FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: R4ML8

Calculation Name: 7F9O-D-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):

PDB ID: 7F9O

Chain ID: D

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 142
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1131676.835918
FMO2-HF: Nuclear repulsion 1076978.449719
FMO2-HF: Total energy -54698.3862
FMO2-MP2: Total energy -54859.676665


3D Structure
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:63:GLY)


Summations of interaction energy for fragment #1(A:63:GLY)
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.
59.06660.21-0.002-0.463-0.678-0.002
Interaction energy analysis for fragmet #1(A:63:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.880 / q_NPA : 0.926
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].
3A65VAL00.0440.0363.8427.7178.861-0.002-0.463-0.678-0.002
4A66PRO00.0090.0175.6822.0242.0240.0000.0000.0000.000
5A67PRO0-0.016-0.0188.4402.4272.4270.0000.0000.0000.000
6A68GLN0-0.045-0.04711.5950.2270.2270.0000.0000.0000.000
7A69LEU0-0.023-0.00814.7730.6850.6850.0000.0000.0000.000
8A70ASP-1-0.888-0.94516.674-13.931-13.9310.0000.0000.0000.000
9A71PRO00.0190.02720.2550.3560.3560.0000.0000.0000.000
10A72SER0-0.006-0.01023.0440.2800.2800.0000.0000.0000.000
11A73THR0-0.012-0.00125.1110.1900.1900.0000.0000.0000.000
12A74PRO00.0030.00728.0350.2200.2200.0000.0000.0000.000
13A75SER00.0340.02330.491-0.215-0.2150.0000.0000.0000.000
14A76PRO0-0.026-0.01630.9850.2380.2380.0000.0000.0000.000
15A77ILE0-0.0080.01033.9850.1060.1060.0000.0000.0000.000
16A78PHE0-0.003-0.02137.355-0.017-0.0170.0000.0000.0000.000
17A79GLY00.0210.01839.2930.0360.0360.0000.0000.0000.000
18A80GLY0-0.0050.01539.9600.0770.0770.0000.0000.0000.000
19A81SER0-0.017-0.02139.8720.1130.1130.0000.0000.0000.000
20A82THR00.0290.00040.890-0.158-0.1580.0000.0000.0000.000
21A83GLY00.0050.01639.057-0.017-0.0170.0000.0000.0000.000
22A84GLY00.0140.01136.374-0.264-0.2640.0000.0000.0000.000
23A85LEU0-0.048-0.02631.744-0.100-0.1000.0000.0000.0000.000
24A86LEU00.0700.03335.7020.2650.2650.0000.0000.0000.000
25A87ARG10.9650.97136.2647.7207.7200.0000.0000.0000.000
26A88LYS10.8900.95330.38010.25910.2590.0000.0000.0000.000
27A89ALA0-0.006-0.00731.915-0.245-0.2450.0000.0000.0000.000
28A90GLN0-0.040-0.02732.254-0.068-0.0680.0000.0000.0000.000
29A91VAL0-0.025-0.00234.0490.0760.0760.0000.0000.0000.000
30A92GLU-1-0.866-0.92330.828-9.856-9.8560.0000.0000.0000.000
31A93GLU-1-0.778-0.89226.496-12.354-12.3540.0000.0000.0000.000
32A94PHE0-0.053-0.01927.6920.4630.4630.0000.0000.0000.000
33A95TYR0-0.012-0.00223.480-0.809-0.8090.0000.0000.0000.000
34A96VAL00.0120.00323.1390.6290.6290.0000.0000.0000.000
35A97ILE0-0.014-0.02223.104-0.720-0.7200.0000.0000.0000.000
36A98THR00.0390.03120.9890.4090.4090.0000.0000.0000.000
37A99TRP0-0.011-0.01822.184-0.596-0.5960.0000.0000.0000.000
38A100THR0-0.002-0.00422.7370.0920.0920.0000.0000.0000.000
39A101SER00.001-0.02225.172-0.270-0.2700.0000.0000.0000.000
40A102PRO0-0.0110.00327.7660.1020.1020.0000.0000.0000.000
