# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:25:08 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-(phenylacetyl)glycyl-N~6~-acetyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCC[C@H](NC(=O)CNC(=O)Cc1ccccc1)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
 1VP  1VP  N-(phenylacetyl)glycyl-N~6~-acetyl-L-lysine  peptide  50  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1VP
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
 1VP  C5   C  C      0   0.563  -3.7616  -0.6740   0.5297
 1VP  C4   C  CH2    0  -0.672  -5.0081  -0.6147  -0.3380
 1VP  C3   C  CR6    0   0.138  -5.7202   0.6989  -0.1846
 1VP  C16  C  CR16   0  -0.293  -5.4400   1.7549  -1.0479
 1VP  C17  C  CR16   0  -0.242  -6.0729   2.9817  -0.8975
 1VP  C    C  CR16   0  -0.269  -6.9966   3.1679   0.1228
 1VP  C1   C  CR16   0  -0.244  -7.2812   2.1203   0.9893
 1VP  C2   C  CR16   0  -0.301  -6.6452   0.8955   0.8368
 1VP  O    O  O      0  -0.493  -3.7711  -0.3207   1.7002
 1VP  N    N  NH1    0  -0.639  -2.6691  -1.1533  -0.0765
 1VP  C6   C  CH2    0  -0.382  -1.4169  -1.3278   0.6045
 1VP  C7   C  C      0   0.526  -0.3562  -1.7887  -0.3836
 1VP  O1   O  O      0  -0.503  -0.6506  -2.1398  -1.5189
 1VP  O2   O  O      0  -0.515   5.9774   4.3051  -0.5193
 1VP  C13  C  C      0   0.519   6.5899   3.5150   0.1899
 1VP  C14  C  CH3    0  -0.775   7.9111   3.8742   0.8240
 1VP  N2   N  NH1    0  -0.633   6.1427   2.2764   0.4394
 1VP  C12  C  CH2    0  -0.233   4.8945   1.7638  -0.0863
 1VP  C11  C  CH2    0  -0.473   4.7709   0.2719   0.1792
 1VP  C9   C  CH2    0  -0.453   3.3140  -1.7833  -0.0736
 1VP  C8   C  CH1    0  -0.205   2.0042  -2.3782  -0.5857
 1VP  N1   N  NH1    0  -0.617   0.8900  -1.7532   0.0913
 1VP  C15  C  C      0   0.418   1.9875  -3.9258  -0.4459
 1VP  O3   O  O      0  -0.593   1.0872  -4.4338   0.2423
 1VP  O4   O  OC    -1  -0.614   2.9011  -4.5167  -1.0548
 1VP  H19  H  HCH2   0   0.274  -4.7649  -0.7990  -1.3857
 1VP  H20  H  HCH2   0   0.292  -5.6575  -1.4347  -0.0191
 1VP  H23  H  HCR6   0   0.250  -4.7212   1.6157  -1.8470
 1VP  H24  H  HCR6   0   0.254  -5.8458   3.7913  -1.5793
 1VP  H25  H  HCR6   0   0.254  -7.4940   4.1222   0.2395
 1VP  H22  H  HCR6   0   0.254  -8.0015   2.2556   1.7860
 1VP  H21  H  HCR6   0   0.248  -6.8777   0.0828   1.5141
 1VP  H18  H  HNH1   0   0.401  -2.7075  -1.4445  -1.0418
 1VP  H16  H  HCH2   0   0.272  -1.0996  -0.3976   1.0822
 1VP  H17  H  HCH2   0   0.277  -1.4971  -2.0783   1.3984
 1VP  H12  H  HCH3   0   0.265   8.6546   4.0317   0.0419
 1VP  H13  H  HCH3   0   0.262   7.8109   4.8124   1.3686
 1VP  H14  H  HCH3   0   0.247   8.2902   3.1162   1.5071
 1VP  H11  H  HNH1   0   0.399   6.6658   1.6878   1.0666
 1VP  H9   H  HCH2   0   0.227   4.0469   2.2901   0.3652
 1VP  H10  H  HCH2   0   0.232   4.8475   1.9533  -1.1613
 1VP  H7   H  HCH2   0   0.230   5.6011  -0.2541  -0.3022
