# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:26:04 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-{4-[(2-fluoro-6-methoxy-3'-nitrobiphenyl-3-yl)methyl]phenyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cc2ccc(NC(N)=O)cc2)c(F)c1c3cccc(c3)[N](=O)=O
#
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
 15X  15X  1-{4-[(2-fluoro-6-methoxy-3'-nitrobiphenyl-3-yl)methyl]phenyl}urea  ligand  47  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_15X
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
 15X  C1    C  CR6    0   0.112  -2.4926  -0.2862   0.6835
 15X  C2    C  CR16   0  -0.309  -3.3479   0.5690   0.0014
 15X  C3    C  CR6    0   0.269  -4.1735   1.4186   0.7233
 15X  C4    C  CR16   0  -0.274  -4.1735   1.4434   2.1095
 15X  C5    C  CR16   0  -0.239  -3.3174   0.5868   2.7811
 15X  C6    C  CR16   0  -0.253  -2.4853  -0.2704   2.0770
 15X  C13   C  CR16   0  -0.303   0.1130  -2.8652  -1.4797
 15X  C14   C  CR6    0  -0.084   0.3067  -1.4956  -1.5737
 15X  C15   C  CR6    0   0.570  -0.5747  -0.7050  -0.8494
 15X  C16   C  CR6    0  -0.281  -1.5985  -1.1980  -0.0634
 15X  C17   C  CR6    0   0.382  -1.7587  -2.5914   0.0049
 15X  C18   C  CR16   0  -0.388  -0.8994  -3.4212  -0.7069
 15X  C28   C  CR6    0   0.127   2.4692  -0.2099  -1.5546
 15X  C30   C  CR16   0  -0.281   3.1657  -0.9114  -0.5764
 15X  C31   C  CR16   0  -0.304   4.1574  -0.3214   0.1937
 15X  C32   C  CR6    0   0.364   4.4860   1.0220  -0.0064
 15X  C33   C  CR16   0  -0.343   3.7855   1.7351  -0.9825
 15X  C34   C  CR16   0  -0.310   2.7954   1.1287  -1.7363
 15X  C43   C  CH3    0  -0.440  -2.9849  -4.4169   0.8898
 15X  O43   O  O2     0  -0.459  -2.7719  -3.0229   0.7704
 15X  N47   N  N      1   0.328  -5.0690   2.3104  -0.0002
 15X  O49   O  O     -1  -0.378  -5.0513   2.2783  -1.2080
 15X  N51   N  NH1    0  -0.766   5.4574   1.7233   0.7065
 15X  O51   O  O      0  -0.377  -5.7863   3.0390   0.6435
 15X  C53   C  C      0   0.668   6.3909   1.2427   1.5882
 15X  N55   N  NH2    0  -0.844   7.2084   2.2049   2.0887
 15X  O57   O  O      0  -0.515   6.4658   0.0709   1.9281
 15X  F59   F  F      0  -0.297  -0.4223   0.6271  -0.9108
 15X  H2    H  HCR6   0   0.293  -3.3739   0.5573  -1.0789
 15X  H4    H  HCR6   0   0.300  -4.8192   2.1096   2.6619
 15X  H5    H  HCR6   0   0.280  -3.2987   0.5910   3.8621
 15X  H6    H  HCR6   0   0.272  -1.8156  -0.9267   2.6171
 15X  H13   H  HCR6   0   0.268   0.7705  -3.5268  -2.0302
 15X  H18   H  HCR6   0   0.284  -1.0062  -4.4966  -0.6796
 15X  H26   H  HCH2   0   0.270   1.8681  -1.6730  -2.9942
 15X  H26A  H  HCH2   0   0.266   0.9977  -0.1646  -3.1039
 15X  H30   H  HCR6   0   0.247   2.9321  -1.9549  -0.3974
 15X  H31   H  HCR6   0   0.275   4.6633  -0.9104   0.9402
 15X  H33   H  HCR6   0   0.264   4.0193   2.7795  -1.1547
 15X  H34   H  HCR6   0   0.249   2.2736   1.7151  -2.4830
 15X  H43   H  HCH3   0   0.232  -3.2237  -4.8751  -0.0729
 15X  H43A  H  HCH3   0   0.232  -2.1187  -4.9256   1.3192
 15X  H43B  H  HCH3   0   0.263  -3.8330  -4.5411   1.5581
 15X  HN51  H  HNH1   0   0.408   5.5065   2.7060   0.4862
 15X  HN55  H  HNH2   0   0.401   7.2968   3.1017   1.6405
 15X  HN5A  H  HNH2   0   0.402   8.0220   1.8953   2.5929
 15X  C26   C  CH2    0  -0.580   1.4102  -0.8840  -2.3922

