# 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 15:18:58 2012
#
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-nitro-L-tyrosine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(c1)[N+]([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
NIY        NIY '3-nitro-L-tyrosine       ' L-peptide 26 16 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_NIY
#
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
NIY         N      N   NH2   .         -0.7483   -0.0414    2.1248
NIY         CA     C   CH1   .          0.6282   -0.0270    2.5609
NIY         C      C   C     .          1.3084    1.3171    2.3111
NIY         O      O   O     .          1.3490    1.9677    1.2632
NIY         CB     C   CH2   .          1.4637   -1.1218    1.8639
NIY         CG     C   CR6   .          2.9038   -1.0488    2.2290
NIY         CD1    C   CR16  .          3.8594   -0.7266    1.2750
NIY         CD2    C   CR16  .          3.3092   -1.3098    3.5532
NIY         CE1    C   CR6   .          5.2284   -0.6578    1.6224
NIY         CE2    C   CR16  .          4.6403   -1.2479    3.9120
NIY         CZ     C   CR6   .          5.6286   -0.9199    2.9509
NIY         OH     O   OH1   .          6.8951   -0.8964    3.4459
NIY         NN     N   N     .          6.1941   -0.3095    0.5619
NIY         O1     O   O     .          5.7998   -0.1247   -0.5563
NIY         O2     O   O     .          7.3660   -0.2165    0.8399
NIY         OXT    O   OH1   .          1.9394    1.8374    3.3953
NIY        H       H   HNH2  .         -1.3094    0.5631    2.6902
NIY        H2      H   HNH2  .         -0.8293    0.2219    1.1625
NIY        HA      H   HCH1  .          0.6352   -0.2145    3.6772
NIY        HB2     H   HCH2  .          1.0688   -2.1298    2.1700
NIY        HB3     H   HCH2  .          1.3325   -1.0312    0.7523
NIY        HD1     H   HCR6  .          3.5576   -0.5193    0.2313
NIY        HD2     H   HCR6  .          2.5491   -1.5662    4.3103
NIY        HE2     H   HCR6  .          4.9681   -1.4495    4.9436
NIY        HH      H   HOH1  .          7.1988   -1.7813    3.7097
NIY        HXT     H   HOH1  .          2.3474    2.6888    3.1641
#
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
NIY   N       CA    single        1.444 0.020
NIY   N      H      single        1.000 0.020
NIY   N      H2     single        1.001 0.020
NIY   CA      C     single        1.527 0.020
NIY   CA      CB    single        1.543 0.020
NIY   CA     HA     single        1.132 0.020
NIY   C       O     double        1.234 0.020
NIY   C       OXT   single        1.358 0.020
NIY   CB      CG    single        1.487 0.020
NIY   CB     HB2    single        1.125 0.020
NIY   CB     HB3    single        1.123 0.020
NIY   CG      CD1   aromatic      1.388 0.020
NIY   CG      CD2   aromatic      1.409 0.020
NIY   CD1     CE1   aromatic      1.414 0.020
NIY   CD1    HD1    single        1.106 0.020
NIY   CD2     CE2   aromatic      1.380 0.020
NIY   CD2    HD2    single        1.103 0.020
NIY   CE1     CZ    aromatic      1.412 0.020
NIY   CE1     NN    single        1.476 0.020
NIY   CE2     CZ    aromatic      1.417 0.020
NIY   CE2    HE2    single        1.101 0.020
NIY   CZ      OH    single        1.360 0.020
NIY   OH     HH     single        0.972 0.020
NIY   NN      O1    single        1.200 0.020
NIY   NN      O2    double        1.208 0.020
NIY   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
NIY  H2       N      H            109.82 3.000
NIY  H2       N       CA          111.39 3.000
NIY  H        N       CA          110.98 3.000
NIY  HA       CA      CB          108.94 3.000
NIY  HA       CA      C           107.72 3.000
NIY   CB      CA      C           108.02 3.000
NIY  HA       CA      N           107.58 3.000
NIY   CB      CA      N           111.88 3.000
