# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:02:38 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: (5S)-2-amino-5-(1-ethyl-1H-pyrazol-4-yl)-3-methyl-5-[3-(pyrimidin-5-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1cc(cn1)[C@@]2(N=C(N)N(C)C2=O)c3cccc(c3)c4cncnc4
#
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
 591  591  (5S)-2-amino-5-(1-ethyl-1H-pyrazol-4-yl)-3-methyl-5-[3-(pyrimidin-5-yl)phenyl]-3,5-dihydro-4H-imidazol-4-one  ligand  46  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_591
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
 591  C1    C  CH3   0  -0.660  -4.3998  -4.1110  -0.0573
 591  N1    N  NR5   0  -0.265  -2.3951  -2.7173   0.2751
 591  O1    O  O     0  -0.436  -0.6027   1.3003  -2.1719
 591  C2    C  CH2   0  -0.296  -3.1481  -3.8556   0.7637
 591  N2    N  N     0  -0.289  -1.7143  -2.8058  -0.8612
 591  C3    C  CR15  0   0.046  -2.3664  -1.4788   0.7935
 591  N3    N  NR5   0  -0.516  -2.3378   2.3645  -1.1049
 591  C4    C  CR5   0  -0.088  -1.6026  -0.7053  -0.0541
 591  N4    N  N     0  -0.468  -2.3240   1.3797   0.9269
 591  C5    C  CR15  0  -0.083  -1.2232  -1.5976  -1.0738
 591  C6    C  CR5   0  -0.268  -1.2816   0.7520   0.1470
 591  N6    N  N     0  -0.386   4.8028  -1.1398  -1.6383
 591  C7    C  CR5   0   0.571  -1.3154   1.4723  -1.2109
 591  N7    N  N     0  -0.387   5.7010  -1.3749   0.5323
 591  C8    C  CR5   0   0.676  -2.8834   2.2512   0.1711
 591  C9    C  CH3   0  -0.557  -2.7708   3.2717  -2.1411
 591  C10   C  CR6   0   0.203   0.0971   0.9644   0.7644
 591  C11   C  CR16  0  -0.317   0.2781   1.8609   1.8105
 591  C12   C  CR16  0  -0.224   1.5438   2.0664   2.3454
 591  C13   C  CR16  0  -0.321   2.6403   1.3913   1.8379
 591  C14   C  CR6   0   0.113   2.4757   0.4907   0.7849
 591  C15   C  CR16  0  -0.361   1.2014   0.2843   0.2631
 591  C16   C  CR6   0  -0.046   3.6286  -0.2341   0.2299
 591  C17   C  CR16  0  -0.046   3.7698  -0.4822  -1.1327
 591  C18   C  CR16  0   0.050   5.7210  -1.5554  -0.7794
 591  C19   C  CR16  0  -0.046   4.6597  -0.7222   1.0275
 591  H1    H  HCH3  0   0.236  -4.1522  -4.3166  -1.0980
 591  H1A   H  HCH3  0   0.240  -4.9316  -4.9750   0.3403
 591  H1B   H  HCH3  0   0.234  -5.0716  -3.2536  -0.0232
 591  H2    H  HCH2  0   0.258  -3.4028  -3.6513   1.8025
 591  H2A   H  HCH2  0   0.261  -2.4912  -4.7249   0.7531
 591  H3    H  HCR5  0   0.289  -2.8783  -1.2284   1.7079
 591  H5    H  HCR5  0   0.258  -0.6244  -1.4054  -1.9508
 591  HN5   H  HNH2  0   0.407  -4.2309   3.0023   1.4554
 591  HN5A  H  HNH2  0   0.415  -4.1448   3.8486  -0.0132
 591  H9    H  HCH3  0   0.266  -3.8208   3.1111  -2.3820
 591  H9A   H  HCH3  0   0.265  -2.6231   4.3088  -1.8408
 591  H9B   H  HCH3  0   0.276  -2.1793   3.0852  -3.0329
 591  H11   H  HCR6  0   0.259  -0.5711   2.3928   2.2156
 591  H12   H  HCR6  0   0.261   1.6726   2.7653   3.1615
 591  H13   H  HCR6  0   0.259   3.6243   1.5769   2.2499
 591  H15   H  HCR6  0   0.248   1.0686  -0.4447  -0.5254
 591  H17   H  HCR6  0   0.272   3.0293  -0.1219  -1.8401