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
 15X  C1   C2    aromatic  1.389  0.020  1.389
 15X  C1   C6    aromatic  1.394  0.020  1.394
 15X  C1   C16   single    1.479  0.020  1.479
 15X  C2   C3    aromatic  1.387  0.020  1.387
 15X  C3   C4    aromatic  1.386  0.020  1.386
 15X  C3   N47   single    1.456  0.020  1.456
 15X  C4   C5    aromatic  1.385  0.020  1.385
 15X  C5   C6    aromatic  1.387  0.020  1.387
 15X  C13  C14   aromatic  1.386  0.020  1.386
 15X  C13  C18   aromatic  1.390  0.020  1.390
 15X  C14  C15   aromatic  1.388  0.020  1.388
 15X  C14  C26   single    1.504  0.020  1.504
 15X  C15  C16   aromatic  1.382  0.020  1.382
 15X  C15  F59   single    1.342  0.020  1.342
 15X  C16  C17   aromatic  1.404  0.020  1.404
 15X  C17  C18   aromatic  1.390  0.020  1.390
 15X  C17  O43   single    1.341  0.020  1.341
 15X  C26  C28   single    1.509  0.020  1.509
 15X  C28  C30   aromatic  1.391  0.020  1.391
 15X  C28  C34   aromatic  1.390  0.020  1.390
 15X  C30  C31   aromatic  1.387  0.020  1.387
 15X  C31  C32   aromatic  1.397  0.020  1.397
 15X  C32  C33   aromatic  1.397  0.020  1.397
 15X  C32  N51   single    1.394  0.020  1.394
 15X  C33  C34   aromatic  1.384  0.020  1.384
 15X  C43  O43   single    1.415  0.020  1.415
 15X  N47  O49   single    1.208  0.020  1.208
 15X  N47  O51   double    1.208  0.020  1.208
 15X  N51  C53   single    1.371  0.020  1.371
 15X  C53  N55   single    1.358  0.020  1.358
 15X  C53  O57   double    1.222  0.020  1.222
 15X  C2   H2    single    0.930  0.020  1.080
 15X  C4   H4    single    0.930  0.020  1.080
 15X  C5   H5    single    0.930  0.020  1.080
 15X  C6   H6    single    0.930  0.020  1.080
 15X  C13  H13   single    0.930  0.020  1.080
 15X  C18  H18   single    0.930  0.020  1.080
 15X  C26  H26   single    0.970  0.020  1.090
 15X  C26  H26A  single    0.970  0.020  1.090
 15X  C30  H30   single    0.930  0.020  1.080
 15X  C31  H31   single    0.930  0.020  1.080
 15X  C33  H33   single    0.930  0.020  1.080
 15X  C34  H34   single    0.930  0.020  1.080
 15X  C43  H43   single    0.970  0.020  1.090
 15X  C43  H43A  single    0.970  0.020  1.090
 15X  C43  H43B  single    0.970  0.020  1.090
 15X  N51  HN51  single    0.860  0.020  1.020
 15X  N55  HN55  single    0.890  0.020  1.040
 15X  N55  HN5A  single    0.890  0.020  1.040

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
 15X  C16   C1   C6    120.57  3.000
 15X  C16   C1   C2    120.25  3.000
 15X  C6    C1   C2    119.17  3.000
 15X  H2    C2   C3    120.83  3.000
 15X  H2    C2   C1    119.95  3.000
 15X  C3    C2   C1    119.22  3.000
 15X  N47   C3   C4    119.06  3.000
 15X  N47   C3   C2    118.85  3.000
 15X  C4    C3   C2    122.09  3.000
 15X  H4    C4   C5    120.21  3.000
 15X  H4    C4   C3    121.50  3.000
 15X  C5    C4   C3    118.28  3.000
 15X  H5    C5   C6    119.98  3.000
 15X  H5    C5   C4    119.55  3.000
 15X  C6    C5   C4    120.47  3.000
 15X  H6    C6   C5    119.53  3.000
 15X  H6    C6   C1    119.70  3.000
 15X  C5    C6   C1    120.77  3.000
 15X  H13   C13  C18   118.72  3.000
 15X  H13   C13  C14   118.96  3.000
 15X  C18   C13  C14   122.32  3.000
 15X  C26   C14  C15   121.21  3.000
 15X  C26   C14  C13   122.76  3.000
 15X  C15   C14  C13   116.02  3.000
