# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 21:35:04 2021
#   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  53  24  .  2021-08-14  2022-11-17
;
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  -0.776   -0.0735   0.3130  -0.3310
 MFD  C2    C  CH1   0  -0.367    0.2076   2.4629  -1.6230
 MFD  C1    C  C     0   0.535    1.6017   2.0247  -1.9989
 MFD  O1    O  O     0  -0.450    1.8497   1.3031  -2.9353
 MFD  OXT   O  OH1   0  -0.584    2.5401   2.5164  -1.1991
 MFD  C3    C  CH1   0  -0.139   -0.6597   1.2180  -1.3133
 MFD  CM2   C  CH3   0  -0.656   -0.3786   3.2978  -2.7603
 MFD  C7    C  C1    0  -0.227   -5.5446   1.0893  -1.5257
 MFD  C6    C  C     0   0.114   -4.4949   1.6357  -0.8948
 MFD  C4    C  C1    0  -0.195   -2.0071   1.6505  -0.8190
 MFD  C'    C  CH2   0  -0.555   -6.7007  -1.1905   0.0100
 MFD  C9    C  CH1   0   0.094   -7.4967  -0.3428  -1.0060
 MFD  C8    C  CH1   0  -0.360   -6.9835   1.1066  -1.1203
 MFD  C4'   C  CR16  0  -0.285   -3.1423  -2.9705  -1.6507
 MFD  C3'   C  CR16  0  -0.224   -3.0403  -2.0387  -0.6265
 MFD  C2'   C  CR16  0  -0.300   -4.1874  -1.4799  -0.0803
 MFD  C1'   C  CR6   0   0.145   -5.4512  -1.8158  -0.5560
 MFD  C6'   C  CR16  0  -0.314   -5.5392  -2.7612  -1.5779
 MFD  C5'   C  CR16  0  -0.243   -4.3981  -3.3360  -2.1201
 MFD  O9    O  O2    0  -0.493   -8.8876  -0.3966  -0.7603
 MFD  CM9   C  CH3   0  -0.421   -9.3237   0.1414   0.4652
 MFD  CM8   C  CH3   0  -0.644   -7.8083   1.9090  -2.1298
 MFD  CM6   C  CH3   0  -0.761   -4.5852   2.4351   0.3702
 MFD  HN31  H  HNH2  0   0.350    0.7634  -0.1267  -0.6935
 MFD  HN32  H  HNH2  0   0.342    0.2005   0.8218   0.5017
 MFD  H2    H  HCH1  0   0.257    0.2591   3.0763  -0.7182
 MFD  HXT   H  HOH1  0   0.478    3.4143   2.2127  -1.4890
 MFD  H3    H  HCH1  0   0.243   -0.7872   0.6524  -2.2411
 MFD  HM21  H  HCH3  0   0.247   -1.3626   3.6731  -2.4828
 MFD  HM22  H  HCH3  0   0.243    0.2489   4.1582  -2.9943
 MFD  HM23  H  HCH3  0   0.230   -0.4901   2.7011  -3.6663
 MFD  H7    H  H     0   0.234   -5.3368   0.5283  -2.4354
 MFD  H5    H  H     0   0.226   -3.1309   0.7624  -2.3322
 MFD  H4    H  H     0   0.243   -2.0015   2.2207   0.1078
 MFD  H'1   H  HCH2  0   0.258   -7.3574  -1.9939   0.3585
 MFD  H'2   H  HCH2  0   0.246   -6.4421  -0.5958   0.8903
 MFD  H9    H  HCH1  0   0.224   -7.3886  -0.8072  -1.9927
 MFD  H8    H  HCH1  0   0.238   -7.0787   1.5830  -0.1405
 MFD  H3'   H  HCR6  0   0.249   -2.0686  -1.7135  -0.2745
 MFD  H2'   H  HCR6  0   0.240   -4.0918  -0.7474   0.7121
 MFD  H6'   H  HCR6  0   0.242   -6.5124  -3.0538  -1.9567
 MFD  H5'   H  HCR6  0   0.247   -4.4885  -4.0679  -2.9128
 MFD  HM91  H  HCH3  0   0.210   -9.1597   1.2215   0.5379
 MFD  HM92  H  HCH3  0   0.237  -10.3961  -0.0385   0.5332
 MFD  HM93  H  HCH3  0   0.215   -8.8461  -0.3308   1.3294
 MFD  HM81  H  HCH3  0   0.230   -7.4145   2.9216  -2.2227
 MFD  HM82  H  HCH3  0   0.234   -8.8543   1.9869  -1.8331
 MFD  HM83  H  HCH3  0   0.219   -7.7747   1.4481  -3.1194
 MFD  HM61  H  HCH3  0   0.240   -4.0622   3.3880   0.2658
