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: JK2G9

Calculation Name: 7F9O-p-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: p

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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1745153.886493
FMO2-HF: Nuclear repulsion 1670974.380135
FMO2-HF: Total energy -74179.506358
FMO2-MP2: Total energy -74396.513286


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:40:GLU)


Summations of interaction energy for fragment #1(A:40:GLU)
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.
-22.237-10.1817.265-8.293-11.028-0.005
Interaction energy analysis for fragmet #1(A:40:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.102 / q_NPA : -0.060
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].
3A42PHE00.0150.0192.5690.3992.8530.171-1.143-1.482-0.002
4A43PRO0-0.016-0.0173.1595.9277.5930.239-0.696-1.209-0.004
5A44GLY00.0220.0103.425-2.716-2.1080.010-0.272-0.3460.002
6A45GLN0-0.0200.0014.161-2.508-2.475-0.001-0.028-0.0040.000
7A46PRO0-0.014-0.0073.7575.6276.2120.019-0.128-0.4760.000
8A47ARG10.8550.9412.530-20.888-16.8832.721-2.627-4.0990.033
9A48PRO00.0140.0075.213-1.283-1.253-0.001-0.008-0.0210.000
20A59PHE0-0.039-0.0373.100-0.849-0.1090.079-0.178-0.6410.000
21A60GLY00.0180.0092.263-11.255-9.3894.029-3.206-2.689-0.034
22A61PHE0-0.048-0.0274.2781.7301.799-0.001-0.007-0.0610.000
10A49ALA00.000-0.0058.2900.1360.1360.0000.0000.0000.000
11A50HIS0-0.065-0.03610.5890.3510.3510.0000.0000.0000.000
12A51LEU0-0.0240.0006.817-1.010-1.0100.0000.0000.0000.000
13A52ASP-1-0.840-0.8946.3543.9463.9460.0000.0000.0000.000
14A53GLY0-0.037-0.0197.455-0.566-0.5660.0000.0000.0000.000
15A54SER0-0.060-0.0537.995-0.907-0.9070.0000.0000.0000.000
16A55SER0-0.031-0.02010.912-0.023-0.0230.0000.0000.0000.000
17A56PRO0-0.011-0.00210.279-0.722-0.7220.0000.0000.0000.000
18A57GLY00.0510.0109.3250.3990.3990.0000.0000.0000.000
19A58ASP-1-0.745-0.8616.713-2.400-2.4000.0000.0000.0000.000
23A62ASP-1-0.695-0.8667.2250.8600.8600.0000.0000.0000.000
24A63PRO0-0.046-0.0159.8670.8150.8150.0000.0000.0000.000
25A64LEU0-0.029-0.01411.4130.0990.0990.0000.0000.0000.000
26A65GLY00.0190.02713.6930.0450.0450.0000.0000.0000.000
27A66LEU0-0.007-0.01014.941-0.043-0.0430.0000.0000.0000.000
28A67ALA0-0.032-0.01812.705-0.121-0.1210.0000.0000.0000.000
29A68THR0-0.045-0.01414.8680.0720.0720.0000.0000.0000.000
30A69VAL0-0.0050.00916.3670.0400.0400.0000.0000.0000.000
31A70PRO00.022-0.00318.391-0.164-0.1640.0000.0000.0000.000
32A71GLU-1-0.892-0.95319.4530.0670.0670.0000.0000.0000.000
33A72ASN00.0110.00520.125-0.206-0.2060.0000.0000.0000.000
34A73PHE00.0490.02211.637-0.209-0.2090.0000.0000.0000.000
35A74GLU-1-0.836-0.92017.319-0.701-0.7010.0000.0000.0000.000
36A75ARG10.9800.99319.4450.0270.0270.0000.0000.0000.000
37A76PHE0-0.020-0.01516.937-0.114-0.1140.0000.0000.0000.000
38A77LYS10.8970.95913.8140.2910.2910.0000.0000.0000.000
39A78GLU-1-0.923-0.97017.201-0.692-0.6920.0000.0000.0000.000
40A79SER0-0.0010.00120.436-0.104-0.1040.0000.0000.0000.000
