0.020  0.980
 V08  C37  H6   single  0.970  0.020  1.090
 V08  C37  H7   single  0.970  0.020  1.090
 V08  C37  H8   single  0.970  0.020  1.090
 V08  C9   H9   single  0.970  0.020  1.090
 V08  C9   H10  single  0.970  0.020  1.090
 V08  C9   H11  single  0.970  0.020  1.090
 V08  C16  H12  single  0.930  0.020  1.080

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
 V08  H1   C4   O5   110.23  3.000
 V08  H1   C4   C3   107.72  3.000
 V08  O5   C4   C3   109.47  3.000
 V08  H1   C4   C7   107.40  3.000
 V08  C3   C4   C7   110.61  3.000
 V08  O5   C4   C7   111.33  3.000
 V08  H2   C7   C16  108.39  3.000
 V08  H2   C7   C8   109.09  3.000
 V08  C16  C7   C8   109.61  3.000
 V08  H2   C7   C4   107.61  3.000
 V08  C16  C7   C4   108.21  3.000
 V08  C8   C7   C4   113.78  3.000
 V08  H3   C8   C9   108.05  3.000
 V08  H3   C8   C37  108.25  3.000
 V08  C9   C8   C37  109.87  3.000
 V08  H3   C8   C7   108.28  3.000
 V08  C9   C8   C7   110.24  3.000
 V08  C37  C8   C7   112.03  3.000
 V08  O13  C3   O8   128.16  3.000
 V08  O13  C3   C4   117.74  3.000
 V08  O8   C3   C4   114.09  3.000
 V08  H5   O5   C4   101.81  3.000
 V08  H8   C37  H7   107.54  3.000
 V08  H8   C37  H6   107.20  3.000
 V08  H7   C37  H6   107.85  3.000
 V08  H8   C37  C8   110.32  3.000
 V08  H7   C37  C8   111.05  3.000
 V08  H6   C37  C8   112.67  3.000
 V08  H11  C9   H10  107.78  3.000
 V08  H11  C9   H9   107.56  3.000
 V08  H10  C9   H9   107.06  3.000
 V08  H11  C9   C8   110.85  3.000
 V08  H10  C9   C8   110.81  3.000
 V08  H9   C9   C8   112.56  3.000
 V08  H12  C16  O17  120.22  3.000
 V08  H12  C16  C7   114.60  3.000
 V08  O17  C16  C7   125.17  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
 V08  Var_01  H6   C37  C8  C7    -64.75  30.0  3
 V08  Var_02  H7   C37  C8  C7     56.35  30.0  3
 V08  Var_03  H8   C37  C8  C7    175.49  30.0  3
 V08  Var_04  H9   C9   C8  C7     60.91  30.0  3
 V08  Var_05  H10  C9   C8  C7   -179.24  30.0  3
 V08  Var_06  H11  C9   C8  C7    -59.61  30.0  3
 V08  Var_07  H9   C9   C8  C37  -175.15  30.0  3
 V08  Var_08  H10  C9   C8  C37   -55.30  30.0  3
 V08  Var_09  H11  C9   C8  C37    64.33  30.0  3
 V08  Var_10  H6   C37  C8  C9    172.35  30.0  3
 V08  Var_11  H7   C37  C8  C9    -66.54  30.0  3
 V08  Var_12  H8   C37  C8  C9     52.59  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
 V08  chir_01  C4  O5   C7  C3  positiv
 V08  chir_02  C7  C16  C4  C8  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
 V08  plan-1  C4   0.020
 V08  plan-1  C3   0.020
 V08  plan-1  O13  0.020
 V08  plan-1  O8   0.020
 V08  plan-2  C7   0.020
 V08  plan-2  C16  0.020
 V08  plan-2  O17  0.020
 V08  plan-2  H12  0.020

