# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 26 19:06:16 2016
#
#   Inital geometry file: a 108 line input string
#   Ligand name: (2S)-2-amino-6-{[(2R,4R)-1,4-dihydroxy-3-oxo-5-(phosphonooxy)pentan-2-yl]amino}hexanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN[C@H](CO)C(=O)[C@H](O)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
LRK        LRK '(2S)-2-amino-6-{[(2R,4R)-1,4-dihydroxy-3-oxo-5-(phosphonooxy)pentan-2-yl]amino}hexanoic acid (non-preferred name)' ligand 43 23 .
2016-04-26 2016-04-26
;
CIF prepared directly in eLBOW
;
#
data_comp_LRK
#
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
LRK         C      C   C      0    .       8.0858   -0.3540   -0.1137
LRK         O      O   O      0    .       8.9070   -1.1626    0.4144
LRK         CA     C   CH1    0    .       6.6783   -0.8885   -0.5342
LRK         N      N   NH2    0    .       6.5026   -2.3223   -0.3365
LRK         CB     C   CH2    0    .       5.6083   -0.0354    0.1518
LRK         CG     C   CH2    0    .       4.2153   -0.2889   -0.3863
LRK         CD     C   CH2    0    .       3.1941    0.6163    0.2727
LRK         CE     C   CH2    0    .       1.7953    0.3592   -0.2914
LRK         NZ     N   NH1    0    .       0.7907    1.2493    0.2560
LRK         C3     C   CH1    0    .      -0.5644    0.9817   -0.2202
LRK         C2     C   CH2    0    .      -0.9069    1.8797   -1.4265
LRK         O1     O   OH1    0    .      -0.9302    3.2625   -1.1321
LRK         C5     C   C      0    .      -1.6348    1.0712    0.8890
LRK         O13    O   O      0    .      -1.2834    0.9721    2.0714
LRK         C6     C   CH1    0    .      -3.0745    1.2342    0.4522
LRK         O14    O   OH1    0    .      -3.8526    1.5446    1.5831
LRK         C7     C   CH2    0    .      -3.6004   -0.0299   -0.2946
LRK         O8     O   O2     0    .      -4.6728    0.3016   -1.0716
LRK         P9     P   P      0    .      -6.1858   -0.3627   -0.5112
LRK         O11    O   OP    -1    .      -7.1684    0.0922   -1.5472
LRK         O10    O   O      0    .      -5.8647   -1.8283   -0.4541
LRK         O12    O   OP    -1    .      -6.2527    0.3226    0.8360
LRK         H2     H   HCH1   0    .       6.5981   -0.7175   -1.6483
LRK         H3     H   HNH2   0    .       7.4118   -2.7513   -0.4069
LRK         H4     H   HNH2   0    .       6.1840   -2.4849    0.6021
LRK         H6     H   HCH2   0    .       5.6229   -0.2219    1.2574
LRK         H7     H   HCH2   0    .       5.8914    1.0391   -0.0098
LRK         H8     H   HCH2   0    .       4.2078   -0.1184   -1.4949
LRK         H9     H   HCH2   0    .       3.9288   -1.3599   -0.2171
LRK         H10    H   HCH2   0    .       3.1957    0.4386    1.3800
LRK         H11    H   HCH2   0    .       3.4801    1.6876    0.1069
LRK         H12    H   HCH2   0    .       1.8182    0.5231   -1.4066
LRK         H13    H   HCH2   0    .       1.5422   -0.7311   -0.1253
LRK         H14    H   HNH1   0    .       0.8143    1.2302    1.2605
LRK         H16    H   HCH1   0    .      -0.6557   -0.0867   -0.6009
LRK         H17    H   HCH2   0    .      -0.1169    1.7792   -2.2195
LRK         H18    H   HCH2   0    .      -1.9013    1.5577   -1.8437
LRK         H19    H   HOH1   0    .      -1.4783    3.3748   -0.3453
LRK         H20    H   HCH1   0    .      -3.1343    2.1159   -0.2525
LRK         H21    H   HOH1   0    .      -4.7520    1.1338    1.4369
LRK         H22    H   HCH2   0    .      -2.7561   -0.4092   -0.9450