41A80GLU-1-0.824-0.88013.487-2.822-2.8220.0000.0000.0000.000
42A81ILE00.0210.00417.353-0.141-0.1410.0000.0000.0000.000
43A82TYR0-0.019-0.00519.485-0.022-0.0220.0000.0000.0000.000
44A83HIS0-0.039-0.02720.2680.0360.0360.0000.0000.0000.000
45A84CYS0-0.065-0.02217.237-0.139-0.1390.0000.0000.0000.000
46A85ARG10.8180.88119.9341.3861.3860.0000.0000.0000.000
47A86TRP00.002-0.00322.9000.0430.0430.0000.0000.0000.000
48A87ALA00.0280.01721.8640.0500.0500.0000.0000.0000.000
49A88MET0-0.030-0.03021.692-0.046-0.0460.0000.0000.0000.000
50A89LEU0-0.037-0.00723.6420.0310.0310.0000.0000.0000.000
51A90CYS0-0.005-0.01626.9120.0790.0790.0000.0000.0000.000
52A91VAL00.0160.01924.0070.0480.0480.0000.0000.0000.000
53A92PRO0-0.010-0.00826.7850.0500.0500.0000.0000.0000.000
54A93GLY0-0.0020.00029.5740.0640.0640.0000.0000.0000.000
55A94VAL0-0.012-0.00230.2020.0670.0670.0000.0000.0000.000
56A95LEU00.017-0.00528.7130.0320.0320.0000.0000.0000.000
57A96VAL0-0.035-0.01032.1220.0380.0380.0000.0000.0000.000
58A97PRO0-0.047-0.03734.6760.0370.0370.0000.0000.0000.000
59A98GLU-1-0.826-0.90334.643-0.845-0.8450.0000.0000.0000.000
60A99ALA00.0310.02334.8000.0230.0230.0000.0000.0000.000
61A100LEU0-0.047-0.02536.7010.0330.0330.0000.0000.0000.000
62A101GLY0-0.007-0.00239.6260.0140.0140.0000.0000.0000.000
63A102LEU0-0.071-0.02840.8620.0270.0270.0000.0000.0000.000
64A103GLY00.0370.01940.7430.0310.0310.0000.0000.0000.000
65A104ASN00.0200.01237.923-0.055-0.0550.0000.0000.0000.000
66A105TRP00.0750.02931.7830.0230.0230.0000.0000.0000.000
67A106VAL0-0.010-0.00936.0750.0140.0140.0000.0000.0000.000
68A107LYS10.8910.94538.0710.5270.5270.0000.0000.0000.000
69A108ALA00.0160.02238.6070.0240.0240.0000.0000.0000.000
70A109GLN0-0.021-0.02237.007-0.004-0.0040.0000.0000.0000.000
71A110GLU-1-0.888-0.94741.272-0.403-0.4030.0000.0000.0000.000
72A111TRP0-0.045-0.02143.9610.0330.0330.0000.0000.0000.000
73A112ALA00.0090.00143.7300.0160.0160.0000.0000.0000.000
74A113ALA0-0.037-0.00145.2780.0160.0160.0000.0000.0000.000
75A114LEU0-0.007-0.00447.0620.0210.0210.0000.0000.0000.000
76A115PRO0-0.033-0.01950.262-0.005-0.0050.0000.0000.0000.000
77A116ASP-1-0.960-0.98452.705-0.307-0.3070.0000.0000.0000.000
78A117GLY0-0.0060.01349.232-0.008-0.0080.0000.0000.0000.000
79A118GLN0-0.075-0.04949.0550.0090.0090.0000.0000.0000.000
80A119ALA00.0140.00744.190-0.011-0.0110.0000.0000.0000.000
81A120THR0-0.014-0.02644.9590.0060.0060.0000.0000.0000.000
82A121TYR0-0.039-0.01441.026-0.019-0.0190.0000.0000.0000.000
83A122LEU0-0.005-0.01942.6070.0130.0130.0000.0000.0000.000
84A123GLY00.0750.04344.3970.0050.0050.0000.0000.0000.000
85A124ASN0-0.066-0.02847.5250.0370.0370.0000.0000.0000.000
86A125PRO00.0370.01948.081-0.016-0.0160.0000.0000.0000.000
87A126VAL00.0210.02846.4940.0180.0180.0000.0000.0000.000
88A127PRO00.0170.00049.7690.0040.0040.0000.0000.0000.000
89A128TRP00.0040.00747.3980.0190.0190.0000.0000.0000.000
90A129GLY0-0.009-0.00346.986-0.004-0.0040.0000.0000.0000.000
91A130ASN00.0370.01147.470-0.014-0.0140.0000.0000.0000.000
92A131LEU00.0980.04844.914-0.007-0.0070.0000.0000.0000.000