 15X  F59   C15  C16   117.66  3.000
 15X  F59   C15  C14   117.99  3.000
 15X  C16   C15  C14   124.34  3.000
 15X  C17   C16  C15   117.79  3.000
 15X  C17   C16  C1    121.21  3.000
 15X  C15   C16  C1    121.00  3.000
 15X  O43   C17  C18   124.55  3.000
 15X  O43   C17  C16   115.67  3.000
 15X  C18   C17  C16   119.79  3.000
 15X  H18   C18  C17   121.31  3.000
 15X  H18   C18  C13   118.94  3.000
 15X  C17   C18  C13   119.75  3.000
 15X  C34   C28  C30   117.40  3.000
 15X  C34   C28  C26   121.49  3.000
 15X  C30   C28  C26   121.11  3.000
 15X  H30   C30  C31   118.14  3.000
 15X  H30   C30  C28   119.58  3.000
 15X  C31   C30  C28   122.27  3.000
 15X  H31   C31  C32   120.96  3.000
 15X  H31   C31  C30   119.20  3.000
 15X  C32   C31  C30   119.83  3.000
 15X  N51   C32  C33   116.74  3.000
 15X  N51   C32  C31   125.05  3.000
 15X  C33   C32  C31   118.21  3.000
 15X  H33   C33  C34   119.33  3.000
 15X  H33   C33  C32   119.64  3.000
 15X  C34   C33  C32   121.03  3.000
 15X  H34   C34  C33   118.86  3.000
 15X  H34   C34  C28   119.90  3.000
 15X  C33   C34  C28   121.24  3.000
 15X  H43B  C43  H43A  108.90  3.000
 15X  H43B  C43  H43   108.86  3.000
 15X  H43A  C43  H43   108.93  3.000
 15X  H43B  C43  O43   106.37  3.000
 15X  H43A  C43  O43   111.87  3.000
 15X  H43   C43  O43   111.82  3.000
 15X  C43   O43  C17   118.60  3.000
 15X  O51   N47  O49   123.86  3.000
 15X  O51   N47  C3    118.02  3.000
 15X  O49   N47  C3    118.12  3.000
 15X  HN51  N51  C53   116.68  3.000
 15X  HN51  N51  C32   114.36  3.000
 15X  C53   N51  C32   128.82  3.000
 15X  O57   C53  N55   122.66  3.000
 15X  O57   C53  N51   123.82  3.000
 15X  N55   C53  N51   113.48  3.000
 15X  HN5A  N55  HN55  115.24  3.000
 15X  HN5A  N55  C53   116.96  3.000
 15X  HN55  N55  C53   121.33  3.000
 15X  H26A  C26  H26   105.95  3.000
 15X  H26A  C26  C28   109.41  3.000
 15X  H26   C26  C28   109.52  3.000
 15X  H26A  C26  C14   110.20  3.000
 15X  H26   C26  C14   108.27  3.000
 15X  C28   C26  C14   113.23  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
 15X  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 15X  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 15X  CONST_03  C14   C15  C16  C1    180.00   0.0  0
 15X  CONST_04  C18   C17  C16  C1    180.00   0.0  0
 15X  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 15X  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 15X  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 15X  CONST_10  C16   C1   C2   C3    180.00   0.0  0
 15X  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 15X  CONST_12  C16   C1   C6   C5    180.00   0.0  0
 15X  CONST_15  C16   C15  C14  C13     0.00   0.0  0
 15X  CONST_16  C16   C17  C18  C13     0.00   0.0  0
 15X  CONST_17  C17   C18  C13  C14     0.00   0.0  0
 15X  CONST_18  C17   C16  C15  C14     0.00   0.0  0
 15X  CONST_19  C18   C13  C14  C15     0.00   0.0  0
 15X  CONST_20  C18   C17  C16  C15     0.00   0.0  0
 15X  CONST_21  C32   C31  C30  C28     0.00   0.0  0
 15X  CONST_22  C32   C33  C34  C28     0.00   0.0  0
 15X  CONST_23  C33   C34  C28  C30     0.00   0.0  0
 15X  CONST_24  C33   C32  C31  C30     0.00   0.0  0
 15X  CONST_25  C34   C28  C30  C31     0.00   0.0  0
 15X  CONST_26  C34   C33  C32  C31     0.00   0.0  0
