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: 8QNKY

Calculation Name: 2C2H-B-Xray547

Preferred Name: Ras-related C3 botulinum toxin substrate 3

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | sulfate ion | calcium ion | magnesium ion

Ligand 3-letter code: GDP | SO4 | CA | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C2H

Chain ID: B

ChEMBL ID: CHEMBL6087

UniProt ID: P60763

Base Structure: X-ray

Registration Date: 2025-10-05

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1871386.256818
FMO2-HF: Nuclear repulsion 1801611.62046
FMO2-HF: Total energy -69774.636358
FMO2-MP2: Total energy -69976.385642


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-58.79-51.66810.227-5.278-12.071-0.062
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.801 / q_NPA : 0.905
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].
3A3ALA00.003-0.0062.647-4.551-1.4690.653-1.671-2.064-0.016
4A4ILE00.0310.0205.2491.3091.356-0.001-0.005-0.0400.000
43A43ASN0-0.053-0.0312.483-9.761-9.3682.106-0.892-1.608-0.013
44A44VAL00.0210.0134.4483.3273.398-0.001-0.005-0.0650.000
45A45MET0-0.039-0.0055.078-3.314-3.253-0.0010.000-0.0600.000
50A50PRO0-0.028-0.0022.1481.3651.3692.444-0.573-1.8750.001
51A51VAL00.010-0.0092.597-15.259-13.2533.330-1.785-3.551-0.026
52A52ASN00.0200.0072.7504.4215.7751.678-0.366-2.666-0.008
53A53LEU0-0.004-0.0053.5690.5770.6810.0190.019-0.1420.000
5A5LYS10.7840.9008.47818.32618.3260.0000.0000.0000.000
6A6CYS0-0.012-0.00611.6691.4261.4260.0000.0000.0000.000
7A7VAL00.0010.00813.9960.0950.0950.0000.0000.0000.000
8A8VAL00.0020.00317.3420.4260.4260.0000.0000.0000.000
9A9VAL00.0220.03219.7990.3580.3580.0000.0000.0000.000
10A10GLY00.0830.02623.556-0.003-0.0030.0000.0000.0000.000
11A11ASP-1-0.784-0.86426.676-9.307-9.3070.0000.0000.0000.000
12A12GLY00.001-0.00828.207-0.319-0.3190.0000.0000.0000.000
13A13ALA00.012-0.00329.4130.1270.1270.0000.0000.0000.000
14A14VAL0-0.0120.00325.7260.1310.1310.0000.0000.0000.000
15A15GLY00.0270.02325.434-0.064-0.0640.0000.0000.0000.000
16A16LYS10.8200.93221.68211.15711.1570.0000.0000.0000.000
17A17THR00.0580.00320.414-0.237-0.2370.0000.0000.0000.000
18A18CYS0-0.051-0.01220.318-0.249-0.2490.0000.0000.0000.000
19A19LEU0-0.011-0.01118.401-0.198-0.1980.0000.0000.0000.000
20A20LEU00.0310.01715.020-0.508-0.5080.0000.0000.0000.000
21A21ILE00.0400.04015.600-0.725-0.7250.0000.0000.0000.000
22A22SER0-0.042-0.00517.028-0.398-0.3980.0000.0000.0000.000
23A23TYR0-0.010-0.00910.106-0.093-0.0930.0000.0000.0000.000
24A24THR0-0.052-0.04611.378-0.608-0.6080.0000.0000.0000.000
25A25THR0-0.051-0.04312.603-0.311-0.3110.0000.0000.0000.000
26A26ASN0-0.0230.00715.3380.1340.1340.0000.0000.0000.000
27A27ALA00.0240.01517.0360.6520.6520.0000.0000.0000.000
28A28PHE00.010-0.00520.258-0.237-0.2370.0000.0000.0000.000
