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: ZNGLN

Calculation Name: 2F6E-A-Xray540

Preferred Name: Toxin A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F6E

Chain ID: A

ChEMBL ID: CHEMBL3580504

UniProt ID: P16154

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1010644.768797
FMO2-HF: Nuclear repulsion 962265.848916
FMO2-HF: Total energy -48378.919881
FMO2-MP2: Total energy -48521.020826


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:2:TYR)


Summations of interaction energy for fragment #1(A:2:TYR)
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.
1.7883.645-0.011-0.922-0.9250.001
Interaction energy analysis for fragmet #1(A:2:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.178 / q_NPA : 0.023
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].
4A3TYR0-0.0840.0763.730-0.1890.2310.007-0.194-0.2340.000
5A4PHE00.155-0.0753.871-0.1281.120-0.013-0.702-0.5330.001
6A4PHE0-0.0630.1016.442-0.008-0.0080.0000.0000.0000.000
7A5GLU00.024-0.0987.1290.0520.0520.0000.0000.0000.000
8A5GLU-1-0.857-0.7718.4500.0620.0620.0000.0000.0000.000
9A6PRO00.023-0.11310.6650.0340.0340.0000.0000.0000.000
10A7ASN00.0420.03713.3500.1100.1100.0000.0000.0000.000
11A7ASN0-0.0460.11114.138-0.055-0.0550.0000.0000.0000.000
12A8THR00.064-0.08916.0940.0100.0100.0000.0000.0000.000
13A8THR0-0.0320.05917.497-0.020-0.0200.0000.0000.0000.000
14A9ALA00.129-0.07018.6660.0070.0070.0000.0000.0000.000
15A9ALA0-0.0690.11320.8410.0070.0070.0000.0000.0000.000
16A10ILE00.027-0.12121.590-0.027-0.0270.0000.0000.0000.000
17A10ILE0-0.0390.12924.9010.0010.0010.0000.0000.0000.000
18A11GLY00.024-0.09623.9240.0250.0250.0000.0000.0000.000
19A12ALA00.0940.00222.841-0.034-0.0340.0000.0000.0000.000
20A12ALA0-0.0630.12924.7680.0040.0040.0000.0000.0000.000
21A13ASN00.062-0.12120.7160.0190.0190.0000.0000.0000.000
22A13ASN0-0.1040.06919.4160.0070.0070.0000.0000.0000.000
23A14GLY00.015-0.08516.327-0.018-0.0180.0000.0000.0000.000
24A15TYR00.1680.02213.6180.0540.0540.0000.0000.0000.000
25A15TYR0-0.1380.07012.305-0.046-0.0460.0000.0000.0000.000
26A16LYS0-0.032-0.13715.087-0.008-0.0080.0000.0000.0000.000
27A16LYS10.7611.00518.5590.3250.3250.0000.0000.0000.000
28A17ILE00.112-0.09717.625-0.027-0.0270.0000.0000.0000.000
29A17ILE0-0.0770.11415.596-0.003-0.0030.0000.0000.0000.000
30A18ILE00.056-0.11519.2540.0230.0230.0000.0000.0000.000
31A18ILE0-0.0810.09921.7630.0060.0060.0000.0000.0000.000
32A19ASP00.075-0.07922.950-0.012-0.0120.0000.0000.0000.000
33A19ASP-1-0.889-0.79726.027-0.271-0.2710.0000.0000.0000.000
34A20ASN00.045-0.07021.6190.0010.0010.0000.0000.0000.000
35A20ASN0-0.1200.04122.822-0.013-0.0130.0000.0000.0000.000