 1VP  H8   H  HCH2   0   0.228   4.8610   0.0841   1.2545
 1VP  H5   H  HCH2   0   0.220   2.6235   0.2506   0.1603
 1VP  H6   H  HCH2   0   0.218   3.3492  -0.0911  -1.3962
 1VP  H3   H  HCH2   0   0.237   4.1348  -2.3072  -0.5652
 1VP  H4   H  HCH2   0   0.220   3.4148  -1.9902   0.9990
 1VP  H2   H  HCH1   0   0.241   1.9190  -2.1430  -1.6511
 1VP  H15  H  HNH1   0   0.393   1.0081  -1.5534   1.0735
 1VP  C10  C  CH2    0  -0.412   3.4455  -0.2857  -0.3227

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
 1VP  O1   C7   double    1.224  0.020  1.224
 1VP  C6   C7   single    1.521  0.020  1.521
 1VP  C6   N    single    1.436  0.020  1.436
 1VP  C7   N1   single    1.334  0.020  1.334
 1VP  C14  C13  single    1.509  0.020  1.509
 1VP  N    C5   single    1.338  0.020  1.338
 1VP  N1   C8   single    1.446  0.020  1.446
 1VP  C8   C9   single    1.527  0.020  1.527
 1VP  C8   C15  single    1.554  0.020  1.554
 1VP  O    C5   double    1.223  0.020  1.223
 1VP  C9   C10  single    1.524  0.020  1.524
 1VP  C5   C4   single    1.520  0.020  1.520
 1VP  C13  N2   single    1.340  0.020  1.340
 1VP  C13  O2   double    1.226  0.020  1.226
 1VP  N2   C12  single    1.448  0.020  1.448
 1VP  C15  O3   deloc     1.242  0.020  1.242
 1VP  C15  O4   deloc     1.247  0.020  1.247
 1VP  C4   C3   single    1.502  0.020  1.502
 1VP  C10  C11  single    1.523  0.020  1.523
 1VP  C11  C12  single    1.520  0.020  1.520
 1VP  C3   C16  aromatic  1.392  0.020  1.392
 1VP  C3   C2   aromatic  1.392  0.020  1.392
 1VP  C16  C17  aromatic  1.389  0.020  1.389
 1VP  C2   C1   aromatic  1.388  0.020  1.388
 1VP  C17  C    aromatic  1.389  0.020  1.389
 1VP  C1   C    aromatic  1.389  0.020  1.389
 1VP  C8   H2   single    0.970  0.020  1.090
 1VP  C9   H3   single    0.970  0.020  1.090
 1VP  C9   H4   single    0.970  0.020  1.090
 1VP  C10  H5   single    0.970  0.020  1.090
 1VP  C10  H6   single    0.970  0.020  1.090
 1VP  C11  H7   single    0.970  0.020  1.090
 1VP  C11  H8   single    0.970  0.020  1.090
 1VP  C12  H9   single    0.970  0.020  1.090
 1VP  C12  H10  single    0.970  0.020  1.090
 1VP  N2   H11  single    0.860  0.020  1.020
 1VP  C14  H12  single    0.970  0.020  1.090
 1VP  C14  H13  single    0.970  0.020  1.090
 1VP  C14  H14  single    0.970  0.020  1.090
 1VP  N1   H15  single    0.890  0.020  1.040
 1VP  C6   H16  single    0.970  0.020  1.090
 1VP  C6   H17  single    0.970  0.020  1.090
 1VP  N    H18  single    0.860  0.020  1.020
 1VP  C4   H19  single    0.970  0.020  1.090
 1VP  C4   H20  single    0.970  0.020  1.090
 1VP  C2   H21  single    0.930  0.020  1.080
 1VP  C1   H22  single    0.930  0.020  1.080
 1VP  C16  H23  single    0.930  0.020  1.080
 1VP  C17  H24  single    0.930  0.020  1.080
 1VP  C    H25  single    0.930  0.020  1.080

