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: RYKM8

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 OptH
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 -1010205.088987
FMO2-HF: Nuclear repulsion 961827.089156
FMO2-HF: Total energy -48377.999832
FMO2-MP2: Total energy -48520.107264


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.
1.0743.044-0.02-1.007-0.9420
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 : 0.188 / q_NPA : 0.010
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].
4A3TYR0-0.0590.1033.966-0.0410.3450.004-0.158-0.2310.000
5A4PHE00.141-0.1083.814-0.2831.200-0.019-0.841-0.6240.000
6A4PHE0-0.0620.1226.432-0.011-0.0110.0000.0000.0000.000
7A5GLU00.024-0.1307.048-0.033-0.0330.0000.0000.0000.000
8A5GLU-1-0.962-0.8249.0770.1800.1800.0000.0000.0000.000
9A6PRO00.006-0.11110.4980.0310.0310.0000.0000.0000.000
10A7ASN00.0760.02613.1860.1120.1120.0000.0000.0000.000
11A7ASN0-0.0930.10314.538-0.047-0.0470.0000.0000.0000.000
12A8THR00.052-0.07616.1170.0040.0040.0000.0000.0000.000
13A8THR0-0.0410.05517.296-0.022-0.0220.0000.0000.0000.000
14A9ALA00.141-0.08318.5460.0050.0050.0000.0000.0000.000
15A9ALA0-0.0600.11920.8860.0070.0070.0000.0000.0000.000
16A10ILE00.009-0.12621.428-0.029-0.0290.0000.0000.0000.000
17A10ILE0-0.0250.12024.8180.0010.0010.0000.0000.0000.000
18A11GLY00.014-0.08624.1100.0220.0220.0000.0000.0000.000
19A12ALA00.083-0.02022.668-0.034-0.0340.0000.0000.0000.000
20A12ALA0-0.0640.13124.3400.0030.0030.0000.0000.0000.000
21A13ASN00.073-0.10720.5130.0240.0240.0000.0000.0000.000
22A13ASN0-0.0980.06518.8100.0190.0190.0000.0000.0000.000
23A14GLY0-0.007-0.10016.364-0.024-0.0240.0000.0000.0000.000
24A15TYR00.1630.02013.7020.0520.0520.0000.0000.0000.000
25A15TYR0-0.1240.07812.714-0.030-0.0300.0000.0000.0000.000
26A16LYS0-0.010-0.13815.150-0.024-0.0240.0000.0000.0000.000
27A16LYS10.8211.06618.7910.3390.3390.0000.0000.0000.000
28A17ILE00.123-0.09118.044-0.004-0.0040.0000.0000.0000.000
29A17ILE0-0.0800.10815.685-0.003-0.0030.0000.0000.0000.000
30A18ILE00.049-0.12019.1350.0250.0250.0000.0000.0000.000
31A18ILE0-0.0770.09821.9140.0070.0070.0000.0000.0000.000
32A19ASP00.065-0.07922.770-0.013-0.0130.0000.0000.0000.000
33A19ASP-1-0.910-0.82025.517-0.263-0.2630.0000.0000.0000.000
34A20ASN00.022-0.08421.2010.0070.0070.0000.0000.0000.000
35A20ASN0-0.0970.06222.155-0.019-0.0190.0000.0000.0000.000
36A21LYS00.132-0.10220.035-0.035-0.0350.0000.0000.0000.000
37A21LYS10.7751.02021.2640.3070.3070.0000.0000.0000.000
38A22ASN00.069-0.06916.2200.0260.0260.0000.0000.0000.000
39A22ASN0-0.1020.04614.6000.0310.0310.0000.0000.0000.000