36A21LYS00.143-0.09120.036-0.034-0.0340.0000.0000.0000.000
37A21LYS10.7591.00021.3240.3140.3140.0000.0000.0000.000
38A22ASN00.077-0.05516.0330.0410.0410.0000.0000.0000.000
39A22ASN0-0.0750.04414.1920.0470.0470.0000.0000.0000.000
40A23PHE00.091-0.08817.4200.0100.0100.0000.0000.0000.000
41A23PHE0-0.0700.08919.7050.0120.0120.0000.0000.0000.000
42A24TYR00.142-0.06116.224-0.054-0.0540.0000.0000.0000.000
43A24TYR0-0.0870.09213.0960.0350.0350.0000.0000.0000.000
44A25PHE00.036-0.12717.3120.0290.0290.0000.0000.0000.000
45A25PHE0-0.0990.10619.8110.0030.0030.0000.0000.0000.000
46A26ARG00.116-0.10119.017-0.007-0.0070.0000.0000.0000.000
47A26ARG10.8271.06416.1310.1100.1100.0000.0000.0000.000
48A27ASN00.014-0.08921.207-0.004-0.0040.0000.0000.0000.000
49A27ASN0-0.0790.07623.7940.0040.0040.0000.0000.0000.000
50A28GLY00.070-0.07324.0320.0080.0080.0000.0000.0000.000
51A29LEU00.027-0.03024.493-0.012-0.0120.0000.0000.0000.000
52A29LEU0-0.0460.12025.4910.0020.0020.0000.0000.0000.000
53A30PRO00.055-0.07021.887-0.005-0.0050.0000.0000.0000.000
54A31GLN00.043-0.01119.6420.0340.0340.0000.0000.0000.000
55A31GLN0-0.1060.08018.8120.0210.0210.0000.0000.0000.000
56A32ILE00.147-0.07519.269-0.050-0.0500.0000.0000.0000.000
57A32ILE0-0.1210.10620.8530.0040.0040.0000.0000.0000.000
58A33GLY0-0.066-0.14817.2000.0470.0470.0000.0000.0000.000
59A34VAL00.070-0.01313.368-0.059-0.0590.0000.0000.0000.000
60A34VAL0-0.0620.12911.215-0.006-0.0060.0000.0000.0000.000
61A35PHE00.073-0.09711.3430.1070.1070.0000.0000.0000.000
62A35PHE0-0.0890.08612.5970.0210.0210.0000.0000.0000.000
63A36LYS00.088-0.1167.946-0.162-0.1620.0000.0000.0000.000
64A36LYS10.7731.0235.433-0.125-0.1250.0000.0000.0000.000
65A37GLY00.026-0.0757.9980.3270.3270.0000.0000.0000.000
66A38PRO0-0.028-0.0127.191-0.635-0.6350.0000.0000.0000.000
67A39ASN00.0410.0486.714-0.683-0.6830.0000.0000.0000.000
68A39ASN0-0.1120.0568.559-0.033-0.0330.0000.0000.0000.000
69A40GLY00.093-0.0964.492-0.175-0.127-0.001-0.020-0.0270.000
70A41PHE00.041-0.0075.5310.4260.467-0.0020.000-0.0390.000
71A41PHE0-0.0230.1144.910-0.263-0.2630.0000.0000.0000.000
72A42GLU00.046-0.0967.973-0.061-0.0610.0000.0000.0000.000
73A42GLU-1-0.814-0.77110.560-1.036-1.0360.0000.0000.0000.000
74A43TYR00.124-0.08111.4830.0840.0840.0000.0000.0000.000
75A43TYR0-0.0830.08314.9340.0190.0190.0000.0000.0000.000
76A44PHE00.055-0.09114.867-0.021-0.0210.0000.0000.0000.000
77A44PHE0-0.1470.08612.655-0.010-0.0100.0000.0000.0000.000
78A45ALA00.132-0.09417.3530.0480.0480.0000.0000.0000.000
79A45ALA0-0.0380.10819.558-0.003-0.0030.0000.0000.0000.000
80A46PRO00.048-0.09720.4430.0060.0060.0000.0000.0000.000
81A47ALA00.1440.04824.173-0.028-0.0280.0000.0000.0000.000
