# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 01:22:44 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxo-1,2,5,6,7,8,9,9a-octahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12C[C@]34C[C@H]1C[C@H](O2)[C@H]3[C@](C)(CCC(=O)Nc5c(O)ccc(C(O)=O)c5O)C(=O)C=C4
#
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
 PMN  PMN  '3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxo-1,2,5,6,7,8,9,9a-octahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid'  ligand  59  32  .  2021-08-19  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PMN
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
 PMN  O16   O  O2    0  -0.500  24.5539  28.2747  54.3807
 PMN  O19   O  O     0  -0.417  20.1843  28.6245  50.4380
 PMN  O20   O  O     0  -0.453  18.4134  25.8918  53.2632
 PMN  O30   O  OH1   0  -0.601  18.9400  24.2560  56.7841
 PMN  O32   O  O     0  -0.494  14.9190  29.0675  55.9353
 PMN  O33   O  OH1   0  -0.585  13.7752  27.7616  57.3277
 PMN  N28   N  NH1   0  -0.730  19.3016  26.5279  55.2396
 PMN  C1    C  C     0   0.533  19.3222  26.4122  53.8782
 PMN  C2    C  CH2   0  -0.603  20.5463  27.0042  53.2235
 PMN  C3    C  CH2   0  -0.419  20.4487  28.5363  53.2173
 PMN  C4    C  CR6   0  -0.226  21.4860  29.2701  52.3519
 PMN  C5    C  CR6   0   0.443  21.2752  28.9401  50.8731
 PMN  C6    C  CR16  0  -0.366  22.4166  29.1120  49.9647
 PMN  C7    C  CR16  0  -0.114  23.6592  29.3460  50.3966
 PMN  C8    C  CR6   0  -0.186  24.0437  29.4059  51.8256
 PMN  C9    C  CR16  0  -0.226  22.9212  28.8485  52.7346
 PMN  C10   C  CH1   0  -0.022  23.3434  29.0003  54.2122
 PMN  C11   C  CH2   0  -0.423  23.8076  30.4017  54.5915
 PMN  C12   C  CH1   0  -0.306  25.0326  30.4960  53.6859
 PMN  C13   C  CH2   0  -0.403  24.5391  30.7979  52.2692
 PMN  C14   C  CH2   0  -0.394  25.3203  28.6121  52.1558
 PMN  C15   C  CT    0   0.254  25.5234  29.0050  53.6230
 PMN  C17   C  CH3   0  -0.693  26.9003  28.7368  54.1780
 PMN  C18   C  CH3   0  -0.665  21.1685  30.7734  52.4640
 PMN  C22   C  CR6   0  -0.262  15.9061  27.0501  56.6687
 PMN  C23   C  CR6   0   0.374  17.0854  27.2695  55.9282
 PMN  C24   C  CR6   0   0.092  18.1152  26.3262  55.9747
 PMN  C25   C  CR6   0   0.364  17.9758  25.1730  56.7410
 PMN  C26   C  CR16  0  -0.368  16.8114  24.9541  57.4877
 PMN  C27   C  CR16  0  -0.259  15.8027  25.8845  57.4402
 PMN  HO30  H  HOH1  0   0.477  19.6786  24.5347  56.2227
 PMN  HO31  H  HOH1  0   0.481  16.4750  28.9011  55.2294
 PMN  HO33  H  HOH1  0   0.492  13.1109  28.4605  57.2311
 PMN  HN28  H  HNH1  0   0.411  20.0439  27.0528  55.6805
 PMN  H21   H  HCH2  0   0.265  21.4409  26.6691  53.7544
 PMN  H22   H  HCH2  0   0.272  20.6059  26.6153  52.2080
 PMN  H31   H  HCH2  0   0.258  19.4535  28.8289  52.8780
