# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:20:49 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: methyl 2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@@H]2CO[C@@](C)(O[C@H]2[C@H](O)[C@@H]1NC(C)=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
 6LA  6LA  'methyl 2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside'  D-saccharide  39  21  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6LA
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
 6LA  C8   C  CH3    0  -0.776  17.5896  -18.1604  -1.1889
 6LA  C7   C  C      0   0.523  17.8483  -16.6817  -1.3383
 6LA  O7   O  O      0  -0.500  18.6335  -16.0915  -0.6093
 6LA  N2   N  NH1    0  -0.615  17.1580  -16.0755  -2.3227
 6LA  C2   C  CH1    0  -0.216  17.3249  -14.6865  -2.6663
 6LA  C3   C  CH1    0   0.049  18.3198  -14.4981  -3.8341
 6LA  O3   O  OH1    0  -0.653  19.5160  -15.1939  -3.6234
 6LA  C4   C  CH1    0   0.010  17.6698  -14.9970  -5.1097
 6LA  O4   O  O2     0  -0.502  18.4864  -14.7327  -6.2223
 6LA  CAB  C  CT     0   0.377  17.9099  -15.1448  -7.4419
 6LA  CAK  C  CH3    0  -0.701  18.8323  -14.6508  -8.5424
 6LA  CAL  C  C      0   0.358  17.7870  -16.7063  -7.5556
 6LA  OAN  O  O      0  -0.588  16.9406  -17.1166  -8.3679
 6LA  OAM  O  OC    -1  -0.584  18.5936  -17.3752  -6.8874
 6LA  O6   O  O2     0  -0.490  16.6722  -14.5013  -7.6317
 6LA  C6   C  CH2    0  -0.223  15.7311  -14.7464  -6.6105
 6LA  C5   C  CH1    0   0.007  16.3306  -14.2893  -5.2934
 6LA  O5   O  O2     0  -0.500  15.4709  -14.5808  -4.2182
 6LA  C1   C  CH1    0   0.316  15.9818  -14.0422  -3.0173
 6LA  O1   O  O2     0  -0.481  15.0887  -14.2791  -2.0035
 6LA  CAU  C  CH3    0  -0.411  13.8910  -13.5296  -2.0809
 6LA  H1   H  HCH3   0   0.266  18.4972  -18.7085  -1.4441
 6LA  H2   H  HCH3   0   0.262  17.3571  -18.3864  -0.1491
 6LA  H3   H  HCH3   0   0.248  16.7805  -18.5306  -1.8159
 6LA  H4   H  HNH1   0   0.400  16.5468  -16.6378  -2.8933
 6LA  H5   H  HCH1   0   0.283  17.7211  -14.1689  -1.7894
 6LA  H6   H  HCH1   0   0.214  18.4985  -13.4162  -3.9393
 6LA  H7   H  HOH1   0   0.450  19.9195  -14.8761  -2.8085
 6LA  H8   H  HCH1   0   0.220  17.4862  -16.0778  -5.0175
 6LA  H9   H  HCH3   0   0.234  19.8162  -15.1089  -8.4469
 6LA  H10  H  HCH3   0   0.234  18.4322  -14.9132  -9.5209
 6LA  H11  H  HCH3   0   0.234  18.9503  -13.5667  -8.4960
 6LA  H13  H  HCH2   0   0.246  14.8316  -14.1781  -6.8551
 6LA  H14  H  HCH2   0   0.212  15.4528  -15.8067  -6.5529
 6LA  H15  H  HCH1   0   0.221  16.5090  -13.2029  -5.3528
 6LA  H16  H  HCH1   0   0.204  16.1469  -12.9572  -3.1606
 6LA  H17  H  HCH3   0   0.239  13.3583  -13.6776  -1.1435
 6LA  H18  H  HCH3   0   0.213  14.0925  -12.4600  -2.2006
