# 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 15:12:31 2012
#
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S)-2-amino-6-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}hexanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)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
GPL        GPL '(2S)-2-amino-6-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}hexanoic acid (non-preferred name)' L-peptide 59 33 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_GPL
#
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
GPL         P      P   P     .         -1.4274    3.3542   -0.2283
GPL         O1P    O   O     .         -2.5210    3.3314   -1.1956
GPL         O2P    O   OH1   .         -1.3460    4.8535    0.3672
GPL        O5'     O   O2    .         -1.8187    2.6189    1.1709
GPL        C5'     C   CH2   .         -0.9748    2.7476    2.2828
GPL        C4'     C   CR15  .         -0.4267    1.3690    2.6686
GPL        O4'     O   O     .          0.6338    1.0047    1.7798
GPL        C3'     C   CR15  .          0.1116    1.3265    4.1100
GPL        O3'     O   OH1   .         -0.5229    0.3125    4.8659
GPL        C2'     C   CR15  .          1.6043    0.9474    3.9975
GPL        O2'     O   OH1   .          1.9209   -0.3121    4.5283
GPL        C1'     C   CR15  .          1.9007    0.9670    2.4622
GPL         N9     N   NR5   .          2.7321    2.0587    2.0282
GPL         C8     C   CR15  .          2.7129    3.4197    2.4463
GPL         N7     N   N     .          3.6338    4.1766    1.8320
GPL         C5     C   CR56  .          4.3028    3.3043    0.9665
GPL         C6     C   CR6   .          5.3914    3.5411    0.0463
GPL         O6     O   O     .          5.9997    4.5978   -0.1956
GPL         N1     N   NR16  .          5.8033    2.3877   -0.6683
GPL         C2     C   CR6   .          5.2078    1.1232   -0.4993
GPL         N2     N   NH2   .          5.7178    0.0712   -1.2732
GPL         N3     N   N     .          4.1814    0.8707    0.3597
GPL         C4     C   CR56  .          3.7561    1.9727    1.0713
GPL         N      N   NH2   .          4.0370    2.7903   -5.8234
GPL         CA     C   CH1   .          4.0925    4.0502   -5.1284
GPL         CB     C   CH2   .          2.7589    4.4578   -4.4796
GPL         CG     C   CH2   .          2.0762    3.3206   -3.7474
GPL         CD     C   CH2   .          1.2027    3.8437   -2.6270
GPL         CE     C   CH2   .          0.3495    2.7135   -2.0320
GPL         NZ     N   NH1   .          0.0041    2.8729   -0.6527
GPL         C      C   C     .          5.1706    4.1213   -4.0451
GPL         O      O   O     .          5.5214    3.2303   -3.2557
GPL         OXT    O   OH1   .          5.7942    5.3175   -3.9705
GPL        HOP2    H   HOH1  .         -2.0038    5.4583    0.0331
GPL        H5'1    H   HCH2  .         -0.1390    3.4678    2.0739
GPL        H5'2    H   HCH2  .         -1.6044    3.1365    3.1327
GPL        H4'     H   HCR5  .         -1.2295    0.5922    2.5126
GPL        H3'     H   HCR5  .         -0.0052    2.3192    4.6220
GPL        HO3'    H   HOH1  .         -1.3967    0.6451    5.1087
GPL        H2'     H   HCR5  .          2.2512    1.6664    4.5720
GPL        HO2'    H   HOH1  .          1.1929   -0.9205    4.3366
GPL        H1'     H   HCR5  .          2.3886   -0.0023    2.1368
GPL        H8      H   HCR5  .          2.0012    3.7756    3.1986
GPL        HN1     H   HNR6  .          6.5559    2.4950   -1.3211
GPL        HN21    H   HNH2  .          6.4688    0.2322   -1.9088
GPL        HN22    H   HNH2  .          5.3287   -0.8406   -1.1881
GPL        H2      H   HNH2  .          4.6291    2.1078   -5.3925
GPL        HA      H   HCH1  .          4.3620    4.8446   -5.8914
GPL        HB2     H   HCH2  .          2.9784    5.3016   -3.7719