 PMN  H32   H  HCH2  0   0.246  20.5325  28.9119  54.2404
 PMN  H6    H  HCR6  0   0.261  22.2033  29.0501  48.9036
 PMN  H7    H  HCR6  0   0.267  24.4531  29.4953  49.6698
 PMN  H9    H  HCR6  0   0.266  22.9433  27.7651  52.5555
 PMN  H10   H  HCH1  0   0.240  22.5968  28.5792  54.8890
 PMN  H111  H  HCH2  0   0.242  23.0894  31.1991  54.4122
 PMN  H112  H  HCH2  0   0.251  24.0676  30.4214  55.6520
 PMN  H12   H  HCH1  0   0.248  25.7959  31.1889  54.0404
 PMN  H131  H  HCH2  0   0.250  25.3538  31.1139  51.6120
 PMN  H132  H  HCH2  0   0.252  23.7823  31.5812  52.2445
 PMN  H141  H  HCH2  0   0.251  25.2201  27.5322  52.0288
 PMN  H142  H  HCH2  0   0.240  26.1489  28.9544  51.5286
 PMN  H171  H  HCH3  0   0.231  27.6485  29.2977  53.6175
 PMN  H172  H  HCH3  0   0.234  26.9705  29.0375  55.2247
 PMN  H173  H  HCH3  0   0.234  27.1565  27.6779  54.1086
 PMN  H181  H  HCH3  0   0.248  21.2757  31.1208  53.4906
 PMN  H182  H  HCH3  0   0.246  21.7998  31.3905  51.8280
 PMN  H183  H  HCH3  0   0.250  20.1331  30.9507  52.1707
 PMN  H26   H  HCR6  0   0.274  16.7146  24.0586  58.0863
 PMN  H27   H  HCR6  0   0.277  14.9064  25.7034  58.0175
 PMN  O31   O  OH1   0  -0.602  17.2812  28.3416  55.1742
 PMN  C21   C  C     0   0.592  14.8411  28.0457  56.6046

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
 PMN  O16  C10   single    1.421  0.020  1.421
 PMN  O16  C15   single    1.431  0.020  1.431
 PMN  O19  C5    double    1.216  0.020  1.216
 PMN  O20  C1    double    1.214  0.020  1.214
 PMN  O30  C25   single    1.331  0.020  1.331
 PMN  O30  HO30  single    0.850  0.020  0.980
 PMN  O31  C23   single    1.325  0.020  1.325
 PMN  O31  HO31  single    0.850  0.020  0.980
 PMN  O32  C21   double    1.224  0.020  1.224
 PMN  O33  C21   single    1.319  0.020  1.319
 PMN  O33  HO33  single    0.850  0.020  0.980
 PMN  N28  C1    single    1.366  0.020  1.366
 PMN  N28  C24   single    1.410  0.020  1.410
 PMN  N28  HN28  single    0.890  0.020  1.040
 PMN  C1   C2    single    1.509  0.020  1.509
 PMN  C2   C3    single    1.535  0.020  1.535
 PMN  C2   H21   single    0.970  0.020  1.090
 PMN  C2   H22   single    0.970  0.020  1.090
 PMN  C3   C4    single    1.537  0.020  1.537
 PMN  C3   H31   single    0.970  0.020  1.090
 PMN  C3   H32   single    0.970  0.020  1.090
 PMN  C4   C5    single    1.530  0.020  1.530
 PMN  C4   C9    single    1.544  0.020  1.544
 PMN  C4   C18   single    1.541  0.020  1.541
 PMN  C5   C6    single    1.469  0.020  1.469
 PMN  C6   C7    double    1.336  0.020  1.336
 PMN  C6   H6    single    0.930  0.020  1.080
 PMN  C7   C8    single    1.481  0.020  1.481
 PMN  C7   H7    single    0.930  0.020  1.080
 PMN  C8   C9    single    1.548  0.020  1.548
