# 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 15:29:38 2012
#
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S)-2-amino-4-({[(2S,3S,4R,5R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC=Nc23)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
SIB        SIB '(2S)-2-amino-4-({[(2S,3S,4R,5R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)' L-peptide 45 26 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_SIB
#
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
SIB         N      N   NH2   .          6.3571   -0.1914    1.7868
SIB         CA     C   CH1   .          5.8090   -0.9560    0.6873
SIB         CB     C   CH2   .          4.7820   -0.2374   -0.2091
SIB         CG     C   CH2   .          3.4957    0.0215    0.5302
SIB         SD     S   S2    .          2.3122    0.5469   -0.6751
SIB         C      C   C     .          6.9248   -1.4346   -0.2288
SIB         OXT    O   OH1   .          6.7311   -2.6925   -0.7052
SIB         O      O   O     .          7.9465   -0.8418   -0.5789
SIB        C5'     C   CH2   .          1.1680    1.4531    0.3243
SIB        C4'     C   CH1   .          0.2353    2.2228   -0.5901
SIB        O4'     O   O2    .         -0.5782    1.3217   -1.3597
SIB        C3'     C   CH1   .         -0.7115    3.1565    0.1992
SIB        O3'     O   OH1   .         -0.6985    4.4629   -0.3149
SIB        C2'     C   CH1   .         -2.0950    2.4737    0.1340
SIB        O2'     O   OH1   .         -3.0324    3.4109   -0.3495
SIB        C1'     C   CH1   .         -1.9374    1.3272   -0.9187
SIB         N9     N   NR5   .         -2.3135    0.0205   -0.4198
SIB         C8     C   CR15  .         -1.4857   -1.0979   -0.1669
SIB         N7     N   N     .         -2.1681   -2.1639    0.2968
SIB         C5     C   CR56  .         -3.4969   -1.7468    0.3569
SIB         C6     C   CR6   .         -4.6927   -2.4619    0.7797
SIB         O6     O   O     .         -4.7817   -3.6275    1.1873
SIB         N1     N   NR16  .         -5.8778   -1.6771    0.6936
SIB         C2     C   CR16  .         -5.8626   -0.3668    0.2482
SIB         N3     N   N     .         -4.8090    0.3309   -0.1472
SIB         C4     C   CR56  .         -3.6112   -0.3799   -0.0881
SIB        H       H   HNH2  .          6.3851    0.7868    1.5715
SIB        H2      H   HNH2  .          5.8149   -0.3409    2.6149
SIB        HA      H   HCH1  .          5.3098   -1.8686    1.1364
SIB        HB2     H   HCH2  .          5.2143    0.7272   -0.5850
SIB        HB3     H   HCH2  .          4.5803   -0.8910   -1.1010
SIB        HG2     H   HCH2  .          3.1408   -0.9056    1.0443
SIB        HG3     H   HCH2  .          3.6272    0.8120    1.3083
SIB        HO      H   HOH1  .          7.4731   -2.9416   -1.2816
SIB        H5'1    H   HCH2  .          0.5849    0.7579    0.9773
SIB        H5'2    H   HCH2  .          1.7265    2.1624    0.9838
SIB        H4'     H   HCH1  .          0.8219    2.8044   -1.3582
SIB        H3'     H   HCH1  .         -0.3798    3.2710    1.2681
SIB        HO3'    H   HOH1  .         -1.2140    4.4736   -1.1330
SIB        H2'     H   HCH1  .         -2.3941    2.0931    1.1451
SIB        HO2'    H   HOH1  .         -3.8763    2.9462   -0.4338
SIB        H1'     H   HCH1  .         -2.5529    1.5455   -1.8445
SIB        H8      H   HCR5  .         -0.4025   -1.0516   -0.3465
SIB        HN1     H   HNR6  .         -6.7383   -2.0982    0.9662
SIB        HC2     H   HCR6  .         -6.8445    0.1543    0.2205
#
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
SIB   N       CA    single        1.447 0.020
SIB   N      H      single        1.002 0.020
SIB   N      H2     single        1.001 0.020
SIB   CA      CB    single        1.541 0.020
SIB   CA      C     single        1.521 0.020
SIB   CA     HA     single        1.133 0.020
SIB   CB      CG    single        1.506 0.020
SIB   CB     HB2    single        1.122 0.020
