# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:05:33 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: {3-[(1S,2S,5R)-2-carboxy-3,6-diazabicyclo[3.2.0]heptan-1-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NC[C@@H]2NC[C@]12CCC[B-](O)(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
 VV1  VV1  "3-[(1~{S},2~{S},5~{R})-2-carboxy-3,6-diazabicyclo[3.2.0]heptan-1-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  34  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VV1
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
 VV1  N1   N  N      0  -0.614  13.1587  3.4553  25.2867
 VV1  C4   C  C      0  -0.266  14.5815  3.6488  24.9404
 VV1  C5   C  C      0  -0.097  14.2029  4.6023  23.7914
 VV1  C6   C  CH2    0  -0.415  14.7205  4.3190  22.3889
 VV1  C7   C  CH2    0  -0.454  14.4347  2.9299  21.8201
 VV1  C8   C  CH2    0  -0.656  15.0244  2.7037  20.4249
 VV1  O    O  O      0  -0.599  15.1247  7.6580  22.6100
 VV1  O1   O  OC    -1  -0.609  16.5678  6.6431  23.9803
 VV1  C1   C  CR15   0  -0.204  14.2807  6.1045  24.2096
 VV1  C3   C  C      0  -0.076  12.7343  4.2681  24.1237
 VV1  C2   C  CH2    0  -0.312  12.0279  5.6142  24.3670
 VV1  N    N  NR15   0  -0.582  12.9599  6.6594  23.9692
 VV1  B    B  B     -1   0.475  14.6591  1.2622  19.6892
 VV1  O4   O  OB     0  -0.748  13.2062  1.1480  19.4182
 VV1  O3   O  OB     0  -0.751  15.1600  0.1205  20.5112
 VV1  O2   O  OB     0  -0.735  15.2731  1.1701  18.3532
 VV1  H1   H  H      0   0.332  12.9137  3.8958  26.1656
 VV1  H3   H  H      0   0.210  15.0594  2.7160  24.6301
 VV1  H4   H  H      0   0.214  15.2020  4.0930  25.7234
 VV1  H5   H  HCH2   0   0.203  15.8038  4.4820  22.3760
 VV1  H6   H  HCH2   0   0.200  14.3001  5.0635  21.7029
 VV1  H7   H  HCH2   0   0.186  13.3498  2.7738  21.7902
 VV1  H8   H  HCH2   0   0.186  14.8195  2.1726  22.5146
 VV1  H9   H  HCH2   0   0.147  16.1153  2.8354  20.5012
 VV1  H10  H  HCH2   0   0.149  14.6884  3.5308  19.7822
 VV1  H12  H  HCR5   0   0.209  14.4508  6.1348  25.2946
 VV1  H13  H  H      0   0.218  12.1954  3.6603  23.3911
 VV1  H14  H  HCH2   0   0.209  11.7818  5.7170  25.4307
 VV1  H15  H  HCH2   0   0.230  11.0913  5.7050  23.8149
 VV1  H16  H  HNR5   0   0.328  12.8698  6.8492  22.9778
 VV1  H18  H  H      0   0.408  12.7209  1.3747  20.2136
 VV1  H19  H  H      0   0.406  15.1633  0.3714  21.4368
 VV1  H2   H  H      0   0.409  16.2161  1.3148  18.4524
 VV1  C    C  C      0   0.399  15.4253  6.8827  23.5388

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
 VV1  O2  B    single  1.473  0.020  1.473
 VV1  O4  B    single  1.482  0.020  1.482
 VV1  B   C8   single  1.659  0.020  1.659
