# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 15 18:32:24 2019
#
#   Inital geometry file: a 95 line input string
#   Ligand name: N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Basis set: 6-31G(d,p)
#   Method: UHF
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@H](N)C(O)=O
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Apr 15 18:33:42 2019
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
PYL PYL 'N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine' L-peptide 38 18 . 
2016-04-26 2019-04-15
;
CIF prepared directly in eLBOW
;
#
data_comp_PYL
#
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
PYL         CB2    C   CH3   0     .          5.7414    1.4537    1.4220
PYL         CG2    C   CR15  0     .          4.9472    0.5953    0.4446
PYL         CD2    C   CH2   0     .          5.7007    0.1968   -0.8380
PYL         CE2    C   CR15  0     .          4.5980    0.2567   -1.8636
PYL         N2     N   N     0     .          3.5376    0.8171   -1.5041
PYL         CA2    C   CR15  0     .          3.6783    1.2758   -0.1236
PYL         C2     C   C     0     .          2.4376    1.0310    0.7293
PYL         O2     O   O     0     .          2.5176    1.1253    1.9314
PYL         NZ     N   NH1   0     .          1.3140    0.7486    0.0701
PYL         CE     C   CH2   0     .          0.0408    0.5170    0.7377
PYL         CD     C   CH2   0     .         -1.0376    0.1714   -0.2826
PYL         CG     C   CH2   0     .         -2.4012   -0.0992    0.3561
PYL         CB     C   CH2   0     .         -3.4809   -0.4379   -0.6713
PYL         CA     C   CH1   0     .         -4.8409   -0.7806   -0.0538
PYL         C      C   C     0     .         -5.8994   -0.9131   -1.1925
PYL         OXT    O   OC    -1    .         -6.1593    0.1397   -1.7792
PYL         O      O   O     0     .         -6.3296   -2.0542   -1.3934
PYL         N      N   NH2   0     .         -4.7300   -1.9770    0.7849
PYL         HA     H   HCH1  0     .         -5.1431    0.0592    0.5696
PYL         H      H   HNH2  0     .         -5.4776   -1.9561    1.4528
PYL         H2     H   HNH2  0     .         -4.9853   -2.7320    0.1718
PYL         HB3    H   HCH2  0     .         -3.6251    0.3912   -1.3560
PYL         HB2    H   HCH2  0     .         -3.1519   -1.2903   -1.2676
PYL         HG3    H   HCH2  0     .         -2.3214   -0.9172    1.0652
PYL         HG2    H   HCH2  0     .         -2.7091    0.7791    0.9245
PYL         HD3    H   HCH2  0     .         -1.1245    0.9874   -0.9995
PYL         HD2    H   HCH2  0     .         -0.7229   -0.7061   -0.8465
PYL         HE3    H   HCH2  0     .          0.1563   -0.2880    1.4558
PYL         HE2    H   HCH2  0     .         -0.2359    1.4037    1.2990
PYL         HZ     H   HNH1  0     .          1.3639    0.6806   -0.9201
PYL         HA2    H   HCR5  0     .          3.8037    2.3577   -0.1470
PYL        HE22    H   HCR5  0     .          4.7007   -0.1368   -2.8640
PYL        HD32    H   HCH2  0     .          6.4818    0.9112   -1.0967
PYL        HD22    H   HCH2  0     .          6.1675   -0.7817   -0.7844
PYL        HG22    H   HCR5  0     .          4.6364   -0.3096    0.9572
PYL        HB12    H   HCH3  0     .          6.0757    2.3747    0.9493
PYL        HB22    H   HCH3  0     .          5.1272    1.7093    2.2759
PYL        HB32    H   HCH3  0     .          6.6218    0.9246    1.7770
#
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
PYL   CB2     CG2   single        1.524 0.02   1.524
PYL   CB2    HB12   single        0.970 0.02   1.09
PYL   CB2    HB22   single        0.970 0.02   1.09
PYL   CB2    HB32   single        0.970 0.02   1.09
PYL   CG2     CD2   single        1.540 0.02   1.54
PYL   CG2     CA2   single        1.548 0.02   1.548
PYL   CG2    HG22   single        0.970 0.02   1.09
PYL   CD2     CE2   single        1.507 0.02   1.507
PYL   CD2    HD32   single        0.970 0.02   1.09
PYL   CD2    HD22   single        0.970 0.02   1.09
PYL   CE2     N2    double        1.252 0.02   1.252
PYL   CE2    HE22   single        0.930 0.02   1.08
PYL   N2      CA2   single        1.461 0.02   1.461
PYL   CA2     C2    single        1.525 0.02   1.525
PYL   CA2     HA2   single        0.970 0.02   1.09
PYL   C2      NZ    single        1.333 0.02   1.333
PYL   C2      O2    double        1.208 0.02   1.208
PYL   NZ      CE    single        1.456 0.02   1.456
PYL   NZ      HZ    single        0.860 0.02   1.02
PYL   CE      CD    single        1.524 0.02   1.524
PYL   CE      HE3   single        0.970 0.02   1.09
PYL   CE      HE2   single        0.970 0.02   1.09
PYL   CD      CG    single        1.530 0.02   1.53
PYL   CD      HD3   single        0.970 0.02   1.09
PYL   CD      HD2   single        0.970 0.02   1.09
PYL   CG      CB    single        1.528 0.02   1.528
PYL   CG      HG3   single        0.970 0.02   1.09
PYL   CG      HG2   single        0.970 0.02   1.09