41A103LYS10.9660.97329.9759.3619.3610.0000.0000.0000.000
42A104GLU-1-0.872-0.92233.089-9.253-9.2530.0000.0000.0000.000
43A105GLN0-0.064-0.04332.0460.4170.4170.0000.0000.0000.000
44A106VAL00.0100.00436.105-0.112-0.1120.0000.0000.0000.000
45A107PHE0-0.038-0.02532.609-0.183-0.1830.0000.0000.0000.000
46A108GLU-1-0.826-0.90235.615-8.417-8.4170.0000.0000.0000.000
47A109MET0-0.014-0.01033.859-0.491-0.4910.0000.0000.0000.000
48A110PRO0-0.035-0.03531.0770.1610.1610.0000.0000.0000.000
49A111THR0-0.0230.00734.1930.0380.0380.0000.0000.0000.000
50A112GLY00.0340.03336.8800.2410.2410.0000.0000.0000.000
51A113GLY00.0260.00639.6000.0010.0010.0000.0000.0000.000
52A114ALA0-0.017-0.01538.808-0.210-0.2100.0000.0000.0000.000
53A115ALA00.0050.00835.8980.1370.1370.0000.0000.0000.000
54A116ILE00.015-0.00136.744-0.065-0.0650.0000.0000.0000.000
55A117MET0-0.0610.01931.024-0.195-0.1950.0000.0000.0000.000
56A118ARG10.9000.93732.4669.5549.5540.0000.0000.0000.000
57A119GLU-1-0.865-0.93830.093-10.973-10.9730.0000.0000.0000.000
58A120GLY00.0840.06727.831-0.071-0.0710.0000.0000.0000.000
59A121PRO0-0.053-0.04024.810-0.161-0.1610.0000.0000.0000.000
60A122ASN00.008-0.01126.5050.7430.7430.0000.0000.0000.000
61A123LEU00.0100.00625.664-0.476-0.4760.0000.0000.0000.000
62A124LEU00.006-0.00727.3260.5520.5520.0000.0000.0000.000
63A125LYS10.9470.97927.53910.04510.0450.0000.0000.0000.000
64A126LEU00.001-0.00828.2770.4020.4020.0000.0000.0000.000
65A127ALA00.0480.01129.278-0.334-0.3340.0000.0000.0000.000
66A128ARG0-0.006-0.00329.184-0.048-0.0480.0000.0000.0000.000
67A129LYS10.9830.99319.82914.77114.7710.0000.0000.0000.000
68A130GLU-1-0.888-0.93825.553-10.498-10.4980.0000.0000.0000.000
69A131GLN00.0360.01827.8350.2400.2400.0000.0000.0000.000
70A132CYS00.0010.01124.2340.0620.0620.0000.0000.0000.000
71A133LEU00.0080.00522.057-0.262-0.2620.0000.0000.0000.000
72A134ALA00.0060.01125.0390.0080.0080.0000.0000.0000.000
73A135LEU0-0.006-0.00127.7600.1950.1950.0000.0000.0000.000
74A136GLY00.0550.00824.0990.0340.0340.0000.0000.0000.000
75A137ASN0-0.004-0.00924.790-0.568-0.5680.0000.0000.0000.000
76A138ARG10.8480.92326.4649.5249.5240.0000.0000.0000.000
77A139LEU0-0.009-0.00825.9160.2100.2100.0000.0000.0000.000
78A140ARG10.8730.93821.65613.62013.6200.0000.0000.0000.000
79A141SER0-0.0140.00525.3620.1740.1740.0000.0000.0000.000
80A142LYS10.9400.97328.4049.3149.3140.0000.0000.0000.000
81A143TYR00.008-0.01629.1150.1280.1280.0000.0000.0000.000
82A144LYS10.8370.93026.23510.40510.4050.0000.0000.0000.000
83A145ILE00.0010.02424.848-0.251-0.2510.0000.0000.0000.000
84A146ALA00.0200.01219.556-0.241-0.2410.0000.0000.0000.000
85A147TYR0-0.012-0.01020.3510.5680.5680.0000.0000.0000.000
86A148GLN00.0290.01916.559-0.287-0.2870.0000.0000.0000.000
87A149PHE00.008-0.01718.7730.7570.7570.0000.0000.0000.000
88A150TYR00.0300.01417.202-1.254-1.2540.0000.0000.0000.000
89A151ARG10.8170.89320.46014.55214.5520.0000.0000.0000.000
90A152VAL00.0250.01521.971-0.648-0.6480.0000.0000.0000.000
91A153PHE00.0290.00521.4570.4060.4060.0000.0000.0000.000
