# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 08:50:17 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N~2~-[(2R)-2-(3,5-dichlorophenyl)-2-(dimethylamino)acetyl]-N-({2-[(Z)-iminomethyl]pyrimidin-4-yl}methyl)-L-isoleucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)[C@H](N(C)C)c1cc(Cl)cc(Cl)c1)C(=O)NCc2ccnc(C=N)n2
#
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
 3FU  3FU  N~2~-[(2R)-2-(3,5-dichlorophenyl)-2-(dimethylamino)acetyl]-N-({2-[(Z)-iminomethyl]pyrimidin-4-yl}methyl)-L-isoleucinamide  peptide  60  32  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_3FU
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
 3FU  C11  C   CR6   0  -0.029  -4.6034  -1.1101  -2.0877
 3FU  C12  C   CR16  0  -0.184  -4.8519   0.2508  -2.1951
 3FU  C13  C   CR6   0  -0.029  -4.4156   1.0684  -1.1672
 3FU  C14  C   CR16  0  -0.256  -3.7518   0.5581  -0.0622
 3FU  C7   C   C     0   0.543  -1.3119  -1.5902   0.6048
 3FU  C8   C   CH1   0  -0.218  -2.7183  -1.3657   1.1794
 3FU  C9   C   CR6   0   0.070  -3.5118  -0.8062   0.0173
 3FU  C10  C   CR16  0  -0.214  -3.9365  -1.6503  -1.0036
 3FU  CL1  CL  CL    0  -0.114  -5.1413  -2.1565  -3.3571
 3FU  CL2  CL  CL    0  -0.112  -4.7122   2.7697  -1.2636
 3FU  N21  N   NT    0  -0.406  -3.2823  -2.5911   1.6935
 3FU  N3   N   NH1   0  -0.616  -0.4697  -0.5733   0.8423
 3FU  C2   C   CH1   0  -0.217   0.8315  -0.4492   0.2433
 3FU  C1   C   C     0   0.572   1.8849  -0.2707   1.3402
 3FU  O4   O   O     0  -0.486   1.5991  -0.2516   2.5275
 3FU  C5   C   CH1   0  -0.238   0.8470   0.6274  -0.8662
 3FU  C18  C   CH2   0  -0.419   0.4156   2.0232  -0.4094
 3FU  C20  C   CH3   0  -0.658  -0.0299   0.1785  -2.0334
 3FU  C19  C   CH3   0  -0.681   1.3054   2.7102   0.6192
 3FU  C24  C   CH2   0  -0.291   4.2632   0.0313   1.7687
 3FU  C25  C   CR6   0   0.269   5.5133   0.2756   0.9726
 3FU  C27  C   CR6   0   0.359   6.5334   0.4638  -1.0515
 3FU  C29  C   CR16  0  -0.025   7.8176   0.7379   0.7760
 3FU  C30  C   CR16  0  -0.335   6.7274   0.5240   1.5988
 3FU  N6   N   NH1   0  -0.658   3.1424  -0.1713   0.8940
 3FU  N26  N   N     0  -0.472   5.4272   0.2463  -0.3483
 3FU  N28  N   N     0  -0.396   7.7315   0.7109  -0.5487
 3FU  C31  C   C1    0  -0.105   6.3572   0.4150  -2.5218
 3FU  N32  N   N     0  -0.513   7.3238   0.6050  -3.3099
 3FU  H2   H   HCR6  0   0.302  -5.3710   0.6581  -3.0511
 3FU  H3   H   HCR6  0   0.279  -3.4302   1.2169   0.7342
 3FU  H12  H   HCH3  0   0.203  -2.3595  -2.4815   3.6176
 3FU  H13  H   HCH3  0   0.245  -2.9260  -4.0781   3.1074
 3FU  H14  H   HCH3  0   0.247  -1.4702  -3.4082   2.3954
 3FU  H15  H   HCH3  0   0.204  -4.7066  -1.6641   2.9901
 3FU  H16  H   HCH3  0   0.245  -5.2917  -2.0503   1.3652
 3FU  H17  H   HCH3  0   0.242  -5.0371  -3.3412   2.5299
