# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:14:56 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: ({[(2-ethoxynaphthalen-1-yl)carbonyl]amino}methyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2ccccc2c1C(=O)NCB(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
 NBF  NBF  '({[(2-ethoxynaphthalen-1-yl)carbonyl]amino}methyl)boronic acid'  ligand  36  20  .  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_NBF
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
 NBF  C25   C  CH3   0  -0.700   3.6246   0.1607   2.3407
 NBF  C24   C  CH2   0  -0.190   3.3416   0.1818   0.8585
 NBF  O23   O  O2    0  -0.482   1.9306   0.0759   0.6771
 NBF  C15   C  CR6   0   0.420   1.4145   0.0823  -0.5662
 NBF  C13   C  CR6   0  -0.201   0.0450  -0.0393  -0.6678
 NBF  C11   C  C     0   0.439  -0.7544  -0.2324   0.5839
 NBF  O12   O  O     0  -0.479  -1.1260  -1.3407   0.9538
 NBF  N10   N  NH1   0  -0.606  -1.0238   0.8819   1.2673
 NBF  C7    C  CH2   0  -0.523  -1.7495   0.8310   2.5215
 NBF  B     B  B     0   0.508  -1.0695  -0.1471   3.5757
 NBF  O1    O  OH1   0  -0.620  -1.8663  -0.7027   4.5264
 NBF  O2    O  OH1   0  -0.631   0.2739  -0.3712   3.6044
 NBF  C14   C  CR66  0   0.155  -0.5868  -0.0562  -1.9337
 NBF  C16   C  CR66  0   0.081   0.2086   0.0643  -3.1035
 NBF  C18   C  CR16  0  -0.305  -0.4116   0.0587  -4.3748
 NBF  C20   C  CR16  0  -0.267  -1.7686  -0.0583  -4.4894
 NBF  C22   C  CR16  0  -0.249  -2.5624  -0.1719  -3.3286
 NBF  C17   C  CR16  0  -0.335  -1.9918  -0.1711  -2.0853
 NBF  C19   C  CR16  0  -0.301   1.6067   0.1884  -2.9623
 NBF  C21   C  CR16  0  -0.383   2.2039   0.1985  -1.7329
 NBF  H251  H  HCH3  0   0.251   4.6999   0.2330   2.5002
 NBF  H252  H  HCH3  0   0.238   3.1573   1.0045   2.8493
 NBF  H253  H  HCH3  0   0.239   3.2810  -0.7661   2.8009
 NBF  H241  H  HCH2  0   0.233   3.7082   1.1113   0.4128
 NBF  H242  H  HCH2  0   0.233   3.8468  -0.6527   0.3625
 NBF  H10   H  HNH1  0   0.411  -0.7397   1.7715   0.8912
 NBF  H71   H  HCH2  0   0.265  -1.7543   1.8427   2.9326
 NBF  H72   H  HCH2  0   0.251  -2.7978   0.5670   2.3525
 NBF  HO1   H  HOH1  0   0.487  -1.3910  -1.2425   5.1670
 NBF  HO2   H  HOH1  0   0.476   0.7401   0.0461   2.8730
 NBF  H18   H  HCR6  0   0.258   0.2097   0.1516  -5.2578
 NBF  H20   H  HCR6  0   0.258  -2.2375  -0.0620  -5.4645
 NBF  H22   H  HCR6  0   0.261  -3.6369  -0.2586  -3.4239
 NBF  H17   H  HCR6  0   0.252  -2.6272  -0.2598  -1.2134
 NBF  H19   H  HCR6  0   0.267   2.2195   0.2774  -3.8508
 NBF  H21   H  HCR6  0   0.289   3.2785   0.2941  -1.6703

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
 NBF  C25  C24   single    1.509  0.020  1.509
 NBF  C25  H251  single    0.970  0.020  1.090
 NBF  C25  H252  single    0.970  0.020  1.090
 NBF  C25  H253  single    0.970  0.020  1.090
 NBF  C24  O23   single    1.427  0.020  1.427
 NBF  C24  H241  single    0.970  0.020  1.090
 NBF  C24  H242  single    0.970  0.020  1.090
 NBF  O23  C15   single    1.346  0.020  1.346
 NBF  C15  C13   aromatic  1.379  0.020  1.379
 NBF  C15  C21   aromatic  1.413  0.020  1.413