82A47ALA0-0.0680.10627.5280.0030.0030.0000.0000.0000.000
83A48ASN0-0.086-0.11626.5030.0090.0090.0000.0000.0000.000
84A48ASN0-0.0900.06028.8960.0000.0000.0000.0000.0000.000
85A49THR00.091-0.05923.3230.0150.0150.0000.0000.0000.000
86A49THR0-0.0990.01921.7570.0010.0010.0000.0000.0000.000
87A50ASP00.088-0.09922.7920.0050.0050.0000.0000.0000.000
88A50ASP-1-0.879-0.80222.152-0.341-0.3410.0000.0000.0000.000
89A51ALA00.014-0.08224.1670.0050.0050.0000.0000.0000.000
90A51ALA0-0.0790.09524.812-0.004-0.0040.0000.0000.0000.000
91A52ASN00.045-0.06226.476-0.008-0.0080.0000.0000.0000.000
92A52ASN0-0.1220.04529.5060.0020.0020.0000.0000.0000.000
93A53ASN00.133-0.06323.7400.0100.0100.0000.0000.0000.000
94A53ASN0-0.0990.02823.072-0.001-0.0010.0000.0000.0000.000
95A54ILE00.108-0.05824.8170.0200.0200.0000.0000.0000.000
96A54ILE0-0.0790.08624.7590.0010.0010.0000.0000.0000.000
97A55GLU00.084-0.11423.778-0.030-0.0300.0000.0000.0000.000
98A55GLU-1-0.896-0.81625.568-0.167-0.1670.0000.0000.0000.000
99A56GLY0-0.029-0.11020.6440.0030.0030.0000.0000.0000.000
100A57GLN00.1500.00419.715-0.036-0.0360.0000.0000.0000.000
101A57GLN0-0.1280.08220.4990.0360.0360.0000.0000.0000.000
102A58ALA00.086-0.11016.2770.0360.0360.0000.0000.0000.000
103A58ALA0-0.0930.11815.518-0.020-0.0200.0000.0000.0000.000
104A59ILE0-0.072-0.12816.9850.0210.0210.0000.0000.0000.000
105A59ILE0-0.0790.10818.0490.0070.0070.0000.0000.0000.000
106A60ARG00.213-0.07316.580-0.084-0.0840.0000.0000.0000.000
107A60ARG10.6690.97918.4290.3800.3800.0000.0000.0000.000
108A61TYR00.084-0.10016.6300.0630.0630.0000.0000.0000.000
109A61TYR0-0.1650.05316.2930.0110.0110.0000.0000.0000.000
110A62GLN00.071-0.11215.848-0.069-0.0690.0000.0000.0000.000
111A62GLN0-0.1000.07817.0060.0480.0480.0000.0000.0000.000
112A63ASN00.050-0.03516.2710.0480.0480.0000.0000.0000.000
113A63ASN0-0.0860.05916.935-0.024-0.0240.0000.0000.0000.000
114A64ARG00.103-0.09417.4730.0520.0520.0000.0000.0000.000
115A64ARG10.9001.07019.1480.2620.2620.0000.0000.0000.000
116A65PHE00.131-0.08417.034-0.055-0.0550.0000.0000.0000.000
117A65PHE0-0.0460.11018.298-0.004-0.0040.0000.0000.0000.000
118A66LEU00.067-0.10417.823-0.014-0.0140.0000.0000.0000.000
119A66LEU0-0.0780.11416.417-0.008-0.0080.0000.0000.0000.000
120A67HIS00.091-0.09018.5820.0150.0150.0000.0000.0000.000
121A67HIS0-0.0730.10521.2110.0090.0090.0000.0000.0000.000
122A68LEU00.091-0.10119.695-0.006-0.0060.0000.0000.0000.000
123A68LEU0-0.0880.11217.918-0.005-0.0050.0000.0000.0000.000
124A69LEU0-0.019-0.11719.7880.0140.0140.0000.0000.0000.000
125A69LEU0-0.0410.10820.2540.0000.0000.0000.0000.0000.000
126A70GLY00.062-0.09721.9120.0200.0200.0000.0000.0000.000
