FMODB

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

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FMODB ID: G78R1

Calculation Name: 7F9O-j-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: j

ChEMBL ID:

UniProt ID:

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


IFIE MAP

IFIE Diagram


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 158
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1166704.595816
FMO2-HF: Nuclear repulsion 1106469.10812
FMO2-HF: Total energy -60235.487696
FMO2-MP2: Total energy -60414.10819


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:78:ASP)


Summations of interaction energy for fragment #1(A:78:ASP)
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.
-39.295-34.0811.25-7.512-8.952-0.052
Interaction energy analysis for fragmet #1(A:78:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.053
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
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].
3A80ALA00.0230.0083.879-5.587-4.237-0.002-0.496-0.8520.003
4A81GLY00.0320.0243.5490.8611.4810.015-0.189-0.4460.000
5A82LEU0-0.042-0.0123.328-1.990-0.6700.161-0.492-0.989-0.004
6A83THR00.011-0.0061.997-22.806-23.5167.986-3.925-3.351-0.049
7A84PRO00.0660.0272.9210.2960.7330.031-0.103-0.3650.000
62A139LEU00.0010.0061.919-3.460-3.3782.975-1.217-1.839-0.013
63A140CYS0-0.103-0.0495.2864.1514.213-0.001-0.001-0.0590.000
78A155ARG10.9430.9792.957-19.257-17.2030.085-1.089-1.0510.011
8A85CYS0-0.089-0.0485.6261.4551.4550.0000.0000.0000.000
9A86LYS00.0080.0468.6461.0201.0200.0000.0000.0000.000
10A87GLU-1-0.800-0.9037.044-4.758-4.7580.0000.0000.0000.000
11A88SER0-0.063-0.0148.4540.9140.9140.0000.0000.0000.000
12A89LYS10.9240.9299.8604.3994.3990.0000.0000.0000.000
13A90ALA00.0240.01612.6810.4410.4410.0000.0000.0000.000
14A91PHE00.0610.03112.1270.3580.3580.0000.0000.0000.000
15A92ALA00.0590.03314.1790.3600.3600.0000.0000.0000.000
16A93LYS10.8960.94816.6852.2892.2890.0000.0000.0000.000
17A94ARG10.9050.95816.4442.5582.5580.0000.0000.0000.000
18A95GLU-1-0.827-0.91518.367-1.187-1.1870.0000.0000.0000.000
19A96LYS11.0241.02720.1631.2511.2510.0000.0000.0000.000
20A97GLN0-0.040-0.04722.2910.2520.2520.0000.0000.0000.000
21A98SER0-0.065-0.02622.3200.1340.1340.0000.0000.0000.000
22A99VAL00.0810.02123.7160.1260.1260.0000.0000.0000.000
23A100LYS10.9250.99726.1971.0301.0300.0000.0000.0000.000
24A101LYS10.9260.97526.7661.0821.0820.0000.0000.0000.000
25A102LEU00.0080.00827.3280.0470.0470.0000.0000.0000.000
26A103ASN00.011-0.01528.8890.1000.1000.0000.0000.0000.000
27A104SER0-0.013-0.01032.0250.0480.0480.0000.0000.0000.000
28A105SER0-0.034-0.01333.6730.0530.0530.0000.0000.0000.000
29A106LEU00.0270.01134.1520.0300.0300.0000.0000.0000.000
30A107LYS10.8280.91034.2360.6160.6160.0000.0000.0000.000
31A108LYS10.9510.98038.3850.5430.5430.0000.0000.0000.000
32A109TYR0-0.0180.00538.4440.0040.0040.0000.0000.0000.000
33A110ALA00.0640.04442.764-0.001-0.0010.0000.0000.0000.000
34A111PRO0-0.010-0.02140.876-0.015-0.0150.0000.0000.0000.000
35A112ASP-1-0.861-0.92440.846-0.354-0.3540.0000.0000.0000.000
36A113SER0-0.020-0.00742.502-0.001-0.0010.0000.0000.0000.000
37A114ALA00.0680.02241.284-0.021-0.0210.0000.0000.0000.000
38A115PRO00.019-0.00239.420-0.024-0.0240.0000.0000.0000.000
39A116ALA00.0160.01737.770-0.037-0.0370.0000.0000.0000.000
40A117LEU00.0230.01036.663-0.037-0.0370.0000.0000.0000.000