LRK         H23    H   HCH2   0    .      -3.8668   -0.8165    0.4667
LRK         OXT    O   OC    -1    .       8.3537    0.8578   -0.3474
#
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
LRK   O       C     deloc         1.268 0.020     1.268
LRK   C       CA    single        1.563 0.020     1.563
LRK   CA      N     single        1.458 0.020     1.458
LRK   CA      CB    single        1.531 0.020     1.531
LRK   CG      CB    single        1.515 0.020     1.515
LRK   CG      CD    single        1.515 0.020     1.515
LRK   C2      O1    single        1.414 0.020     1.414
LRK   C2      C3    single        1.542 0.020     1.542
LRK   CE      CD    single        1.530 0.020     1.530
LRK   CE      NZ    single        1.450 0.020     1.450
LRK   C3      NZ    single        1.461 0.020     1.461
LRK   C3      C5    single        1.544 0.020     1.544
LRK   C5      O13   double        1.237 0.020     1.237
LRK   C5      C6    single        1.513 0.020     1.513
LRK   O14     C6    single        1.407 0.020     1.407
LRK   C6      C7    single        1.560 0.020     1.560
LRK   C7      O8    single        1.365 0.020     1.365
LRK   O10     P9    deloc         1.501 0.020     1.501
LRK   O8      P9    single        1.745 0.020     1.745
LRK   P9      O11   deloc         1.499 0.020     1.499
LRK   P9      O12   deloc         1.513 0.020     1.513
LRK   CA      H2    single        0.970 0.020     1.090
LRK   N       H3    single        0.890 0.020     1.040
LRK   N       H4    single        0.890 0.020     1.040
LRK   CB      H6    single        0.970 0.020     1.090
LRK   CB      H7    single        0.970 0.020     1.090
LRK   CG      H8    single        0.970 0.020     1.090
LRK   CG      H9    single        0.970 0.020     1.090
LRK   CD      H10   single        0.970 0.020     1.090
LRK   CD      H11   single        0.970 0.020     1.090
LRK   CE      H12   single        0.970 0.020     1.090
LRK   CE      H13   single        0.970 0.020     1.090
LRK   NZ      H14   single        0.890 0.020     1.040
LRK   C3      H16   single        0.970 0.020     1.090
LRK   C2      H17   single        0.970 0.020     1.090
LRK   C2      H18   single        0.970 0.020     1.090
LRK   O1      H19   single        0.850 0.020     0.980
LRK   C6      H20   single        0.970 0.020     1.090
LRK   O14     H21   single        0.850 0.020     0.980
LRK   C7      H22   single        0.970 0.020     1.090
LRK   C7      H23   single        0.970 0.020     1.090
LRK   C       OXT   deloc         1.263 0.020     1.263
#
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
LRK   OXT     C       CA          117.99 3.000
LRK   OXT     C       O           123.48 3.000
LRK   CA      C       O           118.50 3.000
LRK   H2      CA      CB          107.93 3.000
LRK   H2      CA      N           105.90 3.000
LRK   CB      CA      N           113.77 3.000
LRK   H2      CA      C           106.10 3.000
LRK   CB      CA      C           108.56 3.000
LRK   N       CA      C           114.10 3.000
LRK   H4      N       H3          106.41 3.000
LRK   H4      N       CA          108.92 3.000
LRK   H3      N       CA          107.48 3.000
LRK   H7      CB      H6          107.32 3.000
LRK   H7      CB      CG          109.93 3.000
LRK   H6      CB      CG          109.53 3.000
LRK   H7      CB      CA          107.01 3.000
LRK   H6      CB      CA          109.88 3.000
LRK   CG      CB      CA          112.98 3.000
LRK   H9      CG      H8          107.01 3.000
LRK   H9      CG      CD          109.43 3.000