29A29PRO0-0.016-0.00221.6600.2590.2590.0000.0000.0000.000
30A30GLY0-0.011-0.01824.0750.2230.2230.0000.0000.0000.000
31A31GLU-1-0.869-0.92726.506-9.076-9.0760.0000.0000.0000.000
32A32TYR0-0.103-0.04726.948-0.311-0.3110.0000.0000.0000.000
33A33ILE0-0.024-0.01323.922-0.247-0.2470.0000.0000.0000.000
34A34PRO00.0170.01120.3330.2850.2850.0000.0000.0000.000
35A35THR0-0.009-0.00922.0890.2830.2830.0000.0000.0000.000
36A36VAL0-0.021-0.00823.156-0.159-0.1590.0000.0000.0000.000
37A37PHE0-0.058-0.03021.7380.1470.1470.0000.0000.0000.000
38A38ASP-1-0.768-0.86018.827-14.524-14.5240.0000.0000.0000.000
39A39ASN0-0.055-0.04114.291-0.278-0.2780.0000.0000.0000.000
40A40TYR0-0.034-0.02913.243-0.019-0.0190.0000.0000.0000.000
41A41SER0-0.012-0.0117.665-1.615-1.6150.0000.0000.0000.000
42A42ALA00.0200.0188.0461.3511.3510.0000.0000.0000.000
46A46VAL00.0290.0147.3462.7322.7320.0000.0000.0000.000
47A47ASP-1-0.835-0.9128.973-28.328-28.3280.0000.0000.0000.000
48A48GLY00.0250.0119.9160.3340.3340.0000.0000.0000.000
49A49LYS10.8420.9045.73528.01828.0180.0000.0000.0000.000
54A54GLY00.0270.0137.2061.3801.3800.0000.0000.0000.000
55A55LEU0-0.034-0.0239.9120.9120.9120.0000.0000.0000.000
56A56TRP00.0330.00912.7020.7940.7940.0000.0000.0000.000
57A57ASP-1-0.766-0.87416.368-12.511-12.5110.0000.0000.0000.000
58A58THR0-0.058-0.05619.6700.2480.2480.0000.0000.0000.000
59A59ALA00.0580.04123.1650.2990.2990.0000.0000.0000.000
60A60GLY0-0.017-0.00526.7960.0040.0040.0000.0000.0000.000
61A61GLN0-0.004-0.02328.5780.0720.0720.0000.0000.0000.000
62A62GLU-1-0.917-0.96231.813-8.232-8.2320.0000.0000.0000.000
63A63ASP-1-0.928-0.95633.646-8.983-8.9830.0000.0000.0000.000
64A64TYR00.0480.01928.303-0.253-0.2530.0000.0000.0000.000
65A65ASP-1-0.791-0.86029.797-9.772-9.7720.0000.0000.0000.000
66A66ARG10.8550.91931.3069.1449.1440.0000.0000.0000.000
67A67LEU00.0360.02228.021-0.153-0.1530.0000.0000.0000.000
68A68ARG10.7950.87025.08310.12810.1280.0000.0000.0000.000
69A69PRO00.0370.01024.361-0.584-0.5840.0000.0000.0000.000
70A70LEU0-0.0050.00024.141-0.435-0.4350.0000.0000.0000.000
71A71SER0-0.0070.00120.392-0.646-0.6460.0000.0000.0000.000
72A72TYR0-0.056-0.04219.304-0.996-0.9960.0000.0000.0000.000
73A73PRO00.0180.02619.493-0.594-0.5940.0000.0000.0000.000
74A74GLN0-0.006-0.01214.6700.1580.1580.0000.0000.0000.000
75A75THR0-0.008-0.00914.429-1.482-1.4820.0000.0000.0000.000
76A76ASP-1-0.829-0.89911.331-24.114-24.1140.0000.0000.0000.000
77A77VAL0-0.029-0.02813.8260.8310.8310.0000.0000.0000.000
78A78PHE00.0300.00716.416-0.179-0.1790.0000.0000.0000.000
79A79LEU0-0.019-0.00716.8320.2710.2710.0000.0000.0000.000
80A80ILE00.0190.01020.1750.2130.2130.0000.0000.0000.000
81A81CYS0-0.046-0.01121.8600.0280.0280.0000.0000.0000.000
82A82PHE00.0170.00024.6160.3180.3180.0000.0000.0000.000
83A83SER00.0050.00727.783-0.158-0.1580.0000.0000.0000.000