 591  H18   H  HCR6  0   0.268   6.5688  -2.0930  -1.1885
 591  H19   H  HCR6  0   0.277   4.6340  -0.5911   2.1045
 591  N5    N  NH2   0  -0.848  -3.9557   2.9961   0.4870

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
 591  C1   C2    single    1.518  0.020  1.518
 591  C1   H1    single    0.970  0.020  1.090
 591  C1   H1A   single    0.970  0.020  1.090
 591  C1   H1B   single    0.970  0.020  1.090
 591  N2   N1    aromatic  1.328  0.020  1.328
 591  N1   C3    aromatic  1.343  0.020  1.343
 591  N1   C2    single    1.450  0.020  1.450
 591  C7   O1    double    1.209  0.020  1.209
 591  C2   H2    single    0.970  0.020  1.090
 591  C2   H2A   single    0.970  0.020  1.090
 591  C5   N2    aromatic  1.321  0.020  1.321
 591  C4   C3    aromatic  1.378  0.020  1.378
 591  C3   H3    single    0.930  0.020  1.080
 591  C8   N3    single    1.392  0.020  1.392
 591  N3   C7    single    1.361  0.020  1.361
 591  N3   C9    single    1.444  0.020  1.444
 591  C5   C4    aromatic  1.407  0.020  1.407
 591  C6   C4    single    1.506  0.020  1.506
 591  N4   C8    double    1.282  0.020  1.282
 591  N4   C6    single    1.445  0.020  1.445
 591  C5   H5    single    0.930  0.020  1.080
 591  N5   C8    single    1.343  0.020  1.343
 591  N5   HN5   single    0.890  0.020  1.040
 591  N5   HN5A  single    0.890  0.020  1.040
 591  C10  C6    single    1.526  0.020  1.526
 591  C6   C7    single    1.538  0.020  1.538
 591  N6   C17   aromatic  1.325  0.020  1.325
 591  N6   C18   aromatic  1.324  0.020  1.324
 591  C18  N7    aromatic  1.324  0.020  1.324
 591  N7   C19   aromatic  1.325  0.020  1.325
 591  C9   H9    single    0.970  0.020  1.090
 591  C9   H9A   single    0.970  0.020  1.090
 591  C9   H9B   single    0.970  0.020  1.090
 591  C15  C10   aromatic  1.390  0.020  1.390
 591  C10  C11   aromatic  1.390  0.020  1.390
 591  C12  C11   aromatic  1.389  0.020  1.389
 591  C11  H11   single    0.930  0.020  1.080
 591  C13  C12   aromatic  1.384  0.020  1.384
 591  C12  H12   single    0.930  0.020  1.080
 591  C14  C13   aromatic  1.395  0.020  1.395
 591  C13  H13   single    0.930  0.020  1.080
 591  C16  C14   single    1.471  0.020  1.471
 591  C14  C15   aromatic  1.392  0.020  1.392
 591  C15  H15   single    0.930  0.020  1.080
 591  C17  C16   aromatic  1.392  0.020  1.392
 591  C16  C19   aromatic  1.392  0.020  1.392
 591  C17  H17   single    0.930  0.020  1.080
 591  C18  H18   single    0.930  0.020  1.080
 591  C19  H19   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
 591  H1B   C1   H1A  108.15  3.000
 591  H1B   C1   H1   108.57  3.000
 591  H1A   C1   H1   108.05  3.000
 591  H1B   C1   C2   111.03  3.000
 591  H1A   C1   C2   109.78  3.000
 591  H1    C1   C2   111.16  3.000
 591  C3    N1   N2   112.40  3.000
 591  C3    N1   C2   127.24  3.000
 591  N2    N1   C2   120.16  3.000
 591  H2A   C2   H2   107.45  3.000
 591  H2A   C2   N1   108.06  3.000
 591  H2    C2   N1   107.20  3.000
 591  H2A   C2   C1   110.95  3.000
 591  H2    C2   C1   110.77  3.000
 591  N1    C2   C1   112.22  3.000
 591  C5    N2   N1   105.50  3.000
