# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 26 20:58:44 2016
#
#   Inital geometry file: a 65 line input string
#   Ligand name: O-[(S)-(dimethylamino)(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: CN(C)[P@@](O)(=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
SEN        SEN 'O-[(S)-(dimethylamino)(hydroxy)phosphoryl]-L-serine' ligand 24 13 .
2016-04-26 2016-04-26
;
CIF prepared directly in eLBOW
;
#
data_comp_SEN
#
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
SEN         N      N   NH2    0    .       1.5090   -1.7210    0.2355
SEN         CA     C   CH1    0    .       1.7498   -0.5055   -0.5244
SEN         C      C   C      0    .       3.2498   -0.0938   -0.5872
SEN         O      O   O      0    .       4.0216   -0.3852    0.3753
SEN         CB     C   CH2    0    .       0.9378    0.7180   -0.0373
SEN         OG     O   O2     0    .      -0.4102    0.6166   -0.3988
SEN         P      P   P      0    .      -1.5256    0.3506    0.7994
SEN         O2     O   OP    -1    .      -2.0897    1.6899    1.1377
SEN         O3     O   O      0    .      -0.8458   -0.4749    1.8386
SEN         N1     N   NT     0    .      -2.6721   -0.5435    0.0476
SEN         C1     C   CH3    0    .      -2.5060   -1.9383   -0.0937
SEN         C2     C   CH3    0    .      -3.7604    0.0791   -0.5969
SEN         OXT    O   OC    -1    .       3.6511    0.5207   -1.6201
SEN         H      H   HNH2   0    .       2.2660   -1.8471    0.8856
SEN         HN2    H   HNH2   0    .       0.6631   -1.6119    0.7744
SEN         HA     H   HCH1   0    .       1.4190   -0.7185   -1.5830
SEN         HB     H   HCH2   0    .       1.0261    0.8351    1.0774
SEN         HBA    H   HCH2   0    .       1.3517    1.6322   -0.5487
SEN         H1     H   HCH3   0    .      -3.3743   -2.5140    0.3431
SEN         H1A    H   HCH3   0    .      -2.4318   -2.2614   -1.1730
SEN         H1B    H   HCH3   0    .      -1.5639   -2.2363    0.4461
SEN         H2     H   HCH3   0    .      -3.7027    1.1847   -0.3942
SEN         H2A    H   HCH3   0    .      -3.7661   -0.0941   -1.7135
SEN         H2B    H   HCH3   0    .      -4.7534   -0.3084   -0.2220
#
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
SEN   CA      N     single        1.454 0.020     1.454
SEN   N       H     single        0.860 0.020     1.020
SEN   N       HN2   single        0.890 0.020     1.040
SEN   CA      CB    single        1.547 0.020     1.547
SEN   CA      C     single        1.557 0.020     1.557
SEN   CA      HA    single        0.970 0.020     1.090
SEN   C       O     deloc         1.268 0.020     1.268
SEN   C       OXT   deloc         1.267 0.020     1.267
SEN   OG      CB    single        1.399 0.020     1.399
SEN   CB      HB    single        0.970 0.020     1.090
SEN   CB      HBA   single        0.970 0.020     1.090
SEN   OG      P     single        1.658 0.020     1.658
SEN   N1      P     single        1.637 0.020     1.637
SEN   O3      P     deloc         1.491 0.020     1.491
SEN   P       O2    deloc         1.492 0.020     1.492
SEN   C1      N1    single        1.412 0.020     1.412
SEN   C2      N1    single        1.410 0.020     1.410
SEN   C1      H1    single        0.970 0.020     1.090
SEN   C1      H1A   single        0.970 0.020     1.090
SEN   C1      H1B   single        0.970 0.020     1.090
SEN   C2      H2    single        0.970 0.020     1.090
SEN   C2      H2A   single        0.970 0.020     1.090
SEN   C2      H2B   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
SEN   HN2     N       H           107.42 3.000
SEN   HN2     N       CA          109.13 3.000
SEN   H       N       CA          108.55 3.000
SEN   HA      CA      CB          106.89 3.000
SEN   HA      CA      C           107.12 3.000
SEN   CB      CA      C           108.01 3.000
SEN   HA      CA      N           106.49 3.000
SEN   C       CA      N           113.69 3.000
SEN   CB      CA      N           114.19 3.000
SEN   OXT     C       O           122.52 3.000
SEN   OXT     C       CA          117.79 3.000
SEN   O       C       CA          119.69 3.000
SEN   HBA     CB      HB          109.68 3.000
SEN   HBA     CB      OG          107.19 3.000
SEN   HB      CB      OG          109.84 3.000
SEN   HBA     CB      CA          107.83 3.000
SEN   HB      CB      CA          110.69 3.000
SEN   OG      CB      CA          111.53 3.000
SEN   P       OG      CB          118.22 3.000
SEN   N1      P       O3          109.69 3.000
SEN   O3      P       O2          120.75 3.000
SEN   N1      P       O2          109.25 3.000
SEN   O2      P       OG          105.91 3.000
SEN   O3      P       OG          106.60 3.000
SEN   N1      P       OG          103.11 3.000
SEN   C2      N1      C1          118.78 3.000
SEN   C2      N1      P           120.62 3.000
SEN   C1      N1      P           120.22 3.000
SEN   H1B     C1      H1A         109.12 3.000
SEN   H1B     C1      H1          108.84 3.000
SEN   H1A     C1      H1          105.92 3.000
SEN   H1B     C1      N1          108.17 3.000
SEN   H1A     C1      N1          112.72 3.000
SEN   H1      C1      N1          111.98 3.000
SEN   H2B     C2      H2A         105.71 3.000
SEN   H2B     C2      H2          108.79 3.000
SEN   H2A     C2      H2          109.20 3.000
SEN   H2B     C2      N1          112.04 3.000
SEN   H2A     C2      N1          112.83 3.000
SEN   H2      C2      N1          108.18 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
SEN Var_01         N1      P       OG      CB         -147.74  30.0 3
SEN Var_02         C1      N1      P       OG           82.68  30.0 2
SEN Var_03         HB      CB      OG      P           -13.12  30.0 3
SEN Var_04         H1      C1      N1      P           124.23  30.0 3
SEN Var_05         H2      C2      N1      P            -5.25  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
SEN 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
SEN plan-1     CA 0.020
SEN plan-1      C 0.020
SEN plan-1      O 0.020
SEN plan-1    OXT 0.020
