# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 05:34:51 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: {3-[(3aS,4S,6aR)-4-carboxyhexahydropyrrolo[3,4-b]pyrrol-3a(1H)-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NC[C@@H]2NCC[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
 VUS  VUS  "3-[(3~{a}~{S},4~{S},6~{a}~{R})-4-carboxy-2,3,4,5,6,6~{a}-hexahydro-1~{H}-pyrrolo[2,3-c]pyrrol-3~{a}-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  37  18  .  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_VUS
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
 VUS  N1   N  NH1    0  -0.586  12.6994  3.8716  25.6391
 VUS  C4   C  CH2    0  -0.319  13.9157  3.0879  25.8214
 VUS  C5   C  CH2    0  -0.459  15.0384  3.8228  25.0685
 VUS  C6   C  CR5    0  -0.055  14.2985  4.6688  24.0155
 VUS  C7   C  CH2    0  -0.408  14.7420  4.3930  22.5747
 VUS  C8   C  CH2    0  -0.433  14.5498  2.9687  22.0553
 VUS  O    O  O      0  -0.600  15.4084  7.6185  22.7695
 VUS  O1   O  OC    -1  -0.605  16.6263  6.7255  24.4123
 VUS  C1   C  CR15   0  -0.194  14.3226  6.1941  24.3429
 VUS  C3   C  CR15   0  -0.124  12.8001  4.3641  24.2668
 VUS  C2   C  CH2    0  -0.304  12.0613  5.6913  24.0289
 VUS  N    N  NR15   0  -0.597  13.0676  6.7347  23.8527
 VUS  C9   C  CH2    0  -0.674  15.1318  2.7440  20.6593
 VUS  B    B  B     -1   0.486  14.8743  1.2425  20.0071
 VUS  O4   O  OB     0  -0.740  15.4542  1.1720  18.6458
 VUS  O3   O  OB     0  -0.741  13.4438  0.9520  19.7989
 VUS  O2   O  OB     0  -0.751  15.4327  0.1916  20.9100
 VUS  H1   H  HNH1   0   0.334  12.7344  4.6670  26.2694
 VUS  H3   H  HCH2   0   0.213  13.7623  2.0970  25.3822
 VUS  H4   H  HCH2   0   0.227  14.1232  2.9385  26.8822
 VUS  H5   H  HCH2   0   0.223  15.7506  3.1258  24.6236
 VUS  H6   H  HCH2   0   0.225  15.6075  4.4648  25.7426
 VUS  H7   H  HCH2   0   0.202  15.8053  4.6418  22.4853
 VUS  H8   H  HCH2   0   0.196  14.2223  5.0769  21.8937
 VUS  H9   H  HCH2   0   0.183  13.4809  2.7272  22.0395
 VUS  H10  H  HCH2   0   0.185  14.9986  2.2564  22.7576
 VUS  H12  H  HCR5   0   0.202  14.3372  6.2904  25.4379
 VUS  H13  H  HCR5   0   0.233  12.4294  3.5772  23.6035
 VUS  H14  H  HCH2   0   0.207  11.4173  5.9103  24.8886
 VUS  H15  H  HCH2   0   0.227  11.4063  5.6419  23.1579
 VUS  H16  H  HNR5   0   0.331  13.1860  6.9530  22.8718
 VUS  H18  H  HCH2   0   0.145  16.2087  2.9786  20.7047
 VUS  H19  H  HCH2   0   0.150  14.7130  3.5098  19.9892
 VUS  H21  H  H      0   0.409  13.0114  0.9226  20.6546
 VUS  H22  H  H      0   0.405  16.1385  0.5767  21.4329
 VUS  H2   H  H      0   0.406  16.2876  1.6464  18.6473
 VUS  C    C  C      0   0.400  15.5610  6.9216  23.7929

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
 VUS  O4  B    single  1.481  0.020  1.481
 VUS  O3  B    single  1.475  0.020  1.475
 VUS  B   O2   single  1.494  0.020  1.494
 VUS  B   C9   single  1.657  0.020  1.657
