# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:59:39 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 4-(1,3,2-dioxaborolan-2-yloxy)butan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCCCOB1OCCO1
#
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
 DYB  DYB  4-(1,3,2-dioxaborolan-2-yloxy)butan-1-aminium  ligand  26  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DYB
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
 DYB  BD    B  B     0   0.590   1.9352   0.1216  -0.0604
 DYB  OE1   O  O2    0  -0.456   0.6694   0.5830  -0.0417
 DYB  OE2   O  O2    0  -0.475   2.9927   0.9834  -0.1514
 DYB  CZ2   C  CH2   0  -0.215   4.1818   0.2086  -0.0131
 DYB  OE3   O  O2    0  -0.492   2.2996  -1.1938   0.0088
 DYB  CZ3   C  CH2   0  -0.209   3.7158  -1.2507  -0.1543
 DYB  CZ1   C  CH2   0  -0.134  -0.4408  -0.3028   0.0041
 DYB  CH    C  CH2   0  -0.469  -1.7175   0.5135  -0.0051
 DYB  CQ    C  CH2   0  -0.460  -2.9470  -0.3864   0.0343
 DYB  CI    C  CH2   0  -0.302  -4.2142   0.4432   0.0124
 DYB  NK    N  NT3   1  -0.776  -5.4217  -0.4234   0.0422
 DYB  HZ22  H  HCH2  0   0.243   4.9046   0.4891  -0.7797
 DYB  HZ23  H  HCH2  0   0.234   4.6294   0.4011   0.9647
 DYB  HZ32  H  HCH2  0   0.235   3.9504  -1.6616  -1.1389
 DYB  HZ33  H  HCH2  0   0.244   4.1544  -1.9023   0.6015
 DYB  HZ12  H  HCH2  0   0.225  -0.4006  -0.9197   0.9074
 DYB  HZ13  H  HCH2  0   0.224  -0.4253  -0.9780  -0.8572
 DYB  HH2   H  HCH2  0   0.241  -1.7454   1.1358  -0.9041
 DYB  HH3   H  HCH2  0   0.242  -1.7258   1.1881   0.8556
 DYB  HQ2   H  HCH2  0   0.253  -2.9281  -1.0060   0.9355
 DYB  HQ3   H  HCH2  0   0.253  -2.9381  -1.0653  -0.8233
 DYB  HI2   H  HCH2  0   0.293  -4.2835   1.0466  -0.8903
 DYB  HI3   H  HCH2  0   0.293  -4.2796   1.1019   0.8758
 DYB  HK1   H  HNT3  0   0.479  -6.2797   0.1266   0.0185
 DYB  HK2   H  HNT3  0   0.469  -5.4577  -0.9946   0.8860
 DYB  HK3   H  HNT3  0   0.469  -5.4535  -1.0579  -0.7553

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
 DYB  BD   OE1   single  1.347  0.020  1.347
 DYB  BD   OE2   single  1.367  0.020  1.367
 DYB  BD   OE3   single  1.367  0.020  1.367
 DYB  OE1  CZ1   single  1.421  0.020  1.421
 DYB  OE2  CZ2   single  1.426  0.020  1.426
 DYB  CZ2  CZ3   single  1.538  0.020  1.538
 DYB  CZ2  HZ22  single  0.970  0.020  1.090
 DYB  CZ2  HZ23  single  0.970  0.020  1.090
 DYB  OE3  CZ3   single  1.427  0.020  1.427
 DYB  CZ3  HZ32  single  0.970  0.020  1.090
 DYB  CZ3  HZ33  single  0.970  0.020  1.090
 DYB  CZ1  CH    single  1.515  0.020  1.515
 DYB  CZ1  HZ12  single  0.970  0.020  1.090
 DYB  CZ1  HZ13  single  0.970  0.020  1.090
 DYB  CH   CQ    single  1.524  0.020  1.524
 DYB  CH   HH2   single  0.970  0.020  1.090
 DYB  CH   HH3   single  0.970  0.020  1.090
