# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:51:25 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  51  26  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.570  -3.6071   0.4708  -0.3698
 1VP  C4   C  CH2   0  -0.685  -4.8988   0.0622  -1.0600
 1VP  C3   C  CR6   0   0.150  -6.1068   0.6639  -0.4065
 1VP  C16  C  CR16  0  -0.302  -6.5349   1.9453  -0.7416
 1VP  C17  C  CR16  0  -0.244  -7.6396   2.5095  -0.1183
 1VP  C    C  CR16  0  -0.270  -8.3312   1.7984   0.8543
 1VP  C1   C  CR16  0  -0.242  -7.9123   0.5192   1.1951
 1VP  C2   C  CR16  0  -0.298  -6.8073  -0.0418   0.5677
 1VP  O    O  O     0  -0.488  -3.4877   1.5227   0.2391
 1VP  N    N  NH1   0  -0.644  -2.5989  -0.4023  -0.5088
 1VP  C6   C  CH2   0  -0.371  -1.2819  -0.1342  -0.0054
 1VP  C7   C  C     0   0.533  -0.3226  -1.2189  -0.4570
 1VP  O1   O  O     0  -0.484  -0.6351  -2.0787  -1.2655
 1VP  O2   O  O     0  -0.514   7.0595   3.7358  -0.8271
 1VP  C13  C  C     0   0.520   7.4751   2.9610   0.0268
 1VP  C14  C  CH3   0  -0.777   8.7433   3.2290   0.7990
 1VP  N2   N  NH1   0  -0.634   6.8402   1.8212   0.3346
 1VP  C12  C  CH2   0  -0.233   5.6164   1.3948  -0.3110
 1VP  C11  C  CH2   0  -0.478   5.0905   0.1245   0.3370
 1VP  C9   C  CH2   0  -0.471   3.2726  -1.6214   0.3527
 1VP  C8   C  CH1   0  -0.176   1.9330  -2.0875  -0.2262
 1VP  N1   N  NH1   0  -0.640   0.9010  -1.1358   0.0841
 1VP  C15  C  C     0   0.544   1.5769  -3.4582   0.3309
 1VP  O3   O  O     0  -0.432   0.8147  -3.6495   1.2414
 1VP  O4   O  OH1   0  -0.590   2.2476  -4.4158  -0.2927
 1VP  H19  H  HCH2  0   0.298  -4.8229   0.3937  -2.1002
 1VP  H20  H  HCH2  0   0.280  -4.9796  -1.0262  -1.0915
 1VP  H23  H  HCR6  0   0.248  -6.0061   2.5065  -1.5027
 1VP  H24  H  HCR6  0   0.254  -7.9603   3.5064  -0.3924
 1VP  H25  H  HCR6  0   0.254  -9.1931   2.2374   1.3401
 1VP  H22  H  HCR6  0   0.254  -8.4466  -0.0457   1.9481
 1VP  H21  H  HCR6  0   0.250  -6.4892  -1.0424   0.8367
 1VP  H18  H  HNH1  0   0.404  -2.7291  -1.2467  -1.0453
 1VP  H16  H  HCH2  0   0.284  -0.9091   0.8283  -0.3698
 1VP  H17  H  HCH2  0   0.276  -1.2760  -0.0766   1.0871
 1VP  H12  H  HCH3  0   0.265   9.5898   3.2417   0.1121
 1VP  H13  H  HCH3  0   0.263   8.6863   4.2140   1.2615
 1VP  H14  H  HCH3  0   0.247   8.9434   2.4935   1.5760
 1VP  H11  H  HNH1  0   0.401   7.2451   1.2130   1.0274
 1VP  H9   H  HCH2  0   0.232   4.8658   2.1863  -0.2371
 1VP  H10  H  HCH2  0   0.231   5.7917   1.2230  -1.3775
 1VP  H7   H  HCH2  0   0.235   5.8401  -0.6687   0.2505
 1VP  H8   H  HCH2  0   0.235   4.9389   0.2994   1.4067
 1VP  H5   H  HCH2  0   0.231   3.0378   0.4588  -0.1981
 1VP  H6   H  HCH2  0   0.233   3.9240  -0.5047  -1.3624
 1VP  H3   H  HCH2  0   0.265   4.0113  -2.4123   0.2079
 1VP  H4   H  HCH2  0   0.248   3.1679  -1.4878   1.4342
 1VP  H2   H  HCH1  0   0.289   2.0337  -2.1752  -1.3117
 1VP  H15  H  HNH1  0   0.413   1.0643  -0.4723   0.8259
 1VP  H1   H  HOH1  0   0.485   2.0523  -5.2779   0.1045
 1VP  C10  C  CH2   0  -0.422   3.7822  -0.3370  -0.2905

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    1.221  0.020  1.221
 1VP  C6   C7   single    1.517  0.020  1.517
 1VP  C6   N    single    1.435  0.020  1.435
 1VP  C7   N1   single    1.340  0.020  1.340
 1VP  C14  C13  single    1.509  0.020  1.509
 1VP  N    C5   single    1.341  0.020  1.341
 1VP  N1   C8   single    1.438  0.020  1.438
 1VP  C8   C9   single    1.532  0.020  1.532
 1VP  C8   C15  single    1.522  0.020  1.522
 1VP  O    C5   double    1.221  0.020  1.221
 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   double    1.203  0.020  1.203
 1VP  C15  O4   single    1.325  0.020  1.325
 1VP  C4   C3   single    1.499  0.020  1.499
 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  1.388  0.020  1.388
 1VP  C2   C1   aromatic  1.389  0.020  1.389
 1VP  C17  C    aromatic  1.389  0.020  1.389
