# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 15:38:24 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: diethyl [(1R)-1,5-diaminopentyl]boronate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOB(OCC)[C@@H](N)CCCCN
#
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
 0AY  0AY  'diethyl [(1R)-1,5-diaminopentyl]boronate'  peptide  37  14  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0AY
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
 0AY  N     N  NH2   0  -0.812   1.0295  -1.6343   2.5209
 0AY  CA    C  CH1   0  -0.264   0.4840  -1.4215   1.1739
 0AY  CB    C  CH2   0  -0.449  -1.0355  -1.2098   1.1588
 0AY  CG    C  CH2   0  -0.442  -1.6132  -0.9581  -0.2291
 0AY  CD    C  CH2   0  -0.421  -3.1287  -0.8019  -0.2245
 0AY  CE    C  CH2   0  -0.270  -3.6972  -0.5028  -1.6030
 0AY  NZ    N  NH2   0  -0.801  -5.1431  -0.3367  -1.5479
 0AY  B     B  B     0   0.616   1.2527  -0.1928   0.5067
 0AY  OXT   O  O2    0  -0.452   1.9847  -0.4469  -0.6091
 0AY  C1    C  CH2   0  -0.170   2.8091   0.4327  -1.3623
 0AY  C2    C  CH3   0  -0.680   3.6670  -0.3845  -2.3026
 0AY  O     O  O2    0  -0.456   1.0860   0.9963   1.1405
 0AY  C3    C  CH2   0  -0.166   1.4809   2.3032   0.7546
 0AY  C5    C  CH3   0  -0.676   0.7180   3.3103   1.5862
 0AY  H1N   H  HNH2  0   0.333   0.8435  -0.8145   3.0869
 0AY  H2N   H  HNH2  0   0.334   0.5224  -2.3873   2.9738
 0AY  HA    H  HCH1  0   0.198   0.7046  -2.3262   0.5956
 0AY  H1B   H  HCH2  0   0.208  -1.5255  -2.0880   1.5974
 0AY  H2B   H  HCH2  0   0.203  -1.2835  -0.3651   1.8114
 0AY  H1G   H  HCH2  0   0.216  -1.1684  -0.0523  -0.6590
 0AY  H2G   H  HCH2  0   0.210  -1.3332  -1.7785  -0.8989
 0AY  H1D   H  HCH2  0   0.210  -3.5885  -1.7178   0.1643
 0AY  H2D   H  HCH2  0   0.210  -3.4145   0.0018   0.4614
 0AY  H1E   H  HCH2  0   0.210  -3.2611   0.4297  -1.9730
 0AY  H2E   H  HCH2  0   0.185  -3.3719  -1.2898  -2.2996
 0AY  H1NZ  H  HNH2  0   0.344  -5.4940  -0.1124  -2.4702
 0AY  H2NZ  H  HNH2  0   0.336  -5.5717  -1.2214  -1.3035
 0AY  H11   H  HCH2  0   0.219   2.1885   1.1253  -1.9364
 0AY  H21   H  HCH2  0   0.217   3.4478   1.0276  -0.7058
 0AY  H12   H  HCH3  0   0.231   3.0558  -0.9765  -2.9844
 0AY  H22   H  HCH3  0   0.231   4.2898   0.2788  -2.9022
 0AY  H32   H  HCH3  0   0.230   4.3262  -1.0588  -1.7547
 0AY  H13   H  HCH2  0   0.217   2.5553   2.4333   0.9083
 0AY  H23   H  HCH2  0   0.214   1.2749   2.4737  -0.3047
 0AY  H15   H  HCH3  0   0.230  -0.3567   3.2225   1.4242
 0AY  H25   H  HCH3  0   0.230   0.9182   3.1800   2.6502
 0AY  H35   H  HCH3  0   0.230   1.0188   4.3209   1.3106

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
 0AY  N    CA    single  1.458  0.019  1.458
 0AY  N    H1N   single  0.890  0.020  1.040
 0AY  N    H2N   single  0.890  0.020  1.040
 0AY  CA   B     single  1.596  0.020  1.596
 0AY  CA   HA    single  0.970  0.020  0.970
 0AY  CB   CA    single  1.521  0.033  1.521
 0AY  CB   H1B   single  0.970  0.020  1.090
 0AY  CB   H2B   single  0.970  0.020  1.090
 0AY  CG   CB    single  1.524  0.020  1.524
 0AY  CG   H1G   single  0.970  0.020  1.090
 0AY  CG   H2G   single  0.970  0.020  1.090
 0AY  CD   CG    single  1.524  0.020  1.524
 0AY  CD   H1D   single  0.970  0.020  1.090
 0AY  CD   H2D   single  0.970  0.020  1.090
 0AY  CE   CD    single  1.521  0.020  1.521
 0AY  CE   H1E   single  0.970  0.020  1.090
 0AY  CE   H2E   single  0.970  0.020  1.090
 0AY  NZ   CE    single  1.456  0.020  1.456
 0AY  NZ   H1NZ  single  0.890  0.020  1.040
 0AY  NZ   H2NZ  single  0.890  0.020  1.040
 0AY  B    O     single  1.358  0.020  1.358
 0AY  B    OXT   single  1.359  0.020  1.359