 15X  CONST_27  N47   C3   C2   C1    180.00   0.0  0
 15X  CONST_28  F59   C15  C16  C1      0.00   0.0  0
 15X  CONST_29  O43   C17  C16  C1      0.00   0.0  0
 15X  CONST_30  N47   C3   C4   C5    180.00   0.0  0
 15X  CONST_31  F59   C15  C14  C13   180.00   0.0  0
 15X  CONST_32  O43   C17  C18  C13   180.00   0.0  0
 15X  CONST_33  O43   C17  C16  C15   180.00   0.0  0
 15X  CONST_34  C26   C14  C15  C16   180.00   0.0  0
 15X  CONST_35  F59   C15  C16  C17   180.00   0.0  0
 15X  CONST_36  C26   C14  C13  C18   180.00   0.0  0
 15X  CONST_37  C31   C30  C28  C26   180.00   0.0  0
 15X  CONST_38  C33   C34  C28  C26   180.00   0.0  0
 15X  CONST_39  N51   C32  C31  C30   180.00   0.0  0
 15X  CONST_40  N51   C32  C33  C34   180.00   0.0  0
 15X  CONST_41  H5    C5   C6   C1    180.00   0.0  0
 15X  CONST_42  H6    C6   C1   C2    180.00   0.0  0
 15X  CONST_43  H4    C4   C3   C2    180.00   0.0  0
 15X  CONST_44  H2    C2   C3   C4    180.00   0.0  0
 15X  CONST_45  H18   C18  C13  C14   180.00   0.0  0
 15X  CONST_46  H13   C13  C14  C15   180.00   0.0  0
 15X  CONST_47  H31   C31  C30  C28   180.00   0.0  0
 15X  CONST_48  H33   C33  C34  C28   180.00   0.0  0
 15X  CONST_49  H34   C34  C28  C30   180.00   0.0  0
 15X  CONST_50  H30   C30  C31  C32   180.00   0.0  0
 15X  CONST_51  O49   N47  C3   C2      0.00   0.0  0
 15X  CONST_52  O51   N47  C3   C2    180.00   0.0  0
 15X  CONST_53  O49   N47  C3   C4    180.00   0.0  0
 15X  CONST_54  O51   N47  C3   C4      0.00   0.0  0
 15X  CONST_55  C53   N51  C32  C31     0.00   0.0  0
 15X  CONST_56  C53   N51  C32  C33   180.00   0.0  0
 15X  CONST_57  HN51  N51  C32  C31   180.00   0.0  0
 15X  CONST_58  O57   C53  N51  C32     0.00   0.0  0
 15X  CONST_59  N55   C53  N51  C32   180.00   0.0  0
 15X  CONST_61  HN5A  N55  C53  O57     0.00   0.0  0
 15X  Var_01    C28   C26  C14  C13  -111.89  30.0  2
 15X  Var_02    C30   C28  C26  C14    57.37  30.0  2
 15X  Var_03    H43   C43  O43  C17   -62.14  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
 15X  plan-1  C1    0.020
 15X  plan-1  C2    0.020
 15X  plan-1  C3    0.020
 15X  plan-1  C4    0.020
 15X  plan-1  C5    0.020
 15X  plan-1  C6    0.020
 15X  plan-1  C16   0.020
 15X  plan-1  N47   0.020
 15X  plan-1  H2    0.020
 15X  plan-1  H4    0.020
 15X  plan-1  H5    0.020
 15X  plan-1  H6    0.020
 15X  plan-2  C1    0.020
 15X  plan-2  C13   0.020
 15X  plan-2  C14   0.020
 15X  plan-2  C15   0.020
 15X  plan-2  C16   0.020
 15X  plan-2  C17   0.020
 15X  plan-2  C18   0.020
 15X  plan-2  O43   0.020
 15X  plan-2  F59   0.020
 15X  plan-2  H13   0.020
 15X  plan-2  H18   0.020
 15X  plan-2  C26   0.020
 15X  plan-3  C28   0.020
 15X  plan-3  C30   0.020
 15X  plan-3  C31   0.020
 15X  plan-3  C32   0.020
 15X  plan-3  C33   0.020
 15X  plan-3  C34   0.020
 15X  plan-3  N51   0.020
 15X  plan-3  H30   0.020
 15X  plan-3  H31   0.020
 15X  plan-3  H33   0.020
 15X  plan-3  H34   0.020
 15X  plan-3  C26   0.020
 15X  plan-4  C32   0.020
 15X  plan-4  N51   0.020
 15X  plan-4  C53   0.020
 15X  plan-4  N55   0.020
 15X  plan-4  O57   0.020
 15X  plan-4  HN51  0.020
 15X  plan-4  HN55  0.020
 15X  plan-4  HN5A  0.020
 15X  plan-5  C3    0.020
 15X  plan-5  N47   0.020
 15X  plan-5  O49   0.020
 15X  plan-5  O51   0.020

