# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:15:10 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(2-methoxy-5-methyl-phenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)cc1NC(=O)Nc2ccc3CO[B-](O)(O)c3c2
#
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
 RC4  RC4  1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(2-methoxy-5-methyl-phenyl)urea  ligand  42  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RC4
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
 RC4  C5   C  CR16   0  -0.295   3.4447  -2.4183   0.4116
 RC4  C4   C  CR16   0  -0.352   2.0908  -2.3496   0.1103
 RC4  C3   C  CR6    0   0.350   1.5121  -1.1393  -0.2758
 RC4  C2   C  CR16   0  -0.418   2.3023   0.0079  -0.3640
 RC4  C1   C  CR56   0  -0.045   3.6526  -0.0478  -0.0432
 RC4  C6   C  CR56   0  -0.099   4.2083  -1.2628   0.3431
 RC4  C7   C  CH2    0  -0.148   5.6771  -1.1015   0.6353
 RC4  B1   B  B     -1   0.415   4.8349   1.0584  -0.0526
 RC4  O3   O  OB     0  -0.734   4.5148   2.1861   0.8230
 RC4  C16  C  CH3    0  -0.434  -5.3790  -2.5337   0.5431
 RC4  C11  C  CR16   0  -0.372  -5.4790   0.2795   0.4471
 RC4  C10  C  CR6    0   0.317  -4.3295  -0.4400   0.1519
 RC4  C12  C  CR16   0  -0.304  -5.4825   1.6662   0.3462
 RC4  C13  C  CR6    0   0.077  -4.3536   2.3600  -0.0660
 RC4  C14  C  CR16   0  -0.331  -3.2112   1.6275  -0.3834
 RC4  C9   C  CR6    0   0.281  -3.1768   0.2446  -0.2700
 RC4  O4   O  O      0  -0.502  -0.4726   0.8109   0.3865
 RC4  N1   N  NH1    0  -0.779   0.1452  -1.1435  -0.6162
 RC4  N2   N  NH1    0  -0.771  -2.0452  -0.5083  -0.6078
 RC4  C8   C  C      0   0.695  -0.7646  -0.2028  -0.2230
 RC4  C15  C  CH3    0  -0.722  -4.3495   3.8588  -0.1624
 RC4  O2   O  OB     0  -0.737   5.1238   1.4645  -1.4351
 RC4  O1   O  O      0  -0.583   5.9735   0.2565   0.5192
 RC4  H1   H  HCR6   0   0.233   3.8790  -3.3677   0.7057
 RC4  H2   H  HCR6   0   0.249   1.4745  -3.2391   0.1775
 RC4  H3   H  HCR6   0   0.234   1.8596   0.9383  -0.6959
 RC4  H4   H  HCH2   0   0.188   5.9201  -1.4801   1.6402
 RC4  H5   H  HCH2   0   0.182   6.2725  -1.7172  -0.0598
 RC4  H6   H  H      0   0.428   5.2533   2.7993   0.8820
 RC4  H7   H  HCH3   0   0.229  -5.7554  -2.3002   1.5424
 RC4  H8   H  HCH3   0   0.229  -6.1809  -2.3711  -0.1815
 RC4  H9   H  HCH3   0   0.260  -5.0849  -3.5799   0.5155
 RC4  H10  H  HCR6   0   0.278  -6.3809  -0.2230   0.7690
 RC4  H11  H  HCR6   0   0.248  -6.3896   2.2053   0.5914
 RC4  H12  H  HCR6   0   0.253  -2.3333   2.1472  -0.7415
 RC4  H13  H  HNH1   0   0.400  -0.2100  -2.0204  -0.9651
 RC4  H14  H  HNH1   0   0.401  -2.2229  -1.4340  -0.9666
 RC4  H15  H  HCH3   0   0.244  -4.0223   4.3160   0.7741
 RC4  H16  H  HCH3   0   0.241  -3.6735   4.2075  -0.9432
 RC4  H17  H  HCH3   0   0.241  -5.3436   4.2477  -0.3819
 RC4  H18  H  H      0   0.426   5.9188   2.0048  -1.4753
 RC4  O5   O  O2     0  -0.475  -4.2240  -1.7836   0.2250

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
 RC4  C16  O5   single    1.413  0.020  1.413
 RC4  O5   C10  single    1.350  0.020  1.350
 RC4  C11  C10  aromatic  1.388  0.020  1.388
 RC4  C11  C12  aromatic  1.390  0.020  1.390
 RC4  C10  C9   aromatic  1.406  0.020  1.406
 RC4  C12  C13  aromatic  1.388  0.020  1.388
 RC4  C9   N2   single    1.400  0.020  1.400
 RC4  C9   C14  aromatic  1.388  0.020  1.388
 RC4  C13  C14  aromatic  1.394  0.020  1.394
 RC4  C13  C15  single    1.502  0.020  1.502
