# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:54:27 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2S,3S,4E,6E,8R,9R)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](Cc1ccccc1)[C@H](C)\C=C(C)\C=C\[C@H](N)[C@H](C)C(O)=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
 MFD  MFD  '(2S,3S,4E,6E,8R,9R)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid'  ligand  52  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MFD
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
 MFD  N3    N  NH2    0  -0.782   2.2632  -0.1865  -4.3513
 MFD  C2    C  CH1    0  -0.335   0.1554   0.2468  -5.4981
 MFD  C1    C  C      0   0.419   0.6703  -0.5804  -6.6927
 MFD  O1    O  O      0  -0.622   0.4500  -1.8090  -6.6485
 MFD  OXT   O  OC    -1  -0.619   1.2366   0.0316  -7.6212
 MFD  C3    C  CH1    0  -0.132   0.8091  -0.2408  -4.2007
 MFD  CM2   C  CH3    0  -0.656  -1.3666   0.1657  -5.4207
 MFD  C7    C  C1     0  -0.245  -1.2710  -0.0416   0.2423
 MFD  C6    C  C      0   0.120  -0.7095   0.6824  -0.7391
 MFD  C4    C  C1     0  -0.210   0.3367   0.5332  -3.0051
 MFD  C'    C  CH2    0  -0.544  -1.1698   0.5513   4.0588
 MFD  C9    C  CH1    0   0.093  -0.7519   0.0716   2.6662
 MFD  C8    C  CH1    0  -0.330  -1.7778   0.4263   1.5732
 MFD  C4'   C  C1     0  -0.274   2.0192  -0.1321   6.8660
 MFD  C3'   C  C1     0  -0.241   1.9531   1.0609   6.1579
 MFD  C2'   C  C1     0  -0.309   0.9130   1.2841   5.2655
 MFD  C1'   C  C      0   0.146  -0.0786   0.3257   5.0656
 MFD  C6'   C  C1     0  -0.299  -0.0029  -0.8654   5.7843
 MFD  C5'   C  C1     0  -0.244   1.0353  -1.0941   6.6774
 MFD  O9    O  O2     0  -0.495  -0.5373  -1.3237   2.7057
 MFD  CM9   C  CH3    0  -0.402   0.7694  -1.7287   2.3822
 MFD  CM8   C  CH3    0  -0.667  -3.1658  -0.1590   1.8376
 MFD  CM6   C  CH3    0  -0.757  -0.4893   2.1652  -0.6779
 MFD  HN31  H  HNH2   0   0.340   2.7025  -0.4395  -3.4740
 MFD  HN32  H  HNH2   0   0.333   2.5471   0.7704  -4.5315
 MFD  H2    H  HCH1   0   0.190   0.4398   1.2960  -5.6469
 MFD  H3    H  HCH1   0   0.214   0.5301  -1.2917  -4.0690
 MFD  HM21  H  HCH3   0   0.212  -1.6912  -0.8539  -5.2072
 MFD  HM22  H  HCH3   0   0.221  -1.7664   0.8118  -4.6384
 MFD  HM23  H  HCH3   0   0.221  -1.8253   0.4697  -6.3636
 MFD  H7    H  H      0   0.229  -1.3666  -1.1121   0.0724
 MFD  H5    H  H      0   0.223  -0.4533  -1.0878  -1.9628
 MFD  H4    H  H      0   0.235   0.5400   1.6023  -3.0273
 MFD  H'1   H  HCH2   0   0.246  -1.4191   1.6139   4.0017
 MFD  H'2   H  HCH2   0   0.251  -2.0766   0.0278   4.3705
 MFD  H9    H  HCH1   0   0.227   0.1818   0.5873   2.4010
 MFD  H8    H  HCH1   0   0.243  -1.8635   1.5164   1.5797
 MFD  H2'   H  H      0   0.243   0.8705   2.2192   4.7181
 MFD  H6'   H  H      0   0.240  -0.7678  -1.6196   5.6469
 MFD  H5'   H  H      0   0.250   1.0753  -2.0255   7.2285