84A84LEU00.0010.00428.7080.2820.2820.0000.0000.0000.000
85A85VAL00.0120.01131.6170.2700.2700.0000.0000.0000.000
86A86SER0-0.015-0.01533.2370.2390.2390.0000.0000.0000.000
87A87PRO00.0620.03034.095-0.197-0.1970.0000.0000.0000.000
88A88ALA00.0110.02136.245-0.018-0.0180.0000.0000.0000.000
89A89SER00.016-0.00130.835-0.184-0.1840.0000.0000.0000.000
90A90PHE0-0.005-0.00931.524-0.238-0.2380.0000.0000.0000.000
91A91GLU-1-0.822-0.91132.902-8.130-8.1300.0000.0000.0000.000
92A92ASN0-0.028-0.02832.3900.0800.0800.0000.0000.0000.000
93A93VAL0-0.056-0.02128.656-0.265-0.2650.0000.0000.0000.000
94A94ARG10.7790.84130.8958.0878.0870.0000.0000.0000.000
95A95ALA0-0.036-0.02133.803-0.009-0.0090.0000.0000.0000.000
96A96LYS10.8520.91631.1739.4219.4210.0000.0000.0000.000
97A97TRP0-0.032-0.03427.293-0.304-0.3040.0000.0000.0000.000
98A98TYR00.0460.02427.782-0.435-0.4350.0000.0000.0000.000
99A99PRO00.0080.00629.050-0.238-0.2380.0000.0000.0000.000
100A100GLU-1-0.815-0.88428.119-10.757-10.7570.0000.0000.0000.000
101A101VAL00.0210.01023.384-0.171-0.1710.0000.0000.0000.000
102A102ARG10.8350.91023.48512.02212.0220.0000.0000.0000.000
103A103HIS0-0.0150.00227.3330.0260.0260.0000.0000.0000.000
104A104HIS0-0.058-0.04025.7580.0870.0870.0000.0000.0000.000
105A105CYS0-0.068-0.02322.215-0.710-0.7100.0000.0000.0000.000
106A106PRO00.0110.01724.126-0.062-0.0620.0000.0000.0000.000
107A107HIS00.012-0.01322.6270.1610.1610.0000.0000.0000.000
108A108THR00.0060.03518.028-0.023-0.0230.0000.0000.0000.000
109A109PRO00.0410.03217.4650.9980.9980.0000.0000.0000.000
110A110ILE00.0300.00419.880-0.286-0.2860.0000.0000.0000.000
111A111LEU0-0.0080.01317.9810.3290.3290.0000.0000.0000.000
112A112LEU0-0.057-0.01621.6780.1610.1610.0000.0000.0000.000
113A113VAL00.024-0.01120.4830.0290.0290.0000.0000.0000.000
114A114GLY00.0380.02623.9250.2330.2330.0000.0000.0000.000
115A115THR0-0.017-0.04823.846-0.080-0.0800.0000.0000.0000.000
116A116LYS10.9070.94326.2819.7389.7380.0000.0000.0000.000
117A117LEU00.0040.00726.6580.3410.3410.0000.0000.0000.000
118A118ASP-1-0.878-0.92828.109-9.546-9.5460.0000.0000.0000.000
119A119LEU00.0320.01730.5150.2050.2050.0000.0000.0000.000
120A120ARG10.7490.83630.9589.1619.1610.0000.0000.0000.000
121A121ASP-1-0.892-0.95734.217-8.046-8.0460.0000.0000.0000.000
122A122ASP-1-0.823-0.87835.986-7.403-7.4030.0000.0000.0000.000
123A123LYS10.8370.91537.6976.6186.6180.0000.0000.0000.000
124A124ASP-1-0.843-0.92440.507-6.714-6.7140.0000.0000.0000.000
125A125THR0-0.067-0.06335.6950.0220.0220.0000.0000.0000.000
126A126ILE0-0.038-0.02038.9800.0510.0510.0000.0000.0000.000
127A127GLU-1-0.912-0.94640.849-6.230-6.2300.0000.0000.0000.000
128A128ARG10.9800.97739.4547.2777.2770.0000.0000.0000.000
129A129LEU0-0.062-0.01737.3360.0110.0110.0000.0000.0000.000
130A130ARG10.9760.98841.9806.1836.1830.0000.0000.0000.000
131A131ASP-1-0.938-0.95545.309-6.121-6.1210.0000.0000.0000.000