 6LA  H19  H  HCH3   0   0.220  13.2479  -13.8558  -2.9010

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
 6LA  CAK  CAB  single  1.519  0.020  1.519
 6LA  OAN  CAL  deloc   1.243  0.020  1.243
 6LA  O6   CAB  single  1.408  0.020  1.408
 6LA  O6   C6   single  1.410  0.020  1.410
 6LA  CAB  CAL  single  1.570  0.020  1.570
 6LA  CAB  O4   single  1.411  0.020  1.411
 6LA  CAL  OAM  deloc   1.243  0.020  1.243
 6LA  C6   C5   single  1.518  0.020  1.518
 6LA  O4   C4   single  1.405  0.020  1.405
 6LA  C5   C4   single  1.526  0.020  1.526
 6LA  C5   O5   single  1.407  0.020  1.407
 6LA  C4   C3   single  1.516  0.020  1.516
 6LA  O5   C1   single  1.412  0.020  1.412
 6LA  C3   O3   single  1.400  0.020  1.400
 6LA  C3   C2   single  1.546  0.020  1.546
 6LA  C1   C2   single  1.530  0.020  1.530
 6LA  C1   O1   single  1.372  0.020  1.372
 6LA  C2   N2   single  1.441  0.020  1.441
 6LA  N2   C7   single  1.347  0.020  1.347
 6LA  O1   CAU  single  1.415  0.020  1.415
 6LA  C7   C8   single  1.509  0.020  1.509
 6LA  C7   O7   double  1.223  0.020  1.223
 6LA  C8   H1   single  0.970  0.020  1.090
 6LA  C8   H2   single  0.970  0.020  1.090
 6LA  C8   H3   single  0.970  0.020  1.090
 6LA  N2   H4   single  0.860  0.020  1.020
 6LA  C2   H5   single  0.970  0.020  1.090
 6LA  C3   H6   single  0.970  0.020  1.090
 6LA  O3   H7   single  0.850  0.020  0.980
 6LA  C4   H8   single  0.970  0.020  1.090
 6LA  CAK  H9   single  0.970  0.020  1.090
 6LA  CAK  H10  single  0.970  0.020  1.090
 6LA  CAK  H11  single  0.970  0.020  1.090
 6LA  C6   H13  single  0.970  0.020  1.090
 6LA  C6   H14  single  0.970  0.020  1.090
 6LA  C5   H15  single  0.970  0.020  1.090
 6LA  C1   H16  single  0.970  0.020  1.090
 6LA  CAU  H17  single  0.970  0.020  1.090
 6LA  CAU  H18  single  0.970  0.020  1.090
 6LA  CAU  H19  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
 6LA  H3   C8   H2   108.70  3.000
 6LA  H3   C8   H1   108.23  3.000
 6LA  H2   C8   H1   107.26  3.000
 6LA  H3   C8   C7   113.82  3.000
 6LA  H2   C8   C7   109.54  3.000
 6LA  H1   C8   C7   109.07  3.000
 6LA  N2   C7   O7   123.20  3.000
 6LA  O7   C7   C8   121.60  3.000
 6LA  N2   C7   C8   115.20  3.000
 6LA  H4   N2   C2   118.25  3.000
 6LA  H4   N2   C7   118.28  3.000
 6LA  C2   N2   C7   123.30  3.000
 6LA  H5   C2   C1   107.63  3.000
 6LA  H5   C2   C3   108.38  3.000
 6LA  C1   C2   C3   109.89  3.000
 6LA  H5   C2   N2   107.90  3.000
 6LA  C1   C2   N2   111.03  3.000
 6LA  C3   C2   N2   111.86  3.000
 6LA  H6   C3   C4   108.21  3.000
 6LA  H6   C3   O3   111.34  3.000
 6LA  C4   C3   O3   109.23  3.000
 6LA  H6   C3   C2   107.23  3.000
 6LA  O3   C3   C2   112.07  3.000
