# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:11:48 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-borono-5-{[(thiophen-2-yl)acetyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1cc(NC(=O)Cc2sccc2)cc(c1)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
 H4D  H4D  '3-borono-5-{[(thiophen-2-yl)acetyl]amino}benzoic acid'  ligand  33  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H4D
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
 H4D  N1   N  NH1   0  -0.755  -0.3423   0.8049   0.5120
 H4D  C4   C  CR15  0  -0.239  -5.0097   0.0775   1.3013
 H4D  C5   C  CR15  0  -0.183  -6.1511  -0.3600   0.5730
 H4D  C6   C  CR15  0  -0.470  -6.0066  -0.1965  -0.7696
 H4D  C7   C  CR6   0   0.433   0.9306   0.2756   0.2844
 H4D  C8   C  CR16  0  -0.413   1.9837   1.1886   0.1931
 H4D  C10  C  CR16  0  -0.357   3.5539  -0.5834  -0.1425
 H4D  C13  C  CR16  0  -0.357   1.2037  -1.0816   0.1541
 H4D  O1   O  O     0  -0.446  -1.7006  -1.0155   0.3602
 H4D  C1   C  C     0   0.556  -1.5423   0.1727   0.5543
 H4D  C2   C  CH2   0  -0.687  -2.6936   1.1031   0.9083
 H4D  C3   C  CR5   0  -0.111  -4.0207   0.5662   0.5030
 H4D  S1   S  S2    0   0.209  -4.4839   0.4920  -1.1547
 H4D  C9   C  CR6   0  -0.050   3.2961   0.7822  -0.0190
 H4D  B1   B  B     0   0.519   4.4574   1.8387  -0.1241
 H4D  O2   O  OH1   0  -0.632   4.1088   3.1520  -0.1245
 H4D  O3   O  OH1   0  -0.632   5.7271   1.3629  -0.2089
 H4D  C11  C  CR6   0  -0.039   2.5152  -1.5025  -0.0578
 H4D  C12  C  C     0   0.540   2.7462  -2.9652  -0.1866
 H4D  O4   O  O     0  -0.439   1.8669  -3.7923  -0.1420
 H4D  O5   O  OH1   0  -0.594   4.0234  -3.2763  -0.3554
 H4D  H1   H  HNH1  0   0.421  -0.3623   1.8034   0.6565
 H4D  H2   H  HCR5  0   0.263  -4.9262   0.0321   2.3786
 H4D  H3   H  HCR5  0   0.266  -7.0371  -0.7759   1.0304
 H4D  H4   H  HCR5  0   0.294  -6.7095  -0.4396  -1.5513
 H4D  H5   H  HCR6  0   0.276   1.7616   2.2452   0.2956
 H4D  H6   H  HCR6  0   0.264   4.5667  -0.9219  -0.3098
 H4D  H7   H  HCR6  0   0.289   0.4158  -1.8132   0.2160
 H4D  H8   H  HCH2  0   0.317  -2.6835   1.2315   1.9947
 H4D  H9   H  HCH2  0   0.296  -2.5227   2.0977   0.4879
 H4D  H10  H  HOH1  0   0.487   4.8316   3.7835  -0.1926
 H4D  H11  H  HOH1  0   0.488   4.1221  -4.2375  -0.4255
 H4D  H12  H  HOH1  0   0.486   6.4233   2.0227  -0.2853

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
 H4D  O4   C12  double    1.208  0.020  1.208
 H4D  O5   C12  single    1.325  0.020  1.325
 H4D  C12  C11  single    1.486  0.020  1.486
 H4D  C11  C10  aromatic  1.390  0.020  1.390
 H4D  C11  C13  aromatic  1.394  0.020  1.394
 H4D  C10  C9   aromatic  1.395  0.020  1.395
 H4D  C13  C7   aromatic  1.391  0.020  1.391
 H4D  O2   B1   single    1.359  0.020  1.359
 H4D  C9   B1   single    1.573  0.020  1.573
 H4D  C9   C8   aromatic  1.390  0.020  1.390
