# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:41:22 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O[C@H](C)C(O)=O)[C@H]1O
#
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
 9QG  9QG  'methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactopyranoside'  D-saccharide  35  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9QG
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
 9QG  O1   O  O2     0  -0.497  -2.2257  -2.4602  -0.4457
 9QG  O5   O  O2     0  -0.493  -2.4561  -0.2262  -0.2059
 9QG  C6   C  CH2    0  -0.169  -2.9844   2.0693   0.0871
 9QG  O6   O  OH1    0  -0.669  -4.1917   1.7929   0.7554
 9QG  C1   C  CH1    0   0.295  -1.6754  -1.3389   0.1383
 9QG  C2   C  CH1    0  -0.005  -0.2423  -1.1789  -0.3710
 9QG  C3   C  CH1    0   0.027   0.3379   0.1168   0.1887
 9QG  C4   C  CH1    0  -0.013  -0.5839   1.2970  -0.1140
 9QG  C5   C  CH1    0  -0.006  -1.9926   0.9675   0.3880
 9QG  O2   O  OH1    0  -0.663   0.5678  -2.2391   0.0680
 9QG  O3   O  O2     0  -0.496   1.6171   0.3418  -0.3346
 9QG  O4   O  OH1    0  -0.671  -0.5614   1.5350  -1.5015
 9QG  CAP  C  C      0   0.375   4.0201   0.1385  -0.1444
 9QG  OAQ  O  O      0  -0.598   4.0213   0.2168  -1.3835
 9QG  CAM  C  CH1    0  -0.082   2.6790   0.3026   0.5996
 9QG  CAN  C  CH3    0  -0.682   2.7039   1.5561   1.4701
 9QG  CAO  C  CH3    0  -0.410  -3.4022  -2.9342   0.1801
 9QG  H2   H  HCH2   0   0.204  -2.5451   3.0189   0.4212
 9QG  H3   H  HOH1   0   0.456  -4.8382   2.4514   0.4868
 9QG  H4   H  HCH1   0   0.175  -1.6535  -1.4461   1.2416
 9QG  H5   H  HCH1   0   0.219  -0.2691  -1.1225  -1.4691
 9QG  H6   H  HCH1   0   0.222   0.3685   0.0126   1.2844
 9QG  H7   H  HCH1   0   0.236  -0.2187   2.1701   0.4445
 9QG  H8   H  HCH1   0   0.217  -1.9358   0.8484   1.4832
 9QG  H9   H  HOH1   0   0.451   0.2771  -3.0439  -0.3725
 9QG  H10  H  HOH1   0   0.457  -0.7913   2.4537  -1.6647
 9QG  H12  H  HCH1   0   0.201   2.5597  -0.5691   1.2583
 9QG  H13  H  HCH3   0   0.222   1.7904   1.6571   2.0600
 9QG  H14  H  HCH3   0   0.230   3.5406   1.5158   2.1651
 9QG  H15  H  HCH3   0   0.220   2.8082   2.4551   0.8588
 9QG  H16  H  HCH3   0   0.239  -3.6727  -3.8713  -0.3026
 9QG  H17  H  HCH3   0   0.213  -3.2384  -3.1254   1.2457
 9QG  H18  H  HCH3   0   0.219  -4.2363  -2.2361   0.0779
 9QG  OAR  O  OC    -1  -0.626   5.0047  -0.0501   0.5998
 9QG  H1   H  HCH2   0   0.202  -3.1321   2.1446  -0.9973

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
 9QG  OAQ  CAP  deloc   1.242  0.020  1.242
 9QG  OAR  CAP  deloc   1.249  0.020  1.249
 9QG  CAP  CAM  single  1.542  0.020  1.542
 9QG  CAM  CAN  single  1.526  0.020  1.526
 9QG  CAM  O3   single  1.415  0.020  1.415
 9QG  O3   C3   single  1.400  0.020  1.400
 9QG  C4   C3   single  1.528  0.020  1.528
 9QG  C4   O4   single  1.408  0.020  1.408
 9QG  C4   C5   single  1.531  0.020  1.531
 9QG  C3   C2   single  1.526  0.020  1.526
 9QG  C6   O6   single  1.407  0.020  1.407
 9QG  C6   C5   single  1.513  0.020  1.513
 9QG  C5   O5   single  1.412  0.020  1.412
 9QG  C2   O2   single  1.405  0.020  1.405
 9QG  C2   C1   single  1.529  0.020  1.529
 9QG  O5   C1   single  1.402  0.020  1.402
 9QG  C1   O1   single  1.379  0.020  1.379
 9QG  O1   CAO  single  1.414  0.020  1.414
 9QG  C6   H1   single  0.970  0.020  1.090
 9QG  C6   H2   single  0.970  0.020  1.090
 9QG  O6   H3   single  0.850  0.020  0.980