 VUS  C9  C8   single  1.529  0.020  1.529
 VUS  C8  C7   single  1.528  0.020  1.528
 VUS  C7  C6   single  1.533  0.020  1.533
 VUS  O   C    deloc   1.248  0.020  1.248
 VUS  C   O1   deloc   1.248  0.020  1.248
 VUS  C   C1   single  1.538  0.020  1.538
 VUS  N   C2   single  1.460  0.020  1.460
 VUS  N   C1   single  1.452  0.020  1.452
 VUS  C6  C3   single  1.550  0.020  1.550
 VUS  C6  C1   single  1.560  0.020  1.560
 VUS  C6  C5   single  1.540  0.020  1.540
 VUS  C2  C3   single  1.537  0.020  1.537
 VUS  C3  N1   single  1.462  0.020  1.462
 VUS  C5  C4   single  1.539  0.020  1.539
 VUS  N1  C4   single  1.458  0.020  1.458
 VUS  N1  H1   single  0.890  0.020  1.040
 VUS  C4  H3   single  0.970  0.020  1.090
 VUS  C4  H4   single  0.970  0.020  1.090
 VUS  C5  H5   single  0.970  0.020  1.090
 VUS  C5  H6   single  0.970  0.020  1.090
 VUS  C7  H7   single  0.970  0.020  1.090
 VUS  C7  H8   single  0.970  0.020  1.090
 VUS  C8  H9   single  0.970  0.020  1.090
 VUS  C8  H10  single  0.970  0.020  1.090
 VUS  C1  H12  single  0.970  0.020  1.090
 VUS  C3  H13  single  0.970  0.020  1.090
 VUS  C2  H14  single  0.970  0.020  1.090
 VUS  C2  H15  single  0.970  0.020  1.090
 VUS  N   H16  single  0.890  0.020  1.040
 VUS  C9  H18  single  0.970  0.020  1.090
 VUS  C9  H19  single  0.970  0.020  1.090
 VUS  O3  H21  single  0.850  0.020  0.980
 VUS  O2  H22  single  0.850  0.020  0.980
 VUS  O4  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
 VUS  H1   N1  C3   108.45  3.000
 VUS  H1   N1  C4   108.34  3.000
 VUS  C3   N1  C4   103.95  3.000
 VUS  H4   C4  H3   107.03  3.000
 VUS  H4   C4  C5   113.72  3.000
 VUS  H3   C4  C5   109.77  3.000
 VUS  H4   C4  N1   110.71  3.000
 VUS  H3   C4  N1   108.63  3.000
 VUS  C5   C4  N1   106.90  3.000
 VUS  H6   C5  H5   106.69  3.000
 VUS  H6   C5  C6   110.47  3.000
 VUS  H5   C5  C6   112.68  3.000
 VUS  H6   C5  C4   111.06  3.000
 VUS  H5   C5  C4   111.76  3.000
 VUS  C6   C5  C4   104.26  3.000
 VUS  C3   C6  C1    99.97  3.000
 VUS  C1   C6  C7   111.64  3.000
 VUS  C3   C6  C7   113.39  3.000
 VUS  C1   C6  C5   112.71  3.000
 VUS  C3   C6  C5   104.22  3.000
 VUS  C7   C6  C5   113.88  3.000
 VUS  H8   C7  H7   105.53  3.000
 VUS  H8   C7  C8   108.10  3.000
 VUS  H7   C7  C8   107.82  3.000
 VUS  H8   C7  C6   109.55  3.000
 VUS  H7   C7  C6   108.47  3.000
 VUS  C8   C7  C6   116.80  3.000
 VUS  H10  C8  H9   105.39  3.000
 VUS  H10  C8  C9   109.49  3.000
 VUS  H9   C8  C9   109.01  3.000
 VUS  H10  C8  C7   109.65  3.000
 VUS  H9   C8  C7   109.44  3.000
 VUS  C9   C8  C7   113.54  3.000
 VUS  H12  C1  N    108.37  3.000
 VUS  H12  C1  C    107.70  3.000
 VUS  N    C1  C    113.53  3.000
 VUS  H12  C1  C6   107.15  3.000
 VUS  N    C1  C6   106.25  3.000
 VUS  C    C1  C6   113.57  3.000
 VUS  H13  C3  C2   111.36  3.000
 VUS  H13  C3  C6   111.77  3.000
 VUS  C2   C3  C6   105.66  3.000
