# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:58:00 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (5S)-2-amino-5-(4-methoxy-3-methylphenyl)-3-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1C)[C@@]2(N=C(N)N(C)C2=O)[C@@]34CC5[CH2][CH](C[CH]([CH2]5)C3)C4
#
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
 X17  X17  (5S)-2-amino-5-(4-methoxy-3-methylphenyl)-3-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]-3,5-dihydro-4H-imidazol-4-one  ligand  56  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X17
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
 X17  C1    C  CH3   0  -0.714   3.8415   0.6361  -2.3431
 X17  N1    N  NR5   0  -0.520  -1.0446  -2.8992  -0.4332
 X17  O1    O  O2    0  -0.466   5.1218   0.7216   0.0980
 X17  C2    C  CR6   0   0.022   3.1386   0.3069  -1.0591
 X17  N2    N  N     0  -0.460  -0.6588  -1.5417   1.3176
 X17  O2    O  O     0  -0.450  -0.5940  -1.5636  -2.2297
 X17  C3    C  CR16  0  -0.335   1.8010  -0.0597  -1.0527
 X17  N3    N  NH2   0  -0.847  -1.4520  -3.7031   1.7479
 X17  C4    C  CR6   0   0.128   1.1110  -0.3803   0.1189
 X17  C5    C  CR16  0  -0.304   1.8184  -0.3219   1.3114
 X17  C6    C  CR16  0  -0.372   3.1582   0.0473   1.3415
 X17  C7    C  CR6   0   0.333   3.8237   0.3609   0.1626
 X17  C8    C  CH3   0  -0.434   5.8584   0.8106   1.2998
 X17  C9    C  CR5   0  -0.145  -0.3665  -0.7644   0.1263
 X17  C10   C  CR5   0   0.575  -0.6610  -1.7348  -1.0310
 X17  C11   C  CR5   0   0.660  -1.0279  -2.7050   0.9421
 X17  C13   C  CT    0  -0.046  -1.3201   0.4875   0.0760
 X17  C14   C  CH2   0  -0.420  -1.0335   1.4220  -1.1090
 X17  C15   C  CH1   0  -0.241  -1.9988   2.6120  -1.1014
 X17  C16   C  CH2   0  -0.417  -1.8145   3.4091   0.1903
 X17  C17   C  CH1   0  -0.244  -2.1043   2.4994   1.3848
 X17  C18   C  CH2   0  -0.402  -1.1482   1.3049   1.3666
 X17  C19   C  CH2   0  -0.417  -3.5489   2.0050   1.3040
 X17  C20   C  CH1   0  -0.243  -3.7397   1.2169   0.0084
 X17  C21   C  CH2   0  -0.417  -3.4439   2.1201  -1.1888
 X17  C22   C  CH2   0  -0.427  -2.7845   0.0221  -0.0153
 X17  H1    H  HCH3  0   0.240   4.2492   1.6484  -2.3350
 X17  H1A   H  HCH3  0   0.241   4.6764  -0.0402  -2.5358
 X17  H1B   H  HCH3  0   0.241   3.1551   0.5617  -3.1853
 X17  H3    H  HCR6  0   0.252   1.2922  -0.1026  -2.0063
 X17  HN3   H  HNH2  0   0.400  -1.2691  -3.5725   2.7297
 X17  HN3A  H  HNH2  0   0.408  -1.3499  -4.6562   1.4384
 X17  H5    H  HCR6  0   0.251   1.3268  -0.5725   2.2404
 X17  H6    H  HCR6  0   0.271   3.6655   0.0789   2.2966
 X17  H8    H  HCH3  0   0.226   5.9210  -0.1525   1.8137
 X17  H8A   H  HCH3  0   0.258   6.8623   1.1260   1.0260
 X17  H8B   H  HCH3  0   0.226   5.4329   1.5473   1.9864
 X17  H12   H  HCH3  0   0.260  -0.8300  -4.9422  -0.8565
 X17  H12A  H  HCH3  0   0.262  -2.5002  -4.3377  -0.8859
 X17  H12B  H  HCH3  0   0.273  -1.3796  -3.9289  -2.1906
 X17  H14   H  HCH2  0   0.230  -0.0092   1.7995  -1.0451
 X17  H14A  H  HCH2  0   0.233  -1.1132   0.8849  -2.0567
 X17  H15   H  HCH1  0   0.220  -1.7771   3.2510  -1.9618
 X17  H16   H  HCH2  0   0.218  -0.7947   3.8031   0.2509
 X17  H16A  H  HCH2  0   0.219  -2.4888   4.2726   0.2002
 X17  H17   H  HCH1  0   0.219  -1.9585   3.0561   2.3158
 X17  H18   H  HCH2  0   0.229  -1.3257   0.6668   2.2350
 X17  H18A  H  HCH2  0   0.226  -0.1164   1.6628   1.4427
