# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:10:30 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-{[(3R)-3,4-dihydroxybutyl]oxy}-4-fluoro-6-[(2-fluoro-4-iodophenyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1c(Nc2ccc(I)cc2F)cc(F)cc1OCC[C@@H](O)CO
#
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
 M3K  M3K  2-{[(3R)-3,4-dihydroxybutyl]oxy}-4-fluoro-6-[(2-fluoro-4-iodophenyl)amino]benzamide  ligand  43  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M3K
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
 M3K  C01   C  CR6   0   0.190    1.6549   0.8713   0.0071
 M3K  C02   C  CR16  0  -0.297    2.1283  -0.1587   0.8200
 M3K  C03   C  CR16  0  -0.231    3.4865  -0.3710   1.0015
 M3K  C04   C  CR6   0  -0.232    4.4013   0.4708   0.3883
 M3K  C05   C  CR16  0  -0.368    3.9690   1.5232  -0.4065
 M3K  C06   C  CR6   0   0.479    2.6138   1.6939  -0.5849
 M3K  N07   N  NH1   0  -0.805    0.3152   1.1496  -0.1941
 M3K  C08   C  CR6   0   0.412   -0.7219   0.2513  -0.2463
 M3K  C09   C  CR6   0  -0.286   -2.0468   0.6927  -0.0172
 M3K  C10   C  CR6   0   0.435   -3.0986  -0.2372  -0.1464
 M3K  C11   C  CR16  0  -0.584   -2.8528  -1.5738  -0.4388
 M3K  C12   C  CR6   0   0.590   -1.5388  -1.9544  -0.6241
 M3K  C13   C  CR16  0  -0.534   -0.4744  -1.0932  -0.5456
 M3K  C14   C  C     0   0.521   -2.2860   2.1315   0.3090
 M3K  N15   N  NH2   0  -0.785   -3.2286   2.4257   1.2083
 M3K  O16   O  O     0  -0.509   -1.5889   3.0154  -0.1950
 M3K  C18   C  CH2   0  -0.498   -6.7024   0.1942   0.1381
 M3K  C19   C  CH1   0  -0.010   -7.9780  -0.6327   0.0029
 M3K  C20   C  CH2   0  -0.154   -9.1960   0.2643   0.1499
 M3K  O21   O  OH1   0  -0.662   -8.0052  -1.7208   0.9019
 M3K  O22   O  OH1   0  -0.670  -10.3605  -0.4929  -0.0725
 M3K  I23   I  I     0   0.067    6.4593   0.1656   0.6658
 M3K  C15   C  CH2   0  -0.170   -5.4581  -0.6386  -0.0874
 M3K  F24   F  F     0  -0.306    2.1872   2.7053  -1.3563
 M3K  F26   F  F     0  -0.311   -1.2952  -3.2363  -0.9220
 M3K  O1    O  O2    0  -0.480   -4.3397   0.2367   0.0150
 M3K  H02   H  HCR6  0   0.299    1.4292  -0.8047   1.3333
 M3K  H07   H  HNH1  0   0.414    0.0377   2.1168  -0.3159
 M3K  H03   H  HCR6  0   0.285    3.8094  -1.1855   1.6349
 M3K  H05   H  HCR6  0   0.302    4.6570   2.1991  -0.8968
 M3K  H13   H  HCR6  0   0.300    0.5229  -1.4495  -0.7592
 M3K  H11   H  HCR6  0   0.304   -3.6409  -2.3059  -0.5343
 M3K  H151  H  HNH2  0   0.411   -3.8539   1.7350   1.5829
 M3K  H152  H  HNH2  0   0.405   -3.4317   3.3922   1.4064
 M3K  H181  H  HCH2  0   0.247   -6.7261   1.0063  -0.5933
 M3K  H182  H  HCH2  0   0.240   -6.6653   0.6584   1.1299
 M3K  H19   H  HCH1  0   0.231   -8.0005  -1.0820  -0.9962
