# 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 15:27:44 2012
#
#   Inital geometry file: a 87 line input string
#   Ligand name: O-[bis(propan-2-yloxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CC(C)O[P](=O)(OC[C@H](N)C(O)=O)OC(C)C
#
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
SVY        SVY 'O-[bis(propan-2-yloxy)phosphoryl]-L-serine' L-peptide 37 17 .
2012-08-28 2012-08-28
;
CIF prepared directly in eLBOW
;
#
data_comp_SVY
#
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
SVY         N      N   NH2   .          1.1515    2.1675   -0.5381
SVY         CA     C   CH1   .          2.1346    1.6207    0.3624
SVY         C      C   C     .          3.5657    1.7330   -0.1464
SVY         O      O   O     .          3.9989    1.4503   -1.2679
SVY         CB     C   CH2   .          1.8640    0.1404    0.7305
SVY         OG     O   O2    .          0.5145   -0.0235    1.0916
SVY         C1     C   CH1   .         -1.3629   -3.1646   -0.0738
SVY         C2     C   CH3   .         -0.5046   -4.3465   -0.4942
SVY         C3     C   CH3   .         -2.4625   -3.6159    0.8754
SVY        C1'     C   CH1   .         -2.3005    1.1010   -0.0777
SVY        C2'     C   CH3   .         -3.5444    0.9201   -0.9340
SVY        C3'     C   CH3   .         -2.5913    2.0181    1.0991
SVY         P      P   P     .         -0.4744   -0.7334    0.0415
SVY         O1P    O   O2    .         -0.5292   -2.2287    0.6000
SVY         O2P    O   O2    .         -1.9162   -0.1747    0.4253
SVY         O3P    O   O     .         -0.0655   -0.6024   -1.3552
SVY         OXT    O   OH1   .          4.4624    2.2050    0.7606
SVY        HN1     H   HNH2  .          1.1919    3.1677   -0.5439
SVY        HN2     H   HNH2  .          1.2744    1.8223   -1.4706
SVY        HA      H   HCH1  .          2.0913    2.2217    1.3230
SVY        HBC1    H   HCH2  .          2.1321   -0.5441   -0.1209
SVY        HBC2    H   HCH2  .          2.4740   -0.1072    1.6465
SVY        HOT     H   HOH1  .          5.3461    2.2455    0.3580
SVY        H1      H   HCH1  .         -1.8087   -2.6674   -0.9854
SVY        H2C1    H   HCH3  .          0.2740   -4.0262   -1.2252
SVY        H2C2    H   HCH3  .          0.0049   -4.7857    0.3963
SVY        H2C3    H   HCH3  .         -1.1503   -5.1229   -0.9694
SVY        H3C1    H   HCH3  .         -2.0149   -4.0072    1.8199
SVY        H3C2    H   HCH3  .         -3.1403   -2.7672    1.1318
SVY        H3C3    H   HCH3  .         -3.0615   -4.4229    0.3902
SVY        H1'     H   HCH1  .         -1.4550    1.5176   -0.7009
SVY        H2'1    H   HCH3  .         -4.3611    0.4575   -0.3303
SVY        H2'2    H   HCH3  .         -3.8823    1.9157   -1.3084
SVY        H2'3    H   HCH3  .         -3.3327    0.2576   -1.8068
SVY        H3'1    H   HCH3  .         -3.3494    1.5497    1.7708
SVY        H3'2    H   HCH3  .         -1.6636    2.2085    1.6895
SVY        H3'3    H   HCH3  .         -2.9867    2.9903    0.7197
#
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
SVY   N       CA    single        1.441 0.020
SVY   CA      C     single        1.523 0.020
SVY   C       O     double        1.235 0.020
SVY   CA      CB    single        1.549 0.020
SVY   CB      OG    single        1.407 0.020
SVY   C1      C2    single        1.520 0.020
SVY   C1      C3    single        1.521 0.020
SVY  C1'     C2'    single        1.521 0.020
SVY  C1'     C3'    single        1.520 0.020
SVY   OG      P     single        1.608 0.020
SVY   C1      O1P   single        1.423 0.020
SVY   P       O1P   single        1.597 0.020
SVY  C1'      O2P   single        1.424 0.020
SVY   P       O2P   single        1.593 0.020
SVY   P       O3P   double        1.461 0.020
SVY   C       OXT   single        1.360 0.020
SVY   N      HN1    single        1.001 0.020
SVY   N      HN2    single        1.002 0.020
SVY   CA     HA     single        1.134 0.020
SVY   CB     HBC1   single        1.125 0.020
SVY   CB     HBC2   single        1.128 0.020
SVY   OXT    HOT    single        0.972 0.020
SVY   C1     H1     single        1.130 0.020
SVY   C2     H2C1   single        1.115 0.020
SVY   C2     H2C2   single        1.116 0.020
SVY   C2     H2C3   single        1.116 0.020
SVY   C3     H3C1   single        1.116 0.020
SVY   C3     H3C2   single        1.116 0.020