127A71ASN00.0780.03217.5200.0260.0260.0000.0000.0000.000
128A71ASN0-0.1070.06016.5490.0350.0350.0000.0000.0000.000
129A72ILE00.104-0.08617.421-0.045-0.0450.0000.0000.0000.000
130A72ILE0-0.0610.11217.841-0.001-0.0010.0000.0000.0000.000
131A73TYR00.028-0.10614.3300.0680.0680.0000.0000.0000.000
132A73TYR0-0.0300.09312.391-0.023-0.0230.0000.0000.0000.000
133A74TYR00.111-0.07113.4640.0260.0260.0000.0000.0000.000
134A74TYR0-0.0500.09613.906-0.004-0.0040.0000.0000.0000.000
135A75PHE00.036-0.11512.296-0.068-0.0680.0000.0000.0000.000
136A75PHE0-0.0610.13312.2490.0210.0210.0000.0000.0000.000
137A76GLY00.063-0.06711.7070.0950.0950.0000.0000.0000.000
138A77ASN00.1190.02612.9960.0010.0010.0000.0000.0000.000
139A77ASN0-0.0910.07215.934-0.012-0.0120.0000.0000.0000.000
140A78ASN00.067-0.08411.7680.1090.1090.0000.0000.0000.000
141A78ASN0-0.0350.0868.9630.1440.1440.0000.0000.0000.000
142A79SER00.048-0.06712.610-0.112-0.1120.0000.0000.0000.000
143A79SER0-0.0510.07314.2740.0580.0580.0000.0000.0000.000
144A80LYS00.024-0.1248.7740.1210.1210.0000.0000.0000.000
145A80LYS10.7271.0047.8441.2491.2490.0000.0000.0000.000
146A81ALA00.082-0.0789.4320.0460.0460.0000.0000.0000.000
147A81ALA0-0.0420.1049.2510.0390.0390.0000.0000.0000.000
148A82VAL00.027-0.1207.711-0.436-0.4360.0000.0000.0000.000
149A82VAL0-0.1060.09010.1790.0140.0140.0000.0000.0000.000
150A83THR00.016-0.0976.1710.0390.0390.0000.0000.0000.000
151A83THR0-0.0510.0815.2060.1690.1690.0000.0000.0000.000
152A84GLY00.057-0.0677.541-0.083-0.0830.0000.0000.0000.000
153A85TRP00.0800.0098.687-0.152-0.1520.0000.0000.0000.000
154A85TRP0-0.0920.07712.064-0.064-0.0640.0000.0000.0000.000
155A86GLN00.021-0.10611.594-0.043-0.0430.0000.0000.0000.000
156A86GLN0-0.0730.0829.494-0.072-0.0720.0000.0000.0000.000
157A87THR00.004-0.10213.7740.0440.0440.0000.0000.0000.000
158A87THR0-0.0100.08516.8460.0090.0090.0000.0000.0000.000
159A88ILE00.029-0.10017.450-0.043-0.0430.0000.0000.0000.000
160A88ILE0-0.0650.10115.684-0.002-0.0020.0000.0000.0000.000
161A89ASN00.036-0.07919.3900.0230.0230.0000.0000.0000.000
162A89ASN0-0.0930.06223.087-0.015-0.0150.0000.0000.0000.000
163A90GLY00.045-0.09722.1340.0080.0080.0000.0000.0000.000
164A91ASN00.1090.02222.1510.0190.0190.0000.0000.0000.000
165A91ASN0-0.0960.08721.8480.0080.0080.0000.0000.0000.000
166A92MET00.130-0.09518.476-0.034-0.0340.0000.0000.0000.000
167A92MET0-0.0140.16817.4760.0080.0080.0000.0000.0000.000
168A93TYR00.042-0.08916.4080.0090.0090.0000.0000.0000.000
169A93TYR0-0.0670.08815.773-0.023-0.0230.0000.0000.0000.000
170A94TYR00.151-0.08912.957-0.011-0.0110.0000.0000.0000.000
171A94TYR0-0.0500.11210.4940.0550.0550.0000.0000.0000.000
172A95PHE00.040-0.08211.2060.0000.0000.0000.0000.0000.000