 1VP  C1   C    aromatic  1.389  0.020  1.389
 1VP  O4   H1   single    0.850  0.020  0.980
 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    0.860  0.020  1.020
 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    122.62  3.000
 1VP  O    C5   C4   122.74  3.000
 1VP  N    C5   C4   114.63  3.000
 1VP  H20  C4   H19  106.25  3.000
 1VP  H20  C4   C3   110.67  3.000
 1VP  H19  C4   C3   110.40  3.000
 1VP  H20  C4   C5   110.11  3.000
 1VP  H19  C4   C5   106.93  3.000
 1VP  C3   C4   C5   112.25  3.000
 1VP  C2   C3   C16  118.70  3.000
 1VP  C2   C3   C4   120.47  3.000
 1VP  C16  C3   C4   120.82  3.000
 1VP  H23  C16  C17  119.55  3.000
 1VP  H23  C16  C3   119.72  3.000
 1VP  C17  C16  C3   120.72  3.000
 1VP  H24  C17  C    120.08  3.000
 1VP  H24  C17  C16  119.76  3.000
 1VP  C    C17  C16  120.16  3.000
 1VP  H25  C    C1   120.25  3.000
 1VP  H25  C    C17  120.20  3.000
 1VP  C1   C    C17  119.55  3.000
 1VP  H22  C1   C2   119.75  3.000
 1VP  H22  C1   C    120.17  3.000
 1VP  C2   C1   C    120.08  3.000
 1VP  H21  C2   C1   119.62  3.000
 1VP  H21  C2   C3   119.59  3.000
 1VP  C1   C2   C3   120.78  3.000
 1VP  H18  N    C6   117.47  3.000
 1VP  H18  N    C5   120.20  3.000
 1VP  C6   N    C5   122.14  3.000
 1VP  H17  C6   H16  106.51  3.000
 1VP  H17  C6   C7   109.36  3.000
 1VP  H16  C6   C7   108.32  3.000
 1VP  H17  C6   N    111.41  3.000
 1VP  H16  C6   N    111.11  3.000
 1VP  C7   C6   N    110.02  3.000
 1VP  N1   C7   O1   123.00  3.000
 1VP  N1   C7   C6   114.38  3.000
 1VP  O1   C7   C6   122.61  3.000
 1VP  N2   C13  C14  115.57  3.000
 1VP  N2   C13  O2   122.47  3.000
 1VP  C14  C13  O2   121.96  3.000
 1VP  H14  C14  H13  108.51  3.000
 1VP  H14  C14  H12  108.35  3.000
 1VP  H13  C14  H12  107.31  3.000
 1VP  H14  C14  C13  113.57  3.000
 1VP  H13  C14  C13  109.50  3.000
 1VP  H12  C14  C13  109.40  3.000
 1VP  H11  N2   C12  117.96  3.000
 1VP  H11  N2   C13  118.76  3.000
 1VP  C12  N2   C13  123.25  3.000
 1VP  H10  C12  H9   106.82  3.000
 1VP  H10  C12  C11  109.86  3.000
 1VP  H9   C12  C11  109.79  3.000
 1VP  H10  C12  N2   110.21  3.000
 1VP  H9   C12  N2   109.69  3.000
 1VP  C11  C12  N2   110.40  3.000
 1VP  H8   C11  H7   106.73  3.000
 1VP  H8   C11  C10  109.41  3.000
 1VP  H7   C11  C10  109.65  3.000
 1VP  H8   C11  C12  109.33  3.000
 1VP  H7   C11  C12  109.56  3.000
 1VP  C10  C11  C12  112.02  3.000
 1VP  H4   C9   H3   106.51  3.000
 1VP  H4   C9   C8   109.07  3.000
 1VP  H3   C9   C8   108.73  3.000
 1VP  H4   C9   C10  110.24  3.000
 1VP  H3   C9   C10  109.16  3.000
 1VP  C8   C9   C10  112.91  3.000
 1VP  H2   C8   C15  108.22  3.000
 1VP  H2   C8   N1   109.47  3.000
 1VP  C15  C8   N1   110.44  3.000
 1VP  H2   C8   C9   108.60  3.000
 1VP  C15  C8   C9   109.90  3.000
 1VP  N1   C8   C9   110.17  3.000
 1VP  H15  N1   C8   118.55  3.000
 1VP  H15  N1   C7   119.05  3.000
 1VP  C8   N1   C7   121.80  3.000
 1VP  O4   C15  O3   124.21  3.000
 1VP  O4   C15  C8   111.11  3.000
 1VP  O3   C15  C8   124.66  3.000
 1VP  H1   O4   C15  110.36  3.000
 1VP  H6   C10  H5   106.41  3.000
 1VP  H6   C10  C9   109.12  3.000
 1VP  H5   C10  C9   110.49  3.000
 1VP  H6   C10  C11  109.81  3.000
 1VP  H5   C10  C11  109.24  3.000
 1VP  C9   C10  C11  111.64  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  CONST_23  H1   O4   C15  C8    180.00   0.0  0
 1VP  Var_01    C16  C3   C4   C5     84.89  30.0  2
 1VP  Var_02    N    C5   C4   C3    153.72  30.0  1
 1VP  Var_03    C7   C6   N    C5   -173.12  30.0  1
 1VP  Var_04    O1   C7   C6   N       8.30  30.0  3
 1VP  Var_05    C11  C12  N2   C13  -175.40  30.0  3
 1VP  Var_06    C10  C11  C12  N2    178.48  30.0  1
 1VP  Var_07    C9   C10  C11  C12   179.22  30.0  1
 1VP  Var_08    C8   C9   C10  C11   178.13  30.0  1
 1VP  Var_09    H12  C14  C13  O2    -63.35  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
 1VP  plan-5  H1   0.020

