# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 10:31:52 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: {3-[(2S,3R,4R)-2-carboxy-4-(L-valylamino)pyrrolidin-3-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](N)C(=O)N[C@H]1CN[C@@H]([C@@H]1CCC[B-](O)(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
 0IZ  0IZ  "3-[(2~{S},3~{R},4~{R})-4-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron"  ligand  49  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
;

data_comp_0IZ
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
 0IZ  N1   N  NH1    0  -0.621  13.0360  4.0170  25.8310
 0IZ  C4   C  C      0   0.525  13.5360  2.8776  26.3271
 0IZ  C5   C  CH1    0  -0.109  12.8167  4.2454  24.4164
 0IZ  C6   C  CH2    0  -0.290  11.8818  5.4406  24.2060
 0IZ  C7   C  CH1    0  -0.186  14.1350  6.1849  24.0879
 0IZ  C8   C  C      0   0.399  15.0153  7.0412  23.1577
 0IZ  O1   O  O      0  -0.596  14.4339  7.8050  22.3603
 0IZ  O2   O  OC    -1  -0.609  16.2447  6.8744  23.2778
 0IZ  N2   N  NH1    0  -0.617  12.7418  6.6211  24.1262
 0IZ  C9   C  CH1    0  -0.257  14.0993  4.6916  23.6971
 0IZ  C12  C  CH2    0  -0.674  14.2049  2.6456  20.3433
 0IZ  B    B  B     -1   0.484  14.0579  1.0520  19.9086
 0IZ  O5   O  OB     0  -0.739  14.3015  0.8873  18.4569
 0IZ  O4   O  OB     0  -0.742  12.6883  0.5391  20.0900
 0IZ  O3   O  OB     0  -0.750  14.9810  0.2141  20.7307
 0IZ  O    O  O      0  -0.502  13.7863  1.8894  25.6471
 0IZ  C3   C  CH1    0  -0.168  13.7277  2.8808  27.8424
 0IZ  N    N  NH2    0  -0.811  14.2030  4.1916  28.2599
 0IZ  C1   C  CH1    0  -0.235  12.4036  2.5467  28.5597
 0IZ  C2   C  CH3    0  -0.666  12.6342  2.3563  30.0583
 0IZ  C    C  CH3    0  -0.661  11.7244  1.3057  27.9880
 0IZ  H1   H  HNH1   0   0.396  12.9881  4.7952  26.4742
 0IZ  H2   H  HCH1   0   0.254  12.3890  3.3357  23.9953
 0IZ  H3   H  HCH2   0   0.214  11.1545  5.5121  25.0216
 0IZ  H4   H  HCH2   0   0.225  11.3054  5.2938  23.2880
 0IZ  H5   H  HCH1   0   0.203  14.5680  6.2530  25.0956
 0IZ  H6   H  HCH2   0   0.210  14.9579  4.8350  21.7413
 0IZ  H7   H  HCH2   0   0.201  13.2156  4.9709  21.7288
 0IZ  H9   H  HNH1   0   0.335  12.5663  7.1411  23.2763
 0IZ  H11  H  HCH1   0   0.224  14.9672  4.1626  24.1015
 0IZ  H12  H  HCH2   0   0.185  12.9840  2.5502  22.1123
 0IZ  H13  H  HCH2   0   0.179  14.6906  2.3978  22.4345
 0IZ  H14  H  HCH2   0   0.146  15.2014  3.0399  20.0823
 0IZ  H15  H  HCH2   0   0.150  13.5050  3.2548  19.7525
 0IZ  H17  H  H      0   0.409  12.4526  0.6207  21.0161
 0IZ  H18  H  H      0   0.405  15.7167  0.7543  21.0256
 0IZ  H19  H  HCH1   0   0.222  14.4370  2.0683  28.0590
 0IZ  H20  H  HNH2   0   0.359  14.2777  4.2357  29.2673
 0IZ  H21  H  HNH2   0   0.355  15.1394  4.3492  27.9079
 0IZ  H23  H  HCH1   0   0.224  11.7349  3.4027  28.4169