132A132LYS10.9090.95542.1707.0537.0530.0000.0000.0000.000
133A133LYS10.9370.97345.4026.1776.1770.0000.0000.0000.000
134A134LEU0-0.078-0.04240.249-0.088-0.0880.0000.0000.0000.000
135A135ALA00.0270.00640.6910.1170.1170.0000.0000.0000.000
136A136PRO00.005-0.00235.509-0.112-0.1120.0000.0000.0000.000
137A137ILE0-0.053-0.00132.8910.1100.1100.0000.0000.0000.000
138A138THR00.017-0.01233.803-0.197-0.1970.0000.0000.0000.000
139A139TYR00.0570.02428.029-0.130-0.1300.0000.0000.0000.000
140A140PRO00.004-0.01732.442-0.166-0.1660.0000.0000.0000.000
141A141GLN00.0520.05534.996-0.018-0.0180.0000.0000.0000.000
142A142GLY00.0600.03030.834-0.051-0.0510.0000.0000.0000.000
143A143LEU0-0.008-0.00529.468-0.220-0.2200.0000.0000.0000.000
144A144ALA0-0.056-0.03031.287-0.074-0.0740.0000.0000.0000.000
145A145MET00.0180.02130.900-0.071-0.0710.0000.0000.0000.000
146A146ALA0-0.010-0.01727.813-0.149-0.1490.0000.0000.0000.000
147A147ARG10.9270.96929.3068.7428.7420.0000.0000.0000.000
148A148GLU-1-0.828-0.87131.808-8.493-8.4930.0000.0000.0000.000
149A149ILE0-0.036-0.02727.6130.0090.0090.0000.0000.0000.000
150A150GLY0-0.0080.01428.789-0.263-0.2630.0000.0000.0000.000
151A151SER0-0.059-0.02924.989-0.607-0.6070.0000.0000.0000.000
152A152VAL0-0.007-0.01120.2630.2180.2180.0000.0000.0000.000
153A153LYS10.8180.89821.11713.09113.0910.0000.0000.0000.000
154A154TYR0-0.041-0.03023.3280.0090.0090.0000.0000.0000.000
155A155LEU0-0.009-0.00219.689-0.119-0.1190.0000.0000.0000.000
156A156GLU-1-0.755-0.82223.937-9.267-9.2670.0000.0000.0000.000
157A157CYS0-0.044-0.01821.979-0.280-0.2800.0000.0000.0000.000
158A158SER0-0.049-0.04423.6940.3530.3530.0000.0000.0000.000
159A159ALA00.0350.01221.660-0.269-0.2690.0000.0000.0000.000
160A160LEU00.0080.02922.477-0.268-0.2680.0000.0000.0000.000
161A161THR00.005-0.02925.2870.0630.0630.0000.0000.0000.000
162A162GLN0-0.001-0.01318.510-0.179-0.1790.0000.0000.0000.000
163A163ARG10.9480.98621.0359.3899.3890.0000.0000.0000.000
164A164GLY00.0390.01121.6070.1230.1230.0000.0000.0000.000
165A165LEU0-0.047-0.01317.199-0.375-0.3750.0000.0000.0000.000
166A166LYS10.8590.90511.97618.17418.1740.0000.0000.0000.000
167A167THR00.0210.00514.937-0.874-0.8740.0000.0000.0000.000
168A168VAL00.0080.00116.767-0.329-0.3290.0000.0000.0000.000
169A169PHE00.025-0.00111.879-0.188-0.1880.0000.0000.0000.000
170A170ASP-1-0.809-0.88012.031-20.198-20.1980.0000.0000.0000.000
171A171GLU-1-0.860-0.92813.357-14.715-14.7150.0000.0000.0000.000
172A172ALA0-0.008-0.00213.729-0.006-0.0060.0000.0000.0000.000
173A173ILE00.0130.0018.112-0.524-0.5240.0000.0000.0000.000
174A174ARG10.8570.90411.96716.63516.6350.0000.0000.0000.000
175A175ALA0-0.046-0.02314.8400.7250.7250.0000.0000.0000.000
176A176VAL0-0.056-0.02511.4410.4610.4610.0000.0000.0000.000
177A177LEU-1-0.886-0.9069.253-20.346-20.3460.0000.0000.0000.000