# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:41:59 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-[(4-methylphenyl)sulfonyl]-2,3,1-benzodiazaborinin-1(2H)-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)[S](=O)(=O)N2N=Cc3ccccc3B2O
#
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
 NDT  NDT  2-[(4-methylphenyl)sulfonyl]-2,3,1-benzodiazaborinin-1(2H)-ol  ligand  34  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDT
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
 NDT  C1    C  CR6    0  -0.003  -0.3121  -0.8523  -2.6972
 NDT  C4    C  CR6    0  -0.076   0.5709   0.2350  -2.7096
 NDT  C5    C  CR16   0  -0.332   1.4163   0.3992  -3.8103
 NDT  C6    C  CR16   0  -0.226   1.3788  -0.4958  -4.8648
 NDT  C7    C  CR16   0  -0.259   0.4942  -1.5753  -4.8399
 NDT  C8    C  CR16   0  -0.277  -0.3493  -1.7571  -3.7620
 NDT  C2    C  C1     0  -0.107  -1.1845  -1.0233  -1.5584
 NDT  N1    N  N      0  -0.199  -1.2428  -0.2603  -0.5370
 NDT  N2    N  N     -1  -0.500  -0.4181   0.8204  -0.4787
 NDT  B1    B  B      0   0.560   0.5543   1.1917  -1.4992
 NDT  O1    O  OH1    0  -0.619   1.3802   2.2535  -1.4375
 NDT  S1    S  S      0   1.402  -0.7077   1.6434   0.9730
 NDT  O2    O  OS     0  -0.620  -2.1278   1.8972   1.0820
 NDT  O3    O  OS     0  -0.659   0.2246   2.7648   0.9722
 NDT  C15   C  CR6    0  -0.206  -0.2284   0.4889   2.2085
 NDT  C16   C  CR16   0  -0.210   1.1026   0.4402   2.6061
 NDT  C17   C  CR16   0  -0.283   1.4784  -0.4736   3.5738
 NDT  C18   C  CR6    0   0.116   0.5473  -1.3393   4.1493
 NDT  C19   C  CR16   0  -0.293  -0.7787  -1.2685   3.7270
 NDT  C20   C  CR16   0  -0.202  -1.1774  -0.3594   2.7607
 NDT  C21   C  CH3    0  -0.722   0.9654  -2.3032   5.2167
 NDT  H5    H  HCR6   0   0.265   2.1072   1.2319  -3.8416
 NDT  H6    H  HCR6   0   0.267   2.0362  -0.3601  -5.7136
 NDT  H7    H  HCR6   0   0.271   0.4701  -2.2708  -5.6683
 NDT  H8    H  HCR6   0   0.265  -1.0367  -2.5939  -3.7399
 NDT  H2    H  H      0   0.284  -1.8653  -1.8669  -1.5389
 NDT  HO1   H  HOH1   0   0.494   1.2884   2.7869  -0.6371
 NDT  H16   H  HCR6   0   0.285   1.8420   1.1036   2.1781
 NDT  H17   H  HCR6   0   0.268   2.5134  -0.5107   3.8893
 NDT  H19   H  HCR6   0   0.267  -1.5148  -1.9346   4.1590
 NDT  H20   H  HCR6   0   0.285  -2.2117  -0.3205   2.4497
 NDT  H211  H  HCH3   0   0.260   1.0615  -1.7902   6.1756
 NDT  H212  H  HCH3   0   0.252   0.2380  -3.1031   5.3424
 NDT  H213  H  HCH3   0   0.254   1.9337  -2.7496   4.9928

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
 NDT  C1   C4    aromatic  1.401  0.020  1.401
 NDT  C1   C8    aromatic  1.398  0.020  1.398
 NDT  C1   C2    single    1.445  0.020  1.445
 NDT  C4   C5    aromatic  1.398  0.020  1.398
 NDT  C4   B1    single    1.543  0.020  1.543
 NDT  C5   C6    aromatic  1.384  0.020  1.384
 NDT  C5   H5    single    0.930  0.020  1.080
 NDT  C6   C7    aromatic  1.396  0.020  1.396
