# 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 15:06:19 2012
#
#   Inital geometry file: a 124 line input string
#   Ligand name: (E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]-L-lysine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C1CNC[C@@H](CCC(O)=O)[C@H]1CC(O)=O)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
CYJ        CYJ '(E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]-L-lysine' L-peptide 52 25 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_CYJ
#
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
CYJ         O4     O   O     .          6.3708   -4.9100   -2.3895
CYJ         C11    C   C     .          6.5820   -3.7266   -2.1099
CYJ         O3     O   OH1   .          7.8353   -3.2534   -2.3664
CYJ         C10    C   CH2   .          5.6654   -2.7024   -1.5220
CYJ         C9     C   CH2   .          4.2142   -3.0710   -1.7527
CYJ         C8     C   CH1   .          3.2536   -2.2866   -0.8721
CYJ         C7     C   CH2   .          1.8646   -2.9469   -0.9522
CYJ         N6     N   NH1   .          0.8614   -2.3500   -0.0984
CYJ         C5     C   CH2   .          0.7722   -0.9148   -0.2332
CYJ         C3     C   CH1   .          3.1664   -0.7714   -1.1305
CYJ         C2     C   CH2   .          2.8726   -0.3724   -2.5749
CYJ         C1     C   C     .          2.6647    1.1048   -2.7032
CYJ         O1     O   OH1   .          1.6605    1.4499   -3.5482
CYJ         O2     O   O     .          3.2808    2.0235   -2.1492
CYJ         C4     C   C     .          2.1146   -0.1735   -0.2021
CYJ         NZ     N   N     .          2.1997    0.8816    0.5270
CYJ         CE     C   CH2   .          3.2646    1.1506    1.4540
CYJ         CD     C   CH2   .          3.1650    2.5431    2.0829
CYJ         CG     C   CH2   .          2.9656    3.6198    1.0378
CYJ         CB     C   CH2   .          3.2821    4.9882    1.6024
CYJ         CA     C   CH1   .          3.0656    6.1295    0.5939
CYJ         N      N   NH2   .          1.7529    6.1386   -0.0006
CYJ         C      C   C     .          4.2018    6.0822   -0.4252
CYJ         O      O   O     .          4.2738    5.4196   -1.4675
CYJ         OXT    O   OH1   .          5.2590    6.8793   -0.1278
CYJ        H3      H   HOH1  .          8.3806   -3.9618   -2.7452
CYJ        H101    H   HCH2  .          5.9011   -1.7008   -1.9715
CYJ        H102    H   HCH2  .          5.8871   -2.6403   -0.4219
CYJ        H9C1    H   HCH2  .          4.0821   -4.1638   -1.5216
CYJ        H9C2    H   HCH2  .          3.9605   -2.9536   -2.8379
CYJ        H8      H   HCH1  .          3.6227   -2.3952    0.1905
CYJ        H7C1    H   HCH2  .          1.4932   -2.8920   -2.0145
CYJ        H7C2    H   HCH2  .          1.9595   -4.0338   -0.6776
CYJ        H6      H   HNH1  .          1.0360   -2.5952    0.8602
CYJ        H5C1    H   HCH2  .          0.0868   -0.5322    0.5755
CYJ        H5C2    H   HCH2  .          0.2890   -0.6846   -1.2261
CYJ        HA      H   HCH1  .          4.1800   -0.3417   -0.8760
CYJ        H2C1    H   HCH2  .          3.7498   -0.6210   -3.2320
CYJ        H2C2    H   HCH2  .          1.9774   -0.9138   -2.9797
CYJ        H1      H   HOH1  .          1.5744    2.4213   -3.5900
CYJ        HEC1    H   HCH2  .          4.2972    1.0589    1.0017
CYJ        HEC2    H   HCH2  .          3.1839    0.3867    2.2815
CYJ        HDC1    H   HCH2  .          4.1238    2.7214    2.6376
CYJ        HDC2    H   HCH2  .          2.3296    2.5781    2.8281
CYJ        HGC1    H   HCH2  .          1.9043    3.5864    0.6757
CYJ        HGC2    H   HCH2  .          3.6296    3.4126    0.1524
CYJ        HBC1    H   HCH2  .          4.3583    5.0287    1.9203
CYJ        HBC2    H   HCH2  .          2.6483    5.1809    2.5066
CYJ        HB      H   HCH1  .          3.1840    7.1090    1.1533
CYJ        HN1     H   HNH2  .          1.7660    5.7448   -0.9208
CYJ        HN2     H   HNH2  .          1.3865    7.0691   -0.0427
CYJ        HXT     H   HOH1  .          5.9391    6.7973   -0.8173
#
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
CYJ   O4      C11   double        1.234 0.020
CYJ   C11     O3    single        1.364 0.020
