# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:11:36 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: butyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCO[C@H]1O[C@H](CO)[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
 DEG  DEG  'butyl alpha-D-mannopyranoside'  D-saccharide  36  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DEG
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
 DEG  C3'   C  CH2   0  -0.429  -0.5479  -0.0871   4.5926
 DEG  C4'   C  CH3   0  -0.661  -1.0932  -1.0182   5.6662
 DEG  C1'   C  CH2   0  -0.134  -0.4724   0.4612   2.1343
 DEG  C2'   C  CH2   0  -0.458  -0.9997  -0.4860   3.1927
 DEG  C2    C  CH1   0  -0.030  -1.4809   0.3762  -1.4000
 DEG  O2    O  OH1   0  -0.669  -1.5102   1.3334  -2.4280
 DEG  C3    C  CH1   0   0.003  -0.7326  -0.8537  -1.9071
 DEG  O3    O  OH1   0  -0.674  -1.2660  -1.3542  -3.1109
 DEG  C4    C  CH1   0   0.029   0.7351  -0.5260  -2.1588
 DEG  O4    O  OH1   0  -0.676   1.4676  -1.6877  -2.4710
 DEG  C5    C  CH1   0  -0.008   1.3527   0.0840  -0.8992
 DEG  O5    O  O2    0  -0.499   0.5895   1.1925  -0.4560
 DEG  C6    C  CH2   0  -0.159   2.7590   0.5866  -1.1516
 DEG  O6    O  OH1   0  -0.670   3.3097   1.0258   0.0678
 DEG  O1    O  O2    0  -0.507  -0.9266   0.0245   0.8649
 DEG  C1    C  CH1   0   0.244  -0.7539   0.9329  -0.1721
 DEG  H3'1  H  HCH2  0   0.217  -0.8682   0.9376   4.8016
 DEG  H3'2  H  HCH2  0   0.217   0.5453  -0.0791   4.6358
 DEG  H4'1  H  HCH3  0   0.229  -0.7529  -0.7238   6.6593
 DEG  H4'2  H  HCH3  0   0.218  -2.1847  -1.0128   5.6749
 DEG  H4'3  H  HCH3  0   0.218  -0.7711  -2.0476   5.4983
 DEG  H1'1  H  HCH2  0   0.201  -0.8299   1.4815   2.3307
 DEG  H1'2  H  HCH2  0   0.208   0.6229   0.4915   2.1690
 DEG  H2'1  H  HCH2  0   0.223  -0.6581  -1.5027   2.9756
 DEG  H2'2  H  HCH2  0   0.220  -2.0932  -0.5036   3.1515
 DEG  H2    H  HCH1  0   0.230  -2.4964   0.0840  -1.0976
 DEG  HA    H  HOH1  0   0.455  -2.0708   2.0647  -2.1511
 DEG  H3    H  HCH1  0   0.227  -0.7767  -1.6172  -1.1187
 DEG  HB    H  HOH1  0   0.456  -2.0623  -1.8552  -2.9108
 DEG  H4    H  HCH1  0   0.212   0.8021   0.2083  -2.9757
 DEG  HC    H  HOH1  0   0.452   1.0612  -2.0943  -3.2435
 DEG  H5    H  HCH1  0   0.223   1.3947  -0.6938  -0.1223
 DEG  H6C1  H  HCH2  0   0.210   3.3461  -0.2272  -1.5903
 DEG  H6C2  H  HCH2  0   0.194   2.7202   1.3943  -1.8958
 DEG  H6    H  HOH1  0   0.455   4.2107   1.3146  -0.1017
 DEG  H1    H  HCH1  0   0.232  -1.1753   1.9122   0.1020

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
 DEG  C3'  C4'   single  1.522  0.020  1.522
 DEG  C3'  C2'   single  1.524  0.020  1.524
 DEG  C3'  H3'1  single  0.970  0.020  1.090
 DEG  C3'  H3'2  single  0.970  0.020  1.090
 DEG  C4'  H4'1  single  0.970  0.020  1.090
 DEG  C4'  H4'2  single  0.970  0.020  1.090
 DEG  C4'  H4'3  single  0.970  0.020  1.090
 DEG  C1'  C2'   single  1.515  0.020  1.515
 DEG  C1'  O1    single  1.417  0.020  1.417
 DEG  C1'  H1'1  single  0.970  0.020  1.090
 DEG  C1'  H1'2  single  0.970  0.020  1.090
 DEG  C2'  H2'1  single  0.970  0.020  1.090
 DEG  C2'  H2'2  single  0.970  0.020  1.090
 DEG  C2   O2    single  1.405  0.020  1.405
 DEG  C2   C3    single  1.526  0.020  1.526
 DEG  C2   C1    single  1.532  0.020  1.532
 DEG  C2   H2    single  0.970  0.020  1.090
 DEG  O2   HA    single  0.850  0.020  0.980
 DEG  C3   O3    single  1.409  0.020  1.409
 DEG  C3   C4    single  1.525  0.020  1.525
 DEG  C3   H3    single  0.970  0.020  1.090
 DEG  O3   HB    single  0.850  0.020  0.980