 0IZ  H24  H  HCH3   0   0.235  11.6991  2.0990  30.5573
 0IZ  H25  H  HCH3   0   0.221  13.3415  1.5439  30.2401
 0IZ  H26  H  HCH3   0   0.228  13.0171  3.2503  30.5521
 0IZ  H27  H  HCH3   0   0.228  10.8380  1.0614  28.5747
 0IZ  H28  H  HCH3   0   0.233  11.3987  1.4419  26.9572
 0IZ  H29  H  HCH3   0   0.218  12.3876  0.4386  28.0188
 0IZ  H10  H  H      0   0.406  15.1037  1.3613  18.2293
 0IZ  C10  C  CH2    0  -0.411  14.0473  4.4271  22.1911
 0IZ  C11  C  CH2    0  -0.428  13.9646  2.9466  21.8227

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
 0IZ  O5   B    single  1.481  0.020  1.481
 0IZ  O4   B    single  1.474  0.020  1.474
 0IZ  B    O3   single  1.493  0.020  1.493
 0IZ  B    C12  single  1.658  0.020  1.658
 0IZ  C12  C11  single  1.529  0.020  1.529
 0IZ  C11  C10  single  1.528  0.020  1.528
 0IZ  C10  C9   single  1.530  0.020  1.530
 0IZ  O1   C8   deloc   1.248  0.020  1.248
 0IZ  C8   O2   deloc   1.246  0.020  1.246
 0IZ  C8   C7   single  1.541  0.020  1.541
 0IZ  N2   C6   single  1.463  0.020  1.463
 0IZ  N2   C7   single  1.460  0.020  1.460
 0IZ  C9   C7   single  1.544  0.020  1.544
 0IZ  C9   C5   single  1.537  0.020  1.537
 0IZ  C6   C5   single  1.532  0.020  1.532
 0IZ  C5   N1   single  1.450  0.020  1.450
 0IZ  O    C4   double  1.225  0.020  1.225
 0IZ  N1   C4   single  1.340  0.020  1.340
 0IZ  C4   C3   single  1.527  0.020  1.527
 0IZ  C3   N    single  1.455  0.020  1.455
 0IZ  C3   C1   single  1.543  0.020  1.543
 0IZ  C    C1   single  1.526  0.020  1.526
 0IZ  C1   C2   single  1.528  0.020  1.528
 0IZ  N1   H1   single  0.860  0.020  1.020
 0IZ  C5   H2   single  0.970  0.020  1.090
 0IZ  C6   H3   single  0.970  0.020  1.090
 0IZ  C6   H4   single  0.970  0.020  1.090
 0IZ  C7   H5   single  0.970  0.020  1.090
 0IZ  C10  H6   single  0.970  0.020  1.090
 0IZ  C10  H7   single  0.970  0.020  1.090
 0IZ  N2   H9   single  0.890  0.020  1.040
 0IZ  C9   H11  single  0.970  0.020  1.090
 0IZ  C11  H12  single  0.970  0.020  1.090
 0IZ  C11  H13  single  0.970  0.020  1.090
 0IZ  C12  H14  single  0.970  0.020  1.090
 0IZ  C12  H15  single  0.970  0.020  1.090
 0IZ  O4   H17  single  0.850  0.020  0.980
 0IZ  O3   H18  single  0.850  0.020  0.980
 0IZ  C3   H19  single  0.970  0.020  1.090
 0IZ  N    H20  single  0.890  0.020  1.040
 0IZ  N    H21  single  0.890  0.020  1.040
 0IZ  C1   H23  single  0.970  0.020  1.090
 0IZ  C2   H24  single  0.970  0.020  1.090
 0IZ  C2   H25  single  0.970  0.020  1.090
 0IZ  C2   H26  single  0.970  0.020  1.090
 0IZ  C    H27  single  0.970  0.020  1.090
 0IZ  C    H28  single  0.970  0.020  1.090
 0IZ  C    H29  single  0.970  0.020  1.090
 0IZ  O5   H10  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
 0IZ  H1   N1   C5   119.50  3.000
 0IZ  H1   N1   C4   115.91  3.000
