# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 02:41:58 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: {[(thiophen-2-ylacetyl)amino]methyl}boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)CNC(=O)Cc1sccc1
#
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
 CTB  CTB  '{[(thiophen-2-ylacetyl)amino]methyl}boronic acid'  ligand  23  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CTB
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
 CTB  B    B  B     0   0.516   0.3953  -0.0918   3.4373
 CTB  O1   O  OH1   0  -0.627   1.0242  -1.1845   3.9587
 CTB  O2   O  OH1   0  -0.631   0.8880   1.1799   3.4666
 CTB  C3   C  CH2   0  -0.507  -1.0978  -0.2784   2.9177
 CTB  N4   N  NH1   0  -0.624  -1.3081   0.3814   1.6441
 CTB  C5   C  C     0   0.581  -0.3833   0.3152   0.6888
 CTB  O6   O  O     0  -0.503   0.6786  -0.2825   0.8447
 CTB  C7   C  CH2   0  -0.633  -0.6838   1.0588  -0.5959
 CTB  C8   C  CR5   0  -0.133  -0.3902   0.2576  -1.8207
 CTB  C9   C  CR15  0  -0.237  -1.2111   0.0642  -2.8923
 CTB  C10  C  CR15  0  -0.186  -0.6086  -0.7013  -3.9288
 CTB  C11  C  CR15  0  -0.477   0.6655  -1.0693  -3.6263
 CTB  S1   S  S2    0   0.216   1.1346  -0.5060  -2.0754
 CTB  H1   H  HOH1  0   0.482   1.8959  -1.0201   4.3316
 CTB  H2   H  HOH1  0   0.479   1.7826   1.2728   3.8076
 CTB  H31  H  HCH2  0   0.240  -1.3711  -1.3362   2.8492
 CTB  H32  H  HCH2  0   0.251  -1.7847   0.1705   3.6389
 CTB  H4   H  HNH1  0   0.403  -2.1936   0.8187   1.4506
 CTB  H71  H  HCH2  0   0.280  -1.7221   1.3905  -0.6333
 CTB  H72  H  HCH2  0   0.298  -0.0676   1.9643  -0.5814
 CTB  H9   H  HCR5  0   0.260  -2.2154   0.4624  -2.9421
 CTB  H10  H  HCR5  0   0.263  -1.1057  -0.9675  -4.8508
 CTB  H11  H  HCR5  0   0.290   1.3443  -1.6628  -4.2192

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
 CTB  B    O1   single    1.364  0.020  1.364
 CTB  B    O2   single    1.364  0.020  1.364
 CTB  B    C3   single    1.592  0.020  1.592
 CTB  O1   H1   single    0.850  0.020  0.980
 CTB  O2   H2   single    0.850  0.020  0.980
 CTB  C3   N4   single    1.450  0.020  1.450
 CTB  C3   H31  single    0.970  0.020  1.090
 CTB  C3   H32  single    0.970  0.020  1.090
 CTB  N4   C5   single    1.331  0.020  1.331
 CTB  N4   H4   single    0.860  0.020  1.020
 CTB  C5   O6   double    1.228  0.020  1.228
 CTB  C5   C7   single    1.514  0.020  1.514
 CTB  C7   C8   single    1.493  0.020  1.493
 CTB  C7   H71  single    0.970  0.020  1.090
 CTB  C7   H72  single    0.970  0.020  1.090
 CTB  C8   C9   aromatic  1.364  0.020  1.364
 CTB  C8   S1   aromatic  1.724  0.020  1.724
 CTB  C9   C10  aromatic  1.422  0.020  1.422
 CTB  C9   H9   single    0.930  0.020  1.080
 CTB  C10  C11  aromatic  1.360  0.020  1.360
