# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:47:46 2022
#   Inital geometry file: a 167 line input string
#   Ligand name: N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@H]2C[C@H](O)/C=C/C(=C/C[C@H](O)/C=C/C(=C/[C@@H](NC(=O)C(C)=O)[C@](C)(C(=O)O2)C1=O)C)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
 LC2  LC2  N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide  ligand  66  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LC2
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
 LC2  C1    C  C     0   0.646  53.3454  121.4709  111.8158
 LC2  N1    N  NH1   0  -0.626  56.7508  120.7977  113.2895
 LC2  O1    O  O2    0  -0.438  52.1953  120.8855  111.5278
 LC2  C2    C  C1    0  -0.279  50.3493  122.4180  116.6014
 LC2  O2    O  O     0  -0.417  53.4211  122.6671  111.7166
 LC2  C3    C  C     0   0.151  50.2678  122.3848  115.2625
 LC2  O3    O  OH1   0  -0.677  52.3223  124.6018  118.9232
 LC2  C4    C  C1    0  -0.279  50.0587  121.0885  114.6196
 LC2  O4    O  OH1   0  -0.672  48.2980  119.3512  112.4430
 LC2  C5    C  C1    0  -0.223  49.8603  120.8705  113.3170
 LC2  C6    C  CH1   0   0.008  49.6734  119.4924  112.7604
 LC2  O6    O  O     0  -0.459  57.9893  122.6854  113.0033
 LC2  C7    C  CH2   0  -0.527  50.5119  119.2145  111.5065
 LC2  O7    O  O     0  -0.363  59.0250  119.4702  113.7699
 LC2  C8    C  CH1   0   0.046  52.0092  119.4628  111.5896
 LC2  C9    C  CH1   0  -0.452  52.6947  118.8900  112.8255
 LC2  C10   C  C     0   0.503  54.1556  119.2561  112.7906
 LC2  C11   C  CH3   0  -0.667  52.4826  117.3906  112.9749
 LC2  C12   C  CT    0  -0.407  54.5439  120.5976  112.1684
 LC2  C13   C  CH3   0  -0.758  50.4128  123.5847  114.3777
 LC2  C15   C  CH3   0  -0.641  55.2724  120.3087  110.8379
 LC2  C16   C  C     0   0.469  57.8885  121.4933  113.2366
 LC2  C17   C  C     0   0.295  59.1430  120.6394  113.4967
 LC2  C18   C  CH3   0  -0.766  60.4493  121.3518  113.3869
 LC2  C23   C  CH1   0  -0.137  55.4520  121.4145  113.1302
 LC2  C26   C  C1    0  -0.277  54.7740  121.6112  114.4546
 LC2  C27   C  C     0   0.151  54.3929  122.7751  115.0022
 LC2  C28   C  C1    0  -0.253  53.6268  122.7142  116.2454
 LC2  C29   C  C1    0  -0.234  53.0321  123.7436  116.8486
 LC2  C30   C  CH1   0   0.024  52.0903  123.5656  117.9934
 LC2  C31   C  CH2   0  -0.544  50.6345  123.5925  117.4756
 LC2  HN1   H  HNH1  0   0.408  56.7996  119.8217  113.5446
 LC2  H2    H  H     0   0.237  50.2542  121.4725  117.1302
 LC2  HO3   H  HOH1  0   0.451  51.7038  124.4944  119.6532
 LC2  H4    H  H     0   0.236  50.0821  120.2289  115.2866
 LC2  HO4   H  HOH1  0   0.449  48.1576  118.4640  112.0941
 LC2  H5    H  H     0   0.249  49.8095  121.6951  112.6134
 LC2  H6    H  HCH1  0   0.212  49.9479  118.7707  113.5432
 LC2  H7    H  HCH2  0   0.264  50.3687  118.1698  111.2151
