# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:09:30 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  51  23  .  2022-07-25  2022-07-26
;
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  -0.238  -0.0705  -0.4767   1.7567
 HDQ  C13  C  C      0   0.414   0.3980  -3.3916  -0.5774
 HDQ  B6   B  B     -1   0.427   4.5872   1.9749  -0.4583
 HDQ  C1   C  CT     0  -0.062  -0.1534  -2.5196   0.5784
 HDQ  C17  C  CH1    0  -0.075  -3.4111   0.6054   0.3744
 HDQ  C19  C  CH2    0  -0.289  -5.6175   1.5481   0.0776
 HDQ  C2   C  CH1    0  -0.252   0.8582  -1.4282   1.0097
 HDQ  C20  C  CH2    0  -0.425  -5.1129   2.5649  -0.9351
 HDQ  C21  C  CH2    0  -0.441  -3.8712   2.0329  -1.6423
 HDQ  C22  C  CH2    0  -0.406  -2.8225   1.5902  -0.6278
 HDQ  C3   C  CH2    0  -0.397   1.5881  -0.7448  -0.1459
 HDQ  C4   C  CH2    0  -0.435   2.6363   0.2763   0.2927
 HDQ  C5   C  CH2    0  -0.636   3.4223   0.8869  -0.8657
 HDQ  C9   C  CH2    0  -0.229  -1.4086  -1.7019   0.2502
 HDQ  N10  N  NT     0  -0.417  -1.2200  -0.3988   0.8793
 HDQ  N12  N  NH2    0  -0.803  -0.4335  -3.3301   1.7704
 HDQ  N18  N  NH1    0  -0.606  -4.5636   1.2153   1.0220
 HDQ  O14  O  OC    -1  -0.621   1.2888  -4.2052  -0.2461
 HDQ  O15  O  O      0  -0.600  -0.0548  -3.2313  -1.7273
 HDQ  O23  O  OB     0  -0.749   5.3704   2.3948  -1.6438
 HDQ  O7   O  OB     0  -0.751   3.8943   3.1265   0.1745
 HDQ  O8   O  OB     0  -0.753   5.6153   1.4004   0.4378
 HDQ  H1   H  HCH2   0   0.181  -0.3148  -0.8879   2.7481
 HDQ  H2   H  HCH2   0   0.213   0.3588   0.5163   1.9162
 HDQ  H3   H  HCH2   0   0.215  -2.0989   1.1088   1.9823
 HDQ  H4   H  HCH2   0   0.180  -2.8891  -0.4599   2.1755
 HDQ  H5   H  HCH1   0   0.187  -3.7148  -0.2994  -0.1860
 HDQ  H6   H  HCH2   0   0.226  -6.4680   1.9535   0.6306
 HDQ  H7   H  HCH2   0   0.181  -5.9842   0.6622  -0.4681
 HDQ  H8   H  HCH1   0   0.208   1.6033  -1.8673   1.6826
 HDQ  H9   H  HCH2   0   0.223  -5.9032   2.7900  -1.6552
 HDQ  H10  H  HCH2   0   0.210  -4.8716   3.4986  -0.4181
 HDQ  H11  H  HCH2   0   0.206  -4.1502   1.1766  -2.2664
 HDQ  H12  H  HCH2   0   0.226  -3.4566   2.7865  -2.3161
 HDQ  H13  H  HCH2   0   0.199  -2.4471   2.4617  -0.0794
 HDQ  H14  H  HCH2   0   0.234  -1.9656   1.1328  -1.1259
 HDQ  H15  H  HCH2   0   0.204   2.0987  -1.5001  -0.7512
 HDQ  H16  H  HCH2   0   0.203   0.8643  -0.2576  -0.8070
 HDQ  H17  H  HCH2   0   0.195   2.1606   1.0723   0.8741
 HDQ  H18  H  HCH2   0   0.171   3.3250  -0.2242   0.9877
 HDQ  H19  H  HCH2   0   0.149   2.6996   1.3438  -1.5603
 HDQ  H20  H  HCH2   0   0.151   3.8706   0.0608  -1.4380
 HDQ  H21  H  HCH2   0   0.214  -1.5422  -1.5972  -0.8267
 HDQ  H22  H  HCH2   0   0.187  -2.3033  -2.2144   0.6368