 DYB  CQ   CI    single  1.515  0.020  1.515
 DYB  CQ   HQ2   single  0.970  0.020  1.090
 DYB  CQ   HQ3   single  0.970  0.020  1.090
 DYB  CI   NK    single  1.487  0.020  1.487
 DYB  CI   HI2   single  0.970  0.020  1.090
 DYB  CI   HI3   single  0.970  0.020  1.090
 DYB  NK   HK1   single  0.890  0.020  1.040
 DYB  NK   HK2   single  0.890  0.020  1.040
 DYB  NK   HK3   single  0.890  0.020  1.040

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
 DYB  OE3   BD   OE2   113.82  3.000
 DYB  OE3   BD   OE1   125.40  3.000
 DYB  OE2   BD   OE1   120.78  3.000
 DYB  CZ1   OE1  BD    121.40  3.000
 DYB  CZ2   OE2  BD    107.22  3.000
 DYB  HZ23  CZ2  HZ22  108.20  3.000
 DYB  HZ23  CZ2  CZ3   111.92  3.000
 DYB  HZ22  CZ2  CZ3   112.36  3.000
 DYB  HZ23  CZ2  OE2   109.43  3.000
 DYB  HZ22  CZ2  OE2   110.17  3.000
 DYB  CZ3   CZ2  OE2   104.71  3.000
 DYB  CZ3   OE3  BD    107.29  3.000
 DYB  HZ33  CZ3  HZ32  108.28  3.000
 DYB  HZ33  CZ3  OE3   110.12  3.000
 DYB  HZ32  CZ3  OE3   109.34  3.000
 DYB  HZ33  CZ3  CZ2   112.43  3.000
 DYB  HZ32  CZ3  CZ2   111.99  3.000
 DYB  OE3   CZ3  CZ2   104.62  3.000
 DYB  HZ13  CZ1  HZ12  107.53  3.000
 DYB  HZ13  CZ1  CH    109.85  3.000
 DYB  HZ12  CZ1  CH    109.85  3.000
 DYB  HZ13  CZ1  OE1   110.37  3.000
 DYB  HZ12  CZ1  OE1   110.44  3.000
 DYB  CH    CZ1  OE1   108.80  3.000
 DYB  HH3   CH   HH2   107.21  3.000
 DYB  HH3   CH   CQ    109.74  3.000
 DYB  HH2   CH   CQ    109.67  3.000
 DYB  HH3   CH   CZ1   109.51  3.000
 DYB  HH2   CH   CZ1   109.45  3.000
 DYB  CQ    CH   CZ1   111.18  3.000
 DYB  HQ3   CQ   HQ2   107.11  3.000
 DYB  HQ3   CQ   CI    109.60  3.000
 DYB  HQ2   CQ   CI    109.67  3.000
 DYB  HQ3   CQ   CH    109.86  3.000
 DYB  HQ2   CQ   CH    109.98  3.000
 DYB  CI    CQ   CH    110.55  3.000
 DYB  HI3   CI   HI2   108.59  3.000
 DYB  HI3   CI   NK    106.75  3.000
 DYB  HI2   CI   NK    106.75  3.000
 DYB  HI3   CI   CQ    111.74  3.000
 DYB  HI2   CI   CQ    111.65  3.000
 DYB  NK    CI   CQ    111.10  3.000
 DYB  HK3   NK   HK2   107.31  3.000
 DYB  HK3   NK   HK1   106.93  3.000
 DYB  HK2   NK   HK1   106.97  3.000
 DYB  HK3   NK   CI    111.86  3.000
 DYB  HK2   NK   CI    111.83  3.000
 DYB  HK1   NK   CI    111.63  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
 DYB  Var_01  CZ3  CZ2  OE2  BD     12.69  30.0  1
 DYB  Var_02  CZ2  CZ3  OE3  BD     12.33  30.0  1
 DYB  Var_03  OE3  CZ3  CZ2  OE2   -15.38  30.0  1
 DYB  Var_04  OE3  BD   OE2  CZ2    -5.54  30.0  1
 DYB  Var_05  CH   CZ1  OE1  BD   -179.20  30.0  3
 DYB  Var_06  CQ   CH   CZ1  OE1   179.65  30.0  3
 DYB  Var_07  CI   CQ   CH   CZ1  -179.51  30.0  3
 DYB  Var_08  NK   CI   CQ   CH    179.66  30.0  3
 DYB  Var_09  HK1  NK   CI   CQ   -179.44  30.0  3

