# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 23:36:57 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]oxy]-5-chloranyl-2-(4-oxidanylidenepentoxy)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CCCOc1nc(Oc2ccc3c(CO[B-]3(O)O)c2)c(Cl)cc1C#N
#
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
 6QQ  6QQ  6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]oxy]-5-chloranyl-2-(4-oxidanylidenepentoxy)pyridine-3-carbonitrile  ligand  45  28  .  2022-07-23  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_6QQ
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
 6QQ  C1   C   CH3    0  -0.769   4.2997  -4.8245   0.2756
 6QQ  C2   C   C      0   0.400   2.7976  -4.8866   0.2379
 6QQ  C4   C   CH2    0  -0.575   2.0908  -3.5590   0.3329
 6QQ  C5   C   CH2    0  -0.464   0.5865  -3.6254   0.1288
 6QQ  C6   C   CH2    0  -0.158  -0.0058  -2.2375   0.2383
 6QQ  C8   C   CR6    0   0.577  -2.1528  -1.2597   0.0437
 6QQ  C12  C   CR6    0   0.338  -0.3120   2.2622   0.1948
 6QQ  C15  C   CH2    0  -0.149   2.7924   2.1238  -2.0096
 6QQ  C21  C   CR16   0  -0.386   1.6766   2.6757   1.4569
 6QQ  C23  C   CR6    0  -0.221  -3.6893   0.9894  -0.0469
 6QQ  C27  C   CSP    0   0.053  -4.1379  -2.6813  -0.1707
 6QQ  O3   O   O      0  -0.406   2.1971  -5.9315   0.1245
 6QQ  O7   O   O2     0  -0.454  -1.4274  -2.3582   0.0817
 6QQ  N9   N   N      0  -0.480  -1.5715  -0.0837   0.1265
 6QQ  C10  C   CR6    0   0.599  -2.2933   1.0120   0.0768
 6QQ  O11  O   O2     0  -0.496  -1.7025   2.1961   0.1480
 6QQ  C13  C   CR16   0  -0.336   0.4178   2.1144  -0.9724
 6QQ  C14  C   CR56   0  -0.091   1.7955   2.2454  -0.8872
 6QQ  O16  O   O      0  -0.582   4.0627   2.1978  -1.4418
 6QQ  B17  B   B     -1   0.420   4.0335   2.6228   0.0033
 6QQ  O18  O   OB     0  -0.735   4.7947   1.6821   0.8245
 6QQ  O19  O   OB     0  -0.737   4.4785   4.0144   0.1532
 6QQ  C20  C   CR56   0  -0.049   2.4469   2.5241   0.3105
 6QQ  C22  C   CR16   0  -0.298   0.2916   2.5391   1.4096
 6QQ  CL1  CL  CL     0  -0.093  -4.5822   2.4581  -0.0980
 6QQ  C25  C   CR16   0  -0.058  -4.3108  -0.2340  -0.1271
 6QQ  C26  C   CR6    0  -0.192  -3.5442  -1.3975  -0.0867
 6QQ  N28  N   NS     0  -0.251  -4.6259  -3.7242  -0.2317
 6QQ  H1   H   HCH3   0   0.272   4.6632  -4.5250  -0.7106
 6QQ  H2   H   HCH3   0   0.257   4.6506  -4.0718   0.9812
 6QQ  H3   H   HCH3   0   0.261   4.7343  -5.7909   0.5227
 6QQ  H4   H   HCH2   0   0.277   2.3301  -3.1387   1.3167
 6QQ  H5   H   HCH2   0   0.271   2.5595  -2.8745  -0.3831
 6QQ  H6   H   HCH2   0   0.245   0.3585  -4.0454  -0.8532
 6QQ  H7   H   HCH2   0   0.245   0.1359  -4.2804   0.8772
 6QQ  H8   H   HCH2   0   0.239   0.2147  -1.7893   1.2105
 6QQ  H9   H   HCH2   0   0.241   0.3961  -1.5748  -0.5314
