# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:57:02 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-[(2-chloro-4-iodophenyl)amino]-N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)CONC(=O)c1ccc(F)c(F)c1Nc2ccc(I)cc2Cl
#
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
 3BM  3BM  2-[(2-chloro-4-iodophenyl)amino]-N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluorobenzamide  ligand  40  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3BM
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
 3BM  C01   C   CR6   0   0.430   0.5578   1.1091   0.6197
 3BM  C02   C   CR16  0  -0.313   0.5711   0.5060  -0.6396
 3BM  C03   C   CR16  0  -0.203   1.0461  -0.7804  -0.8200
 3BM  C04   C   CR6   0  -0.255   1.5508  -1.4829   0.2640
 3BM  C05   C   CR16  0  -0.184   1.5818  -0.9042   1.5230
 3BM  C06   C   CR6   0  -0.124   1.0791   0.3750   1.6891
 3BM  N07   N   NH1   0  -0.783   0.0763   2.3863   0.8068
 3BM  C08   C   CR6   0   0.172  -0.9136   2.9745   0.0393
 3BM  C09   C   CR6   0  -0.100  -2.0604   2.2936  -0.3983
 3BM  C10   C   CR16  0  -0.265  -2.9904   2.9450  -1.2003
 3BM  C11   C   CR16  0  -0.414  -2.8377   4.2775  -1.5512
 3BM  C12   C   CR6   0   0.407  -1.7248   4.9498  -1.0949
 3BM  C13   C   CR6   0   0.352  -0.7700   4.3072  -0.3302
 3BM  C14   C   C     0   0.493  -2.3596   0.9162   0.1051
 3BM  N15   N   NH1   0  -0.347  -2.7006   0.0591  -0.8775
 3BM  O16   O   O     0  -0.437  -2.3489   0.6319   1.2857
 3BM  O17   O   O2    0  -0.380  -2.8927  -1.2503  -0.5760
 3BM  C18   C   CH2   0  -0.156  -4.2790  -1.5542  -0.4345
 3BM  C19   C   CH1   0  -0.054  -4.3847  -3.0435  -0.1563
 3BM  C20   C   CH2   0  -0.166  -5.8269  -3.4026   0.1649
 3BM  O21   O   OH1   0  -0.656  -3.8524  -3.8184  -1.2028
 3BM  O22   O   OH1   0  -0.667  -5.8800  -4.7585   0.5333
 3BM  I23   I   I     0   0.063   2.2810  -3.4341   0.0033
 3BM  CL24  CL  CL    0  -0.106   1.0919   1.0772   3.2711
 3BM  F25   F   F     0  -0.295   0.3161   4.9797   0.0593
 3BM  F26   F   F     0  -0.299  -1.5321   6.2322  -1.4039
 3BM  H02   H   HCR6  0   0.295   0.2186   1.0572  -1.5023
 3BM  H03   H   HCR6  0   0.284   1.0325  -1.2104  -1.8118
 3BM  H05   H   HCR6  0   0.298   1.9743  -1.4352   2.3792
 3BM  HN07  H   HNH1  0   0.404   0.4599   2.9258   1.5669
 3BM  H10   H   HCR6  0   0.285  -3.8773   2.4189  -1.5268
 3BM  H11   H   HCR6  0   0.299  -3.5762   4.7885  -2.1534
 3BM  HN15  H   HNH1  0   0.420  -2.4896   0.2430  -1.8496
 3BM  H18   H   HCH2  0   0.229  -4.7097  -0.9828   0.3934
 3BM  H18A  H   HCH2  0   0.226  -4.8206  -1.2870  -1.3496
 3BM  H19   H   HCH1  0   0.242  -3.7737  -3.2712   0.7238
 3BM  H20   H   HCH2  0   0.203  -6.1816  -2.7472   0.9709
 3BM  H20A  H   HCH2  0   0.199  -6.4574  -3.1949  -0.7120
 3BM  HO21  H   HOH1  0   0.445  -4.4034  -3.7025  -1.9848
 3BM  HO22  H   HOH1  0   0.457  -6.7996  -4.9885   0.6927

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
 3BM  C02  C01   aromatic  1.396  0.020  1.396
 3BM  C01  N07   single    1.378  0.020  1.378
 3BM  C01  C06   aromatic  1.398  0.020  1.398
 3BM  C03  C02   aromatic  1.383  0.020  1.383
 3BM  C02  H02   single    0.930  0.020  1.080
 3BM  C03  C04   aromatic  1.387  0.020  1.387
 3BM  C03  H03   single    0.930  0.020  1.080
 3BM  I23  C04   single    2.100  0.020  2.100
 3BM  C04  C05   aromatic  1.386  0.020  1.386
 3BM  C05  C06   aromatic  1.384  0.020  1.384