 NDT  C6   H6    single    0.930  0.020  1.080
 NDT  C7   C8    aromatic  1.381  0.020  1.381
 NDT  C7   H7    single    0.930  0.020  1.080
 NDT  C8   H8    single    0.930  0.020  1.080
 NDT  C2   N1    double    1.276  0.020  1.276
 NDT  C2   H2    single    0.930  0.020  1.080
 NDT  N1   N2    single    1.361  0.020  1.361
 NDT  N2   B1    single    1.458  0.020  1.458
 NDT  N2   S1    single    1.694  0.020  1.694
 NDT  B1   O1    single    1.347  0.020  1.347
 NDT  O1   HO1   single    0.850  0.020  0.980
 NDT  S1   O2    double    1.447  0.020  1.447
 NDT  S1   O3    double    1.458  0.020  1.458
 NDT  S1   C15   single    1.757  0.020  1.757
 NDT  C15  C16   aromatic  1.390  0.020  1.390
 NDT  C15  C20   aromatic  1.388  0.020  1.388
 NDT  C16  C17   aromatic  1.383  0.020  1.383
 NDT  C16  H16   single    0.930  0.020  1.080
 NDT  C17  C18   aromatic  1.396  0.020  1.396
 NDT  C17  H17   single    0.930  0.020  1.080
 NDT  C18  C19   aromatic  1.393  0.020  1.393
 NDT  C18  C21   single    1.498  0.020  1.498
 NDT  C19  C20   aromatic  1.385  0.020  1.385
 NDT  C19  H19   single    0.930  0.020  1.080
 NDT  C20  H20   single    0.930  0.020  1.080
 NDT  C21  H211  single    0.970  0.020  1.090
 NDT  C21  H212  single    0.970  0.020  1.090
 NDT  C21  H213  single    0.970  0.020  1.090

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
 NDT  C2    C1   C8    120.51  3.000
 NDT  C2    C1   C4    118.66  3.000
 NDT  C8    C1   C4    120.83  3.000
 NDT  B1    C4   C5    123.47  3.000
 NDT  B1    C4   C1    117.88  3.000
 NDT  C5    C4   C1    118.65  3.000
 NDT  H5    C5   C6    119.53  3.000
 NDT  H5    C5   C4    119.95  3.000
 NDT  C6    C5   C4    120.53  3.000
 NDT  H6    C6   C7    119.73  3.000
 NDT  H6    C6   C5    120.02  3.000
 NDT  C7    C6   C5    120.25  3.000
 NDT  H7    C7   C8    119.96  3.000
 NDT  H7    C7   C6    119.84  3.000
 NDT  C8    C7   C6    120.19  3.000
 NDT  H8    C8   C7    120.35  3.000
 NDT  H8    C8   C1    120.10  3.000
 NDT  C7    C8   C1    119.55  3.000
 NDT  H2    C2   N1    114.96  3.000
 NDT  H2    C2   C1    119.05  3.000
 NDT  N1    C2   C1    125.99  3.000
 NDT  N2    N1   C2    118.77  3.000
 NDT  S1    N2   B1    126.18  3.000
 NDT  S1    N2   N1    108.60  3.000
 NDT  B1    N2   N1    125.22  3.000
 NDT  O1    B1   N2    125.30  3.000
 NDT  O1    B1   C4    121.22  3.000
 NDT  N2    B1   C4    113.48  3.000
 NDT  HO1   O1   B1    114.52  3.000
 NDT  C15   S1   O3    109.34  3.000
 NDT  C15   S1   O2    109.27  3.000
 NDT  O3    S1   O2    119.52  3.000
 NDT  C15   S1   N2    103.69  3.000
 NDT  O3    S1   N2    105.30  3.000
 NDT  O2    S1   N2    108.52  3.000
 NDT  C20   C15  C16   121.31  3.000
 NDT  C20   C15  S1    119.66  3.000
 NDT  C16   C15  S1    119.03  3.000
 NDT  H16   C16  C17   119.76  3.000
 NDT  H16   C16  C15   121.33  3.000
 NDT  C17   C16  C15   118.92  3.000
 NDT  H17   C17  C18   119.76  3.000
