# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:07:37 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@@H]([C@H](O)[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
 0AI  0AI  'methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranosiduronic acid'  ligand  32  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0AI
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
 0AI  O6    O  O     0  -0.421   3.5861  -0.8518   1.2802
 0AI  C6    C  C     0   0.514   3.2489  -0.2940   0.2720
 0AI  O5    O  O2    0  -0.493   1.0707  -1.1052   0.5609
 0AI  C1    C  CH1   0   0.285  -0.2786  -1.2171   0.2027
 0AI  C5    C  CH1   0  -0.089   1.8378  -0.2840  -0.2825
 0AI  C2    C  CH1   0  -0.139  -0.9558   0.1549   0.1819
 0AI  N2    N  NH1   0  -0.630  -2.3369   0.0294  -0.1978
 0AI  C7    C  C     0   0.524  -3.3674   0.5079   0.5255
 0AI  O7    O  O     0  -0.504  -3.2310   1.0635   1.6064
 0AI  C8    C  CH3   0  -0.780  -4.7288   0.2910  -0.0862
 0AI  C3    C  CH1   0   0.014  -0.1922   1.1066  -0.7351
 0AI  O3    O  OH1   0  -0.658  -0.7654   2.3845  -0.6044
 0AI  C4    C  CH1   0  -0.010   1.2889   1.1387  -0.3431
 0AI  O4    O  OH1   0  -0.671   1.4739   1.7191   0.9227
 0AI  H1    H  HCH1  0   0.249  -0.7293  -1.8405   0.9859
 0AI  H2    H  HCH1  0   0.279  -0.9286   0.5456   1.2002
 0AI  H3    H  HCH1  0   0.235  -0.2637   0.7496  -1.7707
 0AI  HA    H  HNH1  0   0.398  -2.5371  -0.4000  -1.0871
 0AI  H4    H  HCH1  0   0.248   1.8377   1.6879  -1.1215
 0AI  HB    H  HOH1  0   0.461  -0.4876   2.9232  -1.3524
 0AI  H5    H  HCH1  0   0.285   1.8795  -0.6806  -1.3065
 0AI  HC    H  HOH1  0   0.454   0.9738   2.5435   0.9427
 0AI  H8C1  H  HCH3  0   0.267  -5.3209  -0.3475   0.5697
 0AI  H8C2  H  HCH3  0   0.265  -5.2473   1.2462  -0.1636
 0AI  H8C3  H  HCH3  0   0.248  -4.6966  -0.1655  -1.0737
 0AI  HMC1  H  HCH3  0   0.241  -0.4348  -3.5406  -2.0783
 0AI  HMC2  H  HCH3  0   0.222   0.9926  -3.3097  -1.0570
 0AI  HMC3  H  HCH3  0   0.217  -0.5632  -3.7449  -0.3217
 0AI  O71   O  OH1   0  -0.593   4.0666   0.3887  -0.5157
 0AI  H15   H  HOH1  0   0.489   4.9643   0.3875  -0.1505
 0AI  O1    O  O2    0  -0.499  -0.4499  -1.7975  -1.0470
 0AI  CM    C  CH3   0  -0.407  -0.0884  -3.1631  -1.1184

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
 0AI  C6   O6    double  1.201  0.020  1.201
 0AI  C1   C2    single  1.530  0.020  1.530
 0AI  C1   O1    single  1.389  0.020  1.389
 0AI  C1   O5    single  1.401  0.020  1.401
 0AI  C1   H1    single  0.970  0.020  1.090
 0AI  C5   C6    single  1.516  0.020  1.516
 0AI  C5   O5    single  1.405  0.020  1.405
 0AI  C5   H5    single  0.970  0.020  1.090
 0AI  O1   CM    single  1.414  0.020  1.414
 0AI  CM   HMC1  single  0.970  0.020  1.090
 0AI  CM   HMC2  single  0.970  0.020  1.090
 0AI  CM   HMC3  single  0.970  0.020  1.090
 0AI  C2   C3    single  1.526  0.020  1.526
 0AI  C2   N2    single  1.438  0.020  1.438
 0AI  C2   H2    single  0.970  0.020  1.090
 0AI  N2   HA    single  0.860  0.020  1.020
 0AI  C7   C8    single  1.508  0.020  1.508
 0AI  C7   N2    single  1.347  0.020  1.347
 0AI  C7   O7    double  1.223  0.020  1.223
 0AI  C8   H8C1  single  0.970  0.020  1.090
 0AI  C8   H8C2  single  0.970  0.020  1.090
 0AI  C8   H8C3  single  0.970  0.020  1.090
 0AI  C3   C4    single  1.532  0.020  1.532
 0AI  C3   O3    single  1.407  0.020  1.407
