# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:24:09 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: [3-(aminomethyl)-3-hydroxyazetidin-1-yl]{3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(O)CN(C1)C(=O)c2ccc(F)c(F)c2Nc3ccc(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
 YQY  YQY  '[3-(aminomethyl)-3-hydroxyazetidin-1-yl]{3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}methanone'  ligand  41  26  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YQY
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
 YQY  F26   F  F     0  -0.300   1.8332  -4.0421  -1.0610
 YQY  C9    C  CR6   0   0.346   2.1959  -3.3924   0.0512
 YQY  C10   C  CR6   0   0.407   2.7975  -4.0941   1.0749
 YQY  F22   F  F     0  -0.301   3.0102  -5.4010   0.9107
 YQY  C11   C  CR16  0  -0.421   3.1456  -3.4688   2.2544
 YQY  C12   C  CR16  0  -0.282   2.8915  -2.1133   2.3736
 YQY  C13   C  CR6   0  -0.059   2.3359  -1.3770   1.3326
 YQY  C16   C  C     0   0.460   2.1643   0.0928   1.5556
 YQY  O18   O  O     0  -0.480   1.5938   0.5230   2.5501
 YQY  N17   N  N     0  -0.429   2.6962   0.8905   0.6321
 YQY  C21   C  C     0  -0.272   2.7575   2.3408   0.6234
 YQY  C20   C  C     0   0.202   3.9183   2.2474  -0.3870
 YQY  O23   O  OH1   0  -0.674   3.7018   2.9327  -1.5753
 YQY  C24   C  CH2   0  -0.333   5.2665   2.6423   0.2024
 YQY  N25   N  NH2   0  -0.815   6.2743   2.5504  -0.8416
 YQY  C19   C  C     0  -0.287   3.6756   0.7084  -0.4300
 YQY  C8    C  CR6   0   0.200   1.9463  -2.0246   0.1502
 YQY  N7    N  NH1   0  -0.783   1.3418  -1.3862  -0.9169
 YQY  C5    C  CR6   0   0.165   0.3557  -0.4172  -0.8130
 YQY  C6    C  CR6   0   0.495   0.2136   0.5295  -1.8259
 YQY  F15   F  F     0  -0.307   1.0354   0.4529  -2.8840
 YQY  C1    C  CR16  0  -0.371  -0.7310   1.5309  -1.7906
 YQY  C4    C  CR16  0  -0.275  -0.5303  -0.3359   0.2586
 YQY  C3    C  CR16  0  -0.227  -1.4800   0.6714   0.3329
 YQY  C2    C  CR6   0  -0.232  -1.5743   1.6013  -0.6902
 YQY  I14   I  I     0   0.064  -3.0065   3.1330  -0.5876
 YQY  H11   H  HCR6  0   0.294   3.6087  -4.0285   3.0553
 YQY  H12   H  HCR6  0   0.279   3.1693  -1.6064   3.2878
 YQY  H211  H  H     0   0.253   1.8517   2.8049   0.2247
 YQY  H212  H  H     0   0.254   3.0001   2.7922   1.5885
 YQY  H191  H  H     0   0.253   4.5150   0.0632  -0.1603
 YQY  H192  H  H     0   0.252   3.2436   0.3669  -1.3703
 YQY  H23   H  HOH1  0   0.441   4.5877   3.0358  -1.9636
 YQY  H241  H  HCH2  0   0.248   5.2057   3.6830   0.5310
 YQY  H242  H  HCH2  0   0.221   5.4813   2.0410   1.0943
 YQY  H251  H  HNH2  0   0.369   7.0869   3.0998  -0.5987
 YQY  H252  H  HNH2  0   0.357   6.5947   1.5960  -0.9468
 YQY  H7    H  HNH1  0   0.408   1.5091  -1.7705  -1.8334
 YQY  H4    H  HCR6  0   0.295  -0.4831  -1.0702   1.0515
 YQY  H1    H  HCR6  0   0.301  -0.7832   2.2388  -2.6070
 YQY  H3    H  HCR6  0   0.283  -2.1435   0.7051   1.1855

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
 YQY  F26  C9    single    1.338  0.020  1.338
 YQY  C9   C10   aromatic  1.379  0.020  1.379
 YQY  C9   C8    aromatic  1.394  0.020  1.394
 YQY  C10  F22   single    1.334  0.020  1.334
 YQY  C10  C11   aromatic  1.380  0.020  1.380
 YQY  C11  C12   aromatic  1.384  0.020  1.384
 YQY  C12  C13   aromatic  1.391  0.020  1.391
 YQY  C13  C16   single    1.497  0.020  1.497
 YQY  C13  C8    aromatic  1.403  0.020  1.403
 YQY  C16  O18   double    1.225  0.020  1.225
 YQY  C16  N17   single    1.331  0.020  1.331
 YQY  N17  C21   single    1.452  0.020  1.452
 YQY  N17  C19   single    1.456  0.020  1.456