41A118ALA00.0200.01435.569-0.029-0.0290.0000.0000.0000.000
42A119ILE0-0.015-0.00932.986-0.051-0.0510.0000.0000.0000.000
43A120GLN00.0180.01231.444-0.068-0.0680.0000.0000.0000.000
44A121ALA00.0790.04831.081-0.046-0.0460.0000.0000.0000.000
45A122THR0-0.143-0.09729.192-0.064-0.0640.0000.0000.0000.000
46A123ILE0-0.043-0.02627.444-0.102-0.1020.0000.0000.0000.000
47A124ASP-1-0.866-0.93326.266-0.786-0.7860.0000.0000.0000.000
48A125LYS10.9940.99825.4780.7730.7730.0000.0000.0000.000
49A126THR0-0.078-0.04022.598-0.095-0.0950.0000.0000.0000.000
50A127LYS10.9360.97721.6630.8080.8080.0000.0000.0000.000
51A128ARG10.9090.94420.0210.9310.9310.0000.0000.0000.000
52A129ARG10.9220.97018.6431.4681.4680.0000.0000.0000.000
53A130PHE0-0.032-0.01816.584-0.139-0.1390.0000.0000.0000.000
54A131GLU-1-0.907-0.96515.927-1.706-1.7060.0000.0000.0000.000
55A132ASN00.0190.01516.5210.0350.0350.0000.0000.0000.000
56A133TYR00.008-0.01112.987-0.013-0.0130.0000.0000.0000.000
57A134GLY00.0110.00412.177-0.481-0.4810.0000.0000.0000.000
58A135LYS00.0070.00913.2740.2420.2420.0000.0000.0000.000
59A136PHE0-0.025-0.01312.4980.2950.2950.0000.0000.0000.000
60A137GLY00.0310.0098.1720.1930.1930.0000.0000.0000.000
61A138LEU0-0.0250.0006.744-1.778-1.7780.0000.0000.0000.000
64A141GLY00.0620.0426.822-1.478-1.4780.0000.0000.0000.000
65A142SER00.017-0.0079.3180.1120.1120.0000.0000.0000.000
66A143ASP-1-0.886-0.93210.570-2.801-2.8010.0000.0000.0000.000
67A144GLY0-0.072-0.05312.0950.4980.4980.0000.0000.0000.000
68A145LEU00.009-0.00811.9250.5850.5850.0000.0000.0000.000
69A146PRO00.0160.01310.007-0.809-0.8090.0000.0000.0000.000
70A147HIS0-0.041-0.0298.0040.8570.8570.0000.0000.0000.000
71A148LEU00.0390.0318.136-0.963-0.9630.0000.0000.0000.000
72A149ILE0-0.013-0.0055.613-0.151-0.1510.0000.0000.0000.000
73A150VAL00.0240.0049.0390.6770.6770.0000.0000.0000.000
74A151SER0-0.039-0.02310.3550.2660.2660.0000.0000.0000.000
75A152GLY00.0160.01412.2960.3750.3750.0000.0000.0000.000
76A153ASP-1-0.868-0.9277.8633.9003.9000.0000.0000.0000.000
77A154GLN0-0.007-0.01411.367-0.558-0.5580.0000.0000.0000.000
79A156HIS0-0.023-0.0156.222-1.848-1.8480.0000.0000.0000.000
80A157TRP00.0040.0079.264-0.329-0.3290.0000.0000.0000.000
81A158GLY00.0560.02612.9460.1720.1720.0000.0000.0000.000
82A159GLU-1-0.932-0.96911.673-2.467-2.4670.0000.0000.0000.000
83A160PHE0-0.020-0.02214.9420.0450.0450.0000.0000.0000.000
84A161ILE00.0470.02816.1920.0610.0610.0000.0000.0000.000
85A162THR00.003-0.00218.304-0.001-0.0010.0000.0000.0000.000
86A163PRO00.0250.00518.4100.0530.0530.0000.0000.0000.000
87A164GLY00.0440.03520.6790.0220.0220.0000.0000.0000.000
88A165VAL00.002-0.01422.3850.0400.0400.0000.0000.0000.000
89A166LEU0-0.0130.01224.0730.0290.0290.0000.0000.0000.000
90A167PHE00.009-0.00625.0400.0170.0170.0000.0000.0000.000
91A168LEU00.0180.00325.5480.0230.0230.0000.0000.0000.000
92A169TYR0-0.038-0.00228.3290.0240.0240.0000.0000.0000.000
93A170ILE00.0130.00229.6920.0150.0150.0000.0000.0000.000
94A171ALA00.008-0.00430.6260.0130.0130.0000.0000.0000.000
95A172GLY00.0390.01432.1690.0130.0130.0000.0000.0000.000
96A173TRP0-0.0310.00134.0480.0190.0190.0000.0000.0000.000
97A174ILE0-0.026-0.02333.8690.0100.0100.0000.0000.0000.000
98A175GLY00.0190.01236.3690.0070.0070.0000.0000.0000.000
99A176TRP0-0.017-0.00537.9460.0110.0110.0000.0000.0000.000
100A177VAL0-0.0190.00139.7830.0090.0090.0000.0000.0000.000
101A178GLY00.0230.02041.1430.0060.0060.0000.0000.0000.000
