# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 09:38:38 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: (2S,3R)-3-{[(2S,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-2-aminobutanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1NC(C)=O)[C@H](N)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
 TNY  TNY  '(2S,3R)-3-{[(2S,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-2-aminobutanoic acid (non-preferred name)'  L-peptide  43  22  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TNY
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
 TNY  C     C  C      0   0.414  -2.1717   2.3256   9.7811
 TNY  N     N  NH2    0  -0.788  -0.2044   0.7182   9.9104
 TNY  O     O  O      0  -0.599  -1.3426   3.2014   9.4423
 TNY  C1    C  CH1    0   0.287  -1.9473   2.5111  13.3864
 TNY  C2    C  CH1    0  -0.143  -1.3582   3.9183  13.5455
 TNY  N2    N  NH1    0  -0.648  -1.4329   4.6273  12.2942
 TNY  C3    C  CH1    0   0.055   0.0640   3.8189  14.0974
 TNY  O3    O  OH1    0  -0.660   0.5700   5.1174  14.2589
 TNY  C4    C  CH1    0  -0.019   0.0502   3.0200  15.4058
 TNY  O4    O  OH1    0  -0.673  -0.6388   3.7668  16.3796
 TNY  C5    C  CH1    0  -0.004  -0.6030   1.6597  15.1492
 TNY  O5    O  O2     0  -0.503  -1.8998   1.8123  14.5960
 TNY  C6    C  CH2    0  -0.200  -0.7995   0.8228  16.4030
 TNY  O6    O  OH1    0  -0.668   0.4496   0.6787  17.0361
 TNY  C7    C  C      0   0.508  -1.9209   5.8766  12.1750
 TNY  O7    O  O      0  -0.503  -2.3307   6.5381  13.1200
 TNY  C8    C  CH3    0  -0.791  -1.9152   6.4262  10.7685
 TNY  CA    C  CH1    0  -0.230  -1.6063   0.9472  10.2148
 TNY  CB    C  CH1    0   0.056  -1.8806   0.7789  11.7125
 TNY  OG1   O  O2     0  -0.518  -1.2483   1.8748  12.3726
 TNY  CG2   C  CH3    0  -0.666  -1.3913  -0.5447  12.2708
 TNY  OXT   O  OC    -1  -0.595  -3.4088   2.4516   9.8348
 TNY  H     H  HNH2   0   0.337  -0.1008   0.6386   8.9065
 TNY  H2    H  HNH2   0   0.327   0.3101   1.5571  10.1510
 TNY  H1    H  HCH1   0   0.237  -3.0134   2.5876  13.1359
 TNY  H9    H  HCH1   0   0.265  -1.9806   4.4559  14.2628
 TNY  HN2   H  HNH1   0   0.405  -1.1522   4.1396  11.4511
 TNY  H3    H  HCH1   0   0.214   0.6767   3.2512  13.3825
 TNY  HO3   H  HOH1   0   0.449   1.5064   5.0528  14.4723
 TNY  H4    H  HCH1   0   0.234   1.0927   2.8449  15.7057
 TNY  HO4   H  HOH1   0   0.454  -0.3830   3.4472  17.2497
 TNY  H5    H  HCH1   0   0.225   0.0462   1.1022  14.4605
 TNY  H6    H  HCH2   0   0.200  -1.5365   1.3089  17.0549
 TNY  H6A   H  HCH2   0   0.219  -1.2224  -0.1468  16.1102
 TNY  HO6   H  HOH1   0   0.459   0.3228   0.1741  17.8440
 TNY  H8    H  HCH3   0   0.253  -2.8497   6.9513  10.5769
 TNY  H8A   H  HCH3   0   0.259  -1.1081   7.1544  10.6701
 TNY  H8B   H  HCH3   0   0.248  -1.7768   5.6573  10.0109
 TNY  HA    H  HCH1   0   0.222  -2.1885   0.1686   9.7104
 TNY  HB    H  HCH1   0   0.211  -2.9652   0.8494  11.8561
