# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 22 17:35:49 2016
#
#   Inital geometry file: a 54 line input string
#   Ligand name: D-norleucine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](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
DNE        DNE 'D-norleucine             ' ligand 21 9 .
2016-04-22 2016-04-22
;
CIF prepared directly in eLBOW
;
#
data_comp_DNE
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
DNE         N      N   NH2    0    .       5.5261   -0.5744   -3.9867
DNE         CA     C   CH1    0    .       4.5833    0.5280   -3.8194
DNE         C      C   C      0    .       4.6655    1.2095   -2.4141
DNE         O      O   O      0    .       5.7419    1.0913   -1.7606
DNE         CB     C   CH2    0    .       4.7594    1.6011   -4.9003
DNE         CG     C   CH2    0    .       3.5138    2.4530   -5.0154
DNE         CD     C   CH2    0    .       3.7355    3.6355   -5.9341
DNE         CE     C   CH3    0    .       2.4860    4.4654   -6.0799
DNE         OXT    O   OC    -1    .       3.6464    1.8285   -1.9981
DNE         H      H   HNH2   0    .       5.4490   -1.1587   -3.1717
DNE         H2     H   HNH2   0    .       6.4564   -0.1922   -3.9662
DNE         HA     H   HCH1   0    .       3.5491    0.0881   -3.9194
DNE         HB2    H   HCH2   0    .       5.6367    2.2462   -4.6324
DNE         HB3    H   HCH2   0    .       4.9796    1.1304   -5.8948
DNE         HG2    H   HCH2   0    .       2.6669    1.8300   -5.4062
DNE         HG3    H   HCH2   0    .       3.2209    2.8058   -3.9864
DNE         HD2    H   HCH2   0    .       4.5632    4.2731   -5.5248
DNE         HD3    H   HCH2   0    .       4.0666    3.2744   -6.9436
DNE         HE1    H   HCH3   0    .       1.6582    3.8569   -6.5180
DNE         HE2    H   HCH3   0    .       2.6706    5.3415   -6.7476
DNE         HE3    H   HCH3   0    .       2.1508    4.8429   -5.0835
#
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
_chem_comp_bond.value_dist_neutron
DNE   N       CA    single        1.460 0.020     1.460
DNE   N       H     single        0.860 0.020     1.020
DNE   N       H2    single        0.890 0.020     1.040
DNE   CA      C     single        1.564 0.020     1.564
DNE   CA      CB    single        1.533 0.020     1.533
DNE   CA      HA    single        0.970 0.020     1.090
DNE   C       O     deloc         1.265 0.020     1.265
DNE   C       OXT   deloc         1.263 0.020     1.263
DNE   CB      CG    single        1.514 0.020     1.514
DNE   CB      HB2   single        0.970 0.020     1.090
DNE   CB      HB3   single        0.970 0.020     1.090
DNE   CG      CD    single        1.514 0.020     1.514
DNE   CG      HG2   single        0.970 0.020     1.090
DNE   CG      HG3   single        0.970 0.020     1.090
DNE   CD      CE    single        1.507 0.020     1.507
DNE   CD      HD2   single        0.970 0.020     1.090
DNE   CD      HD3   single        0.970 0.020     1.090
DNE   CE      HE1   single        0.970 0.020     1.090
DNE   CE      HE2   single        0.970 0.020     1.090
DNE   CE      HE3   single        0.970 0.020     1.090
#
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
DNE   H2      N       H           105.96 3.000
DNE   H2      N       CA          107.94 3.000
DNE   H       N       CA          107.23 3.000
DNE   HA      CA      CB          108.40 3.000
DNE   HA      CA      C           107.33 3.000
DNE   CB      CA      C           108.81 3.000
DNE   HA      CA      N           106.70 3.000
DNE   CB      CA      N           111.93 3.000
DNE   C       CA      N           113.45 3.000
DNE   OXT     C       O           124.22 3.000
DNE   OXT     C       CA          117.85 3.000
DNE   O       C       CA          117.92 3.000
DNE   HB3     CB      HB2         107.43 3.000
DNE   HB3     CB      CG          109.28 3.000
DNE   HB2     CB      CG          109.77 3.000
DNE   HB3     CB      CA          110.72 3.000
DNE   HB2     CB      CA          108.91 3.000
DNE   CG      CB      CA          110.67 3.000
DNE   HG3     CG      HG2         107.21 3.000
DNE   HG3     CG      CD          110.35 3.000
DNE   HG2     CG      CD          109.46 3.000
DNE   HG3     CG      CB          108.71 3.000
DNE   HG2     CG      CB          109.59 3.000
DNE   CD      CG      CB          111.43 3.000
DNE   HD3     CD      HD2         107.06 3.000
DNE   HD3     CD      CE          109.56 3.000
DNE   HD2     CD      CE          109.51 3.000
DNE   HD3     CD      CG          109.74 3.000
DNE   HD2     CD      CG          109.30 3.000
DNE   CE      CD      CG          111.56 3.000
DNE   HE3     CE      HE2         108.53 3.000
DNE   HE3     CE      HE1         108.15 3.000
DNE   HE2     CE      HE1         108.39 3.000
DNE   HE3     CE      CD          110.40 3.000
DNE   HE2     CE      CD          110.66 3.000
DNE   HE1     CE      CD          110.63 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
DNE Var_01         CD      CG      CB      CA          171.98  30.0 3
DNE Var_02         CE      CD      CG      CB          178.48  30.0 3
DNE Var_03         HE1     CE      CD      CG          -60.72  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
DNE chir_01   CA      N       C       CB    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
DNE plan-1     CA 0.020
DNE plan-1      C 0.020
DNE plan-1      O 0.020
DNE plan-1    OXT 0.020