 YQY  C21  C20   single    1.542  0.020  1.542
 YQY  C20  O23   single    1.389  0.020  1.389
 YQY  C20  C24   single    1.523  0.020  1.523
 YQY  C20  C19   single    1.559  0.020  1.559
 YQY  C24  N25   single    1.454  0.020  1.454
 YQY  C8   N7    single    1.383  0.020  1.383
 YQY  N7   C5    single    1.386  0.020  1.386
 YQY  C5   C6    aromatic  1.394  0.020  1.394
 YQY  C5   C4    aromatic  1.393  0.020  1.393
 YQY  C6   F15   single    1.342  0.020  1.342
 YQY  C6   C1    aromatic  1.377  0.020  1.377
 YQY  C1   C2    aromatic  1.388  0.020  1.388
 YQY  C4   C3    aromatic  1.386  0.020  1.386
 YQY  C3   C2    aromatic  1.386  0.020  1.386
 YQY  C2   I14   single    2.100  0.020  2.100
 YQY  C11  H11   single    0.930  0.020  1.080
 YQY  C12  H12   single    0.930  0.020  1.080
 YQY  C21  H211  single    0.970  0.020  1.090
 YQY  C21  H212  single    0.970  0.020  1.090
 YQY  C19  H191  single    0.970  0.020  1.090
 YQY  C19  H192  single    0.970  0.020  1.090
 YQY  O23  H23   single    0.850  0.020  0.980
 YQY  C24  H241  single    0.970  0.020  1.090
 YQY  C24  H242  single    0.970  0.020  1.090
 YQY  N25  H251  single    0.890  0.020  1.040
 YQY  N25  H252  single    0.890  0.020  1.040
 YQY  N7   H7    single    0.860  0.020  1.020
 YQY  C4   H4    single    0.930  0.020  1.080
 YQY  C1   H1    single    0.930  0.020  1.080
 YQY  C3   H3    single    0.930  0.020  1.080

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
 YQY  C8    C9   C10   121.64  3.000
 YQY  C8    C9   F26   119.14  3.000
 YQY  C10   C9   F26   119.22  3.000
 YQY  C11   C10  F22   120.59  3.000
 YQY  C11   C10  C9    120.93  3.000
 YQY  F22   C10  C9    118.46  3.000
 YQY  H11   C11  C12   121.45  3.000
 YQY  H11   C11  C10   120.44  3.000
 YQY  C12   C11  C10   118.10  3.000
 YQY  H12   C12  C13   119.16  3.000
 YQY  H12   C12  C11   118.98  3.000
 YQY  C13   C12  C11   121.82  3.000
 YQY  C8    C13  C16   123.16  3.000
 YQY  C8    C13  C12   119.82  3.000
 YQY  C16   C13  C12   117.01  3.000
 YQY  N17   C16  O18   122.62  3.000
 YQY  N17   C16  C13   116.06  3.000
 YQY  O18   C16  C13   121.30  3.000
 YQY  C19   N17  C21    95.29  3.000
 YQY  C19   N17  C16   134.41  3.000
 YQY  C21   N17  C16   128.30  3.000
 YQY  H212  C21  H211  109.31  3.000
 YQY  H212  C21  C20   115.89  3.000
 YQY  H211  C21  C20   114.24  3.000
 YQY  H212  C21  N17   114.64  3.000
 YQY  H211  C21  N17   113.04  3.000
 YQY  C20   C21  N17    88.58  3.000
 YQY  C19   C20  C24   113.86  3.000
 YQY  C19   C20  O23   116.06  3.000
 YQY  C24   C20  O23   109.95  3.000
 YQY  C19   C20  C21    87.74  3.000
 YQY  C24   C20  C21   113.39  3.000
 YQY  O23   C20  C21   114.42  3.000
 YQY  H23   O23  C20   104.59  3.000
 YQY  H242  C24  H241  106.76  3.000
 YQY  H242  C24  N25   114.42  3.000
 YQY  H241  C24  N25   108.34  3.000
 YQY  H242  C24  C20   110.23  3.000
 YQY  H241  C24  C20   108.29  3.000
 YQY  N25   C24  C20   108.62  3.000
 YQY  H252  N25  H251  106.44  3.000
 YQY  H252  N25  C24   110.71  3.000
 YQY  H251  N25  C24   110.52  3.000
 YQY  H192  C19  H191  109.42  3.000
 YQY  H192  C19  C20   113.27  3.000
 YQY  H191  C19  C20   117.17  3.000
 YQY  H192  C19  N17   113.70  3.000
 YQY  H191  C19  N17   114.24  3.000
 YQY  C20   C19  N17    87.77  3.000
 YQY  N7    C8   C13   123.96  3.000
 YQY  N7    C8   C9    118.46  3.000
 YQY  C13   C8   C9    117.58  3.000
 YQY  H7    N7   C5    116.92  3.000
 YQY  H7    N7   C8    116.95  3.000
 YQY  C5    N7   C8    125.16  3.000
 YQY  C4    C5   C6    117.04  3.000
