# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:34:16 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-O-[(1R)-1-carboxyethyl]-2-[carboxy(methyl)amino]-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O)[C@@H]1N(C)C(O)=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
 MDP  MDP  3-O-[(1R)-1-carboxyethyl]-2-[carboxy(methyl)amino]-2-deoxy-alpha-D-glucopyranose  D-saccharide  38  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_MDP
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
 MDP  C1    C  CH1    0   0.304  38.7919  51.5492  49.4921
 MDP  O1    O  OH1    0  -0.652  39.7542  52.3055  48.8554
 MDP  C2    C  CH1    0  -0.140  37.4048  51.9967  49.0227
 MDP  N2    N  NT     0  -0.481  37.1467  53.3871  49.2762
 MDP  C3    C  CH1    0   0.042  36.3288  51.0727  49.6236
 MDP  O3    O  O2     0  -0.498  35.0772  51.3705  49.0661
 MDP  C4    C  CH1    0   0.029  36.6681  49.6133  49.3403
 MDP  O4    O  OH1    0  -0.667  35.7503  48.7921  50.0235
 MDP  C5    C  CH1    0  -0.009  38.1023  49.3254  49.8051
 MDP  O5    O  O2     0  -0.500  39.0003  50.1947  49.1538
 MDP  C6    C  CH2    0  -0.196  38.5511  47.8990  49.5676
 MDP  O6    O  OH1    0  -0.668  38.4210  47.5770  48.2030
 MDP  C7    C  CH1    0  -0.089  34.2086  52.1547  49.8609
 MDP  C8    C  C      0   0.373  33.2595  52.9875  48.9675
 MDP  O8    O  O      0  -0.620  32.4792  53.7295  49.6007
 MDP  O9    O  OC    -1  -0.596  33.3446  52.8654  47.7340
 MDP  C9    C  CH3    0  -0.662  33.4224  51.2822  50.8346
 MDP  C10   C  C      0   0.522  36.9916  54.3039  48.2138
 MDP  O10   O  O      0  -0.644  36.9046  55.5072  48.5408
 MDP  O11   O  OC    -1  -0.640  36.9433  53.8421  47.0533
 MDP  C11   C  CH3    0  -0.526  37.3040  53.8891  50.6179
 MDP  H1    H  HCH1   0   0.170  38.8710  51.6445  50.5907
 MDP  HO1   H  HOH1   0   0.456  40.5889  52.2198  49.3281
 MDP  H2    H  HCH1   0   0.245  37.3765  51.8702  47.9384
 MDP  H3    H  HCH1   0   0.197  36.3125  51.1943  50.7197
 MDP  H4    H  HCH1   0   0.211  36.6095  49.4564  48.2548
 MDP  HO4   H  HOH1   0   0.452  35.7073  47.9413  49.5782
 MDP  H5    H  HCH1   0   0.211  38.1428  49.4843  50.8970
 MDP  H61   H  HCH2   0   0.214  39.5886  47.8002  49.9137
 MDP  H62   H  HCH2   0   0.205  37.9483  47.2409  50.2047
 MDP  HO6   H  HOH1   0   0.456  38.6180  46.6428  48.0934
 MDP  H7    H  HCH1   0   0.214  34.7902  52.8759  50.4489
 MDP  H91   H  HCH3   0   0.215  32.7844  51.8979  51.4655
 MDP  H92   H  HCH3   0   0.209  32.7889  50.5679  50.3044
 MDP  H93   H  HCH3   0   0.216  34.0892  50.7158  51.4865
 MDP  H111  H  HCH3   0   0.206  38.2849  54.3431  50.8034
 MDP  H112  H  HCH3   0   0.225  36.5477  54.6369  50.8512
 MDP  H113  H  HCH3   0   0.216  37.1824  53.0824  51.3414

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
 MDP  C1   O1    single  1.380  0.020  1.380
 MDP  C1   C2    single  1.531  0.020  1.531
 MDP  C1   O5    single  1.412  0.020  1.412
 MDP  C1   H1    single  0.970  0.020  1.090
 MDP  O1   HO1   single  0.850  0.020  0.980
 MDP  C2   N2    single  1.437  0.020  1.437
 MDP  C2   C3    single  1.540  0.020  1.540
 MDP  C2   H2    single  0.970  0.020  1.090
 MDP  N2   C10   single  1.412  0.020  1.412
 MDP  N2   C11   single  1.441  0.020  1.441
 MDP  C3   O3    single  1.402  0.020  1.402
 MDP  C3   C4    single  1.525  0.020  1.525
 MDP  C3   H3    single  0.970  0.020  1.090
 MDP  O3   C7    single  1.415  0.020  1.415
 MDP  C4   O4    single  1.408  0.020  1.408
 MDP  C4   C5    single  1.535  0.020  1.535
 MDP  C4   H4    single  0.970  0.020  1.090
 MDP  O4   HO4   single  0.850  0.020  0.980
 MDP  C5   O5    single  1.409  0.020  1.409
 MDP  C5   C6    single  1.514  0.020  1.514
 MDP  C5   H5    single  0.970  0.020  1.090
 MDP  C6   O6    single  1.408  0.020  1.408
 MDP  C6   H61   single  0.970  0.020  1.090
 MDP  C6   H62   single  0.970  0.020  1.090