 X17  H19   H  HCH2  0   0.219  -3.7868   1.3775   2.1690
 X17  H19A  H  HCH2  0   0.219  -4.2377   2.8559   1.3308
 X17  H20   H  HCH1  0   0.221  -4.7684   0.8484  -0.0515
 X17  H21   H  HCH2  0   0.220  -4.1290   2.9744  -1.1961
 X17  H21A  H  HCH2  0   0.219  -3.6070   1.5757  -2.1246
 X17  H22   H  HCH2  0   0.226  -2.9484  -0.5388  -0.9422
 X17  H22A  H  HCH2  0   0.232  -3.0139  -0.6530   0.8140
 X17  C12   C  CH3   0  -0.554  -1.4640  -4.0961  -1.1205

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
 X17  C2   C1    single    1.500  0.020  1.500
 X17  C1   H1    single    0.970  0.020  1.090
 X17  C1   H1A   single    0.970  0.020  1.090
 X17  C1   H1B   single    0.970  0.020  1.090
 X17  C11  N1    single    1.389  0.020  1.389
 X17  N1   C12   single    1.442  0.020  1.442
 X17  N1   C10   single    1.364  0.020  1.364
 X17  C8   O1    single    1.412  0.020  1.412
 X17  C7   O1    single    1.349  0.020  1.349
 X17  C7   C2    aromatic  1.402  0.020  1.402
 X17  C3   C2    aromatic  1.387  0.020  1.387
 X17  N2   C11   double    1.277  0.020  1.277
 X17  N2   C9    single    1.452  0.020  1.452
 X17  C10  O2    double    1.213  0.020  1.213
 X17  C4   C3    aromatic  1.397  0.020  1.397
 X17  C3   H3    single    0.930  0.020  1.080
 X17  N3   C11   single    1.351  0.020  1.351
 X17  N3   HN3   single    0.890  0.020  1.040
 X17  N3   HN3A  single    0.890  0.020  1.040
 X17  C5   C4    aromatic  1.388  0.020  1.388
 X17  C9   C4    single    1.527  0.020  1.527
 X17  C5   C6    aromatic  1.390  0.020  1.390
 X17  C5   H5    single    0.930  0.020  1.080
 X17  C6   C7    aromatic  1.390  0.020  1.390
 X17  C6   H6    single    0.930  0.020  1.080
 X17  C8   H8    single    0.970  0.020  1.090
 X17  C8   H8A   single    0.970  0.020  1.090
 X17  C8   H8B   single    0.970  0.020  1.090
 X17  C13  C9    single    1.574  0.020  1.574
 X17  C9   C10   single    1.539  0.020  1.539
 X17  C12  H12   single    0.970  0.020  1.090
 X17  C12  H12A  single    0.970  0.020  1.090
 X17  C12  H12B  single    0.970  0.020  1.090
 X17  C22  C13   single    1.539  0.020  1.539
 X17  C14  C13   single    1.536  0.020  1.536
 X17  C13  C18   single    1.537  0.020  1.537
 X17  C15  C14   single    1.532  0.020  1.532
 X17  C14  H14   single    0.970  0.020  1.090
 X17  C14  H14A  single    0.970  0.020  1.090
 X17  C21  C15   single    1.529  0.020  1.529
 X17  C15  C16   single    1.529  0.020  1.529
 X17  C15  H15   single    0.970  0.020  1.090
 X17  C16  C17   single    1.529  0.020  1.529
 X17  C16  H16   single    0.970  0.020  1.090
 X17  C16  H16A  single    0.970  0.020  1.090
 X17  C19  C17   single    1.529  0.020  1.529
 X17  C17  C18   single    1.530  0.020  1.530
 X17  C17  H17   single    0.970  0.020  1.090
 X17  C18  H18   single    0.970  0.020  1.090
 X17  C18  H18A  single    0.970  0.020  1.090
 X17  C20  C19   single    1.528  0.020  1.528
 X17  C19  H19   single    0.970  0.020  1.090
 X17  C19  H19A  single    0.970  0.020  1.090
 X17  C21  C20   single    1.529  0.020  1.529
 X17  C20  C22   single    1.530  0.020  1.530
 X17  C20  H20   single    0.970  0.020  1.090
 X17  C21  H21   single    0.970  0.020  1.090
 X17  C21  H21A  single    0.970  0.020  1.090
 X17  C22  H22   single    0.970  0.020  1.090
 X17  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
 X17  H1B   C1   H1A   107.65  3.000