 0IZ  C5   N1   C4   123.50  3.000
 0IZ  C3   C4   O    121.78  3.000
 0IZ  C3   C4   N1   114.36  3.000
 0IZ  O    C4   N1   123.82  3.000
 0IZ  H2   C5   C9   112.90  3.000
 0IZ  H2   C5   C6   111.02  3.000
 0IZ  C9   C5   C6   102.62  3.000
 0IZ  H2   C5   N1   107.75  3.000
 0IZ  C6   C5   N1   110.45  3.000
 0IZ  C9   C5   N1   112.10  3.000
 0IZ  H4   C6   H3   106.49  3.000
 0IZ  H4   C6   N2   111.86  3.000
 0IZ  H3   C6   N2   112.23  3.000
 0IZ  H4   C6   C5   109.40  3.000
 0IZ  H3   C6   C5   110.73  3.000
 0IZ  N2   C6   C5   106.16  3.000
 0IZ  H5   C7   C9   107.52  3.000
 0IZ  H5   C7   N2   109.47  3.000
 0IZ  C9   C7   N2   105.87  3.000
 0IZ  H5   C7   C8   107.10  3.000
 0IZ  C9   C7   C8   113.45  3.000
 0IZ  N2   C7   C8   113.27  3.000
 0IZ  O2   C8   O1   127.08  3.000
 0IZ  O2   C8   C7   115.54  3.000
 0IZ  O1   C8   C7   117.37  3.000
 0IZ  H9   N2   C7   107.28  3.000
 0IZ  H9   N2   C6   111.01  3.000
 0IZ  C7   N2   C6   108.74  3.000
 0IZ  H11  C9   C10  107.89  3.000
 0IZ  H11  C9   C7   110.85  3.000
 0IZ  C10  C9   C7   114.65  3.000
 0IZ  H11  C9   C5   110.41  3.000
 0IZ  C7   C9   C5   100.47  3.000
 0IZ  C10  C9   C5   112.46  3.000
 0IZ  H15  C12  H14  104.47  3.000
 0IZ  H15  C12  B    109.57  3.000
 0IZ  H14  C12  B    111.19  3.000
 0IZ  H15  C12  C11  108.10  3.000
 0IZ  H14  C12  C11  107.50  3.000
 0IZ  B    C12  C11  115.40  3.000
 0IZ  O3   B    O4   108.15  3.000
 0IZ  O3   B    O5   112.06  3.000
 0IZ  O4   B    O5   103.58  3.000
 0IZ  O3   B    C12  109.88  3.000
 0IZ  O4   B    C12  112.61  3.000
 0IZ  O5   B    C12  110.44  3.000
 0IZ  H10  O5   B    108.37  3.000
 0IZ  H17  O4   B    108.52  3.000
 0IZ  H18  O3   B    109.11  3.000
 0IZ  H19  C3   C1   107.57  3.000
 0IZ  H19  C3   N    113.46  3.000
 0IZ  C1   C3   N    110.00  3.000
 0IZ  H19  C3   C4   105.95  3.000
 0IZ  C1   C3   C4   110.68  3.000
 0IZ  N    C3   C4   109.11  3.000
 0IZ  H21  N    H20  105.74  3.000
 0IZ  H21  N    C3   110.02  3.000
 0IZ  H20  N    C3   110.44  3.000
 0IZ  H23  C1   C    108.36  3.000
 0IZ  H23  C1   C2   108.50  3.000
 0IZ  C    C1   C2   109.47  3.000
 0IZ  H23  C1   C3   107.11  3.000
 0IZ  C2   C1   C3   110.70  3.000
 0IZ  C    C1   C3   112.58  3.000
 0IZ  H26  C2   H25  107.87  3.000
 0IZ  H26  C2   H24  106.69  3.000
 0IZ  H25  C2   H24  107.67  3.000
 0IZ  H26  C2   C1   113.25  3.000
 0IZ  H25  C2   C1   110.71  3.000
 0IZ  H24  C2   C1   110.40  3.000
 0IZ  H29  C    H28  107.90  3.000
 0IZ  H29  C    H27  107.49  3.000
 0IZ  H28  C    H27  107.09  3.000
 0IZ  H29  C    C1   111.40  3.000
 0IZ  H28  C    C1   112.70  3.000
 0IZ  H27  C    C1   110.03  3.000
 0IZ  H7   C10  H6   105.85  3.000
 0IZ  H7   C10  C11  109.76  3.000
 0IZ  H6   C10  C11  107.88  3.000
 0IZ  H7   C10  C9   110.81  3.000
 0IZ  H6   C10  C9   108.17  3.000
