# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 16:20:03 2019
#
#   Inital geometry file: a 74 line input string
#   Ligand name: 3-amino-6-carbamimidamido-3,4,5,6-tetradeoxy-L-erythro-hexonic acid
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=N)[C@H](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
00W        00W '3-amino-6-carbamimidamido-3,4,5,6-tetradeoxy-L-erythro-hexonic acid' ligand 29 14 .
2019-03-22 2019-03-22
;
CIF prepared directly in eLBOW
;
#
data_comp_00W
#
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
00W         C      C   CH1    0  -0.078    2.5910    0.5821    0.3955
00W         N      N   NH2    0  -0.337    1.6245   -1.7513    0.3567
00W         O      O   OH1    0  -0.369    2.3805    1.8551   -0.1895
00W         CA     C   CH1    0  -0.044    1.4466   -0.3667   -0.0503
00W         CB     C   CH2    0  -0.150    0.1161    0.2210    0.4441
00W         NE     N   NH1    0  -0.282   -3.5439   -0.4552   -0.2808
00W         CG     C   CH2    0  -0.162   -1.0731   -0.4892   -0.1629
00W         CZ     C   C      0   0.149   -4.8123    0.1911   -0.1258
00W         CX     C   C      0   0.309    3.9767    0.0032    0.0140
00W         NH1    N   N      0  -0.337   -4.9468    1.2488    0.6392
00W         NH2    N   NH2    0  -0.372   -5.8991   -0.4166   -0.8581
00W         HN     H   HNH2   0   0.171    2.4999   -2.0838   -0.0171
00W         HA     H   HCH1   0   0.089    1.4300   -0.3553   -1.1808
00W         HB     H   HCH2   0   0.070    0.0627    0.1644    1.5621
00W         HBA    H   HCH2   0   0.098    0.1022    1.3069    0.1597
00W         HD     H   HCH2   0   0.079   -2.3168    1.2910   -0.0783
00W         HDA    H   HCH2   0   0.102   -2.4556    0.2062    1.3732
00W         HNE    H   HNH1   0   0.184   -3.3945   -0.7777   -1.2181
00W         HG     H   HCH2   0   0.072   -0.9753   -0.4896   -1.2806
00W         HGA    H   HCH2   0   0.100   -1.0891   -1.5588    0.1724
00W        HNH1    H   H      0   0.133   -5.8843    1.5642    0.7628
00W        HNH2    H   HNH2   0   0.176   -5.7039   -1.3284   -1.2122
00W        HNHA    H   HNH2   0   0.171   -6.7556   -0.4083   -0.3467
00W         H41    H   HCH1   0   0.078    2.5422    0.7354    1.5074
00W         H42    H   HOH1   0   0.225    3.0630    1.9693   -0.8718
00W         H2     H   HNH2   0   0.125    1.7040   -1.7909    1.3566
00W         OXT    O   OC    -1  -0.570    4.3793   -1.0352    0.6079
00W         OX     O   O      0  -0.570    4.6232    0.6217   -0.8792
00W         CD     C   CH2    0  -0.057   -2.3684    0.2122    0.2502
#
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
00W   C       CA    single        1.552 0.020     1.552
00W   N       HN    single        0.890 0.020     1.040
00W   O       C     single        1.417 0.020     1.417
00W   CA      N     single        1.454 0.020     1.454
00W   CA      CB    single        1.536 0.020     1.536
00W   CA      HA    single        0.970 0.020     1.090
00W   CB      CG    single        1.512 0.020     1.512
00W   CB      HB    single        0.970 0.020     1.090
00W   CB      HBA   single        0.970 0.020     1.090
00W   CD      NE    single        1.452 0.020     1.452
00W   CD      HD    single        0.970 0.020     1.090
00W   CD      HDA   single        0.970 0.020     1.090
00W   NE      CZ    single        1.432 0.020     1.432
00W   NE      HNE   single        0.890 0.020     1.040
00W   CG      CD    single        1.530 0.020     1.530
00W   CG      HG    single        0.970 0.020     1.090
00W   CG      HGA   single        0.970 0.020     1.090
00W   CZ      NH1   double        1.312 0.020     1.312
00W   CZ      NH2   single        1.445 0.020     1.445
00W   CX      C     single        1.549 0.020     1.549
00W   CX      OX    deloc         1.264 0.020     1.264
