# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 26 19:11:54 2016
#
#   Inital geometry file: a 101 line input string
#   Ligand name: O-phosphono-L-seryl-N-[(3S)-3-amino-3-carboxypropyl]glycinamide
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC(=O)CNC(=O)[C@@H](N)CO[P](O)(O)=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
LYV        LYV 'O-phosphono-L-seryl-N-[(3S)-3-amino-3-carboxypropyl]glycinamide' L-peptide 38 22 .
2016-04-26 2016-04-26
;
CIF prepared directly in eLBOW
;
#
data_comp_LYV
#
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
LYV         N      N   NH2    0    .       6.7463    0.3005    1.9376
LYV         CA     C   CH1    0    .       6.6117   -0.2621    0.5995
LYV         C      C   C      0    .       7.8530   -0.0200   -0.3220
LYV         O      O   O      0    .       8.8543    0.5826    0.1677
LYV         CB     C   CH2    0    .       5.3570    0.2061   -0.1402
LYV         CG     C   CH2    0    .       4.0820   -0.2607    0.5622
LYV         ND     N   NH1    0    .       2.8740    0.1234   -0.1247
LYV         CE     C   C      0    .       1.6843   -0.5518    0.0144
LYV         CZ     C   CH2    0    .       0.4955   -0.0744   -0.8437
LYV         N1     N   NH1    0    .      -0.7256    0.0230   -0.1169
LYV         C2     C   C      0    .      -1.6085    1.0918   -0.2693
LYV         OZ1    O   O      0    .      -1.2767    2.0450   -1.0059
LYV         C4     C   CH1    0    .      -2.9487    0.9902    0.4713
LYV         C5     C   CH2    0    .      -3.9453    0.1805   -0.4340
LYV         N6     N   NH2    0    .      -3.4297    2.2915    0.8956
LYV         O7     O   O      0    .       1.5840   -1.5524    0.7566
LYV         P      P   P      0    .      -6.5242    0.4872   -0.0503
LYV         O1     O   O2     0    .      -4.9932   -0.2655    0.3179
LYV         O2     O   O      0    .      -6.5685    0.3717   -1.5490
LYV         O3     O   OP    -1    .      -7.5033   -0.3450    0.7248
LYV         O4     O   OP    -1    .      -6.2472    1.8747    0.4759
LYV         H1     H   HNH2   0    .       7.7196    0.2399    2.1919
LYV         H2     H   HNH2   0    .       6.5230    1.2792    1.9016
LYV         H4     H   HCH1   0    .       6.5394   -1.3813    0.7371
LYV         H6     H   HCH2   0    .       5.3611    1.3236   -0.2288
LYV         H7     H   HCH2   0    .       5.4118   -0.2163   -1.1792
LYV         H8     H   HCH2   0    .       4.0959   -1.3843    0.6586
LYV         H9     H   HCH2   0    .       4.0529    0.1636    1.6076
LYV         H10    H   HNH1   0    .       2.9094    0.9307   -0.6970
LYV         H11    H   HCH2   0    .       0.7092    0.9232   -1.3248
LYV         H12    H   HCH2   0    .       0.4060   -0.8472   -1.6652
LYV         H13    H   HNH1   0    .      -0.9937   -0.7580    0.4326
LYV         H14    H   HCH1   0    .      -2.8069    0.3878    1.4175
LYV         H15    H   HCH2   0    .      -4.2926    0.8273   -1.2878
LYV         H16    H   HCH2   0    .      -3.3658   -0.6988   -0.8474
LYV         H17    H   HNH2   0    .      -3.4472    2.9045    0.0996
LYV         H18    H   HNH2   0    .      -4.4030    2.1691    1.1862
LYV         OXT    O   OC    -1    .       7.8111   -0.4640   -1.5027
#
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
LYV   N       CA    single        1.458 0.020     1.458
LYV   CA      CB    single        1.530 0.020     1.530
LYV   CA      C     single        1.565 0.020     1.565
LYV   CB      CG    single        1.529 0.020     1.529
LYV   ND      CG    single        1.442 0.020     1.442
LYV   ND      CE    single        1.375 0.020     1.375
LYV   C       O     deloc         1.267 0.020     1.267
LYV   N6      C4    single        1.451 0.020     1.451
LYV   C5      C4    single        1.571 0.020     1.571
LYV   C5      O1    single        1.365 0.020     1.365
LYV   CZ      CE    single        1.542 0.020     1.542
LYV   CZ      N1    single        1.424 0.020     1.424
LYV   CE      O7    double        1.250 0.020     1.250
LYV   C4      C2    single        1.535 0.020     1.535
LYV   O1      P     single        1.745 0.020     1.745
LYV   N1      C2    single        1.395 0.020     1.395
LYV   O2      P     deloc         1.504 0.020     1.504
LYV   C2      OZ1   double        1.249 0.020     1.249
LYV   P       O3    deloc         1.501 0.020     1.501
LYV   P       O4    deloc         1.510 0.020     1.510
LYV   N       H1    single        0.890 0.020     1.040
LYV   N       H2    single        0.890 0.020     1.040
LYV   CA      H4    single        0.970 0.020     1.090
LYV   CB      H6    single        0.970 0.020     1.090
LYV   CB      H7    single        0.970 0.020     1.090
LYV   CG      H8    single        0.970 0.020     1.090
LYV   CG      H9    single        0.970 0.020     1.090
LYV   ND      H10   single        0.860 0.020     1.020
LYV   CZ      H11   single        0.970 0.020     1.090
LYV   CZ      H12   single        0.970 0.020     1.090