40A23PHE00.101-0.07417.6640.0080.0080.0000.0000.0000.000
41A23PHE0-0.0660.08820.1150.0090.0090.0000.0000.0000.000
42A24TYR00.141-0.08216.472-0.048-0.0480.0000.0000.0000.000
43A24TYR0-0.0960.10513.1740.0330.0330.0000.0000.0000.000
44A25PHE00.064-0.11917.4880.0360.0360.0000.0000.0000.000
45A25PHE0-0.1200.10320.0260.0020.0020.0000.0000.0000.000
46A26ARG00.149-0.08719.072-0.004-0.0040.0000.0000.0000.000
47A26ARG10.8791.08915.9250.0330.0330.0000.0000.0000.000
48A27ASN00.016-0.10121.110-0.002-0.0020.0000.0000.0000.000
49A27ASN0-0.0740.07924.5880.0100.0100.0000.0000.0000.000
50A28GLY00.051-0.07023.7350.0040.0040.0000.0000.0000.000
51A29LEU00.023-0.04424.281-0.013-0.0130.0000.0000.0000.000
52A29LEU0-0.0510.12325.4000.0020.0020.0000.0000.0000.000
53A30PRO00.030-0.07721.879-0.003-0.0030.0000.0000.0000.000
54A31GLN00.061-0.01820.0580.0240.0240.0000.0000.0000.000
55A31GLN0-0.1340.07919.1180.0190.0190.0000.0000.0000.000
56A32ILE00.102-0.08519.736-0.046-0.0460.0000.0000.0000.000
57A32ILE0-0.1070.11220.5990.0040.0040.0000.0000.0000.000
58A33GLY0-0.061-0.14917.2360.0480.0480.0000.0000.0000.000
59A34VAL00.079-0.00513.505-0.068-0.0680.0000.0000.0000.000
60A34VAL0-0.0660.12011.373-0.006-0.0060.0000.0000.0000.000
61A35PHE00.060-0.11611.5540.1110.1110.0000.0000.0000.000
62A35PHE0-0.0770.10212.6540.0250.0250.0000.0000.0000.000
63A36LYS00.099-0.1208.072-0.144-0.1440.0000.0000.0000.000
64A36LYS10.8061.0864.696-0.872-0.830-0.001-0.004-0.0360.000
65A37GLY00.040-0.0638.1720.2490.2490.0000.0000.0000.000
66A38PRO0-0.010-0.0147.109-0.658-0.6580.0000.0000.0000.000
67A39ASN00.0240.0296.315-0.770-0.7700.0000.0000.0000.000
68A39ASN0-0.1150.0628.092-0.148-0.1480.0000.0000.0000.000
69A40GLY00.108-0.0914.935-0.115-0.085-0.002-0.005-0.0240.000
70A41PHE00.036-0.0125.9250.3140.343-0.0020.001-0.0270.000
71A41PHE0-0.0200.1125.358-0.195-0.1950.0000.0000.0000.000
72A42GLU00.058-0.1008.366-0.032-0.0320.0000.0000.0000.000
73A42GLU-1-0.847-0.77810.431-1.050-1.0500.0000.0000.0000.000
74A43TYR00.127-0.08611.7850.0860.0860.0000.0000.0000.000
75A43TYR0-0.0790.09015.2110.0180.0180.0000.0000.0000.000
76A44PHE00.077-0.08515.195-0.018-0.0180.0000.0000.0000.000
77A44PHE0-0.1560.09012.839-0.014-0.0140.0000.0000.0000.000
78A45ALA00.117-0.10517.5630.0520.0520.0000.0000.0000.000
79A45ALA0-0.0410.10619.573-0.003-0.0030.0000.0000.0000.000
80A46PRO00.051-0.09220.5890.0020.0020.0000.0000.0000.000
81A47ALA00.1500.03224.306-0.025-0.0250.0000.0000.0000.000
82A47ALA0-0.0750.11027.6810.0030.0030.0000.0000.0000.000
83A48ASN0-0.096-0.11026.6290.0080.0080.0000.0000.0000.000
84A48ASN0-0.0730.06029.170-0.007-0.0070.0000.0000.0000.000