 RC4  N2   C8   single    1.372  0.020  1.372
 RC4  C8   N1   single    1.366  0.020  1.366
 RC4  C8   O4   double    1.218  0.020  1.218
 RC4  N1   C3   single    1.409  0.020  1.409
 RC4  C3   C4   aromatic  1.396  0.020  1.396
 RC4  C3   C2   aromatic  1.396  0.020  1.396
 RC4  C4   C5   aromatic  1.389  0.020  1.389
 RC4  C2   C1   aromatic  1.389  0.020  1.389
 RC4  C5   C6   aromatic  1.387  0.020  1.387
 RC4  C1   C6   aromatic  1.391  0.020  1.391
 RC4  C1   B1   single    1.619  0.020  1.619
 RC4  O2   B1   single    1.470  0.020  1.470
 RC4  C6   C7   single    1.506  0.020  1.506
 RC4  O1   C7   single    1.395  0.020  1.395
 RC4  O1   B1   single    1.505  0.020  1.505
 RC4  B1   O3   single    1.463  0.020  1.463
 RC4  C5   H1   single    0.930  0.020  1.080
 RC4  C4   H2   single    0.930  0.020  1.080
 RC4  C2   H3   single    0.930  0.020  1.080
 RC4  C7   H4   single    0.970  0.020  1.090
 RC4  C7   H5   single    0.970  0.020  1.090
 RC4  O3   H6   single    0.850  0.020  0.980
 RC4  C16  H7   single    0.970  0.020  1.090
 RC4  C16  H8   single    0.970  0.020  1.090
 RC4  C16  H9   single    0.970  0.020  1.090
 RC4  C11  H10  single    0.930  0.020  1.080
 RC4  C12  H11  single    0.930  0.020  1.080
 RC4  C14  H12  single    0.930  0.020  1.080
 RC4  N1   H13  single    0.860  0.020  1.020
 RC4  N2   H14  single    0.860  0.020  1.020
 RC4  C15  H15  single    0.970  0.020  1.090
 RC4  C15  H16  single    0.970  0.020  1.090
 RC4  C15  H17  single    0.970  0.020  1.090
 RC4  O2   H18  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
 RC4  H1   C5   C6   121.48  3.000
 RC4  H1   C5   C4   119.51  3.000
 RC4  C6   C5   C4   119.01  3.000
 RC4  H2   C4   C3   119.53  3.000
 RC4  H2   C4   C5   120.01  3.000
 RC4  C3   C4   C5   120.47  3.000
 RC4  N1   C3   C2   122.45  3.000
 RC4  C2   C3   C4   119.69  3.000
 RC4  N1   C3   C4   117.81  3.000
 RC4  H3   C2   C1   120.18  3.000
 RC4  H3   C2   C3   119.62  3.000
 RC4  C1   C2   C3   120.19  3.000
 RC4  B1   C1   C6   107.86  3.000
 RC4  B1   C1   C2   132.93  3.000
 RC4  C6   C1   C2   119.18  3.000
 RC4  C7   C6   C1   110.48  3.000
 RC4  C7   C6   C5   128.07  3.000
 RC4  C1   C6   C5   121.44  3.000
 RC4  H5   C7   H4   105.31  3.000
 RC4  H5   C7   O1   112.10  3.000
 RC4  H4   C7   O1   111.34  3.000
 RC4  H5   C7   C6   110.14  3.000
 RC4  H4   C7   C6   110.82  3.000
 RC4  O1   C7   C6   107.18  3.000
 RC4  O1   B1   O2   110.84  3.000
 RC4  O1   B1   O3   110.41  3.000
 RC4  O2   B1   O3   113.14  3.000
 RC4  O3   B1   C1   111.31  3.000
 RC4  O1   B1   C1   100.73  3.000
 RC4  O2   B1   C1   109.74  3.000
 RC4  H6   O3   B1   111.11  3.000
 RC4  H9   C16  H8   108.96  3.000
 RC4  H9   C16  H7   108.78  3.000
 RC4  H8   C16  H7   108.76  3.000
 RC4  H9   C16  O5   106.50  3.000
 RC4  H8   C16  O5   111.80  3.000
 RC4  H7   C16  O5   111.95  3.000
 RC4  H10  C11  C12  118.87  3.000
 RC4  H10  C11  C10  120.88  3.000
 RC4  C12  C11  C10  120.25  3.000
 RC4  O5   C10  C9   115.91  3.000
 RC4  C9   C10  C11  119.38  3.000
 RC4  O5   C10  C11  124.70  3.000
 RC4  H11  C12  C13  119.97  3.000
 RC4  H11  C12  C11  118.82  3.000
 RC4  C13  C12  C11  121.21  3.000
 RC4  C15  C13  C14  120.50  3.000
 RC4  C15  C13  C12  121.35  3.000
 RC4  C14  C13  C12  118.15  3.000
 RC4  H12  C14  C9   119.07  3.000
 RC4  H12  C14  C13  119.24  3.000
 RC4  C9   C14  C13  121.69  3.000
 RC4  N2   C9   C14  122.41  3.000
 RC4  C14  C9   C10  119.31  3.000