 MFD  HM91  H  HCH3   0   0.226   0.8199  -2.8116   2.4975
 MFD  HM92  H  HCH3   0   0.206   1.0363  -1.4809   1.3489
 MFD  HM93  H  HCH3   0   0.207   1.5159  -1.2795   3.0461
 MFD  HM81  H  HCH3   0   0.223  -3.1343  -1.2472   1.9070
 MFD  HM82  H  HCH3   0   0.234  -3.6012   0.2241   2.7610
 MFD  HM83  H  HCH3   0   0.235  -3.8474   0.1005   1.0267
 MFD  HM61  H  HCH3   0   0.248  -0.8674   2.6128   0.2381
 MFD  HM62  H  HCH3   0   0.239   0.5745   2.4038  -0.7459
 MFD  HM63  H  HCH3   0   0.238  -0.9754   2.6665  -1.5176
 MFD  C5    C  C1     0  -0.290  -0.2676  -0.0156  -1.9474
 MFD  H4'   H  H      0   0.251   2.8286  -0.3082   7.5630
 MFD  H3'   H  H      0   0.251   2.7105   1.8208   6.3028

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
 MFD  N3   C3    single    1.463  0.020  1.463
 MFD  N3   HN31  single    0.890  0.020  1.040
 MFD  N3   HN32  single    0.890  0.020  1.040
 MFD  C2   C1    single    1.542  0.020  1.542
 MFD  C2   C3    single    1.532  0.020  1.532
 MFD  C2   CM2   single    1.526  0.020  1.526
 MFD  C2   H2    single    0.970  0.020  1.090
 MFD  C1   O1    deloc     1.249  0.020  1.249
 MFD  C1   OXT   deloc     1.248  0.020  1.248
 MFD  C3   C4    single    1.501  0.020  1.501
 MFD  C3   H3    single    0.970  0.020  1.090
 MFD  CM2  HM21  single    0.970  0.020  1.090
 MFD  CM2  HM22  single    0.970  0.020  1.090
 MFD  CM2  HM23  single    0.970  0.020  1.090
 MFD  C7   C6    double    1.343  0.020  1.343
 MFD  C7   C8    single    1.499  0.020  1.499
 MFD  C7   H7    single    0.930  0.020  1.080
 MFD  C6   C5    single    1.464  0.020  1.464
 MFD  C6   CM6   single    1.500  0.020  1.500
 MFD  C5   C4    double    1.336  0.020  1.336
 MFD  C5   H5    single    0.930  0.020  1.080
 MFD  C4   H4    single    0.930  0.020  1.080
 MFD  C'   C9    single    1.531  0.020  1.531
 MFD  C'   C1'   single    1.502  0.020  1.502
 MFD  C'   H'1   single    0.970  0.020  1.090
 MFD  C'   H'2   single    0.970  0.020  1.090
 MFD  C9   C8    single    1.540  0.020  1.540
 MFD  C9   O9    single    1.412  0.020  1.412
 MFD  C9   H9    single    0.970  0.020  1.090
 MFD  C8   CM8   single    1.529  0.020  1.529
 MFD  C8   H8    single    0.970  0.020  1.090
 MFD  C4'  C3'   aromatic  1.389  0.020  1.389
 MFD  C4'  C5'   aromatic  1.389  0.020  1.389
 MFD  C4'  H4'   single    0.930  0.020  1.080
 MFD  C3'  C2'   aromatic  1.389  0.020  1.389
 MFD  C3'  H3'   single    0.930  0.020  1.080
 MFD  C2'  C1'   aromatic  1.393  0.020  1.393
 MFD  C2'  H2'   single    0.930  0.020  1.080
 MFD  C1'  C6'   aromatic  1.393  0.020  1.393
 MFD  C6'  C5'   aromatic  1.388  0.020  1.388
 MFD  C6'  H6'   single    0.930  0.020  1.080
 MFD  C5'  H5'   single    0.930  0.020  1.080
 MFD  O9   CM9   single    1.406  0.020  1.406
 MFD  CM9  HM91  single    0.970  0.020  1.090
 MFD  CM9  HM92  single    0.970  0.020  1.090