GPL        HB3     H   HCH2  .          2.0798    4.8521   -5.2796
GPL        HG2     H   HCH2  .          2.8442    2.6237   -3.3167
GPL        HG3     H   HCH2  .          1.4567    2.7250   -4.4688
GPL        HD2     H   HCH2  .          0.5307    4.6508   -3.0189
GPL        HD3     H   HCH2  .          1.8542    4.3093   -1.8410
GPL        HE2     H   HCH2  .         -0.6089    2.6302   -2.6261
GPL        HE3     H   HCH2  .          0.9157    1.7432   -2.1629
GPL        HZ      H   HNH1  .          0.7745    2.8063   -0.0315
GPL        HXT     H   HOH1  .          6.4742    5.3275   -3.2705
GPL        H       H   HNH2  .          4.2947    2.8988   -6.7846
#
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
GPL   P       O1P   double        1.460 0.020
GPL   P       O2P   single        1.615 0.020
GPL   P      O5'    single        1.628 0.020
GPL   P       NZ    single        1.569 0.020
GPL   O2P    HOP2   single        0.954 0.020
GPL  O5'     C5'    single        1.402 0.020
GPL  C5'     C4'    single        1.533 0.020
GPL  C5'     H5'1   single        1.123 0.020
GPL  C5'     H5'2   single        1.127 0.020
GPL  C4'     O4'    single        1.431 0.020
GPL  C4'     C3'    single        1.539 0.020
GPL  C4'     H4'    single        1.128 0.020
GPL  O4'     C1'    single        1.439 0.020
GPL  C3'     O3'    single        1.415 0.020
GPL  C3'     C2'    single        1.544 0.020
GPL  C3'     H3'    single        1.123 0.020
GPL  O3'     HO3'   single        0.966 0.020
GPL  C2'     O2'    single        1.403 0.020
GPL  C2'     C1'    single        1.564 0.020
GPL  C2'     H2'    single        1.125 0.020
GPL  O2'     HO2'   single        0.968 0.020
GPL  C1'      N9    single        1.439 0.020
GPL  C1'     H1'    single        1.133 0.020
GPL   N9      C8    aromatic      1.424 0.020
GPL   N9      C4    aromatic      1.404 0.020
GPL   C8      N7    aromatic      1.341 0.020
GPL   C8     H8     single        1.095 0.020
GPL   N7      C5    aromatic      1.399 0.020
GPL   C5      C6    single        1.445 0.020
GPL   C5      C4    aromatic      1.443 0.020
GPL   C6      O6    double        1.243 0.020
GPL   C6      N1    single        1.418 0.020
GPL   N1      C2    single        1.408 0.020
GPL   N1     HN1    single        1.002 0.020
GPL   C2      N2    single        1.402 0.020
GPL   C2      N3    double        1.362 0.020
GPL   N2     HN21   single        0.997 0.020
GPL   N2     HN22   single        0.995 0.020
GPL   N3      C4    single        1.379 0.020
GPL   N       CA    single        1.440 0.020
GPL   N      H      single        1.001 0.020
GPL   N      H2     single        1.001 0.020
GPL   CA      CB    single        1.538 0.020
GPL   CA      C     single        1.530 0.020
GPL   CA     HA     single        1.134 0.020
GPL   CB      CG    single        1.515 0.020
GPL   CB     HB2    single        1.123 0.020
GPL   CB     HB3    single        1.121 0.020
GPL   CG      CD    single        1.514 0.020
GPL   CG     HG2    single        1.123 0.020
GPL   CG     HG3    single        1.122 0.020
GPL   CD      CE    single        1.536 0.020
GPL   CD     HD2    single        1.121 0.020
GPL   CD     HD3    single        1.122 0.020
GPL   CE      NZ    single        1.431 0.020
GPL   CE     HE2    single        1.131 0.020
GPL   CE     HE3    single        1.131 0.020
GPL   NZ     HZ     single        0.992 0.020
GPL   C       O     double        1.241 0.020
GPL   C       OXT   single        1.351 0.020
GPL   OXT    HXT    single        0.976 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
GPL   NZ      P      O5'          108.25 3.000
GPL   NZ      P       O2P         109.79 3.000
GPL  O5'      P       O2P          96.57 3.000
GPL   NZ      P       O1P         119.96 3.000
GPL  O5'      P       O1P         112.47 3.000
GPL   O2P     P       O1P         107.25 3.000
