# 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 15:28:11 2012
#
#   Inital geometry file: a 67 line input string
#   Ligand name: O-[(R)-ethoxy(methyl)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CCO[P@@](C)(=O)OC[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
SVX        SVX 'O-[(R)-ethoxy(methyl)phosphoryl]-L-serine' L-peptide 27 13 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_SVX
#
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
SVX         N      N   NH2   .         -2.1909    0.3917    1.7546
SVX         CA     C   CH1   .         -2.1254    0.7713    0.3609
SVX         C      C   C     .         -3.1556    0.0005   -0.4484
SVX         CB     C   CH2   .         -0.7669    0.5467   -0.3377
SVX         O      O   O     .         -3.4062   -1.2066   -0.4269
SVX         OG     O   O2    .          0.2515    0.7468    0.6159
SVX         P1     P   P     .          1.7465    0.4804    0.0523
SVX         C4     C   CH3   .          2.6617    1.6017    0.7973
SVX         OXT    O   OH1   .         -3.8760    0.7800   -1.2970
SVX         C2     C   CH2   .          1.7113   -2.1345    0.1969
SVX         O6     O   O     .          1.7478    0.3642   -1.4001
SVX         O5     O   O2    .          2.1004   -0.9090    0.7849
SVX         C1     C   CH3   .          2.9385   -2.9345   -0.1814
SVX        HN1     H   HNH2  .         -2.1255   -0.6029    1.8568
SVX        HN2     H   HNH2  .         -1.4362    0.8285    2.2501
SVX        HA      H   HCH1  .         -2.3683    1.8754    0.3032
SVX        HBC1    H   HCH2  .         -0.6781   -0.5040   -0.7291
SVX        HBC2    H   HCH2  .         -0.6283    1.2808   -1.1789
SVX        HOT     H   HOH1  .         -4.5144    0.2317   -1.7834
SVX        H4C1    H   HCH3  .          3.3590    1.1618    1.5554
SVX        H4C2    H   HCH3  .          3.2998    2.1762    0.0797
SVX        H4C3    H   HCH3  .          2.0541    2.3619    1.3515
SVX        H2C1    H   HCH2  .          1.1197   -2.6958    0.9748
SVX        H2C2    H   HCH2  .          1.0638   -1.9393   -0.7030
SVX        H1C1    H   HCH3  .          3.4975   -2.4403   -1.0113
SVX        H1C2    H   HCH3  .          3.6218   -3.0327    0.6954
SVX        H1C3    H   HCH3  .          2.6244   -3.9518   -0.5158
#
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
SVX   CB      OG    single        1.409 0.020
SVX   OG      P1    single        1.620 0.020
SVX   P1      C4    single        1.628 0.020
SVX   C       OXT   single        1.359 0.020
SVX   P1      O6    double        1.457 0.020
SVX   C2      O5    single        1.414 0.020
SVX   P1      O5    single        1.610 0.020
SVX   C2      C1    single        1.513 0.020
SVX   N      HN1    single        1.002 0.020
SVX   N      HN2    single        1.003 0.020
SVX   CA     HA     single        1.132 0.020
SVX   CB     HBC1   single        1.125 0.020
SVX   CB     HBC2   single        1.125 0.020
SVX   OXT    HOT    single        0.972 0.020
SVX   C4     H4C1   single        1.120 0.020
SVX   C4     H4C2   single        1.119 0.020
SVX   C4     H4C3   single        1.120 0.020
SVX   C2     H2C1   single        1.127 0.020
SVX   C2     H2C2   single        1.126 0.020
SVX   C1     H1C1   single        1.116 0.020
SVX   C1     H1C2   single        1.116 0.020
SVX   C1     H1C3   single        1.116 0.020
SVX   N       CA    single        1.446 0.020
SVX   CA      C     single        1.520 0.020
SVX   CA      CB    single        1.544 0.020
SVX   C       O     double        1.233 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
SVX  HN2      N      HN1          109.44 3.000
SVX  HN2      N       CA          109.13 3.000
SVX  HN1      N       CA          110.85 3.000
SVX  HA       CA      CB          107.92 3.000
SVX   CB      CA      C           106.36 3.000
SVX  HA       CA      C           108.79 3.000
SVX   CB      CA      N           115.96 3.000
SVX   C       CA      N           110.45 3.000
SVX  HA       CA      N           107.18 3.000
SVX   OXT     C       O           117.69 3.000
SVX   O       C       CA          128.68 3.000
SVX   OXT     C       CA          113.63 3.000
SVX  HBC2     CB     HBC1         109.85 3.000
SVX  HBC2     CB      OG          108.92 3.000
SVX  HBC1     CB      OG          108.12 3.000
SVX  HBC2     CB      CA          110.60 3.000
SVX  HBC1     CB      CA          111.27 3.000
SVX   OG      CB      CA          108.00 3.000
SVX   P1      OG      CB          114.09 3.000
SVX   O5      P1      O6          112.62 3.000
SVX   O5      P1      C4          105.22 3.000
SVX   O6      P1      C4          120.71 3.000
SVX   O5      P1      OG          100.75 3.000
SVX   O6      P1      OG          111.15 3.000
SVX   C4      P1      OG          104.26 3.000
SVX  H4C3     C4     H4C2         106.15 3.000
SVX  H4C3     C4     H4C1         105.63 3.000
SVX  H4C2     C4     H4C1         106.30 3.000
SVX  H4C3     C4      P1          112.89 3.000
SVX  H4C2     C4      P1          112.38 3.000
SVX  H4C1     C4      P1          112.91 3.000
SVX  HOT      OXT     C           109.70 3.000
SVX  H2C2     C2     H2C1         109.65 3.000
SVX  H2C2     C2      C1          111.00 3.000
SVX  H2C1     C2      C1          109.57 3.000
SVX  H2C2     C2      O5          109.91 3.000
SVX  H2C1     C2      O5          106.81 3.000
SVX   C1      C2      O5          109.82 3.000
SVX   C2      O5      P1          119.89 3.000
SVX  H1C3     C1     H1C2         109.12 3.000
SVX  H1C3     C1     H1C1         108.77 3.000
SVX  H1C2     C1     H1C1         108.45 3.000
SVX  H1C3     C1      C2          109.19 3.000
SVX  H1C2     C1      C2          110.29 3.000
SVX  H1C1     C1      C2          110.98 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
SVX CONST_01       HOT     OXT     C       CA          180.00   0.0 0
SVX Var_01         C4      P1      OG      CB          143.70  30.0 3
SVX Var_02         C1      C2      O5      P1          115.55  30.0 1
SVX Var_03        H4C1     C4      P1      OG          110.17  30.0 3
SVX Var_04        HBC1     CB      OG      P1           56.84  30.0 1
SVX Var_05        H1C1     C1      C2      O5          -67.66  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
SVX chir_01   CA      N       C       CB    positiv
SVX chir_02   P1      C4      O6      O5    both
#
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
SVX plan-1     CA 0.020
SVX plan-1      C 0.020
SVX plan-1      O 0.020
SVX plan-1    OXT 0.020
SVX plan-1    HOT 0.020
