# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 09:43:32 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-acetyl-O-(4-hydroxy-3,5-dinitrophenyl)-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccc(Oc2cc(c(O)c(c2)[N+]([O-])=O)[N+]([O-])=O)cc1)C(O)=O
#
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
 P28  P28  N-acetyl-O-(4-hydroxy-3,5-dinitrophenyl)-L-tyrosine  ligand  43  29  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P28
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
 P28  C1    C  CR6    0   0.146   2.7378  -1.0617   2.3637
 P28  C2    C  CR16   0  -0.290   3.4163  -1.7639   3.3544
 P28  C3    C  CR16   0  -0.287   4.7840  -1.6210   3.5287
 P28  C4    C  CR6    0   0.265   5.4800  -0.7600   2.6976
 P28  C5    C  CR16   0  -0.280   4.8296  -0.0270   1.7192
 P28  C6    C  CR16   0  -0.302   3.4601  -0.1789   1.5648
 P28  C7    C  CH2    0  -0.514   1.2888  -1.3220   2.0901
 P28  C8    C  CH1    0  -0.200   1.1009  -2.4781   1.0798
 P28  C9    C  C      0   0.419  -0.4006  -2.5887   0.7237
 P28  O9    O  O      0  -0.606  -1.1415  -2.9494   1.6556
 P28  O10   O  OC    -1  -0.595  -0.7376  -2.2768  -0.4340
 P28  N8    N  NH1    0  -0.614   1.8993  -2.2800  -0.1025
 P28  C81   C  C      0   0.532   3.1383  -2.7643  -0.2791
 P28  C82   C  CH3    0  -0.768   3.7989  -2.3721  -1.5787
 P28  O81   O  O      0  -0.496   3.7198  -3.4531   0.5507
 P28  O41   O  O2     0  -0.512   6.8390  -0.6030   2.8772
 P28  C1'   C  CR6    0   0.386   7.6863  -1.2838   2.0726
 P28  C2'   C  CR16   0  -0.399   7.3080  -2.2725   1.1868
 P28  C3'   C  CR6    0   0.201   8.2816  -2.9187   0.4255
 P28  N3    N  N      1   0.368   7.8385  -3.9637  -0.4670
 P28  O31   O  O      0  -0.424   8.6857  -4.5660  -1.1140
 P28  O32   O  O     -1  -0.335   6.6658  -4.2045  -0.5451
 P28  C4'   C  CR6    0   0.348   9.6496  -2.5985   0.5003
 P28  O4'   O  OH1    0  -0.578  10.6097  -3.2012  -0.1689
 P28  C5'   C  CR6    0   0.182   9.9732  -1.5767   1.4092
 P28  N5    N  N      1   0.341  11.3541  -1.1487   1.5617
 P28  O51   O  O      0  -0.359  12.0453  -1.0992   0.5759
 P28  O52   O  O     -1  -0.369  11.7174  -0.8427   2.6724
 P28  C6'   C  CR16   0  -0.332   9.0310  -0.9477   2.1902
 P28  H2    H  HCR6   0   0.249   2.8715  -2.4482   3.9943
 P28  H3    H  HCR6   0   0.268   5.3044  -2.1712   4.3026
 P28  H5    H  HCR6   0   0.270   5.3843   0.6565   1.0879
 P28  H6    H  HCR6   0   0.252   2.9496   0.3952   0.8011
 P28  H71   H  HCH2   0   0.241   0.8190  -0.4192   1.6894
 P28  H72   H  HCH2   0   0.248   0.7610  -1.5831   3.0083
 P28  H8    H  HCH1   0   0.246   1.4251  -3.4049   1.5573
 P28  HN8   H  HNH1   0   0.379   1.4460  -1.7888  -0.8569
 P28  H821  H  HCH3   0   0.256   4.6111  -1.6766  -1.3622
 P28  H822  H  HCH3   0   0.255   4.2405  -3.2469  -2.0524