 6QQ  H10  H   HCH2   0   0.193   2.6520   1.1798  -2.5577
 6QQ  H11  H   HCH2   0   0.186   2.6189   2.9223  -2.7504
 6QQ  H12  H   HCR6   0   0.234   2.1417   2.9009   2.4109
 6QQ  H13  H   HCR6   0   0.249  -0.0804   1.9001  -1.9118
 6QQ  H14  H   H      0   0.429   5.7313   1.7094   0.6090
 6QQ  H15  H   H      0   0.427   5.3862   4.1237  -0.1456
 6QQ  H16  H   HCR6   0   0.253  -0.3136   2.6509   2.3012
 6QQ  H17  H   HCR6   0   0.314  -5.3859  -0.2975  -0.2234

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
 6QQ  CL1  C23  single    1.720  0.020  1.720
 6QQ  C25  C23  aromatic  1.375  0.020  1.375
 6QQ  C25  C26  aromatic  1.394  0.020  1.394
 6QQ  C23  C10  aromatic  1.402  0.020  1.402
 6QQ  N28  C27  triple    1.153  0.020  1.153
 6QQ  C27  C26  single    1.417  0.020  1.417
 6QQ  C26  C8   aromatic  1.404  0.020  1.404
 6QQ  C10  O11  single    1.325  0.020  1.325
 6QQ  C10  N9   aromatic  1.313  0.020  1.313
 6QQ  O11  C12  single    1.393  0.020  1.393
 6QQ  C8   N9   aromatic  1.314  0.020  1.314
 6QQ  C8   O7   single    1.317  0.020  1.317
 6QQ  C13  C12  aromatic  1.385  0.020  1.385
 6QQ  C13  C14  aromatic  1.387  0.020  1.387
 6QQ  O7   C6   single    1.435  0.020  1.435
 6QQ  C12  C22  aromatic  1.384  0.020  1.384
 6QQ  C14  C15  single    1.506  0.020  1.506
 6QQ  C14  C20  aromatic  1.392  0.020  1.392
 6QQ  C15  O16  single    1.393  0.020  1.393
 6QQ  C6   C5   single    1.513  0.020  1.513
 6QQ  C22  C21  aromatic  1.393  0.020  1.393
 6QQ  C4   C5   single    1.520  0.020  1.520
 6QQ  C4   C2   single    1.507  0.020  1.507
 6QQ  C20  C21  aromatic  1.389  0.020  1.389
 6QQ  C20  B17  single    1.619  0.020  1.619
 6QQ  O16  B17  single    1.507  0.020  1.507
 6QQ  C2   C1   single    1.504  0.020  1.504
 6QQ  C2   O3   double    1.211  0.020  1.211
 6QQ  B17  O19  single    1.469  0.020  1.469
 6QQ  B17  O18  single    1.462  0.020  1.462
 6QQ  C1   H1   single    0.970  0.020  1.090
 6QQ  C1   H2   single    0.970  0.020  1.090
 6QQ  C1   H3   single    0.970  0.020  1.090
 6QQ  C4   H4   single    0.970  0.020  1.090
 6QQ  C4   H5   single    0.970  0.020  1.090
 6QQ  C5   H6   single    0.970  0.020  1.090
 6QQ  C5   H7   single    0.970  0.020  1.090
 6QQ  C6   H8   single    0.970  0.020  1.090
 6QQ  C6   H9   single    0.970  0.020  1.090
 6QQ  C15  H10  single    0.970  0.020  1.090
 6QQ  C15  H11  single    0.970  0.020  1.090
 6QQ  C21  H12  single    0.930  0.020  1.080
 6QQ  C13  H13  single    0.930  0.020  1.080
 6QQ  O18  H14  single    0.850  0.020  0.980
 6QQ  O19  H15  single    0.850  0.020  0.980
 6QQ  C22  H16  single    0.930  0.020  1.080
 6QQ  C25  H17  single    0.930  0.020  1.080

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