 VV1  B   O3   single  1.493  0.020  1.493
 VV1  C8  C7   single  1.531  0.020  1.531
 VV1  C7  C6   single  1.528  0.020  1.528
 VV1  C6  C5   single  1.521  0.020  1.521
 VV1  O   C    deloc   1.247  0.020  1.247
 VV1  C   O1   deloc   1.248  0.020  1.248
 VV1  C   C1   single  1.538  0.020  1.538
 VV1  C5  C3   single  1.542  0.020  1.542
 VV1  C5  C1   single  1.561  0.020  1.561
 VV1  C5  C4   single  1.540  0.020  1.540
 VV1  N   C2   single  1.456  0.020  1.456
 VV1  N   C1   single  1.453  0.020  1.453
 VV1  C2  C3   single  1.540  0.020  1.540
 VV1  C3  N1   single  1.481  0.020  1.481
 VV1  C4  N1   single  1.477  0.020  1.477
 VV1  N1  H1   single  0.890  0.020  1.040
 VV1  C4  H3   single  0.970  0.020  1.090
 VV1  C4  H4   single  0.970  0.020  1.090
 VV1  C6  H5   single  0.970  0.020  1.090
 VV1  C6  H6   single  0.970  0.020  1.090
 VV1  C7  H7   single  0.970  0.020  1.090
 VV1  C7  H8   single  0.970  0.020  1.090
 VV1  C8  H9   single  0.970  0.020  1.090
 VV1  C8  H10  single  0.970  0.020  1.090
 VV1  C1  H12  single  0.970  0.020  1.090
 VV1  C3  H13  single  0.970  0.020  1.090
 VV1  C2  H14  single  0.970  0.020  1.090
 VV1  C2  H15  single  0.970  0.020  1.090
 VV1  N   H16  single  0.890  0.020  1.040
 VV1  O4  H18  single  0.850  0.020  0.980
 VV1  O3  H19  single  0.850  0.020  0.980
 VV1  O2  H2   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
 VV1  H1   N1  C3   111.92  3.000
 VV1  H1   N1  C4   112.29  3.000
 VV1  C3   N1  C4    91.15  3.000
 VV1  H4   C4  H3   107.58  3.000
 VV1  H4   C4  C5   114.97  3.000
 VV1  H3   C4  C5   115.08  3.000
 VV1  H4   C4  N1   115.59  3.000
 VV1  H3   C4  N1   112.08  3.000
 VV1  C5   C4  N1    91.10  3.000
 VV1  C3   C5  C1   101.43  3.000
 VV1  C1   C5  C6   114.15  3.000
 VV1  C3   C5  C6   118.83  3.000
 VV1  C1   C5  C4   112.55  3.000
 VV1  C3   C5  C4    86.51  3.000
 VV1  C6   C5  C4   119.25  3.000
 VV1  H6   C6  H5   105.71  3.000
 VV1  H6   C6  C7   108.22  3.000
 VV1  H5   C6  C7   108.40  3.000
 VV1  H6   C6  C5   108.66  3.000
 VV1  H5   C6  C5   108.64  3.000
 VV1  C7   C6  C5   116.67  3.000
 VV1  H8   C7  H7   105.42  3.000
 VV1  H8   C7  C8   109.86  3.000
 VV1  H7   C7  C8   109.58  3.000
 VV1  H8   C7  C6   109.04  3.000
 VV1  H7   C7  C6   108.94  3.000
 VV1  C8   C7  C6   113.67  3.000
 VV1  H10  C8  H9   104.66  3.000
 VV1  H10  C8  B    109.08  3.000
 VV1  H9   C8  B    110.65  3.000
 VV1  H10  C8  C7   107.68  3.000
 VV1  H9   C8  C7   107.50  3.000
 VV1  B    C8  C7   116.58  3.000
 VV1  H12  C1  N    107.08  3.000
 VV1  H12  C1  C    107.55  3.000
 VV1  N    C1  C    114.27  3.000
