# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 09:00:46 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (3~{S})-3-methyl-2-oxidanylidene-pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(O)=O)C(=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
 ROQ  ROQ  "(3~{S})-3-methyl-2-oxidanylidene-pentanedioic acid"  ligand  17  11  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ROQ
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
 ROQ  C01  C  C      0   0.266  21.6579  25.4687  29.2306
 ROQ  C02  C  CH1    0  -0.338  20.2447  25.0030  29.4827
 ROQ  C03  C  CH2    0  -0.570  19.2840  25.9087  28.7028
 ROQ  C04  C  CH3    0  -0.652  19.9021  24.9652  30.9640
 ROQ  C05  C  C      0   0.334  22.2380  25.2682  27.8043
 ROQ  C06  C  C      0   0.411  17.8266  25.3942  28.6408
 ROQ  O01  O  O      0  -0.410  22.3394  25.9768  30.0958
 ROQ  O02  O  OC    -1  -0.583  23.0205  26.1441  27.4063
 ROQ  O03  O  O      0  -0.582  21.8734  24.2286  27.2263
 ROQ  O04  O  OC    -1  -0.610  16.9389  26.2676  28.5871
 ROQ  O05  O  O      0  -0.603  17.6638  24.1583  28.6079
 ROQ  H01  H  HCH1   0   0.236  20.1478  24.0008  29.0606
 ROQ  H02  H  HCH2   0   0.236  19.6249  26.0077  27.6651
 ROQ  H03  H  HCH2   0   0.208  19.3037  26.9181  29.1241
 ROQ  H04  H  HCH3   0   0.220  20.5889  24.3294  31.5245
 ROQ  H05  H  HCH3   0   0.210  19.9319  25.9607  31.4095
 ROQ  H06  H  HCH3   0   0.224  18.8980  24.5673  31.1084

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
 ROQ  O03  C05  deloc   1.244  0.020  1.244
 ROQ  O05  C06  deloc   1.247  0.020  1.247
 ROQ  O02  C05  deloc   1.240  0.020  1.240
 ROQ  C05  C01  single  1.553  0.020  1.553
 ROQ  C06  C03  single  1.547  0.020  1.547
 ROQ  C06  O04  deloc   1.247  0.020  1.247
 ROQ  C03  C02  single  1.534  0.020  1.534
 ROQ  C01  C02  single  1.509  0.020  1.509
 ROQ  C01  O01  double  1.213  0.020  1.213
 ROQ  C02  C04  single  1.521  0.020  1.521
 ROQ  C02  H01  single  0.970  0.020  1.090
 ROQ  C03  H02  single  0.970  0.020  1.090
 ROQ  C03  H03  single  0.970  0.020  1.090
 ROQ  C04  H04  single  0.970  0.020  1.090
 ROQ  C04  H05  single  0.970  0.020  1.090
 ROQ  C04  H06  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
 ROQ  O01  C01  C05  119.96  3.000
 ROQ  O01  C01  C02  122.43  3.000
 ROQ  C05  C01  C02  117.61  3.000
 ROQ  H01  C02  C04  109.50  3.000
 ROQ  H01  C02  C03  106.86  3.000
 ROQ  C04  C02  C03  111.65  3.000
 ROQ  H01  C02  C01  107.56  3.000
 ROQ  C04  C02  C01  112.41  3.000
 ROQ  C03  C02  C01  108.63  3.000
 ROQ  H03  C03  H02  105.99  3.000
 ROQ  H03  C03  C06  109.84  3.000
 ROQ  H02  C03  C06  106.56  3.000
 ROQ  H03  C03  C02  109.75  3.000
 ROQ  H02  C03  C02  109.86  3.000
 ROQ  C06  C03  C02  114.46  3.000
 ROQ  H06  C04  H05  107.71  3.000
 ROQ  H06  C04  H04  107.41  3.000
 ROQ  H05  C04  H04  107.74  3.000
 ROQ  H06  C04  C02  110.22  3.000
 ROQ  H05  C04  C02  111.65  3.000
 ROQ  H04  C04  C02  111.91  3.000
 ROQ  O03  C05  O02  128.76  3.000
 ROQ  O02  C05  C01  116.06  3.000
 ROQ  O03  C05  C01  115.16  3.000
 ROQ  O05  C06  O04  126.89  3.000
 ROQ  O04  C06  C03  116.08  3.000
 ROQ  O05  C06  C03  116.99  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
 ROQ  Var_01  O05  C06  C03  C02   -33.28  30.0  2
 ROQ  Var_02  O04  C06  C03  C02   148.88  30.0  2
 ROQ  Var_03  O03  C05  C01  C02   -35.66  30.0  2
 ROQ  Var_04  O02  C05  C01  C02   145.86  30.0  2
 ROQ  Var_05  O03  C05  C01  O01   143.92  30.0  2
 ROQ  Var_06  O02  C05  C01  O01   -34.56  30.0  2
 ROQ  Var_07  H02  C03  C06  O04   -89.47  30.0  3
 ROQ  Var_08  H03  C03  C06  O04    24.91  30.0  3
 ROQ  Var_09  H02  C03  C06  O05    88.37  30.0  3
 ROQ  Var_10  H03  C03  C06  O05  -157.24  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
 ROQ  chir_01  C02  C03  C01  C04  negativ

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
 ROQ  plan-1  C01  0.020
 ROQ  plan-1  C02  0.020
 ROQ  plan-1  C05  0.020
 ROQ  plan-1  O01  0.020
 ROQ  plan-2  C01  0.020
 ROQ  plan-2  C05  0.020
 ROQ  plan-2  O02  0.020
 ROQ  plan-2  O03  0.020
 ROQ  plan-3  C03  0.020
 ROQ  plan-3  C06  0.020
 ROQ  plan-3  O04  0.020
 ROQ  plan-3  O05  0.020

