# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 21:25:11 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cc(NC(=O)NC(N)=O)ccc1C)c2cccc3ccccc23
#
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
 Y95  Y95  5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide  ligand  51  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y95
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
 Y95  O28  O  O     0  -0.515  54.9941  38.7390  -0.2086
 Y95  C27  C  C     0   0.651  54.5887  37.5876  -0.2289
 Y95  N29  N  NH2   0  -0.822  55.3618  36.5181  -0.4387
 Y95  N25  N  NH1   0  -0.752  53.2245  37.3627  -0.0259
 Y95  C24  C  C     0   0.774  52.5389  36.1680   0.0088
 Y95  O26  O  O     0  -0.499  53.0722  35.0836  -0.1564
 Y95  N01  N  NH1   0  -0.786  51.2108  36.3375   0.2451
 Y95  C19  C  CR6   0   0.379  50.2193  35.3597   0.3610
 Y95  C13  C  CR16  0  -0.343  50.4215  33.9938   0.1786
 Y95  C3   C  CR6   0  -0.058  49.3595  33.1016   0.3012
 Y95  C10  C  CR6   0   0.075  48.0683  33.5330   0.6143
 Y95  C16  C  CH3   0  -0.732  46.9066  32.5939   0.7682
 Y95  C17  C  CR16  0  -0.289  47.8933  34.9002   0.8083
 Y95  C21  C  CR16  0  -0.331  48.9358  35.7997   0.6810
 Y95  C1   C  C     0   0.492  49.6390  31.6543   0.0363
 Y95  O7   O  O     0  -0.471  48.9925  31.0030  -0.7693
 Y95  N2   N  NH1   0  -0.635  50.6626  31.1393   0.7401
 Y95  C6   C  CH1   0  -0.146  51.1094  29.7727   0.5738
 Y95  C01  C  CH3   0  -0.671  51.9046  29.3549   1.8073
 Y95  C5   C  CR6   0   0.118  51.9320  29.5840  -0.6877
 Y95  C8   C  CR66  0   0.097  51.9556  28.3240  -1.3555
 Y95  C11  C  CR66  0   0.111  52.7712  28.1687  -2.5113
 Y95  C12  C  CR16  0  -0.333  53.5476  29.2568  -2.9715
 Y95  C9   C  CR16  0  -0.241  53.5190  30.4499  -2.3086
 Y95  C4   C  CR16  0  -0.334  52.7091  30.6069  -1.1670
 Y95  C18  C  CR16  0  -0.310  52.7986  26.9250  -3.1852
 Y95  C22  C  CR16  0  -0.261  52.0576  25.8664  -2.7390
 Y95  C20  C  CR16  0  -0.248  51.2504  26.0117  -1.5936
 Y95  C14  C  CR16  0  -0.343  51.2020  27.2037  -0.9224
 Y95  H1   H  HNH2  0   0.408  56.3507  36.6589  -0.5509
 Y95  H2   H  HNH2  0   0.422  54.9920  35.5817  -0.4203
 Y95  H3   H  HNH1  0   0.420  52.7099  38.2182   0.1247
 Y95  H4   H  HNH1  0   0.421  50.8821  37.2814   0.3846
 Y95  H5   H  HCR6  0   0.295  51.3983  33.6199  -0.0817
 Y95  H6   H  HCH3  0   0.243  47.1552  31.7356   1.3930
 Y95  H7   H  HCH3  0   0.245  46.0642  33.1052   1.2317
 Y95  H8   H  HCH3  0   0.252  46.5726  32.2050  -0.1934
 Y95  H9   H  HCR6  0   0.259  46.9127  35.2761   1.0727
 Y95  H10  H  HCR6  0   0.276  48.7481  36.8558   0.8355
 Y95  H11  H  HNH1  0   0.409  51.1116  31.7125   1.4370