 LC2  H7A   H  HCH2  0   0.268  50.1202  119.8124  110.6783
 LC2  H8    H  HCH1  0   0.271  52.4614  119.0260  110.6915
 LC2  H9    H  HCH1  0   0.306  52.2882  119.4108  113.7069
 LC2  H11   H  HCH3  0   0.258  53.0438  117.0030  113.8220
 LC2  H11A  H  HCH3  0   0.250  51.4333  117.1590  113.1464
 LC2  H11B  H  HCH3  0   0.244  52.8045  116.8559  112.0806
 LC2  H13   H  HCH3  0   0.248  51.2693  123.4652  113.7104
 LC2  H13A  H  HCH3  0   0.239  49.5332  123.7187  113.7441
 LC2  H13B  H  HCH3  0   0.243  50.5578  124.5041  114.9390
 LC2  H14   H  HCH3  0   0.243  55.0568  124.7986  115.1706
 LC2  H14A  H  HCH3  0   0.251  55.3682  124.0999  113.5918
 LC2  H14B  H  HCH3  0   0.248  53.7323  124.5756  114.0409
 LC2  H15   H  HCH3  0   0.266  56.1233  119.6519  111.0036
 LC2  H15A  H  HCH3  0   0.264  54.6187  119.8279  110.1090
 LC2  H15B  H  HCH3  0   0.267  55.6352  121.2407  110.4049
 LC2  H18   H  HCH3  0   0.268  61.2752  120.6683  113.5670
 LC2  H18A  H  HCH3  0   0.276  60.5560  121.7983  112.3972
 LC2  H18B  H  HCH3  0   0.277  60.4949  122.1719  114.1050
 LC2  H23   H  HCH1  0   0.294  55.6232  122.3736  112.6458
 LC2  H26   H  H     0   0.255  54.5534  120.7002  115.0062
 LC2  H28   H  H     0   0.233  53.4885  121.7206  116.6643
 LC2  H29   H  H     0   0.250  53.1218  124.7527  116.4558
 LC2  H30   H  HCH1  0   0.216  52.2644  122.5808  118.4503
 LC2  H31   H  HCH2  0   0.244  50.4524  124.5453  116.9750
 LC2  H31A  H  HCH2  0   0.252  49.9670  123.5595  118.3443
 LC2  O5    O  O     0  -0.381  55.0155  118.5297  113.2296
 LC2  C14   C  CH3   0  -0.755  54.6555  124.1263  114.4108

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
 LC2  C1   O1    single  1.322  0.020  1.322
 LC2  C1   O2    double  1.203  0.020  1.203
 LC2  C1   C12   single  1.524  0.020  1.524
 LC2  N1   C16   single  1.335  0.020  1.335
 LC2  N1   C23   single  1.447  0.020  1.447
 LC2  O1   C8    single  1.436  0.020  1.436
 LC2  C2   C3    double  1.342  0.020  1.342
 LC2  C2   C31   single  1.492  0.020  1.492
 LC2  C3   C4    single  1.462  0.020  1.462
 LC2  C3   C13   single  1.498  0.020  1.498
 LC2  O3   C30   single  1.411  0.020  1.411
 LC2  C4   C5    double  1.335  0.020  1.335
 LC2  O4   C6    single  1.419  0.020  1.419
 LC2  C5   C6    single  1.498  0.020  1.498
 LC2  O5   C10   double  1.208  0.020  1.208
 LC2  C6   C7    single  1.534  0.020  1.534
 LC2  O6   C16   double  1.219  0.020  1.219
 LC2  C7   C8    single  1.520  0.020  1.520
 LC2  O7   C17   double  1.206  0.020  1.206
 LC2  C8   C9    single  1.525  0.020  1.525
 LC2  C9   C10   single  1.507  0.020  1.507
 LC2  C9   C11   single  1.522  0.020  1.522
 LC2  C10  C12   single  1.529  0.020  1.529
 LC2  C12  C15   single  1.544  0.020  1.544
 LC2  C12  C23   single  1.555  0.020  1.555
 LC2  C14  C27   single  1.498  0.020  1.498
 LC2  C16  C17   single  1.540  0.020  1.540
