# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:20:01 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: N-(tert-butoxycarbonyl)-L-alanyl-N-{(1R)-5-ammonio-1-[hydroxy(methoxy)boranyl]pentyl}-L-valinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COB(O)[C@H](CCCC[NH3+])NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)OC(C)(C)C)C(C)C
#
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
 0ZY  0ZY  N-(tert-butoxycarbonyl)-L-alanyl-N-{(1R)-5-ammonio-1-[hydroxy(methoxy)boranyl]pentyl}-L-valinamide  peptide  70  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0ZY
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
 0ZY  O1    O  O     0  -0.521    5.6179  -0.4539   1.6901
 0ZY  C     C  C     0   0.766    5.6079   0.0724   0.5947
 0ZY  O2    O  O2    0  -0.504    6.6723   0.2867  -0.1774
 0ZY  CT    C  CT    0   0.192    8.0135  -0.1192   0.2032
 0ZY  C1    C  CH3   0  -0.671    8.1079  -1.6348   0.3298
 0ZY  C2    C  CH3   0  -0.660    8.8603   0.3552  -0.9718
 0ZY  C3    C  CH3   0  -0.673    8.4622   0.5821   1.4803
 0ZY  N     N  NH1   0  -0.660    4.4928   0.5195  -0.0179
 0ZY  CA    C  CH1   0  -0.204    3.2085   0.5139   0.6327
 0ZY  C4    C  C     0   0.560    2.1279   0.4660  -0.4428
 0ZY  O     O  O     0  -0.489    2.3189   0.9031  -1.5678
 0ZY  CB    C  CH3   0  -0.649    2.9982   1.7447   1.5185
 0ZY  N1    N  NH1   0  -0.643    0.9586  -0.0389  -0.0281
 0ZY  CA1   C  CH1   0  -0.176   -0.2164  -0.1159  -0.8626
 0ZY  C5    C  C     0   0.580   -1.4325   0.0318   0.0352
 0ZY  O3    O  O     0  -0.495   -1.4457  -0.4139   1.1809
 0ZY  CB1   C  CH1   0  -0.240   -0.2590  -1.4277  -1.6849
 0ZY  CG1   C  CH3   0  -0.665   -0.2803  -2.6805  -0.8169
 0ZY  CG2   C  CH3   0  -0.668   -1.4005  -1.4337  -2.6953
 0ZY  N2    N  NH1   0  -0.641   -2.5036   0.6217  -0.4936
 0ZY  CA2   C  CH1   0  -0.285   -3.7209   0.7762   0.2890
 0ZY  CB2   C  CH2   0  -0.484   -4.9138   0.9239  -0.6589
 0ZY  CG    C  CH2   0  -0.451   -6.2223   1.1762   0.0800
 0ZY  CD    C  CH2   0  -0.446   -7.4114   1.2102  -0.8723
 0ZY  CE    C  CH2   0  -0.303   -8.7045   1.4439  -0.1186
 0ZY  NZ    N  NT3   1  -0.777   -9.8681   1.4392  -1.0442
 0ZY  B     B  B     0   0.570   -3.8993  -0.5067   1.2420
 0ZY  O4    O  OH1   0  -0.620   -4.0471  -1.7561   0.7044
 0ZY  O21   O  O2    0  -0.440   -4.1513  -0.4502   2.5760
 0ZY  C6    C  CH3   0  -0.419   -4.0026   0.7376   3.3241
 0ZY  H11   H  HCH3  0   0.234    7.7646  -2.1268  -0.5819
 0ZY  H12   H  HCH3  0   0.234    9.1501  -1.9174   0.4838
 0ZY  H13   H  HCH3  0   0.246    7.5335  -2.0161   1.1710
 0ZY  H21   H  HCH3  0   0.237    8.8111   1.4393  -1.0859
 0ZY  H22   H  HCH3  0   0.230    9.9032   0.0830  -0.8114
 0ZY  H23   H  HCH3  0   0.237    8.5349  -0.1047  -1.9062
 0ZY  H31   H  HCH3  0   0.246    7.9548   0.2012   2.3635
 0ZY  H32   H  HCH3  0   0.234    9.5330   0.4231   1.6147