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
 1VP  N    C5   O    122.92  3.000
 1VP  O    C5   C4   121.92  3.000
 1VP  N    C5   C4   115.15  3.000
 1VP  H20  C4   H19  106.60  3.000
 1VP  H20  C4   C3   110.15  3.000
 1VP  H19  C4   C3   110.57  3.000
 1VP  H20  C4   C5   106.94  3.000
 1VP  H19  C4   C5   111.02  3.000
 1VP  C3   C4   C5   111.39  3.000
 1VP  C2   C3   C16  118.78  3.000
 1VP  C2   C3   C4   120.90  3.000
 1VP  C16  C3   C4   120.30  3.000
 1VP  H23  C16  C17  119.71  3.000
 1VP  H23  C16  C3   119.55  3.000
 1VP  C17  C16  C3   120.74  3.000
 1VP  H24  C17  C    120.13  3.000
 1VP  H24  C17  C16  119.80  3.000
 1VP  C    C17  C16  120.07  3.000
 1VP  H25  C    C1   120.23  3.000
 1VP  H25  C    C17  120.20  3.000
 1VP  C1   C    C17  119.57  3.000
 1VP  H22  C1   C2   119.73  3.000
 1VP  H22  C1   C    120.08  3.000
 1VP  C2   C1   C    120.19  3.000
 1VP  H21  C2   C1   119.66  3.000
 1VP  H21  C2   C3   119.70  3.000
 1VP  C1   C2   C3   120.64  3.000
 1VP  H18  N    C6   116.86  3.000
 1VP  H18  N    C5   120.38  3.000
 1VP  C6   N    C5   122.72  3.000
 1VP  H17  C6   H16  106.72  3.000
 1VP  H17  C6   C7   108.32  3.000
 1VP  H16  C6   C7   109.84  3.000
 1VP  H17  C6   N    111.29  3.000
 1VP  H16  C6   N    110.92  3.000
 1VP  C7   C6   N    109.68  3.000
 1VP  N1   C7   O1   124.22  3.000
 1VP  N1   C7   C6   114.33  3.000
 1VP  O1   C7   C6   121.44  3.000
 1VP  N2   C13  C14  115.72  3.000
 1VP  N2   C13  O2   122.46  3.000
 1VP  C14  C13  O2   121.82  3.000
 1VP  H14  C14  H13  108.54  3.000
 1VP  H14  C14  H12  108.26  3.000
 1VP  H13  C14  H12  107.27  3.000
 1VP  H14  C14  C13  113.76  3.000
 1VP  H13  C14  C13  109.55  3.000
 1VP  H12  C14  C13  109.26  3.000
 1VP  H11  N2   C12  117.85  3.000
 1VP  H11  N2   C13  118.87  3.000
 1VP  C12  N2   C13  123.17  3.000
 1VP  H10  C12  H9   106.80  3.000
 1VP  H10  C12  C11  109.78  3.000
 1VP  H9   C12  C11  109.67  3.000
 1VP  H10  C12  N2   109.44  3.000
 1VP  H9   C12  N2   110.32  3.000
 1VP  C11  C12  N2   110.73  3.000
 1VP  H8   C11  H7   106.68  3.000
 1VP  H8   C11  C10  109.41  3.000
 1VP  H7   C11  C10  109.83  3.000
 1VP  H8   C11  C12  109.45  3.000
 1VP  H7   C11  C12  109.46  3.000
 1VP  C10  C11  C12  111.87  3.000
 1VP  H4   C9   H3   106.32  3.000
 1VP  H4   C9   C8   109.47  3.000
 1VP  H3   C9   C8   107.89  3.000
 1VP  H4   C9   C10  109.71  3.000
 1VP  H3   C9   C10  109.47  3.000
 1VP  C8   C9   C10  113.71  3.000
 1VP  H2   C8   C15  107.51  3.000
 1VP  H2   C8   N1   107.64  3.000
 1VP  C15  C8   N1   112.34  3.000
 1VP  H2   C8   C9   108.03  3.000
 1VP  C15  C8   C9   111.53  3.000
 1VP  N1   C8   C9   109.60  3.000
 1VP  H15  N1   C8   116.82  3.000
 1VP  H15  N1   C7   117.45  3.000
 1VP  C8   N1   C7   122.79  3.000
 1VP  O4   C15  O3   127.44  3.000
 1VP  O4   C15  C8   114.84  3.000
 1VP  O3   C15  C8   117.72  3.000
