# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun 11 14:05:56 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (5R)-2-amino-5-[4-(difluoromethoxy)phenyl]-5-[4-fluoro-3-(5-fluoropent-1-yn-1-yl)phenyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@](C1=O)(c2ccc(OC(F)F)cc2)c3ccc(F)c(c3)C#CCCCF)N
#
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
 ZOO  ZOO  (5R)-2-amino-5-[4-(difluoromethoxy)phenyl]-5-[4-fluoro-3-(5-fluoropent-1-yn-1-yl)phenyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one  ligand  50  31  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZOO
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
 ZOO  C1    C  CH3   0  -0.555   0.5035   4.7784   0.1746
 ZOO  F1    F  F     0  -0.333   6.4490  -1.9779   0.5937
 ZOO  N1    N  NR5   0  -0.518   0.5276   3.3641  -0.1139
 ZOO  O1    O  O     0  -0.434   1.4491   2.5524   1.8261
 ZOO  C2    C  CR5   0   0.574   0.9956   2.3940   0.7170
 ZOO  F2    F  F     0  -0.333   5.2006  -3.5467  -0.1980
 ZOO  N2    N  N     0  -0.457   0.1863   1.4797  -1.3098
 ZOO  O2    O  O2    0  -0.511   5.5481  -1.7170  -1.4357
 ZOO  C3    C  CR5   0  -0.245   0.7933   1.0811  -0.0575
 ZOO  F3    F  F     0  -0.379  -8.4485   0.3592  -2.3625
 ZOO  N3    N  NH2   0  -0.843  -0.3691   3.5322  -2.2860
 ZOO  C4    C  CR5   0   0.675   0.0784   2.7576  -1.2832
 ZOO  F4    F  F     0  -0.294  -2.6004  -2.1193   3.0859
 ZOO  C5    C  CR6   0   0.193   2.1004   0.3577  -0.3506
 ZOO  C6    C  CR16  0  -0.267   2.0196  -0.8708  -1.0053
 ZOO  C7    C  CR16  0  -0.299   3.1588  -1.5748  -1.3506
 ZOO  C8    C  CR6   0   0.325   4.4036  -1.0426  -1.0450
 ZOO  C9    C  CR16  0  -0.293   4.5091   0.1786  -0.4071
 ZOO  C10   C  CR16  0  -0.326   3.3558   0.8761  -0.0636
 ZOO  C11   C  CH1   0   0.667   6.0924  -2.5936  -0.5589
 ZOO  C12   C  CR6   0   0.139  -0.1283   0.2015   0.7766
 ZOO  C13   C  CR16  0  -0.256   0.3494  -0.3995   1.9408
 ZOO  C14   C  CR16  0  -0.411  -0.4817  -1.1803   2.7263
 ZOO  C15   C  CR6   0   0.507  -1.7929  -1.3609   2.3363
 ZOO  C16   C  CR6   0  -0.296  -2.3066  -0.7852   1.1809
 ZOO  C17   C  CR16  0  -0.338  -1.4477   0.0034   0.4074
 ZOO  C18   C  CSP   0   0.172  -3.6595  -1.0021   0.7974
 ZOO  C19   C  CSP   0   0.072  -4.8009  -1.1815   0.4552
 ZOO  C20   C  CH2   0  -0.638  -6.1730  -1.3846   0.0169
 ZOO  C21   C  CH2   0  -0.497  -6.6256  -0.3247  -0.9917
 ZOO  C22   C  CH2   0  -0.002  -8.0357  -0.6117  -1.4519
 ZOO  H1    H  HCH3  0   0.269   1.1102   5.3307  -0.5417
 ZOO  H1A   H  HCH3  0   0.265  -0.5164   5.1617   0.1573