 0ZY  H33   H  HCH3  0   0.235    8.2941   1.6583   1.4162
 0ZY  H     H  HNH1  0   0.395    4.5680   1.0077  -0.8975
 0ZY  HA    H  HCH1  0   0.277    3.1370  -0.3833   1.2510
 0ZY  HB1   H  HCH3  0   0.238    2.0314   1.7140   2.0209
 0ZY  HB2   H  HCH3  0   0.250    3.7712   1.7882   2.2849
 0ZY  HB3   H  HCH3  0   0.236    3.0464   2.6600   0.9279
 0ZY  H1    H  HNH1  0   0.406    0.8887  -0.4207   0.9032
 0ZY  HA1   H  HCH1  0   0.287   -0.1871   0.7177  -1.5690
 0ZY  HB    H  HCH1  0   0.252    0.6769  -1.4242  -2.2528
 0ZY  HG11  H  HCH3  0   0.222   -1.1999  -2.7610  -0.2350
 0ZY  HG12  H  HCH3  0   0.238   -0.2168  -3.5686  -1.4471
 0ZY  HG13  H  HCH3  0   0.232    0.5607  -2.7138  -0.1235
 0ZY  HG21  H  HCH3  0   0.212   -2.3781  -1.5074  -2.2158
 0ZY  HG22  H  HCH3  0   0.236   -1.3995  -0.5335  -3.3126
 0ZY  HG23  H  HCH3  0   0.246   -1.3035  -2.2907  -3.3614
 0ZY  HN    H  HNH1  0   0.402   -2.4265   1.0943  -1.3817
 0ZY  HNZ   H  HNT3  0   0.469   -9.7879   2.1640  -1.7565
 0ZY  HNZA  H  HNT3  0   0.469   -9.9626   0.5477  -1.5295
 0ZY  HNZB  H  HNT3  0   0.478  -10.7445   1.6026  -0.5500
 0ZY  HO    H  HOH1  0   0.464   -3.9230  -1.7888  -0.2479
 0ZY  HA2   H  HCH1  0   0.253   -3.6438   1.6992   0.8770
 0ZY  HB4   H  HCH2  0   0.248   -4.7319   1.7536  -1.3503
 0ZY  HBA   H  HCH2  0   0.227   -5.0106   0.0290  -1.2828
 0ZY  HG    H  HCH2  0   0.246   -6.3935   0.3980   0.8305
 0ZY  HGA   H  HCH2  0   0.239   -6.1603   2.1234   0.6241
 0ZY  HD    H  HCH2  0   0.251   -7.2687   2.0007  -1.6146
 0ZY  HDA   H  HCH2  0   0.249   -7.4686   0.2632  -1.4168
 0ZY  HE    H  HCH2  0   0.292   -8.8871   0.6654   0.6192
 0ZY  HEA   H  HCH2  0   0.292   -8.7092   2.4078   0.3860
 0ZY  H2    H  HCH3  0   0.216   -4.6558   1.5368   2.9655
 0ZY  HC    H  HCH3  0   0.240   -4.2707   0.5251   4.3581
 0ZY  HF    H  HCH3  0   0.221   -2.9723   1.0994   3.3054

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
 0ZY  O1    C     double  1.215  0.020  1.215
 0ZY  C     O2    single  1.332  0.020  1.332
 0ZY  C     N     single  1.349  0.020  1.349
 0ZY  O2    CT    single  1.452  0.020  1.452
 0ZY  CT    C1    single  1.524  0.020  1.524
 0ZY  CT    C2    single  1.524  0.020  1.524
 0ZY  CT    C3    single  1.525  0.020  1.525
 0ZY  C1    H11   single  0.970  0.020  1.090
 0ZY  C1    H12   single  0.970  0.020  1.090
 0ZY  C1    H13   single  0.970  0.020  1.090
 0ZY  C2    H21   single  0.970  0.020  1.090
 0ZY  C2    H22   single  0.970  0.020  1.090
 0ZY  C2    H23   single  0.970  0.020  1.090
 0ZY  C3    H31   single  0.970  0.020  1.090
 0ZY  C3    H32   single  0.970  0.020  1.090
 0ZY  C3    H33   single  0.970  0.020  1.090
 0ZY  N     CA    single  1.458  0.019  1.458
 0ZY  N     H     single  0.860  0.020  0.860
 0ZY  CA    C4    single  1.525  0.020  1.525
 0ZY  CA    CB    single  1.521  0.033  1.521
