# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:37:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-[(3~{S},4~{R})-4-azanyl-4-carboxy-1-[[(2~{S})-piperidin-2-yl]methyl]pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CN(C[C@@H]2CCCCN2)C[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
 HDQ  HDQ  3-[(3~{S},4~{R})-4-azanyl-4-carboxy-1-[[(2~{S})-piperidin-2-yl]methyl]pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide  ligand  52  23  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HDQ
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
 HDQ  C11  C  CH2    0  -0.240  -0.0914  -0.5054   1.7266
 HDQ  C13  C  C      0   0.547   0.2854  -3.3396  -0.6787
 HDQ  B6   B  B     -1   0.428   4.5427   1.9867  -0.4938
 HDQ  C1   C  CT     0  -0.060  -0.1986  -2.5003   0.4969
 HDQ  C17  C  CH1    0  -0.077  -3.4279   0.6330   0.3744
 HDQ  C19  C  CH2    0  -0.289  -5.6321   1.5881   0.1055
 HDQ  C2   C  CH1    0  -0.265   0.8319  -1.4388   0.9504
 HDQ  C20  C  CH2    0  -0.425  -5.1268   2.6298  -0.8805
 HDQ  C21  C  CH2    0  -0.441  -3.8859   2.1165  -1.6024
 HDQ  C22  C  CH2    0  -0.406  -2.8372   1.6430  -0.6018
 HDQ  C3   C  CH2    0  -0.411   1.5452  -0.7325  -0.2032
 HDQ  C4   C  CH2    0  -0.436   2.5986   0.2789   0.2453
 HDQ  C5   C  CH2    0  -0.638   3.3746   0.9046  -0.9107
 HDQ  C9   C  CH2    0  -0.225  -1.4373  -1.6580   0.1612
 HDQ  N10  N  NT     0  -0.420  -1.2396  -0.3910   0.8514
 HDQ  N12  N  NH2    0  -0.786  -0.5129  -3.3485   1.6409
 HDQ  N18  N  NH1    0  -0.605  -4.5776   1.2276   1.0393
 HDQ  O14  O  OH1    0  -0.597   1.3711  -4.0390  -0.3594
 HDQ  O15  O  O      0  -0.436  -0.2412  -3.4157  -1.7614
 HDQ  O23  O  OB     0  -0.748   5.3147   2.4248  -1.6797
 HDQ  O7   O  OB     0  -0.751   3.8541   3.1259   0.1635
 HDQ  O8   O  OB     0  -0.752   5.5787   1.3977   0.3831
 HDQ  H1   H  HCH2   0   0.197  -0.3371  -0.9411   2.7059
 HDQ  H2   H  HCH2   0   0.227   0.3519   0.4761   1.9107
 HDQ  H3   H  HCH2   0   0.222  -2.1124   1.0881   1.9949
 HDQ  H4   H  HCH2   0   0.189  -2.9084  -0.4822   2.1463
 HDQ  H5   H  HCH1   0   0.189  -3.7336  -0.2568  -0.2090
 HDQ  H6   H  HCH2   0   0.227  -6.4800   1.9813   0.6708
 HDQ  H7   H  HCH2   0   0.182  -6.0029   0.7175  -0.4614
 HDQ  H8   H  HCH1   0   0.236   1.5796  -1.8989   1.6045
 HDQ  H9   H  HCH2   0   0.224  -5.9172   2.8750  -1.5938
 HDQ  H10  H  HCH2   0   0.210  -4.8841   3.5493  -0.3392
 HDQ  H11  H  HCH2   0   0.207  -4.1644   1.2801  -2.2530
 HDQ  H12  H  HCH2   0   0.227  -3.4695   2.8897  -2.2525
 HDQ  H13  H  HCH2   0   0.201  -2.4571   2.4979  -0.0313
