# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:25:04 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1Oc2c(C[C@@H]1NC(=O)C3CCCCC3)cccc2C(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
 C6S  C6S  '(3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid'  ligand  42  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C6S
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
 C6S  O01   O  OH1    0  -0.596   0.3336   2.3207  -1.2216
 C6S  B02   B  B      0   0.514   0.8319   1.1902  -0.6767
 C6S  O03   O  O2     0  -0.460   2.1649   0.9154  -0.7870
 C6S  C04   C  CR6    0   0.358   2.7241  -0.2158  -0.2664
 C6S  C05   C  CR6    0   0.041   1.9179  -1.3244   0.0024
 C6S  C06   C  CH2    0  -0.522   0.4410  -1.2507  -0.2658
 C6S  C07   C  CH1    0  -0.261  -0.0958   0.1492   0.0642
 C6S  N08   N  NH1    0  -0.659  -1.4930   0.3092  -0.2602
 C6S  C09   C  C      0   0.575  -2.4904  -0.1630   0.5074
 C6S  O10   O  O      0  -0.505  -2.2938  -0.7199   1.5808
 C6S  C11   C  CH1    0  -0.389  -3.8854   0.0281  -0.0519
 C6S  C12   C  CH2    0  -0.416  -4.8004   0.7136   0.9653
 C6S  C13   C  CH2    0  -0.436  -6.2101   0.8764   0.4064
 C6S  C14   C  CH2    0  -0.429  -6.7930  -0.4644  -0.0281
 C6S  C15   C  CH2    0  -0.435  -5.8802  -1.1653  -1.0291
 C6S  C16   C  CH2    0  -0.415  -4.4680  -1.3264  -0.4765
 C6S  C17   C  CR16   0  -0.338   2.5172  -2.4748   0.4986
 C6S  C18   C  CR16   0  -0.252   3.8908  -2.5342   0.6875
 C6S  C19   C  CR16   0  -0.306   4.6723  -1.4316   0.3800
 C6S  C20   C  CR6    0  -0.153   4.1044  -0.2444  -0.0777
 C6S  C21   C  C      0   0.377   5.0026   0.9613  -0.3247
 C6S  O22   O  O      0  -0.589   4.6073   2.0548   0.1139
 C6S  O23   O  OC    -1  -0.601   6.0734   0.7262  -0.9162
 C6S  H01   H  HOH1   0   0.497   0.9858   2.8715  -1.6696
 C6S  H07   H  HCH1   0   0.270   0.0262   0.3076   1.1436
 C6S  H061  H  HCH2   0   0.255   0.2453  -1.4721  -1.3217
 C6S  H062  H  HCH2   0   0.261  -0.0814  -2.0137   0.3133
 C6S  H17   H  HCR6   0   0.248   1.8979  -3.3330   0.7315
 C6S  H08   H  HNH1   0   0.401  -1.7385   0.7309  -1.1410
 C6S  H11   H  HCH1   0   0.240  -3.8359   0.6652  -0.9435
 C6S  H121  H  HCH2   0   0.219  -4.8373   0.1153   1.8805
 C6S  H122  H  HCH2   0   0.236  -4.3885   1.6881   1.2408
 C6S  H161  H  HCH2   0   0.235  -3.8212  -1.7920  -1.2250
 C6S  H162  H  HCH2   0   0.220  -4.4859  -1.9960   0.3886
 C6S  H131  H  HCH2   0   0.230  -6.8531   1.3462   1.1544
 C6S  H132  H  HCH2   0   0.211  -6.1841   1.5561  -0.4521
 C6S  H141  H  HCH2   0   0.210  -6.9207  -1.1041   0.8521
 C6S  H142  H  HCH2   0   0.228  -7.7879  -0.3242  -0.4578
 C6S  H151  H  HCH2   0   0.231  -6.2879  -2.1435  -1.2948
 C6S  H152  H  HCH2   0   0.212  -5.8403  -0.5836  -1.9566
 C6S  H18   H  HCR6   0   0.247   4.3479  -3.4383   1.0680
 C6S  H19   H  HCR6   0   0.247   5.7453  -1.4812   0.5133

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
 C6S  O01  B02   single    1.350  0.020  1.350
 C6S  B02  O03   single    1.365  0.020  1.365
 C6S  B02  C07   single    1.579  0.020  1.579
 C6S  O03  C04   single    1.365  0.020  1.365
 C6S  C04  C05   aromatic  1.397  0.020  1.397
 C6S  C04  C20   aromatic  1.393  0.020  1.393
 C6S  C05  C06   single    1.503  0.020  1.503
 C6S  C05  C17   aromatic  1.389  0.020  1.389