 ZOO  H1B   H  HCH3  0   0.278   0.9100   4.9372   1.1691
 ZOO  HN3   H  HNH2  0   0.414  -0.7314   4.4495  -2.0840
 ZOO  HN3A  H  HNH2  0   0.408  -0.8327   3.0568  -3.0430
 ZOO  H6    H  HCR6  0   0.263   1.0512  -1.2892  -1.2486
 ZOO  H7    H  HCR6  0   0.274   3.0779  -2.5212  -1.8690
 ZOO  H9    H  HCR6  0   0.275   5.4800   0.6026  -0.1885
 ZOO  H10   H  HCR6  0   0.260   3.4717   1.8261   0.4390
 ZOO  H11   H  HCH1  0   0.214   6.9635  -3.0555  -1.0170
 ZOO  H13   H  HCR6  0   0.268   1.3800  -0.2697   2.2432
 ZOO  H14   H  HCR6  0   0.285  -0.1144  -1.6479   3.6300
 ZOO  H17   H  HCR6  0   0.268  -1.8270   0.4564  -0.4977
 ZOO  H20   H  HCH2  0   0.275  -6.2605  -2.3824  -0.4238
 ZOO  H20A  H  HCH2  0   0.277  -6.8333  -1.3784   0.8890
 ZOO  H21   H  HCH2  0   0.250  -6.5792   0.6633  -0.5295
 ZOO  H21A  H  HCH2  0   0.249  -5.9488  -0.3223  -1.8483
 ZOO  H22   H  HCH2  0   0.207  -8.7326  -0.6040  -0.6117
 ZOO  H22A  H  HCH2  0   0.207  -8.0967  -1.5843  -1.9450

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
 ZOO  C1   N1    single    1.444  0.020  1.444
 ZOO  F1   C11   single    1.355  0.020  1.355
 ZOO  N1   C2    single    1.360  0.020  1.360
 ZOO  N1   C4    single    1.392  0.020  1.392
 ZOO  O1   C2    double    1.209  0.020  1.209
 ZOO  C2   C3    single    1.538  0.020  1.538
 ZOO  F2   C11   single    1.354  0.020  1.354
 ZOO  N2   C3    single    1.448  0.020  1.448
 ZOO  N2   C4    double    1.283  0.020  1.283
 ZOO  O2   C8    single    1.385  0.020  1.385
 ZOO  O2   C11   single    1.354  0.020  1.354
 ZOO  C3   C5    single    1.522  0.020  1.522
 ZOO  C3   C12   single    1.523  0.020  1.523
 ZOO  F3   C22   single    1.394  0.020  1.394
 ZOO  N3   C4    single    1.344  0.020  1.344
 ZOO  F4   C15   single    1.338  0.020  1.338
 ZOO  C5   C6    aromatic  1.394  0.020  1.394
 ZOO  C5   C10   aromatic  1.388  0.020  1.388
 ZOO  C6   C7    aromatic  1.383  0.020  1.383
 ZOO  C7   C8    aromatic  1.388  0.020  1.388
 ZOO  C8   C9    aromatic  1.382  0.020  1.382
 ZOO  C9   C10   aromatic  1.391  0.020  1.391
 ZOO  C12  C13   aromatic  1.394  0.020  1.394
 ZOO  C12  C17   aromatic  1.384  0.020  1.384
 ZOO  C13  C14   aromatic  1.385  0.020  1.385
 ZOO  C14  C15   aromatic  1.380  0.020  1.380
 ZOO  C15  C16   aromatic  1.389  0.020  1.389
 ZOO  C16  C17   aromatic  1.399  0.020  1.399
 ZOO  C16  C18   single    1.423  0.020  1.423
 ZOO  C18  C19   triple    1.205  0.020  1.205
 ZOO  C19  C20   single    1.455  0.020  1.455
 ZOO  C20  C21   single    1.532  0.020  1.532