85A49THR00.110-0.05723.6280.0170.0170.0000.0000.0000.000
86A49THR0-0.1060.02122.1530.0020.0020.0000.0000.0000.000
87A50ASP00.076-0.12923.1160.0110.0110.0000.0000.0000.000
88A50ASP-1-0.969-0.84622.483-0.321-0.3210.0000.0000.0000.000
89A51ALA00.006-0.10424.496-0.003-0.0030.0000.0000.0000.000
90A51ALA0-0.0640.10225.479-0.003-0.0030.0000.0000.0000.000
91A52ASN00.003-0.06727.056-0.010-0.0100.0000.0000.0000.000
92A52ASN0-0.1270.04429.6420.0080.0080.0000.0000.0000.000
93A53ASN00.168-0.05923.9060.0070.0070.0000.0000.0000.000
94A53ASN0-0.0870.05423.232-0.001-0.0010.0000.0000.0000.000
95A54ILE00.113-0.05825.1000.0200.0200.0000.0000.0000.000
96A54ILE0-0.0850.08224.6860.0010.0010.0000.0000.0000.000
97A55GLU00.083-0.12624.025-0.028-0.0280.0000.0000.0000.000
98A55GLU-1-0.896-0.80125.652-0.145-0.1450.0000.0000.0000.000
99A56GLY0-0.020-0.10520.9210.0040.0040.0000.0000.0000.000
100A57GLN00.1670.00819.763-0.036-0.0360.0000.0000.0000.000
101A57GLN0-0.1150.10020.8790.0300.0300.0000.0000.0000.000
102A58ALA00.038-0.12816.1960.0460.0460.0000.0000.0000.000
103A58ALA0-0.0710.11815.388-0.021-0.0210.0000.0000.0000.000
104A59ILE0-0.073-0.13517.328-0.004-0.0040.0000.0000.0000.000
105A59ILE0-0.0900.10518.1120.0080.0080.0000.0000.0000.000
106A60ARG00.176-0.10216.751-0.078-0.0780.0000.0000.0000.000
107A60ARG10.7541.05018.5490.3700.3700.0000.0000.0000.000
108A61TYR00.090-0.11117.1210.0600.0600.0000.0000.0000.000
109A61TYR0-0.1440.06016.5680.0080.0080.0000.0000.0000.000
110A62GLN00.038-0.11116.269-0.055-0.0550.0000.0000.0000.000
111A62GLN0-0.1100.07417.1300.0440.0440.0000.0000.0000.000
112A63ASN00.084-0.04716.5500.0430.0430.0000.0000.0000.000
113A63ASN0-0.0850.06817.142-0.026-0.0260.0000.0000.0000.000
114A64ARG00.103-0.12417.4680.0500.0500.0000.0000.0000.000
115A64ARG10.9151.10619.0410.2220.2220.0000.0000.0000.000
116A65PHE00.110-0.08517.373-0.045-0.0450.0000.0000.0000.000
117A65PHE0-0.0420.11818.348-0.005-0.0050.0000.0000.0000.000
118A66LEU00.056-0.11118.135-0.013-0.0130.0000.0000.0000.000
119A66LEU0-0.0900.11716.558-0.008-0.0080.0000.0000.0000.000
120A67HIS00.109-0.09618.7780.0190.0190.0000.0000.0000.000
121A67HIS0-0.0760.11522.5120.0090.0090.0000.0000.0000.000
122A68LEU00.096-0.11419.810-0.014-0.0140.0000.0000.0000.000
123A68LEU0-0.0890.11718.062-0.005-0.0050.0000.0000.0000.000
124A69LEU0-0.034-0.12419.8990.0170.0170.0000.0000.0000.000
125A69LEU0-0.0540.11320.0800.0000.0000.0000.0000.0000.000
126A70GLY00.045-0.09921.8660.0200.0200.0000.0000.0000.000
127A71ASN00.0930.03617.7490.0270.0270.0000.0000.0000.000
128A71ASN0-0.0840.07916.8190.0330.0330.0000.0000.0000.000
