# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 00:12:49 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](O)([C@H](CC(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
 MIC  MIC  '3-carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentaric acid'  ligand  24  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MIC
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
 MIC  C1    C  C     0   0.530   0.0408  -0.3131   2.3336
 MIC  O1    O  O     0  -0.432  -0.1317   0.3048   3.3511
 MIC  O2    O  OH1   0  -0.593  -0.3213  -1.5758   2.1619
 MIC  C2    C  CT    0   0.111   0.7996   0.2354   1.1184
 MIC  CM2   C  CH3   0  -0.674   2.2106  -0.3552   1.1984
 MIC  O7    O  OH1   0  -0.658   0.9318   1.6230   1.2288
 MIC  C3    C  CH1   0  -0.402   0.1130  -0.1726  -0.2034
 MIC  C4    C  CH2   0  -0.584   0.7810   0.4611  -1.4290
 MIC  C5    C  C     0   0.558   0.5624  -0.3293  -2.6937
 MIC  O3    O  O     0  -0.441   0.4466  -1.5279  -2.7445
 MIC  O4    O  OH1   0  -0.590   0.5751   0.4485  -3.7676
 MIC  C6    C  C     0   0.593  -1.3542   0.1950  -0.1815
 MIC  O5    O  O     0  -0.436  -1.9160   0.6961   0.7627
 MIC  O6    O  OH1   0  -0.583  -1.9564  -0.0803  -1.3248
 MIC  HO2   H  HOH1  0   0.487  -0.7436  -1.9181   2.9647
 MIC  HM21  H  HCH3  0   0.251   2.2023  -1.4325   1.0410
 MIC  HM22  H  HCH3  0   0.258   2.8602   0.0909   0.4457
 MIC  HM23  H  HCH3  0   0.261   2.6555  -0.1514   2.1725
 MIC  HO7   H  HOH1  0   0.450   0.0650   2.0202   1.3719
 MIC  H3    H  HCH1  0   0.317   0.1755  -1.2603  -0.3061
 MIC  H41   H  HCH2  0   0.291   0.4732   1.4969  -1.5694
 MIC  H42   H  HCH2  0   0.312   1.8652   0.4910  -1.2887
 MIC  HO4   H  HOH1  0   0.482   0.4976  -0.0916  -4.5687
 MIC  HO6   H  HOH1  0   0.490  -2.8891   0.1837  -1.2912

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
 MIC  C1   O1    double  1.203  0.020  1.203
 MIC  C1   O2    single  1.325  0.020  1.325
 MIC  C1   C2    single  1.534  0.020  1.534
 MIC  O2   HO2   single  0.850  0.020  0.980
 MIC  C2   CM2   single  1.532  0.020  1.532
 MIC  C2   O7    single  1.398  0.020  1.398
 MIC  C2   C3    single  1.544  0.020  1.544
 MIC  CM2  HM21  single  0.970  0.020  1.090
 MIC  CM2  HM22  single  0.970  0.020  1.090
 MIC  CM2  HM23  single  0.970  0.020  1.090
 MIC  O7   HO7   single  0.850  0.020  0.980
 MIC  C3   C4    single  1.533  0.020  1.533
 MIC  C3   C6    single  1.513  0.020  1.513
 MIC  C3   H3    single  0.970  0.020  1.090
 MIC  C4   C5    single  1.507  0.020  1.507
 MIC  C4   H41   single  0.970  0.020  1.090
 MIC  C4   H42   single  0.970  0.020  1.090
 MIC  C5   O3    double  1.205  0.020  1.205
 MIC  C5   O4    single  1.326  0.020  1.326
 MIC  O4   HO4   single  0.850  0.020  0.980
 MIC  C6   O5    double  1.208  0.020  1.208
 MIC  C6   O6    single  1.321  0.020  1.321
 MIC  O6   HO6   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
 MIC  C2    C1   O2    111.92  3.000
 MIC  C2    C1   O1    123.87  3.000
 MIC  O2    C1   O1    124.06  3.000
 MIC  HO2   O2   C1    110.38  3.000
 MIC  C3    C2   O7    111.82  3.000
 MIC  C3    C2   CM2   110.63  3.000
 MIC  O7    C2   CM2   106.94  3.000
 MIC  C3    C2   C1    111.33  3.000
 MIC  O7    C2   C1    109.82  3.000
 MIC  CM2   C2   C1    106.05  3.000
 MIC  HM23  CM2  HM22  107.30  3.000
 MIC  HM23  CM2  HM21  108.50  3.000
 MIC  HM22  CM2  HM21  108.04  3.000
 MIC  HM23  CM2  C2    110.52  3.000
 MIC  HM22  CM2  C2    110.81  3.000
 MIC  HM21  CM2  C2    111.53  3.000
 MIC  HO7   O7   C2    109.60  3.000
 MIC  H3    C3   C6    107.36  3.000
 MIC  H3    C3   C4    108.12  3.000
 MIC  C6    C3   C4    109.50  3.000
 MIC  H3    C3   C2    108.51  3.000
 MIC  C6    C3   C2    110.77  3.000
 MIC  C4    C3   C2    112.42  3.000
 MIC  H42   C4   H41   105.70  3.000
 MIC  H42   C4   C5    105.41  3.000
 MIC  H41   C4   C5    110.45  3.000
 MIC  H42   C4   C3    109.92  3.000
 MIC  H41   C4   C3    111.90  3.000
 MIC  C5    C4   C3    113.01  3.000
 MIC  O4    C5   O3    123.37  3.000
 MIC  O4    C5   C4    111.75  3.000
 MIC  O3    C5   C4    124.81  3.000
 MIC  HO4   O4   C5    109.98  3.000
 MIC  O6    C6   O5    123.44  3.000
 MIC  O6    C6   C3    112.27  3.000
 MIC  O5    C6   C3    124.29  3.000
 MIC  HO6   O6   C6    110.58  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
 MIC  CONST_01  HO2  O2  C1  O1    0.00   0.0  0
 MIC  CONST_02  HO6  O6  C6  C3  180.00   0.0  0
 MIC  CONST_03  HO4  O4  C5  C4  180.00   0.0  0
 MIC  Var_01    O3   C5  C4  C3  -31.79  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
 MIC  chir_01  C2  CM2  O7  C3  negativ
 MIC  chir_02  C3  C2   C4  C6  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
 MIC  plan-1  C1   0.020
 MIC  plan-1  O1   0.020
 MIC  plan-1  O2   0.020
 MIC  plan-1  C2   0.020
 MIC  plan-1  HO2  0.020
 MIC  plan-2  C4   0.020
 MIC  plan-2  C5   0.020
 MIC  plan-2  O3   0.020
 MIC  plan-2  O4   0.020
 MIC  plan-2  HO4  0.020
 MIC  plan-3  C3   0.020
 MIC  plan-3  C6   0.020
 MIC  plan-3  O5   0.020
 MIC  plan-3  O6   0.020
 MIC  plan-3  HO6  0.020

