# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 07:11:16 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: 2,4-dihydroxy-3-({3-[(2R,4aR,8S,8aR,9R)-9-hydroxy-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CCC(=O)Nc2c(O)ccc(C(O)=O)c2O)[C@@H]3C[C@@H]4C[C@@H](O)[C@]3(CC4=C)C=CC1=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
 N3A  N3A  '2,4-dihydroxy-3-({3-[(2R,4aR,8S,8aR,9R)-9-hydroxy-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid'  ligand  59  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N3A
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
 N3A  C1    C  CH1   0  -0.337  -0.3947  72.1562  68.0581
 N3A  O19   O  O     0  -0.416  -3.3897  68.8293  72.1599
 N3A  O20   O  O     0  -0.459  -6.1979  68.0380  68.7950
 N3A  N28   N  NH1   0  -0.729  -5.4770  69.2402  67.0241
 N3A  C11   C  C     0   0.532  -5.4782  68.9093  68.3482
 N3A  C2    C  CH2   0  -0.597  -4.4956  69.6852  69.1889
 N3A  C3    C  CH2   0  -0.409  -3.2199  68.8522  69.3566
 N3A  C4    C  CR6   0  -0.228  -2.1159  69.4739  70.2263
 N3A  C5    C  CR6   0   0.444  -2.5529  69.5712  71.6824
 N3A  C6    C  CR16  0  -0.365  -1.8479  70.5460  72.5259
 N3A  C7    C  CR16  0  -0.101  -1.0187  71.4720  72.0371
 N3A  C8    C  CR6   0  -0.221  -0.7707  71.6954  70.5834
 N3A  C9    C  CR16  0  -0.233  -1.7646  70.8889  69.7227
 N3A  C10   C  CH2   0  -0.423  -1.3361  70.9594  68.2474
 N3A  C14   C  CH2   0  -0.467  -1.0232  73.1810  70.2476
 N3A  C15   C  C     0   0.223  -0.9976  73.3491  68.7458
 N3A  C17   C  C2    0  -0.634  -1.4688  74.4168  68.1113
 N3A  C18   C  CH3   0  -0.673  -0.9427  68.4743  70.2318
 N3A  C28   C  CH1   0   0.111   0.6900  71.3759  70.1977
 N3A  C29   C  CH2   0  -0.479   0.9347  71.8292  68.7436
 N3A  O30   O  OH1   0  -0.602  -8.0127  69.8860  66.1313
 N3A  O32   O  OH1   0  -0.639  -4.4170  64.9761  64.4493
 N3A  O33   O  O     0  -0.436  -6.2203  64.5930  63.1991
 N3A  C22   C  CR6   0  -0.258  -6.1933  66.4969  64.6185
 N3A  C23   C  CR6   0   0.360  -5.5152  67.2887  65.5664
 N3A  C24   C  CR6   0   0.100  -6.1349  68.4375  66.0688
 N3A  C25   C  CR6   0   0.365  -7.4131  68.7977  65.6527
 N3A  C26   C  CR16  0  -0.366  -8.0933  68.0149  64.7144
 N3A  C27   C  CR16  0  -0.259  -7.4779  66.8924  64.2204
 N3A  O34   O  OH1   0  -0.672   1.5363  72.0221  71.1231
 N3A  H1    H  HCH1  0   0.244  -0.2382  72.3547  66.9961
 N3A  HN28  H  HNH1  0   0.410  -4.7765  69.8904  66.6973
 N3A  H2    H  HCH2  0   0.256  -4.2797  70.6469  68.7204
 N3A  H2A   H  HCH2  0   0.275  -4.9544  69.8885  70.1567
 N3A  H3    H  HCH2  0   0.255  -3.4877  67.8830  69.7805
 N3A  H3A   H  HCH2  0   0.251  -2.7968  68.6432  68.3693
 N3A  H6    H  HCR6  0   0.260  -2.0271  70.4797  73.5932
