# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:04:58 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@H](CCC(O)=O)C(O)=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
 48Y  48Y  '(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid'  ligand  24  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_48Y
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
 48Y  OAB  O  OH1   0  -0.591  -2.8348  -0.0844  -1.5928
 48Y  CAK  C  C     0   0.506  -2.8532  -0.5978  -0.3704
 48Y  OAF  O  O     0  -0.427  -3.8462  -0.7116   0.2973
 48Y  CAM  C  CH1   0  -0.077  -1.4665  -1.0606   0.0664
 48Y  OAD  O  OH1   0  -0.648  -1.4675  -1.4302   1.4085
 48Y  CAN  C  CH1   0  -0.406  -0.3638  -0.0549  -0.3113
 48Y  CAL  C  C     0   0.571  -0.7111   1.3178   0.2123
 48Y  OAG  O  OH1   0  -0.578  -0.1137   2.2953  -0.4456
 48Y  OAC  O  O     0  -0.447  -1.4547   1.5058   1.1482
 48Y  CAI  C  CH2   0  -0.426   0.9988  -0.5360   0.2201
 48Y  CAH  C  CH2   0  -0.586   2.1808   0.1550  -0.4416
 48Y  CAJ  C  C     0   0.556   3.5024  -0.4329  -0.0288
 48Y  OAE  O  O     0  -0.444   3.6481  -1.3409   0.7509
 48Y  OAA  O  OH1   0  -0.596   4.5185   0.1747  -0.6328
 48Y  H1   H  HOH1  0   0.488  -3.7292   0.1726  -1.8651
 48Y  H2   H  HCH1  0   0.303  -1.2566  -1.9728  -0.5053
 48Y  H3   H  HOH1  0   0.448  -1.6590  -0.6491   1.9405
 48Y  H4   H  HCH1  0   0.299  -0.3004  -0.0105  -1.4017
 48Y  H5   H  HOH1  0   0.486  -0.3334   3.1529  -0.0491
 48Y  H6   H  HCH2  0   0.254   1.0479  -0.4190   1.3033
 48Y  H7   H  HCH2  0   0.262   1.0595  -1.6083   0.0221
 48Y  H8   H  HCH2  0   0.283   2.1054   0.0863  -1.5312
 48Y  H9   H  HCH2  0   0.289   2.2076   1.2233  -0.2157
 48Y  H10  H  HOH1  0   0.480   5.3565  -0.2215  -0.3510

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
 48Y  OAE  CAJ  double  1.206  0.020  1.206
 48Y  OAA  CAJ  single  1.329  0.020  1.329
 48Y  CAJ  CAH  single  1.504  0.020  1.504
 48Y  CAH  CAI  single  1.521  0.020  1.521
 48Y  CAI  CAN  single  1.540  0.020  1.540
 48Y  OAD  CAM  single  1.392  0.020  1.392
 48Y  OAC  CAL  double  1.210  0.020  1.210
 48Y  CAM  CAN  single  1.540  0.020  1.540
 48Y  CAM  CAK  single  1.526  0.020  1.526
 48Y  CAN  CAL  single  1.510  0.020  1.510
 48Y  CAL  OAG  single  1.321  0.020  1.321
 48Y  CAK  OAF  double  1.202  0.020  1.202
 48Y  CAK  OAB  single  1.326  0.020  1.326
 48Y  OAB  H1   single  0.850  0.020  0.980
 48Y  CAM  H2   single  0.970  0.020  1.090
 48Y  OAD  H3   single  0.850  0.020  0.980
 48Y  CAN  H4   single  0.970  0.020  1.090
 48Y  OAG  H5   single  0.850  0.020  0.980
 48Y  CAI  H6   single  0.970  0.020  1.090
 48Y  CAI  H7   single  0.970  0.020  1.090
 48Y  CAH  H8   single  0.970  0.020  1.090
 48Y  CAH  H9   single  0.970  0.020  1.090
 48Y  OAA  H10  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
 48Y  H1   OAB  CAK  110.41  3.000
 48Y  CAM  CAK  OAF  124.27  3.000
 48Y  OAF  CAK  OAB  124.07  3.000
 48Y  CAM  CAK  OAB  111.64  3.000
 48Y  H2   CAM  CAN  106.16  3.000
 48Y  H2   CAM  OAD  106.37  3.000
 48Y  CAN  CAM  OAD  114.24  3.000
 48Y  H2   CAM  CAK  106.08  3.000
 48Y  CAN  CAM  CAK  112.49  3.000
 48Y  OAD  CAM  CAK  110.85  3.000
 48Y  H3   OAD  CAM  108.48  3.000
 48Y  H4   CAN  CAI  107.79  3.000
 48Y  H4   CAN  CAL  108.81  3.000
 48Y  CAI  CAN  CAL  111.59  3.000
 48Y  H4   CAN  CAM  108.23  3.000
 48Y  CAL  CAN  CAM  110.13  3.000
 48Y  CAI  CAN  CAM  110.18  3.000
 48Y  OAC  CAL  OAG  123.24  3.000
 48Y  OAG  CAL  CAN  113.33  3.000
 48Y  OAC  CAL  CAN  123.43  3.000
 48Y  H5   OAG  CAL  110.38  3.000
 48Y  H7   CAI  H6   106.43  3.000
 48Y  H7   CAI  CAH  108.91  3.000
 48Y  H6   CAI  CAH  110.39  3.000
 48Y  H7   CAI  CAN  107.07  3.000
 48Y  H6   CAI  CAN  110.43  3.000
 48Y  CAH  CAI  CAN  113.31  3.000
 48Y  H9   CAH  H8   105.61  3.000
 48Y  H9   CAH  CAJ  107.70  3.000
 48Y  H8   CAH  CAJ  108.02  3.000
 48Y  H9   CAH  CAI  111.93  3.000
 48Y  H8   CAH  CAI  110.56  3.000
 48Y  CAJ  CAH  CAI  112.70  3.000
 48Y  OAA  CAJ  OAE  123.08  3.000
 48Y  OAA  CAJ  CAH  111.61  3.000
 48Y  OAE  CAJ  CAH  125.31  3.000
 48Y  H10  OAA  CAJ  110.01  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
 48Y  CONST_01  H1   OAB  CAK  OAF     0.00   0.0  0
 48Y  CONST_02  H5   OAG  CAL  CAN   180.00   0.0  0
 48Y  CONST_03  H10  OAA  CAJ  CAH   180.00   0.0  0
 48Y  Var_01    CAJ  CAH  CAI  CAN  -173.45  30.0  1
 48Y  Var_02    OAE  CAJ  CAH  CAI    -0.88  30.0  2

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
 48Y  chir_01  CAM  OAD  CAN  CAK  positiv
 48Y  chir_02  CAN  CAI  CAM  CAL  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
 48Y  plan-1  OAB  0.020
 48Y  plan-1  CAK  0.020
 48Y  plan-1  OAF  0.020
 48Y  plan-1  CAM  0.020
 48Y  plan-1  H1   0.020
 48Y  plan-2  CAN  0.020
 48Y  plan-2  CAL  0.020
 48Y  plan-2  OAG  0.020
 48Y  plan-2  OAC  0.020
 48Y  plan-2  H5   0.020
 48Y  plan-3  CAH  0.020
 48Y  plan-3  CAJ  0.020
 48Y  plan-3  OAE  0.020
 48Y  plan-3  OAA  0.020
 48Y  plan-3  H10  0.020

