# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 22 16:25:42 2019
#
#   Inital geometry file: a 51 line input string
#   Ligand name: O-thiophosphono-L-serine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[P](O)(S)=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
2RX        2RX 'O-thiophosphono-L-serine ' L-peptide 17 11 .
2019-03-22 2019-03-22
;
CIF prepared directly in eLBOW
;
#
data_comp_2RX
#
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
2RX         N      N   NH2    0  -0.337    1.9235    1.8108    0.2705
2RX         C      C   C      0   0.308    3.3460   -0.2682   -0.0246
2RX         O      O   O      0  -0.607    4.1857    0.4641   -0.6315
2RX         CA     C   CH1    0  -0.131    2.0316    0.3797    0.5141
2RX         CB     C   CH2    0   0.029    0.8341   -0.4384   -0.0048
2RX         OG     O   O2     0  -0.735   -0.2997   -0.2516    0.8099
2RX         P40    P   P      0   2.538   -1.6225    0.4354    0.1883
2RX         S41    S   S2     0  -0.927   -2.8429   -1.3871   -0.4263
2RX         O42    O   OP    -1  -1.107   -2.4434    0.9381    1.3015
2RX         O43    O   O      0  -1.099   -1.3004    1.1662   -1.0435
2RX         H1     H   HNH2   0   0.135    2.8453    2.1595    0.0603
2RX         H2     H   HNH2   0   0.128    1.3582    1.9743   -0.5437
2RX         H5     H   HCH1   0   0.091    2.0574    0.2554    1.6369
2RX         H6     H   HCH2   0   0.076    0.5846   -0.1703   -1.0674
2RX         H7     H   HCH2   0   0.102    1.1165   -1.5276    0.0634
2RX         H8     H   H      0   0.122   -3.5100   -1.4674    0.7113
2RX         O1     O   OC    -1  -0.586    3.5446   -1.4969    0.1982
#
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
2RX   O43     P40   deloc         1.468 0.020     1.468
2RX   O42     P40   deloc         1.472 0.020     1.472
2RX   P40     OG    single        1.615 0.020     1.615
2RX   P40     S41   single        2.278 0.020     2.278
2RX   OG      CB    single        1.409 0.020     1.409
2RX   O       C     deloc         1.269 0.020     1.269
2RX   N       CA    single        1.456 0.020     1.456
2RX   CB      CA    single        1.540 0.020     1.540
2RX   C       CA    single        1.561 0.020     1.561
2RX   N       H1    single        0.890 0.020     1.040
2RX   N       H2    single        0.890 0.020     1.040
2RX   CA      H5    single        0.970 0.020     1.090
2RX   CB      H6    single        0.970 0.020     1.090
2RX   CB      H7    single        0.970 0.020     1.090
2RX   S41     H8    single        1.200 0.020     1.300
2RX   C       O1    deloc         1.264 0.020     1.264
#
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
2RX   H2      N       H1          106.82 3.000
2RX   H2      N       CA          109.72 3.000
2RX   H1      N       CA          107.88 3.000
2RX   O1      C       CA          118.33 3.000
2RX   O1      C       O           122.77 3.000
2RX   CA      C       O           118.87 3.000
2RX   H5      CA      CB          107.10 3.000
2RX   H5      CA      C           106.14 3.000
2RX   CB      CA      C           108.53 3.000
2RX   H5      CA      N           106.03 3.000
2RX   C       CA      N           114.38 3.000
2RX   CB      CA      N           114.08 3.000
2RX   H7      CB      H6          110.08 3.000
2RX   H7      CB      OG          107.15 3.000
2RX   H6      CB      OG          109.66 3.000
2RX   H7      CB      CA          107.34 3.000
2RX   H6      CB      CA          111.37 3.000
2RX   OG      CB      CA          111.13 3.000
2RX   P40     OG      CB          119.54 3.000
2RX   O43     P40     O42         125.94 3.000
2RX   O42     P40     S41         100.28 3.000
2RX   O43     P40     S41         106.83 3.000
2RX   S41     P40     OG          101.68 3.000
2RX   O42     P40     OG          108.12 3.000
2RX   O43     P40     OG          110.80 3.000
2RX   H8      S41     P40          94.98 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
2RX Var_01         O43     P40     OG      CB          -18.58  30.0 1
2RX Var_02         H6      CB      OG      P40          -7.01  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
2RX 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
2RX plan-1      C 0.020
2RX plan-1      O 0.020
2RX plan-1     CA 0.020
2RX plan-1     O1 0.020