 N3A  H7    H  HCR6  0   0.271  -0.5227  72.1419  72.7310
 N3A  H9    H  HCR6  0   0.263  -2.6974  71.4605  69.8048
 N3A  H10   H  HCH2  0   0.246  -2.2110  71.0598  67.6018
 N3A  H10A  H  HCH2  0   0.238  -0.8211  70.0493  67.9275
 N3A  H14   H  HCH2  0   0.260  -1.9844  73.5028  70.6570
 N3A  H14A  H  HCH2  0   0.264  -0.2587  73.8053  70.7181
 N3A  H17   H  H     0   0.231  -1.4177  74.5032  67.0325
 N3A  H17A  H  H     0   0.229  -1.9203  75.2443  68.6461
 N3A  H18   H  HCH3  0   0.246  -0.4459  68.4356  69.2618
 N3A  H18A  H  HCH3  0   0.246  -0.1909  68.7036  70.9860
 N3A  H18B  H  HCH3  0   0.253  -1.3157  67.4714  70.4449
 N3A  H28   H  HCH1  0   0.231   0.8411  70.2955  70.2645
 N3A  H29   H  HCH2  0   0.250   1.4586  71.0514  68.1834
 N3A  H29A  H  HCH2  0   0.245   1.5756  72.7149  68.7399
 N3A  HO30  H  HOH1  0   0.477  -7.4136  70.3498  66.7346
 N3A  HO31  H  HOH1  0   0.488  -3.9361  66.2356  65.6364
 N3A  HO32  H  HOH1  0   0.499  -4.0805  64.1714  64.0256
 N3A  H26   H  HCR6  0   0.274  -9.0861  68.2948  64.3896
 N3A  H27   H  HCR6  0   0.275  -8.0026  66.2867  63.4940
 N3A  HO34  H  HOH1  0   0.453   2.4477  71.8432  70.8720
 N3A  O31   O  OH1   0  -0.600  -4.2994  67.0383  66.0442
 N3A  C21   C  C     0   0.577  -5.6463  65.2760  64.0115

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
 N3A  C1   C10   single    1.534  0.020  1.534
 N3A  C1   C15   single    1.503  0.020  1.503
 N3A  C1   C29   single    1.531  0.020  1.531
 N3A  C1   H1    single    0.970  0.020  1.090
 N3A  C5   O19   double    1.216  0.020  1.216
 N3A  C11  O20   double    1.215  0.020  1.215
 N3A  C24  N28   single    1.411  0.020  1.411
 N3A  N28  C11   single    1.365  0.020  1.365
 N3A  N28  HN28  single    0.860  0.020  1.020
 N3A  C11  C2    single    1.508  0.020  1.508
 N3A  C2   C3    single    1.533  0.020  1.533
 N3A  C2   H2    single    0.970  0.020  1.090
 N3A  C2   H2A   single    0.970  0.020  1.090
 N3A  C3   C4    single    1.537  0.020  1.537
 N3A  C3   H3    single    0.970  0.020  1.090
 N3A  C3   H3A   single    0.970  0.020  1.090
 N3A  C9   C4    single    1.543  0.020  1.543
 N3A  C4   C18   single    1.541  0.020  1.541
 N3A  C4   C5    single    1.523  0.020  1.523
 N3A  C5   C6    single    1.469  0.020  1.469
 N3A  C7   C6    double    1.336  0.020  1.336
 N3A  C6   H6    single    0.930  0.020  1.080
 N3A  C8   C7    single    1.492  0.020  1.492
 N3A  C7   H7    single    0.930  0.020  1.080
 N3A  C9   C8    single    1.542  0.020  1.542
 N3A  C14  C8    single    1.544  0.020  1.544
 N3A  C28  C8    single    1.544  0.020  1.544
 N3A  C10  C9    single    1.538  0.020  1.538
 N3A  C9   H9    single    0.970  0.020  1.090
 N3A  C10  H10   single    0.970  0.020  1.090
 N3A  C10  H10A  single    0.970  0.020  1.090