 RC4  N2   C9   C10  118.25  3.000
 RC4  H13  N1   C8   117.62  3.000
 RC4  H13  N1   C3   115.34  3.000
 RC4  C8   N1   C3   125.06  3.000
 RC4  H14  N2   C8   117.95  3.000
 RC4  H14  N2   C9   115.91  3.000
 RC4  C8   N2   C9   124.54  3.000
 RC4  N2   C8   N1   112.80  3.000
 RC4  N1   C8   O4   123.86  3.000
 RC4  N2   C8   O4   123.33  3.000
 RC4  H17  C15  H16  107.90  3.000
 RC4  H17  C15  H15  107.25  3.000
 RC4  H16  C15  H15  107.13  3.000
 RC4  H17  C15  C13  111.50  3.000
 RC4  H16  C15  C13  111.52  3.000
 RC4  H15  C15  C13  111.32  3.000
 RC4  H18  O2   B1   110.91  3.000
 RC4  B1   O1   C7   112.92  3.000
 RC4  C10  O5   C16  118.46  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
 RC4  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 RC4  CONST_02  C2   C1   C6   C5      0.00   0.0  0
 RC4  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 RC4  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 RC4  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 RC4  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 RC4  CONST_07  C14  C9   C10  C11     0.00   0.0  0
 RC4  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 RC4  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 RC4  CONST_10  C13  C14  C9   C10     0.00   0.0  0
 RC4  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 RC4  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 RC4  CONST_13  N1   C3   C4   C5    180.00   0.0  0
 RC4  CONST_14  N1   C3   C2   C1    180.00   0.0  0
 RC4  CONST_15  N2   C9   C10  C11   180.00   0.0  0
 RC4  CONST_16  C15  C13  C12  C11   180.00   0.0  0
 RC4  CONST_17  O5   C10  C11  C12   180.00   0.0  0
 RC4  CONST_18  N2   C9   C14  C13   180.00   0.0  0
 RC4  CONST_19  O5   C10  C9   C14   180.00   0.0  0
 RC4  CONST_20  C15  C13  C14  C9    180.00   0.0  0
 RC4  CONST_21  H3   C2   C3   C4    180.00   0.0  0
 RC4  CONST_22  H1   C5   C4   C3    180.00   0.0  0
 RC4  CONST_23  H2   C4   C3   C2    180.00   0.0  0
 RC4  CONST_24  H11  C12  C11  C10   180.00   0.0  0
 RC4  CONST_25  H12  C14  C9   C10   180.00   0.0  0
 RC4  CONST_26  H10  C11  C12  C13   180.00   0.0  0
 RC4  CONST_33  O4   C8   N1   C3      0.00   0.0  0
 RC4  CONST_34  O4   C8   N2   C9      0.00   0.0  0
 RC4  CONST_35  N2   C8   N1   C3    180.00   0.0  0
 RC4  CONST_36  N1   C8   N2   C9    180.00   0.0  0
 RC4  Var_01    O1   C7   C6   C5   -175.98  30.0  1
 RC4  Var_02    O1   B1   C1   C2    175.90  30.0  1
 RC4  Var_03    C11  C10  O5   C16     4.14  30.0  2
 RC4  Var_04    H15  C15  C13  C12    90.65  30.0  2
 RC4  Var_05    H7   C16  O5   C10   -63.15  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
 RC4  plan-1  C11  0.020
 RC4  plan-1  C10  0.020
 RC4  plan-1  C12  0.020
 RC4  plan-1  C13  0.020
 RC4  plan-1  C14  0.020
 RC4  plan-1  C9   0.020
 RC4  plan-1  N2   0.020
 RC4  plan-1  C15  0.020
 RC4  plan-1  H10  0.020
 RC4  plan-1  H11  0.020
 RC4  plan-1  H12  0.020
 RC4  plan-1  O5   0.020
 RC4  plan-2  C5   0.020
 RC4  plan-2  C4   0.020
 RC4  plan-2  C3   0.020
 RC4  plan-2  C2   0.020
 RC4  plan-2  C1   0.020
 RC4  plan-2  C6   0.020
 RC4  plan-2  C7   0.020
 RC4  plan-2  B1   0.020
 RC4  plan-2  N1   0.020
 RC4  plan-2  H1   0.020
 RC4  plan-2  H2   0.020
 RC4  plan-2  H3   0.020
 RC4  plan-3  C3   0.020
 RC4  plan-3  C9   0.020
 RC4  plan-3  O4   0.020
 RC4  plan-3  N1   0.020
 RC4  plan-3  N2   0.020
 RC4  plan-3  C8   0.020
 RC4  plan-3  H13  0.020
 RC4  plan-3  H14  0.020