 LC2  C17  C18   single  1.492  0.020  1.492
 LC2  C23  C26   single  1.501  0.020  1.501
 LC2  C26  C27   double  1.342  0.020  1.342
 LC2  C27  C28   single  1.462  0.020  1.462
 LC2  C28  C29   double  1.333  0.020  1.333
 LC2  C29  C30   single  1.493  0.020  1.493
 LC2  C30  C31   single  1.545  0.020  1.545
 LC2  N1   HN1   single  0.860  0.020  1.020
 LC2  C2   H2    single  0.930  0.020  1.080
 LC2  O3   HO3   single  0.850  0.020  0.980
 LC2  C4   H4    single  0.930  0.020  1.080
 LC2  O4   HO4   single  0.850  0.020  0.980
 LC2  C5   H5    single  0.930  0.020  1.080
 LC2  C6   H6    single  0.970  0.020  1.090
 LC2  C7   H7    single  0.970  0.020  1.090
 LC2  C7   H7A   single  0.970  0.020  1.090
 LC2  C8   H8    single  0.970  0.020  1.090
 LC2  C9   H9    single  0.970  0.020  1.090
 LC2  C11  H11   single  0.970  0.020  1.090
 LC2  C11  H11A  single  0.970  0.020  1.090
 LC2  C11  H11B  single  0.970  0.020  1.090
 LC2  C13  H13   single  0.970  0.020  1.090
 LC2  C13  H13A  single  0.970  0.020  1.090
 LC2  C13  H13B  single  0.970  0.020  1.090
 LC2  C14  H14   single  0.970  0.020  1.090
 LC2  C14  H14A  single  0.970  0.020  1.090
 LC2  C14  H14B  single  0.970  0.020  1.090
 LC2  C15  H15   single  0.970  0.020  1.090
 LC2  C15  H15A  single  0.970  0.020  1.090
 LC2  C15  H15B  single  0.970  0.020  1.090
 LC2  C18  H18   single  0.970  0.020  1.090
 LC2  C18  H18A  single  0.970  0.020  1.090
 LC2  C18  H18B  single  0.970  0.020  1.090
 LC2  C23  H23   single  0.970  0.020  1.090
 LC2  C26  H26   single  0.930  0.020  1.080
 LC2  C28  H28   single  0.930  0.020  1.080
 LC2  C29  H29   single  0.930  0.020  1.080
 LC2  C30  H30   single  0.970  0.020  1.090
 LC2  C31  H31   single  0.970  0.020  1.090
 LC2  C31  H31A  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
 LC2  C12   C1   O2    122.65  3.000
 LC2  C12   C1   O1    118.72  3.000
 LC2  O2    C1   O1    118.50  3.000
 LC2  HN1   N1   C23   118.90  3.000
 LC2  HN1   N1   C16   118.20  3.000
 LC2  C23   N1   C16   122.60  3.000
 LC2  C8    O1   C1    122.82  3.000
 LC2  H2    C2   C31   114.60  3.000
 LC2  H2    C2   C3    117.28  3.000
 LC2  C31   C2   C3    128.02  3.000
 LC2  C13   C3   C4    117.67  3.000
 LC2  C13   C3   C2    124.31  3.000
 LC2  C4    C3   C2    118.00  3.000
 LC2  HO3   O3   C30   108.18  3.000
 LC2  H4    C4   C5    118.16  3.000
 LC2  H4    C4   C3    115.33  3.000
 LC2  C5    C4   C3    126.50  3.000
 LC2  HO4   O4   C6    108.30  3.000
 LC2  H5    C5   C6    116.89  3.000
 LC2  H5    C5   C4    121.02  3.000
 LC2  C6    C5   C4    122.08  3.000
 LC2  H6    C6   C7    109.06  3.000
 LC2  H6    C6   C5    107.95  3.000
 LC2  C7    C6   C5    113.72  3.000
 LC2  H6    C6   O4    109.64  3.000
 LC2  C7    C6   O4    109.21  3.000
 LC2  C5    C6   O4    107.20  3.000
 LC2  H7A   C7   H7    105.86  3.000
