# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 03:43:50 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2E)-3-[2-(3-cyclopentyl-5,5-dimethyl-2-oxoimidazolidin-1-yl)phenyl]-N-hydroxyprop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CN(C2CCCC2)C(=O)N1c3ccccc3/C=C/C(=O)NO
#
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
 M7Y  M7Y  (2E)-3-[2-(3-cyclopentyl-5,5-dimethyl-2-oxoimidazolidin-1-yl)phenyl]-N-hydroxyprop-2-enamide  ligand  50  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M7Y
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
 M7Y  C4   C  CR6   0   0.280  -0.6645  -1.8133   0.2766
 M7Y  C5   C  CR6   0   0.109  -1.9673  -1.3083   0.3996
 M7Y  C6   C  CR16  0  -0.333  -3.0023  -2.1994   0.7017
 M7Y  C7   C  C1    0  -0.220  -2.2149   0.1227   0.2440
 M7Y  C8   C  C1    0  -0.414  -3.3941   0.6874  -0.0260
 M7Y  C17  C  CR5   0   0.060   0.8792  -0.7381  -1.4333
 M7Y  C21  C  CR15  0  -0.073   3.5739   0.4652   0.8534
 M7Y  C22  C  CH2   0  -0.473   4.8817   0.3472   0.0345
 M7Y  C24  C  CH2   0  -0.446   4.7542   2.6050   0.8019
 M7Y  C1   C  CR16  0  -0.234  -2.7553  -3.5472   0.8851
 M7Y  C2   C  CR16  0  -0.271  -1.4587  -4.0362   0.7761
 M7Y  C3   C  CR16  0  -0.251  -0.4219  -3.1695   0.4740
 M7Y  C9   C  C     0   0.540  -3.5026   2.1565  -0.1617
 M7Y  N10  N  NH1   0  -0.395  -4.7621   2.5577  -0.4444
 M7Y  O11  O  OH1   0  -0.541  -5.0644   3.8847  -0.4126
 M7Y  O12  O  O     0  -0.474  -2.5589   2.9238  -0.0690
 M7Y  N13  N  NR5   0  -0.623   0.3993  -0.9445  -0.0530
 M7Y  C14  C  CR5   0   0.707   1.4170  -0.7205   0.8484
 M7Y  N15  N  NR5   0  -0.507   2.4413  -0.1310   0.1802
 M7Y  C16  C  CH2   0  -0.273   2.0228   0.2451  -1.1506
 M7Y  C19  C  CH3   0  -0.653   1.4176  -2.0390  -2.0284
 M7Y  O20  O  O     0  -0.517   1.3832  -1.0072   2.0334
 M7Y  C23  C  CH2   0  -0.446   5.2331   1.7729  -0.3850
 M7Y  C25  C  CH2   0  -0.463   3.4036   1.9762   1.1405
 M7Y  H1   H  HCR6  0   0.259  -4.0120  -1.8275   0.8213
 M7Y  H2   H  H     0   0.262  -1.3522   0.7702   0.3489
 M7Y  H3   H  H     0   0.273  -4.2886   0.0920  -0.1744
 M7Y  H4   H  HCR5  0   0.260   3.6839  -0.0787   1.7906
 M7Y  H5   H  HCH2  0   0.244   5.6689  -0.0498   0.6785
 M7Y  H6   H  HCH2  0   0.243   4.7895  -0.3467  -0.8023
 M7Y  H7   H  HCH2  0   0.221   5.4502   2.4905   1.6377
 M7Y  H8   H  HCH2  0   0.234   4.6812   3.6712   0.5834
 M7Y  H9   H  HCR6  0   0.265  -3.5716  -4.2157   1.1251
 M7Y  H10  H  HCR6  0   0.265  -1.2570  -5.0883   0.9272
 M7Y  H11  H  HCR6  0   0.265   0.5888  -3.5452   0.3835
 M7Y  H12  H  HNH1  0   0.415  -5.5563   1.9462  -0.3150
 M7Y  H13  H  HOH1  0   0.479  -5.0936   4.1743  -1.3334
 M7Y  H14  H  HCH2  0   0.258   2.8272   0.1493  -1.8804
 M7Y  H15  H  HCH2  0   0.243   1.6623   1.2811  -1.1810
 M7Y  H16  H  HCH3  0   0.247   0.2481   0.0292  -3.3333
 M7Y  H17  H  HCH3  0   0.241  -1.0295  -0.8077  -2.4601
 M7Y  H18  H  HCH3  0   0.236  -0.5399   0.8203  -1.9701
 M7Y  H19  H  HCH3  0   0.237   2.2079  -2.4638  -1.4072
 M7Y  H20  H  HCH3  0   0.241   0.6296  -2.7852  -2.1363