 HDQ  H24  H  HNH2   0   0.328  -1.2259  -3.9345   1.5811
 HDQ  H25  H  HNH2   0   0.327   0.3526  -3.9576   1.9019
 HDQ  H27  H  HNH1   0   0.341  -4.9342   0.5757   1.7147
 HDQ  H31  H  H      0   0.417   4.5509   3.7915   0.4014
 HDQ  H32  H  H      0   0.417   5.1769   0.9912   1.1866
 HDQ  H23  H  H      0   0.417   4.7558   2.5870  -2.3550
 HDQ  C16  C  CH2    0  -0.267  -2.3950   0.2050   1.4394

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  1.482  0.020  1.482
 HDQ  O7   B6   single  1.486  0.020  1.486
 HDQ  B6   O8   single  1.480  0.020  1.480
 HDQ  B6   C5   single  1.645  0.020  1.645
 HDQ  C5   C4   single  1.527  0.020  1.527
 HDQ  C4   C3   single  1.528  0.020  1.528
 HDQ  C3   C2   single  1.528  0.020  1.528
 HDQ  C2   C11  single  1.525  0.020  1.525
 HDQ  C2   C1   single  1.549  0.020  1.549
 HDQ  N12  C1   single  1.468  0.020  1.468
 HDQ  C11  N10  single  1.448  0.020  1.448
 HDQ  O15  C13  deloc   1.246  0.020  1.246
 HDQ  C1   C13  single  1.549  0.020  1.549
 HDQ  C1   C9   single  1.534  0.020  1.534
 HDQ  C13  O14  deloc   1.251  0.020  1.251
 HDQ  N10  C9   single  1.459  0.020  1.459
 HDQ  N10  C16  single  1.435  0.020  1.435
 HDQ  C16  C17  single  1.525  0.020  1.525
 HDQ  N18  C17  single  1.456  0.020  1.456
 HDQ  N18  C19  single  1.454  0.020  1.454
 HDQ  C17  C22  single  1.523  0.020  1.523
 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  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   107.15  3.000
 HDQ  H2   C11  N10  110.56  3.000
 HDQ  H1   C11  N10  112.93  3.000
 HDQ  H2   C11  C2   113.51  3.000
 HDQ  H1   C11  C2   110.07  3.000
 HDQ  N10  C11  C2   102.72  3.000
 HDQ  O15  C13  O14  125.93  3.000
 HDQ  O14  C13  C1   114.95  3.000
 HDQ  O15  C13  C1   119.12  3.000
 HDQ  O8   B6   O7   111.53  3.000
 HDQ  O8   B6   O23  103.13  3.000
 HDQ  O7   B6   O23  111.58  3.000
 HDQ  O8   B6   C5   112.65  3.000
 HDQ  O7   B6   C5   106.73  3.000
 HDQ  O23  B6   C5   111.32  3.000
 HDQ  N12  C1   C9   108.17  3.000
 HDQ  C9   C1   C2   102.61  3.000
 HDQ  N12  C1   C2   106.70  3.000
 HDQ  C9   C1   C13  115.58  3.000
 HDQ  N12  C1   C13  111.28  3.000
 HDQ  C2   C1   C13  111.82  3.000
 HDQ  H5   C17  N18  110.52  3.000
 HDQ  H5   C17  C22  107.54  3.000
 HDQ  N18  C17  C22  109.13  3.000
 HDQ  H5   C17  C16  108.76  3.000
 HDQ  C22  C17  C16  111.82  3.000
 HDQ  N18  C17  C16  109.07  3.000
 HDQ  H7   C19  H6   106.83  3.000
 HDQ  H7   C19  N18  112.24  3.000
 HDQ  H6   C19  N18  108.69  3.000
 HDQ  H7   C19  C20  108.52  3.000
 HDQ  H6   C19  C20  110.31  3.000
 HDQ  N18  C19  C20  110.18  3.000
 HDQ  H8   C2   C3   108.59  3.000
 HDQ  H8   C2   C1   109.43  3.000
 HDQ  C3   C2   C1   114.61  3.000
 HDQ  H8   C2   C11  111.31  3.000
 HDQ  C1   C2   C11  100.27  3.000
