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: Q5MKY

Calculation Name: 7WG5-A-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | 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 | dodecyl-alpha-d-maltoside | phylloquinone | iron/sulfur cluster | fe2/s2 (inorganic) cluster

Ligand 3-letter code: CLA | CHL | DGD | XAT | LUT | SQD | BCR | LMG | LHG | LMU | PQN | SF4 | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7WG5

Chain ID: A

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1998300.620998
FMO2-HF: Nuclear repulsion 1919418.591178
FMO2-HF: Total energy -78882.02982
FMO2-MP2: Total energy -79113.550276


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:46:ARG)


Summations of interaction energy for fragment #1(A:46:ARG)
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.
-332.638-330.1340.903-18.276-25.136-0.201
Interaction energy analysis for fragmet #1(A:46:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.656 / q_NPA : 1.815
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].
3A48THR00.001-0.0202.217-11.581-9.8994.911-2.157-4.437-0.013
4A49TRP00.0650.0444.1859.5369.7770.001-0.051-0.1920.000
10A55PRO0-0.028-0.0122.3661.3971.8663.197-0.874-2.7910.003
11A56PRO00.0580.0324.4461.6821.812-0.001-0.014-0.1140.000
12A57PRO0-0.033-0.0204.316-10.036-9.928-0.001-0.016-0.0910.000
14A59LEU0-0.028-0.0053.2203.8014.4140.018-0.284-0.348-0.002
15A60ASP-1-0.881-0.9651.999-136.167-136.27214.243-7.437-6.701-0.077
16A61GLY0-0.0280.0042.96116.19615.1160.4652.174-1.559-0.003
17A62ASN0-0.040-0.0133.8904.8045.0000.006-0.010-0.1930.000
21A66ASP-1-0.778-0.8631.683-158.156-160.77917.537-8.524-6.390-0.102
22A67TYR0-0.026-0.0303.2316.1637.3200.025-0.380-0.802-0.003
23A68GLY00.0590.0152.5234.5086.2990.402-0.872-1.321-0.005
24A69PHE0-0.049-0.0243.2488.8848.8130.1000.169-0.1970.001
5A50LEU0-0.015-0.0027.8096.1536.1530.0000.0000.0000.000
6A51PRO0-0.035-0.0148.799-4.265-4.2650.0000.0000.0000.000
7A52GLY00.014-0.0029.4894.3144.3140.0000.0000.0000.000
8A53LEU0-0.0090.0089.4773.8763.8760.0000.0000.0000.000
9A54ASN0-0.032-0.0136.873-6.361-6.3610.0000.0000.0000.000
13A58TYR0-0.010-0.0086.3881.7121.7120.0000.0000.0000.000
18A63LEU00.0530.0146.0826.2096.2090.0000.0000.0000.000
19A64ALA00.0260.0137.045-4.502-4.5020.0000.0000.0000.000
20A65GLY00.010-0.0166.9201.5411.5410.0000.0000.0000.000
25A70ASP-1-0.737-0.8536.881-43.419-43.4190.0000.0000.0000.000
26A71PRO0-0.048-0.0248.6950.0970.0970.0000.0000.0000.000
27A72LEU0-0.030-0.01911.4002.6092.6090.0000.0000.0000.000
28A73GLY00.0530.05611.8592.2282.2280.0000.0000.0000.000
29A74LEU0-0.044-0.02712.2801.8951.8950.0000.0000.0000.000
30A75GLY0-0.040-0.0429.8261.7161.7160.0000.0000.0000.000
31A76GLU-1-0.952-0.97410.281-38.692-38.6920.0000.0000.0000.000
32A77ASP-1-0.809-0.89911.551-31.428-31.4280.0000.0000.0000.000
33A78PRO00.0270.00612.269-1.411-1.4110.0000.0000.0000.000
34A79GLU-1-1.000-1.01513.306-27.696-27.6960.0000.0000.0000.000
35A80SER0-0.008-0.00614.7751.1171.1170.0000.0000.0000.000
36A81LEU0-0.0010.0068.142-0.305-0.3050.0000.0000.0000.000
37A82LYS10.9210.96312.31531.01031.0100.0000.0000.0000.000
38A83TRP00.0180.01414.3740.8510.8510.0000.0000.0000.000
39A84TYR00.015-0.00313.2291.5041.5040.0000.0000.0000.000