 X17  H1B   C1   H1    107.73  3.000
 X17  H1A   C1   H1    106.87  3.000
 X17  H1B   C1   C2    110.58  3.000
 X17  H1A   C1   C2    111.93  3.000
 X17  H1    C1   C2    111.85  3.000
 X17  C12   N1   C11   126.25  3.000
 X17  C12   N1   C10   125.54  3.000
 X17  C11   N1   C10   108.13  3.000
 X17  C8    O1   C7    118.55  3.000
 X17  C7    C2   C3    118.52  3.000
 X17  C3    C2   C1    120.92  3.000
 X17  C7    C2   C1    120.56  3.000
 X17  C11   N2   C9    107.73  3.000
 X17  H3    C3   C4    119.86  3.000
 X17  H3    C3   C2    117.39  3.000
 X17  C4    C3   C2    122.74  3.000
 X17  HN3A  N3   HN3   113.82  3.000
 X17  HN3A  N3   C11   118.94  3.000
 X17  HN3   N3   C11   115.38  3.000
 X17  C9    C4   C5    119.98  3.000
 X17  C9    C4   C3    122.68  3.000
 X17  C5    C4   C3    117.34  3.000
 X17  H5    C5   C6    118.78  3.000
 X17  H5    C5   C4    119.81  3.000
 X17  C6    C5   C4    121.40  3.000
 X17  H6    C6   C7    121.18  3.000
 X17  H6    C6   C5    118.61  3.000
 X17  C7    C6   C5    120.21  3.000
 X17  C6    C7   C2    119.78  3.000
 X17  C6    C7   O1    124.19  3.000
 X17  C2    C7   O1    116.03  3.000
 X17  H8B   C8   H8A   108.79  3.000
 X17  H8B   C8   H8    108.70  3.000
 X17  H8A   C8   H8    108.73  3.000
 X17  H8B   C8   O1    111.95  3.000
 X17  H8A   C8   O1    106.59  3.000
 X17  H8    C8   O1    111.98  3.000
 X17  C13   C9   C10   111.19  3.000
 X17  C10   C9   C4    109.89  3.000
 X17  C13   C9   C4    112.70  3.000
 X17  C10   C9   N2    103.94  3.000
 X17  C13   C9   N2    109.26  3.000
 X17  C4    C9   N2    109.48  3.000
 X17  C9    C10  O2    130.08  3.000
 X17  C9    C10  N1    105.22  3.000
 X17  O2    C10  N1    124.70  3.000
 X17  N3    C11  N2    126.04  3.000
 X17  N3    C11  N1    118.91  3.000
 X17  N2    C11  N1    114.96  3.000
 X17  C22   C13  C18   108.48  3.000
 X17  C18   C13  C14   107.66  3.000
 X17  C22   C13  C14   108.40  3.000
 X17  C18   C13  C9    109.16  3.000
 X17  C14   C13  C9    113.29  3.000
 X17  C22   C13  C9    109.74  3.000
 X17  H14A  C14  H14   106.78  3.000
 X17  H14A  C14  C15   109.89  3.000
 X17  H14   C14  C15   108.76  3.000
 X17  H14A  C14  C13   110.89  3.000
 X17  H14   C14  C13   109.86  3.000
 X17  C15   C14  C13   110.56  3.000
 X17  H15   C15  C21   109.53  3.000
 X17  H15   C15  C16   109.60  3.000
 X17  C21   C15  C16   109.26  3.000
 X17  H15   C15  C14   108.78  3.000
 X17  C16   C15  C14   109.46  3.000
 X17  C21   C15  C14   110.20  3.000
 X17  H16A  C16  H16   106.81  3.000
 X17  H16A  C16  C17   110.19  3.000
 X17  H16   C16  C17   110.32  3.000
 X17  H16A  C16  C15   110.14  3.000
 X17  H16   C16  C15   110.28  3.000
 X17  C17   C16  C15   109.09  3.000
 X17  H17   C17  C19   109.59  3.000
 X17  H17   C17  C18   108.90  3.000
 X17  C19   C17  C18   109.71  3.000
 X17  H17   C17  C16   109.67  3.000
 X17  C18   C17  C16   109.67  3.000
 X17  C19   C17  C16   109.28  3.000
 X17  H18A  C18  H18   106.80  3.000
 X17  H18A  C18  C17   109.44  3.000
 X17  H18   C18  C17   110.19  3.000
 X17  H18A  C18  C13   109.73  3.000
 X17  H18   C18  C13   109.80  3.000
 X17  C17   C18  C13   110.81  3.000
 X17  H19A  C19  H19   106.82  3.000
 X17  H19A  C19  C20   110.05  3.000
 X17  H19   C19  C20   110.30  3.000
 X17  H19A  C19  C17   109.99  3.000
 X17  H19   C19  C17   110.42  3.000
 X17  C20   C19  C17   109.24  3.000
