# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-1137 (Mon Aug 22 05:16:00 2012)
#   - file written: Tue Aug 28 15:29:48 2012
#
#   Inital geometry file: a 95 line input string
#   Ligand name: (2S)-3-{[(2S,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-2-aminopropanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1OC[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
TNR        TNR '(2S)-3-{[(2S,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-2-aminopropanoic acid (non-preferred name)' L-peptide 41 21 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_TNR
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
TNR         OXT    O   OH1   .          0.3099    0.1955    4.8719
TNR         C      C   C     .          1.3495   -0.1008    4.0482
TNR         O      O   O     .          2.2146   -0.8697    4.4704
TNR         CA     C   CH1   .          1.2682    0.5896    2.6976
TNR         N      N   NH2   .          2.5101    1.2648    2.3978
TNR         CB     C   CH2   .          0.8212   -0.4901    1.6854
TNR         O1     O   O2    .          0.3026    0.2212    0.5596
TNR         C1     C   CH1   .         -0.2019   -0.6262   -0.4542
TNR         C2     C   CH1   .         -0.0027    0.0617   -1.8373
TNR         N2     N   NH1   .          1.3727    0.3437   -2.1420
TNR         C7     C   C     .          2.2491   -0.6308   -2.5832
TNR         C8     C   CH3   .          3.6677   -0.2066   -2.8689
TNR         O7     O   O     .          1.8705   -1.8104   -2.7351
TNR         C3     C   CH1   .         -0.8955    1.3264   -1.9189
TNR         O3     O   OH1   .         -0.8031    1.9266   -3.1916
TNR         C4     C   CH1   .         -2.3574    0.9648   -1.5853
TNR         O4     O   OH1   .         -2.9109    0.1590   -2.6112
TNR         C5     C   CH1   .         -2.4073    0.3173   -0.1987
TNR         O5     O   O2    .         -1.5712   -0.8476   -0.1634
TNR         C6     C   CH2   .         -3.8138   -0.1685    0.1645
TNR         O6     O   OH1   .         -3.8784   -0.5725    1.5138
TNR        HB      H   HOH1  .          0.4172   -0.2735    5.7165
TNR        HCA     H   HCH1  .          0.4595    1.3804    2.7427
TNR        H       H   HNH2  .          3.2769    0.6199    2.3901
TNR        H2      H   HNH2  .          2.4376    1.7137    1.5049
TNR        HB2     H   HCH2  .          0.0143   -1.1287    2.1300
TNR        HB3     H   HCH2  .          1.6837   -1.1297    1.3636
TNR        HC1     H   HCH1  .          0.2675   -1.6518   -0.4400
TNR        HC2     H   HCH1  .         -0.3832   -0.6939   -2.5940
TNR        HN2     H   HNH1  .          1.6809    1.2792   -2.0237
TNR        HC81    H   HCH3  .          4.2481   -1.1015   -3.2005
TNR        HC82    H   HCH3  .          3.6889    0.5617   -3.6795
TNR        HC83    H   HCH3  .          4.1441    0.2169   -1.9517
TNR        HC3     H   HCH1  .         -0.5250    2.1080   -1.1980
TNR        HO3     H   HOH1  .         -1.2982    1.3700   -3.8098
TNR        HC4     H   HCH1  .         -2.9818    1.9017   -1.6026
TNR        HO4     H   HOH1  .         -2.7100   -0.7657   -2.4111
TNR        HC5     H   HCH1  .         -2.0432    1.0520    0.5713
TNR        HC61    H   HCH2  .         -4.5408    0.6812    0.0732
TNR        HC62    H   HCH2  .         -4.1146   -1.0079   -0.5166
TNR        HO6     H   HOH1  .         -3.2828   -1.3265    1.6137
#
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
TNR   OXT     C     single        1.359 0.020
TNR   OXT    HB     single        0.972 0.020
TNR   C       O     double        1.232 0.020
TNR   C       CA    single        1.519 0.020
TNR   CA      N     single        1.445 0.020
TNR   CA      CB    single        1.546 0.020
TNR   CA     HCA    single        1.132 0.020
TNR   N      H      single        1.002 0.020
TNR   N      H2     single        1.002 0.020
TNR   CB      O1    single        1.429 0.020
TNR   CB     HB2    single        1.121 0.020
TNR   CB     HB3    single        1.121 0.020
TNR   O1      C1    single        1.414 0.020
TNR   C1      C2    single        1.558 0.020
TNR   C1      O5    single        1.417 0.020
TNR   C1     HC1    single        1.128 0.020
TNR   C2      N2    single        1.437 0.020
TNR   C2      C3    single        1.550 0.020
TNR   C2     HC2    single        1.135 0.020
TNR   N2      C7    single        1.383 0.020
TNR   N2     HN2    single        0.992 0.020
TNR   C7      C8    single        1.508 0.020
TNR   C7      O7    double        1.248 0.020
TNR   C8     HC81   single        1.117 0.020
TNR   C8     HC82   single        1.117 0.020
TNR   C8     HC83   single        1.117 0.020
TNR   C3      O3    single        1.410 0.020
TNR   C3      C4    single        1.542 0.020
TNR   C3     HC3    single        1.126 0.020
TNR   O3     HO3    single        0.968 0.020
TNR   C4      O4    single        1.417 0.020
TNR   C4      C5    single        1.531 0.020
TNR   C4     HC4    single        1.126 0.020