 NDT  H17   C17  C16   119.10  3.000
 NDT  C18   C17  C16   121.14  3.000
 NDT  C21   C18  C19   120.95  3.000
 NDT  C21   C18  C17   120.46  3.000
 NDT  C19   C18  C17   118.58  3.000
 NDT  H19   C19  C20   119.11  3.000
 NDT  H19   C19  C18   119.66  3.000
 NDT  C20   C19  C18   121.24  3.000
 NDT  H20   C20  C19   119.99  3.000
 NDT  H20   C20  C15   121.19  3.000
 NDT  C19   C20  C15   118.82  3.000
 NDT  H213  C21  H212  108.45  3.000
 NDT  H213  C21  H211  107.15  3.000
 NDT  H212  C21  H211  107.63  3.000
 NDT  H213  C21  C18   111.42  3.000
 NDT  H212  C21  C18   111.63  3.000
 NDT  H211  C21  C18   110.37  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
 NDT  CONST_01  C6    C5   C4   C1     0.00   0.0  0
 NDT  CONST_02  C6    C7   C8   C1     0.00   0.0  0
 NDT  CONST_03  C7    C8   C1   C4     0.00   0.0  0
 NDT  CONST_04  C7    C6   C5   C4     0.00   0.0  0
 NDT  CONST_05  C8    C1   C4   C5     0.00   0.0  0
 NDT  CONST_06  C8    C7   C6   C5     0.00   0.0  0
 NDT  CONST_07  C18   C17  C16  C15    0.00   0.0  0
 NDT  CONST_08  C18   C19  C20  C15    0.00   0.0  0
 NDT  CONST_09  C19   C20  C15  C16    0.00   0.0  0
 NDT  CONST_10  C19   C18  C17  C16    0.00   0.0  0
 NDT  CONST_11  C20   C15  C16  C17    0.00   0.0  0
 NDT  CONST_12  C20   C19  C18  C17    0.00   0.0  0
 NDT  CONST_13  C17   C16  C15  S1   180.00   0.0  0
 NDT  CONST_14  C19   C20  C15  S1   180.00   0.0  0
 NDT  CONST_15  C21   C18  C17  C16  180.00   0.0  0
 NDT  CONST_16  C21   C18  C19  C20  180.00   0.0  0
 NDT  CONST_17  H5    C5   C4   C1   180.00   0.0  0
 NDT  CONST_18  H7    C7   C8   C1   180.00   0.0  0
 NDT  CONST_19  H8    C8   C1   C4   180.00   0.0  0
 NDT  CONST_20  H6    C6   C5   C4   180.00   0.0  0
 NDT  CONST_21  H17   C17  C16  C15  180.00   0.0  0
 NDT  CONST_22  H19   C19  C20  C15  180.00   0.0  0
 NDT  CONST_23  H20   C20  C15  C16  180.00   0.0  0
 NDT  CONST_24  H16   C16  C17  C18  180.00   0.0  0
 NDT  Var_01    C16   C15  S1   N2    86.60  30.0  2
 NDT  Var_02    H211  C21  C18  C17   78.25  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
 NDT  chir_01  N2  S1  B1  N1  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
 NDT  plan-1  S1   0.020
 NDT  plan-1  C15  0.020
 NDT  plan-1  C16  0.020
 NDT  plan-1  C17  0.020
 NDT  plan-1  C18  0.020
 NDT  plan-1  C19  0.020
 NDT  plan-1  C20  0.020
 NDT  plan-1  C21  0.020
 NDT  plan-1  H16  0.020
 NDT  plan-1  H17  0.020
 NDT  plan-1  H19  0.020
 NDT  plan-1  H20  0.020
 NDT  plan-2  C1   0.020
 NDT  plan-2  C4   0.020
 NDT  plan-2  C5   0.020
 NDT  plan-2  C6   0.020
 NDT  plan-2  C7   0.020
 NDT  plan-2  C8   0.020
 NDT  plan-2  C2   0.020
 NDT  plan-2  N1   0.020
 NDT  plan-2  N2   0.020
 NDT  plan-2  B1   0.020
 NDT  plan-2  O1   0.020
 NDT  plan-2  S1   0.020
 NDT  plan-2  H5   0.020
 NDT  plan-2  H6   0.020
 NDT  plan-2  H7   0.020
 NDT  plan-2  H8   0.020
 NDT  plan-2  H2   0.020

