# 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 14:51:37 2012
#
#   Inital geometry file: a 69 line input string
#   Ligand name: (1R,5S)-5-amino-1,5-dicarboxypentan-1-aminium
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC[C@@H]([NH3+])C(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
6CL        6CL '(1R,5S)-5-amino-1,5-dicarboxypentan-1-aminium' L-peptide 28 13 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_6CL
#
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
6CL         N      N   NH2   .          0.7420   -1.5331    0.7776
6CL         CA     C   CH1   .          0.0216   -2.0470    1.9174
6CL         CB     C   CH2   .          0.4428   -3.4764    2.2982
6CL         CG     C   CH2   .          0.2058   -4.4382    1.1520
6CL         CD     C   CH2   .          0.3670   -5.8709    1.6175
6CL         CE     C   CH1   .          0.4521   -6.8907    0.4764
6CL         CZ     C   C     .          1.7728   -6.7556   -0.2750
6CL         OH1    O   O     .          1.9327   -6.2060   -1.3648
6CL         OH2    O   OH1   .          2.8089   -7.3132    0.3786
6CL         NZ     N   NT3   .         -0.6858   -6.7635   -0.4989
6CL         C      C   C     .          0.1476   -1.1866    3.1714
6CL         O      O   O     .          1.0351   -0.3792    3.4510
6CL         OXT    O   OH1   .         -0.8616   -1.3608    4.0646
6CL        H2      H   HNH2  .          0.3994   -0.6260    0.5248
6CL        H       H   HNH2  .          1.7231   -1.4679    0.9705
6CL        HA      H   HCH1  .         -1.0794   -2.0596    1.6501
6CL        HB2     H   HCH2  .         -0.1607   -3.7816    3.1947
6CL        HB3     H   HCH2  .          1.5248   -3.4932    2.5909
6CL        HG2     H   HCH2  .         -0.8298   -4.2738    0.7502
6CL        HG3     H   HCH2  .          0.9326   -4.2148    0.3244
6CL        HD2     H   HCH2  .          1.3238   -5.9770    2.2055
6CL        HD3     H   HCH2  .         -0.4755   -6.1505    2.3053
6CL        HE      H   HCH1  .          0.4083   -7.9366    0.9152
6CL        HH2     H   HOH1  .          3.6311   -7.2015   -0.1410
6CL        HZ1     H   HNT3  .         -0.8311   -7.6553   -0.9850
6CL        HZ2     H   HNT3  .         -0.4518   -6.0475   -1.2015
6CL        HZ3     H   HNT3  .         -1.5384   -6.4898   -0.0021
6CL        HXT     H   HOH1  .         -0.7216   -0.7856    4.8381
#
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
6CL   N       CA    single        1.443 0.020
6CL   N      H2     single        1.002 0.020
6CL   N      H      single        1.002 0.020
6CL   CA      CB    single        1.538 0.020
6CL   CA      C     single        1.526 0.020
6CL   CA     HA     single        1.133 0.020
6CL   CB      CG    single        1.515 0.020
6CL   CB     HB2    single        1.123 0.020
6CL   CB     HB3    single        1.121 0.020
6CL   CG      CD    single        1.515 0.020
6CL   CG     HG2    single        1.123 0.020
6CL   CG     HG3    single        1.124 0.020
6CL   CD      CE    single        1.533 0.020
6CL   CD     HD2    single        1.128 0.020
6CL   CD     HD3    single        1.123 0.020
6CL   CE      CZ    single        1.525 0.020
6CL   CE      NZ    single        1.504 0.020
6CL   CE     HE     single        1.135 0.020
6CL   CZ      OH1   double        1.231 0.020
6CL   CZ      OH2   single        1.346 0.020
6CL   OH2    HH2    single        0.979 0.020
6CL   NZ     HZ1    single        1.026 0.020
6CL   NZ     HZ2    single        1.030 0.020
6CL   NZ     HZ3    single        1.024 0.020
6CL   C       O     double        1.232 0.020
6CL   C       OXT   single        1.359 0.020
6CL   OXT    HXT    single        0.974 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
6CL  H        N      H2           108.93 3.000
6CL  H        N       CA          111.09 3.000
6CL  H2       N       CA          110.55 3.000
6CL  HA       CA      C           106.29 3.000
6CL  HA       CA      CB          108.31 3.000
6CL   C       CA      CB          107.33 3.000
6CL  HA       CA      N           107.62 3.000
6CL   C       CA      N           114.02 3.000
6CL   CB      CA      N           112.94 3.000
6CL  HB3      CB     HB2          107.84 3.000
6CL  HB3      CB      CG          109.81 3.000
6CL  HB2      CB      CG          110.32 3.000
6CL  HB3      CB      CA          110.06 3.000
6CL  HB2      CB      CA          107.64 3.000
6CL   CG      CB      CA          111.09 3.000
6CL  HG3      CG     HG2          107.68 3.000
6CL  HG3      CG      CD          110.21 3.000
6CL  HG2      CG      CD          110.28 3.000
6CL  HG3      CG      CB          109.25 3.000
6CL  HG2      CG      CB          108.79 3.000
6CL   CD      CG      CB          110.57 3.000
6CL  HD3      CD     HD2          107.08 3.000
6CL  HD3      CD      CE          109.39 3.000
6CL  HD2      CD      CE          106.17 3.000
6CL  HD3      CD      CG          110.11 3.000
6CL  HD2      CD      CG          109.83 3.000
6CL   CE      CD      CG          113.98 3.000
6CL  HE       CE      NZ          107.42 3.000
6CL  HE       CE      CZ          107.79 3.000
6CL   NZ      CE      CZ          109.15 3.000
6CL  HE       CE      CD          108.85 3.000
6CL   NZ      CE      CD          112.61 3.000
6CL   CZ      CE      CD          110.85 3.000
6CL   OH2     CZ      OH1         120.99 3.000
6CL   OH2     CZ      CE          112.99 3.000
6CL   OH1     CZ      CE          126.02 3.000
6CL  HH2      OH2     CZ          109.97 3.000
6CL  HZ3      NZ     HZ2          109.52 3.000
6CL  HZ3      NZ     HZ1          110.14 3.000
6CL  HZ2      NZ     HZ1          108.25 3.000
6CL  HZ3      NZ      CE          109.75 3.000
6CL  HZ2      NZ      CE          109.22 3.000
6CL  HZ1      NZ      CE          109.93 3.000
6CL   OXT     C       O           118.02 3.000
6CL   OXT     C       CA          113.99 3.000
6CL   O       C       CA          127.99 3.000
6CL  HXT      OXT     C           109.85 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
6CL CONST_01       HXT     OXT     C       CA         -180.00   0.0 0
6CL CONST_02       HH2     OH2     CZ      CE         -180.00   0.0 0
6CL Var_01         CD      CG      CB      CA         -169.05  30.0 3
6CL Var_02         CE      CD      CG      CB         -167.21  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
6CL chir_01   CA      N       CB      C     negativ
6CL chir_02   CE      NZ      CD      CZ    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
6CL plan-1     CE 0.020
6CL plan-1     CZ 0.020
6CL plan-1    OH1 0.020
6CL plan-1    OH2 0.020
6CL plan-1    HH2 0.020
6CL plan-2     CA 0.020
6CL plan-2      C 0.020
6CL plan-2      O 0.020
6CL plan-2    OXT 0.020
6CL plan-2    HXT 0.020