 591  H3    C3   C4   130.90  3.000
 591  H3    C3   N1   122.13  3.000
 591  C4    C3   N1   106.97  3.000
 591  C9    N3   C8   126.25  3.000
 591  C9    N3   C7   125.54  3.000
 591  C8    N3   C7   108.21  3.000
 591  C6    C4   C5   130.77  3.000
 591  C6    C4   C3   125.38  3.000
 591  C5    C4   C3   103.84  3.000
 591  C8    N4   C6   106.96  3.000
 591  H5    C5   C4   128.73  3.000
 591  H5    C5   N2   119.98  3.000
 591  C4    C5   N2   111.29  3.000
 591  C10   C6   C7   108.18  3.000
 591  C7    C6   N4   104.91  3.000
 591  C10   C6   N4   111.90  3.000
 591  C7    C6   C4   109.32  3.000
 591  C10   C6   C4   112.42  3.000
 591  N4    C6   C4   109.80  3.000
 591  C18   N6   C17  116.68  3.000
 591  C6    C7   N3   104.76  3.000
 591  C6    C7   O1   128.51  3.000
 591  N3    C7   O1   126.73  3.000
 591  C19   N7   C18  116.69  3.000
 591  N5    C8   N4   125.91  3.000
 591  N5    C8   N3   118.90  3.000
 591  N4    C8   N3   115.12  3.000
 591  H9B   C9   H9A  108.41  3.000
 591  H9B   C9   H9   108.55  3.000
 591  H9A   C9   H9   109.39  3.000
 591  H9B   C9   N3   108.55  3.000
 591  H9A   C9   N3   111.07  3.000
 591  H9    C9   N3   110.81  3.000
 591  C15   C10  C11  118.92  3.000
 591  C11   C10  C6   120.82  3.000
 591  C15   C10  C6   120.25  3.000
 591  H11   C11  C12  119.91  3.000
 591  H11   C11  C10  119.82  3.000
 591  C12   C11  C10  120.26  3.000
 591  H12   C12  C13  119.82  3.000
 591  H12   C12  C11  119.62  3.000
 591  C13   C12  C11  120.56  3.000
 591  H13   C13  C14  120.33  3.000
 591  H13   C13  C12  119.79  3.000
 591  C14   C13  C12  119.87  3.000
 591  C16   C14  C15  120.20  3.000
 591  C15   C14  C13  119.11  3.000
 591  C16   C14  C13  120.69  3.000
 591  H15   C15  C14  119.03  3.000
 591  H15   C15  C10  119.66  3.000
 591  C14   C15  C10  121.28  3.000
 591  C19   C16  C17  115.04  3.000
 591  C19   C16  C14  122.50  3.000
 591  C17   C16  C14  122.46  3.000
 591  H17   C17  C16  120.63  3.000
 591  H17   C17  N6   116.61  3.000
 591  C16   C17  N6   122.75  3.000
 591  H18   C18  N7   116.95  3.000
 591  H18   C18  N6   116.95  3.000
 591  N7    C18  N6   126.10  3.000
 591  H19   C19  C16  120.59  3.000
 591  H19   C19  N7   116.68  3.000
 591  C16   C19  N7   122.73  3.000
 591  HN5A  N5   HN5  114.93  3.000
 591  HN5A  N5   C8   120.19  3.000
 591  HN5   N5   C8   116.61  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
 591  CONST_01  C4   C5   N2   N1     0.00   0.0  0
 591  CONST_02  C5   C4   C3   N1     0.00   0.0  0
 591  CONST_03  C4   C3   N1   N2     0.00   0.0  0
 591  CONST_04  C3   C4   C5   N2     0.00   0.0  0
 591  CONST_05  C5   N2   N1   C3     0.00   0.0  0
 591  CONST_06  C14  C16  C17  N6   180.00   0.0  0
 591  CONST_07  C19  C16  C17  N6     0.00   0.0  0
 591  CONST_08  C19  N7   C18  N6     0.00   0.0  0
 591  CONST_09  C17  N6   C18  N7     0.00   0.0  0
 591  CONST_10  C14  C16  C19  N7   180.00   0.0  0
 591  CONST_11  C17  C16  C19  N7     0.00   0.0  0
 591  CONST_12  C13  C14  C15  C10    0.00   0.0  0
 591  CONST_13  C16  C14  C15  C10  180.00   0.0  0
