# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:18:40 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(3-oxo-1,2-oxazinan-2-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCONC(=O)c1cc(CN2OCCCC2=O)c(F)c(F)c1Nc3ccc(I)cc3F
#
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
 3OR  3OR  3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(3-oxo-1,2-oxazinan-2-yl)methyl]benzamide  ligand  51  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3OR
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
 3OR  C4    C  CR6   0  -0.073   1.2528   0.7835   0.0266
 3OR  C5    C  CR16  0  -0.318   2.3709   0.7646   0.8488
 3OR  C6    C  CR6   0  -0.085   3.1023  -0.3968   1.0627
 3OR  C7    C  CH2   0  -0.377   4.3201  -0.3988   1.9490
 3OR  C13   C  CR16  0  -0.282  -1.8392  -0.8196   0.3534
 3OR  C15   C  CR6   0  -0.239  -4.1446  -1.2635  -0.1449
 3OR  C17   C  CR16  0  -0.371  -3.8762  -1.1620  -1.5037
 3OR  C20   C  C     0   0.550   6.0406   0.4527   0.4282
 3OR  C22   C  CH2   0  -0.571   7.2488   0.1512  -0.4268
 3OR  C24   C  CH2   0  -0.202   6.8171  -2.2026   0.1985
 3OR  C26   C  C     0   0.494   0.4899   2.0561  -0.1667
 3OR  C1    C  CR6   0   0.047   0.8360  -0.3837  -0.6156
 3OR  N2    N  NH1   0  -0.745  -0.2719  -0.4003  -1.4798
 3OR  C3    C  CR6   0   0.200  -1.5333  -0.7051  -1.0010
 3OR  N8    N  NT    0  -0.192   5.5466  -0.5385   1.1961
 3OR  C9    C  CR6   0   0.413   2.6869  -1.5436   0.4136
 3OR  F10   F  F     0  -0.291   3.3525  -2.6873   0.5749
 3OR  C11   C  CR6   0   0.440   1.5703  -1.5403  -0.4035
 3OR  F12   F  F     0  -0.287   1.2014  -2.6734  -0.9984
 3OR  C14   C  CR16  0  -0.239  -3.1299  -1.0939   0.7825
 3OR  C18   C  CR6   0   0.483  -2.5874  -0.8834  -1.8972
 3OR  F19   F  F     0  -0.313  -2.3179  -0.7802  -3.2113
 3OR  O21   O  O     0  -0.496   5.4667   1.5331   0.3791
 3OR  C23   C  CH2   0  -0.464   7.8869  -1.2166  -0.2065
 3OR  O25   O  O2    0  -0.388   6.2010  -1.7371   1.3930
 3OR  O27   O  O     0  -0.439  -0.7029   2.1605   0.0324
 3OR  N28   N  NH1   0  -0.351   1.2910   3.0731  -0.5395
 3OR  O29   O  O2    0  -0.382   0.7562   4.2908  -0.8059
 3OR  C30   C  CH2   0  -0.170   0.9036   5.1731   0.3099
 3OR  C31   C  CH2   0  -0.193   0.3971   6.5325  -0.0914
 3OR  O32   O  OH1   0  -0.669  -0.9917   6.4745  -0.3121
 3OR  H5    H  HCR6  0   0.279   2.6874   1.6699   1.3500
 3OR  H7    H  HCH2  0   0.289   4.3422   0.5271   2.5236
 3OR  H7A   H  HCH2  0   0.301   4.2804  -1.2149   2.6688
 3OR  H13   H  HCR6  0   0.280  -1.0628  -0.6967   1.0960
 3OR  H17   H  HCR6  0   0.298  -4.6427  -1.2885  -2.2567
 3OR  H22   H  HCH2  0   0.281   6.8966   0.2422  -1.4580
 3OR  H22A  H  HCH2  0   0.286   7.9696   0.9574  -0.2831
 3OR  H24   H  HCH2  0   0.230   6.0675  -2.3352  -0.5901
 3OR  H24A  H  HCH2  0   0.264   7.2295  -3.1774   0.4552
 3OR  HN2   H  HNH1  0   0.403  -0.0718  -0.7193  -2.4163
 3OR  H14   H  HCR6  0   0.281  -3.3211  -1.1738   1.8436
 3OR  H23   H  HCH2  0   0.256   8.3893  -1.5512  -1.1145
 3OR  H23A  H  HCH2  0   0.248   8.6418  -1.1670   0.5804
 3OR  HN28  H  HNH1  0   0.420   2.2305   2.9286  -0.8857
 3OR  H30   H  HCH2  0   0.229   0.3507   4.7907   1.1737
 3OR  H30A  H  HCH2  0   0.231   1.9584   5.2586   0.5874