 P28  H823  H  HCH3   0   0.239   3.1217  -1.8917  -2.2831
 P28  H2'   H  HCR6   0   0.349   6.2692  -2.5627   1.0784
 P28  HO4   H  HOH1   0   0.493  10.2060  -3.9141  -0.7054
 P28  H6'   H  HCR6   0   0.326   9.3263  -0.1720   2.8845

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
 P28  C1   C2    aromatic  1.391  0.020  1.391
 P28  C1   C6    aromatic  1.393  0.020  1.393
 P28  C1   C7    single    1.497  0.020  1.497
 P28  C2   C3    aromatic  1.386  0.020  1.386
 P28  C2   H2    single    0.930  0.020  1.080
 P28  C3   C4    aromatic  1.384  0.020  1.384
 P28  C3   H3    single    0.930  0.020  1.080
 P28  C4   C5    aromatic  1.385  0.020  1.385
 P28  C4   O41   single    1.380  0.020  1.380
 P28  C5   C6    aromatic  1.386  0.020  1.386
 P28  C5   H5    single    0.930  0.020  1.080
 P28  C6   H6    single    0.930  0.020  1.080
 P28  C7   C8    single    1.547  0.020  1.547
 P28  C7   H71   single    0.970  0.020  1.090
 P28  C7   H72   single    0.970  0.020  1.090
 P28  C8   C9    single    1.547  0.020  1.547
 P28  C8   N8    single    1.440  0.020  1.440
 P28  C8   H8    single    0.970  0.020  1.090
 P28  C9   O9    deloc     1.244  0.020  1.244
 P28  C9   O10   deloc     1.245  0.020  1.245
 P28  N8   C81   single    1.342  0.020  1.342
 P28  N8   HN8   single    0.860  0.020  1.020
 P28  C81  C82   single    1.510  0.020  1.510
 P28  C81  O81   double    1.225  0.020  1.225
 P28  C82  H821  single    0.970  0.020  1.090
 P28  C82  H822  single    0.970  0.020  1.090
 P28  C82  H823  single    0.970  0.020  1.090
 P28  O41  C1'   single    1.352  0.020  1.352
 P28  C1'  C2'   aromatic  1.380  0.020  1.380
 P28  C1'  C6'   aromatic  1.391  0.020  1.391
 P28  C2'  C3'   aromatic  1.395  0.020  1.395
 P28  C2'  H2'   single    0.930  0.020  1.080
 P28  C3'  N3    single    1.444  0.020  1.444
 P28  C3'  C4'   aromatic  1.407  0.020  1.407
 P28  N3   O31   double    1.224  0.020  1.224
 P28  N3   O32   single    1.200  0.020  1.200
 P28  C4'  O4'   single    1.316  0.020  1.316
 P28  C4'  C5'   aromatic  1.405  0.020  1.405
 P28  O4'  HO4   single    0.850  0.020  0.980
 P28  C5'  N5    single    1.454  0.020  1.454
 P28  C5'  C6'   aromatic  1.376  0.020  1.376
 P28  N5   O51   double    1.205  0.020  1.205
 P28  N5   O52   single    1.208  0.020  1.208
 P28  C6'  H6'   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
 P28  C7    C1   C6    120.48  3.000
 P28  C7    C1   C2    120.95  3.000
 P28  C6    C1   C2    118.40  3.000
 P28  H2    C2   C3    119.13  3.000
 P28  H2    C2   C1    119.61  3.000
 P28  C3    C2   C1    121.25  3.000
 P28  H3    C3   C4    120.23  3.000
 P28  H3    C3   C2    120.78  3.000
 P28  C4    C3   C2    118.99  3.000
 P28  O41   C4   C5    119.63  3.000
 P28  O41   C4   C3    119.20  3.000
