# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX
#   - file written: Thu Aug 18 15:38:59 2022
#
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH+]cc(CO[P](O)(O)=O)c(C=NCCCC[C@H](N)C(O)=O)c1O
#   Template file: LLP_neutron.pdb
#
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
LLP        LLP "(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid"
 ligand 45 25 .
2013-08-26 2022-08-18
;
CIF prepared directly in eLBOW
;
#
data_comp_LLP
#
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
LLP        C2'     C   CH3    0    .      -2.9035    1.8571    3.9201
LLP         C2     C   CR6    0    .      -1.5499    1.0147    3.7458
LLP         N1     N   NR16   1    .      -1.0905    0.2444    4.8038
LLP         C6     C   CR16   0    .       0.0684   -0.5123    4.7114
LLP         C5     C   CR6    0    .       0.8336   -0.5070    3.4747
LLP        C5'     C   CH2    0    .       2.2176   -1.3107    3.3867
LLP         OP4    O   O2     0    .       2.4891   -1.9091    4.7003
LLP         P      P   P      0    .       4.1362   -2.1613    5.1670
LLP         OP1    O   OP    -1    .       4.3336   -3.6693    5.6153
LLP         OP2    O   OP    -1    .       4.4965   -1.1993    6.3748
LLP         OP3    O   O      0    .       5.0877   -1.8463    3.9386
LLP         C4     C   CR6    0    .       0.3827    0.2889    2.3435
LLP        C4'     C   C1     0    .       1.1668    0.2366    0.9451
LLP         NZ     N   N      0    .       0.5327   -0.1128   -0.1505
LLP         CE     C   CH2    0    .       1.2780   -0.1626   -1.4798
LLP         CD     C   CH2    0    .       0.3720   -0.8651   -2.6014
LLP         CG     C   CH2    0    .       0.0745    0.1083   -3.8405
LLP         CB     C   CH2    0    .      -0.9995   -0.5118   -4.8566
LLP         CA     C   CH1    0    .      -1.8553    0.4955   -5.4286
LLP         N      N   NH2    0    .      -3.0959   -0.0947   -5.8224
LLP         C      C   C      0    .      -1.1825    1.1093   -6.6337
LLP         OXT    O   OC    -1    .      -1.3003    2.4053   -6.8678
LLP         O      O   O      0    .      -0.5053    0.3451   -7.4732
LLP         C3     C   CR6    0    .      -0.8374    1.0693    2.4790
LLP         O3     O   OH1    0    .      -1.3017    1.9396    1.3887
LLP         H1Z    H   HNR6   0    .      -1.6360    0.2338    5.7014
LLP         HA     H   HCH1   0    .      -2.0671    1.3615   -4.6026
LLP        H2'1    H   HCH3   0    .      -3.6463    1.5549    3.1092
LLP        H2'2    H   HCH3   0    .      -3.3539    1.6450    4.9466
LLP        H2'3    H   HCH3   0    .      -2.6729    2.9704    3.8287
LLP         H6     H   HCR6   0    .       0.4182   -1.1335    5.5978
LLP        H5'1    H   HCH2   0    .       3.0600   -0.5955    3.1091
LLP        H5'2    H   HCH2   0    .       2.1359   -2.1309    2.6008
LLP        H4'1    H   H      0    .       2.2716    0.5020    0.9026
LLP         HE2    H   HCH2   0    .       2.2418   -0.7553   -1.3490
LLP         HE3    H   HCH2   0    .       1.5302    0.8980   -1.8098
LLP         HD3    H   HCH2   0    .      -0.6174   -1.1788   -2.1331
LLP         HD2    H   HCH2   0    .       0.9107   -1.7931   -2.9826
LLP         HG3    H   HCH2   0    .       1.0469    0.2982   -4.4022
LLP         HG2    H   HCH2   0    .      -0.3223    1.0994   -3.4439
LLP         HB3    H   HCH2   0    .      -0.4463   -1.0467   -5.6969
LLP         HB2    H   HCH2   0    .      -1.6422   -1.2678   -4.2978
LLP         H      H   HNH2   0    .      -3.0285   -0.4200   -6.8237
LLP         HN2    H   HNH2   0    .      -3.8676    0.6185   -5.7357
LLP         HO3    H   HOH1   0    .      -1.1625    2.8883    1.6409
#
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
