# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 14:43:21 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: O-(5-methyl-2-nitrophenyl)-D-tyrosinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(c(Oc2ccc(C[C@@H](N)C(N)=O)cc2)c1)[N+]([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
 YWO  YWO  O-(5-methyl-2-nitrophenyl)-D-tyrosinamide  ligand  40  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YWO
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
 YWO  C1    C  CR16   0  -0.257  -4.9569   0.5197   0.1906
 YWO  N1    N  N      1   0.333  -4.2265  -1.7953   0.1361
 YWO  O1    O  O2     0  -0.489  -1.6070  -0.8378  -0.2292
 YWO  C2    C  CR6    0   0.150  -3.9113  -0.3873   0.0570
 YWO  N2    N  NH2    0  -0.786   4.6412  -1.5437  -0.8397
 YWO  O2    O  O      0  -0.388  -5.1773  -2.1182   0.8141
 YWO  C3    C  CR6    0   0.417  -2.5996   0.0645  -0.1425
 YWO  N3    N  NH2    0  -0.798   6.6003   0.2177   1.5036
 YWO  O3    O  O     -1  -0.377  -3.5473  -2.5779  -0.4849
 YWO  C4    C  CR16   0  -0.398  -2.3790   1.4372  -0.2083
 YWO  O4    O  O      0  -0.492   6.8382   0.1543  -0.7396
 YWO  C5    C  CR6    0   0.123  -3.4217   2.3477  -0.0958
 YWO  C6    C  CR16   0  -0.313  -4.7188   1.8739   0.1059
 YWO  C7    C  CR6    0   0.278  -0.2969  -0.4081  -0.1955
 YWO  C8    C  CR16   0  -0.277   0.3052  -0.1364   1.0233
 YWO  C9    C  CR16   0  -0.299   1.6368   0.2467   1.0461
 YWO  C10   C  CR6    0   0.130   2.3751   0.3667  -0.1306
 YWO  C11   C  CR16   0  -0.317   1.7427   0.0832  -1.3382
 YWO  C12   C  CR16   0  -0.286   0.4085  -0.3006  -1.3802
 YWO  C13   C  CH3    0  -0.721  -3.1568   3.8170  -0.2110
 YWO  C14   C  CH2    0  -0.530   3.8291   0.7324  -0.0856
 YWO  C15   C  CH1    0  -0.210   4.7200  -0.5088   0.1663
 YWO  C16   C  C      0   0.520   6.1628  -0.0293   0.2630
 YWO  H1    H  HCR6   0   0.296  -5.9635   0.1590   0.3478
 YWO  HN2   H  HNH2   0   0.355   3.6852  -1.8619  -0.9363
 YWO  HN2A  H  HNH2   0   0.344   4.9179  -1.1733  -1.7410
 YWO  HN3   H  HNH2   0   0.402   7.5155   0.6093   1.6578
 YWO  HN3A  H  HNH2   0   0.408   6.0306   0.0416   2.3127
 YWO  H4    H  HCR6   0   0.290  -1.3727   1.8084  -0.3521
 YWO  H6    H  HCR6   0   0.267  -5.5436   2.5682   0.1957
 YWO  H8    H  HCR6   0   0.278  -0.2578  -0.2247   1.9441
 YWO  H9    H  HCR6   0   0.258   2.1059   0.4604   1.9991
 YWO  H11   H  HCR6   0   0.262   2.2941   0.1757  -2.2658
 YWO  H12   H  HCR6   0   0.277  -0.0733  -0.5157  -2.3253
 YWO  H13   H  HCH3   0   0.262  -3.3654   4.1616  -1.2258
 YWO  H13A  H  HCH3   0   0.255  -3.7958   4.3874   0.4619
 YWO  H13B  H  HCH3   0   0.253  -2.1194   4.0587   0.0129
 YWO  H14   H  HCH2   0   0.259   4.1310   1.1940  -1.0292
 YWO  H14A  H  HCH2   0   0.259   4.0033   1.4680   0.7040
 YWO  H15   H  HCH1   0   0.262   4.4208  -0.9453   1.1241

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
 YWO  C1   C2    aromatic  1.391  0.020  1.391
 YWO  C1   C6    aromatic  1.378  0.020  1.378
 YWO  N1   C2    single    1.445  0.020  1.445
 YWO  N1   O2    double    1.212  0.020  1.212
 YWO  N1   O3    single    1.208  0.020  1.208
 YWO  O1   C3    single    1.344  0.020  1.344
 YWO  O1   C7    single    1.379  0.020  1.379
 YWO  C2   C3    aromatic  1.402  0.020  1.402
 YWO  N2   C15   single    1.445  0.020  1.445
 YWO  C3   C4    aromatic  1.392  0.020  1.392
 YWO  N3   C16   single    1.338  0.020  1.338