 MFD  CM9  HM93  single    0.970  0.020  1.090
 MFD  CM8  HM81  single    0.970  0.020  1.090
 MFD  CM8  HM82  single    0.970  0.020  1.090
 MFD  CM8  HM83  single    0.970  0.020  1.090
 MFD  CM6  HM61  single    0.970  0.020  1.090
 MFD  CM6  HM62  single    0.970  0.020  1.090
 MFD  CM6  HM63  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
 MFD  HN32  N3   HN31  105.55  3.000
 MFD  HN32  N3   C3    109.36  3.000
 MFD  HN31  N3   C3    109.43  3.000
 MFD  H2    C2   CM2   108.43  3.000
 MFD  H2    C2   C3    107.97  3.000
 MFD  CM2   C2   C3    111.45  3.000
 MFD  H2    C2   C1    108.75  3.000
 MFD  CM2   C2   C1    110.11  3.000
 MFD  C3    C2   C1    110.05  3.000
 MFD  OXT   C1   O1    126.07  3.000
 MFD  OXT   C1   C2    117.71  3.000
 MFD  O1    C1   C2    116.20  3.000
 MFD  H3    C3   C4    108.59  3.000
 MFD  H3    C3   C2    107.36  3.000
 MFD  C4    C3   C2    112.09  3.000
 MFD  H3    C3   N3    107.53  3.000
 MFD  C4    C3   N3    112.08  3.000
 MFD  C2    C3   N3    108.97  3.000
 MFD  HM23  CM2  HM22  107.48  3.000
 MFD  HM23  CM2  HM21  107.71  3.000
 MFD  HM22  CM2  HM21  107.71  3.000
 MFD  HM23  CM2  C2    111.13  3.000
 MFD  HM22  CM2  C2    111.75  3.000
 MFD  HM21  CM2  C2    110.87  3.000
 MFD  H7    C7   C8    114.58  3.000
 MFD  H7    C7   C6    116.95  3.000
 MFD  C8    C7   C6    128.47  3.000
 MFD  CM6   C6   C5    117.43  3.000
 MFD  CM6   C6   C7    124.37  3.000
 MFD  C5    C6   C7    118.20  3.000
 MFD  H4    C4   C5    120.26  3.000
 MFD  H4    C4   C3    115.57  3.000
 MFD  C5    C4   C3    124.15  3.000
 MFD  H'2   C'   H'1   106.95  3.000
 MFD  H'2   C'   C1'   109.87  3.000
 MFD  H'1   C'   C1'   110.29  3.000
 MFD  H'2   C'   C9    109.63  3.000
 MFD  H'1   C'   C9    108.62  3.000
 MFD  C1'   C'   C9    111.37  3.000
 MFD  H9    C9   O9    109.96  3.000
 MFD  H9    C9   C8    106.65  3.000
 MFD  O9    C9   C8    110.39  3.000
 MFD  H9    C9   C'    107.72  3.000
 MFD  O9    C9   C'    109.00  3.000
 MFD  C8    C9   C'    113.04  3.000
 MFD  H8    C8   CM8   108.02  3.000
 MFD  H8    C8   C9    106.11  3.000
 MFD  CM8   C8   C9    113.18  3.000
 MFD  H8    C8   C7    110.06  3.000
 MFD  CM8   C8   C7    109.93  3.000
 MFD  C9    C8   C7    109.44  3.000
 MFD  H4'   C4'  C5'   120.29  3.000
 MFD  H4'   C4'  C3'   120.24  3.000
 MFD  C5'   C4'  C3'   119.47  3.000
 MFD  H3'   C3'  C2'   119.82  3.000
 MFD  H3'   C3'  C4'   120.09  3.000
 MFD  C2'   C3'  C4'   120.10  3.000
 MFD  H2'   C2'  C1'   119.53  3.000
 MFD  H2'   C2'  C3'   119.50  3.000
 MFD  C1'   C2'  C3'   120.98  3.000
 MFD  C6'   C1'  C2'   118.38  3.000
 MFD  C6'   C1'  C'    120.91  3.000
 MFD  C2'   C1'  C'    120.66  3.000
 MFD  H6'   C6'  C5'   119.67  3.000
 MFD  H6'   C6'  C1'   119.45  3.000
 MFD  C5'   C6'  C1'   120.88  3.000
 MFD  H5'   C5'  C6'   119.77  3.000
 MFD  H5'   C5'  C4'   120.03  3.000