 ZOO  C21  C22   single    1.511  0.020  1.511
 ZOO  C1   H1    single    0.970  0.020  1.090
 ZOO  C1   H1A   single    0.970  0.020  1.090
 ZOO  C1   H1B   single    0.970  0.020  1.090
 ZOO  N3   HN3   single    0.890  0.020  1.040
 ZOO  N3   HN3A  single    0.890  0.020  1.040
 ZOO  C6   H6    single    0.930  0.020  1.080
 ZOO  C7   H7    single    0.930  0.020  1.080
 ZOO  C9   H9    single    0.930  0.020  1.080
 ZOO  C10  H10   single    0.930  0.020  1.080
 ZOO  C11  H11   single    0.970  0.020  1.090
 ZOO  C13  H13   single    0.930  0.020  1.080
 ZOO  C14  H14   single    0.930  0.020  1.080
 ZOO  C17  H17   single    0.930  0.020  1.080
 ZOO  C20  H20   single    0.970  0.020  1.090
 ZOO  C20  H20A  single    0.970  0.020  1.090
 ZOO  C21  H21   single    0.970  0.020  1.090
 ZOO  C21  H21A  single    0.970  0.020  1.090
 ZOO  C22  H22   single    0.970  0.020  1.090
 ZOO  C22  H22A  single    0.970  0.020  1.090

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
 ZOO  H1B   C1   H1A  108.27  3.000
 ZOO  H1B   C1   H1   108.63  3.000
 ZOO  H1A   C1   H1   109.43  3.000
 ZOO  H1B   C1   N1   108.66  3.000
 ZOO  H1A   C1   N1   110.92  3.000
 ZOO  H1    C1   N1   110.86  3.000
 ZOO  C4    N1   C2   108.27  3.000
 ZOO  C4    N1   C1   126.12  3.000
 ZOO  C2    N1   C1   125.61  3.000
 ZOO  C3    C2   O1   128.57  3.000
 ZOO  C3    C2   N1   104.83  3.000
 ZOO  O1    C2   N1   126.59  3.000
 ZOO  C4    N2   C3   106.96  3.000
 ZOO  C11   O2   C8   117.70  3.000
 ZOO  C12   C3   C5   110.52  3.000
 ZOO  C12   C3   N2   112.28  3.000
 ZOO  C5    C3   N2   108.92  3.000
 ZOO  C12   C3   C2   107.27  3.000
 ZOO  C5    C3   C2   112.94  3.000
 ZOO  N2    C3   C2   104.82  3.000
 ZOO  HN3A  N3   HN3  114.54  3.000
 ZOO  HN3A  N3   C4   116.24  3.000
 ZOO  HN3   N3   C4   119.69  3.000
 ZOO  N3    C4   N2   125.93  3.000
 ZOO  N3    C4   N1   118.90  3.000
 ZOO  N2    C4   N1   115.11  3.000
 ZOO  C10   C5   C6   118.58  3.000
 ZOO  C10   C5   C3   124.00  3.000
 ZOO  C6    C5   C3   117.34  3.000
 ZOO  H6    C6   C7   118.94  3.000
 ZOO  H6    C6   C5   119.86  3.000
 ZOO  C7    C6   C5   121.20  3.000
 ZOO  H7    C7   C8   120.52  3.000
 ZOO  H7    C7   C6   120.22  3.000
 ZOO  C8    C7   C6   119.25  3.000
 ZOO  C9    C8   C7   120.60  3.000
 ZOO  C9    C8   O2   119.84  3.000
 ZOO  C7    C8   O2   119.50  3.000
 ZOO  H9    C9   C10  119.85  3.000
 ZOO  H9    C9   C8   120.55  3.000
 ZOO  C10   C9   C8   119.60  3.000
 ZOO  H10   C10  C9   117.82  3.000
 ZOO  H10   C10  C5   121.41  3.000