 PMN  C8   C13   single    1.543  0.020  1.543
 PMN  C8   C14   single    1.539  0.020  1.539
 PMN  C9   C10   single    1.544  0.020  1.544
 PMN  C9   H9    single    0.970  0.020  1.090
 PMN  C10  C11   single    1.524  0.020  1.524
 PMN  C10  H10   single    0.970  0.020  1.090
 PMN  C11  C12   single    1.526  0.020  1.526
 PMN  C11  H111  single    0.970  0.020  1.090
 PMN  C11  H112  single    0.970  0.020  1.090
 PMN  C12  C13   single    1.530  0.020  1.530
 PMN  C12  C15   single    1.571  0.020  1.571
 PMN  C12  H12   single    0.970  0.020  1.090
 PMN  C13  H131  single    0.970  0.020  1.090
 PMN  C13  H132  single    0.970  0.020  1.090
 PMN  C14  C15   single    1.532  0.020  1.532
 PMN  C14  H141  single    0.970  0.020  1.090
 PMN  C14  H142  single    0.970  0.020  1.090
 PMN  C15  C17   single    1.509  0.020  1.509
 PMN  C17  H171  single    0.970  0.020  1.090
 PMN  C17  H172  single    0.970  0.020  1.090
 PMN  C17  H173  single    0.970  0.020  1.090
 PMN  C18  H181  single    0.970  0.020  1.090
 PMN  C18  H182  single    0.970  0.020  1.090
 PMN  C18  H183  single    0.970  0.020  1.090
 PMN  C21  C22   single    1.459  0.020  1.459
 PMN  C22  C23   aromatic  1.410  0.020  1.410
 PMN  C22  C27   aromatic  1.402  0.020  1.402
 PMN  C23  C24   aromatic  1.397  0.020  1.397
 PMN  C24  C25   aromatic  1.392  0.020  1.392
 PMN  C25  C26   aromatic  1.400  0.020  1.400
 PMN  C26  C27   aromatic  1.373  0.020  1.373
 PMN  C26  H26   single    0.930  0.020  1.080
 PMN  C27  H27   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
 PMN  C15   O16  C10   104.69  3.000
 PMN  HO30  O30  C25   109.59  3.000
 PMN  HO33  O33  C21   110.12  3.000
 PMN  HN28  N28  C24   117.70  3.000
 PMN  HN28  N28  C1    117.88  3.000
 PMN  C24   N28  C1    121.32  3.000
 PMN  C2    C1   N28   114.28  3.000
 PMN  C2    C1   O20   123.74  3.000
 PMN  N28   C1   O20   121.97  3.000
 PMN  H22   C2   H21   107.38  3.000
 PMN  H22   C2   C3    110.86  3.000
 PMN  H21   C2   C3    111.10  3.000
 PMN  H22   C2   C1    107.99  3.000
 PMN  H21   C2   C1    109.45  3.000
 PMN  C3    C2   C1    109.98  3.000
 PMN  H32   C3   H31   105.59  3.000
 PMN  H32   C3   C4    108.13  3.000
 PMN  H31   C3   C4    108.20  3.000
 PMN  H32   C3   C2    109.53  3.000
 PMN  H31   C3   C2    109.07  3.000
 PMN  C4    C3   C2    115.83  3.000
 PMN  C18   C4   C9    116.10  3.000
 PMN  C18   C4   C5    104.62  3.000
 PMN  C9    C4   C5    107.99  3.000
 PMN  C18   C4   C3    106.60  3.000
 PMN  C9    C4   C3    110.94  3.000
 PMN  C5    C4   C3    110.38  3.000
 PMN  C6    C5   C4    117.75  3.000
 PMN  C6    C5   O19   120.41  3.000
 PMN  C4    C5   O19   121.70  3.000
 PMN  H6    C6   C7    120.62  3.000
 PMN  H6    C6   C5    116.48  3.000