93A132PRO0-0.012-0.01946.281-0.006-0.0060.0000.0000.0000.000
94A133THR0-0.012-0.00647.5470.0060.0060.0000.0000.0000.000
95A134ILE0-0.0010.00842.669-0.005-0.0050.0000.0000.0000.000
96A135LEU00.0750.05042.560-0.009-0.0090.0000.0000.0000.000
97A136ALA0-0.0020.00043.0570.0010.0010.0000.0000.0000.000
98A137ILE0-0.031-0.02442.1170.0030.0030.0000.0000.0000.000
99A138GLU-1-0.916-0.96038.383-0.521-0.5210.0000.0000.0000.000
100A139PHE0-0.014-0.02139.2240.0010.0010.0000.0000.0000.000
101A140LEU0-0.056-0.01740.6250.0050.0050.0000.0000.0000.000
102A141ALA0-0.025-0.02139.4240.0030.0030.0000.0000.0000.000
103A142ILE0-0.019-0.00334.087-0.018-0.0180.0000.0000.0000.000
104A143ALA00.0670.04835.957-0.002-0.0020.0000.0000.0000.000
105A144PHE00.0020.00537.4110.0100.0100.0000.0000.0000.000
106A145ALA00.000-0.00135.9610.0050.0050.0000.0000.0000.000
107A146GLU-1-0.898-0.96032.149-0.508-0.5080.0000.0000.0000.000
108A147GLN00.0090.01633.2010.0180.0180.0000.0000.0000.000
109A148GLN0-0.036-0.02335.248-0.009-0.0090.0000.0000.0000.000
110A149ARG10.9180.96431.2150.5970.5970.0000.0000.0000.000
111A150THR0-0.026-0.03229.760-0.019-0.0190.0000.0000.0000.000
112A151MET00.006-0.00231.5170.0490.0490.0000.0000.0000.000
113A152GLU-1-0.827-0.88131.618-0.245-0.2450.0000.0000.0000.000
114A153LYS10.7150.83429.6370.1790.1790.0000.0000.0000.000
115A154ASP-1-0.775-0.86727.113-0.392-0.3920.0000.0000.0000.000
116A155PRO0-0.0030.00624.2390.0380.0380.0000.0000.0000.000
117A156GLU-1-0.924-0.98822.170-0.921-0.9210.0000.0000.0000.000
118A157LYS10.8940.92023.9830.5380.5380.0000.0000.0000.000
119A158LYS10.7760.90424.9710.4100.4100.0000.0000.0000.000
120A159LYS10.8610.96119.3910.6010.6010.0000.0000.0000.000
121A160TYR0-0.004-0.02218.477-0.171-0.1710.0000.0000.0000.000
122A161PRO00.0490.05024.1050.0650.0650.0000.0000.0000.000
123A162GLY00.0550.02227.8290.0510.0510.0000.0000.0000.000
124A163GLY00.0250.01229.0270.0420.0420.0000.0000.0000.000
125A164ALA00.0250.00032.503-0.012-0.0120.0000.0000.0000.000
126A165PHE0-0.050-0.03530.191-0.006-0.0060.0000.0000.0000.000
127A166ASP-1-0.827-0.90628.279-1.007-1.0070.0000.0000.0000.000
128A167PRO00.0090.01430.9990.0260.0260.0000.0000.0000.000
129A168LEU0-0.0140.01032.0430.0260.0260.0000.0000.0000.000
130A169GLY00.0220.01529.8950.0030.0030.0000.0000.0000.000
131A170PHE0-0.014-0.04125.678-0.036-0.0360.0000.0000.0000.000
132A171SER0-0.060-0.03024.417-0.133-0.1330.0000.0000.0000.000
133A172LYS10.8020.91125.4850.9320.9320.0000.0000.0000.000
134A173ASP-1-0.855-0.93122.799-1.149-1.1490.0000.0000.0000.000
135A174PRO00.0090.00221.370-0.143-0.1430.0000.0000.0000.000
136A175ALA00.0520.02017.900-0.117-0.1170.0000.0000.0000.000
137A176LYS10.9680.98117.4691.2101.2100.0000.0000.0000.000
138A177PHE00.0290.01419.255-0.184-0.1840.0000.0000.0000.000
139A178GLU-1-0.904-0.95914.743-2.010-2.0100.0000.0000.0000.000
140A179GLU-1-0.904-0.94913.768-4.406-4.4060.0000.0000.0000.000
141A180LEU0-0.077-0.05215.356-0.298-0.2980.0000.0000.0000.000
142A181LYS10.9440.99416.2381.5341.5340.0000.0000.0000.000
