# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 06:22:35 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (3R)-3-{[(benzyloxy)carbonyl]amino}-2-oxo-4-phenylbutane-1-diazonium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N[C@H](Cc1ccccc1)C(=O)C[N+]#N)OCc2ccccc2
#
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
 ZFB  ZFB  (3R)-3-{[(benzyloxy)carbonyl]amino}-2-oxo-4-phenylbutane-1-diazonium  L-peptide  42  24  .  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_ZFB
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
 ZFB  N1    N  NH1   0  -0.667   0.5971  -0.0809  -0.1989
 ZFB  C1    C  C     0   0.792  -0.2765  -0.8261   0.5093
 ZFB  O1    O  O     0  -0.517   0.0819  -1.7124   1.2631
 ZFB  O2    O  O2    0  -0.467  -1.5345  -0.4902   0.2687
 ZFB  C2    C  CH2   0  -0.249  -2.5549  -1.2378   0.9543
 ZFB  C3    C  CR6   0   0.074  -3.8734  -0.7154   0.4751
 ZFB  C4    C  CR16  0  -0.288  -4.4846  -1.2690  -0.6463
 ZFB  C5    C  CR16  0  -0.242  -5.6949  -0.7697  -1.1068
 ZFB  C6    C  CR16  0  -0.260  -6.3042   0.2914  -0.4492
 ZFB  C7    C  CR16  0  -0.242  -5.7006   0.8495   0.6704
 ZFB  C8    C  CR16  0  -0.288  -4.4900   0.3478   1.1283
 ZFB  C9    C  CH1   0  -0.169   1.9953  -0.2450   0.0671
 ZFB  C10   C  C     0   0.388   2.3795  -1.6959  -0.1672
 ZFB  O3    O  O     0  -0.317   2.0814  -2.3499  -1.1191
 ZFB  C11   C  CH2   0  -0.398   3.2680  -2.2602   0.9497
 ZFB  N2    N  N     1   0.286   3.6831  -3.5668   0.5808
 ZFB  N3    N  N     0   0.124   3.9661  -4.5595   0.2390
 ZFB  C12   C  CH2   0  -0.554   2.8454   0.6382  -0.8601
 ZFB  C13   C  CR6   0   0.120   2.5527   2.0985  -0.6469
 ZFB  C14   C  CR16  0  -0.294   3.0489   2.7605   0.4748
 ZFB  C15   C  CR16  0  -0.238   2.7589   4.0993   0.6900
 ZFB  C16   C  CR16  0  -0.264   1.9656   4.7957  -0.2146
 ZFB  C17   C  CR16  0  -0.240   1.4699   4.1462  -1.3356
 ZFB  C18   C  CR16  0  -0.321   1.7637   2.8047  -1.5500
 ZFB  HN1   H  HNH1  0   0.419   0.2765   0.6997  -0.7522
 ZFB  H21   H  HCH2  0   0.257  -2.4491  -2.3001   0.7287
 ZFB  H22   H  HCH2  0   0.257  -2.4481  -1.1021   2.0318
 ZFB  H4    H  HCR6  0   0.256  -4.0149  -2.0992  -1.1606
 ZFB  H5    H  HCR6  0   0.259  -6.1648  -1.2108  -1.9762
 ZFB  H6    H  HCR6  0   0.260  -7.2502   0.6789  -0.8047
 ZFB  H7    H  HCR6  0   0.259  -6.1747   1.6722   1.1896
 ZFB  H8    H  HCR6  0   0.256  -4.0236   0.7831   2.0043
 ZFB  H9    H  HCH1  0   0.306   2.2272   0.0169   1.1072
 ZFB  H111  H  HCH2  0   0.406   4.1800  -1.6841   1.1213
 ZFB  H112  H  HCH2  0   0.414   2.7182  -2.3621   1.8881
 ZFB  H121  H  HCH2  0   0.293   3.8998   0.4367  -0.6585
 ZFB  H122  H  HCH2  0   0.290   2.6561   0.3531  -1.8967
 ZFB  H14   H  HCR6  0   0.255   3.6732   2.2269   1.1827
 ZFB  H15   H  HCR6  0   0.260   3.1560   4.6015   1.5625
 ZFB  H16   H  HCR6  0   0.260   1.7385   5.8402  -0.0462
 ZFB  H17   H  HCR6  0   0.261   0.8562   4.6819  -2.0480
 ZFB  H18   H  HCR6  0   0.262   1.3807   2.3072  -2.4337

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
 ZFB  N1   C1    single    1.349  0.020  1.349
 ZFB  N1   C9    single    1.433  0.020  1.433
 ZFB  N1   HN1   single    0.860  0.020  1.020
 ZFB  C1   O1    double    1.217  0.020  1.217
 ZFB  C1   O2    single    1.324  0.020  1.324
 ZFB  O2   C2    single    1.439  0.020  1.439
 ZFB  C2   C3    single    1.497  0.020  1.497
 ZFB  C2   H21   single    0.970  0.020  1.090
 ZFB  C2   H22   single    0.970  0.020  1.090