 M7Y  H21  H  HCH3  0   0.243   1.8316  -1.8530  -3.0200
 M7Y  H22  H  HCH2  0   0.235   6.2935   1.9017  -0.6055
 M7Y  H23  H  HCH2  0   0.222   4.6757   2.0576  -1.2826
 M7Y  H24  H  HCH2  0   0.233   2.6327   2.3968   0.4893
 M7Y  H25  H  HCH2  0   0.243   3.0843   2.1612   2.1666
 M7Y  C18  C  CH3   0  -0.655  -0.1774  -0.1374  -2.3428

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
 M7Y  C18  C17  single    1.518  0.020  1.518
 M7Y  C19  C17  single    1.528  0.020  1.528
 M7Y  C17  C16  single    1.534  0.020  1.534
 M7Y  C17  N13  single    1.476  0.020  1.476
 M7Y  C2   C1   aromatic  1.390  0.020  1.390
 M7Y  C2   C3   aromatic  1.385  0.020  1.385
 M7Y  C1   C6   aromatic  1.382  0.020  1.382
 M7Y  C3   C4   aromatic  1.392  0.020  1.392
 M7Y  N10  O11  single    1.361  0.020  1.361
 M7Y  N10  C9   single    1.352  0.020  1.352
 M7Y  C16  N15  single    1.445  0.020  1.445
 M7Y  C6   C5   aromatic  1.399  0.020  1.399
 M7Y  C8   C9   single    1.479  0.020  1.479
 M7Y  C8   C7   double    1.335  0.020  1.335
 M7Y  C4   C5   aromatic  1.403  0.020  1.403
 M7Y  C4   N13  single    1.412  0.020  1.412
 M7Y  C5   C7   single    1.461  0.020  1.461
 M7Y  N13  C14  single    1.378  0.020  1.378
 M7Y  C9   O12  double    1.220  0.020  1.220
 M7Y  N15  C14  single    1.358  0.020  1.358
 M7Y  N15  C21  single    1.446  0.020  1.446
 M7Y  C14  O20  double    1.220  0.020  1.220
 M7Y  C22  C21  single    1.548  0.020  1.548
 M7Y  C22  C23  single    1.527  0.020  1.527
 M7Y  C21  C25  single    1.547  0.020  1.547
 M7Y  C23  C24  single    1.527  0.020  1.527
 M7Y  C25  C24  single    1.528  0.020  1.528
 M7Y  C6   H1   single    0.930  0.020  1.080
 M7Y  C7   H2   single    0.930  0.020  1.080
 M7Y  C8   H3   single    0.930  0.020  1.080
 M7Y  C21  H4   single    0.970  0.020  1.090
 M7Y  C22  H5   single    0.970  0.020  1.090
 M7Y  C22  H6   single    0.970  0.020  1.090
 M7Y  C24  H7   single    0.970  0.020  1.090
 M7Y  C24  H8   single    0.970  0.020  1.090
 M7Y  C1   H9   single    0.930  0.020  1.080
 M7Y  C2   H10  single    0.930  0.020  1.080
 M7Y  C3   H11  single    0.930  0.020  1.080
 M7Y  N10  H12  single    0.890  0.020  1.040
 M7Y  O11  H13  single    0.850  0.020  0.980
 M7Y  C16  H14  single    0.970  0.020  1.090
 M7Y  C16  H15  single    0.970  0.020  1.090
 M7Y  C18  H16  single    0.970  0.020  1.090
 M7Y  C18  H17  single    0.970  0.020  1.090
 M7Y  C18  H18  single    0.970  0.020  1.090
 M7Y  C19  H19  single    0.970  0.020  1.090
 M7Y  C19  H20  single    0.970  0.020  1.090
 M7Y  C19  H21  single    0.970  0.020  1.090
 M7Y  C23  H22  single    0.970  0.020  1.090
 M7Y  C23  H23  single    0.970  0.020  1.090
 M7Y  C25  H24  single    0.970  0.020  1.090
 M7Y  C25  H25  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
 M7Y  N13  C4   C3   120.08  3.000
 M7Y  N13  C4   C5   119.91  3.000
 M7Y  C3   C4   C5   120.02  3.000
 M7Y  C7   C5   C6   121.45  3.000
 M7Y  C7   C5   C4   120.05  3.000
 M7Y  C6   C5   C4   118.48  3.000
 M7Y  H1   C6   C1   119.13  3.000