LLP   C2     C2'    single        1.604 0.020     1.604
LLP   N1      C2    aromatic      1.387 0.020     1.387
LLP   C6      N1    aromatic      1.387 0.020     1.387
LLP   C5      C6    aromatic      1.454 0.020     1.454
LLP   OP4    C5'    single        1.469 0.020     1.469
LLP   P       OP4   single        1.730 0.020     1.730
LLP   OP1     P     deloc         1.586 0.020     1.586
LLP   OP2     P     deloc         1.586 0.020     1.586
LLP   OP3     P     deloc         1.585 0.020     1.585
LLP  C5'      C5    single        1.603 0.020     1.603
LLP   C4      C5    aromatic      1.455 0.020     1.455
LLP   NZ     C4'    double        1.313 0.020     1.313
LLP   CE      NZ    single        1.525 0.020     1.525
LLP   CD      CE    single        1.604 0.020     1.604
LLP   CG      CD    single        1.604 0.020     1.604
LLP   CB      CG    single        1.603 0.020     1.603
LLP   CA      CB    single        1.440 0.020     1.440
LLP   N       CA    single        1.429 0.020     1.429
LLP   C       CA    single        1.511 0.020     1.511
LLP   OXT     C     deloc         1.322 0.020     1.322
LLP   O       C     deloc         1.322 0.020     1.322
LLP  C4'      C4    single        1.604 0.020     1.604
LLP   C3      C4    aromatic      1.455 0.020     1.455
LLP   O3      C3    single        1.470 0.020     1.470
LLP   C2      C3    aromatic      1.454 0.020     1.454
LLP   H1Z     N1    single        0.868 0.020     1.014
LLP   HA      CA    single        0.939 0.020     1.096
LLP  H2'1    C2'    single        0.939 0.020     1.096
LLP  H2'2    C2'    single        0.939 0.020     1.096
LLP  H2'3    C2'    single        0.939 0.020     1.096
LLP   H6      C6    single        0.929 0.020     1.085
LLP  H5'1    C5'    single        0.970 0.020     1.090
LLP  H5'2    C5'    single        0.970 0.020     1.090
LLP  H4'1    C4'    single        0.930 0.020     1.080
LLP   HE2     CE    single        0.970 0.020     1.090
LLP   HE3     CE    single        0.970 0.020     1.090
LLP   HD3     CD    single        0.970 0.020     1.090
LLP   HD2     CD    single        0.970 0.020     1.090
LLP   HG3     CG    single        0.970 0.020     1.090
LLP   HG2     CG    single        0.970 0.020     1.090
LLP   HB3     CB    single        0.970 0.020     1.090
LLP   HB2     CB    single        0.970 0.020     1.090
LLP   H       N     single        0.860 0.020     1.020
LLP   HN2     N     single        0.890 0.020     1.040
LLP   HO3     O3    single        0.850 0.020     0.980
#
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
LLP  H2'3    C2'     H2'2         109.47 3.000
LLP  H2'3    C2'     H2'1         109.47 3.000
LLP  H2'2    C2'     H2'1         109.47 3.000
LLP  H2'3    C2'      C2          109.47 3.000
LLP  H2'2    C2'      C2          109.47 3.000
LLP  H2'1    C2'      C2          109.47 3.000
LLP   C3      C2      N1          121.53 3.000
LLP   C3      C2     C2'          119.23 3.000
LLP   N1      C2     C2'          119.23 3.000
LLP   H1Z     N1      C6          119.04 3.000
LLP   H1Z     N1      C2          119.04 3.000
LLP   C6      N1      C2          121.93 3.000
LLP   H6      C6      C5          120.19 3.000
LLP   H6      C6      N1          120.19 3.000
LLP   C5      C6      N1          119.62 3.000
LLP   C4      C5     C5'          119.95 3.000
LLP   C4      C5      C6          120.02 3.000
LLP  C5'      C5      C6          119.94 3.000
LLP  H5'2    C5'     H5'1         109.70 3.000
LLP  H5'2    C5'      OP4         109.69 3.000
LLP  H5'1    C5'      OP4         109.69 3.000
LLP  H5'2    C5'      C5          109.70 3.000
LLP  H5'1    C5'      C5          109.69 3.000
LLP   OP4    C5'      C5          108.35 3.000