SVY   C3     H3C3   single        1.116 0.020
SVY  C1'     H1'    single        1.130 0.020
SVY  C2'     H2'1   single        1.116 0.020
SVY  C2'     H2'2   single        1.116 0.020
SVY  C2'     H2'3   single        1.116 0.020
SVY  C3'     H3'1   single        1.116 0.020
SVY  C3'     H3'2   single        1.116 0.020
SVY  C3'     H3'3   single        1.116 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
SVY  HN2      N      HN1          109.51 3.000
SVY  HN2      N       CA          111.54 3.000
SVY  HN1      N       CA          110.82 3.000
SVY  HA       CA      CB          107.37 3.000
SVY  HA       CA      C           106.25 3.000
SVY   CB      CA      C           108.30 3.000
SVY  HA       CA      N           107.59 3.000
SVY   CB      CA      N           113.08 3.000
SVY   C       CA      N           113.85 3.000
SVY   OXT     C       O           116.99 3.000
SVY   OXT     C       CA          114.98 3.000
SVY   O       C       CA          128.03 3.000
SVY  HBC2     CB     HBC1         110.62 3.000
SVY  HBC2     CB      OG          106.54 3.000
SVY  HBC1     CB      OG          110.61 3.000
SVY  HBC2     CB      CA          107.96 3.000
SVY  HBC1     CB      CA          111.10 3.000
SVY   OG      CB      CA          109.87 3.000
SVY   P       OG      CB          118.29 3.000
SVY  H1       C1      O1P         108.89 3.000
SVY  H1       C1      C3          110.41 3.000
SVY   O1P     C1      C3          108.85 3.000
SVY  H1       C1      C2          109.99 3.000
SVY   O1P     C1      C2          108.15 3.000
SVY   C3      C1      C2          110.50 3.000
SVY  H2C3     C2     H2C2         109.28 3.000
SVY  H2C3     C2     H2C1         108.95 3.000
SVY  H2C2     C2     H2C1         108.50 3.000
SVY  H2C3     C2      C1          109.39 3.000
SVY  H2C2     C2      C1          110.07 3.000
SVY  H2C1     C2      C1          110.63 3.000
SVY  H3C3     C3     H3C2         108.89 3.000
SVY  H3C3     C3     H3C1         109.25 3.000
SVY  H3C2     C3     H3C1         108.40 3.000
SVY  H3C3     C3      C1          109.35 3.000
SVY  H3C2     C3      C1          110.91 3.000
SVY  H3C1     C3      C1          110.02 3.000
SVY  H1'     C1'      O2P         108.86 3.000
SVY  H1'     C1'     C3'          110.34 3.000
SVY   O2P    C1'     C3'          108.58 3.000
SVY  H1'     C1'     C2'          110.20 3.000
SVY   O2P    C1'     C2'          108.24 3.000
SVY  C3'     C1'     C2'          110.56 3.000
SVY  H2'3    C2'     H2'2         108.95 3.000
SVY  H2'3    C2'     H2'1         108.41 3.000
SVY  H2'2    C2'     H2'1         109.25 3.000
SVY  H2'3    C2'     C1'          110.84 3.000
SVY  H2'2    C2'     C1'          109.29 3.000
SVY  H2'1    C2'     C1'          110.07 3.000
SVY  H3'3    C3'     H3'2         109.01 3.000
SVY  H3'3    C3'     H3'1         109.24 3.000
SVY  H3'2    C3'     H3'1         108.53 3.000
SVY  H3'3    C3'     C1'          109.28 3.000
SVY  H3'2    C3'     C1'          110.70 3.000
SVY  H3'1    C3'     C1'          110.05 3.000
SVY   O3P     P       O2P         116.88 3.000
SVY   O3P     P       O1P         115.33 3.000
SVY   O2P     P       O1P         102.30 3.000
SVY   O3P     P       OG          114.37 3.000
SVY   O2P     P       OG          104.14 3.000
SVY   O1P     P       OG          101.89 3.000
SVY   P       O1P     C1          118.05 3.000
SVY   P       O2P    C1'          118.25 3.000
SVY  HOT      OXT     C           109.73 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
SVY CONST_01       HOT     OXT     C       CA         -180.00   0.0 0
SVY Var_01         O1P     P       OG      CB           98.95  30.0 3
SVY Var_02        H3C1     C3      C1      C2           64.07  30.0 3
SVY Var_03        H2C1     C2      C1      C3          177.49  30.0 3
SVY Var_04        H3'1    C3'     C1'     C2'           63.90  30.0 3
SVY Var_05        H2'1    C2'     C1'     C3'          -60.78  30.0 3
SVY Var_06        HBC1     CB      OG      P           -18.10  30.0 1
SVY Var_07        H1       C1      O1P     P             4.21  30.0 1
SVY Var_08        H1'     C1'      O2P     P            -0.08  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
SVY 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
SVY plan-1     CA 0.020
SVY plan-1      C 0.020
SVY plan-1      O 0.020
SVY plan-1    OXT 0.020
SVY plan-1    HOT 0.020