 ZOO  C9    C10  C5   120.77  3.000
 ZOO  H11   C11  O2   108.93  3.000
 ZOO  H11   C11  F2   109.93  3.000
 ZOO  O2    C11  F2   111.31  3.000
 ZOO  H11   C11  F1   109.93  3.000
 ZOO  O2    C11  F1   111.25  3.000
 ZOO  F2    C11  F1   105.45  3.000
 ZOO  C17   C12  C13  119.18  3.000
 ZOO  C17   C12  C3   120.89  3.000
 ZOO  C13   C12  C3   119.93  3.000
 ZOO  H13   C13  C14  118.74  3.000
 ZOO  H13   C13  C12  120.53  3.000
 ZOO  C14   C13  C12  120.73  3.000
 ZOO  H14   C14  C15  120.15  3.000
 ZOO  H14   C14  C13  120.92  3.000
 ZOO  C15   C14  C13  118.93  3.000
 ZOO  C16   C15  C14  122.15  3.000
 ZOO  C16   C15  F4   118.54  3.000
 ZOO  C14   C15  F4   119.30  3.000
 ZOO  C18   C16  C17  121.37  3.000
 ZOO  C18   C16  C15  120.83  3.000
 ZOO  C17   C16  C15  117.79  3.000
 ZOO  H17   C17  C16  118.93  3.000
 ZOO  H17   C17  C12  119.86  3.000
 ZOO  C16   C17  C12  121.21  3.000
 ZOO  C19   C18  C16  180.00  3.000
 ZOO  C20   C19  C18  180.00  3.000
 ZOO  H20A  C20  H20  106.14  3.000
 ZOO  H20A  C20  C21  110.04  3.000
 ZOO  H20   C20  C21  110.00  3.000
 ZOO  H20A  C20  C19  109.17  3.000
 ZOO  H20   C20  C19  108.91  3.000
 ZOO  C21   C20  C19  112.37  3.000
 ZOO  H21A  C21  H21  107.69  3.000
 ZOO  H21A  C21  C22  109.88  3.000
 ZOO  H21   C21  C22  109.91  3.000
 ZOO  H21A  C21  C20  109.57  3.000
 ZOO  H21   C21  C20  109.56  3.000
 ZOO  C22   C21  C20  110.18  3.000
 ZOO  H22A  C22  H22  108.55  3.000
 ZOO  H22A  C22  C21  111.03  3.000
 ZOO  H22   C22  C21  111.10  3.000
 ZOO  H22A  C22  F3   108.00  3.000
 ZOO  H22   C22  F3   107.99  3.000
 ZOO  C21   C22  F3   110.07  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
 ZOO  CONST_01  C8    C7   C6   C5     0.00   0.0  0
 ZOO  CONST_02  C8    C9   C10  C5     0.00   0.0  0
 ZOO  CONST_03  C9    C10  C5   C6     0.00   0.0  0
 ZOO  CONST_04  C9    C8   C7   C6     0.00   0.0  0
 ZOO  CONST_05  C10   C5   C6   C7     0.00   0.0  0
 ZOO  CONST_06  C10   C9   C8   C7     0.00   0.0  0
 ZOO  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 ZOO  CONST_08  C15   C16  C17  C12    0.00   0.0  0
 ZOO  CONST_09  C16   C17  C12  C13    0.00   0.0  0
 ZOO  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 ZOO  CONST_11  C17   C12  C13  C14    0.00   0.0  0
 ZOO  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 ZOO  CONST_13  C7    C6   C5   C3   180.00   0.0  0
 ZOO  CONST_14  C9    C10  C5   C3   180.00   0.0  0
 ZOO  CONST_15  C14   C13  C12  C3   180.00   0.0  0
 ZOO  CONST_16  C16   C17  C12  C3   180.00   0.0  0
 ZOO  CONST_17  C3    N2   C4   N1     0.00   0.0  0