 591  CONST_14  C13  C12  C11  C10    0.00   0.0  0
 591  CONST_15  C14  C15  C10  C11    0.00   0.0  0
 591  CONST_16  C14  C13  C12  C11    0.00   0.0  0
 591  CONST_17  C15  C10  C11  C12    0.00   0.0  0
 591  CONST_18  C16  C14  C13  C12  180.00   0.0  0
 591  CONST_19  C15  C14  C13  C12    0.00   0.0  0
 591  CONST_24  C18  N6   C17  C16    0.00   0.0  0
 591  CONST_25  C18  N7   C19  C16    0.00   0.0  0
 591  CONST_26  C6   C4   C3   N1   180.00   0.0  0
 591  CONST_27  C6   C4   C5   N2   180.00   0.0  0
 591  CONST_28  C14  C15  C10  C6   180.00   0.0  0
 591  CONST_29  C12  C11  C10  C6   180.00   0.0  0
 591  CONST_30  C6   N4   C8   N3     0.00   0.0  0
 591  CONST_31  C7   N3   C8   N4     0.00   0.0  0
 591  CONST_32  C8   N3   C7   C6     0.00   0.0  0
 591  CONST_33  C5   N2   N1   C2   180.00   0.0  0
 591  CONST_34  C4   C3   N1   C2   180.00   0.0  0
 591  CONST_35  C8   N3   C7   O1   180.00   0.0  0
 591  CONST_36  C9   N3   C8   N4   180.00   0.0  0
 591  CONST_37  C7   N3   C8   N5   180.00   0.0  0
 591  CONST_38  C6   N4   C8   N5   180.00   0.0  0
 591  CONST_39  C9   N3   C7   C6   180.00   0.0  0
 591  CONST_40  H5   C5   N2   N1   180.00   0.0  0
 591  CONST_41  H3   C3   N1   N2   180.00   0.0  0
 591  CONST_42  H15  C15  C10  C6     0.00   0.0  0
 591  CONST_43  H11  C11  C10  C6     0.00   0.0  0
 591  CONST_44  H12  C12  C11  C10  180.00   0.0  0
 591  CONST_45  H13  C13  C12  C11  180.00   0.0  0
 591  CONST_46  H17  C17  C16  C14    0.00   0.0  0
 591  CONST_47  H19  C19  C16  C14    0.00   0.0  0
 591  CONST_48  H18  C18  N6   C17  180.00   0.0  0
 591  CONST_49  C9   N3   C7   O1     0.00   0.0  0
 591  CONST_50  C9   N3   C8   N5     0.00   0.0  0
 591  CONST_51  HN5  N5   C8   N3   180.00   0.0  0
 591  Var_01    N2   N1   C2   C1   -72.46  30.0  1
 591  Var_02    H9   C9   N3   C7   122.06  30.0  3
 591  Var_03    H1   C1   C2   N1    60.26  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
 591  chir_01  C6  N4  C10  C7  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
 591  plan-1  N1    0.020
 591  plan-1  C2    0.020
 591  plan-1  N2    0.020
 591  plan-1  C3    0.020
 591  plan-1  C4    0.020
 591  plan-1  C5    0.020
 591  plan-1  C6    0.020
 591  plan-1  H3    0.020
 591  plan-1  H5    0.020
 591  plan-2  N6    0.020
 591  plan-2  N7    0.020
 591  plan-2  C14   0.020
 591  plan-2  C16   0.020
 591  plan-2  C17   0.020
 591  plan-2  C18   0.020
 591  plan-2  C19   0.020
 591  plan-2  H17   0.020
 591  plan-2  H18   0.020
 591  plan-2  H19   0.020
 591  plan-3  C6    0.020
 591  plan-3  C10   0.020
 591  plan-3  C11   0.020
 591  plan-3  C12   0.020
 591  plan-3  C13   0.020
 591  plan-3  C14   0.020
 591  plan-3  C15   0.020
 591  plan-3  C16   0.020
 591  plan-3  H11   0.020
 591  plan-3  H12   0.020
 591  plan-3  H13   0.020
 591  plan-3  H15   0.020
 591  plan-4  O1    0.020
 591  plan-4  N3    0.020
 591  plan-4  N4    0.020
 591  plan-4  C6    0.020
 591  plan-4  C7    0.020
 591  plan-4  C8    0.020
 591  plan-4  C9    0.020
 591  plan-4  HN5   0.020
 591  plan-4  HN5A  0.020
 591  plan-4  N5    0.020