 VV1  H12  C1  C5   107.39  3.000
 VV1  N    C1  C5   106.13  3.000
 VV1  C    C1  C5   114.02  3.000
 VV1  H13  C3  C2   111.44  3.000
 VV1  H13  C3  C5   116.44  3.000
 VV1  C2   C3  C5   106.35  3.000
 VV1  H13  C3  N1   111.23  3.000
 VV1  C2   C3  N1   119.16  3.000
 VV1  C5   C3  N1    90.88  3.000
 VV1  H15  C2  H14  106.88  3.000
 VV1  H15  C2  N    110.58  3.000
 VV1  H14  C2  N    109.96  3.000
 VV1  H15  C2  C3   112.75  3.000
 VV1  H14  C2  C3   109.77  3.000
 VV1  N    C2  C3   106.90  3.000
 VV1  H16  N   C2   110.17  3.000
 VV1  H16  N   C1   108.32  3.000
 VV1  C2   N   C1   105.22  3.000
 VV1  O2   B   O3   108.16  3.000
 VV1  O3   B   O4   111.75  3.000
 VV1  O2   B   O4   103.76  3.000
 VV1  O3   B   C8   110.26  3.000
 VV1  O4   B   C8   111.33  3.000
 VV1  O2   B   C8   111.39  3.000
 VV1  H18  O4  B    109.03  3.000
 VV1  H19  O3  B    109.42  3.000
 VV1  H2   O2  B    107.85  3.000
 VV1  C1   C   O1   115.45  3.000
 VV1  C1   C   O    117.40  3.000
 VV1  O1   C   O    127.13  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
 VV1  Var_01  C3   N1  C4  C5     4.66  30.0  1
 VV1  Var_02  C3   C2  N   C1   -29.77  30.0  1
 VV1  Var_03  H1   N1  C4  C5  -109.66  30.0  1
 VV1  Var_04  H14  C2  N   C1    89.35  30.0  1
 VV1  Var_05  H15  C2  N   C1  -152.85  30.0  1
 VV1  Var_06  H16  N   C2  C3    86.78  30.0  1
 VV1  Var_07  H3   C4  N1  C3  -113.08  30.0  1
 VV1  Var_08  H4   C4  N1  C3   123.17  30.0  1
 VV1  Var_09  C8   C7  C6  C5  -178.13  30.0  1
 VV1  Var_10  H7   C7  C6  C5    59.37  30.0  1
 VV1  Var_11  H8   C7  C6  C5   -55.20  30.0  1
 VV1  Var_12  B    C8  C7  C6  -175.44  30.0  1
 VV1  Var_13  O2   B   C8  C7   179.51  30.0  3
 VV1  Var_14  O4   B   C8  C7    64.22  30.0  3
 VV1  Var_15  O3   B   C8  C7   -60.40  30.0  3
 VV1  Var_16  H9   C8  C7  C6    59.73  30.0  1
 VV1  Var_17  H10  C8  C7  C6   -52.54  30.0  1
 VV1  Var_18  H5   C6  C7  C8   -55.17  30.0  3
 VV1  Var_19  H6   C6  C7  C8    59.03  30.0  3
 VV1  Var_20  H7   C7  C8  B    -53.29  30.0  3
 VV1  Var_21  H8   C7  C8  B     62.08  30.0  3
 VV1  Var_22  H9   C8  B   O4  -172.56  30.0  3
 VV1  Var_23  H10  C8  B   O4   -57.95  30.0  3
 VV1  Var_24  H9   C8  B   O3    62.82  30.0  3
 VV1  Var_25  H10  C8  B   O3   177.43  30.0  3
 VV1  Var_26  H9   C8  B   O2   -57.27  30.0  3
 VV1  Var_27  H10  C8  B   O2    57.34  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
 VV1  chir_01  C5  C3  C1  C4  negativ
 VV1  chir_02  C1  N   C   C5  positiv
 VV1  chir_03  C3  N1  C2  C5  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
 VV1  plan-1  O   0.020
 VV1  plan-1  O1  0.020
 VV1  plan-1  C1  0.020
 VV1  plan-1  C   0.020

