# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:25:27 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-amino-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-3-methoxy-6-methylcyclohexa-2,5-diene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=C(N)C(=O)C(=C(C/C=C(C)/CCC=C(C)C)C1=O)C
#
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
 4YP  4YP  2-amino-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-3-methoxy-6-methylcyclohexa-2,5-diene-1,4-dione  ligand  47  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4YP
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
 4YP  CAB  C  CH3   0  -0.704   6.5516   1.5029  -1.4593
 4YP  CAO  C  C     0   0.082   5.1309   1.2321  -1.0553
 4YP  CAC  C  CH3   0  -0.720   4.1027   1.8165  -1.9783
 4YP  CAI  C  C1    0  -0.259   4.8508   0.5269   0.0436
 4YP  CAK  C  CH2   0  -0.488   3.5008   0.1599   0.5767
 4YP  CAM  C  CH2   0  -0.496   3.1620  -1.3165   0.3162
 4YP  CAP  C  C     0   0.128   1.8590  -1.7227   0.9469
 4YP  CAD  C  CH3   0  -0.754   1.8410  -1.8280   2.4496
 4YP  CAJ  C  C1    0  -0.262   0.7880  -1.9575   0.1875
 4YP  CAL  C  CH2   0  -0.594  -0.5832  -2.3422   0.6714
 4YP  CAS  C  CR6   0  -0.016  -1.5824  -1.3132   0.2240
 4YP  CAV  C  CR6   0   0.355  -1.8766  -0.2098   1.1997
 4YP  OAH  O  O     0  -0.412  -1.3681  -0.2231   2.3097
 4YP  CAQ  C  CR6   0  -0.101  -2.1481  -1.3185  -0.9954
 4YP  CAE  C  CH3   0  -0.723  -1.9084  -2.3491  -2.0523
 4YP  CAU  C  CR6   0   0.364  -3.0709  -0.2305  -1.3821
 4YP  OAG  O  O     0  -0.372  -3.6042  -0.2108  -2.4712
 4YP  CAR  C  CR6   0   0.198  -3.3526   0.8795  -0.4190
 4YP  NAF  N  NH2   0  -0.813  -4.1731   1.8423  -0.8554
 4YP  CAT  C  CR6   0   0.138  -2.7744   0.8546   0.8082
 4YP  OAN  O  O2    0  -0.488  -3.0455   1.8412   1.7061
 4YP  CAA  C  CH3   0  -0.412  -2.0662   2.8742   1.7437
 4YP  H1   H  HCH3  0   0.230   6.7685   1.0776  -2.4426
 4YP  H2   H  HCH3  0   0.230   6.7362   2.5773  -1.5408
 4YP  H3   H  HCH3  0   0.235   7.2669   1.0904  -0.7479
 4YP  H4   H  HCH3  0   0.235   4.1864   2.9062  -2.0070
 4YP  H5   H  HCH3  0   0.235   4.2666   1.4688  -3.0015
 4YP  H6   H  HCH3  0   0.238   3.0792   1.5673  -1.7057
 4YP  H7   H  H     0   0.221   5.6902   0.1432   0.6199
 4YP  H8   H  HCH2  0   0.236   3.4856   0.3489   1.6545
 4YP  H9   H  HCH2  0   0.236   2.7135   0.7825   0.1482
 4YP  H10  H  HCH2  0   0.235   3.1288  -1.4840  -0.7631
 4YP  H11  H  HCH2  0   0.232   3.9715  -1.9423   0.7085
 4YP  H12  H  HCH3  0   0.245   1.6799  -2.8581   2.7748
 4YP  H13  H  HCH3  0   0.241   2.7850  -1.5017   2.8851
 4YP  H14  H  HCH3  0   0.250   1.0464  -1.2250   2.8885
 4YP  H15  H  H     0   0.233   0.8883  -1.8599  -0.8908
 4YP  H16  H  HCH2  0   0.271  -0.8562  -3.3197   0.2681
 4YP  H17  H  HCH2  0   0.275  -0.6039  -2.4373   1.7551
 4YP  H18  H  HCH3  0   0.259  -1.3682  -1.9188  -2.8978
 4YP  H19  H  HCH3  0   0.254  -1.3246  -3.1891  -1.6866
 4YP  H20  H  HCH3  0   0.259  -2.8484  -2.7400  -2.4416
 4YP  H21  H  HNH2  0   0.405  -4.6638   1.7198  -1.7249
 4YP  H22  H  HNH2  0   0.406  -4.5412   2.5231  -0.2136
 4YP  H23  H  HCH3  0   0.221  -1.9344   3.3384   0.7627
 4YP  H24  H  HCH3  0   0.240  -2.4219   3.6300   2.4418
