# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 15:38:25 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alanylglycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](C(=O)NO)C(=O)N[C@H](C)C(=O)NCC(N)=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
 01S  01S  N-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alanylglycinamide  peptide  43  21  .  2022-03-07  2022-03-07
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_01S
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
 01S  N     N  NH1   0  -0.369   3.2744  -1.7477   1.2701
 01S  OH    O  OH1   0  -0.540   3.9500  -2.9262   1.3601
 01S  C1    C  C     0   0.553   3.1364  -1.1465   0.0747
 01S  O1    O  O     0  -0.460   3.4228  -1.6661  -0.9862
 01S  CA    C  CH1   0  -0.565   2.5474   0.2535   0.1697
 01S  CB    C  CH2   0  -0.388   3.5541   1.2758  -0.3567
 01S  CG    C  CH1   0  -0.243   3.1710   2.7334  -0.0914
 01S  CD1   C  CH3   0  -0.660   3.1592   3.0594   1.3989
 01S  CD2   C  CH3   0  -0.652   4.1315   3.6566  -0.8344
 01S  C     C  C     0   0.590   1.2551   0.2386  -0.6434
 01S  O     O  O     0  -0.481   1.2149   0.5691  -1.8167
 01S  N1    N  NH1   0  -0.636   0.1863  -0.2073   0.0337
 01S  CA1   C  CH1   0  -0.203  -1.1002  -0.4169  -0.5821
 01S  C2    C  C     0   0.561  -2.1691  -0.3432   0.5031
 01S  O2    O  O     0  -0.491  -1.9065  -0.5181   1.6847
 01S  CB1   C  CH3   0  -0.650  -1.1791  -1.7672  -1.2997
 01S  N2    N  NH1   0  -0.645  -3.4053  -0.1199   0.0508
 01S  CA2   C  CH2   0  -0.372  -4.5551  -0.1057   0.9111
 01S  C3    C  C     0   0.494  -5.8129   0.0676   0.0745
 01S  O3    O  O     0  -0.483  -5.7659   0.1762  -1.1417
 01S  N3    N  NH2   0  -0.798  -6.9446   0.0895   0.7825
 01S  HN    H  HNH1  0   0.420   3.1950  -1.2396   2.1396
 01S  HOH   H  HOH1  0   0.480   3.2773  -3.6178   1.4066
 01S  HA    H  HCH1  0   0.288   2.3071   0.4795   1.2130
 01S  HB1   H  HCH2  0   0.237   4.5256   1.0818   0.1100
 01S  HB2   H  HCH2  0   0.242   3.6894   1.1178  -1.4280
 01S  HG    H  HCH1  0   0.224   2.1660   2.9105  -0.4894
 01S  HD11  H  HCH3  0   0.232   2.9193   4.1105   1.5654
 01S  HD12  H  HCH3  0   0.228   2.4209   2.4731   1.9479
 01S  HD13  H  HCH3  0   0.216   4.1370   2.8653   1.8466
 01S  HD21  H  HCH3  0   0.227   4.1064   3.4736  -1.9100
 01S  HD22  H  HCH3  0   0.227   3.8793   4.7052  -0.6695
 01S  HD23  H  HCH3  0   0.215   5.1600   3.5080  -0.4963
 01S  H     H  HNH1  0   0.399   0.2765  -0.4682   1.0046
 01S  HA1   H  HCH1  0   0.282  -1.2722   0.3822  -1.3070
 01S  HB11  H  HCH3  0   0.239  -2.1401  -1.8917  -1.7983
 01S  HB21  H  HCH3  0   0.252  -0.3997  -1.8349  -2.0574
 01S  HB3   H  HCH3  0   0.237  -1.0486  -2.5887  -0.5950
 01S  H1    H  HNH1  0   0.405  -3.5716   0.0387  -0.9325
 01S  HA2   H  HCH2  0   0.284  -4.6297  -1.0353   1.4825
 01S  HA3   H  HCH2  0   0.283  -4.4965   0.7083   1.6400
 01S  HN1   H  HNH2  0   0.414  -6.9501   0.0063   1.7848
 01S  HN2   H  HNH2  0   0.409  -7.8326   0.2034   0.3216

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
 01S  N    OH    single  1.361  0.020  1.361
 01S  N    C1    single  1.345  0.020  1.345