 MDP  O6   HO6   single  0.850  0.020  0.980
 MDP  C7   C8    single  1.547  0.020  1.547
 MDP  C7   C9    single  1.526  0.020  1.526
 MDP  C7   H7    single  0.970  0.020  1.090
 MDP  C8   O8    deloc   1.249  0.020  1.249
 MDP  C8   O9    deloc   1.242  0.020  1.242
 MDP  C9   H91   single  0.970  0.020  1.090
 MDP  C9   H92   single  0.970  0.020  1.090
 MDP  C9   H93   single  0.970  0.020  1.090
 MDP  C10  O10   deloc   1.250  0.020  1.250
 MDP  C10  O11   deloc   1.250  0.020  1.250
 MDP  C11  H111  single  0.970  0.020  1.090
 MDP  C11  H112  single  0.970  0.020  1.090
 MDP  C11  H113  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
 MDP  H1    C1   O5    108.08  3.000
 MDP  H1    C1   C2    110.14  3.000
 MDP  O5    C1   C2    109.92  3.000
 MDP  H1    C1   O1    111.19  3.000
 MDP  O5    C1   O1    108.20  3.000
 MDP  C2    C1   O1    109.28  3.000
 MDP  HO1   O1   C1    109.23  3.000
 MDP  H2    C2   C3    107.45  3.000
 MDP  H2    C2   N2    106.42  3.000
 MDP  C3    C2   N2    112.72  3.000
 MDP  H2    C2   C1    107.10  3.000
 MDP  C3    C2   C1    109.75  3.000
 MDP  N2    C2   C1    113.04  3.000
 MDP  C11   N2   C10   119.10  3.000
 MDP  C11   N2   C2    118.80  3.000
 MDP  C10   N2   C2    121.02  3.000
 MDP  H3    C3   C4    107.07  3.000
 MDP  H3    C3   O3    111.01  3.000
 MDP  C4    C3   O3    109.15  3.000
 MDP  H3    C3   C2    109.38  3.000
 MDP  C4    C3   C2    110.25  3.000
 MDP  O3    C3   C2    109.94  3.000
 MDP  C7    O3   C3    116.26  3.000
 MDP  H4    C4   C5    108.80  3.000
 MDP  H4    C4   O4    111.19  3.000
 MDP  C5    C4   O4    110.65  3.000
 MDP  H4    C4   C3    107.97  3.000
 MDP  C5    C4   C3    109.34  3.000
 MDP  O4    C4   C3    108.84  3.000
 MDP  HO4   O4   C4    108.69  3.000
 MDP  H5    C5   C6    106.25  3.000
 MDP  H5    C5   O5    110.17  3.000
 MDP  C6    C5   O5    108.65  3.000
 MDP  H5    C5   C4    107.86  3.000
 MDP  C6    C5   C4    113.97  3.000
 MDP  O5    C5   C4    109.86  3.000
 MDP  C5    O5   C1    112.77  3.000
 MDP  H62   C6   H61   106.40  3.000
 MDP  H62   C6   O6    112.03  3.000
 MDP  H61   C6   O6    111.85  3.000
 MDP  H62   C6   C5    108.14  3.000
 MDP  H61   C6   C5    108.38  3.000
 MDP  O6    C6   C5    109.88  3.000
 MDP  HO6   O6   C6    108.30  3.000
 MDP  H7    C7   C9    107.88  3.000
 MDP  H7    C7   C8    106.31  3.000
 MDP  C9    C7   C8    111.12  3.000
 MDP  H7    C7   O3    109.87  3.000
 MDP  C9    C7   O3    110.98  3.000
 MDP  C8    C7   O3    110.53  3.000
 MDP  O9    C8   O8    127.18  3.000
 MDP  O9    C8   C7    118.59  3.000
 MDP  O8    C8   C7    114.23  3.000
 MDP  H93   C9   H92   107.75  3.000
 MDP  H93   C9   H91   107.80  3.000
 MDP  H92   C9   H91   108.14  3.000
 MDP  H93   C9   C7    111.31  3.000
 MDP  H92   C9   C7    111.29  3.000
 MDP  H91   C9   C7    110.41  3.000
 MDP  O11   C10  O10   126.57  3.000
 MDP  O11   C10  N2    117.58  3.000
 MDP  O10   C10  N2    115.84  3.000
 MDP  H113  C11  H112  106.77  3.000
 MDP  H113  C11  H111  107.08  3.000
 MDP  H112  C11  H111  107.50  3.000
 MDP  H113  C11  N2    110.36  3.000
 MDP  H112  C11  N2    111.28  3.000
 MDP  H111  C11  N2    113.53  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
 MDP  Var_01  O10   C10  N2  C2  -173.09  30.0  2
 MDP  Var_02  H111  C11  N2  C2    95.53  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
 MDP  chir_01  C1  O1  C2  O5  negativ
 MDP  chir_02  C2  N2  C3  C1  positiv
 MDP  chir_03  C3  O3  C4  C2  negativ
 MDP  chir_04  C4  O4  C5  C3  positiv
 MDP  chir_05  C5  O5  C4  C6  negativ
 MDP  chir_06  C7  O3  C9  C8  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
 MDP  plan-1  C7   0.020
 MDP  plan-1  C8   0.020
 MDP  plan-1  O8   0.020
 MDP  plan-1  O9   0.020
 MDP  plan-2  N2   0.020
 MDP  plan-2  C10  0.020
 MDP  plan-2  O10  0.020
 MDP  plan-2  O11  0.020