00W   NH1    HNH1   single        0.890 0.020     1.040
00W   NH2    HNH2   single        0.890 0.020     1.040
00W   NH2    HNHA   single        0.890 0.020     1.040
00W   C       H41   single        0.970 0.020     1.090
00W   O       H42   single        0.850 0.020     0.980
00W   N       H2    single        0.890 0.020     1.040
00W   CX      OXT   deloc         1.262 0.020     1.262
#
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
00W   H41     C       CX          109.48 3.000
00W   H41     C       CA          109.61 3.000
00W   CX      C       CA          111.12 3.000
00W   H41     C       O           106.24 3.000
00W   CX      C       O           111.53 3.000
00W   CA      C       O           108.73 3.000
00W   H2      N       HN          106.71 3.000
00W   H2      N       CA          109.03 3.000
00W   HN      N       CA          108.45 3.000
00W   H42     O       C           106.93 3.000
00W   HA      CA      CB          107.77 3.000
00W   HA      CA      N           106.93 3.000
00W   CB      CA      N           112.35 3.000
00W   HA      CA      C           106.97 3.000
00W   CB      CA      C           108.20 3.000
00W   N       CA      C           114.30 3.000
00W   HBA     CB      HB          107.52 3.000
00W   HBA     CB      CG          110.05 3.000
00W   HB      CB      CG          109.83 3.000
00W   HBA     CB      CA          107.41 3.000
00W   HB      CB      CA          110.06 3.000
00W   CG      CB      CA          111.85 3.000
00W   HNE     NE      CZ          112.24 3.000
00W   HNE     NE      CD          111.66 3.000
00W   CZ      NE      CD          118.03 3.000
00W   HGA     CG      HG          107.39 3.000
00W   HGA     CG      CD          110.16 3.000
00W   HG      CG      CD          110.06 3.000
00W   HGA     CG      CB          109.83 3.000
00W   HG      CG      CB          109.35 3.000
00W   CD      CG      CB          110.00 3.000
00W   NH2     CZ      NH1         123.88 3.000
00W   NH2     CZ      NE          114.94 3.000
00W   NH1     CZ      NE          121.18 3.000
00W   OXT     CX      OX          124.88 3.000
00W   OXT     CX      C           118.47 3.000
00W   OX      CX      C           116.65 3.000
00W  HNH1     NH1     CZ          115.07 3.000
00W  HNHA     NH2    HNH2         110.96 3.000
00W  HNHA     NH2     CZ          112.49 3.000
00W  HNH2     NH2     CZ          114.66 3.000
00W   HDA     CD      HD          107.38 3.000
00W   HDA     CD      CG          109.40 3.000
00W   HD      CD      CG          108.71 3.000
00W   CG      CD      NE          112.08 3.000
00W   HDA     CD      NE          107.42 3.000
00W   HD      CD      NE          111.71 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
00W CONST_01       NH1     CZ      NE      CD           -9.94   0.0 0
00W CONST_02       NH2     CZ      NE      CD          170.53   0.0 0
00W CONST_03      HNH1     NH1     CZ      NE         -173.46   0.0 0
00W CONST_04      HNH2     NH2     CZ      NE           13.78   0.0 0
00W CONST_05      HNHA     NH2     CZ      NE          141.81   0.0 0
00W CONST_06       HNE     NE      CZ      NH1        -141.96   0.0 0
00W Var_01         CD      CG      CB      CA         -174.59  30.0 3
00W Var_02         NE      CD      CG      CB         -178.50  30.0 3
00W Var_03         CZ      NE      CD      CG         -171.74  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
00W chir_01   C       CA      O       CX    positiv
00W chir_02   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
00W plan-1     NE 0.020
00W plan-1     CZ 0.020
00W plan-1    NH1 0.020
00W plan-1    NH2 0.020
00W plan-1    HNE 0.020
00W plan-1   HNH1 0.020
00W plan-1   HNH2 0.020
00W plan-1   HNHA 0.020
00W plan-1     CD 0.020
00W plan-2      C 0.020
00W plan-2     CX 0.020
00W plan-2    OXT 0.020
00W plan-2     OX 0.020