 TNY  HG21  H  HCH3   0   0.228  -1.6813  -0.6630  13.3151
 TNY  HG22  H  HCH3   0   0.220  -1.8288  -1.3721  11.7097
 TNY  HG23  H  HCH3   0   0.223  -0.3080  -0.6290  12.1987

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
 TNY  C    O     deloc   1.231  0.020  1.231
 TNY  C    CA    single  1.525  0.021  1.525
 TNY  C    OXT   deloc   1.245  0.020  1.245
 TNY  N    CA    single  1.458  0.019  1.458
 TNY  N    H     single  0.860  0.020  0.860
 TNY  N    H2    single  0.890  0.020  1.040
 TNY  C1   C2    single  1.534  0.020  1.534
 TNY  C1   O5    single  1.398  0.020  1.398
 TNY  C1   OG1   single  1.386  0.020  1.386
 TNY  C1   H1    single  0.970  0.020  1.090
 TNY  C2   N2    single  1.440  0.020  1.440
 TNY  C2   C3    single  1.529  0.020  1.529
 TNY  C2   H9    single  0.970  0.020  1.090
 TNY  N2   C7    single  1.346  0.020  1.346
 TNY  N2   HN2   single  0.860  0.020  1.020
 TNY  C3   O3    single  1.403  0.020  1.403
 TNY  C3   C4    single  1.533  0.020  1.533
 TNY  C3   H3    single  0.970  0.020  1.090
 TNY  O3   HO3   single  0.850  0.020  0.980
 TNY  C4   O4    single  1.407  0.020  1.407
 TNY  C4   C5    single  1.531  0.020  1.531
 TNY  C4   H4    single  0.970  0.020  1.090
 TNY  O4   HO4   single  0.850  0.020  0.980
 TNY  C5   O5    single  1.418  0.020  1.418
 TNY  C5   C6    single  1.520  0.020  1.520
 TNY  C5   H5    single  0.970  0.020  1.090
 TNY  C6   O6    single  1.408  0.020  1.408
 TNY  C6   H6    single  0.970  0.020  1.090
 TNY  C6   H6A   single  0.970  0.020  1.090
 TNY  O6   HO6   single  0.850  0.020  0.980
 TNY  C7   O7    double  1.224  0.020  1.224
 TNY  C7   C8    single  1.510  0.020  1.510
 TNY  C8   H8    single  0.970  0.020  1.090
 TNY  C8   H8A   single  0.970  0.020  1.090
 TNY  C8   H8B   single  0.970  0.020  1.090
 TNY  CA   CB    single  1.540  0.027  1.540
 TNY  CA   HA    single  0.970  0.020  0.970
 TNY  CB   OG1   single  1.427  0.020  1.427
 TNY  CB   CG2   single  1.518  0.020  1.518
 TNY  CB   HB    single  0.970  0.020  1.090
 TNY  CG2  HG21  single  0.970  0.020  1.090
 TNY  CG2  HG22  single  0.970  0.020  1.090
 TNY  CG2  HG23  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
 TNY  OXT   C    CA    116.11  3.000
 TNY  OXT   C    O     126.78  3.000
 TNY  CA    C    O     120.80  1.700
 TNY  H2    N    H     104.40  3.000
 TNY  H2    N    CA    108.05  3.000
 TNY  H     N    CA    114.00  3.000
 TNY  H1    C1   OG1   110.78  3.000
 TNY  H1    C1   O5    105.38  3.000
 TNY  OG1   C1   O5    112.72  3.000
 TNY  H1    C1   C2    109.44  3.000
 TNY  OG1   C1   C2    107.66  3.000
 TNY  O5    C1   C2    110.85  3.000
 TNY  H9    C2   C3    108.99  3.000
 TNY  H9    C2   N2    107.39  3.000
 TNY  C3    C2   N2    113.21  3.000
 TNY  H9    C2   C1    107.52  3.000
 TNY  C3    C2   C1    109.58  3.000
 TNY  N2    C2   C1    109.97  3.000
 TNY  HN2   N2   C7    118.24  3.000
 TNY  HN2   N2   C2    118.13  3.000
 TNY  C7    N2   C2    123.54  3.000