 3FU  H25  H   HCH1  0   0.254  -2.6648  -0.5867   1.9614
 3FU  H26  H   HCR6  0   0.281  -3.7521  -2.7137  -0.9406
 3FU  H22  H   HNH1  0   0.400  -0.7557   0.1398   1.4939
 3FU  H1   H   HCH1  0   0.299   1.0589  -1.4067  -0.2335
 3FU  H23  H   HCH1  0   0.227   1.8733   0.6990  -1.2430
 3FU  H4   H   HCH2  0   0.236   0.3784   2.6501  -1.3041
 3FU  H5   H   HCH2  0   0.213  -0.6155   1.9826  -0.0437
 3FU  H9   H   HCH3  0   0.223  -1.0862   0.1618  -1.7566
 3FU  H10  H   HCH3  0   0.238   0.0747   0.8706  -2.8698
 3FU  H11  H   HCH3  0   0.233   0.2400  -0.8175  -2.3873
 3FU  H6   H   HCH3  0   0.239   1.0121   3.7544   0.7315
 3FU  H7   H   HCH3  0   0.223   1.2391   2.2566   1.6076
 3FU  H8   H   HCH3  0   0.221   2.3524   2.6935   0.3113
 3FU  H18  H   HCH2  0   0.280   4.4237  -0.8331   2.4213
 3FU  H19  H   HCH2  0   0.277   4.0958   0.8868   2.4299
 3FU  H20  H   HCR6  0   0.286   8.7950   0.9382   1.1988
 3FU  H21  H   HCR6  0   0.290   6.8208   0.5510   2.6753
 3FU  H24  H   HNH1  0   0.411   3.3493  -0.2014  -0.0938
 3FU  H28  H   H     0   0.244   5.3340   0.2035  -2.8362
 3FU  H29  H   H     0   0.360   7.0085   0.5324  -4.2733
 3FU  O17  O   O     0  -0.470  -1.0401  -2.5666  -0.0707
 3FU  C22  C   CH3   0  -0.539  -2.4664  -3.1552   2.7544
 3FU  C23  C   CH3   0  -0.529  -4.6403  -2.3929   2.1681

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
 3FU  N32  C31  double    1.261  0.020  1.261
 3FU  N28  C29  aromatic  1.328  0.020  1.328
 3FU  N28  C27  aromatic  1.323  0.020  1.323
 3FU  C29  C30  aromatic  1.382  0.020  1.382
 3FU  C31  C27  single    1.482  0.020  1.482
 3FU  C27  N26  aromatic  1.329  0.020  1.329
 3FU  C30  C25  aromatic  1.389  0.020  1.389
 3FU  N26  C25  aromatic  1.324  0.020  1.324
 3FU  C25  C24  single    1.502  0.020  1.502
 3FU  C19  C18  single    1.524  0.020  1.524
 3FU  C24  N6   single    1.436  0.020  1.436
 3FU  C18  C5   single    1.531  0.020  1.531
 3FU  N6   C1   single    1.338  0.020  1.338
 3FU  C5   C20  single    1.527  0.020  1.527
 3FU  C5   C2   single    1.546  0.020  1.546
 3FU  C1   C2   single    1.531  0.020  1.531
 3FU  C1   O4   double    1.221  0.020  1.221
 3FU  C2   N3   single    1.438  0.020  1.438
 3FU  N3   C7   single    1.342  0.020  1.342
 3FU  C7   O17  double    1.218  0.020  1.218
 3FU  C7   C8   single    1.536  0.020  1.536
 3FU  C22  N21  single    1.452  0.020  1.452
 3FU  N21  C8   single    1.444  0.020  1.444
 3FU  N21  C23  single    1.452  0.020  1.452
 3FU  CL2  C13  single    1.730  0.020  1.730
 3FU  C14  C13  aromatic  1.386  0.020  1.386
 3FU  C14  C9   aromatic  1.387  0.020  1.387
 3FU  C8   C9   single    1.514  0.020  1.514
 3FU  C13  C12  aromatic  1.384  0.020  1.384
 3FU  C9   C10  aromatic  1.391  0.020  1.391
 3FU  C12  C11  aromatic  1.388  0.020  1.388