 0AI  C3   H3    single  0.970  0.020  1.090
 0AI  O3   HB    single  0.850  0.020  0.980
 0AI  C4   C5    single  1.526  0.020  1.526
 0AI  C4   O4    single  1.405  0.020  1.405
 0AI  C4   H4    single  0.970  0.020  1.090
 0AI  O4   HC    single  0.850  0.020  0.980
 0AI  C6   O71   single  1.325  0.020  1.325
 0AI  O71  H15   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
 0AI  O71   C6   C5    110.71  3.000
 0AI  O71   C6   O6    124.43  3.000
 0AI  C5    C6   O6    124.86  3.000
 0AI  C5    O5   C1    114.78  3.000
 0AI  H1    C1   C2    109.71  3.000
 0AI  H1    C1   O1    110.74  3.000
 0AI  C2    C1   O1    107.94  3.000
 0AI  H1    C1   O5    104.98  3.000
 0AI  O1    C1   O5    112.48  3.000
 0AI  C2    C1   O5    110.99  3.000
 0AI  H5    C5   C4    108.24  3.000
 0AI  C4    C5   O5    111.86  3.000
 0AI  H5    C5   O5    111.66  3.000
 0AI  C4    C5   C6    110.82  3.000
 0AI  H5    C5   C6    107.64  3.000
 0AI  O5    C5   C6    106.54  3.000
 0AI  H2    C2   C3    108.96  3.000
 0AI  H2    C2   N2    107.56  3.000
 0AI  C3    C2   N2    112.11  3.000
 0AI  H2    C2   C1    107.30  3.000
 0AI  N2    C2   C1    110.51  3.000
 0AI  C3    C2   C1    110.23  3.000
 0AI  HA    N2   C7    118.26  3.000
 0AI  C7    N2   C2    124.20  3.000
 0AI  HA    N2   C2    117.46  3.000
 0AI  C8    C7   O7    121.63  3.000
 0AI  O7    C7   N2    123.42  3.000
 0AI  C8    C7   N2    114.94  3.000
 0AI  H8C3  C8   H8C2  108.50  3.000
 0AI  H8C3  C8   H8C1  108.44  3.000
 0AI  H8C2  C8   H8C1  107.33  3.000
 0AI  H8C3  C8   C7    113.68  3.000
 0AI  H8C2  C8   C7    109.41  3.000
 0AI  H8C1  C8   C7    109.30  3.000
 0AI  H3    C3   C4    108.12  3.000
 0AI  H3    C3   O3    110.89  3.000
 0AI  C4    C3   O3    110.55  3.000
 0AI  H3    C3   C2    109.36  3.000
 0AI  O3    C3   C2    107.86  3.000
 0AI  C4    C3   C2    110.06  3.000
 0AI  HB    O3   C3    108.57  3.000
 0AI  H4    C4   O4    111.46  3.000
 0AI  H4    C4   C3    108.17  3.000
 0AI  O4    C4   C3    111.49  3.000
 0AI  H4    C4   C5    108.32  3.000
 0AI  O4    C4   C5    107.58  3.000
 0AI  C3    C4   C5    109.77  3.000
 0AI  HC    O4   C4    107.67  3.000
 0AI  H15   O71  C6    110.31  3.000
 0AI  CM    O1   C1    114.67  3.000
 0AI  HMC3  CM   HMC2  108.47  3.000
 0AI  HMC3  CM   HMC1  108.63  3.000
 0AI  HMC2  CM   HMC1  108.55  3.000
 0AI  HMC3  CM   O1    111.44  3.000
 0AI  HMC2  CM   O1    112.30  3.000
 0AI  HMC1  CM   O1    107.35  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
 0AI  CONST_01  C8    C7   N2  C2  180.00   0.0  0
 0AI  CONST_02  O7    C7   N2  C2    0.00   0.0  0
 0AI  CONST_03  H15   O71  C6  C5  180.00   0.0  0
 0AI  CONST_04  HA    N2   C7  O7  180.00   0.0  0
 0AI  Var_01    HMC1  CM   O1  C1  169.86  30.0  3
 0AI  Var_02    H8C1  C8   C7  N2  117.19  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
 0AI  chir_01  C1  C2  O1  O5  negativ
 0AI  chir_02  C5  O5  C6  C4  positiv
 0AI  chir_03  C2  N2  C1  C3  negativ
 0AI  chir_04  C3  O3  C2  C4  positiv
 0AI  chir_05  C4  O4  C3  C5  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
 0AI  plan-1  C2   0.020
 0AI  plan-1  N2   0.020
 0AI  plan-1  C7   0.020
 0AI  plan-1  O7   0.020
 0AI  plan-1  C8   0.020
 0AI  plan-1  HA   0.020
 0AI  plan-2  O6   0.020
 0AI  plan-2  C6   0.020
 0AI  plan-2  C5   0.020
 0AI  plan-2  O71  0.020
 0AI  plan-2  H15  0.020