 HDQ  H14  H  HCH2   0   0.234  -1.9834   1.1978  -1.1160
 HDQ  H15  H  HCH2   0   0.211   2.0536  -1.4698  -0.8333
 HDQ  H16  H  HCH2   0   0.218   0.8127  -0.2303  -0.8431
 HDQ  H17  H  HCH2   0   0.201   2.1268   1.0655   0.8418
 HDQ  H18  H  HCH2   0   0.178   3.2916  -0.2342   0.9257
 HDQ  H19  H  HCH2   0   0.152   2.6475   1.3716  -1.5936
 HDQ  H20  H  HCH2   0   0.153   3.8197   0.0867  -1.4967
 HDQ  H21  H  HCH2   0   0.228  -1.5497  -1.5004  -0.9136
 HDQ  H22  H  HCH2   0   0.214  -2.3411  -2.1811   0.5028
 HDQ  H24  H  HNH2   0   0.352  -1.2622  -3.9922   1.4172
 HDQ  H25  H  HNH2   0   0.351   0.2870  -3.9066   1.9133
 HDQ  H27  H  HNH1   0   0.342  -4.9495   0.5710   1.7151
 HDQ  H29  H  HOH1   0   0.481   1.6416  -4.5911  -1.1078
 HDQ  H31  H  H      0   0.418   4.5114   3.7886   0.3956
 HDQ  H32  H  H      0   0.417   5.1517   1.0000   1.1445
 HDQ  H23  H  H      0   0.417   4.6935   2.6317  -2.3810
 HDQ  C16  C  CH2    0  -0.271  -2.4143   0.2012   1.4291

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
 HDQ  O23  B6   single  1.481  0.020  1.481
 HDQ  O7   B6   single  1.485  0.020  1.485
 HDQ  B6   O8   single  1.480  0.020  1.480
 HDQ  B6   C5   single  1.646  0.020  1.646
 HDQ  C5   C4   single  1.526  0.020  1.526
 HDQ  C4   C3   single  1.528  0.020  1.528
 HDQ  C3   C2   single  1.529  0.020  1.529
 HDQ  C2   C11  single  1.525  0.020  1.525
 HDQ  C2   C1   single  1.547  0.020  1.547
 HDQ  N12  C1   single  1.458  0.020  1.458
 HDQ  C11  N10  single  1.448  0.020  1.448
 HDQ  O15  C13  double  1.206  0.020  1.206
 HDQ  C1   C13  single  1.523  0.020  1.523
 HDQ  C1   C9   single  1.535  0.020  1.535
 HDQ  C13  O14  single  1.330  0.020  1.330
 HDQ  N10  C9   single  1.456  0.020  1.456
 HDQ  N10  C16  single  1.437  0.020  1.437
 HDQ  C16  C17  single  1.525  0.020  1.525
 HDQ  N18  C17  single  1.455  0.020  1.455
 HDQ  N18  C19  single  1.454  0.020  1.454
 HDQ  C17  C22  single  1.524  0.020  1.524
 HDQ  C19  C20  single  1.521  0.020  1.521
 HDQ  C22  C21  single  1.525  0.020  1.525
 HDQ  C21  C20  single  1.525  0.020  1.525
 HDQ  C11  H1   single  0.970  0.020  1.090
 HDQ  C11  H2   single  0.970  0.020  1.090
 HDQ  C16  H3   single  0.970  0.020  1.090
 HDQ  C16  H4   single  0.970  0.020  1.090
 HDQ  C17  H5   single  0.970  0.020  1.090
 HDQ  C19  H6   single  0.970  0.020  1.090
 HDQ  C19  H7   single  0.970  0.020  1.090
 HDQ  C2   H8   single  0.970  0.020  1.090
 HDQ  C20  H9   single  0.970  0.020  1.090
 HDQ  C20  H10  single  0.970  0.020  1.090
 HDQ  C21  H11  single  0.970  0.020  1.090
 HDQ  C21  H12  single  0.970  0.020  1.090
