# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:15:36 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N~6~-[(1R)-2-{[(1S)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(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
 VB1  VB1  N~6~-[(1R)-2-{[(1S)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine  L-peptide  44  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_VB1
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
 VB1  C1    C  C      0   0.404   6.9925   1.2236  -0.0265
 VB1  C2    C  CH1    0  -0.202   5.8965   0.2377  -0.4837
 VB1  C3    C  CH2    0  -0.428   4.5425   0.7502   0.0354
 VB1  CAV   C  CH1    0  -0.205  -4.9505   0.7673  -0.2626
 VB1  C4    C  CH2    0  -0.421   3.3470  -0.0334  -0.4916
 VB1  C7    C  CH2    0  -0.580   2.0306   0.5129   0.0417
 VB1  C10   C  C      0   0.574   0.8159  -0.2171  -0.4892
 VB1  N11   N  NH1    0  -0.630  -0.2475  -0.2057   0.3384
 VB1  C12   C  CH1    0  -0.238  -1.5256  -0.7846   0.0262
 VB1  C13   C  C      0   0.576  -2.6361   0.2340   0.2850
 VB1  N14   N  NH2    0  -0.801   6.2307  -1.1186  -0.0779
 VB1  O15   O  O      0  -0.498   0.7987  -0.7520  -1.5881
 VB1  C16   C  CH2    0  -0.530  -1.8187  -2.0201   0.8799
 VB1  S17   S  S2     0  -0.246  -0.5626  -3.2943   0.5355
 VB1  O18   O  O      0  -0.498  -2.5470   1.0363   1.2034
 VB1  O19   O  OC    -1  -0.621   7.0980   2.2782  -0.6852
 VB1  O20   O  O      0  -0.610   7.6506   0.9143   0.9870
 VB1  N29   N  NH1    0  -0.611  -3.6754   0.1500  -0.5487
 VB1  C31   C  C      0   0.421  -5.7349  -0.0019   0.8360
 VB1  C33   C  CH2    0  -0.453  -5.7665   0.9028  -1.5467
 VB1  O42   O  O      0  -0.587  -5.2270  -1.0405   1.2916
 VB1  O43   O  OC    -1  -0.614  -6.8241   0.5121   1.1585
 VB1  H321  H  HCH3   0   0.220  -4.1437   1.2736  -2.9507
 VB1  H322  H  HCH3   0   0.229  -5.7141   1.8497  -3.4954
 VB1  H323  H  HCH3   0   0.218  -4.8362   2.7315  -2.2475
 VB1  H331  H  HCH2   0   0.220  -6.0019  -0.0924  -1.9401
 VB1  H332  H  HCH2   0   0.236  -6.7200   1.3598  -1.2826
 VB1  HAV   H  HCH1   0   0.240  -4.7526   1.7748   0.1152
 VB1  H29   H  HNH1   0   0.391  -3.6793  -0.6153  -1.2059
 VB1  H12   H  HCH1   0   0.285  -1.5186  -1.0727  -1.0264
 VB1  H161  H  HCH2   0   0.273  -1.7968  -1.7566   1.9377
 VB1  H162  H  HCH2   0   0.284  -2.8118  -2.3994   0.6435
 VB1  H11   H  HNH1   0   0.397  -0.1644   0.2581   1.2303
 VB1  H17   H  HSH1   0   0.227  -1.0642  -4.2344   1.3436
 VB1  H7C1  H  HCH2   0   0.251   2.0306   0.4944   1.1348
 VB1  H7C2  H  HCH2   0   0.270   1.9270   1.5670  -0.2390
 VB1  H4C1  H  HCH2   0   0.224   3.3467   0.0011  -1.5837
 VB1  H4C2  H  HCH2   0   0.214   3.4348  -1.0882  -0.2146
 VB1  H3C1  H  HCH2   0   0.208   4.5486   0.7238   1.1316
 VB1  H3C2  H  HCH2   0   0.213   4.4290   1.8008  -0.2493
 VB1  H2    H  HCH1   0   0.198   5.8561   0.2637  -1.5792
 VB1  H141  H  HNH2   0   0.326   6.4402  -1.1116   0.9126
 VB1  H142  H  HNH2   0   0.332   5.4380  -1.7349  -0.2065
 VB1  C32   C  CH3    0  -0.660  -5.0753   1.7332  -2.6194