 NBF  C13  C11   single    1.498  0.020  1.498
 NBF  C13  C14   aromatic  1.415  0.020  1.415
 NBF  C11  O12   double    1.226  0.020  1.226
 NBF  C11  N10   single    1.335  0.020  1.335
 NBF  N10  C7    single    1.450  0.020  1.450
 NBF  N10  H10   single    0.860  0.020  1.020
 NBF  C7   B     single    1.591  0.020  1.591
 NBF  C7   H71   single    0.970  0.020  1.090
 NBF  C7   H72   single    0.970  0.020  1.090
 NBF  B    O1    single    1.359  0.020  1.359
 NBF  B    O2    single    1.362  0.020  1.362
 NBF  O1   HO1   single    0.850  0.020  0.980
 NBF  O2   HO2   single    0.850  0.020  0.980
 NBF  C14  C16   aromatic  1.420  0.020  1.420
 NBF  C14  C17   aromatic  1.418  0.020  1.418
 NBF  C16  C18   aromatic  1.415  0.020  1.415
 NBF  C16  C19   aromatic  1.411  0.020  1.411
 NBF  C18  C20   aromatic  1.367  0.020  1.367
 NBF  C18  H18   single    0.930  0.020  1.080
 NBF  C20  C22   aromatic  1.411  0.020  1.411
 NBF  C20  H20   single    0.930  0.020  1.080
 NBF  C22  C17   aromatic  1.368  0.020  1.368
 NBF  C22  H22   single    0.930  0.020  1.080
 NBF  C17  H17   single    0.930  0.020  1.080
 NBF  C19  C21   aromatic  1.367  0.020  1.367
 NBF  C19  H19   single    0.930  0.020  1.080
 NBF  C21  H21   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
 NBF  H253  C25  H252  109.01  3.000
 NBF  H253  C25  H251  107.80  3.000
 NBF  H252  C25  H251  107.66  3.000
 NBF  H253  C25  C24   111.55  3.000
 NBF  H252  C25  C24   111.53  3.000
 NBF  H251  C25  C24   109.15  3.000
 NBF  H242  C24  H241  107.97  3.000
 NBF  H242  C24  O23   110.02  3.000
 NBF  H241  C24  O23   110.04  3.000
 NBF  H242  C24  C25   110.36  3.000
 NBF  H241  C24  C25   110.43  3.000
 NBF  O23   C24  C25   108.02  3.000
 NBF  C15   O23  C24   119.76  3.000
 NBF  C21   C15  C13   120.08  3.000
 NBF  C21   C15  O23   123.27  3.000
 NBF  C13   C15  O23   116.65  3.000
 NBF  C14   C13  C11   120.52  3.000
 NBF  C14   C13  C15   120.70  3.000
 NBF  C11   C13  C15   118.68  3.000
 NBF  N10   C11  O12   122.62  3.000
 NBF  N10   C11  C13   115.34  3.000
 NBF  O12   C11  C13   122.04  3.000
 NBF  H10   N10  C7    119.70  3.000
 NBF  H10   N10  C11   119.31  3.000
 NBF  C7    N10  C11   120.97  3.000
 NBF  H72   C7   H71   106.10  3.000
 NBF  H72   C7   B     111.32  3.000
 NBF  H71   C7   B     108.79  3.000
 NBF  H72   C7   N10   110.76  3.000
 NBF  H71   C7   N10   107.18  3.000
 NBF  B     C7   N10   112.39  3.000
 NBF  O2    B    O1    119.74  3.000
 NBF  O2    B    C7    122.46  3.000
 NBF  O1    B    C7    117.66  3.000
 NBF  HO1   O1   B     113.89  3.000
 NBF  HO2   O2   B     112.98  3.000
 NBF  C17   C14  C16   118.29  3.000
 NBF  C17   C14  C13   122.62  3.000
 NBF  C16   C14  C13   119.08  3.000
 NBF  C19   C16  C18   121.66  3.000
 NBF  C19   C16  C14   118.70  3.000
 NBF  C18   C16  C14   119.64  3.000
 NBF  H18   C18  C20   120.55  3.000
 NBF  H18   C18  C16   118.73  3.000
 NBF  C20   C18  C16   120.72  3.000
 NBF  H20   C20  C22   119.83  3.000
 NBF  H20   C20  C18   120.40  3.000
 NBF  C22   C20  C18   119.77  3.000
 NBF  H22   C22  C17   119.61  3.000
 NBF  H22   C22  C20   119.51  3.000