 YWO  C4   C5    aromatic  1.389  0.020  1.389
 YWO  O4   C16   double    1.223  0.020  1.223
 YWO  C5   C6    aromatic  1.396  0.020  1.396
 YWO  C5   C13   single    1.497  0.020  1.497
 YWO  C7   C8    aromatic  1.386  0.020  1.386
 YWO  C7   C12   aromatic  1.383  0.020  1.383
 YWO  C8   C9    aromatic  1.386  0.020  1.386
 YWO  C9   C10   aromatic  1.394  0.020  1.394
 YWO  C10  C11   aromatic  1.392  0.020  1.392
 YWO  C10  C14   single    1.500  0.020  1.500
 YWO  C11  C12   aromatic  1.389  0.020  1.389
 YWO  C14  C15   single    1.548  0.020  1.548
 YWO  C15  C16   single    1.523  0.020  1.523
 YWO  C1   H1    single    0.930  0.020  1.080
 YWO  N2   HN2   single    0.890  0.020  1.040
 YWO  N2   HN2A  single    0.890  0.020  1.040
 YWO  N3   HN3   single    0.860  0.020  1.020
 YWO  N3   HN3A  single    0.860  0.020  1.020
 YWO  C4   H4    single    0.930  0.020  1.080
 YWO  C6   H6    single    0.930  0.020  1.080
 YWO  C8   H8    single    0.930  0.020  1.080
 YWO  C9   H9    single    0.930  0.020  1.080
 YWO  C11  H11   single    0.930  0.020  1.080
 YWO  C12  H12   single    0.930  0.020  1.080
 YWO  C13  H13   single    0.970  0.020  1.090
 YWO  C13  H13A  single    0.970  0.020  1.090
 YWO  C13  H13B  single    0.970  0.020  1.090
 YWO  C14  H14   single    0.970  0.020  1.090
 YWO  C14  H14A  single    0.970  0.020  1.090
 YWO  C15  H15   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
 YWO  H1    C1   C6    119.87  3.000
 YWO  H1    C1   C2    119.77  3.000
 YWO  C6    C1   C2    120.35  3.000
 YWO  O3    N1   O2    123.79  3.000
 YWO  O3    N1   C2    118.72  3.000
 YWO  O2    N1   C2    117.48  3.000
 YWO  C7    O1   C3    119.38  3.000
 YWO  C3    C2   N1    121.74  3.000
 YWO  C3    C2   C1    120.47  3.000
 YWO  N1    C2   C1    117.79  3.000
 YWO  HN2A  N2   HN2   106.74  3.000
 YWO  HN2A  N2   C15   110.03  3.000
 YWO  HN2   N2   C15   110.06  3.000
 YWO  C4    C3   C2    118.22  3.000
 YWO  C4    C3   O1    122.82  3.000
 YWO  C2    C3   O1    118.94  3.000
 YWO  HN3A  N3   HN3   117.38  3.000
 YWO  HN3A  N3   C16   121.90  3.000
 YWO  HN3   N3   C16   120.71  3.000
 YWO  H4    C4   C5    118.95  3.000
 YWO  H4    C4   C3    119.46  3.000
 YWO  C5    C4   C3    121.59  3.000
 YWO  C13   C5   C6    120.58  3.000
 YWO  C13   C5   C4    120.28  3.000
 YWO  C6    C5   C4    119.14  3.000
 YWO  H6    C6   C5    120.18  3.000
 YWO  H6    C6   C1    119.60  3.000
 YWO  C5    C6   C1    120.22  3.000
 YWO  C12   C7   C8    121.08  3.000
 YWO  C12   C7   O1    119.20  3.000
 YWO  C8    C7   O1    119.68  3.000
 YWO  H8    C8   C9    120.54  3.000
 YWO  H8    C8   C7    120.38  3.000
 YWO  C9    C8   C7    119.08  3.000
 YWO  H9    C9   C10   119.74  3.000
 YWO  H9    C9   C8    119.01  3.000
 YWO  C10   C9   C8    121.25  3.000
 YWO  C14   C10  C11   121.06  3.000
 YWO  C14   C10  C9    120.59  3.000
 YWO  C11   C10  C9    118.29  3.000
 YWO  H11   C11  C12   119.13  3.000
 YWO  H11   C11  C10   119.61  3.000
 YWO  C12   C11  C10   121.25  3.000
 YWO  H12   C12  C11   120.59  3.000
 YWO  H12   C12  C7    120.36  3.000
 YWO  C11   C12  C7    119.05  3.000
 YWO  H13B  C13  H13A  108.41  3.000
 YWO  H13B  C13  H13   107.65  3.000
 YWO  H13A  C13  H13   107.27  3.000
 YWO  H13B  C13  C5    111.75  3.000
 YWO  H13A  C13  C5    111.26  3.000
 YWO  H13   C13  C5    110.33  3.000
 YWO  H14A  C14  H14   107.18  3.000
