# 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 15:26:51 2012
#
#   Inital geometry file: a 75 line input string
#   Ligand name: O-(diethoxyphosphoryl)-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CCO[P](=O)(OCC)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
SDP        SDP 'O-(diethoxyphosphoryl)-L-serine' L-peptide 31 15 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_SDP
#
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
SDP         N      N   NH2   .          4.4877    4.2859   -1.2517
SDP         CA     C   CH1   .          4.8724    2.8963   -1.2693
SDP         CB     C   CH2   .          3.8025    2.0278   -1.9680
SDP         OG     O   O2    .          4.1860    0.6772   -1.7993
SDP         C      C   C     .          6.2031    2.6512   -1.9751
SDP         O      O   O     .          6.5156    2.9334   -3.1350
SDP         C31    C   CH2   .          0.6831   -0.6191   -1.1024
SDP         C32    C   CH3   .         -0.2849    0.5407   -1.1861
SDP         C41    C   CH2   .          2.7636   -0.2511   -4.6792
SDP         C42    C   CH3   .          1.6644   -1.0533   -5.3406
SDP         O1     O   O2    .          2.0045   -0.1384   -0.9441
SDP         O2     O   O2    .          2.3466    0.1814   -3.3975
SDP         O3     O   O     .          3.5081   -1.8071   -2.2183
SDP         P      P   P     .          3.0688   -0.4246   -2.1042
SDP         OXT    O   OH1   .          7.1401    2.0451   -1.2030
SDP        H       H   HNH2  .          4.5667    4.7000   -2.1596
SDP        H2      H   HNH2  .          5.0365    4.7994   -0.5920
SDP        HA      H   HCH1  .          4.9746    2.5359   -0.2011
SDP        HB2     H   HCH2  .          3.7548    2.2508   -3.0676
SDP        HB3     H   HCH2  .          2.7973    2.1805   -1.4892
SDP        H311    H   HCH2  .          0.6256   -1.2695   -2.0198
SDP        H312    H   HCH2  .          0.4558   -1.2364   -0.1873
SDP        H321    H   HCH3  .         -1.3291    0.1474   -1.1726
SDP        H322    H   HCH3  .         -0.1408    1.2268   -0.3177
SDP        H323    H   HCH3  .         -0.1336    1.1264   -2.1239
SDP        H411    H   HCH2  .          2.9659    0.6809   -5.2796
SDP        H412    H   HCH2  .          3.7114   -0.8516   -4.5859
SDP        H421    H   HCH3  .          1.9538   -1.2684   -6.3967
SDP        H422    H   HCH3  .          1.4946   -2.0205   -4.8105
SDP        H423    H   HCH3  .          0.7085   -0.4773   -5.3331
SDP        HXT     H   HOH1  .          7.9583    1.9203   -1.7127
#
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
SDP   N       CA    single        1.442 0.020
SDP   N      H      single        1.001 0.020
SDP   N      H2     single        1.000 0.020
SDP   CA      CB    single        1.545 0.020
SDP   CA      C     single        1.526 0.020
SDP   CA     HA     single        1.132 0.020
SDP   CB      OG    single        1.414 0.020
SDP   CB     HB2    single        1.123 0.020
SDP   CB     HB3    single        1.124 0.020
SDP   OG      P     single        1.598 0.020
SDP   C       O     double        1.234 0.020
SDP   C       OXT   single        1.357 0.020
SDP   C31     C32   single        1.513 0.020
SDP   C31     O1    single        1.415 0.020
SDP   C31    H311   single        1.126 0.020
SDP   C31    H312   single        1.127 0.020
SDP   C32    H321   single        1.116 0.020
SDP   C32    H322   single        1.116 0.020
SDP   C32    H323   single        1.116 0.020
SDP   C41     C42   single        1.513 0.020
SDP   C41     O2    single        1.415 0.020
SDP   C41    H411   single        1.127 0.020