 3OR  H31   H  HCH2  0   0.214   0.6582   7.2198   0.7230
 3OR  H31A  H  HCH2  0   0.210   0.9425   6.8750  -0.9804
 3OR  HO32  H  HOH1  0   0.457  -1.2915   7.3546  -0.5563
 3OR  I16   I  I     0   0.054  -6.1010  -1.6799   0.4944

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
 3OR  C26  C4    single    1.496  0.020  1.496
 3OR  C4   C1    aromatic  1.396  0.020  1.396
 3OR  C4   C5    aromatic  1.388  0.020  1.388
 3OR  C5   C6    aromatic  1.389  0.020  1.389
 3OR  C5   H5    single    0.930  0.020  1.080
 3OR  C6   C9    aromatic  1.382  0.020  1.382
 3OR  C6   C7    single    1.506  0.020  1.506
 3OR  C7   N8    single    1.446  0.020  1.446
 3OR  C7   H7    single    0.970  0.020  1.090
 3OR  C7   H7A   single    0.970  0.020  1.090
 3OR  C3   C13   aromatic  1.393  0.020  1.393
 3OR  C13  C14   aromatic  1.387  0.020  1.387
 3OR  C13  H13   single    0.930  0.020  1.080
 3OR  C17  C15   aromatic  1.389  0.020  1.389
 3OR  C15  I16   single    2.100  0.020  2.100
 3OR  C15  C14   aromatic  1.385  0.020  1.385
 3OR  C18  C17   aromatic  1.376  0.020  1.376
 3OR  C17  H17   single    0.930  0.020  1.080
 3OR  O21  C20   double    1.224  0.020  1.224
 3OR  C20  N8    single    1.348  0.020  1.348
 3OR  C20  C22   single    1.511  0.020  1.511
 3OR  C22  C23   single    1.525  0.020  1.525
 3OR  C22  H22   single    0.970  0.020  1.090
 3OR  C22  H22A  single    0.970  0.020  1.090
 3OR  O25  C24   single    1.422  0.020  1.422
 3OR  C24  C23   single    1.510  0.020  1.510
 3OR  C24  H24   single    0.970  0.020  1.090
 3OR  C24  H24A  single    0.970  0.020  1.090
 3OR  O27  C26   double    1.214  0.020  1.214
 3OR  C26  N28   single    1.347  0.020  1.347
 3OR  N2   C1    single    1.405  0.020  1.405
 3OR  C1   C11   aromatic  1.386  0.020  1.386
 3OR  N2   C3    single    1.383  0.020  1.383
 3OR  N2   HN2   single    0.890  0.020  1.040
 3OR  C18  C3    aromatic  1.395  0.020  1.395
 3OR  N8   O25   single    1.380  0.020  1.380
 3OR  C11  C9    aromatic  1.384  0.020  1.384
 3OR  C9   F10   single    1.333  0.020  1.333
 3OR  C11  F12   single    1.332  0.020  1.332
 3OR  C14  H14   single    0.930  0.020  1.080
 3OR  F19  C18   single    1.345  0.020  1.345
 3OR  C23  H23   single    0.970  0.020  1.090
 3OR  C23  H23A  single    0.970  0.020  1.090
 3OR  O29  N28   single    1.356  0.020  1.356
 3OR  N28  HN28  single    0.860  0.020  1.020
 3OR  C30  O29   single    1.430  0.020  1.430
 3OR  C31  C30   single    1.505  0.020  1.505
 3OR  C30  H30   single    0.970  0.020  1.090
 3OR  C30  H30A  single    0.970  0.020  1.090
 3OR  O32  C31   single    1.407  0.020  1.407
 3OR  C31  H31   single    0.970  0.020  1.090
 3OR  C31  H31A  single    0.970  0.020  1.090
 3OR  O32  HO32  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
 3OR  C1    C4   C26  119.97  3.000
 3OR  C1    C4   C5   120.11  3.000
 3OR  C26   C4   C5   119.92  3.000
 3OR  H5    C5   C6   118.30  3.000
 3OR  H5    C5   C4   119.91  3.000
 3OR  C6    C5   C4   121.79  3.000
 3OR  C9    C6   C7   121.23  3.000
 3OR  C7    C6   C5   121.17  3.000
 3OR  C9    C6   C5   117.60  3.000
 3OR  H7A   C7   H7   106.80  3.000
 3OR  H7A   C7   N8   107.62  3.000