 6QQ  H3   C1   H2   109.75  3.000
 6QQ  H3   C1   H1   108.39  3.000
 6QQ  H2   C1   H1   106.73  3.000
 6QQ  H3   C1   C2   111.59  3.000
 6QQ  H2   C1   C2   111.49  3.000
 6QQ  H1   C1   C2   108.72  3.000
 6QQ  O3   C2   C4   122.26  3.000
 6QQ  O3   C2   C1   122.24  3.000
 6QQ  C4   C2   C1   115.50  3.000
 6QQ  H5   C4   H4   104.69  3.000
 6QQ  H5   C4   C5   111.28  3.000
 6QQ  H4   C4   C5   110.69  3.000
 6QQ  H5   C4   C2   107.97  3.000
 6QQ  H4   C4   C2   106.97  3.000
 6QQ  C5   C4   C2   114.67  3.000
 6QQ  H7   C5   H6   107.43  3.000
 6QQ  H7   C5   C6   109.83  3.000
 6QQ  H6   C5   C6   109.64  3.000
 6QQ  H7   C5   C4   110.04  3.000
 6QQ  H6   C5   C4   110.13  3.000
 6QQ  C6   C5   C4   109.74  3.000
 6QQ  H9   C6   H8   107.68  3.000
 6QQ  H9   C6   O7   109.79  3.000
 6QQ  H8   C6   O7   109.35  3.000
 6QQ  H9   C6   C5   111.19  3.000
 6QQ  H8   C6   C5   111.19  3.000
 6QQ  O7   C6   C5   107.63  3.000
 6QQ  C26  C8   N9   122.13  3.000
 6QQ  N9   C8   O7   120.06  3.000
 6QQ  C26  C8   O7   117.81  3.000
 6QQ  C22  C12  C13  122.09  3.000
 6QQ  C22  C12  O11  118.31  3.000
 6QQ  C13  C12  O11  119.53  3.000
 6QQ  H11  C15  H10  105.45  3.000
 6QQ  H11  C15  O16  112.25  3.000
 6QQ  H10  C15  O16  111.39  3.000
 6QQ  H11  C15  C14  109.76  3.000
 6QQ  H10  C15  C14  110.86  3.000
 6QQ  O16  C15  C14  107.19  3.000
 6QQ  H12  C21  C22  118.46  3.000
 6QQ  H12  C21  C20  120.70  3.000
 6QQ  C22  C21  C20  120.84  3.000
 6QQ  C25  C23  CL1  121.58  3.000
 6QQ  C25  C23  C10  118.02  3.000
 6QQ  CL1  C23  C10  120.40  3.000
 6QQ  N28  C27  C26  180.00  3.000
 6QQ  C8   O7   C6   118.59  3.000
 6QQ  C10  N9   C8   120.07  3.000
 6QQ  O11  C10  N9   119.91  3.000
 6QQ  N9   C10  C23  122.51  3.000
 6QQ  O11  C10  C23  117.59  3.000
 6QQ  C10  O11  C12  119.29  3.000
 6QQ  H13  C13  C14  121.89  3.000
 6QQ  H13  C13  C12  120.60  3.000
 6QQ  C14  C13  C12  117.51  3.000
 6QQ  C20  C14  C13  122.48  3.000
 6QQ  C20  C14  C15  110.35  3.000
 6QQ  C13  C14  C15  127.17  3.000
 6QQ  B17  O16  C15  112.84  3.000
 6QQ  C20  B17  O19  109.59  3.000
 6QQ  O19  B17  O18  113.23  3.000
 6QQ  C20  B17  O18  111.37  3.000
 6QQ  O18  B17  O16  110.31  3.000
 6QQ  O19  B17  O16  111.06  3.000
 6QQ  C20  B17  O16  100.59  3.000
 6QQ  H14  O18  B17  111.28  3.000
 6QQ  H15  O19  B17  111.22  3.000
 6QQ  B17  C20  C14  107.92  3.000
 6QQ  B17  C20  C21  133.88  3.000
 6QQ  C14  C20  C21  118.19  3.000
 6QQ  H16  C22  C21  121.16  3.000
 6QQ  H16  C22  C12  119.95  3.000
 6QQ  C21  C22  C12  118.89  3.000
 6QQ  H17  C25  C26  120.02  3.000
 6QQ  H17  C25  C23  120.47  3.000
 6QQ  C26  C25  C23  119.51  3.000
 6QQ  C25  C26  C27  121.61  3.000
 6QQ  C27  C26  C8   120.64  3.000