40A85VAL00.0120.01610.472-0.195-0.1950.0000.0000.0000.000
41A86GLN0-0.033-0.02213.2391.7181.7180.0000.0000.0000.000
42A87ALA0-0.013-0.00116.9651.2261.2260.0000.0000.0000.000
43A88GLU-1-0.812-0.88111.145-44.633-44.6330.0000.0000.0000.000
44A89LEU0-0.0110.00714.4120.9080.9080.0000.0000.0000.000
45A90VAL0-0.022-0.00716.8691.2451.2450.0000.0000.0000.000
46A91HIS00.0110.00018.5830.9510.9510.0000.0000.0000.000
47A92SER0-0.041-0.02516.6150.8330.8330.0000.0000.0000.000
48A93ARG10.7990.87818.09030.80130.8010.0000.0000.0000.000
49A94PHE00.004-0.00721.2611.1251.1250.0000.0000.0000.000
50A95ALA00.0060.01220.9210.9240.9240.0000.0000.0000.000
51A96MET0-0.027-0.01118.6910.5230.5230.0000.0000.0000.000
52A97LEU0-0.037-0.01022.9640.8890.8890.0000.0000.0000.000
53A98GLY00.0090.01226.0120.8530.8530.0000.0000.0000.000
54A99VAL00.019-0.00723.5120.6930.6930.0000.0000.0000.000
55A100ALA0-0.023-0.00426.5220.6210.6210.0000.0000.0000.000
56A101GLY0-0.013-0.01428.2170.7120.7120.0000.0000.0000.000
57A102ILE0-0.0030.00129.0680.6640.6640.0000.0000.0000.000
58A103LEU00.0160.00526.9580.5170.5170.0000.0000.0000.000
59A104PHE0-0.011-0.00231.2260.6220.6220.0000.0000.0000.000
60A105THR00.020-0.00233.6350.4590.4590.0000.0000.0000.000
61A106ASP-1-0.767-0.88733.991-16.814-16.8140.0000.0000.0000.000
62A107LEU00.0100.02333.1870.4100.4100.0000.0000.0000.000
63A108LEU0-0.046-0.00436.4530.5550.5550.0000.0000.0000.000
64A109ARG10.7940.89437.00216.57416.5740.0000.0000.0000.000
65A110THR0-0.057-0.04937.9610.3500.3500.0000.0000.0000.000
66A111THR0-0.049-0.04439.3500.3650.3650.0000.0000.0000.000
67A112GLY00.0240.02641.9940.3410.3410.0000.0000.0000.000
68A113ILE0-0.060-0.01741.6510.3110.3110.0000.0000.0000.000
69A114ARG10.9010.93442.02114.13614.1360.0000.0000.0000.000
70A115ASN00.0060.01343.043-0.411-0.4110.0000.0000.0000.000
71A116LEU0-0.031-0.01139.0060.1430.1430.0000.0000.0000.000
72A117PRO00.0180.01040.0090.0510.0510.0000.0000.0000.000
73A118VAL00.0560.02237.402-0.380-0.3800.0000.0000.0000.000
74A119TRP00.0290.00331.2060.1320.1320.0000.0000.0000.000
75A120TYR00.003-0.00535.885-0.080-0.0800.0000.0000.0000.000
76A121GLU-1-0.950-0.96536.742-14.209-14.2090.0000.0000.0000.000
77A122ALA0-0.024-0.01037.3350.3640.3640.0000.0000.0000.000
78A123GLY0-0.011-0.00738.7570.1920.1920.0000.0000.0000.000
79A124ALA0-0.009-0.00439.4410.2280.2280.0000.0000.0000.000
80A125VAL00.0210.01042.7140.4840.4840.0000.0000.0000.000
81A126LYS10.8440.92444.41412.94712.9470.0000.0000.0000.000
82A127PHE00.007-0.00341.5580.0680.0680.0000.0000.0000.000
83A128ASP-1-0.930-0.96047.391-11.690-11.6900.0000.0000.0000.000
84A129PHE00.0220.00743.8340.0830.0830.0000.0000.0000.000
85A130ALA00.0000.00045.665-0.021-0.0210.0000.0000.0000.000
86A131SER00.0130.01946.792-0.152-0.1520.0000.0000.0000.000
87A132THR00.0840.02642.051-0.057-0.0570.0000.0000.0000.000
88A133LYS10.9520.96942.28812.45512.4550.0000.0000.0000.000
89A134THR00.0140.01043.947-0.013-0.0130.0000.0000.0000.000
90A135LEU00.0160.00640.296-0.184-0.1840.0000.0000.0000.000
91A136ILE00.0330.02238.139-0.329-0.3290.0000.0000.0000.000
92A137VAL00.0100.01038.492-0.322-0.3220.0000.0000.0000.000
93A138VAL00.009-0.00139.638-0.164-0.1640.0000.0000.0000.000
94A139GLN00.0080.00532.9350.0170.0170.0000.0000.0000.000
95A140PHE0-0.021-0.01234.894-0.432-0.4320.0000.0000.0000.000
