# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 20:38:15 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)OCc1ccccc1)B(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
 0P2  0P2  N~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide  peptide  49  24  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_0P2
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
 0P2  C1    C  C     0   0.755  -13.4391  18.3384  38.6447
 0P2  O1    O  O     0  -0.504  -13.8200  19.4659  38.8798
 0P2  O2    O  O2    0  -0.480  -14.2161  17.3628  38.1602
 0P2  C2    C  CH2   0  -0.255  -15.6115  17.6382  38.0335
 0P2  C3    C  CR6   0   0.069  -16.3167  17.5793  39.3592
 0P2  C4    C  CR16  0  -0.292  -17.0243  18.6745  39.8414
 0P2  C5    C  CR16  0  -0.240  -17.6923  18.6050  41.0579
 0P2  C6    C  CR16  0  -0.262  -17.6459  17.4400  41.8102
 0P2  C7    C  CR16  0  -0.241  -16.9350  16.3425  41.3384
 0P2  C8    C  CR16  0  -0.281  -16.2780  16.4116  40.1190
 0P2  N     N  NH1   0  -0.648  -12.1830  17.8967  38.8505
 0P2  CA    C  CH1   0  -0.205  -11.1252  18.8205  39.1635
 0P2  C     C  C     0   0.544  -10.8697  19.7750  37.9894
 0P2  O     O  O     0  -0.487  -11.1063  19.4428  36.8390
 0P2  CB    C  CH3   0  -0.674   -9.8519  18.0446  39.4844
 0P2  N1    N  NH1   0  -0.655  -10.3318  20.9499  38.3482
 0P2  CA1   C  CH1   0  -0.246   -9.9373  22.0095  37.4239
 0P2  CB1   C  CH1   0  -0.233  -10.8625  23.2384  37.5284
 0P2  CG1   C  CH2   0  -0.438  -11.0259  23.7657  38.9585
 0P2  CG2   C  CH3   0  -0.663  -12.2217  22.9336  36.8986
 0P2  CD1   C  CH3   0  -0.664  -11.6845  25.1390  39.0324
 0P2  B     B  B     0   0.535   -8.3634  22.2471  37.5823
 0P2  O11   O  OH1   0  -0.620   -7.5663  21.4495  36.8167
 0P2  O21   O  OH1   0  -0.619   -7.8969  23.1740  38.4611
 0P2  H21   H  HCH2  0   0.254  -15.7787  18.5992  37.5449
 0P2  H22   H  HCH2  0   0.262  -15.9816  16.8574  37.3690
 0P2  H41   H  HCR6  0   0.252  -17.0559  19.5889  39.2609
 0P2  H51   H  HCR6  0   0.255  -18.2426  19.4638  41.4202
 0P2  H61   H  HCR6  0   0.255  -18.1624  17.3850  42.7598
 0P2  H71   H  HCR6  0   0.255  -16.8982  15.4300  41.9195
 0P2  H81   H  HCR6  0   0.254  -15.7345  15.5474  39.7552
 0P2  H     H  HNH1  0   0.401  -11.9288  16.9881  38.4938
 0P2  HA    H  HCH1  0   0.269  -11.4108  19.4010  40.0452
 0P2  HB1   H  HCH3  0   0.252   -9.0505  18.7232  39.7710
 0P2  HB2   H  HCH3  0   0.255  -10.0249  17.3576  40.3122
 0P2  HB3   H  HCH3  0   0.241   -9.5161  17.4675  38.6216
 0P2  HN2   H  HNH1  0   0.403  -10.2029  21.1204  39.3338
 0P2  HA1   H  HCH1  0   0.243  -10.0769  21.5928  36.4235
 0P2  HB    H  HCH1  0   0.217  -10.3900  24.0298  36.9329
 0P2  HG11  H  HCH2  0   0.208  -11.6212  23.0542  39.5399
 0P2  HG12  H  HCH2  0   0.237  -10.0531  23.8236  39.4487
 0P2  HG21  H  HCH3  0   0.230  -12.8740  23.8067  36.9014
 0P2  HG22  H  HCH3  0   0.224  -12.1130  22.6131  35.8613
 0P2  HG23  H  HCH3  0   0.215  -12.7386  22.1384  37.4408
 0P2  HD11  H  HCH3  0   0.227  -11.7198  25.4972  40.0618
 0P2  HD12  H  HCH3  0   0.215  -11.1287  25.8738  38.4468
 0P2  HD13  H  HCH3  0   0.220  -12.7088  25.1268  38.6597
 0P2  HO1   H  HOH1  0   0.480   -6.6168  21.5518  36.9430
 0P2  HO2   H  HOH1  0   0.482   -6.9389  23.2520  38.5264

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
 0P2  C1   O1    double    1.213  0.020  1.213
 0P2  C1   O2    single    1.338  0.020  1.338
 0P2  O2   C2    single    1.428  0.020  1.428
 0P2  C2   C3    single    1.503  0.020  1.503
 0P2  C2   H21   single    0.970  0.020  1.090
 0P2  C2   H22   single    0.970  0.020  1.090