 Y95  H12  H  HCH1  0   0.257  50.2144  29.1508   0.5149
 Y95  H13  H  HCH3  0   0.249  51.2864  29.4099   2.7040
 Y95  H14  H  HCH3  0   0.250  52.2591  28.3302   1.7060
 Y95  H15  H  HCH3  0   0.237  52.7771  29.9954   1.9443
 Y95  H16  H  HCR6  0   0.255  54.1655  29.1284  -3.8519
 Y95  H17  H  HCR6  0   0.256  54.1171  31.2827  -2.6547
 Y95  H18  H  HCR6  0   0.246  52.7086  31.5656  -0.6639
 Y95  H19  H  HCR6  0   0.256  53.4228  26.8262  -4.0653
 Y95  H20  H  HCR6  0   0.258  52.0886  24.9189  -3.2608
 Y95  H21  H  HCR6  0   0.260  50.6621  25.1741  -1.2421
 Y95  H22  H  HCR6  0   0.249  50.5708  27.2758  -0.0474

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
 Y95  C22  C18  aromatic  1.367  0.020  1.367
 Y95  C22  C20  aromatic  1.409  0.020  1.409
 Y95  C18  C11  aromatic  1.415  0.020  1.415
 Y95  C20  C14  aromatic  1.369  0.020  1.369
 Y95  N29  C27  single    1.336  0.020  1.336
 Y95  C11  C12  aromatic  1.414  0.020  1.414
 Y95  C11  C8   aromatic  1.423  0.020  1.423
 Y95  C14  C8   aromatic  1.418  0.020  1.418
 Y95  O26  C24  double    1.220  0.020  1.220
 Y95  C12  C9   aromatic  1.365  0.020  1.365
 Y95  C27  O28  double    1.221  0.020  1.221
 Y95  C27  N25  single    1.397  0.020  1.397
 Y95  C8   C5   aromatic  1.426  0.020  1.426
 Y95  O7   C1   double    1.221  0.020  1.221
 Y95  C24  N25  single    1.378  0.020  1.378
 Y95  C24  N01  single    1.360  0.020  1.360
 Y95  C9   C4   aromatic  1.408  0.020  1.408
 Y95  N01  C19  single    1.397  0.020  1.397
 Y95  C13  C19  aromatic  1.393  0.020  1.393
 Y95  C13  C3   aromatic  1.392  0.020  1.392
 Y95  C5   C4   aromatic  1.371  0.020  1.371
 Y95  C5   C6   single    1.518  0.020  1.518
 Y95  C1   C3   single    1.498  0.020  1.498
 Y95  C1   N2   single    1.345  0.020  1.345
 Y95  C19  C21  aromatic  1.394  0.020  1.394
 Y95  C3   C10  aromatic  1.397  0.020  1.397
 Y95  C21  C17  aromatic  1.383  0.020  1.383
 Y95  C10  C17  aromatic  1.392  0.020  1.392
 Y95  C10  C16  single    1.502  0.020  1.502
 Y95  C6   N2   single    1.447  0.020  1.447
 Y95  C6   C01  single    1.526  0.020  1.526
 Y95  N29  H1   single    0.860  0.020  1.020
 Y95  N29  H2   single    0.860  0.020  1.020
 Y95  N25  H3   single    0.860  0.020  1.020
 Y95  N01  H4   single    0.860  0.020  1.020
 Y95  C13  H5   single    0.930  0.020  1.080
 Y95  C16  H6   single    0.970  0.020  1.090
 Y95  C16  H7   single    0.970  0.020  1.090
 Y95  C16  H8   single    0.970  0.020  1.090
 Y95  C17  H9   single    0.930  0.020  1.080
 Y95  C21  H10  single    0.930  0.020  1.080
 Y95  N2   H11  single    0.860  0.020  1.020
 Y95  C6   H12  single    0.970  0.020  1.090
 Y95  C01  H13  single    0.970  0.020  1.090
