# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:47:29 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  21  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 GRAND
;

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   0.385  -0.0495  -0.4062   2.3584
 MIC  O1    O  O      0  -0.549  -0.4834   0.3438   3.2525
 MIC  O2    O  OC    -1  -0.665  -0.1998  -1.6469   2.3042
 MIC  C2    C  CT     0   0.120   0.7863   0.2279   1.2095
 MIC  CM2   C  CH3    0  -0.658   2.2190  -0.2815   1.3555
 MIC  O7    O  OH1    0  -0.728   0.8226   1.6330   1.3069
 MIC  C3    C  CH1    0  -0.301   0.1640  -0.1880  -0.1468
 MIC  C4    C  CH2    0  -0.571   0.9350   0.3662  -1.3533
 MIC  C5    C  C      0   0.375   0.3548  -0.1289  -2.6852
 MIC  O3    O  O      0  -0.492   0.5275  -1.3357  -2.9589
 MIC  O4    O  OC    -1  -0.776  -0.2402   0.7028  -3.4016
 MIC  C6    C  C      0   0.382  -1.2949   0.2904  -0.2306
 MIC  O5    O  O      0  -0.488  -1.5103   1.4786   0.1439
 MIC  O6    O  OC    -1  -0.703  -2.1575  -0.4858  -0.6685
 MIC  HM21  H  HCH3   0   0.188   2.2708  -1.3582   1.1972
 MIC  HM22  H  HCH3   0   0.172   2.8922   0.1979   0.6429
 MIC  HM23  H  HCH3   0   0.260   2.6061  -0.0735   2.3567
 MIC  HO7   H  HOH1   0   0.400  -0.0640   1.8876   0.9618
 MIC  H3    H  HCH1   0   0.201   0.1831  -1.2764  -0.2084
 MIC  H41   H  HCH2   0   0.245   0.9338   1.4572  -1.3185
 MIC  H42   H  HCH2   0   0.204   1.9793   0.0439  -1.2857

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    deloc   1.245  0.020  1.245
 MIC  C1   O2    deloc   1.251  0.020  1.251
 MIC  C1   C2    single  1.556  0.020  1.556
 MIC  C2   CM2   single  1.528  0.020  1.528
 MIC  C2   O7    single  1.409  0.020  1.409
 MIC  C2   C3    single  1.549  0.020  1.549
 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  1.535  0.020  1.535
 MIC  C3   C6    single  1.538  0.020  1.538
 MIC  C3   H3    single  0.970  0.020  1.090
 MIC  C4   C5    single  1.535  0.020  1.535
 MIC  C4   H41   single  0.970  0.020  1.090
 MIC  C4   H42   single  0.970  0.020  1.090
 MIC  C5   O3    deloc   1.249  0.020  1.249
 MIC  C5   O4    deloc   1.249  0.020  1.249
 MIC  C6   O5    deloc   1.264  0.020  1.264
 MIC  C6   O6    deloc   1.240  0.020  1.240

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    115.90  3.000
 MIC  C2    C1   O1    118.16  3.000
 MIC  O2    C1   O1    125.92  3.000
 MIC  C3    C2   O7    109.79  3.000
 MIC  C3    C2   CM2   111.77  3.000
 MIC  O7    C2   CM2   107.57  3.000
 MIC  C3    C2   C1    108.74  3.000
 MIC  O7    C2   C1    111.67  3.000
 MIC  CM2   C2   C1    107.30  3.000
 MIC  HM23  CM2  HM22  107.22  3.000
 MIC  HM23  CM2  HM21  107.71  3.000
 MIC  HM22  CM2  HM21  108.06  3.000
 MIC  HM23  CM2  C2    110.86  3.000
 MIC  HM22  CM2  C2    111.70  3.000
 MIC  HM21  CM2  C2    111.11  3.000
 MIC  HO7   O7   C2    102.15  3.000
 MIC  H3    C3   C6    108.91  3.000
 MIC  H3    C3   C4    107.89  3.000
 MIC  C6    C3   C4    108.74  3.000
 MIC  H3    C3   C2    108.09  3.000
 MIC  C6    C3   C2    110.20  3.000
 MIC  C4    C3   C2    112.92  3.000
 MIC  H42   C4   H41   107.05  3.000
 MIC  H42   C4   C5    108.61  3.000
 MIC  H41   C4   C5    110.47  3.000
 MIC  H42   C4   C3    108.91  3.000
 MIC  H41   C4   C3    109.59  3.000
 MIC  C5    C4   C3    112.07  3.000
 MIC  O4    C5   O3    125.70  3.000
 MIC  O4    C5   C4    117.60  3.000
 MIC  O3    C5   C4    116.71  3.000
 MIC  O6    C6   O5    125.05  3.000
 MIC  O6    C6   C3    118.97  3.000
 MIC  O5    C6   C3    115.97  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  Var_01  O3  C5  C4  C3  -70.53  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-2  C4  0.020
 MIC  plan-2  C5  0.020
 MIC  plan-2  O3  0.020
 MIC  plan-2  O4  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