 3FU  C10  C11  aromatic  1.383  0.020  1.383
 3FU  C11  CL1  single    1.731  0.020  1.731
 3FU  C2   H1   single    0.970  0.020  1.090
 3FU  C12  H2   single    0.930  0.020  1.080
 3FU  C14  H3   single    0.930  0.020  1.080
 3FU  C18  H4   single    0.970  0.020  1.090
 3FU  C18  H5   single    0.970  0.020  1.090
 3FU  C19  H6   single    0.970  0.020  1.090
 3FU  C19  H7   single    0.970  0.020  1.090
 3FU  C19  H8   single    0.970  0.020  1.090
 3FU  C20  H9   single    0.970  0.020  1.090
 3FU  C20  H10  single    0.970  0.020  1.090
 3FU  C20  H11  single    0.970  0.020  1.090
 3FU  C22  H12  single    0.970  0.020  1.090
 3FU  C22  H13  single    0.970  0.020  1.090
 3FU  C22  H14  single    0.970  0.020  1.090
 3FU  C23  H15  single    0.970  0.020  1.090
 3FU  C23  H16  single    0.970  0.020  1.090
 3FU  C23  H17  single    0.970  0.020  1.090
 3FU  C24  H18  single    0.970  0.020  1.090
 3FU  C24  H19  single    0.970  0.020  1.090
 3FU  C29  H20  single    0.930  0.020  1.080
 3FU  C30  H21  single    0.930  0.020  1.080
 3FU  N3   H22  single    0.860  0.020  1.020
 3FU  C5   H23  single    0.970  0.020  1.090
 3FU  N6   H24  single    0.860  0.020  1.020
 3FU  C8   H25  single    0.970  0.020  1.090
 3FU  C10  H26  single    0.930  0.020  1.080
 3FU  C31  H28  single    0.930  0.020  1.080
 3FU  N32  H29  single    0.890  0.020  1.040

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
 3FU  CL1  C11  C10  119.26  3.000
 3FU  CL1  C11  C12  118.72  3.000
 3FU  C10  C11  C12  122.02  3.000
 3FU  H2   C12  C13  121.13  3.000
 3FU  H2   C12  C11  121.13  3.000
 3FU  C13  C12  C11  117.74  3.000
 3FU  CL2  C13  C14  119.25  3.000
 3FU  C14  C13  C12  121.70  3.000
 3FU  CL2  C13  C12  119.05  3.000
 3FU  H3   C14  C9   120.33  3.000
 3FU  H3   C14  C13  120.31  3.000
 3FU  C9   C14  C13  119.36  3.000
 3FU  N3   C7   O17  124.45  3.000
 3FU  O17  C7   C8   121.94  3.000
 3FU  N3   C7   C8   113.45  3.000
 3FU  H25  C8   N21  111.42  3.000
 3FU  H25  C8   C9   107.93  3.000
 3FU  N21  C8   C9   112.47  3.000
 3FU  H25  C8   C7   108.88  3.000
 3FU  C9   C8   C7   104.29  3.000
 3FU  N21  C8   C7   111.53  3.000
 3FU  C10  C9   C8   119.93  3.000
 3FU  C10  C9   C14  120.12  3.000
 3FU  C8   C9   C14  119.86  3.000
 3FU  H26  C10  C9   120.13  3.000
 3FU  H26  C10  C11  120.81  3.000
 3FU  C9   C10  C11  119.06  3.000
 3FU  C8   N21  C23  111.46  3.000
 3FU  C23  N21  C22  109.85  3.000
 3FU  C8   N21  C22  111.74  3.000
 3FU  H22  N3   C2   117.73  3.000
 3FU  H22  N3   C7   118.21  3.000
 3FU  C2   N3   C7   124.05  3.000
 3FU  H1   C2   C5   107.14  3.000
 3FU  H1   C2   C1   105.74  3.000
 3FU  C5   C2   C1   115.22  3.000
 3FU  H1   C2   N3   107.11  3.000
 3FU  C1   C2   N3   109.52  3.000
 3FU  C5   C2   N3   111.60  3.000