 Y95  C01  H14  single    0.970  0.020  1.090
 Y95  C01  H15  single    0.970  0.020  1.090
 Y95  C12  H16  single    0.930  0.020  1.080
 Y95  C9   H17  single    0.930  0.020  1.080
 Y95  C4   H18  single    0.930  0.020  1.080
 Y95  C18  H19  single    0.930  0.020  1.080
 Y95  C22  H20  single    0.930  0.020  1.080
 Y95  C20  H21  single    0.930  0.020  1.080
 Y95  C14  H22  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
 Y95  N25  C27  N29  117.31  3.000
 Y95  N25  C27  O28  118.27  3.000
 Y95  N29  C27  O28  124.42  3.000
 Y95  H2   N29  H1   119.58  3.000
 Y95  H2   N29  C27  121.94  3.000
 Y95  H1   N29  C27  118.34  3.000
 Y95  H3   N25  C24  118.51  3.000
 Y95  H3   N25  C27  112.51  3.000
 Y95  C24  N25  C27  128.97  3.000
 Y95  N01  C24  O26  124.16  3.000
 Y95  N01  C24  N25  112.48  3.000
 Y95  O26  C24  N25  123.36  3.000
 Y95  H4   N01  C19  114.32  3.000
 Y95  H4   N01  C24  117.31  3.000
 Y95  C19  N01  C24  128.34  3.000
 Y95  C21  C19  C13  118.25  3.000
 Y95  C21  C19  N01  116.84  3.000
 Y95  C13  C19  N01  124.91  3.000
 Y95  H5   C13  C3   119.35  3.000
 Y95  H5   C13  C19  120.23  3.000
 Y95  C3   C13  C19  120.40  3.000
 Y95  C1   C3   C10  120.70  3.000
 Y95  C10  C3   C13  121.79  3.000
 Y95  C1   C3   C13  117.47  3.000
 Y95  C17  C10  C16  120.18  3.000
 Y95  C16  C10  C3   123.02  3.000
 Y95  C17  C10  C3   116.79  3.000
 Y95  H8   C16  H7   107.82  3.000
 Y95  H8   C16  H6   107.13  3.000
 Y95  H7   C16  H6   107.59  3.000
 Y95  H8   C16  C10  111.71  3.000
 Y95  H7   C16  C10  110.39  3.000
 Y95  H6   C16  C10  112.00  3.000
 Y95  H9   C17  C21  118.64  3.000
 Y95  H9   C17  C10  119.26  3.000
 Y95  C21  C17  C10  122.10  3.000
 Y95  H10  C21  C17  119.36  3.000
 Y95  H10  C21  C19  119.98  3.000
 Y95  C17  C21  C19  120.66  3.000
 Y95  N2   C1   O7   122.96  3.000
 Y95  N2   C1   C3   114.81  3.000
 Y95  O7   C1   C3   122.22  3.000
 Y95  H11  N2   C6   118.61  3.000
 Y95  H11  N2   C1   118.89  3.000
 Y95  C6   N2   C1   122.45  3.000
 Y95  H12  C6   C5   109.19  3.000
 Y95  H12  C6   C01  108.36  3.000
 Y95  C5   C6   C01  110.82  3.000
 Y95  H12  C6   N2   106.92  3.000
 Y95  C01  C6   N2   109.06  3.000
 Y95  C5   C6   N2   112.34  3.000
 Y95  H15  C01  H14  107.68  3.000
 Y95  H15  C01  H13  108.70  3.000
 Y95  H14  C01  H13  107.96  3.000
 Y95  H15  C01  C6   110.95  3.000
 Y95  H14  C01  C6   110.61  3.000
 Y95  H13  C01  C6   110.82  3.000
 Y95  C4   C5   C8   119.08  3.000
 Y95  C4   C5   C6   120.33  3.000
 Y95  C8   C5   C6   120.53  3.000
 Y95  C14  C8   C11  117.81  3.000
 Y95  C14  C8   C5   123.11  3.000
 Y95  C11  C8   C5   119.09  3.000
 Y95  C18  C11  C12  120.72  3.000