 P28  C5    C4   C3    121.15  3.000
 P28  H5    C5   C6    120.67  3.000
 P28  H5    C5   C4    120.35  3.000
 P28  C6    C5   C4    118.99  3.000
 P28  H6    C6   C5    119.08  3.000
 P28  H6    C6   C1    119.73  3.000
 P28  C5    C6   C1    121.19  3.000
 P28  H72   C7   H71   107.34  3.000
 P28  H72   C7   C8    108.19  3.000
 P28  H71   C7   C8    108.99  3.000
 P28  H72   C7   C1    110.86  3.000
 P28  H71   C7   C1    109.82  3.000
 P28  C8    C7   C1    111.52  3.000
 P28  H8    C8   N8    108.14  3.000
 P28  H8    C8   C9    109.16  3.000
 P28  N8    C8   C9    111.03  3.000
 P28  H8    C8   C7    108.22  3.000
 P28  N8    C8   C7    111.47  3.000
 P28  C9    C8   C7    108.76  3.000
 P28  O10   C9   O9    127.43  3.000
 P28  O10   C9   C8    117.30  3.000
 P28  O9    C9   C8    115.24  3.000
 P28  HN8   N8   C81   119.51  3.000
 P28  HN8   N8   C8    115.61  3.000
 P28  C81   N8   C8    124.76  3.000
 P28  O81   C81  C82   121.42  3.000
 P28  O81   C81  N8    123.51  3.000
 P28  C82   C81  N8    115.05  3.000
 P28  H823  C82  H822  108.99  3.000
 P28  H823  C82  H821  108.07  3.000
 P28  H822  C82  H821  107.26  3.000
 P28  H823  C82  C81   113.54  3.000
 P28  H822  C82  C81   110.08  3.000
 P28  H821  C82  C81   108.70  3.000
 P28  C1'   O41  C4    118.84  3.000
 P28  C6'   C1'  C2'   119.49  3.000
 P28  C6'   C1'  O41   115.70  3.000
 P28  C2'   C1'  O41   124.81  3.000
 P28  H2'   C2'  C3'   119.36  3.000
 P28  H2'   C2'  C1'   121.23  3.000
 P28  C3'   C2'  C1'   119.40  3.000
 P28  C4'   C3'  N3    119.73  3.000
 P28  C4'   C3'  C2'   122.98  3.000
 P28  N3    C3'  C2'   117.29  3.000
 P28  O32   N3   O31   122.90  3.000
 P28  O32   N3   C3'   119.04  3.000
 P28  O31   N3   C3'   118.05  3.000
 P28  C5'   C4'  O4'   119.59  3.000
 P28  C5'   C4'  C3'   115.07  3.000
 P28  O4'   C4'  C3'   125.30  3.000
 P28  HO4   O4'  C4'   108.13  3.000
 P28  C6'   C5'  N5    117.15  3.000
 P28  C6'   C5'  C4'   122.81  3.000
 P28  N5    C5'  C4'   120.04  3.000
 P28  O52   N5   O51   124.70  3.000
 P28  O52   N5   C5'   117.18  3.000
 P28  O51   N5   C5'   118.11  3.000
 P28  H6'   C6'  C5'   120.33  3.000
 P28  H6'   C6'  C1'   119.42  3.000
 P28  C5'   C6'  C1'   120.23  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
 P28  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 P28  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 P28  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 P28  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 P28  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 P28  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 P28  CONST_07  C4'   C3'  C2'  C1'    0.00   0.0  0
 P28  CONST_08  C4'   C5'  C6'  C1'    0.00   0.0  0
 P28  CONST_09  C5'   C6'  C1'  C2'    0.00   0.0  0