 3OR  H7    C7   N8   109.84  3.000
 3OR  H7A   C7   C6   111.13  3.000
 3OR  H7    C7   C6   108.99  3.000
 3OR  N8    C7   C6   112.31  3.000
 3OR  H13   C13  C14  118.55  3.000
 3OR  H13   C13  C3   120.04  3.000
 3OR  C14   C13  C3   121.41  3.000
 3OR  I16   C15  C14  120.20  3.000
 3OR  C14   C15  C17  120.30  3.000
 3OR  I16   C15  C17  119.50  3.000
 3OR  H17   C17  C18  119.22  3.000
 3OR  H17   C17  C15  122.38  3.000
 3OR  C18   C17  C15  118.40  3.000
 3OR  O21   C20  N8   120.00  3.000
 3OR  N8    C20  C22  117.96  3.000
 3OR  O21   C20  C22  121.89  3.000
 3OR  H22A  C22  H22  105.99  3.000
 3OR  H22A  C22  C23  111.55  3.000
 3OR  H22   C22  C23  110.21  3.000
 3OR  H22A  C22  C20  107.84  3.000
 3OR  H22   C22  C20  105.05  3.000
 3OR  C23   C22  C20  115.59  3.000
 3OR  H24A  C24  H24  108.67  3.000
 3OR  H24A  C24  O25  105.01  3.000
 3OR  H24   C24  O25  110.34  3.000
 3OR  H24A  C24  C23  112.29  3.000
 3OR  H24   C24  C23  111.74  3.000
 3OR  O25   C24  C23  108.57  3.000
 3OR  N28   C26  O27  124.38  3.000
 3OR  N28   C26  C4   112.00  3.000
 3OR  O27   C26  C4   123.58  3.000
 3OR  C11   C1   N2   120.12  3.000
 3OR  C11   C1   C4   117.98  3.000
 3OR  N2    C1   C4   121.88  3.000
 3OR  HN2   N2   C3   115.61  3.000
 3OR  HN2   N2   C1   114.71  3.000
 3OR  C3    N2   C1   120.58  3.000
 3OR  C18   C3   N2   119.66  3.000
 3OR  C18   C3   C13  116.63  3.000
 3OR  N2    C3   C13  123.70  3.000
 3OR  O25   N8   C20  123.12  3.000
 3OR  O25   N8   C7   114.33  3.000
 3OR  C20   N8   C7   122.45  3.000
 3OR  C11   C9   F10  118.46  3.000
 3OR  F10   C9   C6   120.34  3.000
 3OR  C11   C9   C6   121.20  3.000
 3OR  F12   C11  C9   119.03  3.000
 3OR  F12   C11  C1   119.66  3.000
 3OR  C9    C11  C1   121.32  3.000
 3OR  H14   C14  C15  121.23  3.000
 3OR  H14   C14  C13  118.86  3.000
 3OR  C15   C14  C13  119.91  3.000
 3OR  F19   C18  C3   117.80  3.000
 3OR  F19   C18  C17  118.84  3.000
 3OR  C3    C18  C17  123.36  3.000
 3OR  H23A  C23  H23  107.19  3.000
 3OR  H23A  C23  C24  109.04  3.000
 3OR  H23   C23  C24  110.45  3.000
 3OR  H23A  C23  C22  110.65  3.000
 3OR  H23   C23  C22  110.35  3.000
 3OR  C24   C23  C22  109.14  3.000
 3OR  N8    O25  C24  111.71  3.000
 3OR  HN28  N28  O29  115.29  3.000
 3OR  HN28  N28  C26  122.62  3.000
 3OR  O29   N28  C26  119.85  3.000
 3OR  C30   O29  N28  111.10  3.000
 3OR  H30A  C30  H30  108.31  3.000
 3OR  H30A  C30  C31  108.75  3.000
 3OR  H30   C30  C31  110.85  3.000
 3OR  H30A  C30  O29  110.21  3.000
 3OR  H30   C30  O29  110.38  3.000
 3OR  C31   C30  O29  108.33  3.000
 3OR  H31A  C31  H31  106.70  3.000
 3OR  H31A  C31  O32  112.10  3.000
 3OR  H31   C31  O32  112.15  3.000
 3OR  H31A  C31  C30  109.30  3.000
 3OR  H31   C31  C30  106.72  3.000
 3OR  O32   C31  C30  109.67  3.000
 3OR  HO32  O32  C31  108.05  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
 3OR  CONST_01  C9   C11  C1   C4      0.00   0.0  0
 3OR  CONST_02  C9   C6   C5   C4      0.00   0.0  0
 3OR  CONST_03  C11  C1   C4   C5      0.00   0.0  0
 3OR  CONST_04  C11  C9   C6   C5      0.00   0.0  0
 3OR  CONST_05  C1   C4   C5   C6      0.00   0.0  0
 3OR  CONST_06  C1   C11  C9   C6      0.00   0.0  0
 3OR  CONST_07  C17  C18  C3   C13     0.00   0.0  0