TNR   O4     HO4    single        0.967 0.020
TNR   C5      O5    single        1.434 0.020
TNR   C5      C6    single        1.532 0.020
TNR   C5     HC5    single        1.125 0.020
TNR   C6      O6    single        1.410 0.020
TNR   C6     HC61   single        1.122 0.020
TNR   C6     HC62   single        1.122 0.020
TNR   O6     HO6    single        0.966 0.020
#
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
TNR  HB       OXT     C           109.70 3.000
TNR   CA      C       O           128.75 3.000
TNR   CA      C       OXT         113.50 3.000
TNR   O       C       OXT         117.74 3.000
TNR  HCA      CA      CB          107.90 3.000
TNR  HCA      CA      N           107.21 3.000
TNR   CB      CA      N           116.04 3.000
TNR  HCA      CA      C           108.69 3.000
TNR   CB      CA      C           106.27 3.000
TNR   N       CA      C           110.54 3.000
TNR  H2       N      H            109.69 3.000
TNR  H2       N       CA          109.40 3.000
TNR  H        N       CA          111.02 3.000
TNR  HB3      CB     HB2          110.04 3.000
TNR  HB3      CB      O1          109.70 3.000
TNR  HB2      CB      O1          109.56 3.000
TNR  HB3      CB      CA          111.34 3.000
TNR  HB2      CB      CA          110.26 3.000
TNR   O1      CB      CA          105.85 3.000
TNR   C1      O1      CB          113.32 3.000
TNR  HC1      C1      O5          104.92 3.000
TNR  HC1      C1      C2          111.07 3.000
TNR   O5      C1      C2          112.01 3.000
TNR  HC1      C1      O1          112.78 3.000
TNR   O5      C1      O1          106.93 3.000
TNR   C2      C1      O1          109.04 3.000
TNR  HC2      C2      C3          108.35 3.000
TNR  HC2      C2      N2          108.08 3.000
TNR   C3      C2      N2          112.33 3.000
TNR  HC2      C2      C1          104.78 3.000
TNR   C3      C2      C1          109.47 3.000
TNR   N2      C2      C1          113.42 3.000
TNR  HN2      N2      C7          120.38 3.000
TNR  HN2      N2      C2          117.21 3.000
TNR   C7      N2      C2          122.41 3.000
TNR   O7      C7      C8          121.88 3.000
TNR   O7      C7      N2          120.84 3.000
TNR   C8      C7      N2          117.28 3.000
TNR  HC83     C8     HC82         109.09 3.000
TNR  HC83     C8     HC81         109.02 3.000
TNR  HC82     C8     HC81         109.01 3.000
TNR  HC83     C8      C7          110.63 3.000
TNR  HC82     C8      C7          110.42 3.000
TNR  HC81     C8      C7          108.65 3.000
TNR  HC3      C3      C4          109.64 3.000
TNR  HC3      C3      O3          105.12 3.000
TNR   C4      C3      O3          110.92 3.000
TNR  HC3      C3      C2          110.06 3.000
TNR   C4      C3      C2          110.07 3.000
TNR   O3      C3      C2          110.91 3.000
TNR  HO3      O3      C3          107.35 3.000
TNR  HC4      C4      C5          110.35 3.000
TNR  HC4      C4      O4          104.21 3.000
TNR   C5      C4      O4          113.73 3.000
TNR  HC4      C4      C3          109.09 3.000
TNR   C5      C4      C3          109.02 3.000
TNR   O4      C4      C3          110.30 3.000
TNR  HO4      O4      C4          108.22 3.000
TNR  HC5      C5      C6          110.00 3.000
TNR  HC5      C5      O5          108.97 3.000
TNR   C6      C5      O5          105.77 3.000
TNR  HC5      C5      C4          109.46 3.000
TNR   C6      C5      C4          112.26 3.000
TNR   O5      C5      C4          110.29 3.000
TNR   C5      O5      C1          115.55 3.000
TNR  HC62     C6     HC61         110.09 3.000
TNR  HC62     C6      O6          110.75 3.000
TNR  HC61     C6      O6          105.38 3.000
TNR  HC62     C6      C5          109.84 3.000
TNR  HC61     C6      C5          109.60 3.000
TNR   O6      C6      C5          111.09 3.000
TNR  HO6      O6      C6          107.12 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
TNR CONST_01       C8      C7      N2      C2         -180.00   0.0 0
TNR CONST_02       O7      C7      N2      C2           -0.00   0.0 0
TNR CONST_03      HN2      N2      C7      C8            0.00   0.0 0
TNR CONST_04       HB      OXT     C       O            -0.00   0.0 0
TNR Var_01        HB2      CB      O1      C1          -58.95  30.0 2
TNR Var_02        HC81     C8      C7      N2          179.28  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
TNR chir_01   CA      C       N       CB    negativ
TNR chir_02   C1      O1      O5      C2    negativ
TNR chir_03   C2      N2      C3      C1    positiv
TNR chir_04   C3      O3      C2      C4    positiv
TNR chir_05   C4      O4      C5      C3    negativ
TNR chir_06   C5      O5      C4      C6    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
TNR plan-1     C2 0.020
TNR plan-1     N2 0.020
TNR plan-1     C7 0.020
TNR plan-1     C8 0.020
TNR plan-1     O7 0.020
TNR plan-1    HN2 0.020
TNR plan-2    OXT 0.020
TNR plan-2      C 0.020
TNR plan-2      O 0.020
TNR plan-2     CA 0.020
TNR plan-2     HB 0.020