96A141LEU00.008-0.00135.717-0.258-0.2580.0000.0000.0000.000
97A142LEU0-0.022-0.00736.078-0.221-0.2210.0000.0000.0000.000
98A143MET00.0160.01230.007-0.520-0.5200.0000.0000.0000.000
99A144GLY00.0350.03131.337-0.580-0.5800.0000.0000.0000.000
100A145PHE0-0.016-0.00332.572-0.340-0.3400.0000.0000.0000.000
101A146ALA00.0060.00229.854-0.255-0.2550.0000.0000.0000.000
102A147GLU-1-0.784-0.86825.893-23.300-23.3000.0000.0000.0000.000
103A148THR0-0.034-0.02727.741-0.538-0.5380.0000.0000.0000.000
104A149LYS10.9110.96629.48617.48417.4840.0000.0000.0000.000
105A150ARG10.8370.88522.10623.84823.8480.0000.0000.0000.000
106A151TYR0-0.031-0.01824.370-0.632-0.6320.0000.0000.0000.000
107A152MET00.0370.00125.559-0.273-0.2730.0000.0000.0000.000
108A153ASP-1-0.941-0.95123.854-23.883-23.8830.0000.0000.0000.000
109A154PHE0-0.019-0.01317.694-0.597-0.5970.0000.0000.0000.000
110A155VAL0-0.037-0.01522.160-0.711-0.7110.0000.0000.0000.000
111A156SER0-0.069-0.03224.6510.7160.7160.0000.0000.0000.000
112A157PRO00.0620.02522.7140.6950.6950.0000.0000.0000.000
113A158GLY0-0.0200.00725.3190.1900.1900.0000.0000.0000.000
114A159SER0-0.039-0.04028.6861.0401.0400.0000.0000.0000.000
115A160GLN0-0.042-0.04328.4870.3960.3960.0000.0000.0000.000
116A161ALA00.0010.00131.7300.3730.3730.0000.0000.0000.000
117A162LYS10.8790.96430.98519.19519.1950.0000.0000.0000.000
118A163GLU-1-0.850-0.92535.794-15.280-15.2800.0000.0000.0000.000
119A164GLY0-0.014-0.00538.332-0.150-0.1500.0000.0000.0000.000
120A165SER0-0.073-0.03235.375-0.190-0.1900.0000.0000.0000.000
121A166PHE0-0.023-0.01236.888-0.306-0.3060.0000.0000.0000.000
122A167PHE00.000-0.01435.794-0.026-0.0260.0000.0000.0000.000
123A168PHE0-0.008-0.00938.837-0.058-0.0580.0000.0000.0000.000
124A169GLY00.0340.02741.5130.1300.1300.0000.0000.0000.000
125A170LEU0-0.075-0.02936.596-0.169-0.1690.0000.0000.0000.000
126A171GLU-1-0.854-0.94335.912-16.069-16.0690.0000.0000.0000.000
127A172ALA00.0330.01634.516-0.299-0.2990.0000.0000.0000.000
128A173ALA0-0.057-0.03232.171-0.459-0.4590.0000.0000.0000.000
129A174LEU0-0.047-0.02729.543-0.482-0.4820.0000.0000.0000.000
130A175GLU-1-0.900-0.95127.283-21.331-21.3310.0000.0000.0000.000
131A176GLY00.0780.06425.132-0.350-0.3500.0000.0000.0000.000
132A177LEU0-0.060-0.02821.836-1.018-1.0180.0000.0000.0000.000
133A178GLU-1-0.876-0.95816.049-35.894-35.8940.0000.0000.0000.000
134A179PRO0-0.030-0.00316.4130.9320.9320.0000.0000.0000.000
135A180GLY00.0740.03417.245-1.648-1.6480.0000.0000.0000.000
136A181TYR0-0.092-0.06514.293-1.000-1.0000.0000.0000.0000.000
137A182PRO00.0310.01720.3300.2130.2130.0000.0000.0000.000
138A183GLY00.0130.02523.7380.5520.5520.0000.0000.0000.000
139A184GLY00.1070.05725.1690.5580.5580.0000.0000.0000.000
140A185PRO0-0.035-0.04728.929-0.118-0.1180.0000.0000.0000.000
141A186LEU0-0.0110.00731.1960.4250.4250.0000.0000.0000.000
142A187LEU0-0.007-0.00226.6290.1000.1000.0000.0000.0000.000
143A188ASN0-0.027-0.01423.737-0.103-0.1030.0000.0000.0000.000
144A189PRO00.0340.02326.9890.0040.0040.0000.0000.0000.000
145A190LEU00.0090.00727.8660.2230.2230.0000.0000.0000.000
146A191GLY0-0.0040.00025.218-0.060-0.0600.0000.0000.0000.000
147A192LEU0-0.015-0.01422.4600.1830.1830.0000.0000.0000.000
148A193ALA0-0.026-0.00419.350-0.643-0.6430.0000.0000.0000.000