173A95PHE0-0.1380.09210.441-0.063-0.0630.0000.0000.0000.000
174A96MET00.163-0.1139.2930.1940.1940.0000.0000.0000.000
175A96MET0-0.0820.14710.7830.0080.0080.0000.0000.0000.000
176A97PRO00.004-0.1344.891-0.166-0.1660.0000.0000.0000.000
177A98ASP00.038-0.0084.8020.6340.734-0.002-0.006-0.0920.000
178A98ASP-1-0.862-0.7928.2930.9740.9740.0000.0000.0000.000
179A99THR0-0.083-0.1647.142-0.301-0.3010.0000.0000.0000.000
180A99THR0-0.0410.06310.447-0.072-0.0720.0000.0000.0000.000
181A100ALA00.062-0.0598.270-0.151-0.1510.0000.0000.0000.000
182A100ALA0-0.0290.1038.203-0.085-0.0850.0000.0000.0000.000
183A101MET00.088-0.1149.453-0.132-0.1320.0000.0000.0000.000
184A101MET0-0.1120.10012.7440.0150.0150.0000.0000.0000.000
185A102ALA00.074-0.09412.7910.1280.1280.0000.0000.0000.000
186A102ALA0-0.0590.09216.129-0.014-0.0140.0000.0000.0000.000
187A103ALA00.075-0.10315.108-0.003-0.0030.0000.0000.0000.000
188A103ALA0-0.0880.11415.5120.0130.0130.0000.0000.0000.000
189A104ALA00.054-0.14416.663-0.028-0.0280.0000.0000.0000.000
190A104ALA0-0.0680.12019.372-0.008-0.0080.0000.0000.0000.000
191A105GLY0-0.077-0.13020.2160.0120.0120.0000.0000.0000.000
192A106GLY00.0190.00223.256-0.004-0.0040.0000.0000.0000.000
193A107LEU00.062-0.02122.938-0.001-0.0010.0000.0000.0000.000
194A107LEU0-0.0690.09924.168-0.003-0.0030.0000.0000.0000.000
195A108PHE00.015-0.09718.804-0.003-0.0030.0000.0000.0000.000
196A108PHE0-0.0780.08517.2220.0120.0120.0000.0000.0000.000
197A109GLU00.128-0.10419.327-0.028-0.0280.0000.0000.0000.000
198A109GLU-1-0.991-0.83519.2230.4720.4720.0000.0000.0000.000
199A110ILE00.017-0.12615.3980.0730.0730.0000.0000.0000.000
200A110ILE0-0.1110.08613.454-0.014-0.0140.0000.0000.0000.000
201A111ASP00.036-0.09414.589-0.074-0.0740.0000.0000.0000.000
202A111ASP-1-0.952-0.84712.6721.0331.0330.0000.0000.0000.000
203A112GLY00.041-0.10415.502-0.043-0.0430.0000.0000.0000.000
204A113VAL00.055-0.01118.825-0.053-0.0530.0000.0000.0000.000
205A113VAL0-0.0920.09719.564-0.006-0.0060.0000.0000.0000.000
206A114ILE00.104-0.09219.6800.0450.0450.0000.0000.0000.000
207A114ILE0-0.0590.11322.756-0.007-0.0070.0000.0000.0000.000
208A115TYR0-0.002-0.12020.729-0.031-0.0310.0000.0000.0000.000
209A115TYR0-0.0480.09418.021-0.031-0.0310.0000.0000.0000.000
210A116PHE00.121-0.06921.9780.0180.0180.0000.0000.0000.000
211A116PHE0-0.0730.08424.923-0.005-0.0050.0000.0000.0000.000
212A117PHE00.027-0.12220.552-0.010-0.0100.0000.0000.0000.000
213A117PHE0-0.0880.12416.8130.0180.0180.0000.0000.0000.000
214A118GLY00.060-0.07421.939-0.003-0.0030.0000.0000.0000.000
215A119VAL00.059-0.01822.7630.0170.0170.0000.0000.0000.000
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