LRK   H8      CG      CD          109.54 3.000
LRK   H9      CG      CB          109.95 3.000
LRK   H8      CG      CB          109.38 3.000
LRK   CD      CG      CB          111.43 3.000
LRK   H11     CD      H10         107.28 3.000
LRK   H11     CD      CE          109.83 3.000
LRK   H10     CD      CE          109.80 3.000
LRK   H11     CD      CG          109.55 3.000
LRK   H10     CD      CG          109.50 3.000
LRK   CE      CD      CG          110.81 3.000
LRK   H13     CE      H12         106.85 3.000
LRK   H13     CE      NZ          112.41 3.000
LRK   H12     CE      NZ          107.36 3.000
LRK   H13     CE      CD          108.20 3.000
LRK   H12     CE      CD          108.77 3.000
LRK   NZ      CE      CD          113.02 3.000
LRK   H14     NZ      C3          110.12 3.000
LRK   H14     NZ      CE          110.46 3.000
LRK   C3      NZ      CE          114.03 3.000
LRK   H16     C3      C5          103.84 3.000
LRK   H16     C3      C2          105.50 3.000
LRK   C5      C3      C2          111.97 3.000
LRK   H16     C3      NZ          110.82 3.000
LRK   C5      C3      NZ          113.47 3.000
LRK   C2      C3      NZ          110.74 3.000
LRK   H18     C2      H17         109.51 3.000
LRK   H18     C2      O1          110.02 3.000
LRK   H17     C2      O1          104.24 3.000
LRK   H18     C2      C3          108.64 3.000
LRK   H17     C2      C3          110.10 3.000
LRK   O1      C2      C3          114.22 3.000
LRK   H19     O1      C2          107.03 3.000
LRK   C6      C5      O13         123.68 3.000
LRK   C6      C5      C3          117.28 3.000
LRK   O13     C5      C3          119.01 3.000
LRK   H20     C6      C7          108.41 3.000
LRK   H20     C6      O14         107.44 3.000
LRK   C7      C6      O14         112.15 3.000
LRK   H20     C6      C5          108.32 3.000
LRK   C7      C6      C5          111.82 3.000
LRK   O14     C6      C5          108.53 3.000
LRK   H21     O14     C6          106.82 3.000
LRK   H23     C7      H22         109.32 3.000
LRK   H23     C7      O8          111.62 3.000
LRK   H22     C7      O8          109.91 3.000
LRK   H23     C7      C6          108.79 3.000
LRK   H22     C7      C6          107.18 3.000
LRK   O8      C7      C6          109.91 3.000
LRK   P9      O8      C7          113.94 3.000
LRK   O12     P9      O10         114.69 3.000
LRK   O12     P9      O11         116.68 3.000
LRK   O10     P9      O11         117.57 3.000
LRK   O12     P9      O8           98.74 3.000
LRK   O11     P9      O8          103.35 3.000
LRK   O10     P9      O8          101.45 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
LRK Var_01         CD      CG      CB      CA         -177.47  30.0 1
LRK Var_02         CE      CD      CG      CB          179.39  30.0 3
LRK Var_03         NZ      CE      CD      CG         -176.95  30.0 1
LRK Var_04         C3      NZ      CE      CD         -177.25  30.0 3
LRK Var_05         O10     P9      O8      C7          -55.51  30.0 3
LRK Var_06         H22     C7      O8      P9          131.19  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
LRK chir_01   CA      C       N       CB    negativ
LRK chir_02   C3      NZ      C2      C5    positiv
LRK chir_03   C6      O14     C5      C7    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
LRK plan-1     C3 0.020
LRK plan-1     C5 0.020
LRK plan-1    O13 0.020
LRK plan-1     C6 0.020
LRK plan-2      C 0.020
LRK plan-2      O 0.020
LRK plan-2     CA 0.020
LRK plan-2    OXT 0.020