92A154PRO0-0.012-0.01026.275-0.038-0.0380.0000.0000.0000.000
93A155ASN0-0.0030.00025.0680.1350.1350.0000.0000.0000.000
94A156GLY00.0110.01426.4040.1000.1000.0000.0000.0000.000
95A157GLU-1-0.931-0.95320.575-15.571-15.5710.0000.0000.0000.000
96A158VAL00.003-0.00219.3430.2640.2640.0000.0000.0000.000
97A159GLN00.0160.01917.226-0.354-0.3540.0000.0000.0000.000
98A160TYR00.0300.00412.2450.2550.2550.0000.0000.0000.000
99A161LEU0-0.088-0.05915.516-0.555-0.5550.0000.0000.0000.000
100A162HIS0-0.0250.00415.450-0.658-0.6580.0000.0000.0000.000
101A163PRO00.0200.00012.7210.3140.3140.0000.0000.0000.000
102A164LYS10.8880.96511.54221.38621.3860.0000.0000.0000.000
103A165ASP-1-0.873-0.9516.249-41.512-41.5120.0000.0000.0000.000
104A166GLY0-0.0020.0108.216-1.683-1.6830.0000.0000.0000.000
105A167VAL0-0.042-0.0239.9012.1322.1320.0000.0000.0000.000
106A168TYR00.004-0.00512.1840.1650.1650.0000.0000.0000.000
107A169PRO00.020-0.00115.013-0.442-0.4420.0000.0000.0000.000
108A170GLU-1-0.883-0.93616.045-14.387-14.3870.0000.0000.0000.000
109A171LYS10.9410.98913.25921.21621.2160.0000.0000.0000.000
110A172VAL00.0210.00513.773-0.956-0.9560.0000.0000.0000.000
111A173ASN00.0170.0037.8882.5952.5950.0000.0000.0000.000
112A174ALA00.0260.0058.7730.9140.9140.0000.0000.0000.000
113A175GLY00.0420.0136.555-4.052-4.0520.0000.0000.0000.000
114A176ARG10.7960.9237.63522.77422.7740.0000.0000.0000.000
115A177GLN00.0110.0009.9421.9991.9990.0000.0000.0000.000
116A178GLY00.0450.02512.9040.4830.4830.0000.0000.0000.000
117A179VAL0-0.027-0.01916.1260.7990.7990.0000.0000.0000.000
118A180GLY00.0260.01618.5140.1970.1970.0000.0000.0000.000
119A181GLN0-0.041-0.01318.932-0.258-0.2580.0000.0000.0000.000
120A182ASN00.0090.00023.010-0.097-0.0970.0000.0000.0000.000
121A183PHE0-0.005-0.00620.6290.1920.1920.0000.0000.0000.000
122A184ARG10.9170.94326.77610.30910.3090.0000.0000.0000.000
123A185SER0-0.0170.00130.5460.0450.0450.0000.0000.0000.000
124A186ILE00.0970.02932.8020.1640.1640.0000.0000.0000.000
125A187GLY0-0.002-0.00333.8660.1100.1100.0000.0000.0000.000
126A188LYS10.8820.94434.8098.6518.6510.0000.0000.0000.000
127A189ASN00.0200.02433.625-0.356-0.3560.0000.0000.0000.000
128A190VAL00.0350.04136.0580.2290.2290.0000.0000.0000.000
129A191SER00.0370.00838.412-0.058-0.0580.0000.0000.0000.000
130A192PRO00.015-0.02141.280-0.055-0.0550.0000.0000.0000.000
131A193ILE0-0.046-0.01342.3710.0410.0410.0000.0000.0000.000
132A194GLU-1-0.891-0.94940.446-7.432-7.4320.0000.0000.0000.000
133A195VAL0-0.0040.00937.028-0.141-0.1410.0000.0000.0000.000
134A196LYS10.9260.98939.8426.6906.6900.0000.0000.0000.000
135A197PHE0-0.017-0.02742.9810.0810.0810.0000.0000.0000.000
136A198THR0-0.010-0.00338.149-0.140-0.1400.0000.0000.0000.000
137A199GLY00.009-0.00135.8230.0680.0680.0000.0000.0000.000
138A200LYS10.7620.88130.42310.08610.0860.0000.0000.0000.000
139A201ASN00.0150.00232.6240.4810.4810.0000.0000.0000.000
140A202SER00.0240.00534.082-0.207-0.2070.0000.0000.0000.000
141A203PHE0-0.045-0.03430.2610.0160.0160.0000.0000.0000.000
142A204ASP-2-1.693-1.80728.726-21.586-21.5860.0000.0000.0000.000