143A182LEU00.0020.0089.246-0.266-0.2660.0000.0000.0000.000
144A183LYS10.8620.93213.1332.6482.6480.0000.0000.0000.000
145A184GLU-1-0.801-0.87115.204-1.796-1.7960.0000.0000.0000.000
146A185ILE00.0390.02512.2290.0010.0010.0000.0000.0000.000
147A186LYS10.9160.9569.9376.6826.6820.0000.0000.0000.000
148A187ASN00.009-0.00413.593-0.093-0.0930.0000.0000.0000.000
149A188GLY00.0360.01917.2310.2040.2040.0000.0000.0000.000
150A189ARG10.7930.8658.9464.7204.7200.0000.0000.0000.000
151A190LEU0-0.014-0.01114.2950.1390.1390.0000.0000.0000.000
152A191ALA0-0.0100.00717.4060.2240.2240.0000.0000.0000.000
153A192MET00.0360.01718.5090.2370.2370.0000.0000.0000.000
154A193LEU0-0.030-0.01515.0160.1410.1410.0000.0000.0000.000
155A194ALA0-0.0060.00619.6100.1540.1540.0000.0000.0000.000
156A195PHE00.0110.01022.7330.1440.1440.0000.0000.0000.000
157A196VAL0-0.003-0.00821.3440.1270.1270.0000.0000.0000.000
158A197GLY00.0210.01323.4310.1020.1020.0000.0000.0000.000
159A198PHE00.000-0.01524.9210.0840.0840.0000.0000.0000.000
160A199CYS0-0.048-0.01327.0940.1150.1150.0000.0000.0000.000
161A200VAL00.0470.01925.4700.0750.0750.0000.0000.0000.000
162A201GLN00.0210.02528.5850.0880.0880.0000.0000.0000.000
163A202GLN0-0.017-0.00830.4460.0820.0820.0000.0000.0000.000
164A203SER0-0.100-0.05331.2530.0620.0620.0000.0000.0000.000
165A204ALA00.0170.00231.6760.0460.0460.0000.0000.0000.000
166A205TYR0-0.029-0.01133.7080.0280.0280.0000.0000.0000.000
167A206PRO0-0.037-0.01936.077-0.017-0.0170.0000.0000.0000.000
168A207GLY0-0.049-0.01537.8080.0240.0240.0000.0000.0000.000
169A208THR0-0.0140.00134.5290.0030.0030.0000.0000.0000.000
170A209GLY00.0480.02435.364-0.012-0.0120.0000.0000.0000.000
171A210PRO0-0.023-0.02930.019-0.014-0.0140.0000.0000.0000.000
172A211LEU0-0.028-0.01031.773-0.050-0.0500.0000.0000.0000.000
173A212GLU-1-0.864-0.92333.495-0.666-0.6660.0000.0000.0000.000
174A213ASN00.0190.00132.2910.0560.0560.0000.0000.0000.000
175A214LEU0-0.036-0.00428.591-0.017-0.0170.0000.0000.0000.000
176A215ALA0-0.006-0.01131.783-0.003-0.0030.0000.0000.0000.000
177A216THR0-0.023-0.03435.0810.0210.0210.0000.0000.0000.000
178A217HIS0-0.055-0.02329.474-0.045-0.0450.0000.0000.0000.000
179A218LEU0-0.042-0.02830.9910.0100.0100.0000.0000.0000.000
180A219ALA0-0.032-0.00933.4150.0180.0180.0000.0000.0000.000
181A220ASP-1-0.862-0.91736.094-0.579-0.5790.0000.0000.0000.000
182A221PRO00.0250.01231.906-0.003-0.0030.0000.0000.0000.000
183A222TRP0-0.049-0.03829.541-0.033-0.0330.0000.0000.0000.000
184A223HIS10.7770.86834.1810.6110.6110.0000.0000.0000.000
185A224ASN00.0650.06535.3550.0450.0450.0000.0000.0000.000
186A225ASN0-0.006-0.00930.214-0.078-0.0780.0000.0000.0000.000
187A226ILE00.0490.01225.9650.0310.0310.0000.0000.0000.000
188A227GLY00.0080.01430.1660.0370.0370.0000.0000.0000.000
189A228ASP-1-0.930-0.95631.825-0.520-0.5200.0000.0000.0000.000
190A229ILE0-0.119-0.06231.1980.0330.0330.0000.0000.0000.000
191A230VAL0-0.054-0.01827.8990.0210.0210.0000.0000.0000.000
192A231ILE0-0.017-0.01731.039-0.018-0.0180.0000.0000.0000.000
193A232PRO-1-0.942-0.95730.039-0.422-0.4220.0000.0000.0000.000