 N3A  C15  C14   single    1.511  0.020  1.511
 N3A  C14  H14   single    0.970  0.020  1.090
 N3A  C14  H14A  single    0.970  0.020  1.090
 N3A  C17  C15   double    1.328  0.020  1.328
 N3A  C17  H17   single    0.930  0.020  1.080
 N3A  C17  H17A  single    0.930  0.020  1.080
 N3A  C18  H18   single    0.970  0.020  1.090
 N3A  C18  H18A  single    0.970  0.020  1.090
 N3A  C18  H18B  single    0.970  0.020  1.090
 N3A  C29  C28   single    1.543  0.020  1.543
 N3A  C28  O34   single    1.411  0.020  1.411
 N3A  C28  H28   single    0.970  0.020  1.090
 N3A  C29  H29   single    0.970  0.020  1.090
 N3A  C29  H29A  single    0.970  0.020  1.090
 N3A  C25  O30   single    1.331  0.020  1.331
 N3A  O30  HO30  single    0.850  0.020  0.980
 N3A  C23  O31   single    1.330  0.020  1.330
 N3A  O31  HO31  single    0.850  0.020  0.980
 N3A  C21  O32   single    1.339  0.020  1.339
 N3A  O32  HO32  single    0.850  0.020  0.980
 N3A  O33  C21   double    1.207  0.020  1.207
 N3A  C21  C22   single    1.469  0.020  1.469
 N3A  C27  C22   aromatic  1.402  0.020  1.402
 N3A  C22  C23   aromatic  1.409  0.020  1.409
 N3A  C23  C24   aromatic  1.399  0.020  1.399
 N3A  C25  C24   aromatic  1.392  0.020  1.392
 N3A  C26  C25   aromatic  1.399  0.020  1.399
 N3A  C27  C26   aromatic  1.372  0.020  1.372
 N3A  C26  H26   single    0.930  0.020  1.080
 N3A  C27  H27   single    0.930  0.020  1.080
 N3A  O34  HO34  single    0.850  0.020  0.980

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
 N3A  H1    C1   C29   110.48  3.000
 N3A  H1    C1   C15   110.99  3.000
 N3A  C29   C1   C15   108.24  3.000
 N3A  H1    C1   C10   110.48  3.000
 N3A  C29   C1   C10   108.11  3.000
 N3A  C15   C1   C10   108.45  3.000
 N3A  HN28  N28  C24   118.07  3.000
 N3A  HN28  N28  C11   118.07  3.000
 N3A  C24   N28  C11   121.25  3.000
 N3A  C2    C11  N28   114.56  3.000
 N3A  C2    C11  O20   123.35  3.000
 N3A  N28   C11  O20   122.07  3.000
 N3A  H2A   C2   H2    107.46  3.000
 N3A  H2A   C2   C3    110.76  3.000
 N3A  H2    C2   C3    111.17  3.000
 N3A  H2A   C2   C11   108.46  3.000
 N3A  H2    C2   C11   110.06  3.000
 N3A  C3    C2   C11   108.89  3.000
 N3A  H3A   C3   H3    106.00  3.000
 N3A  H3A   C3   C4    108.07  3.000
 N3A  H3    C3   C4    108.40  3.000
 N3A  H3A   C3   C2    109.08  3.000
 N3A  H3    C3   C2    108.72  3.000
 N3A  C4    C3   C2    116.10  3.000
 N3A  C18   C4   C9    115.01  3.000
 N3A  C18   C4   C5    104.86  3.000
 N3A  C9    C4   C5    108.59  3.000
 N3A  C5    C4   C3    111.15  3.000
 N3A  C18   C4   C3    106.65  3.000
 N3A  C9    C4   C3    110.48  3.000
 N3A  C6    C5   C4    116.97  3.000
 N3A  C6    C5   O19   120.63  3.000
 N3A  C4    C5   O19   122.26  3.000
 N3A  H6    C6   C7    120.35  3.000