 C6S  C06  C07   single    1.535  0.020  1.535
 C6S  C07  N08   single    1.443  0.020  1.443
 C6S  N08  C09   single    1.344  0.020  1.344
 C6S  C09  O10   double    1.225  0.020  1.225
 C6S  C09  C11   single    1.515  0.020  1.515
 C6S  C11  C12   single    1.530  0.020  1.530
 C6S  C11  C16   single    1.534  0.020  1.534
 C6S  C12  C13   single    1.525  0.020  1.525
 C6S  C13  C14   single    1.525  0.020  1.525
 C6S  C14  C15   single    1.525  0.020  1.525
 C6S  C15  C16   single    1.525  0.020  1.525
 C6S  C17  C18   aromatic  1.388  0.020  1.388
 C6S  C18  C19   aromatic  1.386  0.020  1.386
 C6S  C19  C20   aromatic  1.393  0.020  1.393
 C6S  C20  C21   single    1.524  0.020  1.524
 C6S  C21  O22   deloc     1.243  0.020  1.243
 C6S  C21  O23   deloc     1.246  0.020  1.246
 C6S  O01  H01   single    0.850  0.020  0.980
 C6S  C07  H07   single    0.970  0.020  1.090
 C6S  C06  H061  single    0.970  0.020  1.090
 C6S  C06  H062  single    0.970  0.020  1.090
 C6S  C17  H17   single    0.930  0.020  1.080
 C6S  N08  H08   single    0.860  0.020  1.020
 C6S  C11  H11   single    0.970  0.020  1.090
 C6S  C12  H121  single    0.970  0.020  1.090
 C6S  C12  H122  single    0.970  0.020  1.090
 C6S  C16  H161  single    0.970  0.020  1.090
 C6S  C16  H162  single    0.970  0.020  1.090
 C6S  C13  H131  single    0.970  0.020  1.090
 C6S  C13  H132  single    0.970  0.020  1.090
 C6S  C14  H141  single    0.970  0.020  1.090
 C6S  C14  H142  single    0.970  0.020  1.090
 C6S  C15  H151  single    0.970  0.020  1.090
 C6S  C15  H152  single    0.970  0.020  1.090
 C6S  C18  H18   single    0.930  0.020  1.080
 C6S  C19  H19   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
 C6S  H01   O01  B02   114.60  3.000
 C6S  C07   B02  O03   118.61  3.000
 C6S  C07   B02  O01   121.64  3.000
 C6S  O03   B02  O01   119.74  3.000
 C6S  C04   O03  B02   122.40  3.000
 C6S  C20   C04  C05   121.96  3.000
 C6S  C20   C04  O03   118.33  3.000
 C6S  C05   C04  O03   119.64  3.000
 C6S  C17   C05  C06   121.90  3.000
 C6S  C17   C05  C04   118.50  3.000
 C6S  C06   C05  C04   119.60  3.000
 C6S  H062  C06  H061  106.53  3.000
 C6S  H062  C06  C07   110.87  3.000
 C6S  H061  C06  C07   109.20  3.000
 C6S  H062  C06  C05   109.97  3.000
 C6S  H061  C06  C05   109.71  3.000
 C6S  C07   C06  C05   110.49  3.000
 C6S  H07   C07  N08   108.22  3.000
 C6S  H07   C07  C06   107.70  3.000
 C6S  N08   C07  C06   113.03  3.000
 C6S  H07   C07  B02   107.52  3.000
 C6S  N08   C07  B02   112.97  3.000
 C6S  C06   C07  B02   107.15  3.000
 C6S  H08   N08  C09   117.75  3.000
 C6S  H08   N08  C07   118.63  3.000
 C6S  C09   N08  C07   123.44  3.000
 C6S  C11   C09  O10   121.91  3.000
 C6S  C11   C09  N08   115.35  3.000
 C6S  O10   C09  N08   122.74  3.000
 C6S  H11   C11  C16   107.75  3.000
 C6S  H11   C11  C12   107.88  3.000
 C6S  C16   C11  C12   110.63  3.000
 C6S  H11   C11  C09   109.37  3.000
 C6S  C16   C11  C09   109.90  3.000
 C6S  C12   C11  C09   111.20  3.000
 C6S  H122  C12  H121  106.82  3.000
 C6S  H122  C12  C13   110.21  3.000
 C6S  H121  C12  C13   109.49  3.000
 C6S  H122  C12  C11   109.97  3.000
 C6S  H121  C12  C11   109.34  3.000
 C6S  C13   C12  C11   110.91  3.000
 C6S  H132  C13  H131  106.48  3.000
 C6S  H132  C13  C14   109.35  3.000
 C6S  H131  C13  C14   110.37  3.000