149A194LYS10.8640.93521.22022.35122.3510.0000.0000.0000.000
150A195ASP-1-0.810-0.90118.637-30.841-30.8410.0000.0000.0000.000
151A196VAL00.0540.01117.246-0.363-0.3630.0000.0000.0000.000
152A197GLN0-0.038-0.01315.350-3.533-3.5330.0000.0000.0000.000
153A198ASN0-0.004-0.01513.875-4.271-4.2710.0000.0000.0000.000
154A199ALA0-0.0400.00215.224-0.231-0.2310.0000.0000.0000.000
155A200HIS00.0250.0046.4014.3514.3510.0000.0000.0000.000
156A201ASP-1-0.809-0.89411.355-38.885-38.8850.0000.0000.0000.000
157A202TRP00.0420.01513.0260.1680.1680.0000.0000.0000.000
158A203LYS10.9130.96612.18340.63040.6300.0000.0000.0000.000
159A204LEU0-0.0280.0007.835-1.202-1.2020.0000.0000.0000.000
160A205LYS10.8170.87811.17835.39835.3980.0000.0000.0000.000
161A206GLU-1-0.803-0.87514.561-31.537-31.5370.0000.0000.0000.000
162A207ILE00.0320.02610.4360.8500.8500.0000.0000.0000.000
163A208LYS10.8690.9379.23350.68550.6850.0000.0000.0000.000
164A209ASN0-0.050-0.03513.3641.9901.9900.0000.0000.0000.000
165A210GLY00.0790.02116.4021.4091.4090.0000.0000.0000.000
166A211ARG10.7710.8529.08250.84950.8490.0000.0000.0000.000
167A212LEU0-0.017-0.00115.0851.0271.0270.0000.0000.0000.000
168A213ALA00.0180.00917.6011.4321.4320.0000.0000.0000.000
169A214MET00.0180.00615.2981.5761.5760.0000.0000.0000.000
170A215MET0-0.0190.00517.4571.4461.4460.0000.0000.0000.000
171A216ALA0-0.0040.00120.1391.1431.1430.0000.0000.0000.000
172A217MET0-0.0230.00422.9841.2891.2890.0000.0000.0000.000
173A218LEU00.0020.00521.4240.9540.9540.0000.0000.0000.000
174A219GLY00.0170.00524.1110.7790.7790.0000.0000.0000.000
175A220PHE0-0.002-0.02625.8780.8080.8080.0000.0000.0000.000
176A221PHE0-0.033-0.02025.3020.7390.7390.0000.0000.0000.000
177A222VAL00.0220.01926.9520.6670.6670.0000.0000.0000.000
178A223GLN00.0150.00829.0940.8100.8100.0000.0000.0000.000
179A224ALA00.0320.02831.2650.5780.5780.0000.0000.0000.000
180A225SER0-0.072-0.02832.3790.5480.5480.0000.0000.0000.000
181A226VAL0-0.033-0.02633.1520.4250.4250.0000.0000.0000.000
182A227THR0-0.037-0.03634.8330.4630.4630.0000.0000.0000.000
183A228HIS0-0.036-0.00236.9690.5640.5640.0000.0000.0000.000
184A229THR0-0.0160.01236.3900.4630.4630.0000.0000.0000.000
185A230GLY0-0.012-0.01735.365-0.360-0.3600.0000.0000.0000.000
186A231PRO00.013-0.00230.3500.0620.0620.0000.0000.0000.000
187A232ILE0-0.029-0.01231.905-0.252-0.2520.0000.0000.0000.000
188A233ASP-1-0.771-0.87934.222-15.963-15.9630.0000.0000.0000.000
189A234ASN00.0310.00233.091-0.114-0.1140.0000.0000.0000.000
190A235LEU0-0.0270.00629.802-0.226-0.2260.0000.0000.0000.000
191A236VAL00.001-0.01133.088-0.035-0.0350.0000.0000.0000.000
192A237GLU-1-0.891-0.94336.420-16.234-16.2340.0000.0000.0000.000
193A238HIS0-0.066-0.04430.428-0.314-0.3140.0000.0000.0000.000
194A239LEU0-0.026-0.04130.9190.0030.0030.0000.0000.0000.000
195A240SER0-0.0540.00034.6880.3750.3750.0000.0000.0000.000
196A241ASN0-0.040-0.03337.2810.3710.3710.0000.0000.0000.000
197A242PRO00.0560.03632.296-0.011-0.0110.0000.0000.0000.000
198A243TRP0-0.031-0.02530.732-0.442-0.4420.0000.0000.0000.000
199A244HIS0-0.020-0.00935.286-0.001-0.0010.0000.0000.0000.000
200A245LYS10.9150.98035.95416.11816.1180.0000.0000.0000.000
201A246THR00.0340.01831.140-0.521-0.5210.0000.0000.0000.000
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