 P28  CONST_10  C5'   C4'  C3'  C2'    0.00   0.0  0
 P28  CONST_11  C6'   C1'  C2'  C3'    0.00   0.0  0
 P28  CONST_12  C6'   C5'  C4'  C3'    0.00   0.0  0
 P28  CONST_13  O41   C4   C3   C2   180.00   0.0  0
 P28  CONST_14  C7    C1   C2   C3   180.00   0.0  0
 P28  CONST_15  C7    C1   C6   C5   180.00   0.0  0
 P28  CONST_16  O41   C4   C5   C6   180.00   0.0  0
 P28  CONST_17  C3'   C2'  C1'  O41  180.00   0.0  0
 P28  CONST_18  C5'   C6'  C1'  O41  180.00   0.0  0
 P28  CONST_19  N3    C3'  C2'  C1'  180.00   0.0  0
 P28  CONST_20  N5    C5'  C6'  C1'  180.00   0.0  0
 P28  CONST_21  O4'   C4'  C3'  C2'  180.00   0.0  0
 P28  CONST_22  N5    C5'  C4'  C3'  180.00   0.0  0
 P28  CONST_23  C5'   C4'  C3'  N3   180.00   0.0  0
 P28  CONST_24  C6'   C5'  C4'  O4'  180.00   0.0  0
 P28  CONST_25  H3    C3   C2   C1   180.00   0.0  0
 P28  CONST_26  H5    C5   C6   C1   180.00   0.0  0
 P28  CONST_27  H6    C6   C1   C2   180.00   0.0  0
 P28  CONST_28  H2    C2   C3   C4   180.00   0.0  0
 P28  CONST_29  H6'   C6'  C1'  C2'  180.00   0.0  0
 P28  CONST_30  H2'   C2'  C3'  C4'  180.00   0.0  0
 P28  CONST_31  O31   N3   C3'  C2'  180.00   0.0  0
 P28  CONST_32  O32   N3   C3'  C2'    0.00   0.0  0
 P28  CONST_33  C4'   C3'  N3   O31    0.00   0.0  0
 P28  CONST_34  C4'   C3'  N3   O32  180.00   0.0  0
 P28  CONST_39  C82   C81  N8   C8   180.00   0.0  0
 P28  CONST_40  O81   C81  N8   C8     0.00   0.0  0
 P28  CONST_41  HN8   N8   C81  C82    0.00   0.0  0
 P28  Var_01    C2'   C1'  O41  C4    -9.10  30.0  2
 P28  Var_02    C8    C7   C1   C2   -87.02  30.0  2
 P28  Var_03    H821  C82  C81  N8   110.14  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
 P28  chir_01  C8  C7  C9  N8  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
 P28  plan-1  C1   0.020
 P28  plan-1  C2   0.020
 P28  plan-1  C3   0.020
 P28  plan-1  C4   0.020
 P28  plan-1  C5   0.020
 P28  plan-1  C6   0.020
 P28  plan-1  C7   0.020
 P28  plan-1  O41  0.020
 P28  plan-1  H2   0.020
 P28  plan-1  H3   0.020
 P28  plan-1  H5   0.020
 P28  plan-1  H6   0.020
 P28  plan-2  O41  0.020
 P28  plan-2  C1'  0.020
 P28  plan-2  C2'  0.020
 P28  plan-2  C3'  0.020
 P28  plan-2  N3   0.020
 P28  plan-2  C4'  0.020
 P28  plan-2  O4'  0.020
 P28  plan-2  C5'  0.020
 P28  plan-2  N5   0.020
 P28  plan-2  C6'  0.020
 P28  plan-2  H2'  0.020
 P28  plan-2  H6'  0.020
 P28  plan-3  C8   0.020
 P28  plan-3  N8   0.020
 P28  plan-3  C81  0.020
 P28  plan-3  C82  0.020
 P28  plan-3  O81  0.020
 P28  plan-3  HN8  0.020
 P28  plan-4  C3'  0.020
 P28  plan-4  N3   0.020
 P28  plan-4  O31  0.020
 P28  plan-4  O32  0.020
 P28  plan-5  C5'  0.020
 P28  plan-5  N5   0.020
 P28  plan-5  O51  0.020
 P28  plan-5  O52  0.020
 P28  plan-6  C8   0.020
 P28  plan-6  C9   0.020
 P28  plan-6  O9   0.020
 P28  plan-6  O10  0.020