 PMN  C7    C6   C5    122.90  3.000
 PMN  H7    C7   C8    116.75  3.000
 PMN  H7    C7   C6    119.17  3.000
 PMN  C8    C7   C6    124.08  3.000
 PMN  C14   C8   C13    97.90  3.000
 PMN  C14   C8   C9    106.84  3.000
 PMN  C13   C8   C9    112.89  3.000
 PMN  C14   C8   C7    113.67  3.000
 PMN  C13   C8   C7    113.41  3.000
 PMN  C9    C8   C7    111.32  3.000
 PMN  H9    C9   C10   104.33  3.000
 PMN  H9    C9   C8    104.17  3.000
 PMN  C10   C9   C8    109.16  3.000
 PMN  H9    C9   C4    104.33  3.000
 PMN  C10   C9   C4    117.68  3.000
 PMN  C8    C9   C4    115.47  3.000
 PMN  H10   C10  C11   114.11  3.000
 PMN  H10   C10  C9    111.60  3.000
 PMN  C11   C10  C9    114.32  3.000
 PMN  H10   C10  O16   108.17  3.000
 PMN  C11   C10  O16   100.40  3.000
 PMN  C9    C10  O16   107.22  3.000
 PMN  H112  C11  H111  107.70  3.000
 PMN  H112  C11  C12   112.58  3.000
 PMN  H111  C11  C12   112.75  3.000
 PMN  H112  C11  C10   109.31  3.000
 PMN  H111  C11  C10   115.58  3.000
 PMN  C12   C11  C10    98.83  3.000
 PMN  H12   C12  C15   113.42  3.000
 PMN  H12   C12  C13   113.67  3.000
 PMN  C15   C12  C13   104.53  3.000
 PMN  H12   C12  C11   114.10  3.000
 PMN  C15   C12  C11   102.47  3.000
 PMN  C13   C12  C11   107.62  3.000
 PMN  H132  C13  H131  107.23  3.000
 PMN  H132  C13  C12   112.76  3.000
 PMN  H131  C13  C12   111.91  3.000
 PMN  H132  C13  C8    114.78  3.000
 PMN  H131  C13  C8    109.10  3.000
 PMN  C12   C13  C8    101.05  3.000
 PMN  H142  C14  H141  108.20  3.000
 PMN  H142  C14  C15   111.61  3.000
 PMN  H141  C14  C15   112.15  3.000
 PMN  H142  C14  C8    110.11  3.000
 PMN  H141  C14  C8    114.14  3.000
 PMN  C15   C14  C8    100.55  3.000
 PMN  C17   C15  C14   115.32  3.000
 PMN  C17   C15  C12   116.05  3.000
 PMN  C14   C15  C12   103.90  3.000
 PMN  C17   C15  O16   109.44  3.000
 PMN  C14   C15  O16   106.64  3.000
 PMN  C12   C15  O16   104.57  3.000
 PMN  H173  C17  H172  108.24  3.000
 PMN  H173  C17  H171  107.78  3.000
 PMN  H172  C17  H171  107.90  3.000
 PMN  H173  C17  C15   111.30  3.000
 PMN  H172  C17  C15   111.26  3.000
 PMN  H171  C17  C15   110.23  3.000
 PMN  H183  C18  H182  107.54  3.000
 PMN  H183  C18  H181  107.16  3.000
 PMN  H182  C18  H181  108.24  3.000
 PMN  H183  C18  C4    109.55  3.000
 PMN  H182  C18  C4    113.04  3.000
 PMN  H181  C18  C4    111.08  3.000
 PMN  C27   C22  C23   118.71  3.000
 PMN  C27   C22  C21   122.52  3.000
 PMN  C23   C22  C21   118.77  3.000
 PMN  C24   C23  C22   119.60  3.000
 PMN  C24   C23  O31   117.14  3.000
 PMN  C22   C23  O31   123.26  3.000
 PMN  C25   C24  C23   120.26  3.000
 PMN  C25   C24  N28   119.33  3.000
 PMN  C23   C24  N28   120.41  3.000
 PMN  C26   C25  C24   120.42  3.000
 PMN  C26   C25  O30   118.50  3.000
