# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 16:57:20 2020
#   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  58  32  .  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_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   3.0639  -1.3334  -1.7417
 PMN  O19   O  O      0  -0.417   2.1481   3.2892   1.7576
 PMN  O20   O  O      0  -0.469  -1.9193   2.2116   0.6007
 PMN  O32   O  O      0  -0.637  -4.6652  -2.2043   2.1117
 PMN  O33   O  OC    -1  -0.553  -6.7640  -2.0429   1.3920
 PMN  N28   N  NH1    0  -0.730  -1.8716   0.6023  -0.9847
 PMN  C1    C  C      0   0.541  -1.2796   1.4938  -0.1448
 PMN  C2    C  CH2    0  -0.598   0.2296   1.5162  -0.1996
 PMN  C3    C  CH2    0  -0.414   0.8014   0.9275   1.0924
 PMN  C4    C  CR6    0  -0.219   2.3332   0.9516   1.2209
 PMN  C5    C  CR6    0   0.440   2.8445   2.3891   1.3293
 PMN  C6    C  CR16   0  -0.365   4.2555   2.6339   0.9955
 PMN  C7    C  CR16   0  -0.113   5.0305   1.7180   0.4075
 PMN  C8    C  CR6    0  -0.184   4.5489   0.3911  -0.0419
 PMN  C9    C  CR16   0  -0.233   3.0040   0.3162  -0.0157
 PMN  C10   C  CH1    0  -0.021   2.5574  -1.1019  -0.4336
 PMN  C11   C  CH2    0  -0.421   3.2426  -2.2290   0.3295
 PMN  C12   C  CH1    0  -0.308   4.6790  -1.9770  -0.1229
 PMN  C13   C  CH2    0  -0.402   5.2187  -0.7945   0.6851
 PMN  C14   C  CH2    0  -0.394   4.9883   0.0358  -1.4742
 PMN  C15   C  CT     0   0.255   4.4830  -1.4078  -1.5739
 PMN  C17   C  CH3    0  -0.691   5.0804  -2.2259  -2.6920
 PMN  C18   C  CH3    0  -0.668   2.6799   0.3209   2.5821
 PMN  C22   C  C      0  -0.316  -5.0743  -0.8598   0.2301
 PMN  C23   C  C      0   0.363  -3.7017  -0.5583   0.1363
 PMN  C24   C  C      0   0.070  -3.2459   0.2893  -0.8800
 PMN  C25   C  C      0   0.342  -4.1441   0.8444  -1.7882
 PMN  C26   C  C1     0  -0.385  -5.5053   0.5463  -1.7038
 PMN  C27   C  C1     0  -0.283  -5.9426  -0.2965  -0.6998
 PMN  HO30  H  HOH1   0   0.470  -2.7647   1.7735  -2.6959
 PMN  HO31  H  HOH1   0   0.461  -3.4316  -1.6315   1.6206
 PMN  HN28  H  HNH1   0   0.405  -1.2743  -0.0397  -1.4851
 PMN  H21   H  HCH2   0   0.254   0.5851   0.9731  -1.0770
 PMN  H22   H  HCH2   0   0.274   0.5457   2.5541  -0.3175
 PMN  H31   H  HCH2   0   0.254   0.3740   1.4650   1.9398
 PMN  H32   H  HCH2   0   0.247   0.4652  -0.1085   1.1966
 PMN  H6    H  HCR6   0   0.261   4.6547   3.6038   1.2694
 PMN  H7    H  HCR6   0   0.266   6.0772   1.9442   0.2239
 PMN  H9    H  HCR6   0   0.264   2.6864   0.9527  -0.8530
 PMN  H10   H  HCH1   0   0.239   1.4691  -1.1880  -0.4694
 PMN  H111  H  HCH2   0   0.241   3.1291  -2.2002   1.4112
 PMN  H112  H  HCH2   0   0.251   2.8532  -3.1880  -0.0189
 PMN  H12   H  HCH1   0   0.248   5.3205  -2.8577  -0.0859
 PMN  H131  H  HCH2   0   0.249   6.3042  -0.7014   0.5966
 PMN  H132  H  HCH2   0   0.252   4.9879  -0.8748   1.7463
 PMN  H141  H  HCH2   0   0.251   4.5541   0.6758  -2.2447
 PMN  H142  H  HCH2   0   0.240   6.0776   0.0919  -1.5608
 PMN  H171  H  HCH3   0   0.234   4.8502  -1.7937  -3.6675
 PMN  H172  H  HCH3   0   0.231   6.1651  -2.2624  -2.5907
 PMN  H173  H  HCH3   0   0.234   4.7067  -3.2510  -2.6747
 PMN  H181  H  HCH3   0   0.248   2.3989  -0.7303   2.6198
 PMN  H182  H  HCH3   0   0.245   3.7373   0.3973   2.8297
 PMN  H183  H  HCH3   0   0.250   2.1278   0.8318   3.3723
 PMN  H26   H  H      0   0.255  -6.1976   0.9765  -2.4155