 3FU  N6   C1   O4   122.88  3.000
 3FU  O4   C1   C2   122.49  3.000
 3FU  N6   C1   C2   114.60  3.000
 3FU  H23  C5   C20  107.11  3.000
 3FU  H23  C5   C18  107.88  3.000
 3FU  C20  C5   C18  109.53  3.000
 3FU  H23  C5   C2   107.56  3.000
 3FU  C20  C5   C2   109.76  3.000
 3FU  C18  C5   C2   114.71  3.000
 3FU  H5   C18  H4   105.22  3.000
 3FU  H5   C18  C19  109.95  3.000
 3FU  H4   C18  C19  108.30  3.000
 3FU  H5   C18  C5   109.35  3.000
 3FU  H4   C18  C5   106.75  3.000
 3FU  C19  C18  C5   116.62  3.000
 3FU  H11  C20  H10  107.87  3.000
 3FU  H11  C20  H9   107.91  3.000
 3FU  H10  C20  H9   107.27  3.000
 3FU  H11  C20  C5   111.98  3.000
 3FU  H10  C20  C5   110.15  3.000
 3FU  H9   C20  C5   111.48  3.000
 3FU  H8   C19  H7   107.93  3.000
 3FU  H8   C19  H6   107.56  3.000
 3FU  H7   C19  H6   106.79  3.000
 3FU  H8   C19  C18  111.28  3.000
 3FU  H7   C19  C18  112.90  3.000
 3FU  H6   C19  C18  110.13  3.000
 3FU  H19  C24  H18  106.23  3.000
 3FU  H19  C24  N6   111.04  3.000
 3FU  H18  C24  N6   111.48  3.000
 3FU  H19  C24  C25  108.69  3.000
 3FU  H18  C24  C25  108.80  3.000
 3FU  N6   C24  C25  110.47  3.000
 3FU  N26  C25  C30  120.71  3.000
 3FU  N26  C25  C24  118.10  3.000
 3FU  C30  C25  C24  121.19  3.000
 3FU  C31  C27  N28  119.41  3.000
 3FU  C31  C27  N26  114.89  3.000
 3FU  N28  C27  N26  125.70  3.000
 3FU  H20  C29  N28  116.84  3.000
 3FU  H20  C29  C30  120.51  3.000
 3FU  N28  C29  C30  122.65  3.000
 3FU  H21  C30  C29  121.38  3.000
 3FU  H21  C30  C25  121.95  3.000
 3FU  C29  C30  C25  116.67  3.000
 3FU  H24  N6   C24  116.12  3.000
 3FU  H24  N6   C1   121.10  3.000
 3FU  C24  N6   C1   122.74  3.000
 3FU  C27  N26  C25  118.05  3.000
 3FU  C29  N28  C27  116.22  3.000
 3FU  H28  C31  N32  124.59  3.000
 3FU  H28  C31  C27  113.82  3.000
 3FU  N32  C31  C27  121.59  3.000
 3FU  H29  N32  C31  110.11  3.000
 3FU  H14  C22  H13  107.21  3.000
 3FU  H14  C22  H12  108.19  3.000
 3FU  H13  C22  H12  107.78  3.000
 3FU  H14  C22  N21  111.31  3.000
 3FU  H13  C22  N21  109.18  3.000
 3FU  H12  C22  N21  112.95  3.000
 3FU  H17  C23  H16  107.50  3.000
 3FU  H17  C23  H15  107.84  3.000
 3FU  H16  C23  H15  107.84  3.000
 3FU  H17  C23  N21  109.28  3.000
 3FU  H16  C23  N21  111.18  3.000
 3FU  H15  C23  N21  113.01  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
 3FU  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 3FU  CONST_02  C14  C9   C10  C11     0.00   0.0  0
 3FU  CONST_03  C9   C14  C13  C12     0.00   0.0  0
 3FU  CONST_04  C9   C10  C11  C12     0.00   0.0  0
 3FU  CONST_05  C10  C9   C14  C13     0.00   0.0  0
 3FU  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 3FU  CONST_07  N28  C29  C30  C25     0.00   0.0  0
 3FU  CONST_08  N28  C27  N26  C25     0.00   0.0  0