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
 VB1  C32  C33   single  1.523  0.020  1.523
 VB1  C33  CAV   single  1.527  0.020  1.527
 VB1  CAV  C31   single  1.554  0.020  1.554
 VB1  CAV  N29   single  1.445  0.020  1.445
 VB1  C31  O43   deloc   1.247  0.020  1.247
 VB1  C31  O42   deloc   1.243  0.020  1.243
 VB1  N29  C13   single  1.335  0.020  1.335
 VB1  C13  O18   double  1.223  0.020  1.223
 VB1  C13  C12   single  1.529  0.020  1.529
 VB1  C12  C16   single  1.530  0.020  1.530
 VB1  C12  N11   single  1.437  0.020  1.437
 VB1  C16  S17   single  1.822  0.020  1.822
 VB1  N11  C10   single  1.348  0.020  1.348
 VB1  C10  O15   double  1.222  0.020  1.222
 VB1  C10  C7    single  1.513  0.020  1.513
 VB1  C7   C4    single  1.522  0.020  1.522
 VB1  C4   C3    single  1.523  0.020  1.523
 VB1  C3   C2    single  1.538  0.020  1.538
 VB1  C2   C1    single  1.543  0.020  1.543
 VB1  C2   N14   single  1.455  0.020  1.455
 VB1  C1   O20   deloc   1.247  0.020  1.247
 VB1  C1   O19   deloc   1.248  0.020  1.248
 VB1  C32  H321  single  0.970  0.020  1.090
 VB1  C32  H322  single  0.970  0.020  1.090
 VB1  C32  H323  single  0.970  0.020  1.090
 VB1  C33  H331  single  0.970  0.020  1.090
 VB1  C33  H332  single  0.970  0.020  1.090
 VB1  CAV  HAV   single  0.970  0.020  1.090
 VB1  N29  H29   single  0.890  0.020  1.040
 VB1  C12  H12   single  0.970  0.020  1.090
 VB1  C16  H161  single  0.970  0.020  1.090
 VB1  C16  H162  single  0.970  0.020  1.090
 VB1  N11  H11   single  0.860  0.020  1.020
 VB1  S17  H17   single  1.200  0.020  1.300
 VB1  C7   H7C1  single  0.970  0.020  1.090
 VB1  C7   H7C2  single  0.970  0.020  1.090
 VB1  C4   H4C1  single  0.970  0.020  1.090
 VB1  C4   H4C2  single  0.970  0.020  1.090
 VB1  C3   H3C1  single  0.970  0.020  1.090
 VB1  C3   H3C2  single  0.970  0.020  1.090
 VB1  C2   H2    single  0.970  0.020  1.090
 VB1  N14  H141  single  0.890  0.020  1.040
 VB1  N14  H142  single  0.890  0.020  1.040

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
 VB1  O20   C1   O19   126.43  3.000
 VB1  O19   C1   C2    116.33  3.000
 VB1  O20   C1   C2    117.19  3.000
 VB1  H2    C2   N14   108.02  3.000
 VB1  H2    C2   C3    107.27  3.000
 VB1  N14   C2   C3    114.76  3.000
 VB1  H2    C2   C1    107.87  3.000
 VB1  N14   C2   C1    110.48  3.000
 VB1  C3    C2   C1    108.20  3.000
 VB1  H3C2  C3   H3C1  106.48  3.000
 VB1  H3C2  C3   C4    108.81  3.000
 VB1  H3C1  C3   C4    109.74  3.000
 VB1  H3C2  C3   C2    108.87  3.000
 VB1  H3C1  C3   C2    108.94  3.000
 VB1  C4    C3   C2    113.75  3.000
 VB1  HAV   CAV  C33   107.77  3.000
 VB1  HAV   CAV  C31   107.64  3.000
 VB1  C33   CAV  C31   111.63  3.000
 VB1  HAV   CAV  N29   107.58  3.000
 VB1  C31   CAV  N29   111.96  3.000
 VB1  C33   CAV  N29   110.05  3.000
 VB1  H4C2  C4   H4C1  106.47  3.000
 VB1  H4C2  C4   C7    109.07  3.000
 VB1  H4C1  C4   C7    109.80  3.000
 VB1  H4C2  C4   C3    110.20  3.000
 VB1  H4C1  C4   C3    109.25  3.000