LYV   N1      H13   single        0.860 0.020     1.020
LYV   C4      H14   single        0.970 0.020     1.090
LYV   C5      H15   single        0.970 0.020     1.090
LYV   C5      H16   single        0.970 0.020     1.090
LYV   N6      H17   single        0.890 0.020     1.040
LYV   N6      H18   single        0.890 0.020     1.040
LYV   C       OXT   deloc         1.262 0.020     1.262
#
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
LYV   H2      N       H1          106.40 3.000
LYV   H2      N       CA          108.82 3.000
LYV   H1      N       CA          107.31 3.000
LYV   H4      CA      CB          108.03 3.000
LYV   H4      CA      C           106.01 3.000
LYV   CB      CA      C           108.57 3.000
LYV   H4      CA      N           106.04 3.000
LYV   C       CA      N           114.05 3.000
LYV   CB      CA      N           113.67 3.000
LYV   OXT     C       O           123.71 3.000
LYV   OXT     C       CA          118.04 3.000
LYV   O       C       CA          118.22 3.000
LYV   H7      CB      H6          107.56 3.000
LYV   H7      CB      CG          110.55 3.000
LYV   H6      CB      CG          110.11 3.000
LYV   H7      CB      CA          106.99 3.000
LYV   H6      CB      CA          109.89 3.000
LYV   CG      CB      CA          111.62 3.000
LYV   H9      CG      H8          107.20 3.000
LYV   H9      CG      ND          108.63 3.000
LYV   H8      CG      ND          108.45 3.000
LYV   H9      CG      CB          109.41 3.000
LYV   H8      CG      CB          109.47 3.000
LYV   ND      CG      CB          113.49 3.000
LYV   H10     ND      CE          119.32 3.000
LYV   H10     ND      CG          117.56 3.000
LYV   CE      ND      CG          123.09 3.000
LYV   O7      CE      CZ          121.10 3.000
LYV   O7      CE      ND          121.51 3.000
LYV   CZ      CE      ND          117.31 3.000
LYV   H12     CZ      H11         108.03 3.000
LYV   H12     CZ      N1          110.45 3.000
LYV   H11     CZ      N1          108.64 3.000
LYV   H12     CZ      CE          104.69 3.000
LYV   H11     CZ      CE          111.42 3.000
LYV   N1      CZ      CE          113.46 3.000
LYV   H13     N1      C2          119.53 3.000
LYV   H13     N1      CZ          117.42 3.000
LYV   C2      N1      CZ          122.64 3.000
LYV   C4      C2      OZ1         124.54 3.000
LYV   OZ1     C2      N1          118.74 3.000
LYV   C4      C2      N1          116.70 3.000
LYV   H14     C4      N6          105.95 3.000
LYV   H14     C4      C5          106.69 3.000
LYV   N6      C4      C5          114.86 3.000
LYV   H14     C4      C2          109.25 3.000
LYV   C5      C4      C2          108.06 3.000
LYV   N6      C4      C2          111.79 3.000
LYV   H16     C5      H15         109.10 3.000
LYV   H16     C5      O1          109.92 3.000
LYV   H15     C5      O1          111.64 3.000
LYV   H16     C5      C4          106.63 3.000
LYV   H15     C5      C4          109.66 3.000
LYV   O1      C5      C4          109.76 3.000
LYV   H18     N6      H17         106.35 3.000
LYV   H18     N6      C4          106.93 3.000
LYV   H17     N6      C4          108.74 3.000
LYV   O4      P       O3          116.70 3.000
LYV   O4      P       O2          115.05 3.000
LYV   O3      P       O2          116.93 3.000
LYV   O4      P       O1           99.32 3.000
LYV   O3      P       O1          102.95 3.000
LYV   O2      P       O1          101.72 3.000
LYV   P       O1      C5          114.60 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
LYV CONST_01       CZ      CE      ND      CG         -176.63   0.0 0
LYV CONST_02       O7      CE      ND      CG            0.00   0.0 0
LYV CONST_03       C4      C2      N1      CZ          173.94   0.0 0
LYV CONST_04       OZ1     C2      N1      CZ           -4.81   0.0 0
LYV CONST_05       H10     ND      CE      CZ            5.47   0.0 0
LYV CONST_06       H13     N1      C2      OZ1        -177.30   0.0 0
LYV Var_01         ND      CG      CB      CA         -178.17  30.0 3
LYV Var_02         CE      ND      CG      CB          155.72  30.0 1
LYV Var_03         N1      CZ      CE      ND         -135.08  30.0 1
LYV Var_04         C2      N1      CZ      CE          137.71  30.0 3
LYV Var_05         O2      P       O1      C5           48.85  30.0 3
LYV Var_06         H15     C5      O1      P           -10.21  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
LYV chir_01   CA      N       CB      C     negativ
LYV chir_02   C4      N6      C5      C2    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
LYV plan-1     CG 0.020
LYV plan-1     ND 0.020
LYV plan-1     CE 0.020
LYV plan-1     CZ 0.020
LYV plan-1     O7 0.020
LYV plan-1    H10 0.020
LYV plan-2     CZ 0.020
LYV plan-2     N1 0.020
LYV plan-2     C2 0.020
LYV plan-2    OZ1 0.020
LYV plan-2     C4 0.020
LYV plan-2    H13 0.020
LYV plan-3     CA 0.020
LYV plan-3      C 0.020
LYV plan-3      O 0.020
LYV plan-3    OXT 0.020