 0ZY  CA    HA    single  0.970  0.020  0.970
 0ZY  C4    O     double  1.222  0.020  1.222
 0ZY  C4    N1    single  1.339  0.020  1.339
 0ZY  CB    HB1   single  0.970  0.020  1.090
 0ZY  CB    HB2   single  0.970  0.020  1.090
 0ZY  CB    HB3   single  0.970  0.020  1.090
 0ZY  N1    CA1   single  1.443  0.020  1.443
 0ZY  N1    H1    single  0.860  0.020  1.020
 0ZY  CA1   C5    single  1.519  0.020  1.519
 0ZY  CA1   CB1   single  1.549  0.020  1.549
 0ZY  CA1   HA1   single  0.970  0.020  1.090
 0ZY  C5    O3    double  1.229  0.020  1.229
 0ZY  C5    N2    single  1.332  0.020  1.332
 0ZY  CB1   CG1   single  1.524  0.020  1.524
 0ZY  CB1   CG2   single  1.525  0.020  1.525
 0ZY  CB1   HB    single  0.970  0.020  1.090
 0ZY  CG1   HG11  single  0.970  0.020  1.090
 0ZY  CG1   HG12  single  0.970  0.020  1.090
 0ZY  CG1   HG13  single  0.970  0.020  1.090
 0ZY  CG2   HG21  single  0.970  0.020  1.090
 0ZY  CG2   HG22  single  0.970  0.020  1.090
 0ZY  CG2   HG23  single  0.970  0.020  1.090
 0ZY  N2    CA2   single  1.455  0.020  1.455
 0ZY  CA2   B     single  1.608  0.020  1.608
 0ZY  CA2   HA2   single  0.970  0.020  1.090
 0ZY  CB2   CA2   single  1.531  0.020  1.531
 0ZY  CB2   HB4   single  0.970  0.020  1.090
 0ZY  CB2   HBA   single  0.970  0.020  1.090
 0ZY  CG    CB2   single  1.524  0.020  1.524
 0ZY  CG    HG    single  0.970  0.020  1.090
 0ZY  CG    HGA   single  0.970  0.020  1.090
 0ZY  CD    CG    single  1.524  0.020  1.524
 0ZY  CD    HD    single  0.970  0.020  1.090
 0ZY  CD    HDA   single  0.970  0.020  1.090
 0ZY  CE    CD    single  1.515  0.020  1.515
 0ZY  CE    HE    single  0.970  0.020  1.090
 0ZY  CE    HEA   single  0.970  0.020  1.090
 0ZY  NZ    CE    single  1.487  0.020  1.487
 0ZY  NZ    HNZA  single  0.890  0.020  1.040
 0ZY  NZ    HNZ   single  0.890  0.020  1.040
 0ZY  B     O4    single  1.368  0.020  1.368
 0ZY  B     O21   single  1.359  0.020  1.359
 0ZY  O21   C6    single  1.412  0.020  1.412
 0ZY  C6    H2    single  0.970  0.020  1.090
 0ZY  C6    HC    single  0.970  0.020  1.090
 0ZY  C6    HF    single  0.970  0.020  1.090
 0ZY  HN    N2    single  0.860  0.020  1.020
 0ZY  HNZB  NZ    single  0.890  0.020  1.040
 0ZY  HO    O4    single  0.850  0.020  0.980

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
 0ZY  N     C    O2    110.12  3.000
 0ZY  N     C    O1    124.04  3.000
 0ZY  O2    C    O1    125.84  3.000
 0ZY  CT    O2   C     122.75  3.000
 0ZY  C3    CT   C2    109.83  3.000
 0ZY  C3    CT   C1    111.70  3.000
 0ZY  C2    CT   C1    109.83  3.000
 0ZY  C3    CT   O2    111.27  3.000
 0ZY  C2    CT   O2    102.95  3.000
 0ZY  C1    CT   O2    110.92  3.000
 0ZY  H13   C1   H12   107.73  3.000
 0ZY  H13   C1   H11   108.78  3.000
 0ZY  H12   C1   H11   107.56  3.000
 0ZY  H13   C1   CT    112.34  3.000
 0ZY  H12   C1   CT    109.19  3.000
 0ZY  H11   C1   CT    111.07  3.000