 N3A  H6    C6   C5    116.44  3.000
 N3A  C7    C6   C5    123.21  3.000
 N3A  H7    C7   C8    117.07  3.000
 N3A  H7    C7   C6    118.56  3.000
 N3A  C8    C7   C6    124.31  3.000
 N3A  C28   C8   C14   107.42  3.000
 N3A  C28   C8   C9    111.22  3.000
 N3A  C14   C8   C9    106.04  3.000
 N3A  C28   C8   C7    111.70  3.000
 N3A  C14   C8   C7    109.20  3.000
 N3A  C9    C8   C7    111.01  3.000
 N3A  H9    C9   C10   106.55  3.000
 N3A  H9    C9   C8    103.51  3.000
 N3A  C10   C9   C8    109.38  3.000
 N3A  H9    C9   C4    105.06  3.000
 N3A  C10   C9   C4    114.75  3.000
 N3A  C8    C9   C4    116.37  3.000
 N3A  H10A  C10  H10   106.32  3.000
 N3A  H10A  C10  C9    111.94  3.000
 N3A  H10   C10  C9    110.37  3.000
 N3A  H10A  C10  C1    108.91  3.000
 N3A  H10   C10  C1    110.30  3.000
 N3A  C9    C10  C1    108.97  3.000
 N3A  H14A  C14  H14   106.59  3.000
 N3A  H14A  C14  C15   110.62  3.000
 N3A  H14   C14  C15   110.75  3.000
 N3A  H14A  C14  C8    109.97  3.000
 N3A  H14   C14  C8    110.22  3.000
 N3A  C15   C14  C8    108.69  3.000
 N3A  C17   C15  C14   123.92  3.000
 N3A  C17   C15  C1    124.17  3.000
 N3A  C14   C15  C1    111.91  3.000
 N3A  H17A  C17  H17   116.75  3.000
 N3A  H17A  C17  C15   121.72  3.000
 N3A  H17   C17  C15   121.53  3.000
 N3A  H18B  C18  H18A  107.11  3.000
 N3A  H18B  C18  H18   107.27  3.000
 N3A  H18A  C18  H18   107.99  3.000
 N3A  H18B  C18  C4    109.67  3.000
 N3A  H18A  C18  C4    113.04  3.000
 N3A  H18   C18  C4    111.51  3.000
 N3A  H28   C28  O34   109.25  3.000
 N3A  H28   C28  C29   109.04  3.000
 N3A  O34   C28  C29   112.87  3.000
 N3A  H28   C28  C8    108.66  3.000
 N3A  O34   C28  C8    107.99  3.000
 N3A  C29   C28  C8    108.95  3.000
 N3A  H29A  C29  H29   107.09  3.000
 N3A  H29A  C29  C28   109.52  3.000
 N3A  H29   C29  C28   110.50  3.000
 N3A  H29A  C29  C1    109.54  3.000
 N3A  H29   C29  C1    109.81  3.000
 N3A  C28   C29  C1    110.31  3.000
 N3A  HO30  O30  C25   109.68  3.000
 N3A  HO32  O32  C21   111.20  3.000
 N3A  C27   C22  C23   118.26  3.000
 N3A  C23   C22  C21   124.46  3.000
 N3A  C27   C22  C21   117.28  3.000
 N3A  C24   C23  C22   119.34  3.000
 N3A  C24   C23  O31   115.51  3.000
 N3A  C22   C23  O31   125.15  3.000
 N3A  C25   C24  C23   120.81  3.000
 N3A  C25   C24  N28   118.92  3.000
 N3A  C23   C24  N28   120.26  3.000
 N3A  C26   C25  C24   120.16  3.000
 N3A  C26   C25  O30   118.67  3.000
 N3A  C24   C25  O30   121.17  3.000
 N3A  H26   C26  C27   121.02  3.000
 N3A  H26   C26  C25   120.20  3.000
 N3A  C27   C26  C25   118.77  3.000
 N3A  H27   C27  C26   118.84  3.000
 N3A  H27   C27  C22   118.51  3.000
 N3A  C26   C27  C22   122.65  3.000
 N3A  HO34  O34  C28   108.17  3.000