 CTB  C10  H10  single    0.930  0.020  1.080
 CTB  C11  S1   aromatic  1.715  0.020  1.715
 CTB  C11  H11  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
 CTB  C3   B    O2   117.07  3.000
 CTB  C3   B    O1   117.59  3.000
 CTB  O2   B    O1   124.89  3.000
 CTB  H1   O1   B    115.39  3.000
 CTB  H2   O2   B    115.69  3.000
 CTB  H32  C3   H31  106.34  3.000
 CTB  H32  C3   N4   107.56  3.000
 CTB  H31  C3   N4   110.40  3.000
 CTB  H32  C3   B    109.03  3.000
 CTB  H31  C3   B    111.58  3.000
 CTB  N4   C3   B    111.68  3.000
 CTB  H4   N4   C5   119.66  3.000
 CTB  H4   N4   C3   119.62  3.000
 CTB  C5   N4   C3   120.47  3.000
 CTB  C7   C5   O6   121.20  3.000
 CTB  C7   C5   N4   116.52  3.000
 CTB  O6   C5   N4   122.25  3.000
 CTB  H72  C7   H71  106.53  3.000
 CTB  H72  C7   C8   110.11  3.000
 CTB  H71  C7   C8   108.80  3.000
 CTB  H72  C7   C5   106.44  3.000
 CTB  H71  C7   C5   111.55  3.000
 CTB  C8   C7   C5   113.17  3.000
 CTB  S1   C8   C9   110.69  3.000
 CTB  S1   C8   C7   122.20  3.000
 CTB  C9   C8   C7   127.05  3.000
 CTB  H9   C9   C10  123.91  3.000
 CTB  H9   C9   C8   122.89  3.000
 CTB  C10  C9   C8   113.20  3.000
 CTB  H10  C10  C11  123.64  3.000
 CTB  H10  C10  C9   124.01  3.000
 CTB  C11  C10  C9   112.35  3.000
 CTB  H11  C11  S1   120.35  3.000
 CTB  H11  C11  C10  128.01  3.000
 CTB  S1   C11  C10  111.62  3.000
 CTB  C11  S1   C8    92.13  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
 CTB  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 CTB  CONST_02  C10  C11  S1   C8      0.00   0.0  0
 CTB  CONST_03  C11  S1   C8   C9      0.00   0.0  0
 CTB  CONST_04  S1   C11  C10  C9      0.00   0.0  0
 CTB  CONST_05  S1   C8   C9   C10     0.00   0.0  0
 CTB  CONST_06  C10  C9   C8   C7    180.00   0.0  0
 CTB  CONST_07  C11  S1   C8   C7    180.00   0.0  0
 CTB  CONST_08  H10  C10  C9   C8    180.00   0.0  0
 CTB  CONST_09  H11  C11  S1   C8    180.00   0.0  0
 CTB  CONST_10  H9   C9   C10  C11   180.00   0.0  0
 CTB  CONST_11  O6   C5   N4   C3      0.00   0.0  0
 CTB  CONST_12  C7   C5   N4   C3    180.00   0.0  0
 CTB  CONST_13  H4   N4   C5   O6    180.00   0.0  0
 CTB  Var_01    C9   C8   C7   C5    130.79  30.0  2
 CTB  Var_02    C8   C7   C5   N4   -134.49  30.0  3
 CTB  Var_03    C5   N4   C3   B      41.61  30.0  3
 CTB  Var_04    N4   C3   B    O1   -136.36  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
 CTB  plan-1  C7   0.020
 CTB  plan-1  C8   0.020
 CTB  plan-1  C9   0.020
 CTB  plan-1  C10  0.020
 CTB  plan-1  C11  0.020
 CTB  plan-1  S1   0.020
 CTB  plan-1  H9   0.020
 CTB  plan-1  H10  0.020
 CTB  plan-1  H11  0.020
 CTB  plan-2  C3   0.020
 CTB  plan-2  N4   0.020
 CTB  plan-2  C5   0.020
 CTB  plan-2  O6   0.020
 CTB  plan-2  C7   0.020
 CTB  plan-2  H4   0.020