 TNY  H3    C3   C4    106.91  3.000
 TNY  H3    C3   O3    110.59  3.000
 TNY  C4    C3   O3    112.79  3.000
 TNY  H3    C3   C2    108.50  3.000
 TNY  C4    C3   C2    109.49  3.000
 TNY  O3    C3   C2    108.47  3.000
 TNY  HO3   O3   C3    108.32  3.000
 TNY  H4    C4   C5    108.00  3.000
 TNY  H4    C4   O4    111.11  3.000
 TNY  C5    C4   O4    112.25  3.000
 TNY  H4    C4   C3    107.90  3.000
 TNY  C5    C4   C3    108.90  3.000
 TNY  O4    C4   C3    108.57  3.000
 TNY  HO4   O4   C4    108.63  3.000
 TNY  H5    C5   C6    108.30  3.000
 TNY  H5    C5   O5    110.52  3.000
 TNY  C6    C5   O5    105.23  3.000
 TNY  H5    C5   C4    107.69  3.000
 TNY  C6    C5   C4    113.96  3.000
 TNY  O5    C5   C4    111.10  3.000
 TNY  C5    O5   C1    114.99  3.000
 TNY  H6A   C6   H6    106.92  3.000
 TNY  H6A   C6   O6    111.81  3.000
 TNY  H6    C6   O6    111.97  3.000
 TNY  H6A   C6   C5    108.42  3.000
 TNY  H6    C6   C5    109.44  3.000
 TNY  O6    C6   C5    108.21  3.000
 TNY  HO6   O6   C6    108.34  3.000
 TNY  C8    C7   O7    121.57  3.000
 TNY  C8    C7   N2    114.76  3.000
 TNY  O7    C7   N2    123.66  3.000
 TNY  H8B   C8   H8A   108.33  3.000
 TNY  H8B   C8   H8    109.11  3.000
 TNY  H8A   C8   H8    107.28  3.000
 TNY  H8B   C8   C7    113.06  3.000
 TNY  H8A   C8   C7    109.24  3.000
 TNY  H8    C8   C7    109.64  3.000
 TNY  HA    CA   CB    109.00  3.000
 TNY  HA    CA   N     110.00  3.000
 TNY  CB    CA   N     111.50  1.700
 TNY  HA    CA   C     109.00  3.000
 TNY  CB    CA   C     109.10  2.200
 TNY  N     CA   C     111.00  2.800
 TNY  HB    CB   CG2   109.08  3.000
 TNY  HB    CB   OG1   109.17  3.000
 TNY  CG2   CB   OG1   110.90  3.000
 TNY  HB    CB   CA    107.35  3.000
 TNY  CG2   CB   CA    113.44  3.000
 TNY  OG1   CB   CA    106.77  3.000
 TNY  CB    OG1  C1    117.87  3.000
 TNY  HG23  CG2  HG22  107.82  3.000
 TNY  HG23  CG2  HG21  108.64  3.000
 TNY  HG22  CG2  HG21  107.67  3.000
 TNY  HG23  CG2  CB    111.34  3.000
 TNY  HG22  CG2  CB    110.05  3.000
 TNY  HG21  CG2  CB    111.18  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
 TNY  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 TNY  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 TNY  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 TNY  Var_01    H8   C8  C7  N2  137.76  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
 TNY  chir_01  C1  C2   O5  OG1  positiv
 TNY  chir_02  C2  N2   C3  C1   positiv
 TNY  chir_03  C3  O3   C2  C4   positiv
 TNY  chir_04  C4  O4   C5  C3   negativ
 TNY  chir_05  C5  O5   C4  C6   negativ
 TNY  chir_06  CA  N    C   CB   positiv
 TNY  chir_07  CB  OG1  CA  CG2  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
 TNY  plan-1  C2   0.020
 TNY  plan-1  N2   0.020
 TNY  plan-1  C7   0.020
 TNY  plan-1  O7   0.020
 TNY  plan-1  C8   0.020
 TNY  plan-1  HN2  0.020
 TNY  plan-2  C    0.020
 TNY  plan-2  O    0.020
 TNY  plan-2  CA   0.020
 TNY  plan-2  OXT  0.020