 3OR  CONST_08  C17  C15  C14  C13     0.00   0.0  0
 3OR  CONST_09  C3   C18  C17  C15     0.00   0.0  0
 3OR  CONST_10  C3   C13  C14  C15     0.00   0.0  0
 3OR  CONST_11  C18  C3   C13  C14     0.00   0.0  0
 3OR  CONST_12  C18  C17  C15  C14     0.00   0.0  0
 3OR  CONST_13  O25  N8   C20  C22     0.00   0.0  0
 3OR  CONST_14  F12  C11  C1   C4    180.00   0.0  0
 3OR  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 3OR  CONST_16  N2   C1   C4   C5    180.00   0.0  0
 3OR  CONST_17  F10  C9   C6   C5    180.00   0.0  0
 3OR  CONST_18  C26  C4   C5   C6    180.00   0.0  0
 3OR  CONST_19  F12  C11  C9   C6    180.00   0.0  0
 3OR  CONST_20  C11  C9   C6   C7    180.00   0.0  0
 3OR  CONST_21  F19  C18  C3   C13   180.00   0.0  0
 3OR  CONST_22  I16  C15  C14  C13   180.00   0.0  0
 3OR  CONST_23  F19  C18  C17  C15   180.00   0.0  0
 3OR  CONST_24  N2   C3   C18  C17   180.00   0.0  0
 3OR  CONST_25  C11  C1   C4   C26   180.00   0.0  0
 3OR  CONST_26  F10  C9   C11  C1    180.00   0.0  0
 3OR  CONST_27  C9   C11  C1   N2    180.00   0.0  0
 3OR  CONST_28  C14  C13  C3   N2    180.00   0.0  0
 3OR  CONST_29  C18  C17  C15  I16   180.00   0.0  0
 3OR  CONST_30  C22  C20  N8   C7    180.00   0.0  0
 3OR  CONST_31  O25  N8   C20  O21   180.00   0.0  0
 3OR  CONST_32  H13  C13  C14  C15   180.00   0.0  0
 3OR  CONST_33  H14  C14  C15  C17   180.00   0.0  0
 3OR  CONST_34  H5   C5   C4   C1    180.00   0.0  0
 3OR  CONST_35  H17  C17  C18  C3    180.00   0.0  0
 3OR  CONST_36  O21  C20  N8   C7      0.00   0.0  0
 3OR  CONST_37  O29  N28  C26  C4    180.00   0.0  0
 3OR  CONST_39  O29  N28  C26  O27     0.00   0.0  0
 3OR  Var_01    C24  C23  C22  C20    31.09  30.0  1
 3OR  Var_02    O25  C24  C23  C22   -59.26  30.0  1
 3OR  Var_03    C23  C22  C20  N8     -6.82  30.0  1
 3OR  Var_04    C23  C24  O25  N8     63.92  30.0  1
 3OR  Var_05    C3   N2   C1   C4    -92.24  30.0  2
 3OR  Var_06    N8   C7   C6   C5   -108.47  30.0  2
 3OR  Var_07    C20  N8   C7   C6     71.82  30.0  3
 3OR  Var_08    C1   N2   C3   C13     9.69  30.0  2
 3OR  Var_09    O27  C26  C4   C5   -125.54  30.0  2
 3OR  Var_10    C31  C30  O29  N28   175.30  30.0  1
 3OR  Var_11    O32  C31  C30  O29    66.58  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
 3OR  plan-1  C4    0.020
 3OR  plan-1  C5    0.020
 3OR  plan-1  C6    0.020
 3OR  plan-1  C7    0.020
 3OR  plan-1  C26   0.020
 3OR  plan-1  C1    0.020
 3OR  plan-1  N2    0.020
 3OR  plan-1  C9    0.020
 3OR  plan-1  F10   0.020
 3OR  plan-1  C11   0.020
 3OR  plan-1  F12   0.020
 3OR  plan-1  H5    0.020
 3OR  plan-2  C13   0.020
 3OR  plan-2  C15   0.020
 3OR  plan-2  C17   0.020
 3OR  plan-2  N2    0.020
 3OR  plan-2  C3    0.020
 3OR  plan-2  C14   0.020
 3OR  plan-2  C18   0.020
 3OR  plan-2  F19   0.020
 3OR  plan-2  H13   0.020
 3OR  plan-2  H17   0.020
 3OR  plan-2  H14   0.020
 3OR  plan-2  I16   0.020
 3OR  plan-3  C4    0.020
 3OR  plan-3  C26   0.020
 3OR  plan-3  O27   0.020
 3OR  plan-3  N28   0.020
 3OR  plan-3  O29   0.020
 3OR  plan-3  HN28  0.020
 3OR  plan-4  C7    0.020
 3OR  plan-4  C20   0.020
 3OR  plan-4  C22   0.020
 3OR  plan-4  N8    0.020
 3OR  plan-4  O21   0.020
 3OR  plan-4  O25   0.020