SIB   CB     HB3    single        1.124 0.020
SIB   CG      SD    single        1.769 0.020
SIB   CG     HG2    single        1.118 0.020
SIB   CG     HG3    single        1.117 0.020
SIB   SD     C5'    single        1.769 0.020
SIB   C       O     double        1.232 0.020
SIB   C       OXT   single        1.359 0.020
SIB   OXT    HO     single        0.972 0.020
SIB  C5'     C4'    single        1.516 0.020
SIB  C5'     H5'1   single        1.118 0.020
SIB  C5'     H5'2   single        1.118 0.020
SIB  C4'     O4'    single        1.437 0.020
SIB  C4'     C3'    single        1.546 0.020
SIB  C4'     H4'    single        1.128 0.020
SIB  O4'     C1'    single        1.429 0.020
SIB  C3'     C2'    single        1.544 0.020
SIB  C3'     O3'    single        1.404 0.020
SIB  C3'     H3'    single        1.125 0.020
SIB  O3'     HO3'   single        0.967 0.020
SIB  C2'     C1'    single        1.564 0.020
SIB  C2'     O2'    single        1.411 0.020
SIB  C2'     H2'    single        1.121 0.020
SIB  O2'     HO2'   single        0.967 0.020
SIB  C1'      N9    single        1.448 0.020
SIB  C1'     H1'    single        1.133 0.020
SIB   N9      C4    aromatic      1.398 0.020
SIB   N9      C8    aromatic      1.414 0.020
SIB   C8      N7    aromatic      1.348 0.020
SIB   C8     H8     single        1.099 0.020
SIB   N7      C5    aromatic      1.394 0.020
SIB   C5      C4    aromatic      1.442 0.020
SIB   C5      C6    single        1.456 0.020
SIB   C6      N1    single        1.424 0.020
SIB   C6      O6    double        1.238 0.020
SIB   N1      C2    single        1.384 0.020
SIB   N1     HN1    single        0.996 0.020
SIB   C2      N3    double        1.324 0.020
SIB   C2     HC2    single        1.112 0.020
SIB   N3      C4    single        1.394 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
SIB  H2       N      H            109.80 3.000
SIB  H2       N       CA          110.15 3.000
SIB  H        N       CA          111.30 3.000
SIB  HA       CA      C           107.97 3.000
SIB  HA       CA      CB          108.21 3.000
SIB   C       CA      CB          106.58 3.000
SIB  HA       CA      N           106.94 3.000
SIB   C       CA      N           110.24 3.000
SIB   CB      CA      N           116.61 3.000
SIB  HB3      CB     HB2          107.65 3.000
SIB  HB3      CB      CG          109.65 3.000
SIB  HB2      CB      CG          110.23 3.000
SIB  HB3      CB      CA          108.06 3.000
SIB  HB2      CB      CA          109.82 3.000
SIB   CG      CB      CA          111.34 3.000
SIB  HG3      CG     HG2          107.69 3.000
SIB  HG3      CG      SD          110.07 3.000
SIB  HG2      CG      SD          110.32 3.000
SIB  HG3      CG      CB          111.29 3.000
SIB  HG2      CG      CB          110.75 3.000
SIB   SD      CG      CB          106.74 3.000
SIB  C5'      SD      CG          101.53 3.000
SIB   O       C       OXT         117.64 3.000
SIB   OXT     C       CA          113.44 3.000
SIB   O       C       CA          128.92 3.000
SIB  HO       OXT     C           109.65 3.000
SIB  H5'2    C5'     H5'1         108.09 3.000
SIB  H5'2    C5'     C4'          109.94 3.000
SIB  H5'1    C5'     C4'          110.31 3.000
SIB  H5'2    C5'      SD          109.58 3.000
SIB  H5'1    C5'      SD          110.41 3.000
SIB  C4'     C5'      SD          108.50 3.000
SIB  H4'     C4'     C3'          110.77 3.000
SIB  H4'     C4'     O4'          104.65 3.000
SIB  C3'     C4'     O4'          107.78 3.000
SIB  H4'     C4'     C5'          110.64 3.000
SIB  C3'     C4'     C5'          112.05 3.000
SIB  O4'     C4'     C5'          110.66 3.000
SIB  C1'     O4'     C4'          111.75 3.000
SIB  H3'     C3'     C2'          110.44 3.000
SIB  H3'     C3'     O3'          104.51 3.000
SIB  C2'     C3'     O3'          113.85 3.000
SIB  H3'     C3'     C4'          111.46 3.000
SIB  O3'     C3'     C4'          111.67 3.000
SIB  C2'     C3'     C4'          105.07 3.000