 H4D  C7   C8   aromatic  1.397  0.020  1.397
 H4D  C7   N1   single    1.397  0.020  1.397
 H4D  B1   O3   single    1.359  0.020  1.359
 H4D  N1   C1   single    1.357  0.020  1.357
 H4D  C1   O1   double    1.214  0.020  1.214
 H4D  C1   C2   single    1.522  0.020  1.522
 H4D  C2   C3   single    1.488  0.020  1.488
 H4D  S1   C3   aromatic  1.723  0.020  1.723
 H4D  S1   C6   aromatic  1.715  0.020  1.715
 H4D  C3   C4   aromatic  1.362  0.020  1.362
 H4D  C4   C5   aromatic  1.423  0.020  1.423
 H4D  C6   C5   aromatic  1.360  0.020  1.360
 H4D  N1   H1   single    0.860  0.020  1.020
 H4D  C4   H2   single    0.930  0.020  1.080
 H4D  C5   H3   single    0.930  0.020  1.080
 H4D  C6   H4   single    0.930  0.020  1.080
 H4D  C8   H5   single    0.930  0.020  1.080
 H4D  C10  H6   single    0.930  0.020  1.080
 H4D  C13  H7   single    0.930  0.020  1.080
 H4D  C2   H8   single    0.970  0.020  1.090
 H4D  C2   H9   single    0.970  0.020  1.090
 H4D  O2   H10  single    0.850  0.020  0.980
 H4D  O5   H11  single    0.850  0.020  0.980
 H4D  O3   H12  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
 H4D  H1   N1   C1   116.05  3.000
 H4D  H1   N1   C7   114.59  3.000
 H4D  C1   N1   C7   129.36  3.000
 H4D  H2   C4   C3   122.88  3.000
 H4D  H2   C4   C5   123.98  3.000
 H4D  C3   C4   C5   113.14  3.000
 H4D  H3   C5   C6   123.46  3.000
 H4D  H3   C5   C4   124.02  3.000
 H4D  C6   C5   C4   112.52  3.000
 H4D  H4   C6   S1   120.41  3.000
 H4D  H4   C6   C5   128.22  3.000
 H4D  S1   C6   C5   111.36  3.000
 H4D  C13  C7   C8   118.93  3.000
 H4D  C8   C7   N1   116.74  3.000
 H4D  C13  C7   N1   124.33  3.000
 H4D  H5   C8   C9   119.51  3.000
 H4D  H5   C8   C7   118.44  3.000
 H4D  C9   C8   C7   122.05  3.000
 H4D  H6   C10  C11  120.18  3.000
 H4D  H6   C10  C9   119.56  3.000
 H4D  C11  C10  C9   120.26  3.000
 H4D  H7   C13  C11  119.47  3.000
 H4D  H7   C13  C7   120.93  3.000
 H4D  C11  C13  C7   119.60  3.000
 H4D  C2   C1   O1   122.46  3.000
 H4D  C2   C1   N1   113.04  3.000
 H4D  O1   C1   N1   124.48  3.000
 H4D  H9   C2   H8   105.88  3.000
 H4D  H9   C2   C3   111.28  3.000
 H4D  H8   C2   C3   108.73  3.000
 H4D  H9   C2   C1   110.39  3.000
 H4D  H8   C2   C1   107.20  3.000
 H4D  C3   C2   C1   113.00  3.000
 H4D  S1   C3   C2   121.16  3.000
 H4D  S1   C3   C4   110.69  3.000
 H4D  C2   C3   C4   128.15  3.000
 H4D  C3   S1   C6    92.29  3.000
 H4D  B1   C9   C10  120.99  3.000
 H4D  B1   C9   C8   120.71  3.000
 H4D  C10  C9   C8   118.30  3.000
 H4D  O3   B1   O2   125.33  3.000
 H4D  O3   B1   C9   117.31  3.000
 H4D  O2   B1   C9   117.36  3.000
 H4D  H10  O2   B1   116.21  3.000
 H4D  H12  O3   B1   116.16  3.000
 H4D  C12  C11  C13  117.18  3.000
 H4D  C13  C11  C10  120.86  3.000
 H4D  C12  C11  C10  121.97  3.000
 H4D  O5   C12  O4   123.05  3.000