 PMN  C24   C25  O30   121.07  3.000
 PMN  H26   C26  C27   120.96  3.000
 PMN  H26   C26  C25   119.93  3.000
 PMN  C27   C26  C25   119.11  3.000
 PMN  H27   C27  C26   118.49  3.000
 PMN  H27   C27  C22   119.62  3.000
 PMN  C26   C27  C22   121.89  3.000
 PMN  HO31  O31  C23   107.90  3.000
 PMN  C22   C21  O33   114.76  3.000
 PMN  C22   C21  O32   123.16  3.000
 PMN  O33   C21  O32   122.08  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
 PMN  CONST_01  C25   C24  C23  C22     0.00   0.0  0
 PMN  CONST_02  C25   C26  C27  C22     0.00   0.0  0
 PMN  CONST_03  C26   C27  C22  C23     0.00   0.0  0
 PMN  CONST_04  C26   C25  C24  C23     0.00   0.0  0
 PMN  CONST_05  C27   C22  C23  C24     0.00   0.0  0
 PMN  CONST_06  C27   C26  C25  C24     0.00   0.0  0
 PMN  CONST_07  C23   C24  C25  O30   180.00   0.0  0
 PMN  CONST_08  C27   C26  C25  O30   180.00   0.0  0
 PMN  CONST_09  C27   C22  C23  O31   180.00   0.0  0
 PMN  CONST_10  C25   C24  C23  O31   180.00   0.0  0
 PMN  CONST_11  C22   C23  C24  N28   180.00   0.0  0
 PMN  CONST_12  C26   C25  C24  N28   180.00   0.0  0
 PMN  CONST_13  C24   C23  C22  C21   180.00   0.0  0
 PMN  CONST_14  C26   C27  C22  C21   180.00   0.0  0
 PMN  CONST_15  H26   C26  C27  C22   180.00   0.0  0
 PMN  CONST_16  H27   C27  C22  C23   180.00   0.0  0
 PMN  CONST_20  C24   N28  C1   O20     0.00   0.0  0
 PMN  CONST_22  HO33  O33  C21  C22   180.00   0.0  0
 PMN  Var_01    C7    C6   C5   C4     10.21  30.0  1
 PMN  Var_02    C8    C7   C6   C5      2.54  30.0  1
 PMN  Var_03    C23   C22  C21  O32     0.08  30.0  2
 PMN  Var_04    C4    C3   C2   C1   -168.83  30.0  3
 PMN  Var_05    C3    C2   C1   O20   103.94  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
 PMN  chir_01  C4   C5   C9   C18  negativ
 PMN  chir_02  C8   C13  C9   C7   negativ
 PMN  chir_03  C9   C4   C8   C10  negativ
 PMN  chir_04  C10  O16  C11  C9   negativ
 PMN  chir_05  C12  C11  C13  C15  positiv
 PMN  chir_06  C15  C12  O16  C17  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
 PMN  plan-1  O30   0.020
 PMN  plan-1  N28   0.020
 PMN  plan-1  C22   0.020
 PMN  plan-1  C23   0.020
 PMN  plan-1  C24   0.020
 PMN  plan-1  C25   0.020
 PMN  plan-1  C26   0.020
 PMN  plan-1  C27   0.020
 PMN  plan-1  H26   0.020
 PMN  plan-1  H27   0.020
 PMN  plan-1  O31   0.020
 PMN  plan-1  C21   0.020
 PMN  plan-2  O20   0.020
 PMN  plan-2  N28   0.020
 PMN  plan-2  C1    0.020
 PMN  plan-2  C2    0.020
 PMN  plan-2  C24   0.020
 PMN  plan-2  HN28  0.020
 PMN  plan-3  O19   0.020
 PMN  plan-3  C4    0.020
 PMN  plan-3  C5    0.020
 PMN  plan-3  C6    0.020
 PMN  plan-4  O32   0.020
 PMN  plan-4  O33   0.020
 PMN  plan-4  C22   0.020
 PMN  plan-4  HO33  0.020
 PMN  plan-4  C21   0.020