 C6S  H132  C13  C12   109.36  3.000
 C6S  H131  C13  C12   109.82  3.000
 C6S  C14   C13  C12   111.33  3.000
 C6S  H142  C14  H141  106.54  3.000
 C6S  H142  C14  C15   110.23  3.000
 C6S  H141  C14  C15   109.19  3.000
 C6S  H142  C14  C13   110.31  3.000
 C6S  H141  C14  C13   109.21  3.000
 C6S  C15   C14  C13   111.23  3.000
 C6S  H152  C15  H151  106.45  3.000
 C6S  H152  C15  C16   109.22  3.000
 C6S  H151  C15  C16   109.82  3.000
 C6S  H152  C15  C14   109.47  3.000
 C6S  H151  C15  C14   110.34  3.000
 C6S  C16   C15  C14   111.40  3.000
 C6S  H162  C16  H161  106.88  3.000
 C6S  H162  C16  C15   109.63  3.000
 C6S  H161  C16  C15   110.17  3.000
 C6S  H162  C16  C11   109.13  3.000
 C6S  H161  C16  C11   109.92  3.000
 C6S  C15   C16  C11   111.02  3.000
 C6S  H17   C17  C18   120.17  3.000
 C6S  H17   C17  C05   119.09  3.000
 C6S  C18   C17  C05   120.74  3.000
 C6S  H18   C18  C19   120.30  3.000
 C6S  H18   C18  C17   120.11  3.000
 C6S  C19   C18  C17   119.59  3.000
 C6S  H19   C19  C20   118.92  3.000
 C6S  H19   C19  C18   119.68  3.000
 C6S  C20   C19  C18   121.39  3.000
 C6S  C21   C20  C19   119.16  3.000
 C6S  C21   C20  C04   123.08  3.000
 C6S  C19   C20  C04   117.76  3.000
 C6S  O23   C21  O22   127.38  3.000
 C6S  O23   C21  C20   115.75  3.000
 C6S  O22   C21  C20   116.84  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
 C6S  CONST_01  C18  C17  C05  C04    0.00   0.0  0
 C6S  CONST_02  C18  C19  C20  C04    0.00   0.0  0
 C6S  CONST_03  C19  C20  C04  C05    0.00   0.0  0
 C6S  CONST_04  C19  C18  C17  C05    0.00   0.0  0
 C6S  CONST_05  C20  C04  C05  C17    0.00   0.0  0
 C6S  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 C6S  CONST_07  C21  C20  C04  O03    0.00   0.0  0
 C6S  CONST_08  C21  C20  C04  C05  180.00   0.0  0
 C6S  CONST_09  C21  C20  C19  C18  180.00   0.0  0
 C6S  CONST_10  H17  C17  C05  C04  180.00   0.0  0
 C6S  CONST_11  H19  C19  C20  C04  180.00   0.0  0
 C6S  CONST_12  H18  C18  C17  C05  180.00   0.0  0
 C6S  CONST_13  C11  C09  N08  C07  180.00   0.0  0
 C6S  CONST_14  O10  C09  N08  C07    0.00   0.0  0
 C6S  CONST_15  H08  N08  C09  C11    0.00   0.0  0
 C6S  Var_01    C05  C04  O03  B02   21.16  30.0  1
 C6S  Var_02    C07  B02  O03  C04   -0.83  30.0  1
 C6S  Var_03    C07  C06  C05  C04  -36.66  30.0  1
 C6S  Var_04    C14  C13  C12  C11   56.16  30.0  1
 C6S  Var_05    C14  C15  C16  C11  -55.61  30.0  1
 C6S  Var_06    C15  C14  C13  C12  -55.36  30.0  1
 C6S  Var_07    C16  C15  C14  C13   55.10  30.0  1
 C6S  Var_08    O22  C21  C20  C04   44.65  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
 C6S  chir_01  C07  B02  C06  N08  positiv
 C6S  chir_02  C11  C09  C12  C16  positiv

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
 C6S  plan-1  C07  0.020
 C6S  plan-1  N08  0.020
 C6S  plan-1  C09  0.020
 C6S  plan-1  O10  0.020
 C6S  plan-1  C11  0.020
 C6S  plan-1  H08  0.020
 C6S  plan-2  O03  0.020
 C6S  plan-2  C04  0.020
 C6S  plan-2  C05  0.020
 C6S  plan-2  C06  0.020
 C6S  plan-2  C17  0.020
 C6S  plan-2  C18  0.020
 C6S  plan-2  C19  0.020
 C6S  plan-2  C20  0.020
 C6S  plan-2  C21  0.020
 C6S  plan-2  H17  0.020
 C6S  plan-2  H18  0.020
 C6S  plan-2  H19  0.020
 C6S  plan-3  C20  0.020
 C6S  plan-3  C21  0.020
 C6S  plan-3  O22  0.020
 C6S  plan-3  O23  0.020

