# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:03:53 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: beta-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](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
 BMA  BMA  'beta-D-mannopyranose     '  D-saccharide  24  12  .  2012-04-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BMA
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
 BMA  C1   C  CH1   0   0.289  27.8657   0.0704  -0.9678
 BMA  C2   C  CH1   0  -0.055  28.4031   1.0654   0.0457
 BMA  C3   C  CH1   0   0.026  29.9460   1.0507  -0.0132
 BMA  C4   C  CH1   0  -0.039  30.5228  -0.2852  -0.5203
 BMA  C5   C  CH1   0  -0.005  29.6056  -1.4822  -0.2725
 BMA  C6   C  CH2   0  -0.180  29.6401  -1.9795   1.1701
 BMA  O1   O  OH1   0  -0.659  26.4835   0.1082  -0.9459
 BMA  O2   O  OH1   0  -0.663  27.9010   0.7244   1.3099
 BMA  O3   O  OH1   0  -0.674  30.4020   1.3982   1.2704
 BMA  O4   O  OH1   0  -0.673  30.7491  -0.1058  -1.9056
 BMA  O5   O  O2    0  -0.514  28.2631  -1.2468  -0.6582
 BMA  O6   O  OH1   0  -0.669  30.9132  -2.5449   1.3976
 BMA  H1   H  HCH1  0   0.194  28.2466   0.3530  -1.9603
 BMA  H2   H  HCH1  0   0.229  28.0620   2.0684  -0.2484
 BMA  H3   H  HCH1  0   0.236  30.2497   1.8050  -0.7494
 BMA  H4   H  HCH1  0   0.240  31.4712  -0.4775  -0.0005
 BMA  H5   H  HCH1  0   0.229  29.9765  -2.3132  -0.8908
 BMA  H61  H  HCH2  0   0.207  29.4255  -1.1675   1.8689
 BMA  H62  H  HCH2  0   0.202  28.8434  -2.7254   1.2889
 BMA  HO1  H  HOH1  0   0.458  26.1442  -0.3024  -1.7478
 BMA  HO2  H  HOH1  0   0.452  28.4443   1.1716   1.9683
 BMA  HO3  H  HOH1  0   0.462  31.3428   1.5953   1.2285
 BMA  HO4  H  HOH1  0   0.451  31.0857  -0.9300  -2.2725
 BMA  HO6  H  HOH1  0   0.456  30.9879  -2.7489   2.3336

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
 BMA  C1  C2   single  1.519  0.020  1.519
 BMA  C1  O1   single  1.383  0.020  1.383
 BMA  C1  O5   single  1.410  0.020  1.410
 BMA  C1  H1   single  0.970  0.020  1.090
 BMA  C2  C3   single  1.544  0.020  1.544
 BMA  C2  O2   single  1.402  0.020  1.402
 BMA  C2  H2   single  0.970  0.020  1.090
 BMA  C3  C4   single  1.541  0.020  1.541
 BMA  C3  O3   single  1.406  0.020  1.406
 BMA  C3  H3   single  0.970  0.020  1.090
 BMA  C4  C5   single  1.528  0.020  1.528
 BMA  C4  O4   single  1.415  0.020  1.415
 BMA  C4  H4   single  0.970  0.020  1.090
 BMA  C5  C6   single  1.526  0.020  1.526
 BMA  C5  O5   single  1.417  0.020  1.417
 BMA  C5  H5   single  0.970  0.020  1.090
 BMA  C6  O6   single  1.411  0.020  1.411
 BMA  C6  H61  single  0.970  0.020  1.090
 BMA  C6  H62  single  0.970  0.020  1.090
 BMA  O1  HO1  single  0.850  0.020  0.980
 BMA  O2  HO2  single  0.850  0.020  0.980
 BMA  O3  HO3  single  0.850  0.020  0.980
 BMA  O4  HO4  single  0.850  0.020  0.980
 BMA  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
 BMA  H1   C1  O5   109.90  3.000
 BMA  H1   C1  O1   110.69  3.000
 BMA  O5   C1  O1   107.68  3.000
 BMA  H1   C1  C2   108.14  3.000
 BMA  O5   C1  C2   111.45  3.000
 BMA  O1   C1  C2   108.98  3.000
 BMA  H2   C2  O2   110.61  3.000
 BMA  H2   C2  C3   107.97  3.000
 BMA  O2   C2  C3   112.95  3.000
 BMA  H2   C2  C1   108.02  3.000
 BMA  O2   C2  C1   108.40  3.000
 BMA  C3   C2  C1   108.78  3.000
 BMA  H3   C3  O3   110.68  3.000
 BMA  H3   C3  C4   105.77  3.000
 BMA  O3   C3  C4   113.17  3.000
 BMA  H3   C3  C2   107.20  3.000
 BMA  O3   C3  C2   106.67  3.000
 BMA  C4   C3  C2   113.26  3.000
 BMA  H4   C4  O4   110.33  3.000
 BMA  H4   C4  C5   107.72  3.000
 BMA  O4   C4  C5   110.73  3.000
 BMA  H4   C4  C3   108.62  3.000
 BMA  O4   C4  C3   105.79  3.000
 BMA  C5   C4  C3   113.64  3.000
 BMA  H5   C5  O5   106.98  3.000
 BMA  H5   C5  C6   106.11  3.000
 BMA  O5   C5  C6   109.44  3.000
 BMA  H5   C5  C4   107.35  3.000
 BMA  O5   C5  C4   113.24  3.000
 BMA  C6   C5  C4   113.26  3.000
 BMA  H62  C6  H61  107.05  3.000
 BMA  H62  C6  O6   111.41  3.000
 BMA  H61  C6  O6   111.83  3.000
 BMA  H62  C6  C5   107.89  3.000
 BMA  H61  C6  C5   110.97  3.000
 BMA  O6   C6  C5   107.65  3.000
 BMA  HO1  O1  C1   109.11  3.000
 BMA  HO2  O2  C2   107.53  3.000
 BMA  HO3  O3  C3   109.14  3.000
 BMA  HO4  O4  C4   108.68  3.000
 BMA  C5   O5  C1   118.82  3.000
 BMA  HO6  O6  C6   108.19  3.000

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
 BMA  chir_01  C1  C2  O1  O5  positiv
 BMA  chir_02  C2  O2  C1  C3  positiv
 BMA  chir_03  C3  O3  C2  C4  positiv
 BMA  chir_04  C4  O4  C5  C3  positiv
 BMA  chir_05  C5  O5  C4  C6  negativ