 M3K  HA1   H  HCH2  0   0.236   -5.3776  -1.4388   0.6531
 M3K  HB2   H  HCH2  0   0.233   -5.4829  -1.0981  -1.0814
 M3K  H201  H  HCH2  0   0.192   -9.1890   0.7150   1.1540
 M3K  H202  H  HCH2  0   0.199   -9.1070   1.0911  -0.5666
 M3K  H21   H  HOH1  0   0.443   -7.9914  -1.3730   1.8009
 M3K  H22   H  HOH1  0   0.456  -11.1185   0.0861   0.0458

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
 M3K  C01  C02   aromatic  1.395  0.020  1.395
 M3K  C01  C06   aromatic  1.395  0.020  1.395
 M3K  C01  N07   single    1.383  0.020  1.383
 M3K  C02  C03   aromatic  1.387  0.020  1.387
 M3K  C03  C04   aromatic  1.386  0.020  1.386
 M3K  C04  C05   aromatic  1.388  0.020  1.388
 M3K  C04  I23   single    2.099  0.020  2.099
 M3K  C05  C06   aromatic  1.378  0.020  1.378
 M3K  C06  F24   single    1.342  0.020  1.342
 M3K  N07  C08   single    1.373  0.020  1.373
 M3K  C08  C09   aromatic  1.415  0.020  1.415
 M3K  C08  C13   aromatic  1.399  0.020  1.399
 M3K  C09  C10   aromatic  1.410  0.020  1.410
 M3K  C09  C14   single    1.495  0.020  1.495
 M3K  C10  C11   aromatic  1.390  0.020  1.390
 M3K  C10  O1    single    1.338  0.020  1.338
 M3K  C11  C12   aromatic  1.380  0.020  1.380
 M3K  C12  C13   aromatic  1.371  0.020  1.371
 M3K  C12  F26   single    1.338  0.020  1.338
 M3K  C14  N15   single    1.336  0.020  1.336
 M3K  C14  O16   double    1.233  0.020  1.233
 M3K  C18  C19   single    1.526  0.020  1.526
 M3K  C18  C15   single    1.514  0.020  1.514
 M3K  C19  C20   single    1.520  0.020  1.520
 M3K  C19  O21   single    1.412  0.020  1.412
 M3K  C20  O22   single    1.407  0.020  1.407
 M3K  C15  O1    single    1.424  0.020  1.424
 M3K  C02  H02   single    0.930  0.020  1.080
 M3K  N07  H07   single    0.860  0.020  1.020
 M3K  C03  H03   single    0.930  0.020  1.080
 M3K  C05  H05   single    0.930  0.020  1.080
 M3K  C13  H13   single    0.930  0.020  1.080
 M3K  C11  H11   single    0.930  0.020  1.080
 M3K  N15  H151  single    0.860  0.020  1.020
 M3K  N15  H152  single    0.860  0.020  1.020
 M3K  C18  H181  single    0.970  0.020  1.090
 M3K  C18  H182  single    0.970  0.020  1.090
 M3K  C19  H19   single    0.970  0.020  1.090
 M3K  C15  HA1   single    0.970  0.020  1.090
 M3K  C15  HB2   single    0.970  0.020  1.090
 M3K  C20  H201  single    0.970  0.020  1.090
 M3K  C20  H202  single    0.970  0.020  1.090
 M3K  O21  H21   single    0.850  0.020  0.980
 M3K  O22  H22   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
 M3K  N07   C01  C06   119.04  3.000
 M3K  N07   C01  C02   124.20  3.000
 M3K  C06   C01  C02   116.70  3.000
 M3K  H02   C02  C03   118.66  3.000
 M3K  H02   C02  C01   119.88  3.000
 M3K  C03   C02  C01   121.45  3.000