 0P2  C3   C4    aromatic  1.390  0.020  1.390
 0P2  C3   C8    aromatic  1.394  0.020  1.394
 0P2  C4   C5    aromatic  1.390  0.020  1.390
 0P2  C4   H41   single    0.930  0.020  1.080
 0P2  C5   C6    aromatic  1.388  0.020  1.388
 0P2  C5   H51   single    0.930  0.020  1.080
 0P2  C6   C7    aromatic  1.390  0.020  1.390
 0P2  C6   H61   single    0.930  0.020  1.080
 0P2  C7   C8    aromatic  1.387  0.020  1.387
 0P2  C7   H71   single    0.930  0.020  1.080
 0P2  C8   H81   single    0.930  0.020  1.080
 0P2  N    CA    single    1.458  0.019  1.458
 0P2  N    H     single    0.860  0.020  0.860
 0P2  CA   C     single    1.525  0.021  1.525
 0P2  CA   CB    single    1.521  0.033  1.521
 0P2  CA   HA    single    0.970  0.020  0.970
 0P2  C    O     double    1.231  0.020  1.231
 0P2  CB   HB1   single    0.970  0.020  1.090
 0P2  CB   HB2   single    0.970  0.020  1.090
 0P2  CB   HB3   single    0.970  0.020  1.090
 0P2  N1   CA1   single    1.460  0.020  1.460
 0P2  N1   HN2   single    0.860  0.020  1.020
 0P2  CA1  CB1   single    1.542  0.020  1.542
 0P2  CA1  B     single    1.600  0.020  1.600
 0P2  CA1  HA1   single    0.970  0.020  1.090
 0P2  CB1  CG1   single    1.533  0.020  1.533
 0P2  CB1  CG2   single    1.529  0.020  1.529
 0P2  CB1  HB    single    0.970  0.020  1.090
 0P2  CG1  CD1   single    1.525  0.020  1.525
 0P2  CG1  HG11  single    0.970  0.020  1.090
 0P2  CG1  HG12  single    0.970  0.020  1.090
 0P2  CG2  HG21  single    0.970  0.020  1.090
 0P2  CG2  HG22  single    0.970  0.020  1.090
 0P2  CG2  HG23  single    0.970  0.020  1.090
 0P2  CD1  HD11  single    0.970  0.020  1.090
 0P2  CD1  HD12  single    0.970  0.020  1.090
 0P2  CD1  HD13  single    0.970  0.020  1.090
 0P2  B    O11   single    1.363  0.020  1.363
 0P2  B    O21   single    1.360  0.020  1.360
 0P2  O11  HO1   single    0.850  0.020  0.980
 0P2  O21  HO2   single    0.850  0.020  0.980
 0P2  C1   N     single    1.347  0.020  1.347
 0P2  C    N1    single    1.341  0.020  1.341

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
 0P2  N     C1   O2    110.96  3.000
 0P2  N     C1   O1    124.60  3.000
 0P2  O2    C1   O1    124.44  3.000
 0P2  C2    O2   C1    117.32  3.000
 0P2  H22   C2   H21   107.82  3.000
 0P2  H22   C2   C3    110.51  3.000
 0P2  H21   C2   C3    110.96  3.000
 0P2  H22   C2   O2    104.35  3.000
 0P2  H21   C2   O2    111.06  3.000
 0P2  C3    C2   O2    111.88  3.000
 0P2  C8    C3   C4    119.03  3.000
 0P2  C8    C3   C2    120.05  3.000
 0P2  C4    C3   C2    120.92  3.000
 0P2  H41   C4   C5    119.82  3.000
 0P2  H41   C4   C3    119.60  3.000
 0P2  C5    C4   C3    120.59  3.000
 0P2  H51   C5   C6    120.11  3.000
 0P2  H51   C5   C4    119.85  3.000
 0P2  C6    C5   C4    120.04  3.000
 0P2  H61   C6   C7    120.11  3.000
 0P2  H61   C6   C5    120.16  3.000
 0P2  C7    C6   C5    119.73  3.000
 0P2  H71   C7   C8    119.86  3.000
 0P2  H71   C7   C6    120.04  3.000
 0P2  C8    C7   C6    120.09  3.000
 0P2  H81   C8   C7    119.54  3.000
 0P2  H81   C8   C3    119.94  3.000
 0P2  C7    C8   C3    120.52  3.000
 0P2  H     N    CA    114.00  3.000
 0P2  H     N    C1    118.44  3.000
 0P2  CA    N    C1    120.54  3.000
 0P2  HA    CA   CB    109.00  3.000
 0P2  HA    CA   C     110.00  3.000
 0P2  CB    CA   C     110.50  1.500
 0P2  HA    CA   N     110.00  3.000
 0P2  CB    CA   N     110.40  1.500
 0P2  C     CA   N     111.00  2.800
 0P2  N1    C    O     124.63  3.000
 0P2  N1    C    CA    114.02  3.000
 0P2  O     C    CA    120.80  1.700