 MFD  HM62  H  HCH3  0   0.238   -4.1096   1.9059   1.2001
 MFD  HM63  H  HCH3  0   0.248   -5.6094   2.6535   0.6617
 MFD  C5    C  C1    0  -0.251   -3.1604   1.3453  -1.4153
 MFD  H4'   H  HCR6  0   0.246   -2.2509  -3.4077  -2.0826

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    1.459  0.020  1.459
 MFD  N3   HN31  single    0.890  0.020  1.040
 MFD  N3   HN32  single    0.890  0.020  1.040
 MFD  C2   C1    single    1.509  0.020  1.509
 MFD  C2   C3    single    1.548  0.020  1.548
 MFD  C2   CM2   single    1.528  0.020  1.528
 MFD  C2   H2    single    0.970  0.020  1.090
 MFD  C1   O1    double    1.208  0.020  1.208
 MFD  C1   OXT   single    1.327  0.020  1.327
 MFD  OXT  HXT   single    0.850  0.020  0.980
 MFD  C3   C4    single    1.499  0.020  1.499
 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    1.341  0.020  1.341
 MFD  C7   C8    single    1.495  0.020  1.495
 MFD  C7   H7    single    0.930  0.020  1.080
 MFD  C6   C5    single    1.462  0.020  1.462
 MFD  C6   CM6   single    1.499  0.020  1.499
 MFD  C5   C4    double    1.334  0.020  1.334
 MFD  C5   H5    single    0.930  0.020  1.080
 MFD  C4   H4    single    0.930  0.020  1.080
 MFD  C'   C9    single    1.544  0.020  1.544
 MFD  C'   C1'   single    1.508  0.020  1.508
 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    1.542  0.020  1.542
 MFD  C9   O9    single    1.413  0.020  1.413
 MFD  C9   H9    single    0.970  0.020  1.090
 MFD  C8   CM8   single    1.531  0.020  1.531
 MFD  C8   H8    single    0.970  0.020  1.090
 MFD  C4'  C3'   aromatic  1.388  0.020  1.388
 MFD  C4'  C5'   aromatic  1.390  0.020  1.390
 MFD  C4'  H4'   single    0.930  0.020  1.080
 MFD  C3'  C2'   aromatic  1.388  0.020  1.388
 MFD  C3'  H3'   single    0.930  0.020  1.080
 MFD  C2'  C1'   aromatic  1.391  0.020  1.391
 MFD  C2'  H2'   single    0.930  0.020  1.080
 MFD  C1'  C6'   aromatic  1.395  0.020  1.395
 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    1.408  0.020  1.408
 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  106.78  3.000
 MFD  HN32  N3   C3    110.52  3.000
 MFD  HN31  N3   C3    111.13  3.000
 MFD  H2    C2   CM2   109.09  3.000
 MFD  H2    C2   C3    108.16  3.000
 MFD  CM2   C2   C3    111.92  3.000
 MFD  H2    C2   C1    108.99  3.000
 MFD  CM2   C2   C1    109.13  3.000
 MFD  C3    C2   C1    109.51  3.000
 MFD  OXT   C1   O1    122.90  3.000
 MFD  OXT   C1   C2    113.30  3.000
 MFD  O1    C1   C2    123.80  3.000
 MFD  HXT   OXT  C1    109.95  3.000
 MFD  H3    C3   C4    108.91  3.000
 MFD  H3    C3   C2    108.14  3.000
 MFD  C4    C3   C2    109.73  3.000
 MFD  H3    C3   N3    107.29  3.000
 MFD  C4    C3   N3    108.55  3.000
 MFD  C2    C3   N3    114.10  3.000
 MFD  HM23  CM2  HM22  108.20  3.000
 MFD  HM23  CM2  HM21  107.93  3.000
 MFD  HM22  CM2  HM21  107.62  3.000
 MFD  HM23  CM2  C2    111.02  3.000
 MFD  HM22  CM2  C2    111.72  3.000
 MFD  HM21  CM2  C2    110.20  3.000
 MFD  H7    C7   C8    114.59  3.000
 MFD  H7    C7   C6    116.98  3.000
 MFD  C8    C7   C6    128.40  3.000