 M7Y  H1   C6   C5   119.68  3.000
 M7Y  C1   C6   C5   121.17  3.000
 M7Y  H2   C7   C8   118.04  3.000
 M7Y  H2   C7   C5   116.11  3.000
 M7Y  C8   C7   C5   125.85  3.000
 M7Y  H3   C8   C9   118.17  3.000
 M7Y  H3   C8   C7   121.59  3.000
 M7Y  C9   C8   C7   120.22  3.000
 M7Y  C19  C17  C18  110.41  3.000
 M7Y  C19  C17  C16  110.77  3.000
 M7Y  C18  C17  C16  112.06  3.000
 M7Y  C16  C17  N13   99.18  3.000
 M7Y  C19  C17  N13  111.08  3.000
 M7Y  C18  C17  N13  112.91  3.000
 M7Y  H4   C21  C25  109.82  3.000
 M7Y  H4   C21  N15  105.89  3.000
 M7Y  C25  C21  N15  113.75  3.000
 M7Y  H4   C21  C22  109.38  3.000
 M7Y  C25  C21  C22  105.40  3.000
 M7Y  N15  C21  C22  112.59  3.000
 M7Y  H6   C22  H5   106.39  3.000
 M7Y  H6   C22  C23  113.74  3.000
 M7Y  H5   C22  C23  109.61  3.000
 M7Y  H6   C22  C21  112.51  3.000
 M7Y  H5   C22  C21  108.96  3.000
 M7Y  C23  C22  C21  105.58  3.000
 M7Y  H8   C24  H7   107.35  3.000
 M7Y  H8   C24  C25  112.80  3.000
 M7Y  H7   C24  C25  110.49  3.000
 M7Y  H8   C24  C23  113.45  3.000
 M7Y  H7   C24  C23  109.72  3.000
 M7Y  C25  C24  C23  103.01  3.000
 M7Y  H9   C1   C2   120.25  3.000
 M7Y  H9   C1   C6   119.80  3.000
 M7Y  C2   C1   C6   119.95  3.000
 M7Y  H10  C2   C3   119.97  3.000
 M7Y  H10  C2   C1   120.34  3.000
 M7Y  C3   C2   C1   119.69  3.000
 M7Y  H11  C3   C2   120.02  3.000
 M7Y  H11  C3   C4   119.29  3.000
 M7Y  C2   C3   C4   120.69  3.000
 M7Y  O12  C9   N10  123.37  3.000
 M7Y  O12  C9   C8   124.13  3.000
 M7Y  N10  C9   C8   112.47  3.000
 M7Y  H12  N10  O11  114.35  3.000
 M7Y  H12  N10  C9   121.72  3.000
 M7Y  O11  N10  C9   119.43  3.000
 M7Y  H13  O11  N10  106.07  3.000
 M7Y  C14  N13  C17  110.43  3.000
 M7Y  C14  N13  C4   120.24  3.000
 M7Y  C17  N13  C4   123.30  3.000
 M7Y  O20  C14  N15  126.95  3.000
 M7Y  O20  C14  N13  125.24  3.000
 M7Y  N15  C14  N13  107.81  3.000
 M7Y  C16  N15  C14  110.35  3.000
 M7Y  C14  N15  C21  122.73  3.000
 M7Y  C16  N15  C21  123.25  3.000
 M7Y  H15  C16  H14  107.87  3.000
 M7Y  H15  C16  N15  111.50  3.000
 M7Y  H14  C16  N15  112.33  3.000
 M7Y  H15  C16  C17  110.79  3.000
 M7Y  H14  C16  C17  111.72  3.000
 M7Y  N15  C16  C17  102.64  3.000
 M7Y  H21  C19  H20  107.52  3.000
 M7Y  H21  C19  H19  108.00  3.000
 M7Y  H20  C19  H19  108.26  3.000
 M7Y  H21  C19  C17  110.04  3.000
 M7Y  H20  C19  C17  111.49  3.000
 M7Y  H19  C19  C17  111.39  3.000
 M7Y  H23  C23  H22  107.37  3.000
 M7Y  H23  C23  C24  109.64  3.000
 M7Y  H22  C23  C24  113.44  3.000
 M7Y  H23  C23  C22  110.55  3.000
 M7Y  H22  C23  C22  112.92  3.000
 M7Y  C24  C23  C22  102.90  3.000
 M7Y  H25  C25  H24  106.79  3.000
 M7Y  H25  C25  C24  113.42  3.000
 M7Y  H24  C25  C24  109.45  3.000
 M7Y  H25  C25  C21  111.87  3.000
 M7Y  H24  C25  C21  110.04  3.000
 M7Y  C24  C25  C21  105.28  3.000
 M7Y  H18  C18  H17  108.49  3.000
 M7Y  H18  C18  H16  107.83  3.000
 M7Y  H17  C18  H16  107.51  3.000
 M7Y  H18  C18  C17  112.00  3.000
 M7Y  H17  C18  C17  111.41  3.000
 M7Y  H16  C18  C17  109.45  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