 0ZY  H23   C2   H22   107.83  3.000
 0ZY  H23   C2   H21   108.41  3.000
 0ZY  H22   C2   H21   107.86  3.000
 0ZY  H23   C2   CT    111.30  3.000
 0ZY  H22   C2   CT    109.90  3.000
 0ZY  H21   C2   CT    111.40  3.000
 0ZY  H33   C3   H32   107.59  3.000
 0ZY  H33   C3   H31   108.74  3.000
 0ZY  H32   C3   H31   107.87  3.000
 0ZY  H33   C3   CT    111.05  3.000
 0ZY  H32   C3   CT    108.97  3.000
 0ZY  H31   C3   CT    112.45  3.000
 0ZY  H     N    CA    114.00  3.000
 0ZY  H     N    C     119.66  3.000
 0ZY  CA    N    C     111.00  2.800
 0ZY  HA    CA   CB    109.00  3.000
 0ZY  HA    CA   C4    109.09  3.000
 0ZY  CB    CA   C4    109.63  3.000
 0ZY  HA    CA   N     110.00  3.000
 0ZY  CB    CA   N     110.40  1.500
 0ZY  C4    CA   N     108.26  3.000
 0ZY  N1    C4   O     123.80  3.000
 0ZY  N1    C4   CA    114.32  3.000
 0ZY  O     C4   CA    121.82  3.000
 0ZY  HB3   CB   HB2   108.43  3.000
 0ZY  HB3   CB   HB1   108.21  3.000
 0ZY  HB2   CB   HB1   107.83  3.000
 0ZY  HB3   CB   CA    110.82  3.000
 0ZY  HB2   CB   CA    109.98  3.000
 0ZY  HB1   CB   CA    111.46  3.000
 0ZY  H1    N1   CA1   117.20  3.000
 0ZY  H1    N1   C4    119.27  3.000
 0ZY  CA1   N1   C4    123.49  3.000
 0ZY  HA1   CA1  CB1   107.67  3.000
 0ZY  HA1   CA1  C5    109.24  3.000
 0ZY  CB1   CA1  C5    111.98  3.000
 0ZY  HA1   CA1  N1    108.13  3.000
 0ZY  CB1   CA1  N1    111.99  3.000
 0ZY  C5    CA1  N1    107.75  3.000
 0ZY  N2    C5   O3    121.46  3.000
 0ZY  N2    C5   CA1   116.88  3.000
 0ZY  O3    C5   CA1   121.62  3.000
 0ZY  HB    CB1  CG2   107.24  3.000
 0ZY  HB    CB1  CG1   108.06  3.000
 0ZY  CG2   CB1  CG1   111.33  3.000
 0ZY  HB    CB1  CA1   104.43  3.000
 0ZY  CG2   CB1  CA1   112.07  3.000
 0ZY  CG1   CB1  CA1   113.22  3.000
 0ZY  HG13  CG1  HG12  107.32  3.000
 0ZY  HG13  CG1  HG11  107.98  3.000
 0ZY  HG12  CG1  HG11  107.28  3.000
 0ZY  HG13  CG1  CB1   112.11  3.000
 0ZY  HG12  CG1  CB1   109.84  3.000
 0ZY  HG11  CG1  CB1   112.09  3.000
 0ZY  HG23  CG2  HG22  107.63  3.000
 0ZY  HG23  CG2  HG21  107.17  3.000
 0ZY  HG22  CG2  HG21  107.76  3.000
 0ZY  HG23  CG2  CB1   109.97  3.000
 0ZY  HG22  CG2  CB1   111.77  3.000
 0ZY  HG21  CG2  CB1   112.32  3.000
 0ZY  HN    N2   CA2   119.17  3.000
 0ZY  HN    N2   C5    119.70  3.000
 0ZY  CA2   N2   C5    120.40  3.000
 0ZY  HA2   CA2  B     111.19  3.000
 0ZY  HA2   CA2  CB2   107.79  3.000
 0ZY  B     CA2  CB2   110.95  3.000
 0ZY  CB2   CA2  N2    109.21  3.000
 0ZY  HA2   CA2  N2    108.59  3.000
 0ZY  B     CA2  N2    109.07  3.000
 0ZY  HBA   CB2  HB4   105.91  3.000
 0ZY  HBA   CB2  CG    109.61  3.000
 0ZY  HB4   CB2  CG    108.86  3.000
 0ZY  CG    CB2  CA2   112.64  3.000
 0ZY  HBA   CB2  CA2   110.05  3.000
 0ZY  HB4   CB2  CA2   109.55  3.000
 0ZY  HGA   CG   HG    106.46  3.000
 0ZY  HGA   CG   CD    109.61  3.000
 0ZY  HG    CG   CD    108.80  3.000
