# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:55:23 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1Oc2c(ccc(F)c2C(O)=O)[C@H]3C[C@@H]13
#
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
 RM9  RM9  '(1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid'  ligand  23  16  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RM9
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
 RM9  B12  B  B      0   0.535   2.2260  -1.1951  -0.2006
 RM9  C02  C  C      0   0.378  -1.9104  -1.3845   0.0705
 RM9  C04  C  CR6    0  -0.323  -1.2084  -0.0312  -0.0178
 RM9  C05  C  CR6    0   0.500  -1.9247   1.1466  -0.0800
 RM9  C07  C  CR16   0  -0.420  -1.3335   2.3895  -0.1849
 RM9  C08  C  CR16   0  -0.325   0.0517   2.4490  -0.2135
 RM9  C09  C  CR6    0   0.085   0.8311   1.2991  -0.1391
 RM9  C10  C  CR6    0   0.345   0.1778   0.0674  -0.0540
 RM9  C14  C  CH1    0  -0.476   3.0897   0.0866  -0.1761
 RM9  C15  C  CH2    0  -0.493   3.0508   0.9207   1.0830
 RM9  C16  C  CH1    0  -0.316   2.3096   1.3829  -0.1275
 RM9  F06  F  F      0  -0.320  -3.2709   1.0662  -0.0433
 RM9  O01  O  OC    -1  -0.590  -2.1886  -1.9170  -1.0145
 RM9  O03  O  O      0  -0.591  -2.1294  -1.8027   1.2179
 RM9  O11  O  O2     0  -0.478   0.8632  -1.1095  -0.0215
 RM9  O13  O  OH1    0  -0.598   2.7785  -2.4172  -0.3824
 RM9  H1   H  HCR6   0   0.270  -1.9357   3.2868  -0.2399
 RM9  H2   H  HCR6   0   0.259   0.5405   3.4123  -0.2919
 RM9  H3   H  HCH1   0   0.271   4.0286   0.0976  -0.7183
 RM9  H4   H  HCH2   0   0.257   2.4802   0.5667   1.9335
 RM9  H5   H  HCH2   0   0.269   3.9563   1.4508   1.3480
 RM9  H6   H  HCH1   0   0.272   2.7271   2.2345  -0.6525
 RM9  H8   H  HOH1   0   0.492   2.1476  -3.1457  -0.3959

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
 RM9  C07  C08  aromatic  1.387  0.020  1.387
 RM9  C07  C05  aromatic  1.380  0.020  1.380
 RM9  C08  C09  aromatic  1.391  0.020  1.391
 RM9  F06  C05  single    1.349  0.020  1.349
 RM9  C05  C04  aromatic  1.380  0.020  1.380
 RM9  C09  C16  single    1.481  0.020  1.481
 RM9  C09  C10  aromatic  1.397  0.020  1.397
 RM9  C16  C14  single    1.514  0.020  1.514
 RM9  C16  C15  single    1.493  0.020  1.493
 RM9  C04  C10  aromatic  1.390  0.020  1.390
 RM9  C04  C02  single    1.527  0.020  1.527
 RM9  C10  O11  single    1.362  0.020  1.362
 RM9  C14  C15  single    1.511  0.020  1.511
 RM9  C14  B12  single    1.546  0.020  1.546
 RM9  O13  B12  single    1.353  0.020  1.353
 RM9  O03  C02  deloc     1.241  0.020  1.241
 RM9  B12  O11  single    1.377  0.020  1.377
 RM9  C02  O01  deloc     1.240  0.020  1.240
 RM9  C07  H1   single    0.930  0.020  1.080
 RM9  C08  H2   single    0.930  0.020  1.080
 RM9  C14  H3   single    0.970  0.020  1.090
 RM9  C15  H4   single    0.970  0.020  1.090
 RM9  C15  H5   single    0.970  0.020  1.090
 RM9  C16  H6   single    0.970  0.020  1.090
 RM9  O13  H8   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
 RM9  O13  B12  O11  118.53  3.000
 RM9  O11  B12  C14  119.95  3.000
 RM9  O13  B12  C14  121.52  3.000