 YWO  H14A  C14  C15   109.29  3.000
 YWO  H14   C14  C15   108.66  3.000
 YWO  H14A  C14  C10   109.89  3.000
 YWO  H14   C14  C10   110.17  3.000
 YWO  C15   C14  C10   111.54  3.000
 YWO  H15   C15  C16   109.20  3.000
 YWO  H15   C15  C14   107.74  3.000
 YWO  C16   C15  C14   107.63  3.000
 YWO  H15   C15  N2    107.98  3.000
 YWO  C16   C15  N2    108.73  3.000
 YWO  C14   C15  N2    115.43  3.000
 YWO  C15   C16  O4    121.22  3.000
 YWO  C15   C16  N3    115.25  3.000
 YWO  O4    C16  N3    123.49  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
 YWO  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 YWO  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 YWO  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 YWO  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 YWO  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 YWO  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 YWO  CONST_07  C10   C9   C8   C7     0.00   0.0  0
 YWO  CONST_08  C10   C11  C12  C7     0.00   0.0  0
 YWO  CONST_09  C11   C12  C7   C8     0.00   0.0  0
 YWO  CONST_10  C11   C10  C9   C8     0.00   0.0  0
 YWO  CONST_11  C12   C7   C8   C9     0.00   0.0  0
 YWO  CONST_12  C12   C11  C10  C9     0.00   0.0  0
 YWO  CONST_13  O1    C3   C2   C1   180.00   0.0  0
 YWO  CONST_14  C13   C5   C6   C1   180.00   0.0  0
 YWO  CONST_15  C6    C1   C2   N1   180.00   0.0  0
 YWO  CONST_16  C4    C3   C2   N1   180.00   0.0  0
 YWO  CONST_17  C5    C4   C3   O1   180.00   0.0  0
 YWO  CONST_18  C9    C8   C7   O1   180.00   0.0  0
 YWO  CONST_19  C11   C12  C7   O1   180.00   0.0  0
 YWO  CONST_20  C13   C5   C4   C3   180.00   0.0  0
 YWO  CONST_21  C14   C10  C9   C8   180.00   0.0  0
 YWO  CONST_22  C14   C10  C11  C12  180.00   0.0  0
 YWO  CONST_23  H6    C6   C1   C2   180.00   0.0  0
 YWO  CONST_24  H4    C4   C3   C2   180.00   0.0  0
 YWO  CONST_25  H1    C1   C2   C3   180.00   0.0  0
 YWO  CONST_26  H9    C9   C8   C7   180.00   0.0  0
 YWO  CONST_27  H11   C11  C12  C7   180.00   0.0  0
 YWO  CONST_28  H12   C12  C7   C8   180.00   0.0  0
 YWO  CONST_29  H8    C8   C9   C10  180.00   0.0  0
 YWO  CONST_34  HN3   N3   C16  O4     0.00   0.0  0
 YWO  CONST_35  HN3A  N3   C16  O4   180.00   0.0  0
 YWO  Var_01    C8    C7   O1   C3    81.61  30.0  2
 YWO  Var_02    C15   C14  C10  C9    83.66  30.0  2
 YWO  Var_03    H13   C13  C5   C4    97.08  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
 YWO  chir_01  C15  N2  C14  C16  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
 YWO  plan-1  C1    0.020
 YWO  plan-1  N1    0.020
 YWO  plan-1  O1    0.020
 YWO  plan-1  C2    0.020
 YWO  plan-1  C3    0.020
 YWO  plan-1  C4    0.020
 YWO  plan-1  C5    0.020
 YWO  plan-1  C6    0.020
 YWO  plan-1  C13   0.020
 YWO  plan-1  H1    0.020
 YWO  plan-1  H4    0.020
 YWO  plan-1  H6    0.020
 YWO  plan-2  O1    0.020
 YWO  plan-2  C7    0.020
 YWO  plan-2  C8    0.020
 YWO  plan-2  C9    0.020
 YWO  plan-2  C10   0.020
 YWO  plan-2  C11   0.020
 YWO  plan-2  C12   0.020
 YWO  plan-2  C14   0.020
 YWO  plan-2  H8    0.020
 YWO  plan-2  H9    0.020
 YWO  plan-2  H11   0.020
 YWO  plan-2  H12   0.020
 YWO  plan-3  N3    0.020
 YWO  plan-3  O4    0.020
 YWO  plan-3  C15   0.020
 YWO  plan-3  C16   0.020
 YWO  plan-3  HN3   0.020
 YWO  plan-3  HN3A  0.020
 YWO  plan-4  N1    0.020
 YWO  plan-4  C2    0.020
 YWO  plan-4  O2    0.020
 YWO  plan-4  O3    0.020