PYL   CB      CA    single        1.521 0.02   1.521
PYL   CB      HB3   single        0.970 0.033   1.09
PYL   CB      HB2   single        0.970 0.033   1.09
PYL   CA      C     single        1.525 0.033   1.525
PYL   CA      HA    single        0.970 0.021   1.09
PYL   CA      N     single        1.458 0.02   1.458
PYL   C       OXT   deloc         1.233 0.019   1.233
PYL   C       O     deloc         1.231 0.019   1.231
PYL   N       H     single        0.860 0.02   1.02
PYL   N       H2    single        0.890 0.02   1.04
#
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
PYL  HB32     CB2    HB22         108.48 3.0
PYL  HB32     CB2    HB12         107.77 3.0
PYL  HB22     CB2    HB12         108.50 3.0
PYL  HB32     CB2     CG2         110.94 3.0
PYL  HB22     CB2     CG2         110.08 3.0
PYL  HB12     CB2     CG2         110.99 3.0
PYL  HG22     CG2     CA2         107.77 3.0
PYL  HG22     CG2     CD2         108.52 3.0
PYL   CA2     CG2     CD2         102.07 3.0
PYL  HG22     CG2     CB2         108.41 3.0
PYL   CA2     CG2     CB2         114.51 3.0
PYL   CD2     CG2     CB2         115.15 3.0
PYL  HD22     CD2    HD32         107.13 3.0
PYL  HD22     CD2     CE2         112.58 3.0
PYL  HD32     CD2     CE2         109.69 3.0
PYL  HD22     CD2     CG2         113.74 3.0
PYL  HD32     CD2     CG2         112.26 3.0
PYL   CE2     CD2     CG2         101.45 3.0
PYL  HE22     CE2     N2          120.64 3.0
PYL  HE22     CE2     CD2         123.12 3.0
PYL   N2      CE2     CD2         116.23 3.0
PYL   CA2     N2      CE2         109.28 3.0
PYL   HA2     CA2     C2          105.37 3.0
PYL   HA2     CA2     N2          107.61 3.0
PYL   C2      CA2     N2          113.54 3.0
PYL   HA2     CA2     CG2         110.50 3.0
PYL   C2      CA2     CG2         113.02 3.0
PYL   N2      CA2     CG2         106.72 3.0
PYL   NZ      C2      O2          124.35 3.0
PYL   O2      C2      CA2         119.33 3.0
PYL   NZ      C2      CA2         116.30 3.0
PYL   HZ      NZ      CE          119.33 3.0
PYL   HZ      NZ      C2          117.71 3.0
PYL   CE      NZ      C2          122.95 3.0
PYL   HE2     CE      HE3         106.92 3.0
PYL   HE2     CE      CD          110.55 3.0
PYL   HE3     CE      CD          110.50 3.0
PYL   HE2     CE      NZ          109.27 3.0
PYL   HE3     CE      NZ          109.18 3.0
PYL   CD      CE      NZ          110.35 3.0
PYL   HD2     CD      HD3         106.60 3.0
PYL   HD2     CD      CG          109.33 3.0
PYL   HD3     CD      CG          109.64 3.0
PYL   HD2     CD      CE          108.94 3.0
PYL   HD3     CD      CE          109.09 3.0
PYL   CG      CD      CE          113.03 3.0
PYL   HG2     CG      HG3         106.68 3.0
PYL   HG2     CG      CB          109.23 3.0
PYL   HG3     CG      CB          108.91 3.0
PYL   HG2     CG      CD          109.07 3.0
PYL   HG3     CG      CD          109.91 3.0
PYL   CB      CG      CD          112.84 3.0
PYL   HB2     CB      HB3         106.99 3.0
PYL   HB2     CB      CA          108.25 3.0
PYL   HB3     CB      CA          107.89 3.0
PYL   HB2     CB      CG          109.12 3.0
PYL   HB3     CB      CG          110.41 3.0
PYL   CA      CB      CG          113.93 3.0
PYL   HA      CA      N           110.00 3.0
PYL   N       CA      C           111.00 2.8
PYL   HA      CA      C           110.00 3.0
PYL   N       CA      CB          110.40 1.5
PYL   HA      CA      CB          109.00 3.0
PYL   C       CA      CB          110.50 1.5
PYL   O       C       OXT         129.61 3.0
PYL   O       C       CA          120.80 1.7
PYL   OXT     C       CA          114.69 3.0
PYL   H2      N       H           103.45 3.0
PYL   H2      N       CA          104.17 3.0
PYL   H       N       CA          114.00 3.0
#
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
PYL CONST_01   CE      NZ      C2      CA2        -178.71   0.0 0
PYL CONST_02   HZ      NZ      C2      CA2           2.37   0.0 0
PYL CONST_03   CE      NZ      C2      O2           -0.12   0.0 0
PYL   Var_01   N2      CE2     CD2     CG2          12.87  30.0 1
PYL   Var_02   CD      CE      NZ      C2         -178.03  30.0 3
PYL   Var_03   CG      CD      CE      NZ          179.39  30.0 3
PYL   Var_04   CB      CG      CD      CE          179.70  30.0 3
PYL   Var_05   CA      CB      CG      CD          177.18  30.0 3
#
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
PYL plan-1    CA2 0.020
PYL plan-1    C2  0.020
PYL plan-1    O2  0.020
PYL plan-1    NZ  0.020
PYL plan-1    CE  0.020
PYL plan-1    HZ  0.020
PYL plan-2    CA  0.020
PYL plan-2    C   0.020
PYL plan-2    OXT 0.020
PYL plan-2    O   0.020
PYL plan-3   HE22 0.020
PYL plan-3    CD2 0.020
PYL plan-3    CA2 0.020
PYL plan-3    CE2 0.020
PYL plan-3    N2  0.020
#
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
PYL chir_01   CG2     CB2     CD2     CA2   positiv
PYL chir_02   CA2     N2      CG2     C2    positiv
PYL chir_03   CA      CB      C       N     negativ
#