 ZFB  C3   C4    aromatic  1.392  0.020  1.392
 ZFB  C3   C8    aromatic  1.392  0.020  1.392
 ZFB  C4   C5    aromatic  1.388  0.020  1.388
 ZFB  C4   H4    single    0.930  0.020  1.080
 ZFB  C5   C6    aromatic  1.389  0.020  1.389
 ZFB  C5   H5    single    0.930  0.020  1.080
 ZFB  C6   C7    aromatic  1.389  0.020  1.389
 ZFB  C6   H6    single    0.930  0.020  1.080
 ZFB  C7   C8    aromatic  1.388  0.020  1.388
 ZFB  C7   H7    single    0.930  0.020  1.080
 ZFB  C8   H8    single    0.930  0.020  1.080
 ZFB  C9   C10   single    1.519  0.020  1.519
 ZFB  C9   C12   single    1.537  0.020  1.537
 ZFB  C9   H9    single    0.970  0.020  1.090
 ZFB  C10  O3    double    1.193  0.020  1.193
 ZFB  C10  C11   single    1.535  0.020  1.535
 ZFB  C11  N2    single    1.420  0.020  1.420
 ZFB  C11  H111  single    0.970  0.020  1.090
 ZFB  C11  H112  single    0.970  0.020  1.090
 ZFB  N2   N3    triple    1.087  0.020  1.087
 ZFB  C12  C13   single    1.504  0.020  1.504
 ZFB  C12  H121  single    0.970  0.020  1.090
 ZFB  C12  H122  single    0.970  0.020  1.090
 ZFB  C13  C14   aromatic  1.394  0.020  1.394
 ZFB  C13  C18   aromatic  1.392  0.020  1.392
 ZFB  C14  C15   aromatic  1.387  0.020  1.387
 ZFB  C14  H14   single    0.930  0.020  1.080
 ZFB  C15  C16   aromatic  1.390  0.020  1.390
 ZFB  C15  H15   single    0.930  0.020  1.080
 ZFB  C16  C17   aromatic  1.387  0.020  1.387
 ZFB  C16  H16   single    0.930  0.020  1.080
 ZFB  C17  C18   aromatic  1.390  0.020  1.390
 ZFB  C17  H17   single    0.930  0.020  1.080
 ZFB  C18  H18   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
 ZFB  HN1   N1   C9    120.03  3.000
 ZFB  HN1   N1   C1    120.62  3.000
 ZFB  C9    N1   C1    118.12  3.000
 ZFB  O2    C1   O1    125.23  3.000
 ZFB  O2    C1   N1    112.32  3.000
 ZFB  O1    C1   N1    122.44  3.000
 ZFB  C2    O2   C1    117.09  3.000
 ZFB  H22   C2   H21   108.40  3.000
 ZFB  H22   C2   C3    111.03  3.000
 ZFB  H21   C2   C3    111.04  3.000
 ZFB  H22   C2   O2    109.66  3.000
 ZFB  H21   C2   O2    109.79  3.000
 ZFB  C3    C2   O2    106.91  3.000
 ZFB  C8    C3   C4    119.17  3.000
 ZFB  C8    C3   C2    120.43  3.000
 ZFB  C4    C3   C2    120.39  3.000
 ZFB  H4    C4   C5    119.74  3.000
 ZFB  H4    C4   C3    119.78  3.000
 ZFB  C5    C4   C3    120.48  3.000
 ZFB  H5    C5   C6    120.08  3.000
 ZFB  H5    C5   C4    119.91  3.000
 ZFB  C6    C5   C4    120.01  3.000
 ZFB  H6    C6   C7    120.05  3.000
 ZFB  H6    C6   C5    120.09  3.000
 ZFB  C7    C6   C5    119.86  3.000
 ZFB  H7    C7   C8    119.90  3.000
 ZFB  H7    C7   C6    120.12  3.000
 ZFB  C8    C7   C6    119.98  3.000
 ZFB  H8    C8   C7    119.79  3.000
 ZFB  H8    C8   C3    119.71  3.000
 ZFB  C7    C8   C3    120.50  3.000
 ZFB  H9    C9   C12   108.52  3.000
 ZFB  H9    C9   C10   108.71  3.000
 ZFB  C12   C9   C10   108.42  3.000
 ZFB  H9    C9   N1    110.79  3.000
 ZFB  C12   C9   N1    111.22  3.000
 ZFB  C10   C9   N1    109.12  3.000
 ZFB  C11   C10  O3    121.59  3.000
 ZFB  C11   C10  C9    112.67  3.000
 ZFB  O3    C10  C9    125.70  3.000
 ZFB  H112  C11  H111  109.54  3.000
 ZFB  H112  C11  N2    106.54  3.000
 ZFB  H111  C11  N2    106.39  3.000
 ZFB  H112  C11  C10   111.59  3.000
 ZFB  H111  C11  C10   113.81  3.000
 ZFB  N2    C11  C10   108.58  3.000
 ZFB  N3    N2   C11   180.00  3.000
 ZFB  H122  C12  H121  107.12  3.000
 ZFB  H122  C12  C13   110.75  3.000
 ZFB  H121  C12  C13   109.92  3.000
