# 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 14:59:46 2012
#
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S,5S)-2-amino-5-{[(2R,3S,4R,5R)-3-fluoro-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]oxy}-5-hydroxypentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC[C@@H](O)O[C@H]1O[C@H](CO)[C@@H](O)[C@]1(O)F)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
AR4        AR4 '(2S,5S)-2-amino-5-{[(2R,3S,4R,5R)-3-fluoro-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]oxy}-5-hydroxypentanoic acid (non-preferred name)' L-peptide 38 20 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_AR4
#
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
AR4         N      N   NH2   .         -2.8404   -6.7280   -4.6510
AR4         CA     C   CH1   .         -2.2524   -6.3606   -3.3855
AR4         CB     C   CH2   .         -2.3001   -4.8423   -3.1385
AR4         CG     C   CH2   .         -1.1130   -4.3953   -2.3174
AR4         CD     C   CH1   .         -1.2224   -2.9113   -1.9699
AR4         OE1    O   OH1   .         -0.4603   -2.6796   -0.8138
AR4         OE2    O   O2    .         -0.5565   -2.1637   -2.9924
AR4         C      C   C     .         -2.9199   -7.0513   -2.1972
AR4         OXT    O   OH1   .         -2.0576   -7.6125   -1.3093
AR4        C5'     C   CH2   .         -0.3247    2.0788   -1.5361
AR4        C4'     C   CR15  .          0.1469    0.7343   -2.0881
AR4        O4'     O   O     .         -0.9847   -0.1591   -2.0596
AR4        C1'     C   CR15  .         -1.1011   -0.8950   -3.2637
AR4        C2'     C   CR5   .         -0.1922   -0.2183   -4.3430
AR4        F2'     F   F     .         -0.9244    0.3292   -5.3660
AR4        C3'     C   CR15  .          0.6360    0.8423   -3.5401
AR4        O3'     O   OH1   .          2.0068    0.5125   -3.5579
AR4         O      O   O     .         -4.1262   -7.1572   -1.9543
AR4        O2'     O   OH1   .          0.6533   -1.0955   -5.0388
AR4        H       H   HNH2  .         -3.7822   -6.3967   -4.7233
AR4        H2      H   HNH2  .         -2.8252   -7.7210   -4.7761
AR4        HA      H   HCH1  .         -1.1697   -6.6907   -3.4018
AR4        HB2     H   HCH2  .         -3.2585   -4.5798   -2.6197
AR4        HB3     H   HCH2  .         -2.2876   -4.3063   -4.1253
AR4        HG2     H   HCH2  .         -1.0477   -4.9751   -1.3579
AR4        HG3     H   HCH2  .         -0.1601   -4.5658   -2.8827
AR4        HD      H   HCH1  .         -2.2863   -2.5674   -1.8450
AR4        HE1     H   HOH1  .         -0.6520   -1.7838   -0.5039
AR4        HO      H   HOH1  .         -2.5536   -8.0304   -0.5853
AR4        H5'     H   HOH1  .         -1.4862    1.3283   -0.1897
AR4        H5'2    H   HCH2  .          0.5386    2.7964   -1.5044
AR4        H4'     H   HCR5  .          0.9388    0.2851   -1.4273
AR4        H1'     H   HCR5  .         -2.1863   -0.9332   -3.5424
AR4        H3'     H   HCR5  .          0.4730    1.8667   -3.9677
AR4        H3'1    H   HOH1  .          2.2450    0.3382   -4.4808
AR4        HO2'    H   HOH1  .          0.9642   -1.7741   -4.4210
AR4        H5'1    H   HCH2  .         -1.1490    2.4925   -2.1750
AR4        O5'     O   OH1   .         -0.7534    1.9577   -0.1983
#
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
AR4   N       CA    single        1.443 0.020
AR4   N      H      single        1.001 0.020
AR4   N      H2     single        1.001 0.020
AR4   CA      CB    single        1.539 0.020
AR4   CA      C     single        1.528 0.020
AR4   CA     HA     single        1.132 0.020
AR4   CB      CG    single        1.511 0.020
AR4   CB     HB2    single        1.121 0.020
AR4   CB     HB3    single        1.123 0.020
AR4   CG      CD    single        1.528 0.020
AR4   CG     HG2    single        1.123 0.020
AR4   CG     HG3    single        1.121 0.020
AR4   CD      OE1   single        1.404 0.020
AR4   CD      OE2   single        1.431 0.020
AR4   CD     HD     single        1.125 0.020
AR4   OE1    HE1    single        0.967 0.020
AR4   OE2    C1'    single        1.407 0.020
AR4   C       OXT   single        1.359 0.020
AR4   C       O     double        1.235 0.020
AR4   OXT    HO     single        0.972 0.020
AR4  O5'     C5'    single        1.410 0.020
AR4  O5'     H5'    single        0.966 0.020
AR4  C5'     C4'    single        1.528 0.020
AR4  C5'     H5'1   single        1.122 0.020
AR4  C5'     H5'2   single        1.123 0.020
AR4  C4'     O4'    single        1.442 0.020
