FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: Z97JN
Calculation Name: 7F9O-i-Other547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster
Ligand 3-letter code: CLA | CHL | CL0 | DGD | XAT | LUT | SQD | BCR | LMG | LHG | PQN | SF4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 7F9O
Chain ID: i
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 68 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -391435.015741 |
|---|---|
| FMO2-HF: Nuclear repulsion | 365211.291461 |
| FMO2-HF: Total energy | -26223.72428 |
| FMO2-MP2: Total energy | -26302.456301 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:79:LYS)
Summations of interaction energy for
fragment #1(A:79:LYS)
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| 101.701 | 105.66 | 0.534 | -2.296 | -2.197 | -0.024 |
Interaction energy analysis for fragmet #1(A:79:LYS)
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | A | 81 | PRO | 0 | 0.029 | 0.009 | 2.552 | -22.986 | -19.301 | 0.533 | -2.243 | -1.975 | -0.024 |
| 4 | A | 82 | PRO | 0 | -0.008 | -0.011 | 3.392 | 8.687 | 8.961 | 0.001 | -0.053 | -0.222 | 0.000 |
| 5 | A | 83 | ARG | 1 | 0.886 | 0.946 | 6.303 | 48.188 | 48.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 84 | GLY | 0 | 0.075 | 0.040 | 9.913 | 0.841 | 0.841 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 85 | PRO | 0 | 0.003 | -0.004 | 11.866 | -3.182 | -3.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 86 | LYS | 1 | 0.918 | 0.977 | 8.565 | 54.071 | 54.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 87 | ARG | 1 | 0.965 | 0.962 | 12.324 | 38.858 | 38.858 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 88 | GLY | 0 | 0.036 | 0.044 | 15.925 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 89 | THR | 0 | -0.007 | -0.018 | 16.754 | 0.736 | 0.736 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 90 | LYS | 1 | 0.968 | 0.987 | 19.650 | 22.372 | 22.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 91 | VAL | 0 | 0.005 | 0.009 | 19.899 | -0.642 | -0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 92 | LYS | 1 | 0.856 | 0.923 | 22.931 | 21.077 | 21.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 93 | ILE | 0 | -0.032 | -0.009 | 24.499 | -0.815 | -0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 94 | LEU | 0 | -0.017 | -0.013 | 25.740 | 0.863 | 0.863 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 95 | ARG | 1 | 0.808 | 0.888 | 25.372 | 22.434 | 22.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 96 | ARG | 1 | 0.961 | 0.981 | 28.691 | 17.540 | 17.540 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 97 | GLU | -1 | -0.869 | -0.940 | 31.156 | -18.769 | -18.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 98 | SER | 0 | -0.010 | -0.027 | 29.238 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 99 | TYR | 0 | -0.001 | 0.003 | 32.005 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 100 | TRP | 0 | -0.057 | -0.025 | 29.467 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 101 | TYR | 0 | 0.047 | 0.030 | 30.187 | -0.342 | -0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 102 | ASN | 0 | -0.003 | -0.001 | 30.571 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 103 | GLY | 0 | 0.000 | 0.011 | 30.397 | 0.377 | 0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 104 | THR | 0 | -0.044 | -0.043 | 26.962 | -0.433 | -0.433 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 105 | GLY | 0 | 0.035 | 0.028 | 25.529 | 0.707 | 0.707 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 106 | SER | 0 | -0.067 | -0.027 | 22.200 | -0.661 | -0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 107 | VAL | 0 | 0.027 | 0.018 | 16.154 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 108 | VAL | 0 | -0.034 | -0.017 | 18.824 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 109 | THR | 0 | -0.010 | -0.024 | 14.482 | -2.213 | -2.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 110 | VAL | 0 | 0.012 | -0.007 | 12.216 | 1.835 | 1.835 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 111 | ASP | -1 | -0.883 | -0.913 | 12.062 | -37.665 | -37.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 112 | GLN | 0 | -0.053 | -0.057 | 7.032 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 113 | ASP | -1 | -0.853 | -0.906 | 9.882 | -42.674 | -42.674 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 114 | PRO | 0 | -0.060 | -0.040 | 10.884 | 1.721 | 1.721 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 115 | ASN | 0 | 0.001 | 0.001 | 13.425 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 116 | THR | 0 | -0.013 | 0.005 | 15.214 | 2.551 | 2.551 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 117 | ARG | 1 | 0.963 | 0.969 | 17.711 | 24.043 | 24.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 118 | TYR | 0 | -0.008 | -0.008 | 20.040 | 0.549 | 0.549 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 119 | PRO | 0 | 0.047 | 0.021 | 14.890 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 120 | VAL | 0 | -0.009 | 0.024 | 16.061 | -1.463 | -1.463 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 121 | VAL | 0 | 0.017 | 0.013 | 17.454 | 1.748 | 1.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 122 | VAL | 0 | -0.019 | -0.006 | 19.646 | -0.963 | -0.963 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 123 | ARG | 1 | 0.968 | 0.989 | 22.331 | 24.372 | 24.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 124 | PHE | 0 | 0.024 | 0.007 | 25.273 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 125 | ALA | 0 | -0.005 | 0.001 | 28.488 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 126 | LYS | 1 | 0.931 | 0.955 | 31.448 | 17.355 | 17.355 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 127 | VAL | 0 | 0.046 | 0.044 | 32.585 | -0.524 | -0.524 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 128 | ASN | 0 | 0.025 | 0.017 | 33.366 | 0.529 | 0.529 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 129 | TYR | 0 | 0.045 | -0.007 | 35.575 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 130 | ALA | 0 | -0.020 | 0.007 | 35.298 | 0.314 | 0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 131 | GLY | 0 | 0.037 | 0.027 | 36.384 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 132 | VAL | 0 | -0.016 | -0.002 | 30.090 | -0.439 | -0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 133 | SER | 0 | 0.028 | -0.008 | 30.341 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 134 | THR | 0 | -0.030 | -0.039 | 24.639 | -0.826 | -0.826 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 135 | ASN | 0 | -0.010 | 0.004 | 25.163 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 136 | ASN | 0 | 0.015 | 0.006 | 20.518 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 137 | TYR | 0 | 0.022 | 0.017 | 21.095 | 1.472 | 1.472 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 138 | ALA | 0 | 0.006 | 0.018 | 19.216 | -1.359 | -1.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 139 | LEU | 0 | -0.011 | -0.030 | 13.930 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 140 | ASP | -1 | -0.823 | -0.907 | 18.570 | -26.265 | -26.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 141 | GLU | -1 | -0.813 | -0.890 | 21.606 | -22.199 | -22.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 142 | ILE | 0 | -0.021 | 0.000 | 19.382 | 0.742 | 0.742 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 143 | LYS | 1 | 0.903 | 0.951 | 22.070 | 25.693 | 25.693 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 144 | GLU | -1 | -0.887 | -0.951 | 17.255 | -31.126 | -31.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 145 | VAL | 0 | -0.066 | -0.020 | 20.668 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 146 | ALA | -1 | -0.925 | -0.960 | 22.469 | -24.204 | -24.204 | 0.000 | 0.000 | 0.000 | 0.000 |