 N3A  HO31  O31  C23   110.29  3.000
 N3A  C22   C21  O33   124.85  3.000
 N3A  C22   C21  O32   113.14  3.000
 N3A  O33   C21  O32   122.02  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
 N3A  CONST_01  C25   C26  C27  C22     0.00   0.0  0
 N3A  CONST_02  C25   C24  C23  C22     0.00   0.0  0
 N3A  CONST_03  C26   C27  C22  C23     0.00   0.0  0
 N3A  CONST_04  C26   C25  C24  C23     0.00   0.0  0
 N3A  CONST_05  C27   C22  C23  C24     0.00   0.0  0
 N3A  CONST_06  C27   C26  C25  C24     0.00   0.0  0
 N3A  CONST_07  C22   C23  C24  N28   180.00   0.0  0
 N3A  CONST_08  C26   C25  C24  N28   180.00   0.0  0
 N3A  CONST_09  C23   C24  C25  O30   180.00   0.0  0
 N3A  CONST_10  C27   C26  C25  O30   180.00   0.0  0
 N3A  CONST_11  C27   C22  C23  O31   180.00   0.0  0
 N3A  CONST_12  C25   C24  C23  O31   180.00   0.0  0
 N3A  CONST_13  C26   C27  C22  C21   180.00   0.0  0
 N3A  CONST_14  C24   C23  C22  C21   180.00   0.0  0
 N3A  CONST_15  H26   C26  C27  C22   180.00   0.0  0
 N3A  CONST_16  H27   C27  C22  C23   180.00   0.0  0
 N3A  CONST_20  C24   N28  C11  O20     0.00   0.0  0
 N3A  CONST_21  C24   N28  C11  C2    180.00   0.0  0
 N3A  CONST_22  HO32  O32  C21  C22   180.00   0.0  0
 N3A  Var_01    C8    C14  C15  C1    -14.91  30.0  1
 N3A  Var_02    C7    C6   C5   C4     10.99  30.0  1
 N3A  Var_03    C8    C7   C6   C5      4.18  30.0  1
 N3A  Var_04    C27   C22  C21  O32   179.96  30.0  2
 N3A  Var_05    H17   C17  C15  C1     -1.85   0.0  2
 N3A  Var_06    C4    C3   C2   C11  -178.26  30.0  3
 N3A  Var_07    C3    C2   C11  O20    81.64  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
 N3A  chir_01  C1   C10  C15  C29  negativ
 N3A  chir_02  C4   C5   C9   C3   positiv
 N3A  chir_03  C8   C14  C9   C7   positiv
 N3A  chir_04  C9   C10  C8   C4   positiv
 N3A  chir_05  C28  O34  C29  C8   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
 N3A  plan-1  N28   0.020
 N3A  plan-1  O30   0.020
 N3A  plan-1  C22   0.020
 N3A  plan-1  C23   0.020
 N3A  plan-1  C24   0.020
 N3A  plan-1  C25   0.020
 N3A  plan-1  C26   0.020
 N3A  plan-1  C27   0.020
 N3A  plan-1  H26   0.020
 N3A  plan-1  H27   0.020
 N3A  plan-1  O31   0.020
 N3A  plan-1  C21   0.020
 N3A  plan-2  C1    0.020
 N3A  plan-2  C14   0.020
 N3A  plan-2  C15   0.020
 N3A  plan-2  C17   0.020
 N3A  plan-2  H17   0.020
 N3A  plan-2  H17A  0.020
 N3A  plan-3  O20   0.020
 N3A  plan-3  N28   0.020
 N3A  plan-3  C11   0.020
 N3A  plan-3  C2    0.020
 N3A  plan-3  C24   0.020
 N3A  plan-3  HN28  0.020
 N3A  plan-4  O19   0.020
 N3A  plan-4  C4    0.020
 N3A  plan-4  C5    0.020
 N3A  plan-4  C6    0.020
 N3A  plan-5  O32   0.020
 N3A  plan-5  O33   0.020
 N3A  plan-5  C22   0.020
 N3A  plan-5  HO32  0.020
 N3A  plan-5  C21   0.020