102A179ARG10.8610.91142.2530.0560.0560.0000.0000.0000.000
103A180SER0-0.066-0.04243.9560.0090.0090.0000.0000.0000.000
104A181TYR0-0.019-0.03045.7410.0070.0070.0000.0000.0000.000
105A182LEU00.0190.00846.7920.0040.0040.0000.0000.0000.000
106A183ILE00.0330.01446.9220.0040.0040.0000.0000.0000.000
107A184ALA0-0.0400.00150.0420.0060.0060.0000.0000.0000.000
108A185VAL0-0.009-0.01251.0880.0040.0040.0000.0000.0000.000
109A186SER0-0.034-0.01852.7510.0010.0010.0000.0000.0000.000
110A187GLY00.0060.01954.5510.0030.0030.0000.0000.0000.000
111A188GLU-1-0.900-0.97156.227-0.087-0.0870.0000.0000.0000.000
112A189LYS10.8890.93959.5410.0610.0610.0000.0000.0000.000
113A190LYS10.9570.95559.8450.0930.0930.0000.0000.0000.000
114A191PRO00.1050.07554.584-0.006-0.0060.0000.0000.0000.000
115A192ALA00.1070.06354.479-0.005-0.0050.0000.0000.0000.000
116A193MET0-0.074-0.05455.134-0.008-0.0080.0000.0000.0000.000
117A194ARG10.8840.95954.2380.1090.1090.0000.0000.0000.000
118A195GLU-1-0.915-0.94250.656-0.127-0.1270.0000.0000.0000.000
119A196ILE0-0.043-0.02250.547-0.010-0.0100.0000.0000.0000.000
120A197ILE0-0.056-0.03052.515-0.008-0.0080.0000.0000.0000.000
121A198ILE00.0180.01147.4400.0080.0080.0000.0000.0000.000
122A199ASP-1-0.855-0.93651.767-0.099-0.0990.0000.0000.0000.000
123A200VAL00.014-0.00350.1170.0010.0010.0000.0000.0000.000
124A201GLU-1-0.830-0.88951.012-0.084-0.0840.0000.0000.0000.000
125A202LEU0-0.0100.00550.5540.0040.0040.0000.0000.0000.000
126A203ALA00.030-0.00147.5970.0020.0020.0000.0000.0000.000
127A204ALA0-0.022-0.00647.285-0.002-0.0020.0000.0000.0000.000
128A205ARG10.8160.88947.8100.0810.0810.0000.0000.0000.000
129A206ILE0-0.045-0.01445.6390.0120.0120.0000.0000.0000.000
130A207ILE00.0270.00741.6480.0030.0030.0000.0000.0000.000
131A208PRO0-0.003-0.00541.859-0.006-0.0060.0000.0000.0000.000
132A209ARG10.8910.94241.5160.0720.0720.0000.0000.0000.000
133A210GLY00.0670.03638.6100.0110.0110.0000.0000.0000.000
134A211PHE00.019-0.01534.7460.0030.0030.0000.0000.0000.000
135A212ILE0-0.033-0.01537.3400.0180.0180.0000.0000.0000.000
136A213TRP0-0.0160.00731.5180.0220.0220.0000.0000.0000.000
137A214PRO0-0.035-0.01533.6460.0090.0090.0000.0000.0000.000
138A215VAL00.005-0.00535.7260.0180.0180.0000.0000.0000.000
139A216ALA0-0.012-0.00138.5890.0100.0100.0000.0000.0000.000
140A217ALA00.0650.03638.3580.0060.0060.0000.0000.0000.000
141A218TYR0-0.0080.00336.6570.0090.0090.0000.0000.0000.000
142A219ARG10.9230.95039.399-0.073-0.0730.0000.0000.0000.000
143A220GLU-1-0.744-0.85942.992-0.024-0.0240.0000.0000.0000.000
144A221LEU0-0.009-0.00438.6470.0030.0030.0000.0000.0000.000
145A222ILE0-0.092-0.05240.2550.0090.0090.0000.0000.0000.000
146A223ASN0-0.109-0.05843.7740.0150.0150.0000.0000.0000.000
147A224GLY00.0210.02945.848-0.001-0.0010.0000.0000.0000.000
148A225ASP-1-0.852-0.92147.1130.0090.0090.0000.0000.0000.000
149A226LEU0-0.140-0.06440.056-0.010-0.0100.0000.0000.0000.000
150A227VAL0-0.075-0.04343.098-0.013-0.0130.0000.0000.0000.000
151A228VAL00.0190.01445.9690.0050.0050.0000.0000.0000.000
152A229ASP-1-0.977-0.98048.2370.0080.0080.0000.0000.0000.000
153A230ASP-1-0.918-0.97150.472-0.016-0.0160.0000.0000.0000.000
154A231ALA0-0.045-0.00953.223-0.003-0.0030.0000.0000.0000.000
155A232ASP-1-0.898-0.95351.630-0.060-0.0600.0000.0000.0000.000
156A233ILE0-0.061-0.03552.189-0.011-0.0110.0000.0000.0000.000
157A234GLY0-0.069-0.03554.9090.0060.0060.0000.0000.0000.000
158A235TYR-1-0.963-0.97252.902-0.067-0.0670.0000.0000.0000.000