 M7Y  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 M7Y  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 M7Y  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 M7Y  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 M7Y  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 M7Y  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 M7Y  CONST_07  N13  C4   C5   C6   180.00   0.0  0
 M7Y  CONST_08  N13  C4   C3   C2   180.00   0.0  0
 M7Y  CONST_09  C16  C17  N13  C4   180.00   0.0  0
 M7Y  CONST_10  N15  C14  N13  C4   180.00   0.0  0
 M7Y  CONST_12  C21  N15  C16  C17  180.00   0.0  0
 M7Y  CONST_13  N15  C14  N13  C17    0.00   0.0  0
 M7Y  CONST_14  N13  C14  N15  C21  180.00   0.0  0
 M7Y  CONST_16  C16  N15  C14  N13    0.00   0.0  0
 M7Y  CONST_18  C1   C6   C5   C7   180.00   0.0  0
 M7Y  CONST_19  C3   C4   C5   C7   180.00   0.0  0
 M7Y  CONST_20  N13  C4   C5   C7     0.00   0.0  0
 M7Y  CONST_21  O20  C14  N13  C4     0.00   0.0  0
 M7Y  CONST_22  O20  C14  N13  C17  180.00   0.0  0
 M7Y  CONST_23  O20  C14  N15  C21    0.00   0.0  0
 M7Y  CONST_24  O20  C14  N15  C16  180.00   0.0  0
 M7Y  CONST_25  H10  C2   C3   C4   180.00   0.0  0
 M7Y  CONST_26  H1   C6   C5   C4   180.00   0.0  0
 M7Y  CONST_27  H9   C1   C6   C5   180.00   0.0  0
 M7Y  CONST_28  H11  C3   C4   C5   180.00   0.0  0
 M7Y  CONST_29  C9   C8   C7   C5   180.00   0.0  0
 M7Y  CONST_30  H3   C8   C7   C5     0.00   0.0  0
 M7Y  CONST_31  O11  N10  C9   C8   180.00   0.0  0
 M7Y  CONST_32  O12  C9   N10  O11    0.00   0.0  0
 M7Y  CONST_34  H2   C7   C8   C9     0.00   0.0  0
 M7Y  Var_01    C17  N13  C4   C5   -94.75  30.0  2
 M7Y  Var_02    C24  C23  C22  C21   34.05  30.0  1
 M7Y  Var_03    C23  C24  C25  C21   34.95  30.0  1
 M7Y  Var_04    C25  C24  C23  C22  -42.63  30.0  1
 M7Y  Var_05    C18  C17  N13  C4    62.56  30.0  1
 M7Y  Var_06    H14  C16  N15  C21   55.49  30.0  1
 M7Y  Var_07    C8   C7   C5   C4   160.58  30.0  2
 M7Y  Var_08    H16  C18  C17  N13  177.65  30.0  3
 M7Y  Var_09    H19  C19  C17  N13  -56.26  30.0  3
 M7Y  Var_10    N10  C9   C8   C7   179.55  30.0  2

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
 M7Y  chir_01  C21  N15  C22  C25  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
 M7Y  plan-1  C8   0.020
 M7Y  plan-1  C9   0.020
 M7Y  plan-1  N10  0.020
 M7Y  plan-1  O11  0.020
 M7Y  plan-1  O12  0.020
 M7Y  plan-1  H12  0.020
 M7Y  plan-2  C4   0.020
 M7Y  plan-2  C5   0.020
 M7Y  plan-2  C6   0.020
 M7Y  plan-2  C7   0.020
 M7Y  plan-2  C1   0.020
 M7Y  plan-2  C2   0.020
 M7Y  plan-2  C3   0.020
 M7Y  plan-2  N13  0.020
 M7Y  plan-2  H1   0.020
 M7Y  plan-2  H9   0.020
 M7Y  plan-2  H10  0.020
 M7Y  plan-2  H11  0.020
 M7Y  plan-3  C4   0.020
 M7Y  plan-3  C17  0.020
 M7Y  plan-3  C21  0.020
 M7Y  plan-3  N13  0.020
 M7Y  plan-3  C14  0.020
 M7Y  plan-3  N15  0.020
 M7Y  plan-3  C16  0.020
 M7Y  plan-3  O20  0.020
 M7Y  plan-4  C5   0.020
 M7Y  plan-4  C7   0.020
 M7Y  plan-4  C8   0.020
 M7Y  plan-4  C9   0.020
 M7Y  plan-4  H2   0.020
 M7Y  plan-4  H3   0.020