 LC2  H7A   C7   C8    107.75  3.000
 LC2  H7    C7   C8    107.43  3.000
 LC2  H7A   C7   C6    108.91  3.000
 LC2  H7    C7   C6    108.62  3.000
 LC2  C8    C7   C6    117.66  3.000
 LC2  H8    C8   C9    109.20  3.000
 LC2  H8    C8   C7    107.24  3.000
 LC2  C9    C8   C7    115.20  3.000
 LC2  H8    C8   O1    107.81  3.000
 LC2  C9    C8   O1    110.41  3.000
 LC2  C7    C8   O1    106.69  3.000
 LC2  H9    C9   C11   109.62  3.000
 LC2  H9    C9   C10   105.16  3.000
 LC2  C11   C9   C10   112.14  3.000
 LC2  H9    C9   C8    107.76  3.000
 LC2  C11   C9   C8    112.77  3.000
 LC2  C10   C9   C8    109.02  3.000
 LC2  C12   C10  C9    117.96  3.000
 LC2  C12   C10  O5    119.64  3.000
 LC2  C9    C10  O5    122.39  3.000
 LC2  H11B  C11  H11A  108.03  3.000
 LC2  H11B  C11  H11   108.16  3.000
 LC2  H11A  C11  H11   107.40  3.000
 LC2  H11B  C11  C9    111.19  3.000
 LC2  H11A  C11  C9    111.08  3.000
 LC2  H11   C11  C9    110.84  3.000
 LC2  C23   C12  C15   110.84  3.000
 LC2  C23   C12  C10   110.95  3.000
 LC2  C15   C12  C10   107.84  3.000
 LC2  C23   C12  C1    107.54  3.000
 LC2  C15   C12  C1    106.19  3.000
 LC2  C10   C12  C1    113.40  3.000
 LC2  H13B  C13  H13A  107.65  3.000
 LC2  H13B  C13  H13   107.66  3.000
 LC2  H13A  C13  H13   106.89  3.000
 LC2  H13B  C13  C3    112.67  3.000
 LC2  H13A  C13  C3    111.28  3.000
 LC2  H13   C13  C3    110.44  3.000
 LC2  H15B  C15  H15A  108.12  3.000
 LC2  H15B  C15  H15   108.45  3.000
 LC2  H15A  C15  H15   107.73  3.000
 LC2  H15B  C15  C12   109.84  3.000
 LC2  H15A  C15  C12   112.05  3.000
 LC2  H15   C15  C12   110.54  3.000
 LC2  C17   C16  O6    120.49  3.000
 LC2  C17   C16  N1    113.50  3.000
 LC2  O6    C16  N1    126.00  3.000
 LC2  C18   C17  C16   115.85  3.000
 LC2  C18   C17  O7    124.41  3.000
 LC2  C16   C17  O7    119.74  3.000
 LC2  H18B  C18  H18A  106.58  3.000
 LC2  H18B  C18  H18   109.38  3.000
 LC2  H18A  C18  H18   109.47  3.000
 LC2  H18B  C18  C17   110.31  3.000
 LC2  H18A  C18  C17   110.35  3.000
 LC2  H18   C18  C17   110.65  3.000
 LC2  H23   C23  C26   110.39  3.000
 LC2  H23   C23  C12   106.24  3.000
 LC2  C26   C23  C12   110.54  3.000
 LC2  H23   C23  N1    106.48  3.000
 LC2  C26   C23  N1    111.37  3.000
 LC2  C12   C23  N1    111.62  3.000
 LC2  H26   C26  C27   117.52  3.000
 LC2  H26   C26  C23   115.43  3.000
 LC2  C27   C26  C23   127.03  3.000
 LC2  C28   C27  C26   117.38  3.000
 LC2  C28   C27  C14   117.73  3.000
 LC2  C26   C27  C14   124.86  3.000
 LC2  H28   C28  C29   118.34  3.000
 LC2  H28   C28  C27   115.63  3.000
 LC2  C29   C28  C27   125.91  3.000
 LC2  H29   C29  C30   116.10  3.000
 LC2  H29   C29  C28   121.12  3.000
 LC2  C30   C29  C28   122.43  3.000
 LC2  H30   C30  C31   107.70  3.000
 LC2  H30   C30  C29   108.99  3.000
 LC2  C31   C30  C29   109.59  3.000
 LC2  H30   C30  O3    110.96  3.000