 4YP  H25  H  HCH3  0   0.227  -1.0996   2.5044   2.0911

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
 4YP  CAE  CAQ  single  1.496  0.020  1.496
 4YP  OAG  CAU  double  1.213  0.020  1.213
 4YP  CAD  CAP  single  1.507  0.020  1.507
 4YP  CAQ  CAU  single  1.478  0.020  1.478
 4YP  CAQ  CAS  double  1.344  0.020  1.344
 4YP  CAL  CAS  single  1.502  0.020  1.502
 4YP  CAL  CAJ  single  1.504  0.020  1.504
 4YP  CAU  CAR  single  1.496  0.020  1.496
 4YP  CAS  CAV  single  1.502  0.020  1.502
 4YP  CAP  CAJ  double  1.334  0.020  1.334
 4YP  CAP  CAM  single  1.503  0.020  1.503
 4YP  CAC  CAO  single  1.500  0.020  1.500
 4YP  CAK  CAM  single  1.537  0.020  1.537
 4YP  CAK  CAI  single  1.497  0.020  1.497
 4YP  CAR  NAF  single  1.338  0.020  1.338
 4YP  CAR  CAT  double  1.357  0.020  1.357
 4YP  CAV  CAT  single  1.446  0.020  1.446
 4YP  CAV  OAH  double  1.221  0.020  1.221
 4YP  CAT  OAN  single  1.361  0.020  1.361
 4YP  CAO  CAI  double  1.336  0.020  1.336
 4YP  CAO  CAB  single  1.502  0.020  1.502
 4YP  OAN  CAA  single  1.424  0.020  1.424
 4YP  CAB  H1   single  0.970  0.020  1.090
 4YP  CAB  H2   single  0.970  0.020  1.090
 4YP  CAB  H3   single  0.970  0.020  1.090
 4YP  CAC  H4   single  0.970  0.020  1.090
 4YP  CAC  H5   single  0.970  0.020  1.090
 4YP  CAC  H6   single  0.970  0.020  1.090
 4YP  CAI  H7   single  0.930  0.020  1.080
 4YP  CAK  H8   single  0.970  0.020  1.090
 4YP  CAK  H9   single  0.970  0.020  1.090
 4YP  CAM  H10  single  0.970  0.020  1.090
 4YP  CAM  H11  single  0.970  0.020  1.090
 4YP  CAD  H12  single  0.970  0.020  1.090
 4YP  CAD  H13  single  0.970  0.020  1.090
 4YP  CAD  H14  single  0.970  0.020  1.090
 4YP  CAJ  H15  single  0.930  0.020  1.080
 4YP  CAL  H16  single  0.970  0.020  1.090
 4YP  CAL  H17  single  0.970  0.020  1.090
 4YP  CAE  H18  single  0.970  0.020  1.090
 4YP  CAE  H19  single  0.970  0.020  1.090
 4YP  CAE  H20  single  0.970  0.020  1.090
 4YP  NAF  H21  single  0.890  0.020  1.040
 4YP  NAF  H22  single  0.890  0.020  1.040
 4YP  CAA  H23  single  0.970  0.020  1.090
 4YP  CAA  H24  single  0.970  0.020  1.090
 4YP  CAA  H25  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
 4YP  H3   CAB  H2   108.05  3.000
 4YP  H3   CAB  H1   108.03  3.000
 4YP  H2   CAB  H1   106.36  3.000
 4YP  H3   CAB  CAO  112.16  3.000
 4YP  H2   CAB  CAO  110.92  3.000
 4YP  H1   CAB  CAO  111.08  3.000
 4YP  CAI  CAO  CAC  124.63  3.000
 4YP  CAI  CAO  CAB  121.00  3.000
 4YP  CAC  CAO  CAB  114.37  3.000
 4YP  H6   CAC  H5   107.62  3.000
 4YP  H6   CAC  H4   107.87  3.000
 4YP  H5   CAC  H4   106.33  3.000
 4YP  H6   CAC  CAO  113.66  3.000
 4YP  H5   CAC  CAO  110.44  3.000
 4YP  H4   CAC  CAO  110.61  3.000
 4YP  H7   CAI  CAK  114.87  3.000
 4YP  H7   CAI  CAO  117.40  3.000
 4YP  CAK  CAI  CAO  127.70  3.000
 4YP  H9   CAK  H8   106.16  3.000
 4YP  H9   CAK  CAM  108.81  3.000
 4YP  H8   CAK  CAM  109.25  3.000
 4YP  H9   CAK  CAI  111.77  3.000
 4YP  H8   CAK  CAI  108.71  3.000
 4YP  CAM  CAK  CAI  111.95  3.000
 4YP  H11  CAM  H10  106.76  3.000
 4YP  H11  CAM  CAP  109.62  3.000
 4YP  H10  CAM  CAP  110.28  3.000
 4YP  H11  CAM  CAK  108.97  3.000
 4YP  H10  CAM  CAK  108.74  3.000