 HDQ  C22  H13  single  0.970  0.020  1.090
 HDQ  C22  H14  single  0.970  0.020  1.090
 HDQ  C3   H15  single  0.970  0.020  1.090
 HDQ  C3   H16  single  0.970  0.020  1.090
 HDQ  C4   H17  single  0.970  0.020  1.090
 HDQ  C4   H18  single  0.970  0.020  1.090
 HDQ  C5   H19  single  0.970  0.020  1.090
 HDQ  C5   H20  single  0.970  0.020  1.090
 HDQ  C9   H21  single  0.970  0.020  1.090
 HDQ  C9   H22  single  0.970  0.020  1.090
 HDQ  N12  H24  single  0.890  0.020  1.040
 HDQ  N12  H25  single  0.890  0.020  1.040
 HDQ  N18  H27  single  0.890  0.020  1.040
 HDQ  O14  H29  single  0.850  0.020  0.980
 HDQ  O7   H31  single  0.850  0.020  0.980
 HDQ  O8   H32  single  0.850  0.020  0.980
 HDQ  O23  H23  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
 HDQ  H2   C11  H1   107.25  3.000
 HDQ  H2   C11  N10  110.65  3.000
 HDQ  H1   C11  N10  113.09  3.000
 HDQ  H2   C11  C2   112.95  3.000
 HDQ  H1   C11  C2   110.24  3.000
 HDQ  N10  C11  C2   102.75  3.000
 HDQ  O15  C13  O14  122.58  3.000
 HDQ  O14  C13  C1   111.33  3.000
 HDQ  O15  C13  C1   126.06  3.000
 HDQ  O8   B6   O7   111.59  3.000
 HDQ  O8   B6   O23  103.13  3.000
 HDQ  O7   B6   O23  111.67  3.000
 HDQ  O8   B6   C5   112.66  3.000
 HDQ  O7   B6   C5   106.71  3.000
 HDQ  O23  B6   C5   111.19  3.000
 HDQ  N12  C1   C9   108.47  3.000
 HDQ  C9   C1   C2   103.01  3.000
 HDQ  N12  C1   C2   108.22  3.000
 HDQ  C9   C1   C13  112.95  3.000
 HDQ  N12  C1   C13  110.69  3.000
 HDQ  C2   C1   C13  113.11  3.000
 HDQ  H5   C17  N18  110.55  3.000
 HDQ  H5   C17  C22  107.59  3.000
 HDQ  N18  C17  C22  109.15  3.000
 HDQ  H5   C17  C16  108.69  3.000
 HDQ  C22  C17  C16  111.90  3.000
 HDQ  N18  C17  C16  108.95  3.000
 HDQ  H7   C19  H6   106.81  3.000
 HDQ  H7   C19  N18  112.22  3.000
 HDQ  H6   C19  N18  108.65  3.000
 HDQ  H7   C19  C20  108.61  3.000
 HDQ  H6   C19  C20  110.29  3.000
 HDQ  N18  C19  C20  110.20  3.000
 HDQ  H8   C2   C3   109.04  3.000
 HDQ  H8   C2   C1   109.98  3.000
 HDQ  C3   C2   C1   113.98  3.000
 HDQ  H8   C2   C11  111.50  3.000
 HDQ  C1   C2   C11   99.55  3.000
 HDQ  C3   C2   C11  112.56  3.000
 HDQ  H10  C20  H9   107.15  3.000
 HDQ  H10  C20  C21  109.67  3.000
 HDQ  H9   C20  C21  110.81  3.000
 HDQ  H10  C20  C19  109.18  3.000
 HDQ  H9   C20  C19  109.67  3.000
 HDQ  C21  C20  C19  110.29  3.000
 HDQ  H12  C21  H11  106.49  3.000
 HDQ  H12  C21  C22  110.37  3.000
 HDQ  H11  C21  C22  109.11  3.000
 HDQ  H12  C21  C20  110.71  3.000
 HDQ  H11  C21  C20  109.34  3.000
 HDQ  C22  C21  C20  110.71  3.000
 HDQ  H14  C22  H13  106.98  3.000
 HDQ  H14  C22  C21  110.82  3.000