129A72ILE00.091-0.09417.653-0.044-0.0440.0000.0000.0000.000
130A72ILE0-0.0440.10818.054-0.001-0.0010.0000.0000.0000.000
131A73TYR00.068-0.08814.5990.0730.0730.0000.0000.0000.000
132A73TYR0-0.0460.09112.615-0.029-0.0290.0000.0000.0000.000
133A74TYR00.115-0.08713.7190.0100.0100.0000.0000.0000.000
134A74TYR0-0.0460.10914.163-0.008-0.0080.0000.0000.0000.000
135A75PHE00.041-0.11112.756-0.054-0.0540.0000.0000.0000.000
136A75PHE0-0.0800.12812.4150.0260.0260.0000.0000.0000.000
137A76GLY00.076-0.06512.2510.0850.0850.0000.0000.0000.000
138A77ASN00.1160.01113.594-0.001-0.0010.0000.0000.0000.000
139A77ASN0-0.0860.08415.861-0.015-0.0150.0000.0000.0000.000
140A78ASN00.046-0.09011.9070.0960.0960.0000.0000.0000.000
141A78ASN0-0.0300.0988.9560.1410.1410.0000.0000.0000.000
142A79SER00.030-0.07212.722-0.122-0.1220.0000.0000.0000.000
143A79SER0-0.0200.08314.4480.0520.0520.0000.0000.0000.000
144A80LYS00.052-0.1179.0050.1310.1310.0000.0000.0000.000
145A80LYS10.7821.0428.1851.2621.2620.0000.0000.0000.000
146A81ALA00.050-0.0969.7430.0230.0230.0000.0000.0000.000
147A81ALA0-0.0400.1079.5380.0370.0370.0000.0000.0000.000
148A82VAL00.032-0.1158.040-0.358-0.3580.0000.0000.0000.000
149A82VAL0-0.1060.09210.5440.0080.0080.0000.0000.0000.000
150A83THR00.003-0.1086.9570.0100.0100.0000.0000.0000.000
151A83THR0-0.0360.0805.6280.3670.3670.0000.0000.0000.000
152A84GLY00.035-0.0798.282-0.089-0.0890.0000.0000.0000.000
153A85TRP00.0860.0129.643-0.148-0.1480.0000.0000.0000.000
154A85TRP0-0.0580.09012.871-0.043-0.0430.0000.0000.0000.000
155A86GLN00.002-0.12312.317-0.041-0.0410.0000.0000.0000.000
156A86GLN0-0.0580.09910.146-0.088-0.0880.0000.0000.0000.000
157A87THR00.030-0.08014.5150.0370.0370.0000.0000.0000.000
158A87THR0-0.0210.07817.7390.0090.0090.0000.0000.0000.000
159A88ILE00.063-0.10018.167-0.042-0.0420.0000.0000.0000.000
160A88ILE0-0.0750.10515.994-0.004-0.0040.0000.0000.0000.000
161A89ASN00.037-0.09319.9150.0200.0200.0000.0000.0000.000
162A89ASN0-0.1050.07023.931-0.011-0.0110.0000.0000.0000.000
163A90GLY00.032-0.10422.7120.0090.0090.0000.0000.0000.000
164A91ASN00.0790.01822.5360.0170.0170.0000.0000.0000.000
165A91ASN0-0.0680.09122.3420.0080.0080.0000.0000.0000.000
166A92MET00.105-0.08918.842-0.032-0.0320.0000.0000.0000.000
167A92MET0-0.0740.11017.4710.0080.0080.0000.0000.0000.000
168A93TYR00.074-0.09116.8980.0090.0090.0000.0000.0000.000
169A93TYR0-0.0440.09516.166-0.022-0.0220.0000.0000.0000.000
170A94TYR00.141-0.08013.699-0.019-0.0190.0000.0000.0000.000
171A94TYR0-0.0470.11310.7560.0480.0480.0000.0000.0000.000
172A95PHE00.055-0.08311.7020.0130.0130.0000.0000.0000.000
173A95PHE0-0.1430.08711.059-0.062-0.0620.0000.0000.0000.000