 RM9  O03  C02  O01  128.67  3.000
 RM9  O01  C02  C04  115.65  3.000
 RM9  O03  C02  C04  115.68  3.000
 RM9  C10  C04  C05  117.12  3.000
 RM9  C10  C04  C02  121.52  3.000
 RM9  C05  C04  C02  121.36  3.000
 RM9  F06  C05  C07  118.89  3.000
 RM9  F06  C05  C04  117.76  3.000
 RM9  C07  C05  C04  123.34  3.000
 RM9  H1   C07  C08  121.28  3.000
 RM9  H1   C07  C05  120.81  3.000
 RM9  C08  C07  C05  117.90  3.000
 RM9  H2   C08  C09  119.09  3.000
 RM9  H2   C08  C07  119.37  3.000
 RM9  C09  C08  C07  121.54  3.000
 RM9  C16  C09  C10  121.09  3.000
 RM9  C10  C09  C08  118.04  3.000
 RM9  C16  C09  C08  120.86  3.000
 RM9  O11  C10  C09  121.87  3.000
 RM9  O11  C10  C04  116.09  3.000
 RM9  C09  C10  C04  122.04  3.000
 RM9  H3   C14  C16  116.98  3.000
 RM9  H3   C14  C15  115.69  3.000
 RM9  C16  C14  C15   59.15  3.000
 RM9  H3   C14  B12  118.97  3.000
 RM9  C15  C14  B12  117.17  3.000
 RM9  C16  C14  B12  115.00  3.000
 RM9  H5   C15  H4   114.10  3.000
 RM9  H5   C15  C16  117.54  3.000
 RM9  H4   C15  C16  118.44  3.000
 RM9  H5   C15  C14  116.93  3.000
 RM9  H4   C15  C14  119.17  3.000
 RM9  C16  C15  C14   60.52  3.000
 RM9  H6   C16  C15  116.41  3.000
 RM9  H6   C16  C14  117.31  3.000
 RM9  C15  C16  C14   60.33  3.000
 RM9  H6   C16  C09  115.16  3.000
 RM9  C15  C16  C09  118.98  3.000
 RM9  C14  C16  C09  117.76  3.000
 RM9  C10  O11  B12  123.26  3.000
 RM9  H8   O13  B12  114.66  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
 RM9  CONST_01  C08  C07  C05  C04     0.00   0.0  0
 RM9  CONST_02  C08  C09  C10  C04     0.00   0.0  0
 RM9  CONST_03  C09  C08  C07  C05     0.00   0.0  0
 RM9  CONST_04  C09  C10  C04  C05     0.00   0.0  0
 RM9  CONST_05  C10  C09  C08  C07     0.00   0.0  0
 RM9  CONST_06  C10  C04  C05  C07     0.00   0.0  0
 RM9  CONST_07  C07  C05  C04  C02   180.00   0.0  0
 RM9  CONST_08  C09  C10  C04  C02   180.00   0.0  0
 RM9  CONST_09  O11  C10  C04  C02     0.00   0.0  0
 RM9  CONST_10  F06  C05  C07  C08   180.00   0.0  0
 RM9  CONST_11  F06  C05  C04  C10   180.00   0.0  0
 RM9  CONST_12  H1   C07  C05  C04   180.00   0.0  0
 RM9  CONST_13  H2   C08  C07  C05   180.00   0.0  0
 RM9  Var_01    C09  C16  C14  B12    -1.33  30.0  1
 RM9  Var_02    C09  C10  O11  B12    -6.59  30.0  1
 RM9  Var_03    C14  C16  C09  C08  -174.38  30.0  1
 RM9  Var_04    C14  B12  O11  C10    11.99  30.0  1
 RM9  Var_05    O11  B12  C14  C15    59.07  30.0  1
 RM9  Var_06    O03  C02  C04  C05   -90.91  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
 RM9  chir_01  C14  C16  C15  B12  both
 RM9  chir_02  C16  C09  C14  C15  both

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
 RM9  plan-1  C02  0.020
 RM9  plan-1  C04  0.020
 RM9  plan-1  O01  0.020
 RM9  plan-1  O03  0.020
 RM9  plan-2  C02  0.020
 RM9  plan-2  C04  0.020
 RM9  plan-2  C05  0.020
 RM9  plan-2  C07  0.020
 RM9  plan-2  C08  0.020
 RM9  plan-2  C09  0.020
 RM9  plan-2  C10  0.020
 RM9  plan-2  C16  0.020
 RM9  plan-2  F06  0.020
 RM9  plan-2  O11  0.020
 RM9  plan-2  H1   0.020
 RM9  plan-2  H2   0.020