 PMN  H27   H  H      0   0.251  -6.9974  -0.5300  -0.6295
 PMN  C21   C  C      0   0.492  -5.5636  -1.7690   1.3175
 PMN  O31   O  OH1    0  -0.636  -2.8306  -1.0631   0.9933
 PMN  O30   O  OH1    0  -0.619  -3.7249   1.6712  -2.7572

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    1.422  0.020  1.422
 PMN  O16  C15   single    1.431  0.020  1.431
 PMN  O19  C5    double    1.216  0.020  1.216
 PMN  O20  C1    double    1.217  0.020  1.217
 PMN  O30  C25   single    1.341  0.020  1.341
 PMN  O30  HO30  single    0.850  0.020  0.980
 PMN  O31  C23   single    1.322  0.020  1.322
 PMN  O31  HO31  single    0.850  0.020  0.980
 PMN  O32  C21   deloc     1.276  0.020  1.276
 PMN  O33  C21   deloc     1.233  0.020  1.233
 PMN  N28  C1    single    1.360  0.020  1.360
 PMN  N28  C24   single    1.413  0.020  1.413
 PMN  N28  HN28  single    0.860  0.020  1.020
 PMN  C1   C2    single    1.510  0.020  1.510
 PMN  C2   C3    single    1.531  0.020  1.531
 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    1.540  0.020  1.540
 PMN  C5   C6    single    1.470  0.020  1.470
 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    1.547  0.020  1.547
 PMN  C8   C13   single    1.544  0.020  1.544
 PMN  C8   C14   single    1.540  0.020  1.540
 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    1.527  0.020  1.527
 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    1.533  0.020  1.533
 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    1.499  0.020  1.499
 PMN  C22  C23   aromatic  1.408  0.020  1.408
 PMN  C22  C27   aromatic  1.391  0.020  1.391
 PMN  C23  C24   aromatic  1.400  0.020  1.400
 PMN  C24  C25   aromatic  1.393  0.020  1.393
 PMN  C25  C26   aromatic  1.396  0.020  1.396
 PMN  C26  C27   aromatic  1.382  0.020  1.382
 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   104.70  3.000
 PMN  HN28  N28  C24   118.11  3.000
 PMN  HN28  N28  C1    117.73  3.000
 PMN  C24   N28  C1    121.50  3.000
 PMN  C2    C1   N28   114.97  3.000
 PMN  C2    C1   O20   122.61  3.000
 PMN  N28   C1   O20   122.42  3.000
 PMN  H22   C2   H21   106.98  3.000
 PMN  H22   C2   C3    110.41  3.000
 PMN  H21   C2   C3    111.44  3.000
 PMN  H22   C2   C1    107.90  3.000
 PMN  H21   C2   C1    110.32  3.000
 PMN  C3    C2   C1    109.69  3.000
 PMN  H32   C3   H31   105.79  3.000
 PMN  H32   C3   C4    108.25  3.000
 PMN  H31   C3   C4    108.53  3.000
 PMN  H32   C3   C2    109.26  3.000
 PMN  H31   C3   C2    108.66  3.000
 PMN  C4    C3   C2    115.90  3.000
 PMN  C18   C4   C9    116.21  3.000
 PMN  C18   C4   C5    104.30  3.000
 PMN  C9    C4   C5    107.36  3.000
 PMN  C18   C4   C3    106.97  3.000
 PMN  C9    C4   C3    111.07  3.000
 PMN  C5    C4   C3    110.72  3.000
 PMN  C6    C5   C4    117.46  3.000
 PMN  C6    C5   O19   120.41  3.000
 PMN  C4    C5   O19   121.95  3.000
 PMN  H6    C6   C7    120.72  3.000
 PMN  H6    C6   C5    116.42  3.000
 PMN  C7    C6   C5    122.84  3.000
 PMN  H7    C7   C8    116.64  3.000
 PMN  H7    C7   C6    119.37  3.000
 PMN  C8    C7   C6    123.98  3.000
 PMN  C14   C8   C13    97.88  3.000
 PMN  C14   C8   C9    106.83  3.000
 PMN  C13   C8   C9    112.84  3.000
 PMN  C14   C8   C7    113.34  3.000
 PMN  C13   C8   C7    113.84  3.000
 PMN  C9    C8   C7    111.27  3.000
 PMN  H9    C9   C10   104.02  3.000