 3BM  C05  H05   single    0.930  0.020  1.080
 3BM  C06  CL24  single    1.731  0.020  1.731
 3BM  C08  N07   single    1.384  0.020  1.384
 3BM  N07  HN07  single    0.860  0.020  1.020
 3BM  C13  C08   aromatic  1.390  0.020  1.390
 3BM  C09  C08   aromatic  1.404  0.020  1.404
 3BM  C10  C09   aromatic  1.390  0.020  1.390
 3BM  C09  C14   single    1.497  0.020  1.497
 3BM  C11  C10   aromatic  1.386  0.020  1.386
 3BM  C10  H10   single    0.930  0.020  1.080
 3BM  C11  C12   aromatic  1.378  0.020  1.378
 3BM  C11  H11   single    0.930  0.020  1.080
 3BM  F26  C12   single    1.333  0.020  1.333
 3BM  C12  C13   aromatic  1.382  0.020  1.382
 3BM  C13  F25   single    1.336  0.020  1.336
 3BM  N15  C14   single    1.348  0.020  1.348
 3BM  C14  O16   double    1.214  0.020  1.214
 3BM  N15  O17   single    1.357  0.020  1.357
 3BM  N15  HN15  single    0.890  0.020  1.040
 3BM  O17  C18   single    1.426  0.020  1.426
 3BM  C18  C19   single    1.519  0.020  1.519
 3BM  C18  H18   single    0.970  0.020  1.090
 3BM  C18  H18A  single    0.970  0.020  1.090
 3BM  C19  C20   single    1.520  0.020  1.520
 3BM  C19  O21   single    1.407  0.020  1.407
 3BM  C19  H19   single    0.970  0.020  1.090
 3BM  C20  O22   single    1.406  0.020  1.406
 3BM  C20  H20   single    0.970  0.020  1.090
 3BM  C20  H20A  single    0.970  0.020  1.090
 3BM  O21  HO21  single    0.850  0.020  0.980
 3BM  O22  HO22  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
 3BM  N07   C01  C06  120.88  3.000
 3BM  C06   C01  C02  117.36  3.000
 3BM  N07   C01  C02  121.75  3.000
 3BM  H02   C02  C03  118.78  3.000
 3BM  H02   C02  C01  119.71  3.000
 3BM  C03   C02  C01  121.50  3.000
 3BM  H03   C03  C04  121.35  3.000
 3BM  H03   C03  C02  119.02  3.000
 3BM  C04   C03  C02  119.62  3.000
 3BM  I23   C04  C05  119.54  3.000
 3BM  C05   C04  C03  120.44  3.000
 3BM  I23   C04  C03  120.02  3.000
 3BM  H05   C05  C06  119.38  3.000
 3BM  H05   C05  C04  121.49  3.000
 3BM  C06   C05  C04  119.12  3.000
 3BM  CL24  C06  C05  118.80  3.000
 3BM  CL24  C06  C01  119.27  3.000
 3BM  C05   C06  C01  121.92  3.000
 3BM  HN07  N07  C08  117.57  3.000
 3BM  HN07  N07  C01  117.75  3.000
 3BM  C08   N07  C01  124.67  3.000
 3BM  C13   C08  C09  117.80  3.000
 3BM  C09   C08  N07  123.44  3.000
 3BM  C13   C08  N07  118.75  3.000
 3BM  C14   C09  C10  119.44  3.000
 3BM  C14   C09  C08  120.32  3.000
 3BM  C10   C09  C08  119.94  3.000
 3BM  H10   C10  C11  118.77  3.000
 3BM  H10   C10  C09  119.66  3.000
 3BM  C11   C10  C09  121.52  3.000
 3BM  H11   C11  C12  120.36  3.000
 3BM  H11   C11  C10  121.34  3.000
 3BM  C12   C11  C10  118.30  3.000
 3BM  F26   C12  C13  118.41  3.000
 3BM  C13   C12  C11  120.96  3.000
 3BM  F26   C12  C11  120.62  3.000
 3BM  F25   C13  C12  119.29  3.000
 3BM  F25   C13  C08  119.28  3.000
 3BM  C12   C13  C08  121.43  3.000
 3BM  O16   C14  N15  124.20  3.000
 3BM  O16   C14  C09  122.73  3.000
 3BM  N15   C14  C09  112.99  3.000
 3BM  HN15  N15  O17  114.73  3.000
 3BM  HN15  N15  C14  122.15  3.000
 3BM  O17   N15  C14  119.17  3.000
 3BM  C18   O17  N15  111.41  3.000
 3BM  H18A  C18  H18  108.05  3.000
 3BM  H18A  C18  C19  110.94  3.000
 3BM  H18   C18  C19  110.24  3.000
 3BM  H18A  C18  O17  110.21  3.000
 3BM  H18   C18  O17  110.27  3.000
 3BM  C19   C18  O17  107.14  3.000
 3BM  H19   C19  O21  105.79  3.000
 3BM  H19   C19  C20  108.08  3.000