 0IZ  C11  C10  C9   114.00  3.000
 0IZ  H13  C11  H12  105.30  3.000
 0IZ  H13  C11  C12  109.71  3.000
 0IZ  H12  C11  C12  108.97  3.000
 0IZ  H13  C11  C10  108.33  3.000
 0IZ  H12  C11  C10  109.57  3.000
 0IZ  C12  C11  C10  114.55  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
 0IZ  CONST_01  O    C4   N1   C5      0.00   0.0  0
 0IZ  CONST_02  C3   C4   N1   C5    180.00   0.0  0
 0IZ  CONST_03  H1   N1   C4   O     180.00   0.0  0
 0IZ  CONST_04  H1   N1   C4   C3      0.00   0.0  0
 0IZ  Var_01    C7   N2   C6   C5      7.85  30.0  1
 0IZ  Var_02    H9   N2   C6   C5    125.64  30.0  1
 0IZ  Var_03    H3   C6   N2   C7    128.95  30.0  1
 0IZ  Var_04    H4   C6   N2   C7   -111.42  30.0  1
 0IZ  Var_05    C12  C11  C10  C9   -167.83  30.0  1
 0IZ  Var_06    H12  C11  C10  C9     69.37  30.0  1
 0IZ  Var_07    H13  C11  C10  C9    -45.01  30.0  1
 0IZ  Var_08    B    C12  C11  C10  -177.57  30.0  1
 0IZ  Var_09    O5   B    C12  C11   179.56  30.0  3
 0IZ  Var_10    O4   B    C12  C11    64.29  30.0  3
 0IZ  Var_11    O3   B    C12  C11   -56.33  30.0  3
 0IZ  Var_12    H14  C12  C11  C10    57.73  30.0  1
 0IZ  Var_13    H15  C12  C11  C10   -54.52  30.0  1
 0IZ  Var_14    H6   C10  C11  C12   -47.68  30.0  3
 0IZ  Var_15    H7   C10  C11  C12    67.20  30.0  3
 0IZ  Var_16    H12  C11  C12  B     -54.44  30.0  3
 0IZ  Var_17    H13  C11  C12  B      60.36  30.0  3
 0IZ  Var_18    H14  C12  B    O5    -57.69  30.0  3
 0IZ  Var_19    H15  C12  B    O5     57.29  30.0  3
 0IZ  Var_20    H14  C12  B    O4   -172.95  30.0  3
 0IZ  Var_21    H15  C12  B    O4    -57.97  30.0  3
 0IZ  Var_22    H14  C12  B    O3     66.43  30.0  3
 0IZ  Var_23    H15  C12  B    O3   -178.59  30.0  3
 0IZ  Var_24    H27  C    C1   C3    175.45  30.0  3
 0IZ  Var_25    H28  C    C1   C3    -65.10  30.0  3
 0IZ  Var_26    H29  C    C1   C3     56.35  30.0  3
 0IZ  Var_27    H24  C2   C1   C3   -178.76  30.0  3
 0IZ  Var_28    H25  C2   C1   C3    -59.63  30.0  3
 0IZ  Var_29    H26  C2   C1   C3     61.67  30.0  3
 0IZ  Var_30    H27  C    C1   C2     51.88  30.0  3
 0IZ  Var_31    H28  C    C1   C2    171.32  30.0  3
 0IZ  Var_32    H29  C    C1   C2    -67.23  30.0  3
 0IZ  Var_33    H24  C2   C1   C     -54.09  30.0  3
 0IZ  Var_34    H25  C2   C1   C      65.04  30.0  3
 0IZ  Var_35    H26  C2   C1   C    -173.65  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
 0IZ  chir_01  C5  C9  C6  N1   positiv
 0IZ  chir_02  C7  N2  C9  C8   negativ
 0IZ  chir_03  C9  C5  C7  C10  positiv
 0IZ  chir_04  C3  N   C4  C1   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
 0IZ  plan-1  N1  0.020
 0IZ  plan-1  C4  0.020
 0IZ  plan-1  C5  0.020
 0IZ  plan-1  O   0.020
 0IZ  plan-1  C3  0.020
 0IZ  plan-1  H1  0.020
 0IZ  plan-2  C7  0.020
 0IZ  plan-2  C8  0.020
 0IZ  plan-2  O1  0.020
 0IZ  plan-2  O2  0.020