 VB1  C7    C4   C3    111.90  3.000
 VB1  H7C2  C7   H7C1  105.80  3.000
 VB1  H7C2  C7   C10   107.35  3.000
 VB1  H7C1  C7   C10   110.04  3.000
 VB1  H7C2  C7   C4    109.72  3.000
 VB1  H7C1  C7   C4    110.14  3.000
 VB1  C10   C7   C4    113.47  3.000
 VB1  O15   C10  N11   123.01  3.000
 VB1  O15   C10  C7    122.53  3.000
 VB1  N11   C10  C7    114.45  3.000
 VB1  H11   N11  C12   116.77  3.000
 VB1  H11   N11  C10   118.81  3.000
 VB1  C12   N11  C10   124.40  3.000
 VB1  H12   C12  C16   109.04  3.000
 VB1  H12   C12  C13   110.10  3.000
 VB1  C16   C12  C13   107.72  3.000
 VB1  H12   C12  N11   108.07  3.000
 VB1  C16   C12  N11   111.99  3.000
 VB1  C13   C12  N11   109.92  3.000
 VB1  N29   C13  O18   124.55  3.000
 VB1  O18   C13  C12   120.75  3.000
 VB1  N29   C13  C12   114.70  3.000
 VB1  H142  N14  H141  106.89  3.000
 VB1  H142  N14  C2    110.63  3.000
 VB1  H141  N14  C2    108.30  3.000
 VB1  H162  C16  H161  108.25  3.000
 VB1  H162  C16  S17   110.13  3.000
 VB1  H161  C16  S17   109.78  3.000
 VB1  H162  C16  C12   109.56  3.000
 VB1  H161  C16  C12   110.01  3.000
 VB1  S17   C16  C12   109.10  3.000
 VB1  H17   S17  C16    96.82  3.000
 VB1  H29   N29  C13   117.23  3.000
 VB1  H29   N29  CAV   116.72  3.000
 VB1  C13   N29  CAV   122.44  3.000
 VB1  O43   C31  O42   127.36  3.000
 VB1  O42   C31  CAV   117.82  3.000
 VB1  O43   C31  CAV   114.82  3.000
 VB1  H332  C33  H331  106.26  3.000
 VB1  H332  C33  C32   109.83  3.000
 VB1  H331  C33  C32   109.87  3.000
 VB1  H332  C33  CAV   107.51  3.000
 VB1  H331  C33  CAV   109.64  3.000
 VB1  C32   C33  CAV   113.46  3.000
 VB1  H323  C32  H322  107.72  3.000
 VB1  H323  C32  H321  107.57  3.000
 VB1  H322  C32  H321  107.54  3.000
 VB1  H323  C32  C33   110.99  3.000
 VB1  H322  C32  C33   110.99  3.000
 VB1  H321  C32  C33   111.84  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
 VB1  CONST_03  C12   N11  C10  C7    180.00   0.0  0
 VB1  CONST_04  O15   C10  N11  C12     0.00   0.0  0
 VB1  CONST_05  H11   N11  C10  C7      0.00   0.0  0
 VB1  CONST_06  H29   N29  C13  C12     0.00   0.0  0
 VB1  Var_01    C7    C4   C3   C2   -179.70  30.0  1
 VB1  Var_02    C10   C7   C4   C3    178.46  30.0  1
 VB1  Var_03    N11   C10  C7   C4    151.83  30.0  2
 VB1  Var_04    H321  C32  C33  CAV    63.00  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
 VB1  chir_01  C2   C3   C1   N14  negativ
 VB1  chir_02  CAV  C33  C31  N29  negativ
 VB1  chir_03  C12  N11  C13  C16  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
 VB1  plan-1  C7   0.020
 VB1  plan-1  C10  0.020
 VB1  plan-1  N11  0.020
 VB1  plan-1  C12  0.020
 VB1  plan-1  O15  0.020
 VB1  plan-1  H11  0.020
 VB1  plan-2  CAV  0.020
 VB1  plan-2  C12  0.020
 VB1  plan-2  C13  0.020
 VB1  plan-2  O18  0.020
 VB1  plan-2  N29  0.020
 VB1  plan-2  H29  0.020
 VB1  plan-3  C1   0.020
 VB1  plan-3  C2   0.020
 VB1  plan-3  O19  0.020
 VB1  plan-3  O20  0.020
 VB1  plan-4  CAV  0.020
 VB1  plan-4  C31  0.020
 VB1  plan-4  O42  0.020
 VB1  plan-4  O43  0.020