 M3K  H03   C03  C04   121.30  3.000
 M3K  H03   C03  C02   118.99  3.000
 M3K  C04   C03  C02   119.70  3.000
 M3K  I23   C04  C05   119.43  3.000
 M3K  I23   C04  C03   120.02  3.000
 M3K  C05   C04  C03   120.55  3.000
 M3K  H05   C05  C06   119.31  3.000
 M3K  H05   C05  C04   122.36  3.000
 M3K  C06   C05  C04   118.33  3.000
 M3K  F24   C06  C05   118.73  3.000
 M3K  F24   C06  C01   118.03  3.000
 M3K  C05   C06  C01   123.24  3.000
 M3K  H07   N07  C08   114.39  3.000
 M3K  H07   N07  C01   118.34  3.000
 M3K  C08   N07  C01   127.27  3.000
 M3K  C13   C08  C09   119.99  3.000
 M3K  C13   C08  N07   120.20  3.000
 M3K  C09   C08  N07   119.80  3.000
 M3K  C14   C09  C10   122.38  3.000
 M3K  C14   C09  C08   119.05  3.000
 M3K  C10   C09  C08   118.54  3.000
 M3K  O1    C10  C11   122.00  3.000
 M3K  O1    C10  C09   116.56  3.000
 M3K  C11   C10  C09   121.44  3.000
 M3K  H11   C11  C12   119.73  3.000
 M3K  H11   C11  C10   122.77  3.000
 M3K  C12   C11  C10   117.49  3.000
 M3K  F26   C12  C13   118.22  3.000
 M3K  F26   C12  C11   117.85  3.000
 M3K  C13   C12  C11   123.91  3.000
 M3K  H13   C13  C12   119.87  3.000
 M3K  H13   C13  C08   121.50  3.000
 M3K  C12   C13  C08   118.57  3.000
 M3K  O16   C14  N15   121.08  3.000
 M3K  O16   C14  C09   120.68  3.000
 M3K  N15   C14  C09   118.17  3.000
 M3K  H152  N15  H151  117.46  3.000
 M3K  H152  N15  C14   119.08  3.000
 M3K  H151  N15  C14   122.62  3.000
 M3K  H182  C18  H181  106.96  3.000
 M3K  H182  C18  C15   109.88  3.000
 M3K  H181  C18  C15   109.07  3.000
 M3K  H182  C18  C19   109.75  3.000
 M3K  H181  C18  C19   108.97  3.000
 M3K  C15   C18  C19   112.07  3.000
 M3K  H19   C19  O21   105.32  3.000
 M3K  H19   C19  C20   108.28  3.000
 M3K  O21   C19  C20   112.20  3.000
 M3K  H19   C19  C18   108.66  3.000
 M3K  O21   C19  C18   112.17  3.000
 M3K  C20   C19  C18   109.97  3.000
 M3K  H202  C20  H201  106.65  3.000
 M3K  H202  C20  O22   111.67  3.000
 M3K  H201  C20  O22   111.71  3.000
 M3K  H202  C20  C19   108.45  3.000
 M3K  H201  C20  C19   108.96  3.000
 M3K  O22   C20  C19   109.30  3.000
 M3K  H21   O21  C19   108.39  3.000
 M3K  H22   O22  C20   108.01  3.000
 M3K  HB2   C15  HA1   108.01  3.000
 M3K  HB2   C15  O1    109.93  3.000
 M3K  HA1   C15  O1    110.08  3.000
 M3K  HB2   C15  C18   110.32  3.000
 M3K  HA1   C15  C18   111.24  3.000
 M3K  O1    C15  C18   107.26  3.000
 M3K  C15   O1   C10   120.14  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
 M3K  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 M3K  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 M3K  CONST_03  C05   C06  C01  C02     0.00   0.0  0
 M3K  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 M3K  CONST_05  C06   C01  C02  C03     0.00   0.0  0