NIY   C       CA      N           112.58 3.000
NIY   OXT     C       O           117.43 3.000
NIY   OXT     C       CA          114.43 3.000
NIY   O       C       CA          128.14 3.000
NIY  HB3      CB     HB2          107.49 3.000
NIY  HB3      CB      CG          110.61 3.000
NIY  HB2      CB      CG          108.49 3.000
NIY  HB3      CB      CA          109.06 3.000
NIY  HB2      CB      CA          108.82 3.000
NIY   CG      CB      CA          112.24 3.000
NIY   CD2     CG      CD1         119.39 3.000
NIY   CD2     CG      CB          120.00 3.000
NIY   CD1     CG      CB          120.61 3.000
NIY  HD1      CD1     CE1         119.13 3.000
NIY  HD1      CD1     CG          120.28 3.000
NIY   CE1     CD1     CG          120.59 3.000
NIY  HD2      CD2     CE2         119.78 3.000
NIY  HD2      CD2     CG          119.33 3.000
NIY   CE2     CD2     CG          120.89 3.000
NIY   NN      CE1     CZ          122.30 3.000
NIY   NN      CE1     CD1         117.93 3.000
NIY   CZ      CE1     CD1         119.77 3.000
NIY  HE2      CE2     CZ          118.05 3.000
NIY  HE2      CE2     CD2         121.50 3.000
NIY   CZ      CE2     CD2         120.45 3.000
NIY   OH      CZ      CE2         113.99 3.000
NIY   OH      CZ      CE1         127.10 3.000
NIY   CE2     CZ      CE1         118.91 3.000
NIY  HH       OH      CZ          111.97 3.000
NIY   O2      NN      O1          121.42 3.000
NIY   O2      NN      CE1         119.19 3.000
NIY   O1      NN      CE1         119.39 3.000
NIY  HXT      OXT     C           109.92 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
NIY CONST_01       CZ      CE1     CD1     CG            0.05   0.0 0
NIY CONST_02       CZ      CE2     CD2     CG           -0.03   0.0 0
NIY CONST_03       CE2     CD2     CG      CD1           0.06   0.0 0
NIY CONST_04       CE2     CZ      CE1     CD1          -0.01   0.0 0
NIY CONST_05       CE1     CD1     CG      CD2          -0.07   0.0 0
NIY CONST_06       CE1     CZ      CE2     CD2           0.00   0.0 0
NIY CONST_07       CE1     CD1     CG      CB         -179.98   0.0 0
NIY CONST_08       CE2     CD2     CG      CB          179.97   0.0 0
NIY CONST_09       NN      CE1     CD1     CG         -179.97   0.0 0
NIY CONST_10       OH      CZ      CE1     CD1         179.98   0.0 0
NIY CONST_11       OH      CZ      CE2     CD2        -179.99   0.0 0
NIY CONST_12       NN      CE1     CZ      CE2        -180.00   0.0 0
NIY CONST_13      HE2      CE2     CD2     CG          179.97   0.0 0
NIY CONST_14      HD2      CD2     CG      CD1        -179.97   0.0 0
NIY CONST_15      HD1      CD1     CG      CD2         179.99   0.0 0
NIY CONST_16       O1      NN      CE1     CD1          -1.55   0.0 0
NIY CONST_17       O2      NN      CE1     CD1         178.44   0.0 0
NIY CONST_18       O1      NN      CE1     CZ          178.43   0.0 0
NIY CONST_19       O2      NN      CE1     CZ           -1.58   0.0 0
NIY CONST_20       HXT     OXT     C       CA         -179.99   0.0 0
NIY Var_01         CD1     CG      CB      CA         -114.13  30.0 2
NIY Var_02         O1      NN      CE1     CD1          -1.55  30.0 2
#
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
NIY chir_01   CA      N       C       CB    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
NIY plan-1     CB 0.020
NIY plan-1     CG 0.020
NIY plan-1    CD1 0.020
NIY plan-1    CD2 0.020
NIY plan-1    CE1 0.020
NIY plan-1    CE2 0.020
NIY plan-1     CZ 0.020
NIY plan-1     OH 0.020
NIY plan-1     NN 0.020
NIY plan-1    HD1 0.020
NIY plan-1    HD2 0.020
NIY plan-1    HE2 0.020
NIY plan-2    CE1 0.020
NIY plan-2     NN 0.020
NIY plan-2     O1 0.020
NIY plan-2     O2 0.020
NIY plan-3     CA 0.020
NIY plan-3      C 0.020
NIY plan-3      O 0.020
NIY plan-3    OXT 0.020
NIY plan-3    HXT 0.020