 ZOO  CONST_18  N2    C4   N1   C2     0.00   0.0  0
 ZOO  CONST_19  C4    N1   C2   C3     0.00   0.0  0
 ZOO  CONST_20  C6    C7   C8   O2   180.00   0.0  0
 ZOO  CONST_21  C10   C9   C8   O2   180.00   0.0  0
 ZOO  CONST_22  C13   C14  C15  F4   180.00   0.0  0
 ZOO  CONST_23  C17   C16  C15  F4   180.00   0.0  0
 ZOO  CONST_24  C18   C16  C17  C12  180.00   0.0  0
 ZOO  CONST_25  C18   C16  C15  C14  180.00   0.0  0
 ZOO  CONST_26  C3    C2   N1   C1   180.00   0.0  0
 ZOO  CONST_27  N2    C4   N1   C1   180.00   0.0  0
 ZOO  CONST_28  C4    N1   C2   O1   180.00   0.0  0
 ZOO  CONST_29  N3    C4   N1   C2   180.00   0.0  0
 ZOO  CONST_30  N3    C4   N2   C3   180.00   0.0  0
 ZOO  CONST_31  H6    C6   C5   C3     0.00   0.0  0
 ZOO  CONST_32  H10   C10  C5   C3     0.00   0.0  0
 ZOO  CONST_33  H13   C13  C12  C3     0.00   0.0  0
 ZOO  CONST_34  H17   C17  C12  C3     0.00   0.0  0
 ZOO  CONST_35  H7    C7   C6   C5   180.00   0.0  0
 ZOO  CONST_36  H9    C9   C10  C5   180.00   0.0  0
 ZOO  CONST_37  H14   C14  C13  C12  180.00   0.0  0
 ZOO  CONST_38  O1    C2   N1   C1     0.00   0.0  0
 ZOO  CONST_39  N3    C4   N1   C1     0.00   0.0  0
 ZOO  CONST_41  HN3A  N3   C4   N1   180.00   0.0  0
 ZOO  Var_01    H1    C1   N1   C2   118.66  30.0  3
 ZOO  Var_02    H11   C11  O2   C8   178.66  30.0  3
 ZOO  Var_03    C20   C21  C22  F3   179.59  30.0  2
 ZOO  Var_04    C21   C20  C19  C18  -26.58  30.0  3
 ZOO  Var_05    C22   C21  C20  C19  177.88  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
 ZOO  chir_01  C3  N2  C5  C12  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
 ZOO  plan-1  O2    0.020
 ZOO  plan-1  C3    0.020
 ZOO  plan-1  C5    0.020
 ZOO  plan-1  C6    0.020
 ZOO  plan-1  C7    0.020
 ZOO  plan-1  C8    0.020
 ZOO  plan-1  C9    0.020
 ZOO  plan-1  C10   0.020
 ZOO  plan-1  H6    0.020
 ZOO  plan-1  H7    0.020
 ZOO  plan-1  H9    0.020
 ZOO  plan-1  H10   0.020
 ZOO  plan-2  C3    0.020
 ZOO  plan-2  F4    0.020
 ZOO  plan-2  C12   0.020
 ZOO  plan-2  C13   0.020
 ZOO  plan-2  C14   0.020
 ZOO  plan-2  C15   0.020
 ZOO  plan-2  C16   0.020
 ZOO  plan-2  C17   0.020
 ZOO  plan-2  C18   0.020
 ZOO  plan-2  C19   0.020
 ZOO  plan-2  H13   0.020
 ZOO  plan-2  H14   0.020
 ZOO  plan-2  H17   0.020
 ZOO  plan-3  C1    0.020
 ZOO  plan-3  N1    0.020
 ZOO  plan-3  O1    0.020
 ZOO  plan-3  C2    0.020
 ZOO  plan-3  N2    0.020
 ZOO  plan-3  C3    0.020
 ZOO  plan-3  N3    0.020
 ZOO  plan-3  C4    0.020
 ZOO  plan-3  HN3   0.020
 ZOO  plan-3  HN3A  0.020