 H4D  O5   C12  C11  113.07  3.000
 H4D  O4   C12  C11  123.88  3.000
 H4D  H11  O5   C12  109.90  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
 H4D  CONST_01  C6   S1   C3   C4      0.00   0.0  0
 H4D  CONST_02  S1   C6   C5   C4      0.00   0.0  0
 H4D  CONST_03  S1   C3   C4   C5      0.00   0.0  0
 H4D  CONST_04  C3   S1   C6   C5      0.00   0.0  0
 H4D  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 H4D  CONST_06  C10  C11  C13  C7      0.00   0.0  0
 H4D  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 H4D  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 H4D  CONST_09  C11  C13  C7   C8      0.00   0.0  0
 H4D  CONST_10  C9   C10  C11  C13     0.00   0.0  0
 H4D  CONST_11  C9   C8   C7   C13     0.00   0.0  0
 H4D  CONST_12  C11  C13  C7   N1    180.00   0.0  0
 H4D  CONST_13  C9   C8   C7   N1    180.00   0.0  0
 H4D  CONST_14  C2   C3   C4   C5    180.00   0.0  0
 H4D  CONST_15  C2   C3   S1   C6    180.00   0.0  0
 H4D  CONST_16  C12  C11  C13  C7    180.00   0.0  0
 H4D  CONST_17  B1   C9   C8   C7    180.00   0.0  0
 H4D  CONST_18  C12  C11  C10  C9    180.00   0.0  0
 H4D  CONST_19  C11  C10  C9   B1    180.00   0.0  0
 H4D  CONST_20  H4   C6   C5   C4    180.00   0.0  0
 H4D  CONST_21  H2   C4   C5   C6    180.00   0.0  0
 H4D  CONST_22  H6   C10  C9   C8    180.00   0.0  0
 H4D  CONST_23  H7   C13  C7   C8    180.00   0.0  0
 H4D  CONST_24  H5   C8   C9   C10   180.00   0.0  0
 H4D  CONST_25  H3   C5   C4   C3    180.00   0.0  0
 H4D  CONST_26  C1   N1   C7   C8    180.00   0.0  0
 H4D  CONST_27  C1   N1   C7   C13     0.00   0.0  0
 H4D  CONST_28  H1   N1   C7   C8      0.00   0.0  0
 H4D  CONST_29  O1   C1   N1   C7      0.00   0.0  0
 H4D  CONST_30  C2   C1   N1   C7    180.00   0.0  0
 H4D  CONST_31  H11  O5   C12  C11   180.00   0.0  0
 H4D  Var_01    C1   C2   C3   C4    108.10  30.0  1
 H4D  Var_02    O2   B1   C9   C8     -5.97  30.0  2
 H4D  Var_03    O4   C12  C11  C10  -178.65  30.0  2
 H4D  Var_04    C3   C2   C1   N1    159.89  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
 H4D  plan-1  C4   0.020
 H4D  plan-1  C5   0.020
 H4D  plan-1  C6   0.020
 H4D  plan-1  C2   0.020
 H4D  plan-1  C3   0.020
 H4D  plan-1  S1   0.020
 H4D  plan-1  H2   0.020
 H4D  plan-1  H3   0.020
 H4D  plan-1  H4   0.020
 H4D  plan-2  N1   0.020
 H4D  plan-2  C7   0.020
 H4D  plan-2  C8   0.020
 H4D  plan-2  C10  0.020
 H4D  plan-2  C13  0.020
 H4D  plan-2  C9   0.020
 H4D  plan-2  B1   0.020
 H4D  plan-2  C11  0.020
 H4D  plan-2  C12  0.020
 H4D  plan-2  H5   0.020
 H4D  plan-2  H6   0.020
 H4D  plan-2  H7   0.020
 H4D  plan-3  N1   0.020
 H4D  plan-3  C7   0.020
 H4D  plan-3  O1   0.020
 H4D  plan-3  C1   0.020
 H4D  plan-3  C2   0.020
 H4D  plan-3  H1   0.020
 H4D  plan-4  C11  0.020
 H4D  plan-4  C12  0.020
 H4D  plan-4  O4   0.020
 H4D  plan-4  O5   0.020
 H4D  plan-4  H11  0.020