SDP   C41    H412   single        1.126 0.020
SDP   C42    H421   single        1.116 0.020
SDP   C42    H422   single        1.116 0.020
SDP   C42    H423   single        1.116 0.020
SDP   O1      P     single        1.600 0.020
SDP   O2      P     single        1.600 0.020
SDP   O3      P     double        1.455 0.020
SDP   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
SDP  H2       N      H            110.03 3.000
SDP  H2       N       CA          110.89 3.000
SDP  H        N       CA          111.50 3.000
SDP  HA       CA      C           107.85 3.000
SDP  HA       CA      CB          108.07 3.000
SDP   C       CA      CB          107.72 3.000
SDP  HA       CA      N           108.62 3.000
SDP   C       CA      N           113.15 3.000
SDP   CB      CA      N           111.25 3.000
SDP  HB3      CB     HB2          110.62 3.000
SDP  HB3      CB      OG          108.75 3.000
SDP  HB2      CB      OG          108.54 3.000
SDP  HB3      CB      CA          110.51 3.000
SDP  HB2      CB      CA          111.13 3.000
SDP   OG      CB      CA          107.17 3.000
SDP   P       OG      CB          116.49 3.000
SDP   OXT     C       O           117.52 3.000
SDP   OXT     C       CA          114.25 3.000
SDP   O       C       CA          128.23 3.000
SDP  H312     C31    H311         109.56 3.000
SDP  H312     C31     O1          106.47 3.000
SDP  H311     C31     O1          109.58 3.000
SDP  H312     C31     C32         109.62 3.000
SDP  H311     C31     C32         111.41 3.000
SDP   O1      C31     C32         110.07 3.000
SDP  H323     C32    H322         108.28 3.000
SDP  H323     C32    H321         108.78 3.000
SDP  H322     C32    H321         109.15 3.000
SDP  H323     C32     C31         111.22 3.000
SDP  H322     C32     C31         110.22 3.000
SDP  H321     C32     C31         109.13 3.000
SDP  H412     C41    H411         109.52 3.000
SDP  H412     C41     O2          109.62 3.000
SDP  H411     C41     O2          106.42 3.000
SDP  H412     C41     C42         111.41 3.000
SDP  H411     C41     C42         109.63 3.000
SDP   O2      C41     C42         110.11 3.000
SDP  H423     C42    H422         108.29 3.000
SDP  H423     C42    H421         109.14 3.000
SDP  H422     C42    H421         108.78 3.000
SDP  H423     C42     C41         110.22 3.000
SDP  H422     C42     C41         111.25 3.000
SDP  H421     C42     C41         109.11 3.000
SDP   P       O1      C31         118.64 3.000
SDP   P       O2      C41         118.89 3.000
SDP   O3      P       O2          115.63 3.000
SDP   O3      P       O1          115.31 3.000
SDP   O2      P       O1          102.59 3.000
SDP   O3      P       OG          117.31 3.000
SDP   O2      P       OG          102.04 3.000
SDP   O1      P       OG          101.73 3.000
SDP  HXT      OXT     C           109.89 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
SDP CONST_01       HXT     OXT     C       CA         -180.00   0.0 0
SDP Var_01         O1      P       OG      CB          -66.07  30.0 3
SDP Var_02        H321     C32     C31     O1         -172.48  30.0 3
SDP Var_03        H421     C42     C41     O2          172.46  30.0 3
SDP Var_04        HB2      CB      OG      P           -74.87  30.0 1
SDP Var_05        H311     C31     O1      P             7.11  30.0 1
SDP Var_06        H411     C41     O2      P          -128.79  30.0 1
#
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
SDP chir_01   CA      N       CB      C     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
SDP plan-1     CA 0.020
SDP plan-1      C 0.020
SDP plan-1      O 0.020
SDP plan-1    OXT 0.020
SDP plan-1    HXT 0.020