 3BM  O21   C19  C20  112.71  3.000
 3BM  H19   C19  C18  108.19  3.000
 3BM  O21   C19  C18  112.18  3.000
 3BM  C20   C19  C18  109.65  3.000
 3BM  H20A  C20  H20  106.70  3.000
 3BM  H20A  C20  O22  111.67  3.000
 3BM  H20   C20  O22  111.78  3.000
 3BM  H20A  C20  C19  109.32  3.000
 3BM  H20   C20  C19  108.70  3.000
 3BM  O22   C20  C19  108.60  3.000
 3BM  HO21  O21  C19  108.73  3.000
 3BM  HO22  O22  C20  108.08  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
 3BM  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 3BM  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 3BM  CONST_03  C05   C06  C01  C02     0.00   0.0  0
 3BM  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 3BM  CONST_05  C06   C01  C02  C03     0.00   0.0  0
 3BM  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 3BM  CONST_07  C11   C12  C13  C08     0.00   0.0  0
 3BM  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 3BM  CONST_09  C12   C13  C08  C09     0.00   0.0  0
 3BM  CONST_10  C12   C11  C10  C09     0.00   0.0  0
 3BM  CONST_11  C13   C08  C09  C10     0.00   0.0  0
 3BM  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 3BM  CONST_13  CL24  C06  C01  C02   180.00   0.0  0
 3BM  CONST_14  I23   C04  C03  C02   180.00   0.0  0
 3BM  CONST_15  N07   C01  C02  C03   180.00   0.0  0
 3BM  CONST_16  CL24  C06  C05  C04   180.00   0.0  0
 3BM  CONST_17  N07   C01  C06  C05   180.00   0.0  0
 3BM  CONST_18  I23   C04  C05  C06   180.00   0.0  0
 3BM  CONST_19  C12   C13  C08  N07   180.00   0.0  0
 3BM  CONST_20  C10   C09  C08  N07   180.00   0.0  0
 3BM  CONST_21  F26   C12  C13  C08   180.00   0.0  0
 3BM  CONST_22  F25   C13  C08  C09   180.00   0.0  0
 3BM  CONST_23  F26   C12  C11  C10   180.00   0.0  0
 3BM  CONST_24  C14   C09  C10  C11   180.00   0.0  0
 3BM  CONST_25  F25   C13  C12  C11   180.00   0.0  0
 3BM  CONST_26  C14   C09  C08  C13   180.00   0.0  0
 3BM  CONST_27  H03   C03  C02  C01   180.00   0.0  0
 3BM  CONST_28  H05   C05  C06  C01   180.00   0.0  0
 3BM  CONST_29  H02   C02  C03  C04   180.00   0.0  0
 3BM  CONST_30  H10   C10  C09  C08   180.00   0.0  0
 3BM  CONST_31  H11   C11  C10  C09   180.00   0.0  0
 3BM  CONST_32  O17   N15  C14  C09   180.00   0.0  0
 3BM  CONST_34  O17   N15  C14  O16     0.00   0.0  0
 3BM  Var_01    C13   C08  N07  C01  -138.82  30.0  2
 3BM  Var_02    C08   N07  C01  C02    29.44  30.0  2
 3BM  Var_03    N15   C14  C09  C08  -133.33  30.0  2
 3BM  Var_04    C19   C18  O17  N15   177.74  30.0  3

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
 3BM  chir_01  C19  C18  C20  O21  negativ

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
 3BM  plan-1  C01   0.020
 3BM  plan-1  C02   0.020
 3BM  plan-1  C03   0.020
 3BM  plan-1  C04   0.020
 3BM  plan-1  C05   0.020
 3BM  plan-1  C06   0.020
 3BM  plan-1  N07   0.020
 3BM  plan-1  I23   0.020
 3BM  plan-1  CL24  0.020
 3BM  plan-1  H02   0.020
 3BM  plan-1  H03   0.020
 3BM  plan-1  H05   0.020
 3BM  plan-2  N07   0.020
 3BM  plan-2  C08   0.020
 3BM  plan-2  C09   0.020
 3BM  plan-2  C10   0.020
 3BM  plan-2  C11   0.020
 3BM  plan-2  C12   0.020
 3BM  plan-2  C13   0.020
 3BM  plan-2  C14   0.020
 3BM  plan-2  F25   0.020
 3BM  plan-2  F26   0.020
 3BM  plan-2  H10   0.020
 3BM  plan-2  H11   0.020
 3BM  plan-3  C09   0.020
 3BM  plan-3  C14   0.020
 3BM  plan-3  N15   0.020
 3BM  plan-3  O16   0.020
 3BM  plan-3  O17   0.020
 3BM  plan-3  HN15  0.020