 DEG  C4   O4    single  1.408  0.020  1.408
 DEG  C4   C5    single  1.530  0.020  1.530
 DEG  C4   H4    single  0.970  0.020  1.090
 DEG  O4   HC    single  0.850  0.020  0.980
 DEG  C5   O5    single  1.417  0.020  1.417
 DEG  C5   C6    single  1.515  0.020  1.515
 DEG  C5   H5    single  0.970  0.020  1.090
 DEG  O5   C1    single  1.397  0.020  1.397
 DEG  C6   O6    single  1.408  0.020  1.408
 DEG  C6   H6C1  single  0.970  0.020  1.090
 DEG  C6   H6C2  single  0.970  0.020  1.090
 DEG  O6   H6    single  0.850  0.020  0.980
 DEG  O1   C1    single  1.389  0.020  1.389
 DEG  C1   H1    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
 DEG  H3'2  C3'  H3'1  106.15  3.000
 DEG  H3'2  C3'  C2'   109.54  3.000
 DEG  H3'1  C3'  C2'   109.51  3.000
 DEG  H3'2  C3'  C4'   109.54  3.000
 DEG  H3'1  C3'  C4'   109.47  3.000
 DEG  C2'   C3'  C4'   112.43  3.000
 DEG  H4'3  C4'  H4'2  107.51  3.000
 DEG  H4'3  C4'  H4'1  107.62  3.000
 DEG  H4'2  C4'  H4'1  107.67  3.000
 DEG  H4'3  C4'  C3'   111.26  3.000
 DEG  H4'2  C4'  C3'   111.15  3.000
 DEG  H4'1  C4'  C3'   111.44  3.000
 DEG  H1'2  C1'  H1'1  107.08  3.000
 DEG  H1'2  C1'  O1    110.92  3.000
 DEG  H1'1  C1'  O1    110.00  3.000
 DEG  H1'2  C1'  C2'   110.05  3.000
 DEG  H1'1  C1'  C2'   110.02  3.000
 DEG  O1    C1'  C2'   108.76  3.000
 DEG  H2'2  C2'  H2'1  106.83  3.000
 DEG  H2'2  C2'  C1'   109.36  3.000
 DEG  H2'1  C2'  C1'   109.49  3.000
 DEG  H2'2  C2'  C3'   109.57  3.000
 DEG  H2'1  C2'  C3'   109.44  3.000
 DEG  C1'   C2'  C3'   112.02  3.000
 DEG  H2    C2   C1    108.33  3.000
 DEG  H2    C2   C3    109.28  3.000
 DEG  C1    C2   C3    109.06  3.000
 DEG  H2    C2   O2    111.29  3.000
 DEG  C1    C2   O2    110.41  3.000
 DEG  C3    C2   O2    108.43  3.000
 DEG  HA    O2   C2    108.62  3.000
 DEG  H3    C3   C4    107.85  3.000
 DEG  H3    C3   O3    110.56  3.000
 DEG  C4    C3   O3    107.45  3.000
 DEG  H3    C3   C2    107.57  3.000
 DEG  C4    C3   C2    110.71  3.000
 DEG  O3    C3   C2    112.62  3.000
 DEG  HB    O3   C3    108.71  3.000
 DEG  H4    C4   C5    108.70  3.000
 DEG  H4    C4   O4    110.74  3.000
 DEG  C5    C4   O4    107.54  3.000
 DEG  H4    C4   C3    108.94  3.000
 DEG  C5    C4   C3    109.78  3.000
 DEG  O4    C4   C3    111.10  3.000
 DEG  HC    O4   C4    107.85  3.000
 DEG  H5    C5   C6    108.48  3.000
 DEG  H5    C5   O5    110.65  3.000
 DEG  C6    C5   O5    107.02  3.000
 DEG  H5    C5   C4    108.36  3.000
 DEG  C6    C5   C4    111.72  3.000
 DEG  O5    C5   C4    110.61  3.000
 DEG  C1    O5   C5    115.85  3.000
 DEG  H6C2  C6   H6C1  107.09  3.000
 DEG  H6C2  C6   O6    111.78  3.000
 DEG  H6C1  C6   O6    111.65  3.000
 DEG  H6C2  C6   C5    108.90  3.000
 DEG  H6C1  C6   C5    108.54  3.000
 DEG  O6    C6   C5    108.80  3.000
 DEG  H6    O6   C6    107.92  3.000
 DEG  C1    O1   C1'   115.30  3.000
 DEG  H1    C1   O1    110.38  3.000
 DEG  H1    C1   O5    104.68  3.000
 DEG  O1    C1   O5    113.12  3.000
 DEG  H1    C1   C2    109.95  3.000
 DEG  O1    C1   C2    107.56  3.000
 DEG  O5    C1   C2    111.16  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
 DEG  Var_01  O1    C1'  C2'  C3'  179.73  30.0  1
 DEG  Var_02  C1'   C2'  C3'  C4'  178.97  30.0  3
 DEG  Var_03  H4'1  C4'  C3'  C2'  179.47  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
 DEG  chir_01  C2  O2  C3  C1  negativ
 DEG  chir_02  C3  O3  C2  C4  positiv
 DEG  chir_03  C4  O4  C5  C3  positiv
 DEG  chir_04  C5  O5  C4  C6  negativ
 DEG  chir_05  C1  O5  O1  C2  positiv