 LC2  C31   C30  O3    111.28  3.000
 LC2  C29   C30  O3    108.30  3.000
 LC2  H31A  C31  H31   106.75  3.000
 LC2  H31A  C31  C30   107.91  3.000
 LC2  H31   C31  C30   109.02  3.000
 LC2  H31A  C31  C2    108.93  3.000
 LC2  H31   C31  C2    112.75  3.000
 LC2  C30   C31  C2    111.27  3.000
 LC2  H14B  C14  H14A  108.03  3.000
 LC2  H14B  C14  H14   107.06  3.000
 LC2  H14A  C14  H14   107.38  3.000
 LC2  H14B  C14  C27   110.91  3.000
 LC2  H14A  C14  C27   113.01  3.000
 LC2  H14   C14  C27   110.20  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
 LC2  CONST_01  C23  N1   C16  O6      0.00   0.0  0
 LC2  CONST_02  C23  N1   C16  C17   180.00   0.0  0
 LC2  CONST_03  HN1  N1   C16  O6    180.00   0.0  0
 LC2  Var_01    C6   C5   C4   C3    179.20   0.0  0
 LC2  Var_02    C31  C2   C3   C4    176.19   0.0  0
 LC2  Var_03    C28  C27  C26  C23   173.98   0.0  0
 LC2  Var_04    C30  C29  C28  C27   170.01   0.0  0
 LC2  Var_05    C5   C4   C3   C2    175.01  30.0  1
 LC2  Var_06    C30  C31  C2   C3   -103.21  30.0  1
 LC2  Var_07    C12  C1   O1   C8      2.82  30.0  1
 LC2  Var_08    C29  C28  C27  C26  -171.66  30.0  1
 LC2  Var_09    H4   C4   C5   C6     -0.05   0.0  0
 LC2  Var_10    H28  C28  C29  C30    -5.74   0.0  0
 LC2  Var_11    H13  C13  C3   C2    118.37  30.0  3
 LC2  Var_12    H14  C14  C27  C26  -132.17  30.0  3
 LC2  Var_13    O7   C17  C16  N1     -2.80  30.0  2
 LC2  Var_14    H18  C18  C17  O7      1.13  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
 LC2  chir_01  C6   O4   C5   C7   positiv
 LC2  chir_02  C8   O1   C7   C9   positiv
 LC2  chir_03  C9   C8   C10  C11  positiv
 LC2  chir_04  C12  C10  C1   C23  negativ
 LC2  chir_05  C23  N1   C26  C12  positiv
 LC2  chir_06  C30  O3   C29  C31  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
 LC2  plan-1  N1   0.020
 LC2  plan-1  O6   0.020
 LC2  plan-1  C16  0.020
 LC2  plan-1  C17  0.020
 LC2  plan-1  C23  0.020
 LC2  plan-1  HN1  0.020
 LC2  plan-2  C23  0.020
 LC2  plan-2  C26  0.020
 LC2  plan-2  C27  0.020
 LC2  plan-2  C28  0.020
 LC2  plan-2  H26  0.020
 LC2  plan-2  C14  0.020
 LC2  plan-3  C27  0.020
 LC2  plan-3  C28  0.020
 LC2  plan-3  C29  0.020
 LC2  plan-3  C30  0.020
 LC2  plan-3  H28  0.020
 LC2  plan-3  H29  0.020
 LC2  plan-4  C9   0.020
 LC2  plan-4  C10  0.020
 LC2  plan-4  C12  0.020
 LC2  plan-4  O5   0.020
 LC2  plan-5  O7   0.020
 LC2  plan-5  C16  0.020
 LC2  plan-5  C17  0.020
 LC2  plan-5  C18  0.020
 LC2  plan-6  C1   0.020
 LC2  plan-6  O1   0.020
 LC2  plan-6  O2   0.020
 LC2  plan-6  C12  0.020
 LC2  plan-7  C2   0.020
 LC2  plan-7  C3   0.020
 LC2  plan-7  C4   0.020
 LC2  plan-7  C13  0.020
 LC2  plan-7  C31  0.020
 LC2  plan-7  H2   0.020
 LC2  plan-8  C3   0.020
 LC2  plan-8  C4   0.020
 LC2  plan-8  C5   0.020
 LC2  plan-8  C6   0.020
 LC2  plan-8  H4   0.020
 LC2  plan-8  H5   0.020