 NBF  C17   C22  C20   120.87  3.000
 NBF  H17   C17  C22   119.16  3.000
 NBF  H17   C17  C14   120.15  3.000
 NBF  C22   C17  C14   120.69  3.000
 NBF  H19   C19  C21   119.35  3.000
 NBF  H19   C19  C16   119.07  3.000
 NBF  C21   C19  C16   121.58  3.000
 NBF  H21   C21  C19   119.16  3.000
 NBF  H21   C21  C15   120.99  3.000
 NBF  C19   C21  C15   119.86  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
 NBF  CONST_01  C16   C14  C13  C15     0.00   0.0  0
 NBF  CONST_02  C17   C14  C13  C15   180.00   0.0  0
 NBF  CONST_03  C16   C19  C21  C15     0.00   0.0  0
 NBF  CONST_04  C19   C21  C15  C13     0.00   0.0  0
 NBF  CONST_05  C18   C16  C14  C13   180.00   0.0  0
 NBF  CONST_06  C19   C16  C14  C13     0.00   0.0  0
 NBF  CONST_07  C22   C17  C14  C13   180.00   0.0  0
 NBF  CONST_08  C21   C15  C13  C14     0.00   0.0  0
 NBF  CONST_09  C20   C18  C16  C14     0.00   0.0  0
 NBF  CONST_10  C21   C19  C16  C14     0.00   0.0  0
 NBF  CONST_11  C20   C22  C17  C14     0.00   0.0  0
 NBF  CONST_12  C22   C17  C14  C16     0.00   0.0  0
 NBF  CONST_13  C22   C20  C18  C16     0.00   0.0  0
 NBF  CONST_14  C17   C14  C16  C18     0.00   0.0  0
 NBF  CONST_15  C21   C19  C16  C18   180.00   0.0  0
 NBF  CONST_16  C17   C22  C20  C18     0.00   0.0  0
 NBF  CONST_17  C19   C16  C18  C20   180.00   0.0  0
 NBF  CONST_18  C19   C16  C14  C17   180.00   0.0  0
 NBF  CONST_19  C14   C13  C15  O23   180.00   0.0  0
 NBF  CONST_20  C19   C21  C15  O23   180.00   0.0  0
 NBF  CONST_21  C21   C15  C13  C11   180.00   0.0  0
 NBF  CONST_22  C16   C14  C13  C11   180.00   0.0  0
 NBF  CONST_23  C17   C14  C13  C11     0.00   0.0  0
 NBF  CONST_24  H19   C19  C21  C15   180.00   0.0  0
 NBF  CONST_25  H21   C21  C15  C13   180.00   0.0  0
 NBF  CONST_26  H17   C17  C14  C13     0.00   0.0  0
 NBF  CONST_27  H18   C18  C16  C14   180.00   0.0  0
 NBF  CONST_28  H22   C22  C17  C14   180.00   0.0  0
 NBF  CONST_29  H20   C20  C18  C16   180.00   0.0  0
 NBF  CONST_30  C7    N10  C11  C13   180.00   0.0  0
 NBF  CONST_31  H10   N10  C11  C13     0.00   0.0  0
 NBF  CONST_32  C7    N10  C11  O12     0.00   0.0  0
 NBF  Var_01    C13   C15  O23  C24   179.26  30.0  2
 NBF  Var_02    O12   C11  C13  C15   -98.04  30.0  2
 NBF  Var_03    H241  C24  O23  C15    58.86  30.0  1
 NBF  Var_04    B     C7   N10  C11    54.86  30.0  3
 NBF  Var_05    O1    B    C7   N10  -153.99  30.0  3
 NBF  Var_06    H251  C25  C24  O23   179.57  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
 NBF  plan-1  O23  0.020
 NBF  plan-1  C15  0.020
 NBF  plan-1  C13  0.020
 NBF  plan-1  C11  0.020
 NBF  plan-1  C14  0.020
 NBF  plan-1  C16  0.020
 NBF  plan-1  C18  0.020
 NBF  plan-1  C20  0.020
 NBF  plan-1  C22  0.020
 NBF  plan-1  C17  0.020
 NBF  plan-1  C19  0.020
 NBF  plan-1  C21  0.020
 NBF  plan-1  H18  0.020
 NBF  plan-1  H20  0.020
 NBF  plan-1  H22  0.020
 NBF  plan-1  H17  0.020
 NBF  plan-1  H19  0.020
 NBF  plan-1  H21  0.020
 NBF  plan-2  C13  0.020
 NBF  plan-2  C11  0.020
 NBF  plan-2  O12  0.020
 NBF  plan-2  N10  0.020
 NBF  plan-2  C7   0.020
 NBF  plan-2  H10  0.020