AR4  C4'     C3'    single        1.536 0.020
AR4  C4'     H4'    single        1.125 0.020
AR4  O4'     C1'    single        1.416 0.020
AR4  C1'     C2'    single        1.565 0.020
AR4  C1'     H1'    single        1.121 0.020
AR4  C2'     F2'    single        1.372 0.020
AR4  C2'     C3'    single        1.567 0.020
AR4  C2'     O2'    single        1.403 0.020
AR4  C3'     O3'    single        1.410 0.020
AR4  C3'     H3'    single        1.122 0.020
AR4  O3'     H3'1   single        0.969 0.020
AR4  O2'     HO2'   single        0.969 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
AR4  H2       N      H            109.49 3.000
AR4  H2       N       CA          110.85 3.000
AR4  H        N       CA          111.25 3.000
AR4  HA       CA      C           107.29 3.000
AR4  HA       CA      CB          108.64 3.000
AR4   C       CA      CB          107.92 3.000
AR4  HA       CA      N           107.63 3.000
AR4   C       CA      N           112.89 3.000
AR4   CB      CA      N           112.29 3.000
AR4  HB3      CB     HB2          107.72 3.000
AR4  HB3      CB      CG          109.12 3.000
AR4  HB2      CB      CG          110.54 3.000
AR4  HB3      CB      CA          109.24 3.000
AR4  HB2      CB      CA          109.38 3.000
AR4   CG      CB      CA          110.78 3.000
AR4  HG3      CG     HG2          107.63 3.000
AR4  HG3      CG      CD          108.86 3.000
AR4  HG2      CG      CD          108.14 3.000
AR4  HG3      CG      CB          110.41 3.000
AR4  HG2      CG      CB          110.93 3.000
AR4   CD      CG      CB          110.77 3.000
AR4  HD       CD      OE2         111.08 3.000
AR4  HD       CD      OE1         111.80 3.000
AR4   OE2     CD      OE1         104.45 3.000
AR4  HD       CD      CG          112.94 3.000
AR4   OE2     CD      CG          108.16 3.000
AR4   OE1     CD      CG          107.98 3.000
AR4  HE1      OE1     CD          108.01 3.000
AR4  C1'      OE2     CD          115.39 3.000
AR4   O       C       OXT         117.12 3.000
AR4   O       C       CA          128.20 3.000
AR4   OXT     C       CA          114.68 3.000
AR4  HO       OXT     C           109.90 3.000
AR4  H5'2    C5'     H5'1         110.20 3.000
AR4  H5'2    C5'     C4'          109.58 3.000
AR4  H5'1    C5'     C4'          110.21 3.000
AR4  H5'2    C5'     O5'          105.18 3.000
AR4  H5'1    C5'     O5'          110.40 3.000
AR4  C4'     C5'     O5'          111.16 3.000
AR4  H4'     C4'     C3'          111.05 3.000
AR4  H4'     C4'     O4'          107.06 3.000
AR4  C3'     C4'     O4'          108.19 3.000
AR4  H4'     C4'     C5'          110.88 3.000
AR4  C3'     C4'     C5'          112.21 3.000
AR4  O4'     C4'     C5'          107.21 3.000
AR4  C1'     O4'     C4'          111.70 3.000
AR4  H1'     C1'     C2'          113.92 3.000
AR4  H1'     C1'     O4'          107.98 3.000
AR4  C2'     C1'     O4'          108.30 3.000
AR4  H1'     C1'      OE2         113.07 3.000
AR4  C2'     C1'      OE2         107.34 3.000
AR4  O4'     C1'      OE2         105.83 3.000
AR4  O2'     C2'     C3'          111.02 3.000
AR4  O2'     C2'     F2'          101.61 3.000
AR4  C3'     C2'     F2'          113.20 3.000
AR4  O2'     C2'     C1'          114.94 3.000
AR4  C3'     C2'     C1'          104.26 3.000
AR4  F2'     C2'     C1'          112.13 3.000
AR4  H3'     C3'     O3'          110.49 3.000
AR4  H3'     C3'     C2'          110.24 3.000
AR4  O3'     C3'     C2'          110.43 3.000
AR4  H3'     C3'     C4'          112.22 3.000
AR4  O3'     C3'     C4'          107.76 3.000
AR4  C2'     C3'     C4'          105.57 3.000
AR4  H3'1    O3'     C3'          107.04 3.000
AR4  HO2'    O2'     C2'          108.36 3.000
AR4  H5'     O5'     C5'          107.16 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
AR4 CONST_01       HO      OXT     C       CA         -180.00   0.0 0
AR4 Var_01         CD      CG      CB      CA         -175.11  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
AR4 chir_01   CA      N       CB      C     negativ
AR4 chir_02   CD      OE1     OE2     CG    negativ
AR4 chir_03  C4'     O4'     C5'     C3'    positiv
AR4 chir_04  C1'      OE2    O4'     C2'    negativ
AR4 chir_05  C2'     O2'     C3'     C1'    positiv
AR4 chir_06  C3'     O3'     C2'     C4'    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
AR4 plan-1     CA 0.020
AR4 plan-1      C 0.020
AR4 plan-1    OXT 0.020
AR4 plan-1      O 0.020
AR4 plan-1     HO 0.020