LLP   P       OP4    C5'          118.46 3.000
LLP   OP3     P       OP2         109.47 3.000
LLP   OP3     P       OP1         109.47 3.000
LLP   OP2     P       OP1         109.47 3.000
LLP   OP3     P       OP4         109.47 3.000
LLP   OP2     P       OP4         109.47 3.000
LLP   OP1     P       OP4         109.47 3.000
LLP   C3      C4     C4'          120.57 3.000
LLP   C3      C4      C5          118.75 3.000
LLP  C4'      C4      C5          120.57 3.000
LLP  H4'1    C4'      NZ          120.00 3.000
LLP  H4'1    C4'      C4          120.00 3.000
LLP   NZ     C4'      C4          120.00 3.000
LLP   CE      NZ     C4'          120.00 3.000
LLP   HE3     CE      HE2         109.30 3.000
LLP   HE3     CE      CD          109.29 3.000
LLP   HE2     CE      CD          109.29 3.000
LLP   HE3     CE      NZ          109.29 3.000
LLP   HE2     CE      NZ          109.29 3.000
LLP   CD      CE      NZ          110.36 3.000
LLP   HD2     CD      HD3         108.92 3.000
LLP   HD2     CD      CG          108.89 3.000
LLP   HD3     CD      CG          108.89 3.000
LLP   HD2     CD      CE          108.90 3.000
LLP   HD3     CD      CE          108.90 3.000
LLP   CG      CD      CE          112.29 3.000
LLP   HG2     CG      HG3         108.92 3.000
LLP   HG2     CG      CB          108.90 3.000
LLP   HG3     CG      CB          108.90 3.000
LLP   HG2     CG      CD          108.90 3.000
LLP   HG3     CG      CD          108.90 3.000
LLP   CB      CG      CD          112.28 3.000
LLP   HB2     CB      HB3         108.92 3.000
LLP   HB2     CB      CA          108.89 3.000
LLP   HB3     CB      CA          108.90 3.000
LLP   HB2     CB      CG          108.90 3.000
LLP   HB3     CB      CG          108.89 3.000
LLP   CA      CB      CG          112.28 3.000
LLP   HA      CA      C           109.29 3.000
LLP   HA      CA      N           109.28 3.000
LLP   C       CA      N           109.55 3.000
LLP   HA      CA      CB          109.39 3.000
LLP   C       CA      CB          109.66 3.000
LLP   N       CA      CB          109.66 3.000
LLP   HN2     N       H           109.47 3.000
LLP   HN2     N       CA          109.47 3.000
LLP   H       N       CA          109.47 3.000
LLP   O       C       OXT         119.99 3.000
LLP   O       C       CA          119.99 3.000
LLP   OXT     C       CA          119.99 3.000
LLP   O3      C3      C4          120.89 3.000
LLP   O3      C3      C2          120.89 3.000
LLP   C4      C3      C2          118.15 3.000
LLP   HO3     O3      C3          109.47 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
LLP CONST_01       C5      C6      N1      C2           -0.00   0.0 0
LLP CONST_02       C4      C5      C6      N1           -0.00   0.0 0
LLP CONST_03       C3      C4      C5      C6            0.00   0.0 0
LLP CONST_04       C2      C3      C4      C5           -0.00   0.0 0
LLP CONST_05       N1      C2      C3      C4           -0.00   0.0 0
LLP CONST_06       C6      N1      C2      C3            0.00   0.0 0
LLP CONST_07       C6      N1      C2     C2'          179.58   0.0 0
LLP CONST_08       C4      C3      C2     C2'         -179.58   0.0 0
LLP CONST_09       C4'     C4      C3      C2          176.32   0.0 0
LLP CONST_10       O3      C3      C2      N1         -177.08   0.0 0
LLP CONST_11      C5'      C5      C6      N1          176.48   0.0 0
LLP CONST_12       C4'     C4      C5      C6         -176.32   0.0 0
LLP CONST_13       O3      C3      C4      C5          177.08   0.0 0
LLP CONST_14       C3      C4      C5     C5'         -176.48   0.0 0
LLP CONST_15       H1Z     N1      C6      C5          180.00   0.0 0
LLP CONST_16       H1Z     N1      C2      C3         -180.00   0.0 0