 ZFB  H122  C12  C9    109.07  3.000
 ZFB  H121  C12  C9    108.46  3.000
 ZFB  C13   C12  C9    111.39  3.000
 ZFB  C18   C13  C14   118.88  3.000
 ZFB  C18   C13  C12   120.72  3.000
 ZFB  C14   C13  C12   120.38  3.000
 ZFB  H14   C14  C15   119.62  3.000
 ZFB  H14   C14  C13   119.78  3.000
 ZFB  C15   C14  C13   120.60  3.000
 ZFB  H15   C15  C16   120.10  3.000
 ZFB  H15   C15  C14   119.76  3.000
 ZFB  C16   C15  C14   120.14  3.000
 ZFB  H16   C16  C17   120.18  3.000
 ZFB  H16   C16  C15   120.13  3.000
 ZFB  C17   C16  C15   119.68  3.000
 ZFB  H17   C17  C18   119.74  3.000
 ZFB  H17   C17  C16   120.19  3.000
 ZFB  C18   C17  C16   120.07  3.000
 ZFB  H18   C18  C17   119.60  3.000
 ZFB  H18   C18  C13   119.76  3.000
 ZFB  C17   C18  C13   120.63  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
 ZFB  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 ZFB  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 ZFB  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 ZFB  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 ZFB  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 ZFB  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 ZFB  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 ZFB  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 ZFB  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 ZFB  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 ZFB  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 ZFB  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 ZFB  CONST_13  C5   C4   C3   C2    180.00   0.0  0
 ZFB  CONST_14  C7   C8   C3   C2    180.00   0.0  0
 ZFB  CONST_15  C15  C14  C13  C12   180.00   0.0  0
 ZFB  CONST_16  C17  C18  C13  C12   180.00   0.0  0
 ZFB  CONST_17  H5   C5   C4   C3    180.00   0.0  0
 ZFB  CONST_18  H7   C7   C8   C3    180.00   0.0  0
 ZFB  CONST_19  H8   C8   C3   C4    180.00   0.0  0
 ZFB  CONST_20  H6   C6   C5   C4    180.00   0.0  0
 ZFB  CONST_21  H4   C4   C5   C6    180.00   0.0  0
 ZFB  CONST_22  H15  C15  C14  C13   180.00   0.0  0
 ZFB  CONST_23  H17  C17  C18  C13   180.00   0.0  0
 ZFB  CONST_24  H18  C18  C13  C14   180.00   0.0  0
 ZFB  CONST_25  H16  C16  C15  C14   180.00   0.0  0
 ZFB  CONST_26  H14  C14  C15  C16   180.00   0.0  0
 ZFB  Var_01    C4   C3   C2   O2     89.11  30.0  2
 ZFB  Var_02    C14  C13  C12  C9     75.58  30.0  2
 ZFB  Var_03    C3   C2   O2   C1   -177.58  30.0  3
 ZFB  Var_04    C9   N1   C1   O1     -7.21  30.0  1
 ZFB  Var_05    N2   C11  C10  C9   -174.24  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
 ZFB  chir_01  C9  N1  C10  C12  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
 ZFB  plan-1  C2   0.020
 ZFB  plan-1  C3   0.020
 ZFB  plan-1  C4   0.020
 ZFB  plan-1  C5   0.020
 ZFB  plan-1  C6   0.020
 ZFB  plan-1  C7   0.020
 ZFB  plan-1  C8   0.020
 ZFB  plan-1  H4   0.020
 ZFB  plan-1  H5   0.020
 ZFB  plan-1  H6   0.020
 ZFB  plan-1  H7   0.020
 ZFB  plan-1  H8   0.020
 ZFB  plan-2  C12  0.020
 ZFB  plan-2  C13  0.020
 ZFB  plan-2  C14  0.020
 ZFB  plan-2  C15  0.020
 ZFB  plan-2  C16  0.020
 ZFB  plan-2  C17  0.020
 ZFB  plan-2  C18  0.020
 ZFB  plan-2  H14  0.020
 ZFB  plan-2  H15  0.020
 ZFB  plan-2  H16  0.020
 ZFB  plan-2  H17  0.020
 ZFB  plan-2  H18  0.020
 ZFB  plan-3  C9   0.020
 ZFB  plan-3  C10  0.020
 ZFB  plan-3  O3   0.020
 ZFB  plan-3  C11  0.020
 ZFB  plan-4  N1   0.020
 ZFB  plan-4  C1   0.020
 ZFB  plan-4  O1   0.020
 ZFB  plan-4  O2   0.020