 3FU  CONST_09  C30  C29  N28  C27     0.00   0.0  0
 3FU  CONST_10  C30  C25  N26  C27     0.00   0.0  0
 3FU  CONST_11  N26  C27  N28  C29     0.00   0.0  0
 3FU  CONST_12  N26  C25  C30  C29     0.00   0.0  0
 3FU  CONST_13  CL2  C13  C12  C11   180.00   0.0  0
 3FU  CONST_14  C8   C9   C10  C11   180.00   0.0  0
 3FU  CONST_15  C8   C9   C14  C13   180.00   0.0  0
 3FU  CONST_16  CL1  C11  C12  C13   180.00   0.0  0
 3FU  CONST_17  CL2  C13  C14  C9    180.00   0.0  0
 3FU  CONST_18  CL1  C11  C10  C9    180.00   0.0  0
 3FU  CONST_19  C29  C30  C25  C24   180.00   0.0  0
 3FU  CONST_20  C27  N26  C25  C24   180.00   0.0  0
 3FU  CONST_21  C31  C27  N26  C25   180.00   0.0  0
 3FU  CONST_22  C31  C27  N28  C29   180.00   0.0  0
 3FU  CONST_23  H3   C14  C13  C12   180.00   0.0  0
 3FU  CONST_24  H26  C10  C11  C12   180.00   0.0  0
 3FU  CONST_25  H2   C12  C13  C14   180.00   0.0  0
 3FU  CONST_26  H20  C29  C30  C25   180.00   0.0  0
 3FU  CONST_27  H21  C30  C25  N26   180.00   0.0  0
 3FU  CONST_28  C2   N3   C7   C8    180.00   0.0  0
 3FU  CONST_29  C2   N3   C7   O17     0.00   0.0  0
 3FU  CONST_30  C24  N6   C1   C2    180.00   0.0  0
 3FU  CONST_31  C24  N6   C1   O4      0.00   0.0  0
 3FU  CONST_32  H22  N3   C7   C8      0.00   0.0  0
 3FU  CONST_33  H24  N6   C1   C2      0.00   0.0  0
 3FU  Var_01    N6   C24  C25  C30   178.78  30.0  2
 3FU  Var_02    N32  C31  C27  N26   179.92  30.0  2
 3FU  Var_03    C25  C24  N6   C1   -172.85  30.0  1
 3FU  Var_04    H15  C23  N21  C22    63.43  30.0  3
 3FU  Var_05    H12  C22  N21  C23   -63.86  30.0  3
 3FU  Var_06    H6   C19  C18  C5    169.58  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
 3FU  chir_01  C8  C7  N21  C9   positiv
 3FU  chir_02  C2  N3  C5   C1   negativ
 3FU  chir_03  C5  C2  C20  C18  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
 3FU  plan-1  C11  0.020
 3FU  plan-1  C12  0.020
 3FU  plan-1  C13  0.020
 3FU  plan-1  C14  0.020
 3FU  plan-1  C8   0.020
 3FU  plan-1  C9   0.020
 3FU  plan-1  C10  0.020
 3FU  plan-1  CL1  0.020
 3FU  plan-1  CL2  0.020
 3FU  plan-1  H2   0.020
 3FU  plan-1  H3   0.020
 3FU  plan-1  H26  0.020
 3FU  plan-2  C24  0.020
 3FU  plan-2  C25  0.020
 3FU  plan-2  C27  0.020
 3FU  plan-2  C29  0.020
 3FU  plan-2  C30  0.020
 3FU  plan-2  N26  0.020
 3FU  plan-2  N28  0.020
 3FU  plan-2  C31  0.020
 3FU  plan-2  H20  0.020
 3FU  plan-2  H21  0.020
 3FU  plan-3  C7   0.020
 3FU  plan-3  C8   0.020
 3FU  plan-3  N3   0.020
 3FU  plan-3  C2   0.020
 3FU  plan-3  H22  0.020
 3FU  plan-3  O17  0.020
 3FU  plan-4  C2   0.020
 3FU  plan-4  C1   0.020
 3FU  plan-4  O4   0.020
 3FU  plan-4  C24  0.020
 3FU  plan-4  N6   0.020
 3FU  plan-4  H24  0.020
 3FU  plan-5  C27  0.020
 3FU  plan-5  C31  0.020
 3FU  plan-5  N32  0.020
 3FU  plan-5  H28  0.020
 3FU  plan-5  H29  0.020