CYJ   C11     C10   single        1.495 0.020
CYJ   O3     H3     single        0.971 0.020
CYJ   C10     C9    single        1.515 0.020
CYJ   C10    H101   single        1.123 0.020
CYJ   C10    H102   single        1.124 0.020
CYJ   C9      C8    single        1.521 0.020
CYJ   C9     H9C1   single        1.125 0.020
CYJ   C9     H9C2   single        1.121 0.020
CYJ   C8      C7    single        1.540 0.020
CYJ   C8      C3    single        1.540 0.020
CYJ   C8     H8     single        1.130 0.020
CYJ   C7      N6    single        1.446 0.020
CYJ   C7     H7C1   single        1.127 0.020
CYJ   C7     H7C2   single        1.125 0.020
CYJ   N6      C5    single        1.444 0.020
CYJ   N6     H6     single        1.005 0.020
CYJ   C5      C4    single        1.534 0.020
CYJ   C5     H5C1   single        1.127 0.020
CYJ   C5     H5C2   single        1.128 0.020
CYJ   C3      C2    single        1.527 0.020
CYJ   C3      C4    single        1.525 0.020
CYJ   C3     HA     single        1.130 0.020
CYJ   C2      C1    single        1.497 0.020
CYJ   C2     H2C1   single        1.124 0.020
CYJ   C2     H2C2   single        1.122 0.020
CYJ   C1      O1    single        1.357 0.020
CYJ   C1      O2    double        1.237 0.020
CYJ   O1     H1     single        0.976 0.020
CYJ   C4      NZ    double        1.285 0.020
CYJ   NZ      CE    single        1.437 0.020
CYJ   CE      CD    single        1.531 0.020
CYJ   CE     HEC1   single        1.131 0.020
CYJ   CE     HEC2   single        1.129 0.020
CYJ   CD      CG    single        1.514 0.020
CYJ   CD     HDC1   single        1.122 0.020
CYJ   CD     HDC2   single        1.120 0.020
CYJ   CG      CB    single        1.514 0.020
CYJ   CG     HGC1   single        1.122 0.020
CYJ   CG     HGC2   single        1.126 0.020
CYJ   CB      CA    single        1.538 0.020
CYJ   CB     HBC1   single        1.123 0.020
CYJ   CB     HBC2   single        1.121 0.020
CYJ   CA      N     single        1.441 0.020
CYJ   CA      C     single        1.527 0.020
CYJ   CA     HB     single        1.134 0.020
CYJ   N      HN1    single        1.001 0.020
CYJ   N      HN2    single        1.001 0.020
CYJ   C       O     double        1.237 0.020
CYJ   C       OXT   single        1.357 0.020
CYJ   OXT    HXT    single        0.972 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
CYJ   C10     C11     O3          113.55 3.000
CYJ   C10     C11     O4          129.88 3.000
CYJ   O3      C11     O4          116.57 3.000
CYJ  H3       O3      C11         109.64 3.000
CYJ  H102     C10    H101         107.53 3.000
CYJ  H102     C10     C9          110.58 3.000
CYJ  H101     C10     C9          110.93 3.000
CYJ  H102     C10     C11         107.57 3.000
CYJ  H101     C10     C11         108.97 3.000
CYJ   C9      C10     C11         111.15 3.000
CYJ  H9C2     C9     H9C1         105.91 3.000
CYJ  H9C2     C9      C8          111.33 3.000
CYJ  H9C1     C9      C8          107.93 3.000
CYJ  H9C2     C9      C10         109.81 3.000
CYJ  H9C1     C9      C10         108.52 3.000
CYJ   C8      C9      C10         113.04 3.000
CYJ  H8       C8      C3          105.72 3.000
CYJ  H8       C8      C7          107.60 3.000
CYJ   C3      C8      C7          111.23 3.000
CYJ  H8       C8      C9          106.78 3.000
CYJ   C3      C8      C9          116.49 3.000
CYJ   C7      C8      C9          108.57 3.000
CYJ  H7C2     C7     H7C1         107.76 3.000
CYJ  H7C2     C7      N6          108.25 3.000
CYJ  H7C1     C7      N6          107.93 3.000
CYJ  H7C2     C7      C8          108.99 3.000
CYJ  H7C1     C7      C8          108.99 3.000
CYJ   N6      C7      C8          114.70 3.000
CYJ  H6       N6      C5          110.02 3.000
CYJ  H6       N6      C7          110.00 3.000
CYJ   C5      N6      C7          113.44 3.000
CYJ  H5C2     C5     H5C1         107.57 3.000
CYJ  H5C2     C5      C4          107.11 3.000
CYJ  H5C1     C5      C4          110.71 3.000
CYJ  H5C2     C5      N6          108.15 3.000
CYJ  H5C1     C5      N6          107.93 3.000
CYJ   C4      C5      N6          115.11 3.000
CYJ  HA       C3      C4          109.42 3.000
CYJ  HA       C3      C2          106.64 3.000