 X17  H20   C20  C22   108.85  3.000
 X17  H20   C20  C21   109.76  3.000
 X17  C22   C20  C21   109.18  3.000
 X17  H20   C20  C19   109.71  3.000
 X17  C22   C20  C19   109.75  3.000
 X17  C21   C20  C19   109.57  3.000
 X17  H21A  C21  H21   106.79  3.000
 X17  H21A  C21  C20   110.29  3.000
 X17  H21   C21  C20   110.19  3.000
 X17  H21A  C21  C15   110.46  3.000
 X17  H21   C21  C15   109.92  3.000
 X17  C20   C21  C15   109.16  3.000
 X17  H22A  C22  H22   107.10  3.000
 X17  H22A  C22  C20   109.84  3.000
 X17  H22   C22  C20   108.63  3.000
 X17  H22A  C22  C13   109.95  3.000
 X17  H22   C22  C13   110.32  3.000
 X17  C20   C22  C13   110.91  3.000
 X17  H12B  C12  H12A  108.67  3.000
 X17  H12B  C12  H12   108.24  3.000
 X17  H12A  C12  H12   109.21  3.000
 X17  H12B  C12  N1    108.61  3.000
 X17  H12A  C12  N1    110.97  3.000
 X17  H12   C12  N1    111.08  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
 X17  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 X17  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 X17  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 X17  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 X17  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 X17  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 X17  CONST_07  C9   C4   C3   C2   180.00   0.0  0
 X17  CONST_08  C9   C4   C5   C6   180.00   0.0  0
 X17  CONST_09  C9   N2   C11  N1     0.00   0.0  0
 X17  CONST_10  C10  N1   C11  N2     0.00   0.0  0
 X17  CONST_11  C11  N1   C10  C9     0.00   0.0  0
 X17  CONST_12  C6   C7   C2   C1   180.00   0.0  0
 X17  CONST_13  C4   C3   C2   C1   180.00   0.0  0
 X17  CONST_14  C3   C2   C7   O1   180.00   0.0  0
 X17  CONST_15  C5   C6   C7   O1   180.00   0.0  0
 X17  CONST_16  C12  N1   C11  N2   180.00   0.0  0
 X17  CONST_17  C11  N1   C10  O2   180.00   0.0  0
 X17  CONST_18  C10  N1   C11  N3   180.00   0.0  0
 X17  CONST_19  C9   N2   C11  N3   180.00   0.0  0
 X17  CONST_20  C12  N1   C10  C9   180.00   0.0  0
 X17  CONST_21  H6   C6   C7   C2   180.00   0.0  0
 X17  CONST_22  H5   C5   C4   C3   180.00   0.0  0
 X17  CONST_23  H3   C3   C4   C5   180.00   0.0  0
 X17  CONST_24  C12  N1   C10  O2     0.00   0.0  0
 X17  CONST_25  C12  N1   C11  N3     0.00   0.0  0
 X17  CONST_26  HN3  N3   C11  N1   180.00   0.0  0
 X17  Var_01    H1   C1   C2   C3   121.34  30.0  2
 X17  Var_02    H12  C12  N1   C10  121.47  30.0  3
 X17  Var_03    H8   C8   O1   C7    62.04  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
 X17  chir_01  C9   C4   C13  C10  negativ
 X17  chir_02  C13  C9   C14  C18  positiv
 X17  chir_03  C15  C16  C21  C14  positiv
 X17  chir_04  C17  C18  C19  C16  positiv
 X17  chir_05  C20  C22  C21  C19  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
 X17  plan-1  C1    0.020
 X17  plan-1  O1    0.020
 X17  plan-1  C2    0.020
 X17  plan-1  C3    0.020
 X17  plan-1  C4    0.020
 X17  plan-1  C5    0.020
 X17  plan-1  C6    0.020
 X17  plan-1  C7    0.020
 X17  plan-1  C9    0.020
 X17  plan-1  H3    0.020
 X17  plan-1  H5    0.020
 X17  plan-1  H6    0.020
 X17  plan-2  N1    0.020
 X17  plan-2  N2    0.020
 X17  plan-2  O2    0.020
 X17  plan-2  N3    0.020
 X17  plan-2  C9    0.020
 X17  plan-2  C10   0.020
 X17  plan-2  C11   0.020
 X17  plan-2  HN3   0.020
 X17  plan-2  HN3A  0.020
 X17  plan-2  C12   0.020