 Y95  C12  C11  C8   119.69  3.000
 Y95  C18  C11  C8   119.60  3.000
 Y95  H16  C12  C9   120.68  3.000
 Y95  H16  C12  C11  119.12  3.000
 Y95  C9   C12  C11  120.20  3.000
 Y95  H17  C9   C4   119.43  3.000
 Y95  H17  C9   C12  120.37  3.000
 Y95  C4   C9   C12  120.20  3.000
 Y95  H18  C4   C9   118.39  3.000
 Y95  H18  C4   C5   119.87  3.000
 Y95  C9   C4   C5   121.74  3.000
 Y95  H19  C18  C22  120.45  3.000
 Y95  H19  C18  C11  118.57  3.000
 Y95  C22  C18  C11  120.98  3.000
 Y95  H20  C22  C20  119.92  3.000
 Y95  H20  C22  C18  120.34  3.000
 Y95  C20  C22  C18  119.74  3.000
 Y95  H21  C20  C14  119.70  3.000
 Y95  H21  C20  C22  119.72  3.000
 Y95  C14  C20  C22  120.58  3.000
 Y95  H22  C14  C20  118.40  3.000
 Y95  H22  C14  C8   120.31  3.000
 Y95  C20  C14  C8   121.30  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
 Y95  CONST_01  C10  C3   C13  C19     0.00   0.0  0
 Y95  CONST_02  C10  C17  C21  C19     0.00   0.0  0
 Y95  CONST_03  C17  C21  C19  C13     0.00   0.0  0
 Y95  CONST_04  C17  C10  C3   C13     0.00   0.0  0
 Y95  CONST_05  C21  C19  C13  C3      0.00   0.0  0
 Y95  CONST_06  C21  C17  C10  C3      0.00   0.0  0
 Y95  CONST_07  C18  C11  C8   C5    180.00   0.0  0
 Y95  CONST_08  C12  C11  C8   C5      0.00   0.0  0
 Y95  CONST_09  C20  C14  C8   C5    180.00   0.0  0
 Y95  CONST_10  C12  C9   C4   C5      0.00   0.0  0
 Y95  CONST_11  C22  C18  C11  C8      0.00   0.0  0
 Y95  CONST_12  C9   C12  C11  C8      0.00   0.0  0
 Y95  CONST_13  C22  C20  C14  C8      0.00   0.0  0
 Y95  CONST_14  C9   C4   C5   C8      0.00   0.0  0
 Y95  CONST_15  C20  C22  C18  C11     0.00   0.0  0
 Y95  CONST_16  C4   C9   C12  C11     0.00   0.0  0
 Y95  CONST_17  C20  C14  C8   C11     0.00   0.0  0
 Y95  CONST_18  C4   C5   C8   C11     0.00   0.0  0
 Y95  CONST_19  C22  C18  C11  C12   180.00   0.0  0
 Y95  CONST_20  C14  C8   C11  C12   180.00   0.0  0
 Y95  CONST_21  C18  C11  C12  C9    180.00   0.0  0
 Y95  CONST_22  C14  C8   C5   C4    180.00   0.0  0
 Y95  CONST_23  C14  C20  C22  C18     0.00   0.0  0
 Y95  CONST_24  C14  C8   C11  C18     0.00   0.0  0
 Y95  CONST_25  C3   C13  C19  N01   180.00   0.0  0
 Y95  CONST_26  C17  C21  C19  N01   180.00   0.0  0
 Y95  CONST_27  C1   C3   C13  C19   180.00   0.0  0
 Y95  CONST_28  C16  C10  C3   C13   180.00   0.0  0
 Y95  CONST_29  C21  C17  C10  C16   180.00   0.0  0
 Y95  CONST_30  C1   C3   C10  C17   180.00   0.0  0
 Y95  CONST_31  C11  C8   C5   C6    180.00   0.0  0
 Y95  CONST_32  C14  C8   C5   C6      0.00   0.0  0
 Y95  CONST_33  C9   C4   C5   C6    180.00   0.0  0
 Y95  CONST_34  H9   C17  C21  C19   180.00   0.0  0