GPL  HOP2     O2P     P           115.13 3.000
GPL  C5'     O5'      P           119.70 3.000
GPL  H5'2    C5'     H5'1         109.56 3.000
GPL  H5'2    C5'     C4'          108.68 3.000
GPL  H5'1    C5'     C4'          110.95 3.000
GPL  H5'2    C5'     O5'          107.07 3.000
GPL  H5'1    C5'     O5'          111.06 3.000
GPL  C4'     C5'     O5'          109.41 3.000
GPL  H4'     C4'     C3'          111.06 3.000
GPL  H4'     C4'     O4'          105.44 3.000
GPL  C3'     C4'     O4'          108.39 3.000
GPL  H4'     C4'     C5'          109.27 3.000
GPL  C3'     C4'     C5'          112.68 3.000
GPL  O4'     C4'     C5'          109.74 3.000
GPL  C1'     O4'     C4'          111.38 3.000
GPL  H3'     C3'     C2'          110.53 3.000
GPL  H3'     C3'     O3'          110.08 3.000
GPL  C2'     C3'     O3'          107.24 3.000
GPL  H3'     C3'     C4'          111.48 3.000
GPL  C2'     C3'     C4'          106.06 3.000
GPL  O3'     C3'     C4'          111.30 3.000
GPL  HO3'    O3'     C3'          107.04 3.000
GPL  H2'     C2'     C1'          112.60 3.000
GPL  H2'     C2'     O2'          104.52 3.000
GPL  C1'     C2'     O2'          109.87 3.000
GPL  H2'     C2'     C3'          111.21 3.000
GPL  C1'     C2'     C3'          104.58 3.000
GPL  O2'     C2'     C3'          114.27 3.000
GPL  HO2'    O2'     C2'          108.64 3.000
GPL  H1'     C1'      N9          108.28 3.000
GPL  H1'     C1'     C2'          110.66 3.000
GPL   N9     C1'     C2'          114.52 3.000
GPL  H1'     C1'     O4'          105.39 3.000
GPL   N9     C1'     O4'          110.22 3.000
GPL  C2'     C1'     O4'          107.39 3.000
GPL   C4      N9      C8          105.58 3.000
GPL   C4      N9     C1'          125.47 3.000
GPL   C8      N9     C1'          128.96 3.000
GPL  H8       C8      N7          125.28 3.000
GPL  H8       C8      N9          121.41 3.000
GPL   N7      C8      N9          113.31 3.000
GPL   C5      N7      C8          105.06 3.000
GPL   C4      C5      C6          118.87 3.000
GPL   C4      C5      N7          110.44 3.000
GPL   C6      C5      N7          130.69 3.000
GPL   N1      C6      O6          116.82 3.000
GPL   N1      C6      C5          113.98 3.000
GPL   O6      C6      C5          129.19 3.000
GPL  HN1      N1      C2          119.47 3.000
GPL  HN1      N1      C6          117.35 3.000
GPL   C2      N1      C6          123.17 3.000
GPL   N3      C2      N2          118.89 3.000
GPL   N3      C2      N1          124.12 3.000
GPL   N2      C2      N1          116.99 3.000
GPL  HN22     N2     HN21         119.81 3.000
GPL  HN22     N2      C2          119.87 3.000
GPL  HN21     N2      C2          120.32 3.000
GPL   C4      N3      C2          114.19 3.000
GPL   N3      C4      C5          125.66 3.000
GPL   N3      C4      N9          128.72 3.000
GPL   C5      C4      N9          105.61 3.000
GPL  H2       N      H            109.57 3.000
GPL  H2       N       CA          111.47 3.000
GPL  H        N       CA          111.02 3.000
GPL  HA       CA      C           106.04 3.000
GPL  HA       CA      CB          107.71 3.000
GPL   C       CA      CB          107.45 3.000
GPL  HA       CA      N           107.30 3.000
GPL   C       CA      N           114.18 3.000
GPL   CB      CA      N           113.71 3.000
GPL  HB3      CB     HB2          107.69 3.000
GPL  HB3      CB      CG          109.63 3.000
GPL  HB2      CB      CG          110.33 3.000
GPL  HB3      CB      CA          108.51 3.000
GPL  HB2      CB      CA          107.19 3.000
GPL   CG      CB      CA          113.31 3.000
GPL  HG3      CG     HG2          107.15 3.000
GPL  HG3      CG      CD          109.92 3.000
GPL  HG2      CG      CD          108.97 3.000
GPL  HG3      CG      CB          109.66 3.000
GPL  HG2      CG      CB          110.06 3.000