 1VP  H6   C10  H5   106.23  3.000
 1VP  H6   C10  C9   109.10  3.000
 1VP  H5   C10  C9   110.17  3.000
 1VP  H6   C10  C11  109.54  3.000
 1VP  H5   C10  C11  109.21  3.000
 1VP  C9   C10  C11  112.40  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
 1VP  CONST_01  C    C17  C16  C3      0.00   0.0  0
 1VP  CONST_02  C    C1   C2   C3      0.00   0.0  0
 1VP  CONST_03  C1   C2   C3   C16     0.00   0.0  0
 1VP  CONST_04  C1   C    C17  C16     0.00   0.0  0
 1VP  CONST_05  C2   C3   C16  C17     0.00   0.0  0
 1VP  CONST_06  C2   C1   C    C17     0.00   0.0  0
 1VP  CONST_07  C17  C16  C3   C4    180.00   0.0  0
 1VP  CONST_08  C1   C2   C3   C4    180.00   0.0  0
 1VP  CONST_09  H24  C17  C16  C3    180.00   0.0  0
 1VP  CONST_10  H22  C1   C2   C3    180.00   0.0  0
 1VP  CONST_11  H21  C2   C3   C16   180.00   0.0  0
 1VP  CONST_12  H25  C    C17  C16   180.00   0.0  0
 1VP  CONST_13  H23  C16  C17  C     180.00   0.0  0
 1VP  CONST_14  C6   N    C5   C4    180.00   0.0  0
 1VP  CONST_15  C6   N    C5   O       0.00   0.0  0
 1VP  CONST_16  C8   N1   C7   C6    180.00   0.0  0
 1VP  CONST_17  C8   N1   C7   O1      0.00   0.0  0
 1VP  CONST_18  C12  N2   C13  O2      0.00   0.0  0
 1VP  CONST_19  C12  N2   C13  C14   180.00   0.0  0
 1VP  CONST_20  H18  N    C5   C4      0.00   0.0  0
 1VP  CONST_21  H15  N1   C7   C6      0.00   0.0  0
 1VP  CONST_22  H11  N2   C13  O2    180.00   0.0  0
 1VP  Var_01    C16  C3   C4   C5     92.46  30.0  2
 1VP  Var_02    N    C5   C4   C3   -134.57  30.0  1
 1VP  Var_03    C7   C6   N    C5   -175.78  30.0  2
 1VP  Var_04    O1   C7   C6   N     -10.36  30.0  3
 1VP  Var_05    C11  C12  N2   C13   170.79  30.0  3
 1VP  Var_06    C10  C11  C12  N2    178.11  30.0  1
 1VP  Var_07    C9   C10  C11  C12   179.50  30.0  2
 1VP  Var_08    C8   C9   C10  C11  -179.08  30.0  1
 1VP  Var_09    H12  C14  C13  O2    -64.82  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
 1VP  chir_01  C8  N1  C9  C15  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
 1VP  plan-1  C4   0.020
 1VP  plan-1  C3   0.020
 1VP  plan-1  C16  0.020
 1VP  plan-1  C17  0.020
 1VP  plan-1  C    0.020
 1VP  plan-1  C1   0.020
 1VP  plan-1  C2   0.020
 1VP  plan-1  H23  0.020
 1VP  plan-1  H24  0.020
 1VP  plan-1  H25  0.020
 1VP  plan-1  H22  0.020
 1VP  plan-1  H21  0.020
 1VP  plan-2  C5   0.020
 1VP  plan-2  C4   0.020
 1VP  plan-2  O    0.020
 1VP  plan-2  N    0.020
 1VP  plan-2  C6   0.020
 1VP  plan-2  H18  0.020
 1VP  plan-3  C6   0.020
 1VP  plan-3  C7   0.020
 1VP  plan-3  O1   0.020
 1VP  plan-3  C8   0.020
 1VP  plan-3  N1   0.020
 1VP  plan-3  H15  0.020
 1VP  plan-4  O2   0.020
 1VP  plan-4  C13  0.020
 1VP  plan-4  C14  0.020
 1VP  plan-4  N2   0.020
 1VP  plan-4  C12  0.020
 1VP  plan-4  H11  0.020
 1VP  plan-5  C8   0.020
 1VP  plan-5  C15  0.020
 1VP  plan-5  O3   0.020
 1VP  plan-5  O4   0.020