 HDQ  C3   C2   C11  112.47  3.000
 HDQ  H10  C20  H9   107.16  3.000
 HDQ  H10  C20  C21  109.71  3.000
 HDQ  H9   C20  C21  110.81  3.000
 HDQ  H10  C20  C19  109.21  3.000
 HDQ  H9   C20  C19  109.67  3.000
 HDQ  C21  C20  C19  110.22  3.000
 HDQ  H12  C21  H11  106.52  3.000
 HDQ  H12  C21  C22  110.46  3.000
 HDQ  H11  C21  C22  109.10  3.000
 HDQ  H12  C21  C20  110.75  3.000
 HDQ  H11  C21  C20  109.23  3.000
 HDQ  C22  C21  C20  110.66  3.000
 HDQ  H14  C22  H13  107.02  3.000
 HDQ  H14  C22  C21  110.98  3.000
 HDQ  H13  C22  C21  109.73  3.000
 HDQ  H14  C22  C17  109.43  3.000
 HDQ  H13  C22  C17  108.49  3.000
 HDQ  C21  C22  C17  111.08  3.000
 HDQ  H16  C3   H15  106.36  3.000
 HDQ  H16  C3   C4   109.25  3.000
 HDQ  H15  C3   C4   107.46  3.000
 HDQ  H16  C3   C2   109.87  3.000
 HDQ  H15  C3   C2   109.42  3.000
 HDQ  C4   C3   C2   114.17  3.000
 HDQ  H18  C4   H17  105.52  3.000
 HDQ  H18  C4   C5   109.83  3.000
 HDQ  H17  C4   C5   109.62  3.000
 HDQ  H18  C4   C3   107.89  3.000
 HDQ  H17  C4   C3   109.90  3.000
 HDQ  C5   C4   C3   113.74  3.000
 HDQ  H20  C5   H19  104.52  3.000
 HDQ  H20  C5   C4   107.70  3.000
 HDQ  H19  C5   C4   107.85  3.000
 HDQ  H20  C5   B6   109.68  3.000
 HDQ  H19  C5   B6   110.27  3.000
 HDQ  C4   C5   B6   116.17  3.000
 HDQ  H22  C9   H21  106.98  3.000
 HDQ  H22  C9   N10  111.67  3.000
 HDQ  H21  C9   N10  110.86  3.000
 HDQ  H22  C9   C1   109.98  3.000
 HDQ  H21  C9   C1   111.28  3.000
 HDQ  N10  C9   C1   106.14  3.000
 HDQ  C9   N10  C16  115.99  3.000
 HDQ  C16  N10  C11  115.86  3.000
 HDQ  C9   N10  C11  108.41  3.000
 HDQ  H25  N12  H24  105.12  3.000
 HDQ  H25  N12  C1   107.39  3.000
 HDQ  H24  N12  C1   109.05  3.000
 HDQ  H27  N18  C19  108.87  3.000
 HDQ  H27  N18  C17  109.22  3.000
 HDQ  C19  N18  C17  112.38  3.000
 HDQ  H23  O23  B6   108.13  3.000
 HDQ  H31  O7   B6   108.55  3.000
 HDQ  H32  O8   B6   108.71  3.000
 HDQ  H4   C16  H3   106.64  3.000
 HDQ  H4   C16  N10  111.83  3.000
 HDQ  H3   C16  N10  108.63  3.000
 HDQ  H4   C16  C17  108.92  3.000
 HDQ  H3   C16  C17  108.03  3.000
 HDQ  N10  C16  C17  112.54  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  Var_01  C1   C9   N10  C11   -10.61  30.0  1
 HDQ  Var_02  C20  C19  N18  C17   -61.80  30.0  1
 HDQ  Var_03  C20  C21  C22  C17    53.35  30.0  1
 HDQ  Var_04  C22  C21  C20  C19   -52.80  30.0  1
 HDQ  Var_05  C9   N10  C11  C2     34.90  30.0  1
 HDQ  Var_06  N18  C19  C20  C21    56.34  30.0  1
 HDQ  Var_07  C17  C16  N10  C11   163.92  30.0  3
 HDQ  Var_08  C5   C4   C3   C2    176.25  30.0  2
 HDQ  Var_09  C3   C4   C5   B6   -178.91  30.0  3
 HDQ  Var_10  O23  B6   C5   C4    174.27  30.0  2

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