GPL   CD      CG      CB          111.00 3.000
GPL  HD3      CD     HD2          107.10 3.000
GPL  HD3      CD      CE          110.89 3.000
GPL  HD2      CD      CE          109.41 3.000
GPL  HD3      CD      CG          109.07 3.000
GPL  HD2      CD      CG          109.62 3.000
GPL   CE      CD      CG          110.67 3.000
GPL  HE3      CE     HE2          107.47 3.000
GPL  HE3      CE      NZ          109.15 3.000
GPL  HE2      CE      NZ          108.07 3.000
GPL  HE3      CE      CD          107.95 3.000
GPL  HE2      CE      CD          108.76 3.000
GPL   NZ      CE      CD          115.19 3.000
GPL  HZ       NZ      CE          114.13 3.000
GPL  HZ       NZ      P           124.05 3.000
GPL   CE      NZ      P           121.02 3.000
GPL   OXT     C       O           118.04 3.000
GPL   OXT     C       CA          113.92 3.000
GPL   O       C       CA          128.04 3.000
GPL  HXT      OXT     C           111.74 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
GPL CONST_01       C5      N7      C8      N9            0.02   0.0 0
GPL CONST_02       N7      C5      C4      N9           -0.01   0.0 0
GPL CONST_03       C5      C4      N9      C8            0.02   0.0 0
GPL CONST_04       C4      C5      N7      C8           -0.01   0.0 0
GPL CONST_05       C4      N9      C8      N7           -0.03   0.0 0
GPL CONST_06       N7      C8      N9     C1'         -179.98   0.0 0
GPL CONST_07       C5      C4      N9     C1'          179.98   0.0 0
GPL CONST_08       N3      C4      N9     C1'           -0.03   0.0 0
GPL CONST_09       C2      N1      C6      C5           -0.00   0.0 0
GPL CONST_10       N3      C2      N1      C6            0.00   0.0 0
GPL CONST_11       C4      N3      C2      N1           -0.00   0.0 0
GPL CONST_12       C4      N3      C2      N1           -0.00   0.0 0
GPL CONST_13       N2      C2      N1      C6         -180.00   0.0 0
GPL CONST_14       C2      N1      C6      O6          180.00   0.0 0
GPL CONST_15       C4      N3      C2      N2          180.00   0.0 0
GPL CONST_16       C4      N3      C2      N2          180.00   0.0 0
GPL CONST_17      H8       C8      N9     C1'            0.05   0.0 0
GPL CONST_18       HN1     N1      C6      C5         -180.00   0.0 0
GPL CONST_19      HN21     N2      C2      N1            0.00   0.0 0
GPL CONST_20      HN22     N2      C2      N1         -180.00   0.0 0
GPL CONST_21       HXT     OXT     C       CA         -180.00   0.0 0
GPL Var_01        C4'     C5'     O5'      P          -116.98  30.0 3
GPL Var_02         CD      CE      NZ      P           102.41  30.0 1
GPL Var_03         CE      NZ      P       O1P          15.10  30.0 3
GPL Var_04         NZ      P      O5'     C5'           55.96  30.0 2
GPL Var_05         CD      CG      CB      CA          152.75  30.0 3
GPL Var_06         CE      CD      CG      CB          171.24  30.0 3
GPL Var_07         NZ      CE      CD      CG          151.07  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
GPL chir_02  C4'     C5'     O4'     C3'    negativ
GPL chir_03  C3'     O3'     C4'     C2'    positiv
GPL chir_04  C2'     O2'     C3'     C1'    positiv
GPL chir_05  C1'     O4'      N9     C2'    negativ
GPL chir_06   CA      N       CB      C     negativ
GPL chir_07   P       O2P    O5'      NZ    both
#
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
GPL plan-1    C1' 0.020
GPL plan-1     N9 0.020
GPL plan-1     C8 0.020
GPL plan-1     N7 0.020
GPL plan-1     C5 0.020
GPL plan-1     C6 0.020
GPL plan-1     O6 0.020
GPL plan-1     N1 0.020
GPL plan-1     C2 0.020
GPL plan-1     N2 0.020
GPL plan-1     N3 0.020
GPL plan-1     C4 0.020
GPL plan-1     H8 0.020
GPL plan-1    HN1 0.020
GPL plan-1   HN21 0.020
GPL plan-1   HN22 0.020
GPL plan-2     CA 0.020
GPL plan-2      C 0.020
GPL plan-2      O 0.020
GPL plan-2    OXT 0.020
GPL plan-2    HXT 0.020