 6QQ  C25  C26  C8   117.75  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
 6QQ  CONST_01  C23  C25  C26  C8      0.00   0.0  0
 6QQ  CONST_02  C23  C10  N9   C8      0.00   0.0  0
 6QQ  CONST_03  C20  C14  C13  C12     0.00   0.0  0
 6QQ  CONST_04  C20  C21  C22  C12     0.00   0.0  0
 6QQ  CONST_05  C13  C12  C22  C21     0.00   0.0  0
 6QQ  CONST_06  C13  C14  C20  C21     0.00   0.0  0
 6QQ  CONST_07  C25  C23  C10  N9      0.00   0.0  0
 6QQ  CONST_08  C25  C26  C8   N9      0.00   0.0  0
 6QQ  CONST_09  C26  C25  C23  C10     0.00   0.0  0
 6QQ  CONST_10  C26  C8   N9   C10     0.00   0.0  0
 6QQ  CONST_11  C22  C12  C13  C14     0.00   0.0  0
 6QQ  CONST_12  C22  C21  C20  C14     0.00   0.0  0
 6QQ  CONST_13  O11  C10  N9   C8    180.00   0.0  0
 6QQ  CONST_14  O11  C12  C22  C21   180.00   0.0  0
 6QQ  CONST_15  C27  C26  C25  C23   180.00   0.0  0
 6QQ  CONST_16  N9   C8   C26  C27   180.00   0.0  0
 6QQ  CONST_17  C25  C26  C8   O7    180.00   0.0  0
 6QQ  CONST_18  C10  N9   C8   O7    180.00   0.0  0
 6QQ  CONST_19  CL1  C23  C10  N9    180.00   0.0  0
 6QQ  CONST_20  C25  C23  C10  O11   180.00   0.0  0
 6QQ  CONST_21  C14  C13  C12  O11   180.00   0.0  0
 6QQ  CONST_22  C26  C25  C23  CL1   180.00   0.0  0
 6QQ  CONST_23  H17  C25  C26  C8    180.00   0.0  0
 6QQ  CONST_24  H12  C21  C22  C12   180.00   0.0  0
 6QQ  CONST_25  H13  C13  C14  C15     0.00   0.0  0
 6QQ  CONST_26  H16  C22  C12  C13   180.00   0.0  0
 6QQ  Var_01    C20  B17  O16  C15    10.52  30.0  1
 6QQ  Var_02    O16  B17  C20  C21   174.75  30.0  1
 6QQ  Var_03    O16  C15  C14  C13  -174.25  30.0  1
 6QQ  Var_04    C23  C10  O11  C12  -176.38  30.0  2
 6QQ  Var_05    C13  C12  O11  C10    78.85  30.0  2
 6QQ  Var_06    C26  C8   O7   C6   -178.92  30.0  2
 6QQ  Var_07    H8   C6   O7   C8     63.95  30.0  3
 6QQ  Var_08    C5   C4   C2   C1    173.12  30.0  1
 6QQ  Var_09    C6   C5   C4   C2   -179.65  30.0  3
 6QQ  Var_10    O7   C6   C5   C4   -178.18  30.0  1
 6QQ  Var_11    H1   C1   C2   C4    -78.75  30.0  3

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
 6QQ  plan-1  C8   0.020
 6QQ  plan-1  C23  0.020
 6QQ  plan-1  C27  0.020
 6QQ  plan-1  O7   0.020
 6QQ  plan-1  N9   0.020
 6QQ  plan-1  C10  0.020
 6QQ  plan-1  O11  0.020
 6QQ  plan-1  CL1  0.020
 6QQ  plan-1  C25  0.020
 6QQ  plan-1  C26  0.020
 6QQ  plan-1  N28  0.020
 6QQ  plan-1  H17  0.020
 6QQ  plan-2  C12  0.020
 6QQ  plan-2  C15  0.020
 6QQ  plan-2  C21  0.020
 6QQ  plan-2  O11  0.020
 6QQ  plan-2  C13  0.020
 6QQ  plan-2  C14  0.020
 6QQ  plan-2  B17  0.020
 6QQ  plan-2  C20  0.020
 6QQ  plan-2  C22  0.020
 6QQ  plan-2  H12  0.020
 6QQ  plan-2  H13  0.020
 6QQ  plan-2  H16  0.020
 6QQ  plan-3  C1   0.020
 6QQ  plan-3  C2   0.020
 6QQ  plan-3  C4   0.020
 6QQ  plan-3  O3   0.020