 0AY  OXT  C1    single  1.421  0.020  1.421
 0AY  C1   C2    single  1.513  0.020  1.513
 0AY  C1   H11   single  0.970  0.020  1.090
 0AY  C1   H21   single  0.970  0.020  1.090
 0AY  C2   H12   single  0.970  0.020  1.090
 0AY  C2   H22   single  0.970  0.020  1.090
 0AY  C2   H32   single  0.970  0.020  1.090
 0AY  O    C3    single  1.419  0.020  1.419
 0AY  C3   H13   single  0.970  0.020  1.090
 0AY  C3   H23   single  0.970  0.020  1.090
 0AY  C5   C3    single  1.513  0.020  1.513
 0AY  C5   H15   single  0.970  0.020  1.090
 0AY  C5   H25   single  0.970  0.020  1.090
 0AY  C5   H35   single  0.970  0.020  1.090

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
 0AY  H2N   N    H1N   105.03  3.000
 0AY  H2N   N    CA    109.35  3.000
 0AY  H1N   N    CA    109.08  3.000
 0AY  HA    CA   B     108.54  3.000
 0AY  HA    CA   CB    109.00  3.000
 0AY  B     CA   CB    111.51  3.000
 0AY  CB    CA   N     110.40  1.500
 0AY  HA    CA   N     110.00  3.000
 0AY  B     CA   N     108.43  3.000
 0AY  H2B   CB   H1B   106.13  3.000
 0AY  H2B   CB   CG    109.22  3.000
 0AY  H1B   CB   CG    109.08  3.000
 0AY  CG    CB   CA    114.03  3.000
 0AY  H2B   CB   CA    108.95  3.000
 0AY  H1B   CB   CA    109.14  3.000
 0AY  H2G   CG   H1G   105.97  3.000
 0AY  H2G   CG   CD    109.44  3.000
 0AY  H1G   CG   CD    108.66  3.000
 0AY  CD    CG   CB    113.03  3.000
 0AY  H2G   CG   CB    109.64  3.000
 0AY  H1G   CG   CB    109.84  3.000
 0AY  H2D   CD   H1D   106.36  3.000
 0AY  H2D   CD   CE    109.03  3.000
 0AY  H1D   CD   CE    109.22  3.000
 0AY  CE    CD   CG    112.91  3.000
 0AY  H2D   CD   CG    109.68  3.000
 0AY  H1D   CD   CG    109.43  3.000
 0AY  H2E   CE   H1E   106.13  3.000
 0AY  H2E   CE   NZ    113.52  3.000
 0AY  H1E   CE   NZ    108.14  3.000
 0AY  NZ    CE   CD    111.05  3.000
 0AY  H2E   CE   CD    108.82  3.000
 0AY  H1E   CE   CD    108.98  3.000
 0AY  H2NZ  NZ   H1NZ  105.47  3.000
 0AY  H2NZ  NZ   CE    109.24  3.000
 0AY  H1NZ  NZ   CE    109.57  3.000
 0AY  O     B    OXT   127.83  3.000
 0AY  OXT   B    CA    117.33  3.000
 0AY  O     B    CA    114.84  3.000
 0AY  C1    OXT  B     129.20  3.000
 0AY  H21   C1   H11   107.62  3.000
 0AY  H21   C1   C2    109.65  3.000
 0AY  H11   C1   C2    109.75  3.000
 0AY  H21   C1   OXT   110.96  3.000
 0AY  H11   C1   OXT   109.95  3.000
 0AY  C2    C1   OXT   108.90  3.000
 0AY  H32   C2   H22   107.90  3.000
 0AY  H32   C2   H12   108.50  3.000
 0AY  H22   C2   H12   107.86  3.000
 0AY  H32   C2   C1    111.38  3.000
 0AY  H22   C2   C1    109.72  3.000
 0AY  H12   C2   C1    111.35  3.000
 0AY  C3    O    B     130.22  3.000
 0AY  H23   C3   H13   107.64  3.000
 0AY  H23   C3   C5    109.51  3.000
 0AY  H13   C3   C5    109.83  3.000
 0AY  C5    C3   O     108.87  3.000
 0AY  H23   C3   O     110.79  3.000
 0AY  H13   C3   O     110.18  3.000
 0AY  H35   C5   H25   107.87  3.000
 0AY  H35   C5   H15   108.00  3.000
 0AY  H25   C5   H15   108.44  3.000
 0AY  H35   C5   C3    109.83  3.000
 0AY  H25   C5   C3    111.37  3.000
 0AY  H15   C5   C3    111.22  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
 0AY  Var_01  CD    CG  CB   CA    177.88  30.0  1
 0AY  Var_02  CE    CD  CG   CB    178.00  30.0  1
 0AY  Var_03  NZ    CE  CD   CG   -178.93  30.0  1
 0AY  Var_04  C5    C3  O    B     163.51  30.0  3
 0AY  Var_05  C2    C1  OXT  B     166.36  30.0  3
 0AY  Var_06  H1NZ  NZ  CE   CD    178.37  30.0  3
 0AY  Var_07  H12   C2  C1   OXT    59.47  30.0  3
 0AY  Var_08  H15   C5  C3   O     -61.19  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
 0AY  chir_01  CA  N  B  CB  positiv