 YQY  C4    C5   N7    123.43  3.000
 YQY  C6    C5   N7    119.52  3.000
 YQY  C1    C6   F15   118.80  3.000
 YQY  C1    C6   C5    123.04  3.000
 YQY  F15   C6   C5    118.16  3.000
 YQY  H1    C1   C2    122.39  3.000
 YQY  H1    C1   C6    119.31  3.000
 YQY  C2    C1   C6    118.29  3.000
 YQY  H4    C4   C3    118.93  3.000
 YQY  H4    C4   C5    119.78  3.000
 YQY  C3    C4   C5    121.29  3.000
 YQY  H3    C3   C2    121.31  3.000
 YQY  H3    C3   C4    119.04  3.000
 YQY  C2    C3   C4    119.64  3.000
 YQY  I14   C2   C3    120.00  3.000
 YQY  I14   C2   C1    119.35  3.000
 YQY  C3    C2   C1    120.65  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
 YQY  CONST_01  C12   C11  C10  C9     0.00   0.0  0
 YQY  CONST_02  C12   C13  C8   C9     0.00   0.0  0
 YQY  CONST_03  C13   C8   C9   C10    0.00   0.0  0
 YQY  CONST_04  C13   C12  C11  C10    0.00   0.0  0
 YQY  CONST_05  C8    C9   C10  C11    0.00   0.0  0
 YQY  CONST_06  C8    C13  C12  C11    0.00   0.0  0
 YQY  CONST_07  C2    C1   C6   C5     0.00   0.0  0
 YQY  CONST_08  C2    C3   C4   C5     0.00   0.0  0
 YQY  CONST_09  C3    C4   C5   C6     0.00   0.0  0
 YQY  CONST_10  C3    C2   C1   C6     0.00   0.0  0
 YQY  CONST_11  C4    C5   C6   C1     0.00   0.0  0
 YQY  CONST_12  C4    C3   C2   C1     0.00   0.0  0
 YQY  CONST_13  C11   C10  C9   F26  180.00   0.0  0
 YQY  CONST_14  C13   C8   C9   F26  180.00   0.0  0
 YQY  CONST_15  C16   C13  C8   C9   180.00   0.0  0
 YQY  CONST_16  N7    C8   C9   C10  180.00   0.0  0
 YQY  CONST_17  C8    C9   C10  F22  180.00   0.0  0
 YQY  CONST_18  C12   C11  C10  F22  180.00   0.0  0
 YQY  CONST_19  C16   C13  C12  C11  180.00   0.0  0
 YQY  CONST_20  N7    C8   C13  C12  180.00   0.0  0
 YQY  CONST_21  C1    C6   C5   N7   180.00   0.0  0
 YQY  CONST_22  C3    C4   C5   N7   180.00   0.0  0
 YQY  CONST_23  I14   C2   C1   C6   180.00   0.0  0
 YQY  CONST_24  C4    C5   C6   F15  180.00   0.0  0
 YQY  CONST_25  C2    C1   C6   F15  180.00   0.0  0
 YQY  CONST_26  I14   C2   C3   C4   180.00   0.0  0
 YQY  CONST_27  C21   N17  C16  C13  180.00   0.0  0
 YQY  CONST_29  H11   C11  C10  C9   180.00   0.0  0
 YQY  CONST_30  H12   C12  C11  C10  180.00   0.0  0
 YQY  CONST_31  H1    C1   C6   C5   180.00   0.0  0
 YQY  CONST_32  H3    C3   C4   C5   180.00   0.0  0
 YQY  CONST_33  H4    C4   C5   C6   180.00   0.0  0
 YQY  CONST_34  C21   N17  C16  O18    0.00   0.0  0
 YQY  Var_01    C20   C19  N17  C21    6.11  30.0  1
 YQY  Var_02    C5    N7   C8   C9   139.20  30.0  2
 YQY  Var_03    N17   C16  C13  C12  126.61  30.0  2
 YQY  Var_04    C6    C5   N7   C8   153.26  30.0  2
 YQY  Var_05    H251  N25  C24  C20  159.93  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
 YQY  chir_01  C20  C21  C24  C19  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
 YQY  plan-1  F26  0.020
 YQY  plan-1  C9   0.020
 YQY  plan-1  C10  0.020
 YQY  plan-1  F22  0.020
 YQY  plan-1  C11  0.020
 YQY  plan-1  C12  0.020
 YQY  plan-1  C13  0.020
 YQY  plan-1  C16  0.020
 YQY  plan-1  C8   0.020
 YQY  plan-1  N7   0.020
 YQY  plan-1  H11  0.020
 YQY  plan-1  H12  0.020
 YQY  plan-2  N7   0.020
 YQY  plan-2  C5   0.020
 YQY  plan-2  C6   0.020
 YQY  plan-2  F15  0.020
 YQY  plan-2  C1   0.020
 YQY  plan-2  C4   0.020
 YQY  plan-2  C3   0.020
 YQY  plan-2  C2   0.020
 YQY  plan-2  I14  0.020
 YQY  plan-2  H4   0.020
 YQY  plan-2  H1   0.020
 YQY  plan-2  H3   0.020
 YQY  plan-3  C13  0.020
 YQY  plan-3  C16  0.020
 YQY  plan-3  O18  0.020
 YQY  plan-3  N17  0.020
 YQY  plan-3  C21  0.020
 YQY  plan-3  C19  0.020