 M3K  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 M3K  CONST_07  C11   C10  C09  C08     0.00   0.0  0
 M3K  CONST_08  C11   C12  C13  C08     0.00   0.0  0
 M3K  CONST_09  C12   C13  C08  C09     0.00   0.0  0
 M3K  CONST_10  C12   C11  C10  C09     0.00   0.0  0
 M3K  CONST_11  C13   C08  C09  C10     0.00   0.0  0
 M3K  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 M3K  CONST_13  F24   C06  C01  C02   180.00   0.0  0
 M3K  CONST_14  I23   C04  C03  C02   180.00   0.0  0
 M3K  CONST_15  N07   C01  C02  C03   180.00   0.0  0
 M3K  CONST_16  F24   C06  C05  C04   180.00   0.0  0
 M3K  CONST_17  N07   C01  C06  C05   180.00   0.0  0
 M3K  CONST_18  I23   C04  C05  C06   180.00   0.0  0
 M3K  CONST_19  C10   C09  C08  N07   180.00   0.0  0
 M3K  CONST_20  C12   C13  C08  N07   180.00   0.0  0
 M3K  CONST_21  O1    C10  C09  C08   180.00   0.0  0
 M3K  CONST_22  F26   C12  C13  C08   180.00   0.0  0
 M3K  CONST_23  F26   C12  C11  C10   180.00   0.0  0
 M3K  CONST_24  C14   C09  C10  C11   180.00   0.0  0
 M3K  CONST_25  O1    C10  C11  C12   180.00   0.0  0
 M3K  CONST_26  C14   C09  C08  C13   180.00   0.0  0
 M3K  CONST_27  H03   C03  C02  C01   180.00   0.0  0
 M3K  CONST_28  H05   C05  C06  C01   180.00   0.0  0
 M3K  CONST_29  H02   C02  C03  C04   180.00   0.0  0
 M3K  CONST_30  H13   C13  C08  C09   180.00   0.0  0
 M3K  CONST_31  H11   C11  C10  C09   180.00   0.0  0
 M3K  CONST_32  H151  N15  C14  C09     0.00   0.0  0
 M3K  CONST_33  H152  N15  C14  C09   180.00   0.0  0
 M3K  Var_01    C09   C08  N07  C01   159.11  30.0  2
 M3K  Var_02    C08   N07  C01  C02   -34.10  30.0  2
 M3K  Var_03    N15   C14  C09  C08  -142.24  30.0  2
 M3K  Var_04    C18   C15  O1   C10  -179.83  30.0  1
 M3K  Var_05    O1    C15  C18  C19   177.99  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
 M3K  chir_01  C19  C18  C20  O21  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
 M3K  plan-1  C01   0.020
 M3K  plan-1  C02   0.020
 M3K  plan-1  C03   0.020
 M3K  plan-1  C04   0.020
 M3K  plan-1  C05   0.020
 M3K  plan-1  C06   0.020
 M3K  plan-1  N07   0.020
 M3K  plan-1  I23   0.020
 M3K  plan-1  F24   0.020
 M3K  plan-1  H02   0.020
 M3K  plan-1  H03   0.020
 M3K  plan-1  H05   0.020
 M3K  plan-2  N07   0.020
 M3K  plan-2  C08   0.020
 M3K  plan-2  C09   0.020
 M3K  plan-2  C10   0.020
 M3K  plan-2  C11   0.020
 M3K  plan-2  C12   0.020
 M3K  plan-2  C13   0.020
 M3K  plan-2  C14   0.020
 M3K  plan-2  F26   0.020
 M3K  plan-2  O1    0.020
 M3K  plan-2  H13   0.020
 M3K  plan-2  H11   0.020
 M3K  plan-3  C09   0.020
 M3K  plan-3  C14   0.020
 M3K  plan-3  N15   0.020
 M3K  plan-3  O16   0.020
 M3K  plan-3  H151  0.020
 M3K  plan-3  H152  0.020