174A96MET00.158-0.10610.0640.2210.2210.0000.0000.0000.000
175A96MET0-0.0860.14111.2910.0050.0050.0000.0000.0000.000
176A97PRO00.030-0.1095.602-0.139-0.1390.0000.0000.0000.000
177A98ASP00.021-0.0205.5930.4510.4510.0000.0000.0000.000
178A98ASP-1-0.909-0.8168.2181.1641.1640.0000.0000.0000.000
179A99THR0-0.028-0.1637.482-0.251-0.2510.0000.0000.0000.000
180A99THR0-0.0110.09511.106-0.063-0.0630.0000.0000.0000.000
181A100ALA00.064-0.0678.939-0.155-0.1550.0000.0000.0000.000
182A100ALA0-0.0420.0988.524-0.076-0.0760.0000.0000.0000.000
183A101MET00.040-0.1229.828-0.153-0.1530.0000.0000.0000.000
184A101MET0-0.1030.10013.2020.0060.0060.0000.0000.0000.000
185A102ALA00.104-0.10013.3120.1300.1300.0000.0000.0000.000
186A102ALA0-0.0740.10416.341-0.015-0.0150.0000.0000.0000.000
187A103ALA00.063-0.12915.523-0.015-0.0150.0000.0000.0000.000
188A103ALA0-0.0790.13116.0890.0110.0110.0000.0000.0000.000
189A104ALA00.052-0.14817.130-0.026-0.0260.0000.0000.0000.000
190A104ALA0-0.0690.13119.960-0.008-0.0080.0000.0000.0000.000
191A105GLY0-0.092-0.12920.6920.0080.0080.0000.0000.0000.000
192A106GLY00.0250.00423.521-0.001-0.0010.0000.0000.0000.000
193A107LEU00.048-0.03023.166-0.002-0.0020.0000.0000.0000.000
194A107LEU0-0.0680.10624.466-0.004-0.0040.0000.0000.0000.000
195A108PHE00.042-0.08119.020-0.002-0.0020.0000.0000.0000.000
196A108PHE0-0.0810.08017.2790.0130.0130.0000.0000.0000.000
197A109GLU00.154-0.11019.477-0.031-0.0310.0000.0000.0000.000
198A109GLU-1-1.000-0.82719.7730.4610.4610.0000.0000.0000.000
199A110ILE00.044-0.10815.8390.0800.0800.0000.0000.0000.000
200A110ILE0-0.1340.07813.903-0.018-0.0180.0000.0000.0000.000
201A111ASP00.039-0.11215.365-0.072-0.0720.0000.0000.0000.000
202A111ASP-1-1.025-0.86713.3741.1331.1330.0000.0000.0000.000
203A112GLY00.035-0.10816.211-0.058-0.0580.0000.0000.0000.000
204A113VAL00.0770.00519.312-0.054-0.0540.0000.0000.0000.000
205A113VAL0-0.0910.08919.873-0.008-0.0080.0000.0000.0000.000
206A114ILE00.052-0.08820.2320.0450.0450.0000.0000.0000.000
207A114ILE0-0.0600.10622.911-0.008-0.0080.0000.0000.0000.000
208A115TYR00.025-0.13621.277-0.033-0.0330.0000.0000.0000.000
209A115TYR0-0.0290.10518.471-0.030-0.0300.0000.0000.0000.000
210A116PHE00.101-0.06622.5050.0220.0220.0000.0000.0000.000
211A116PHE0-0.0590.08825.808-0.005-0.0050.0000.0000.0000.000
212A117PHE00.022-0.11921.269-0.013-0.0130.0000.0000.0000.000
213A117PHE0-0.0840.11917.6990.0190.0190.0000.0000.0000.000
214A118GLY00.073-0.06422.715-0.004-0.0040.0000.0000.0000.000
215A119VAL00.077-0.01023.2530.0180.0180.0000.0000.0000.000
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