 01S  N    HN    single  0.890  0.020  1.040
 01S  OH   HOH   single  0.850  0.020  0.980
 01S  C1   O1    double  1.216  0.020  1.216
 01S  C1   CA    single  1.522  0.020  1.522
 01S  CA   CB    single  1.521  0.033  1.521
 01S  CA   C     single  1.525  0.021  1.525
 01S  CA   HA    single  0.970  0.020  0.970
 01S  CB   CG    single  1.530  0.020  1.530
 01S  CB   HB1   single  0.970  0.020  1.090
 01S  CB   HB2   single  0.970  0.020  1.090
 01S  CG   CD1   single  1.526  0.020  1.526
 01S  CG   CD2   single  1.525  0.020  1.525
 01S  CG   HG    single  0.970  0.020  1.090
 01S  CD1  HD11  single  0.970  0.020  1.090
 01S  CD1  HD12  single  0.970  0.020  1.090
 01S  CD1  HD13  single  0.970  0.020  1.090
 01S  CD2  HD21  single  0.970  0.020  1.090
 01S  CD2  HD22  single  0.970  0.020  1.090
 01S  CD2  HD23  single  0.970  0.020  1.090
 01S  C    O     double  1.231  0.020  1.231
 01S  N1   CA1   single  1.442  0.020  1.442
 01S  N1   H     single  0.860  0.020  1.020
 01S  CA1  C2    single  1.525  0.020  1.525
 01S  CA1  CB1   single  1.531  0.020  1.531
 01S  CA1  HA1   single  0.970  0.020  1.090
 01S  C2   O2    double  1.223  0.020  1.223
 01S  CB1  HB11  single  0.970  0.020  1.090
 01S  CB1  HB21  single  0.970  0.020  1.090
 01S  CB1  HB3   single  0.970  0.020  1.090
 01S  N2   CA2   single  1.436  0.020  1.436
 01S  N2   H1    single  0.860  0.020  1.020
 01S  CA2  C3    single  1.520  0.020  1.520
 01S  CA2  HA2   single  0.970  0.020  1.090
 01S  CA2  HA3   single  0.970  0.020  1.090
 01S  C3   O3    double  1.222  0.020  1.222
 01S  N3   HN1   single  0.860  0.020  1.020
 01S  N3   HN2   single  0.860  0.020  1.020
 01S  C    N1    single  1.341  0.020  1.341
 01S  C2   N2    single  1.335  0.020  1.335
 01S  C3   N3    single  1.335  0.020  1.335

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
 01S  HN    N    C1    122.14  3.000
 01S  HN    N    OH    114.67  3.000
 01S  C1    N    OH    119.77  3.000
 01S  HOH   OH   N     106.10  3.000
 01S  CA    C1   O1    122.61  3.000
 01S  CA    C1   N     113.29  3.000
 01S  O1    C1   N     124.09  3.000
 01S  HA    CA   C     110.00  3.000
 01S  HA    CA   CB    109.00  3.000
 01S  C     CA   CB    110.50  1.500
 01S  HA    CA   C1    109.55  3.000
 01S  C     CA   C1    106.58  3.000
 01S  CB    CA   C1    109.81  3.000
 01S  HB2   CB   HB1   106.42  3.000
 01S  HB2   CB   CG    109.82  3.000
 01S  HB1   CB   CG    108.48  3.000
 01S  HB2   CB   CA    108.85  3.000
 01S  HB1   CB   CA    108.61  3.000
 01S  CG    CB   CA    114.36  3.000
 01S  HG    CG   CD2   107.63  3.000
 01S  HG    CG   CD1   108.26  3.000
 01S  CD2   CG   CD1   110.57  3.000
 01S  HG    CG   CB    108.71  3.000
 01S  CD2   CG   CB    109.54  3.000
 01S  CD1   CG   CB    112.01  3.000
 01S  HD13  CD1  HD12  107.70  3.000
 01S  HD13  CD1  HD11  107.78  3.000
 01S  HD12  CD1  HD11  106.99  3.000
 01S  HD13  CD1  CG    110.81  3.000
 01S  HD12  CD1  CG    112.45  3.000
 01S  HD11  CD1  CG    110.90  3.000
 01S  HD23  CD2  HD22  107.54  3.000
 01S  HD23  CD2  HD21  107.68  3.000
 01S  HD22  CD2  HD21  107.75  3.000