 6LA  C4   C3   C2   108.64  3.000
 6LA  H7   O3   C3   108.74  3.000
 6LA  H8   C4   C5   108.62  3.000
 6LA  H8   C4   O4   110.37  3.000
 6LA  C5   C4   O4   109.12  3.000
 6LA  H8   C4   C3   108.93  3.000
 6LA  C5   C4   C3   108.96  3.000
 6LA  O4   C4   C3   110.81  3.000
 6LA  CAB  O4   C4   113.09  3.000
 6LA  O6   CAB  CAL  112.08  3.000
 6LA  CAL  CAB  CAK  108.58  3.000
 6LA  O6   CAB  CAK  106.71  3.000
 6LA  CAL  CAB  O4   112.65  3.000
 6LA  O6   CAB  O4   110.02  3.000
 6LA  CAK  CAB  O4   106.46  3.000
 6LA  H11  CAK  H10  108.49  3.000
 6LA  H11  CAK  H9   108.44  3.000
 6LA  H10  CAK  H9   108.01  3.000
 6LA  H11  CAK  CAB  110.98  3.000
 6LA  H10  CAK  CAB  110.46  3.000
 6LA  H9   CAK  CAB  110.37  3.000
 6LA  OAM  CAL  OAN  128.00  3.000
 6LA  OAM  CAL  CAB  116.45  3.000
 6LA  OAN  CAL  CAB  115.40  3.000
 6LA  C6   O6   CAB  114.18  3.000
 6LA  H14  C6   H13  107.80  3.000
 6LA  H14  C6   C5   110.22  3.000
 6LA  H13  C6   C5   111.29  3.000
 6LA  H14  C6   O6   112.03  3.000
 6LA  H13  C6   O6   107.28  3.000
 6LA  C5   C6   O6   108.21  3.000
 6LA  H15  C5   O5   110.13  3.000
 6LA  H15  C5   C6   108.30  3.000
 6LA  O5   C5   C6   111.06  3.000
 6LA  H15  C5   C4   108.75  3.000
 6LA  O5   C5   C4   110.37  3.000
 6LA  C6   C5   C4   108.15  3.000
 6LA  C1   O5   C5   110.48  3.000
 6LA  H16  C1   O1   111.23  3.000
 6LA  H16  C1   O5   108.53  3.000
 6LA  O1   C1   O5   109.10  3.000
 6LA  H16  C1   C2   108.15  3.000
 6LA  O1   C1   C2   109.22  3.000
 6LA  O5   C1   C2   110.61  3.000
 6LA  CAU  O1   C1   114.79  3.000
 6LA  H19  CAU  H18  108.54  3.000
 6LA  H19  CAU  H17  108.54  3.000
 6LA  H18  CAU  H17  108.48  3.000
 6LA  H19  CAU  O1   112.41  3.000
 6LA  H18  CAU  O1   111.57  3.000
 6LA  H17  CAU  O1   107.17  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
 6LA  CONST_01  C2   N2   C7  C8    180.00   0.0  0
 6LA  CONST_02  C2   N2   C7  O7      0.00   0.0  0
 6LA  CONST_03  H4   N2   C7  C8      0.00   0.0  0
 6LA  Var_01    C5   C6   O6  CAB    58.36  30.0  1
 6LA  Var_02    H17  CAU  O1  C1   -170.30  30.0  3
 6LA  Var_03    H1   C8   C7  O7    -66.30  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
 6LA  chir_01  C2   C3  C1  N2   negativ
 6LA  chir_02  C3   O3  C2  C4   positiv
 6LA  chir_03  C4   O4  C5  C3   positiv
 6LA  chir_04  CAB  O4  O6  CAL  positiv
 6LA  chir_05  C5   O5  C4  C6   negativ
 6LA  chir_06  C1   O5  O1  C2   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
 6LA  plan-1  C8   0.020
 6LA  plan-1  C7   0.020
 6LA  plan-1  O7   0.020
 6LA  plan-1  N2   0.020
 6LA  plan-1  C2   0.020
 6LA  plan-1  H4   0.020
 6LA  plan-2  CAB  0.020
 6LA  plan-2  CAL  0.020
 6LA  plan-2  OAN  0.020
 6LA  plan-2  OAM  0.020