 VUS  H13  C3  N1   107.67  3.000
 VUS  C2   C3  N1   113.77  3.000
 VUS  C6   C3  N1   106.57  3.000
 VUS  H15  C2  H14  106.40  3.000
 VUS  H15  C2  N    110.47  3.000
 VUS  H14  C2  N    110.90  3.000
 VUS  H15  C2  C3   111.90  3.000
 VUS  H14  C2  C3   109.47  3.000
 VUS  N    C2  C3   107.72  3.000
 VUS  H16  N   C2   110.59  3.000
 VUS  H16  N   C1   107.85  3.000
 VUS  C2   N   C1   106.79  3.000
 VUS  H19  C9  H18  104.40  3.000
 VUS  H19  C9  B    109.38  3.000
 VUS  H18  C9  B    111.13  3.000
 VUS  H19  C9  C8   107.99  3.000
 VUS  H18  C9  C8   107.62  3.000
 VUS  B    C9  C8   115.68  3.000
 VUS  O2   B   O3   108.02  3.000
 VUS  O2   B   O4   112.06  3.000
 VUS  O3   B   O4   103.92  3.000
 VUS  O2   B   C9   109.97  3.000
 VUS  O3   B   C9   112.63  3.000
 VUS  O4   B   C9   110.12  3.000
 VUS  H2   O4  B    108.37  3.000
 VUS  H21  O3  B    108.51  3.000
 VUS  H22  O2  B    108.79  3.000
 VUS  C1   C   O1   115.83  3.000
 VUS  C1   C   O    117.33  3.000
 VUS  O1   C   O    126.83  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
 VUS  Var_01  C6   C5  C4  N1   -23.10  30.0  1
 VUS  Var_02  C3   N1  C4  C5    37.09  30.0  1
 VUS  Var_03  C3   C2  N   C1   -15.91  30.0  1
 VUS  Var_04  H5   C5  C4  N1  -145.10  30.0  1
 VUS  Var_05  H6   C5  C4  N1    95.89  30.0  1
 VUS  Var_06  H1   N1  C4  C5   -78.12  30.0  1
 VUS  Var_07  H3   C4  C5  C6    94.55  30.0  1
 VUS  Var_08  H4   C4  C5  C6  -145.60  30.0  1
 VUS  Var_09  H14  C2  N   C1   103.87  30.0  1
 VUS  Var_10  H15  C2  N   C1  -138.41  30.0  1
 VUS  Var_11  H16  N   C2  C3   101.18  30.0  1
 VUS  Var_12  H3   C4  N1  C3   -81.31  30.0  1
 VUS  Var_13  H4   C4  N1  C3   161.45  30.0  1
 VUS  Var_14  C9   C8  C7  C6  -174.74  30.0  1
 VUS  Var_15  H9   C8  C7  C6    63.23  30.0  1
 VUS  Var_16  H10  C8  C7  C6   -51.92  30.0  1
 VUS  Var_17  B    C9  C8  C7  -176.53  30.0  1
 VUS  Var_18  O4   B   C9  C8   178.46  30.0  3
 VUS  Var_19  O3   B   C9  C8    62.97  30.0  3
 VUS  Var_20  O2   B   C9  C8   -57.57  30.0  3
 VUS  Var_21  H18  C9  C8  C7    58.56  30.0  1
 VUS  Var_22  H19  C9  C8  C7   -53.62  30.0  1
 VUS  Var_23  H7   C7  C8  C9   -52.39  30.0  3
 VUS  Var_24  H8   C7  C8  C9    61.24  30.0  3
 VUS  Var_25  H9   C8  C9  B    -54.25  30.0  3
 VUS  Var_26  H10  C8  C9  B     60.56  30.0  3
 VUS  Var_27  H18  C9  B   O4   -58.46  30.0  3
 VUS  Var_28  H19  C9  B   O4    56.28  30.0  3
 VUS  Var_29  H18  C9  B   O3  -173.95  30.0  3
 VUS  Var_30  H19  C9  B   O3   -59.21  30.0  3
 VUS  Var_31  H18  C9  B   O2    65.51  30.0  3
 VUS  Var_32  H19  C9  B   O2  -179.75  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
 VUS  chir_01  C6  C3  C1  C5  negativ
 VUS  chir_02  C1  N   C6  C   negativ
 VUS  chir_03  C3  N1  C6  C2  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
 VUS  plan-1  O   0.020
 VUS  plan-1  O1  0.020
 VUS  plan-1  C1  0.020
 VUS  plan-1  C   0.020