 9QG  C1   H4   single  0.970  0.020  1.090
 9QG  C2   H5   single  0.970  0.020  1.090
 9QG  C3   H6   single  0.970  0.020  1.090
 9QG  C4   H7   single  0.970  0.020  1.090
 9QG  C5   H8   single  0.970  0.020  1.090
 9QG  O2   H9   single  0.850  0.020  0.980
 9QG  O4   H10  single  0.850  0.020  0.980
 9QG  CAM  H12  single  0.970  0.020  1.090
 9QG  CAN  H13  single  0.970  0.020  1.090
 9QG  CAN  H14  single  0.970  0.020  1.090
 9QG  CAN  H15  single  0.970  0.020  1.090
 9QG  CAO  H16  single  0.970  0.020  1.090
 9QG  CAO  H17  single  0.970  0.020  1.090
 9QG  CAO  H18  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
 9QG  CAO  O1   C1   114.65  3.000
 9QG  C5   O5   C1   112.65  3.000
 9QG  H2   C6   H1   107.17  3.000
 9QG  H2   C6   C5   107.88  3.000
 9QG  H1   C6   C5   109.57  3.000
 9QG  H2   C6   O6   111.62  3.000
 9QG  H1   C6   O6   111.55  3.000
 9QG  C5   C6   O6   108.96  3.000
 9QG  H3   O6   C6   108.04  3.000
 9QG  H4   C1   C2   108.84  3.000
 9QG  H4   C1   O5   109.38  3.000
 9QG  C2   C1   O5   110.91  3.000
 9QG  H4   C1   O1   110.54  3.000
 9QG  O5   C1   O1   108.62  3.000
 9QG  C2   C1   O1   108.54  3.000
 9QG  H5   C2   O2   111.39  3.000
 9QG  H5   C2   C3   109.38  3.000
 9QG  O2   C2   C3   107.88  3.000
 9QG  H5   C2   C1   108.36  3.000
 9QG  O2   C2   C1   110.94  3.000
 9QG  C3   C2   C1   108.85  3.000
 9QG  H6   C3   O3   111.21  3.000
 9QG  H6   C3   C4   106.67  3.000
 9QG  O3   C3   C4   110.67  3.000
 9QG  H6   C3   C2   107.17  3.000
 9QG  C4   C3   C2   110.72  3.000
 9QG  O3   C3   C2   110.29  3.000
 9QG  H7   C4   O4   111.17  3.000
 9QG  H7   C4   C5   108.07  3.000
 9QG  O4   C4   C5   111.97  3.000
 9QG  H7   C4   C3   108.21  3.000
 9QG  C5   C4   C3   108.90  3.000
 9QG  O4   C4   C3   108.43  3.000
 9QG  H8   C5   C4   107.54  3.000
 9QG  H8   C5   C6   108.05  3.000
 9QG  C4   C5   C6   112.41  3.000
 9QG  H8   C5   O5   110.08  3.000
 9QG  C6   C5   O5   108.49  3.000
 9QG  C4   C5   O5   110.25  3.000
 9QG  H9   O2   C2   108.30  3.000
 9QG  CAM  O3   C3   115.75  3.000
 9QG  H10  O4   C4   108.98  3.000
 9QG  CAM  CAP  OAQ  118.40  3.000
 9QG  CAM  CAP  OAR  114.47  3.000
 9QG  OAQ  CAP  OAR  127.13  3.000
 9QG  H12  CAM  CAN  108.14  3.000
 9QG  H12  CAM  CAP  107.40  3.000
 9QG  CAN  CAM  CAP  110.39  3.000
 9QG  H12  CAM  O3   109.64  3.000
 9QG  CAN  CAM  O3   111.47  3.000
 9QG  CAP  CAM  O3   109.70  3.000
 9QG  H15  CAN  H14  108.33  3.000
 9QG  H15  CAN  H13  107.83  3.000
 9QG  H14  CAN  H13  107.55  3.000
 9QG  H15  CAN  CAM  110.99  3.000
 9QG  H14  CAN  CAM  110.26  3.000
 9QG  H13  CAN  CAM  111.74  3.000
 9QG  H18  CAO  H17  108.48  3.000
 9QG  H18  CAO  H16  108.60  3.000
 9QG  H17  CAO  H16  108.57  3.000
 9QG  H18  CAO  O1   112.31  3.000
 9QG  H17  CAO  O1   111.39  3.000
 9QG  H16  CAO  O1   107.40  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
 9QG  Var_01  H16  CAO  O1  C1  -174.04  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
 9QG  chir_01  C1   C2  O5   O1   negativ
 9QG  chir_02  C2   O2  C1   C3   negativ
 9QG  chir_03  C3   O3  C4   C2   negativ
 9QG  chir_04  C4   O4  C5   C3   negativ
 9QG  chir_05  C5   O5  C4   C6   negativ
 9QG  chir_06  CAM  O3  CAP  CAN  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
 9QG  plan-1  CAP  0.020
 9QG  plan-1  OAQ  0.020
 9QG  plan-1  CAM  0.020
 9QG  plan-1  OAR  0.020