 MFD  CM6   C6   C5    117.48  3.000
 MFD  CM6   C6   C7    124.54  3.000
 MFD  C5    C6   C7    117.79  3.000
 MFD  H4    C4   C5    120.34  3.000
 MFD  H4    C4   C3    115.30  3.000
 MFD  C5    C4   C3    124.32  3.000
 MFD  H'2   C'   H'1   106.55  3.000
 MFD  H'2   C'   C1'   109.38  3.000
 MFD  H'1   C'   C1'   108.20  3.000
 MFD  H'2   C'   C9    110.68  3.000
 MFD  H'1   C'   C9    107.65  3.000
 MFD  C1'   C'   C9    114.08  3.000
 MFD  H9    C9   O9    103.73  3.000
 MFD  H9    C9   C8    107.39  3.000
 MFD  O9    C9   C8    112.10  3.000
 MFD  H9    C9   C'    107.99  3.000
 MFD  O9    C9   C'    111.84  3.000
 MFD  C8    C9   C'    113.16  3.000
 MFD  H8    C8   CM8   108.39  3.000
 MFD  H8    C8   C9    108.30  3.000
 MFD  CM8   C8   C9    111.24  3.000
 MFD  H8    C8   C7    109.38  3.000
 MFD  CM8   C8   C7    110.23  3.000
 MFD  C9    C8   C7    109.24  3.000
 MFD  H4'   C4'  C5'   120.20  3.000
 MFD  H4'   C4'  C3'   120.32  3.000
 MFD  C5'   C4'  C3'   119.48  3.000
 MFD  H3'   C3'  C2'   119.51  3.000
 MFD  H3'   C3'  C4'   120.46  3.000
 MFD  C2'   C3'  C4'   119.99  3.000
 MFD  H2'   C2'  C1'   119.57  3.000
 MFD  H2'   C2'  C3'   119.15  3.000
 MFD  C1'   C2'  C3'   121.26  3.000
 MFD  C6'   C1'  C2'   118.12  3.000
 MFD  C6'   C1'  C'    120.26  3.000
 MFD  C2'   C1'  C'    121.62  3.000
 MFD  H6'   C6'  C5'   119.31  3.000
 MFD  H6'   C6'  C1'   119.69  3.000
 MFD  C5'   C6'  C1'   121.00  3.000
 MFD  H5'   C5'  C6'   119.82  3.000
 MFD  H5'   C5'  C4'   120.04  3.000
 MFD  C6'   C5'  C4'   120.14  3.000
 MFD  CM9   O9   C9    116.21  3.000
 MFD  HM93  CM9  HM92  108.00  3.000
 MFD  HM93  CM9  HM91  107.93  3.000
 MFD  HM92  CM9  HM91  107.83  3.000
 MFD  HM93  CM9  O9    112.79  3.000
 MFD  HM92  CM9  O9    107.23  3.000
 MFD  HM91  CM9  O9    112.85  3.000
 MFD  HM83  CM8  HM82  107.83  3.000
 MFD  HM83  CM8  HM81  107.67  3.000
 MFD  HM82  CM8  HM81  107.67  3.000
 MFD  HM83  CM8  C8    111.08  3.000
 MFD  HM82  CM8  C8    112.02  3.000
 MFD  HM81  CM8  C8    110.39  3.000
 MFD  HM63  CM6  HM62  107.67  3.000
 MFD  HM63  CM6  HM61  107.55  3.000
 MFD  HM62  CM6  HM61  106.66  3.000
 MFD  HM63  CM6  C6    112.97  3.000
 MFD  HM62  CM6  C6    110.87  3.000
 MFD  HM61  CM6  C6    110.84  3.000
 MFD  H5    C5   C4    118.45  3.000
 MFD  H5    C5   C6    115.58  3.000
 MFD  C4    C5   C6    125.80  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  CONST_14  HXT   OXT  C1   C2    180.00   0.0  0
 MFD  Var_01    C2'   C1'  C'   C9    116.48  30.0  2
 MFD  Var_02    C6    C5   C4   C3    173.62   0.0  2
 MFD  Var_03    C8    C7   C6   C5    172.94   0.0  2
 MFD  Var_04    C4    C5   C6   C7   -170.50  30.0  2
 MFD  Var_05    HM61  CM6  C6   C7   -128.93  30.0  3
 MFD  Var_06    HM91  CM9  O9   C9     65.34  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  H3'  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-2  C2   0.020
 MFD  plan-2  C1   0.020
 MFD  plan-2  O1   0.020
 MFD  plan-2  OXT  0.020
 MFD  plan-2  HXT  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