 4YP  CAP  CAM  CAK  112.30  3.000
 4YP  CAJ  CAP  CAD  123.10  3.000
 4YP  CAJ  CAP  CAM  120.31  3.000
 4YP  CAD  CAP  CAM  116.59  3.000
 4YP  H14  CAD  H13  107.76  3.000
 4YP  H14  CAD  H12  107.13  3.000
 4YP  H13  CAD  H12  106.93  3.000
 4YP  H14  CAD  CAP  111.82  3.000
 4YP  H13  CAD  CAP  111.55  3.000
 4YP  H12  CAD  CAP  111.39  3.000
 4YP  H15  CAJ  CAL  115.22  3.000
 4YP  H15  CAJ  CAP  118.34  3.000
 4YP  CAL  CAJ  CAP  126.43  3.000
 4YP  H17  CAL  H16  106.54  3.000
 4YP  H17  CAL  CAS  110.11  3.000
 4YP  H16  CAL  CAS  109.69  3.000
 4YP  H17  CAL  CAJ  111.10  3.000
 4YP  H16  CAL  CAJ  109.76  3.000
 4YP  CAS  CAL  CAJ  109.59  3.000
 4YP  CAQ  CAS  CAV  120.65  3.000
 4YP  CAV  CAS  CAL  116.10  3.000
 4YP  CAQ  CAS  CAL  123.18  3.000
 4YP  CAT  CAV  OAH  120.84  3.000
 4YP  OAH  CAV  CAS  120.06  3.000
 4YP  CAT  CAV  CAS  119.10  3.000
 4YP  CAU  CAQ  CAE  114.99  3.000
 4YP  CAU  CAQ  CAS  119.81  3.000
 4YP  CAE  CAQ  CAS  125.19  3.000
 4YP  H20  CAE  H19  107.85  3.000
 4YP  H20  CAE  H18  106.95  3.000
 4YP  H19  CAE  H18  107.44  3.000
 4YP  H20  CAE  CAQ  111.18  3.000
 4YP  H19  CAE  CAQ  112.40  3.000
 4YP  H18  CAE  CAQ  110.79  3.000
 4YP  CAR  CAU  OAG  118.89  3.000
 4YP  CAR  CAU  CAQ  119.68  3.000
 4YP  OAG  CAU  CAQ  121.43  3.000
 4YP  CAT  CAR  NAF  124.72  3.000
 4YP  CAT  CAR  CAU  119.23  3.000
 4YP  NAF  CAR  CAU  116.06  3.000
 4YP  H22  NAF  H21  117.10  3.000
 4YP  H22  NAF  CAR  120.23  3.000
 4YP  H21  NAF  CAR  119.57  3.000
 4YP  OAN  CAT  CAR  119.90  3.000
 4YP  OAN  CAT  CAV  118.58  3.000
 4YP  CAR  CAT  CAV  121.53  3.000
 4YP  CAA  OAN  CAT  113.97  3.000
 4YP  H25  CAA  H24  108.69  3.000
 4YP  H25  CAA  H23  108.82  3.000
 4YP  H24  CAA  H23  108.67  3.000
 4YP  H25  CAA  OAN  111.81  3.000
 4YP  H24  CAA  OAN  107.21  3.000
 4YP  H23  CAA  OAN  111.55  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
 4YP  Var_01  CAQ  CAS  CAL  CAJ    83.40  30.0  3
 4YP  Var_02  H18  CAE  CAQ  CAS  -112.16  30.0  3
 4YP  Var_03  H21  NAF  CAR  CAU     9.09  30.0  2
 4YP  Var_04  CAS  CAL  CAJ  CAP   120.43  30.0  1
 4YP  Var_05  H23  CAA  OAN  CAT    57.44  30.0  3
 4YP  Var_06  CAK  CAI  CAO  CAB  -179.42   0.0  2
 4YP  Var_07  CAL  CAJ  CAP  CAM  -178.69   0.0  2
 4YP  Var_08  CAM  CAK  CAI  CAO   104.63  30.0  1
 4YP  Var_09  CAP  CAM  CAK  CAI   175.27  30.0  3
 4YP  Var_10  CAD  CAP  CAM  CAK   -71.02  30.0  2
 4YP  Var_11  H4   CAC  CAO  CAB   -61.68  30.0  3
 4YP  Var_12  H1   CAB  CAO  CAC   -60.83  30.0  3
 4YP  Var_13  H12  CAD  CAP  CAM  -114.42  30.0  3

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
 4YP  plan-1  CAL  0.020
 4YP  plan-1  CAS  0.020
 4YP  plan-1  CAV  0.020
 4YP  plan-1  OAH  0.020
 4YP  plan-1  CAQ  0.020
 4YP  plan-1  CAE  0.020
 4YP  plan-1  CAU  0.020
 4YP  plan-1  OAG  0.020
 4YP  plan-1  CAR  0.020
 4YP  plan-1  NAF  0.020
 4YP  plan-1  CAT  0.020
 4YP  plan-1  OAN  0.020
 4YP  plan-2  CAM  0.020
 4YP  plan-2  CAP  0.020
 4YP  plan-2  CAD  0.020
 4YP  plan-2  CAJ  0.020
 4YP  plan-2  CAL  0.020
 4YP  plan-2  H15  0.020
 4YP  plan-3  CAB  0.020
 4YP  plan-3  CAO  0.020
 4YP  plan-3  CAC  0.020
 4YP  plan-3  CAI  0.020
 4YP  plan-3  CAK  0.020
 4YP  plan-3  H7   0.020