 MFD  C6'   C5'  C4'   120.20  3.000
 MFD  CM9   O9   C9    114.79  3.000
 MFD  HM93  CM9  HM92  108.23  3.000
 MFD  HM93  CM9  HM91  108.16  3.000
 MFD  HM92  CM9  HM91  108.25  3.000
 MFD  HM93  CM9  O9    112.08  3.000
 MFD  HM92  CM9  O9    112.24  3.000
 MFD  HM91  CM9  O9    107.75  3.000
 MFD  HM83  CM8  HM82  107.24  3.000
 MFD  HM83  CM8  HM81  107.62  3.000
 MFD  HM82  CM8  HM81  107.94  3.000
 MFD  HM83  CM8  C8    110.34  3.000
 MFD  HM82  CM8  C8    111.99  3.000
 MFD  HM81  CM8  C8    111.51  3.000
 MFD  HM63  CM6  HM62  106.58  3.000
 MFD  HM63  CM6  HM61  107.70  3.000
 MFD  HM62  CM6  HM61  107.52  3.000
 MFD  HM63  CM6  C6    110.92  3.000
 MFD  HM62  CM6  C6    110.87  3.000
 MFD  HM61  CM6  C6    112.96  3.000
 MFD  H5    C5   C4    118.08  3.000
 MFD  H5    C5   C6    115.46  3.000
 MFD  C4    C5   C6    126.46  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
 MFD  CONST_01  C1'   C2'  C3'  C4'     0.00   0.0  0
 MFD  CONST_02  C1'   C6'  C5'  C4'     0.00   0.0  0
 MFD  CONST_03  C6'   C5'  C4'  C3'     0.00   0.0  0
 MFD  CONST_04  C6'   C1'  C2'  C3'     0.00   0.0  0
 MFD  CONST_05  C5'   C4'  C3'  C2'     0.00   0.0  0
 MFD  CONST_06  C5'   C6'  C1'  C2'     0.00   0.0  0
 MFD  CONST_07  C3'   C2'  C1'  C'    180.00   0.0  0
 MFD  CONST_08  C5'   C6'  C1'  C'    180.00   0.0  0
 MFD  CONST_09  H2'   C2'  C3'  C4'   180.00   0.0  0
 MFD  CONST_10  H6'   C6'  C5'  C4'   180.00   0.0  0
 MFD  CONST_11  H5'   C5'  C4'  C3'   180.00   0.0  0
 MFD  CONST_12  H4'   C4'  C3'  C2'   180.00   0.0  0
 MFD  CONST_13  H3'   C3'  C2'  C1'   180.00   0.0  0
 MFD  Var_01    C2'   C1'  C'   C9     87.56  30.0  2
 MFD  Var_02    C6    C5   C4   C3    177.91   0.0  2
 MFD  Var_03    C8    C7   C6   C5    178.81   0.0  2
 MFD  Var_04    C4    C5   C6   C7   -178.29  30.0  2
 MFD  Var_05    HM61  CM6  C6   C7     -2.15  30.0  3
 MFD  Var_06    HM91  CM9  O9   C9    177.16  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
 MFD  chir_01  C2  C1  C3  CM2  positiv
 MFD  chir_02  C3  N3  C2  C4   positiv
 MFD  chir_03  C9  C'  C8  O9   positiv
 MFD  chir_04  C8  C7  C9  CM8  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
 MFD  plan-1  C'   0.020
 MFD  plan-1  C4'  0.020
 MFD  plan-1  C3'  0.020
 MFD  plan-1  C2'  0.020
 MFD  plan-1  C1'  0.020
 MFD  plan-1  C6'  0.020
 MFD  plan-1  C5'  0.020
 MFD  plan-1  H2'  0.020
 MFD  plan-1  H6'  0.020
 MFD  plan-1  H5'  0.020
 MFD  plan-1  H4'  0.020
 MFD  plan-1  H3'  0.020
 MFD  plan-2  C2   0.020
 MFD  plan-2  C1   0.020
 MFD  plan-2  O1   0.020
 MFD  plan-2  OXT  0.020
 MFD  plan-3  C7   0.020
 MFD  plan-3  C6   0.020
 MFD  plan-3  C8   0.020
 MFD  plan-3  CM6  0.020
 MFD  plan-3  H7   0.020
 MFD  plan-3  C5   0.020
 MFD  plan-4  C3   0.020
 MFD  plan-4  C6   0.020
 MFD  plan-4  C4   0.020
 MFD  plan-4  H5   0.020
 MFD  plan-4  H4   0.020
 MFD  plan-4  C5   0.020