 01S  HD23  CD2  CG    111.08  3.000
 01S  HD22  CD2  CG    111.26  3.000
 01S  HD21  CD2  CG    111.35  3.000
 01S  N1    C    O     123.32  3.000
 01S  N1    C    CA    114.13  3.000
 01S  O     C    CA    120.80  1.700
 01S  H     N1   CA1   116.94  3.000
 01S  H     N1   C     120.01  3.000
 01S  CA1   N1   C     122.94  3.000
 01S  HA1   CA1  CB1   109.02  3.000
 01S  HA1   CA1  C2    109.05  3.000
 01S  CB1   CA1  C2    109.88  3.000
 01S  HA1   CA1  N1    108.51  3.000
 01S  CB1   CA1  N1    111.99  3.000
 01S  C2    CA1  N1    108.33  3.000
 01S  N2    C2   O2    123.37  3.000
 01S  N2    C2   CA1   114.59  3.000
 01S  O2    C2   CA1   122.01  3.000
 01S  HB3   CB1  HB21  108.49  3.000
 01S  HB3   CB1  HB11  108.37  3.000
 01S  HB21  CB1  HB11  107.80  3.000
 01S  HB3   CB1  CA1   110.81  3.000
 01S  HB21  CB1  CA1   110.12  3.000
 01S  HB11  CB1  CA1   111.14  3.000
 01S  H1    N2   CA2   116.74  3.000
 01S  H1    N2   C2    120.57  3.000
 01S  CA2   N2   C2    122.69  3.000
 01S  HA3   CA2  HA2   106.73  3.000
 01S  HA3   CA2  C3    109.03  3.000
 01S  HA2   CA2  C3    109.14  3.000
 01S  HA3   CA2  N2    111.32  3.000
 01S  HA2   CA2  N2    111.05  3.000
 01S  C3    CA2  N2    109.50  3.000
 01S  N3    C3   O3    123.98  3.000
 01S  N3    C3   CA2   114.29  3.000
 01S  O3    C3   CA2   121.73  3.000
 01S  HN2   N3   HN1   117.44  3.000
 01S  HN2   N3   C3    120.44  3.000
 01S  HN1   N3   C3    122.12  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
 01S  CONST_01  O1    C1   N    OH      0.00   0.0  0
 01S  CONST_02  CA    C1   N    OH    180.00   0.0  0
 01S  CONST_03  CA1   N1   C    CA    180.00   0.0  0
 01S  CONST_04  CA1   N1   C    O       0.00   0.0  0
 01S  CONST_05  CA2   N2   C2   CA1   180.00   0.0  0
 01S  CONST_06  CA2   N2   C2   O2      0.00   0.0  0
 01S  CONST_07  HN    N    C1   O1    180.00   0.0  0
 01S  CONST_08  H     N1   C    CA      0.00   0.0  0
 01S  CONST_09  H1    N2   C2   CA1     0.00   0.0  0
 01S  CONST_10  HN1   N3   C3   CA2     0.00   0.0  0
 01S  CONST_11  HN2   N3   C3   CA2   180.00   0.0  0
 01S  Var_01    CD1   CG   CB   CA     65.28  30.0  3
 01S  Var_02    C3    CA2  N2   C2   -175.65  30.0  3
 01S  Var_03    O3    C3   CA2  N2     -0.24  30.0  3
 01S  Var_04    HD11  CD1  CG   CB    177.96  30.0  3
 01S  Var_05    HD21  CD2  CG   CB     59.42  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
 01S  chir_01  CA   C1  CB  C    negativ
 01S  chir_02  CA1  N1  C2  CB1  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
 01S  plan-1  N    0.020
 01S  plan-1  OH   0.020
 01S  plan-1  C1   0.020
 01S  plan-1  O1   0.020
 01S  plan-1  CA   0.020
 01S  plan-1  HN   0.020
 01S  plan-2  CA   0.020
 01S  plan-2  C    0.020
 01S  plan-2  O    0.020
 01S  plan-2  N1   0.020
 01S  plan-2  CA1  0.020
 01S  plan-2  H    0.020
 01S  plan-3  CA1  0.020
 01S  plan-3  C2   0.020
 01S  plan-3  O2   0.020
 01S  plan-3  N2   0.020
 01S  plan-3  CA2  0.020
 01S  plan-3  H1   0.020
 01S  plan-4  CA2  0.020
 01S  plan-4  C3   0.020
 01S  plan-4  O3   0.020
 01S  plan-4  N3   0.020
 01S  plan-4  HN1  0.020
 01S  plan-4  HN2  0.020

