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: 2M17R
Calculation Name: 5V2C-H-Xray547
Preferred Name:
Target Type:
Ligand Name: chlorophyll a | pheophytin a | protoporphyrin ix containing fe | digalactosyl diacyl glycerol (dgdg) | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone | heme c | 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 | dodecyl-beta-d-maltoside | ca-mn4-o5 cluster | nonaethylene glycol | heptyl 1-thio-beta-d-glucopyranoside | 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol | hexaethylene glycol | n1-methylated histidine | pentaethylene glycol | n-formylmethionine | tetraethylene glycol | bicarbonate ion | triethylene glycol | calcium ion | 1,2-ethanediol | fe (ii) ion | chloride ion
Ligand 3-letter code: CLA | PHO | HEM | DGD | PL9 | HEC | SQD | BCR | LMG | LHG | LMT | OEX | 2PE | HTG | PE8 | P6G | MHS | 1PE | FME | PG4 | BCT | PGE | CA | EDO | FE2 | CL
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5V2C
Chain ID: H
UniProt ID: P0A387
Base Structure: X-ray
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 | 65 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -262439.253548 |
|---|---|
| FMO2-HF: Nuclear repulsion | 237515.946311 |
| FMO2-HF: Total energy | -24923.307237 |
| FMO2-MP2: Total energy | -24996.549348 |
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:2:ALA)
Summations of interaction energy for
fragment #1(A:2:ALA)
| 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. |
| 29.249 | 30.618 | -0.008 | -0.591 | -0.77 | -0.001 |
Interaction energy analysis for fragmet #1(A:2:ALA)
| 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 | 4 | ARG | 1 | 0.882 | 0.914 | 3.873 | 33.044 | 34.413 | -0.008 | -0.591 | -0.770 | -0.001 |
| 4 | A | 5 | THR | 0 | 0.011 | -0.008 | 6.422 | 2.422 | 2.422 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 6 | TRP | 0 | 0.092 | 0.049 | 9.604 | -0.552 | -0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 7 | LEU | 0 | 0.066 | 0.033 | 12.441 | 0.364 | 0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 8 | GLY | 0 | -0.005 | -0.005 | 8.374 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 9 | ASP | -1 | -0.827 | -0.893 | 8.778 | -31.298 | -31.298 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 10 | ILE | 0 | -0.003 | 0.002 | 10.609 | 0.931 | 0.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 11 | LEU | 0 | 0.013 | 0.000 | 11.590 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 12 | ARG | 1 | 0.852 | 0.925 | 5.800 | 31.632 | 31.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 13 | PRO | 0 | 0.010 | 0.001 | 10.752 | -0.314 | -0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 14 | LEU | 0 | 0.034 | 0.034 | 13.994 | 0.487 | 0.487 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 15 | ASN | 0 | -0.017 | 0.006 | 9.417 | 1.344 | 1.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 16 | SER | 0 | -0.052 | -0.035 | 10.803 | -2.140 | -2.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 17 | GLU | -1 | -0.798 | -0.886 | 12.612 | -15.307 | -15.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 18 | TYR | 0 | 0.012 | 0.001 | 13.142 | 0.845 | 0.845 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 19 | GLY | 0 | 0.005 | 0.000 | 15.116 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 20 | LYS | 1 | 0.803 | 0.908 | 18.175 | 14.828 | 14.828 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 21 | VAL | 0 | 0.007 | 0.005 | 20.377 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 22 | ALA | 0 | -0.006 | 0.001 | 24.044 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 23 | PRO | 0 | 0.014 | -0.010 | 27.511 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 24 | GLY | 0 | 0.011 | 0.011 | 30.173 | 0.312 | 0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 25 | TRP | 0 | 0.054 | 0.022 | 31.029 | -0.242 | -0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 26 | GLY | 0 | 0.013 | 0.030 | 31.412 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 27 | THR | 0 | 0.012 | -0.004 | 31.185 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 28 | THR | 0 | 0.010 | -0.005 | 32.867 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 29 | PRO | 0 | 0.011 | -0.008 | 34.614 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | LEU | 0 | 0.024 | 0.021 | 35.515 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | MET | 0 | -0.001 | 0.001 | 32.385 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | ALA | 0 | 0.025 | 0.008 | 35.548 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 33 | VAL | 0 | 0.006 | 0.009 | 38.520 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 34 | PHE | 0 | 0.005 | -0.006 | 36.428 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 35 | MET | 0 | -0.026 | -0.010 | 35.880 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLY | 0 | 0.019 | 0.017 | 38.684 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | LEU | 0 | -0.004 | -0.011 | 41.537 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | PHE | 0 | -0.003 | -0.001 | 36.958 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | LEU | 0 | 0.011 | 0.009 | 40.929 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | VAL | 0 | 0.017 | 0.003 | 42.927 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | PHE | 0 | -0.009 | -0.001 | 41.359 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | LEU | 0 | -0.006 | -0.014 | 39.627 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | LEU | 0 | -0.016 | 0.004 | 44.123 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | ILE | 0 | 0.023 | 0.016 | 47.563 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | ILE | 0 | -0.011 | -0.012 | 43.358 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | LEU | 0 | -0.030 | 0.000 | 46.879 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | GLU | -1 | -0.890 | -0.969 | 48.580 | -5.806 | -5.806 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 48 | ILE | 0 | 0.000 | 0.020 | 50.692 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 49 | TYR | 0 | -0.040 | -0.020 | 47.577 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 50 | ASN | 0 | -0.074 | -0.034 | 51.605 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 51 | SER | 0 | -0.029 | -0.010 | 53.705 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 52 | THR | 0 | -0.020 | -0.010 | 55.182 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 53 | LEU | 0 | -0.057 | -0.029 | 52.590 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 54 | ILE | 0 | -0.008 | -0.005 | 55.823 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 55 | LEU | 0 | -0.008 | -0.015 | 54.239 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 56 | ASP | -1 | -0.868 | -0.933 | 58.478 | -4.995 | -4.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 57 | GLY | 0 | -0.046 | -0.030 | 58.762 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 58 | VAL | 0 | -0.052 | -0.017 | 54.108 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 59 | ASN | 0 | -0.012 | -0.007 | 56.860 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 60 | VAL | 0 | 0.013 | 0.013 | 53.552 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 61 | SER | 0 | -0.010 | -0.005 | 55.987 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 62 | TRP | 0 | 0.011 | -0.006 | 51.721 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 63 | LYS | 1 | 0.886 | 0.939 | 56.911 | 4.965 | 4.965 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 64 | ALA | 0 | 0.021 | 0.019 | 55.517 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 65 | LEU | 0 | -0.028 | -0.008 | 53.569 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 66 | GLY | -1 | -0.947 | -0.962 | 58.047 | -5.248 | -5.248 | 0.000 | 0.000 | 0.000 | 0.000 |