CYJ   C4      C3      C2          109.92 3.000
CYJ  HA       C3      C8          106.60 3.000
CYJ   C4      C3      C8          108.82 3.000
CYJ   C2      C3      C8          115.27 3.000
CYJ  H2C2     C2     H2C1         107.77 3.000
CYJ  H2C2     C2      C1          109.54 3.000
CYJ  H2C1     C2      C1          106.05 3.000
CYJ  H2C2     C2      C3          111.64 3.000
CYJ  H2C1     C2      C3          110.18 3.000
CYJ   C1      C2      C3          111.44 3.000
CYJ   O2      C1      O1          117.29 3.000
CYJ   O2      C1      C2          128.69 3.000
CYJ   O1      C1      C2          114.02 3.000
CYJ  H1       O1      C1          110.19 3.000
CYJ   NZ      C4      C3          128.42 3.000
CYJ   NZ      C4      C5          117.79 3.000
CYJ   C3      C4      C5          113.69 3.000
CYJ   CE      NZ      C4          124.65 3.000
CYJ  HEC2     CE     HEC1         107.67 3.000
CYJ  HEC2     CE      CD          108.03 3.000
CYJ  HEC1     CE      CD          107.30 3.000
CYJ  HEC2     CE      NZ          107.05 3.000
CYJ  HEC1     CE      NZ          113.79 3.000
CYJ   CD      CE      NZ          112.76 3.000
CYJ  HDC2     CD     HDC1         107.67 3.000
CYJ  HDC2     CD      CG          109.81 3.000
CYJ  HDC1     CD      CG          109.93 3.000
CYJ  HDC2     CD      CE          110.50 3.000
CYJ  HDC1     CD      CE          106.98 3.000
CYJ   CG      CD      CE          111.83 3.000
CYJ  HGC2     CG     HGC1         107.37 3.000
CYJ  HGC2     CG      CB          109.66 3.000
CYJ  HGC1     CG      CB          110.19 3.000
CYJ  HGC2     CG      CD          109.53 3.000
CYJ  HGC1     CG      CD          109.04 3.000
CYJ   CB      CG      CD          110.98 3.000
CYJ  HBC2     CB     HBC1         107.90 3.000
CYJ  HBC2     CB      CA          108.77 3.000
CYJ  HBC1     CB      CA          107.07 3.000
CYJ  HBC2     CB      CG          109.76 3.000
CYJ  HBC1     CB      CG          109.79 3.000
CYJ   CA      CB      CG          113.38 3.000
CYJ  HB       CA      C           106.16 3.000
CYJ  HB       CA      N           107.04 3.000
CYJ   C       CA      N           113.74 3.000
CYJ  HB       CA      CB          107.62 3.000
CYJ   C       CA      CB          108.05 3.000
CYJ   N       CA      CB          113.78 3.000
CYJ  HN2      N      HN1          109.38 3.000
CYJ  HN2      N       CA          110.89 3.000
CYJ  HN1      N       CA          111.40 3.000
CYJ   OXT     C       O           116.99 3.000
CYJ   OXT     C       CA          114.53 3.000
CYJ   O       C       CA          128.48 3.000
CYJ  HXT      OXT     C           109.88 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
CYJ CONST_01       H3      O3      C11     O4           -0.01   0.0 0
CYJ CONST_02       H1      O1      C1      C2         -179.97   0.0 0
CYJ CONST_03       HXT     OXT     C       CA         -180.00   0.0 0
CYJ Var_01         C5      N6      C7      C8           50.36  30.0 1
CYJ Var_02         C4      C5      N6      C7          -47.21  30.0 1
CYJ Var_03         C3      C4      C5      N6           48.84  30.0 1
CYJ Var_04         C8      C9      C10     C11         164.49  30.0 3
CYJ Var_05         O1      C1      C2      C3         -139.76  30.0 3
CYJ Var_06         CD      CE      NZ      C4          174.62  30.0 3
CYJ Var_07         C9      C10     C11     O4          -22.14  30.0 3
CYJ Var_08         CG      CD      CE      NZ          -49.70  30.0 3
CYJ Var_09         CB      CG      CD      CE         -162.93  30.0 3
CYJ Var_10         CA      CB      CG      CD         -178.65  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
CYJ chir_01   C8      C9      C7      C3    positiv
CYJ chir_02   C3      C4      C2      C8    positiv
CYJ chir_03   CA      CB      N       C     positiv
#
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
CYJ plan-1     O4 0.020
CYJ plan-1    C11 0.020
CYJ plan-1     O3 0.020
CYJ plan-1    C10 0.020
CYJ plan-1     H3 0.020
CYJ plan-2     C2 0.020
CYJ plan-2     C1 0.020
CYJ plan-2     O1 0.020
CYJ plan-2     O2 0.020
CYJ plan-2     H1 0.020
CYJ plan-3     CA 0.020
CYJ plan-3      C 0.020
CYJ plan-3      O 0.020
CYJ plan-3    OXT 0.020
CYJ plan-3    HXT 0.020