 HDQ  H13  C22  C21  109.75  3.000
 HDQ  H14  C22  C17  109.55  3.000
 HDQ  H13  C22  C17  108.55  3.000
 HDQ  C21  C22  C17  111.08  3.000
 HDQ  H16  C3   H15  106.45  3.000
 HDQ  H16  C3   C4   109.23  3.000
 HDQ  H15  C3   C4   107.13  3.000
 HDQ  H16  C3   C2   109.92  3.000
 HDQ  H15  C3   C2   109.85  3.000
 HDQ  C4   C3   C2   113.96  3.000
 HDQ  H18  C4   H17  105.68  3.000
 HDQ  H18  C4   C5   109.87  3.000
 HDQ  H17  C4   C5   109.72  3.000
 HDQ  H18  C4   C3   107.91  3.000
 HDQ  H17  C4   C3   109.79  3.000
 HDQ  C5   C4   C3   113.55  3.000
 HDQ  H20  C5   H19  104.60  3.000
 HDQ  H20  C5   C4   107.71  3.000
 HDQ  H19  C5   C4   107.92  3.000
 HDQ  H20  C5   B6   109.67  3.000
 HDQ  H19  C5   B6   110.29  3.000
 HDQ  C4   C5   B6   116.00  3.000
 HDQ  H22  C9   H21  106.86  3.000
 HDQ  H22  C9   N10  112.24  3.000
 HDQ  H21  C9   N10  110.79  3.000
 HDQ  H22  C9   C1   109.55  3.000
 HDQ  H21  C9   C1   112.18  3.000
 HDQ  N10  C9   C1   105.32  3.000
 HDQ  C9   N10  C16  115.99  3.000
 HDQ  C16  N10  C11  115.96  3.000
 HDQ  C9   N10  C11  108.98  3.000
 HDQ  H25  N12  H24  107.07  3.000
 HDQ  H25  N12  C1   111.18  3.000
 HDQ  H24  N12  C1   110.84  3.000
 HDQ  H27  N18  C19  108.84  3.000
 HDQ  H27  N18  C17  109.27  3.000
 HDQ  C19  N18  C17  112.38  3.000
 HDQ  H29  O14  C13  110.00  3.000
 HDQ  H23  O23  B6   108.15  3.000
 HDQ  H31  O7   B6   108.57  3.000
 HDQ  H32  O8   B6   108.89  3.000
 HDQ  H4   C16  H3   106.77  3.000
 HDQ  H4   C16  N10  111.77  3.000
 HDQ  H3   C16  N10  108.44  3.000
 HDQ  H4   C16  C17  109.04  3.000
 HDQ  H3   C16  C17  108.14  3.000
 HDQ  N10  C16  C17  112.45  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
 HDQ  CONST_01  H29  O14  C13  C1    180.00   0.0  0
 HDQ  Var_01    C1   C9   N10  C11    -8.83  30.0  1
 HDQ  Var_02    C20  C19  N18  C17   -61.78  30.0  1
 HDQ  Var_03    C20  C21  C22  C17    53.20  30.0  1
 HDQ  Var_04    C22  C21  C20  C19   -52.65  30.0  1
 HDQ  Var_05    C9   N10  C11  C2     34.14  30.0  1
 HDQ  Var_06    N18  C19  C20  C21    56.22  30.0  1
 HDQ  Var_07    C17  C16  N10  C11   164.30  30.0  3
 HDQ  Var_08    C5   C4   C3   C2    175.84  30.0  1
 HDQ  Var_09    C3   C4   C5   B6   -179.07  30.0  3
 HDQ  Var_10    O23  B6   C5   C4    174.39  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
 HDQ  chir_01  C1   C2   C13  C9   positiv
 HDQ  chir_02  C17  N18  C16  C22  positiv
 HDQ  chir_03  C2   C3   C11  C1   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
 HDQ  plan-1  C13  0.020
 HDQ  plan-1  C1   0.020
 HDQ  plan-1  O14  0.020
 HDQ  plan-1  O15  0.020
 HDQ  plan-1  H29  0.020