 Y95  CONST_35  H10  C21  C19  C13   180.00   0.0  0
 Y95  CONST_36  H5   C13  C3   C10   180.00   0.0  0
 Y95  CONST_37  H22  C14  C8   C5      0.00   0.0  0
 Y95  CONST_38  H17  C9   C4   C5    180.00   0.0  0
 Y95  CONST_39  H19  C18  C11  C8    180.00   0.0  0
 Y95  CONST_40  H16  C12  C11  C8    180.00   0.0  0
 Y95  CONST_41  H21  C20  C14  C8    180.00   0.0  0
 Y95  CONST_42  H18  C4   C5   C8    180.00   0.0  0
 Y95  CONST_43  H20  C22  C18  C11   180.00   0.0  0
 Y95  CONST_44  C13  C19  N01  C24     0.00   0.0  0
 Y95  CONST_45  C21  C19  N01  C24   180.00   0.0  0
 Y95  CONST_46  H4   N01  C19  C13   180.00   0.0  0
 Y95  CONST_47  C19  N01  C24  O26     0.00   0.0  0
 Y95  CONST_48  C6   N2   C1   C3    180.00   0.0  0
 Y95  CONST_49  C19  N01  C24  N25   180.00   0.0  0
 Y95  CONST_50  H11  N2   C1   C3      0.00   0.0  0
 Y95  CONST_51  C24  N25  C27  O28   180.00   0.0  0
 Y95  CONST_52  O26  C24  N25  C27     0.00   0.0  0
 Y95  CONST_53  C6   N2   C1   O7      0.00   0.0  0
 Y95  CONST_54  N01  C24  N25  C27   180.00   0.0  0
 Y95  CONST_55  C24  N25  C27  N29     0.00   0.0  0
 Y95  CONST_56  H1   N29  C27  O28     0.00   0.0  0
 Y95  CONST_57  H2   N29  C27  O28   180.00   0.0  0
 Y95  CONST_58  H3   N25  C27  O28     0.00   0.0  0
 Y95  Var_01    O7   C1   C3   C13  -126.03  30.0  2
 Y95  Var_02    H6   C16  C10  C3     47.07  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
 Y95  chir_01  C6  C5  N2  C01  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
 Y95  plan-1  N01  0.020
 Y95  plan-1  C19  0.020
 Y95  plan-1  C13  0.020
 Y95  plan-1  C3   0.020
 Y95  plan-1  C10  0.020
 Y95  plan-1  C16  0.020
 Y95  plan-1  C17  0.020
 Y95  plan-1  C21  0.020
 Y95  plan-1  C1   0.020
 Y95  plan-1  H5   0.020
 Y95  plan-1  H9   0.020
 Y95  plan-1  H10  0.020
 Y95  plan-2  C6   0.020
 Y95  plan-2  C5   0.020
 Y95  plan-2  C8   0.020
 Y95  plan-2  C11  0.020
 Y95  plan-2  C12  0.020
 Y95  plan-2  C9   0.020
 Y95  plan-2  C4   0.020
 Y95  plan-2  C18  0.020
 Y95  plan-2  C22  0.020
 Y95  plan-2  C20  0.020
 Y95  plan-2  C14  0.020
 Y95  plan-2  H16  0.020
 Y95  plan-2  H17  0.020
 Y95  plan-2  H18  0.020
 Y95  plan-2  H19  0.020
 Y95  plan-2  H20  0.020
 Y95  plan-2  H21  0.020
 Y95  plan-2  H22  0.020
 Y95  plan-3  O28  0.020
 Y95  plan-3  C27  0.020
 Y95  plan-3  N29  0.020
 Y95  plan-3  N25  0.020
 Y95  plan-3  C24  0.020
 Y95  plan-3  O26  0.020
 Y95  plan-3  N01  0.020
 Y95  plan-3  C19  0.020
 Y95  plan-3  H1   0.020
 Y95  plan-3  H2   0.020
 Y95  plan-3  H3   0.020
 Y95  plan-3  H4   0.020
 Y95  plan-4  C3   0.020
 Y95  plan-4  C1   0.020
 Y95  plan-4  O7   0.020
 Y95  plan-4  N2   0.020
 Y95  plan-4  C6   0.020
 Y95  plan-4  H11  0.020