LLP CONST_17       H6      C6      N1      C2          180.00   0.0 0
LLP CONST_18       H6      C6      C5      C4         -180.00   0.0 0
LLP Var_01         OP4    C5'      C5      C6           -2.11  30.0 2
LLP Var_02         NZ      C4'     C4      C5          122.31  30.0 3
LLP Var_03         C4      C5     C5'      OP4         174.38  30.0 2
LLP Var_04         C3      C4      C4'     NZ          -53.94  30.0 2
LLP Var_05        H2'1    C2'      C2      N1         -123.01  30.0 2
LLP Var_06        H2'2    C2'      C2      N1           -3.01  30.0 2
LLP Var_07        H2'3    C2'      C2      N1          116.99  30.0 2
LLP Var_08        H5'1    C5'      C5      C6         -121.83  30.0 2
LLP Var_09        H5'2    C5'      C5      C6          117.61  30.0 2
LLP Var_10        H4'1     C4'     C4      C5          -57.69  30.0 3
LLP Var_11        H5'1    C5'      C5      C4           54.65  30.0 2
LLP Var_12        H5'2    C5'      C5      C4          -65.90  30.0 2
LLP Var_13        H4'1     C4'     C4      C3          126.06  30.0 3
LLP Var_14        H2'1    C2'      C2      C3           56.58  30.0 2
LLP Var_15        H2'2    C2'      C2      C3          176.58  30.0 2
LLP Var_16        H2'3    C2'      C2      C3          -63.41  30.0 2
LLP Var_17         CE      NZ      C4'     C4         -180.00   0.0 2
LLP Var_18         P       OP4    C5'      C5         -151.04  30.0 1
LLP Var_19         OP1     P       OP4    C5'         -127.49  30.0 3
LLP Var_20         OP2     P       OP4    C5'          112.50  30.0 3
LLP Var_21         OP3     P       OP4    C5'           -7.49  30.0 3
LLP Var_22         CD      CE      NZ      C4'         169.68  30.0 1
LLP Var_23         CG      CD      CE      NZ          119.81  30.0 1
LLP Var_24         CB      CG      CD      CE         -171.70  30.0 2
LLP Var_25         CA      CB      CG      CD          144.60  30.0 2
LLP Var_26        H4'1     C4'     NZ      CE           -0.00   0.0 2
LLP Var_27        H5'1    C5'      OP4     P           -31.32  30.0 3
LLP Var_28        H5'2    C5'      OP4     P            89.23  30.0 3
LLP Var_29         HE2     CE      NZ      C4'          49.47  30.0 1
LLP Var_30         HE3     CE      NZ      C4'         -70.10  30.0 1
LLP Var_31         HD3     CD      CE      NZ           -0.87  30.0 1
LLP Var_32         HD2     CD      CE      NZ         -119.52  30.0 1
LLP Var_33         HG3     CG      CD      CE           67.63  30.0 2
LLP Var_34         HG2     CG      CD      CE          -51.02  30.0 2
LLP Var_35         HB3     CB      CG      CD          -94.72  30.0 2
LLP Var_36         HB2     CB      CG      CD           23.92  30.0 2
LLP Var_37         HE2     CE      CD      CG         -119.98  30.0 3
LLP Var_38         HE3     CE      CD      CG           -0.41  30.0 3
LLP Var_39         HD3     CD      CG      CB          -51.02  30.0 3
LLP Var_40         HD2     CD      CG      CB           67.62  30.0 3
LLP Var_41         HG3     CG      CB      CA          -94.72  30.0 3
LLP Var_42         HG2     CG      CB      CA           23.92  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
LLP chir_01   CA      CB      N       C     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
LLP plan-1    C2' 0.020
LLP plan-1     C2 0.020
LLP plan-1     N1 0.020
LLP plan-1     C6 0.020
LLP plan-1     C5 0.020
LLP plan-1    C5' 0.020
LLP plan-1     C4 0.020
LLP plan-1    C4' 0.020
LLP plan-1     C3 0.020
LLP plan-1     O3 0.020
LLP plan-1    H1Z 0.020
LLP plan-1     H6 0.020
LLP plan-2     CA 0.020
LLP plan-2      C 0.020
LLP plan-2    OXT 0.020
LLP plan-2      O 0.020
LLP plan-3     C4 0.020
LLP plan-3    C4' 0.020
LLP plan-3     NZ 0.020
LLP plan-3     CE 0.020
LLP plan-3   H4'1 0.020