SIB  HO3'    O3'     C3'          108.37 3.000
SIB  H2'     C2'     C1'          112.64 3.000
SIB  H2'     C2'     O2'          110.93 3.000
SIB  C1'     C2'     O2'          108.86 3.000
SIB  H2'     C2'     C3'          110.55 3.000
SIB  O2'     C2'     C3'          108.42 3.000
SIB  C1'     C2'     C3'          105.20 3.000
SIB  HO2'    O2'     C2'          106.88 3.000
SIB  H1'     C1'      N9          108.31 3.000
SIB  H1'     C1'     C2'          110.73 3.000
SIB   N9     C1'     C2'          113.78 3.000
SIB  H1'     C1'     O4'          105.38 3.000
SIB   N9     C1'     O4'          110.48 3.000
SIB  C2'     C1'     O4'          107.84 3.000
SIB   C4      N9      C8          105.93 3.000
SIB   C8      N9     C1'          128.54 3.000
SIB   C4      N9     C1'          125.53 3.000
SIB  H8       C8      N7          126.05 3.000
SIB  H8       C8      N9          120.96 3.000
SIB   N7      C8      N9          112.99 3.000
SIB   C5      N7      C8          105.11 3.000
SIB   C4      C5      C6          119.34 3.000
SIB   C6      C5      N7          130.42 3.000
SIB   C4      C5      N7          110.24 3.000
SIB   N1      C6      O6          118.62 3.000
SIB   O6      C6      C5          128.10 3.000
SIB   N1      C6      C5          113.29 3.000
SIB  HN1      N1      C2          119.86 3.000
SIB  HN1      N1      C6          118.00 3.000
SIB   C2      N1      C6          122.14 3.000
SIB  HC2      C2      N3          116.63 3.000
SIB  HC2      C2      N1          116.23 3.000
SIB   N3      C2      N1          127.14 3.000
SIB   C4      N3      C2          113.72 3.000
SIB   N3      C4      C5          124.37 3.000
SIB   N3      C4      N9          129.90 3.000
SIB   C5      C4      N9          105.73 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
SIB CONST_01       N7      C5      C4      N9           -0.00   0.0 0
SIB CONST_02       C5      N7      C8      N9            0.00   0.0 0
SIB CONST_03       C5      C4      N9      C8            0.00   0.0 0
SIB CONST_04       C4      C5      N7      C8           -0.00   0.0 0
SIB CONST_05       C4      N9      C8      N7           -0.00   0.0 0
SIB CONST_06       C5      C4      N9     C1'          180.00   0.0 0
SIB CONST_07       N3      C4      N9     C1'           -0.00   0.0 0
SIB CONST_08       N7      C8      N9     C1'         -180.00   0.0 0
SIB CONST_09       C2      N1      C6      C5            0.00   0.0 0
SIB CONST_10       N3      C2      N1      C6            0.00   0.0 0
SIB CONST_11       C4      N3      C2      N1           -0.00   0.0 0
SIB CONST_12       C4      N3      C2      N1           -0.00   0.0 0
SIB CONST_13       C2      N1      C6      O6          180.00   0.0 0
SIB CONST_14      H8       C8      N9     C1'            0.00   0.0 0
SIB CONST_15       HN1     N1      C6      C5          180.00   0.0 0
SIB CONST_16       HC2     C2      N1      C6          180.00   0.0 0
SIB CONST_17       HO      OXT     C       CA          180.00   0.0 0
SIB Var_01        C4'     C5'      SD      CG          168.30  30.0 3
SIB Var_02         SD      CG      CB      CA         -169.10  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
SIB chir_01   CA      N       CB      C     negativ
SIB chir_02  C4'     O4'     C5'     C3'    positiv
SIB chir_03  C3'     O3'     C4'     C2'    positiv
SIB chir_04  C2'     O2'     C3'     C1'    positiv
SIB chir_05  C1'     O4'      N9     C2'    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
SIB plan-1    C1' 0.020
SIB plan-1     N9 0.020
SIB plan-1     C8 0.020
SIB plan-1     N7 0.020
SIB plan-1     C5 0.020
SIB plan-1     C6 0.020
SIB plan-1     O6 0.020
SIB plan-1     N1 0.020
SIB plan-1     C2 0.020
SIB plan-1     N3 0.020
SIB plan-1     C4 0.020
SIB plan-1     H8 0.020
SIB plan-1    HN1 0.020
SIB plan-1    HC2 0.020
SIB plan-2     CA 0.020
SIB plan-2      C 0.020
SIB plan-2    OXT 0.020
SIB plan-2      O 0.020
SIB plan-2     HO 0.020