 PMN  H9    C9   C8    104.35  3.000
 PMN  C10   C9   C8    109.18  3.000
 PMN  H9    C9   C4    104.27  3.000
 PMN  C10   C9   C4    117.97  3.000
 PMN  C8    C9   C4    115.32  3.000
 PMN  H10   C10  C11   113.96  3.000
 PMN  H10   C10  C9    111.67  3.000
 PMN  C11   C10  C9    114.43  3.000
 PMN  H10   C10  O16   108.18  3.000
 PMN  C11   C10  O16   100.38  3.000
 PMN  C9    C10  O16   107.18  3.000
 PMN  H112  C11  H111  107.65  3.000
 PMN  H112  C11  C12   112.69  3.000
 PMN  H111  C11  C12   112.85  3.000
 PMN  H112  C11  C10   109.23  3.000
 PMN  H111  C11  C10   115.56  3.000
 PMN  C12   C11  C10    98.77  3.000
 PMN  H12   C12  C15   113.43  3.000
 PMN  H12   C12  C13   113.50  3.000
 PMN  C15   C12  C13   104.58  3.000
 PMN  H12   C12  C11   114.22  3.000
 PMN  C15   C12  C11   102.48  3.000
 PMN  C13   C12  C11   107.62  3.000
 PMN  H132  C13  H131  107.19  3.000
 PMN  H132  C13  C12   112.51  3.000
 PMN  H131  C13  C12   111.92  3.000
 PMN  H132  C13  C8    115.06  3.000
 PMN  H131  C13  C8    109.10  3.000
 PMN  C12   C13  C8    101.06  3.000
 PMN  H142  C14  H141  108.06  3.000
 PMN  H142  C14  C15   111.80  3.000
 PMN  H141  C14  C15   112.03  3.000
 PMN  H142  C14  C8    110.24  3.000
 PMN  H141  C14  C8    114.07  3.000
 PMN  C15   C14  C8    100.59  3.000
 PMN  C17   C15  C14   115.36  3.000
 PMN  C17   C15  C12   116.01  3.000
 PMN  C14   C15  C12   103.89  3.000
 PMN  C17   C15  O16   109.51  3.000
 PMN  C14   C15  O16   106.60  3.000
 PMN  C12   C15  O16   104.53  3.000
 PMN  H173  C17  H172  107.93  3.000
 PMN  H173  C17  H171  108.30  3.000
 PMN  H172  C17  H171  107.83  3.000
 PMN  H173  C17  C15   111.23  3.000
 PMN  H172  C17  C15   110.08  3.000
 PMN  H171  C17  C15   111.35  3.000
 PMN  H183  C18  H182  107.09  3.000
 PMN  H183  C18  H181  107.24  3.000
 PMN  H182  C18  H181  108.10  3.000
 PMN  H183  C18  C4    109.54  3.000
 PMN  H182  C18  C4    113.02  3.000
 PMN  H181  C18  C4    111.59  3.000
 PMN  C27   C22  C23   118.49  3.000
 PMN  C27   C22  C21   121.77  3.000
 PMN  C23   C22  C21   119.74  3.000
 PMN  C24   C23  C22   119.69  3.000
 PMN  C24   C23  O31   119.16  3.000
 PMN  C22   C23  O31   121.15  3.000
 PMN  C25   C24  C23   120.32  3.000
 PMN  C25   C24  N28   119.38  3.000
 PMN  C23   C24  N28   120.30  3.000
 PMN  C26   C25  C24   120.29  3.000
 PMN  C26   C25  O30   118.70  3.000
 PMN  C24   C25  O30   121.01  3.000
 PMN  H26   C26  C27   121.19  3.000
 PMN  H26   C26  C25   119.95  3.000
 PMN  C27   C26  C25   118.86  3.000
 PMN  H27   C27  C26   119.15  3.000
 PMN  H27   C27  C22   118.51  3.000
 PMN  C26   C27  C22   122.34  3.000
 PMN  C22   C21  O33   119.74  3.000
 PMN  C22   C21  O32   115.38  3.000
 PMN  O33   C21  O32   124.89  3.000
 PMN  HO31  O31  C23   102.67  3.000
 PMN  HO30  O30  C25   109.25  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_21  C24  N28  C1   C2    180.00   0.0  0
 PMN  Var_01    C7   C6   C5   C4     11.07  30.0  1
 PMN  Var_02    C8   C7   C6   C5      3.53  30.0  1
 PMN  Var_03    C23  C22  C21  O32     0.72  30.0  2
 PMN  Var_04    C4   C3   C2   C1   -176.78  30.0  3
 PMN  Var_05    C3   C2   C1   O20    69.68  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  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  C21   0.020
 PMN  plan-1  O31   0.020
 PMN  plan-1  O30   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  C21   0.020