 0ZY  CD    CG   CB2   111.76  3.000
 0ZY  HGA   CG   CB2   109.63  3.000
 0ZY  HG    CG   CB2   110.42  3.000
 0ZY  HDA   CD   HD    107.14  3.000
 0ZY  HDA   CD   CE    109.67  3.000
 0ZY  HD    CD   CE    109.73  3.000
 0ZY  CE    CD   CG    111.01  3.000
 0ZY  HDA   CD   CG    109.42  3.000
 0ZY  HD    CD   CG    109.78  3.000
 0ZY  HEA   CE   HE    108.59  3.000
 0ZY  HEA   CE   NZ    106.75  3.000
 0ZY  HE    CE   NZ    106.77  3.000
 0ZY  NZ    CE   CD    110.96  3.000
 0ZY  HEA   CE   CD    111.79  3.000
 0ZY  HE    CE   CD    111.73  3.000
 0ZY  HNZB  NZ   HNZA  106.94  3.000
 0ZY  HNZB  NZ   HNZ   107.01  3.000
 0ZY  HNZA  NZ   HNZ   107.24  3.000
 0ZY  HNZB  NZ   CE    111.75  3.000
 0ZY  HNZ   NZ   CE    111.79  3.000
 0ZY  HNZA  NZ   CE    111.82  3.000
 0ZY  O21   B    O4    113.81  3.000
 0ZY  O21   B    CA2   124.69  3.000
 0ZY  O4    B    CA2   120.51  3.000
 0ZY  HO    O4   B     113.98  3.000
 0ZY  C6    O21  B     122.40  3.000
 0ZY  HF    C6   HC    108.25  3.000
 0ZY  HF    C6   H2    108.43  3.000
 0ZY  HC    C6   H2    107.88  3.000
 0ZY  HF    C6   O21   111.66  3.000
 0ZY  HC    C6   O21   108.24  3.000
 0ZY  H2    C6   O21   112.24  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
 0ZY  CONST_01  CA1   N1   C4   CA    180.00   0.0  0
 0ZY  CONST_02  CA1   N1   C4   O       0.00   0.0  0
 0ZY  CONST_03  CA2   N2   C5   CA1   180.00   0.0  0
 0ZY  CONST_04  CA2   N2   C5   O3      0.00   0.0  0
 0ZY  CONST_05  H1    N1   C4   CA      0.00   0.0  0
 0ZY  CONST_06  HN    N2   C5   CA1     0.00   0.0  0
 0ZY  Var_01    CA    N    C    O1      5.45  30.0  2
 0ZY  Var_02    C1    CT   O2   C      63.39  30.0  3
 0ZY  Var_03    N     C    O2   CT   -178.46  30.0  1
 0ZY  Var_04    CD    CG   CB2  CA2  -175.50  30.0  1
 0ZY  Var_05    CE    CD   CG   CB2   179.26  30.0  1
 0ZY  Var_06    NZ    CE   CD   CG   -178.42  30.0  1
 0ZY  Var_07    H11   C1   CT   O2     54.04  30.0  3
 0ZY  Var_08    H21   C2   CT   O2     61.82  30.0  3
 0ZY  Var_09    H31   C3   CT   O2     72.52  30.0  3
 0ZY  Var_10    HG11  CG1  CB1  CA1    66.04  30.0  3
 0ZY  Var_11    HG21  CG2  CB1  CA1   -69.93  30.0  3
 0ZY  Var_12    HNZA  NZ   CE   CD     60.59  30.0  3
 0ZY  Var_13    H2    C6   O21  B      60.60  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
 0ZY  chir_01  CA   N   C4   CB   positiv
 0ZY  chir_02  CA1  N1  C5   CB1  positiv
 0ZY  chir_03  CA2  N2  CB2  B    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
 0ZY  plan-1  CA   0.020
 0ZY  plan-1  C4   0.020
 0ZY  plan-1  O    0.020
 0ZY  plan-1  N1   0.020
 0ZY  plan-1  CA1  0.020
 0ZY  plan-1  H1   0.020
 0ZY  plan-2  CA1  0.020
 0ZY  plan-2  C5   0.020
 0ZY  plan-2  O3   0.020
 0ZY  plan-2  N2   0.020
 0ZY  plan-2  CA2  0.020
 0ZY  plan-2  HN   0.020
 0ZY  plan-3  O1   0.020
 0ZY  plan-3  C    0.020
 0ZY  plan-3  O2   0.020
 0ZY  plan-3  N    0.020