 0P2  HB3   CB   HB2   108.43  3.000
 0P2  HB3   CB   HB1   108.15  3.000
 0P2  HB2   CB   HB1   108.06  3.000
 0P2  HB3   CB   CA    111.08  3.000
 0P2  HB2   CB   CA    110.36  3.000
 0P2  HB1   CB   CA    110.67  3.000
 0P2  HN2   N1   CA1   117.47  3.000
 0P2  HN2   N1   C     117.44  3.000
 0P2  CA1   N1   C     125.08  3.000
 0P2  HA1   CA1  B     105.84  3.000
 0P2  HA1   CA1  CB1   106.82  3.000
 0P2  B     CA1  CB1   117.74  3.000
 0P2  HA1   CA1  N1    105.56  3.000
 0P2  B     CA1  N1    108.11  3.000
 0P2  CB1   CA1  N1    111.92  3.000
 0P2  HB    CB1  CG2   107.65  3.000
 0P2  HB    CB1  CG1   107.70  3.000
 0P2  CG2   CB1  CG1   110.99  3.000
 0P2  HB    CB1  CA1   106.24  3.000
 0P2  CG2   CB1  CA1   110.29  3.000
 0P2  CG1   CB1  CA1   113.66  3.000
 0P2  HG12  CG1  HG11  106.31  3.000
 0P2  HG12  CG1  CD1   108.40  3.000
 0P2  HG11  CG1  CD1   108.94  3.000
 0P2  HG12  CG1  CB1   110.03  3.000
 0P2  HG11  CG1  CB1   109.26  3.000
 0P2  CD1   CG1  CB1   113.64  3.000
 0P2  HG23  CG2  HG22  107.77  3.000
 0P2  HG23  CG2  HG21  107.38  3.000
 0P2  HG22  CG2  HG21  107.30  3.000
 0P2  HG23  CG2  CB1   111.18  3.000
 0P2  HG22  CG2  CB1   111.20  3.000
 0P2  HG21  CG2  CB1   111.80  3.000
 0P2  HD13  CD1  HD12  107.61  3.000
 0P2  HD13  CD1  HD11  107.22  3.000
 0P2  HD12  CD1  HD11  107.56  3.000
 0P2  HD13  CD1  CG1   112.29  3.000
 0P2  HD12  CD1  CG1   111.12  3.000
 0P2  HD11  CD1  CG1   110.83  3.000
 0P2  O21   B    O11   124.15  3.000
 0P2  O21   B    CA1   120.18  3.000
 0P2  O11   B    CA1   115.65  3.000
 0P2  HO1   O11  B     116.14  3.000
 0P2  HO2   O21  B     116.11  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
 0P2  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 0P2  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 0P2  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 0P2  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 0P2  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 0P2  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 0P2  CONST_07  C5    C4   C3   C2    180.00   0.0  0
 0P2  CONST_08  C7    C8   C3   C2    180.00   0.0  0
 0P2  CONST_09  H51   C5   C4   C3    180.00   0.0  0
 0P2  CONST_10  H71   C7   C8   C3    180.00   0.0  0
 0P2  CONST_11  H81   C8   C3   C4    180.00   0.0  0
 0P2  CONST_12  H61   C6   C5   C4    180.00   0.0  0
 0P2  CONST_13  H41   C4   C5   C6    180.00   0.0  0
 0P2  CONST_14  CA1   N1   C    CA    180.00   0.0  0
 0P2  CONST_15  CA1   N1   C    O       0.00   0.0  0
 0P2  CONST_16  HN2   N1   C    CA      0.00   0.0  0
 0P2  Var_01    C4    C3   C2   O2    122.44  30.0  2
 0P2  Var_02    C3    C2   O2   C1    -76.72  30.0  3
 0P2  Var_03    CA    N    C1   O1    -10.71  30.0  2
 0P2  Var_04    N     C1   O2   C2    173.11  30.0  1
 0P2  Var_05    HD11  CD1  CG1  CB1  -176.36  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
 0P2  chir_01  CA   N    C    CB   positiv
 0P2  chir_02  CA1  N1   CB1  B    negativ
 0P2  chir_03  CB1  CA1  CG1  CG2  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
 0P2  plan-1  C2   0.020
 0P2  plan-1  C3   0.020
 0P2  plan-1  C4   0.020
 0P2  plan-1  C5   0.020
 0P2  plan-1  C6   0.020
 0P2  plan-1  C7   0.020
 0P2  plan-1  C8   0.020
 0P2  plan-1  H41  0.020
 0P2  plan-1  H51  0.020
 0P2  plan-1  H61  0.020
 0P2  plan-1  H71  0.020
 0P2  plan-1  H81  0.020
 0P2  plan-2  CA   0.020
 0P2  plan-2  C    0.020
 0P2  plan-2  O    0.020
 0P2  plan-2  N1   0.020
 0P2  plan-2  CA1  0.020
 0P2  plan-2  HN2  0.020
 0P2  plan-3  C1   0.020
 0P2  plan-3  O1   0.020
 0P2  plan-3  O2   0.020
 0P2  plan-3  N    0.020

