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: JV279

Calculation Name: 2CLS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-triphosphate

Ligand 3-letter code: GTP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CLS

Chain ID: A

ChEMBL ID:

UniProt ID: Q92730

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1927802.081384
FMO2-HF: Nuclear repulsion 1855321.060933
FMO2-HF: Total energy -72481.020451
FMO2-MP2: Total energy -72684.751248


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
-137.509-136.2435.07-2.551-3.789-0.021
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.913
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].
3A12ALA00.0540.0442.858-0.4342.4630.490-1.333-2.055-0.011
4A13ARG10.8240.8944.13129.23029.3170.000-0.018-0.0700.000
50A59GLN0-0.032-0.0211.972-7.948-9.6484.581-1.189-1.694-0.010
52A61VAL00.0360.0095.120-6.189-6.207-0.001-0.0110.0300.000
5A14CYS0-0.0130.0017.3650.4420.4420.0000.0000.0000.000
6A15LYS10.7960.90710.67315.65315.6530.0000.0000.0000.000
7A16LEU00.0190.00514.2900.6290.6290.0000.0000.0000.000
8A17VAL00.0160.00017.1460.3510.3510.0000.0000.0000.000
9A18LEU0-0.0110.01120.8790.1000.1000.0000.0000.0000.000
10A19VAL00.0170.02123.7780.3920.3920.0000.0000.0000.000
11A20GLY00.0800.03527.146-0.123-0.1230.0000.0000.0000.000
12A21ASP-1-0.799-0.89130.383-8.752-8.7520.0000.0000.0000.000
13A22VAL00.008-0.00832.870-0.255-0.2550.0000.0000.0000.000
14A23GLN0-0.006-0.00434.4690.2150.2150.0000.0000.0000.000
15A24CYS0-0.090-0.02530.626-0.060-0.0600.0000.0000.0000.000
16A25GLY00.0870.02029.8570.0320.0320.0000.0000.0000.000
17A26LYS10.8390.92426.32910.20110.2010.0000.0000.0000.000
18A27THR00.009-0.02025.794-0.282-0.2820.0000.0000.0000.000
19A28ALA0-0.011-0.00526.642-0.267-0.2670.0000.0000.0000.000
20A29MET0-0.020-0.00723.595-0.264-0.2640.0000.0000.0000.000
21A30LEU00.0370.01820.483-0.510-0.5100.0000.0000.0000.000
22A31GLN0-0.035-0.01622.468-0.377-0.3770.0000.0000.0000.000
23A32VAL00.0070.01523.790-0.205-0.2050.0000.0000.0000.000
24A33LEU0-0.072-0.03217.261-0.383-0.3830.0000.0000.0000.000
25A34ALA0-0.015-0.01719.303-0.749-0.7490.0000.0000.0000.000
26A35LYS10.8390.92420.22311.91011.9100.0000.0000.0000.000
27A36ASP-1-0.921-0.93622.720-13.991-13.9910.0000.0000.0000.000
28A37CYS0-0.026-0.01624.9550.7220.7220.0000.0000.0000.000
29A38TYR00.0330.00627.875-0.274-0.2740.0000.0000.0000.000
30A39PRO0-0.075-0.02629.3950.2910.2910.0000.0000.0000.000
31A40GLU-1-0.848-0.93432.469-8.608-8.6080.0000.0000.0000.000
32A41THR0-0.066-0.02735.7650.2990.2990.0000.0000.0000.000
33A42TYR00.018-0.00633.937-0.279-0.2790.0000.0000.0000.000
34A43VAL00.0410.01633.6580.2650.2650.0000.0000.0000.000
35A44PRO0-0.060-0.03333.522-0.239-0.2390.0000.0000.0000.000
36A45THR00.0120.01427.9670.1260.1260.0000.0000.0000.000
37A46VAL0-0.035-0.01031.1420.2150.2150.0000.0000.0000.000
38A47PHE00.009-0.03126.418-0.022-0.0220.0000.0000.0000.000
39A48GLU-1-0.927-0.94625.191-10.946-10.9460.0000.0000.0000.000
40A49ASN0-0.045-0.02919.403-0.904-0.9040.0000.0000.0000.000
41A50TYR00.0000.00719.7680.4610.4610.0000.0000.0000.000
42A51THR0-0.028-0.00513.959-0.511-0.5110.0000.0000.0000.000
43A52ALA00.0530.01914.6350.8180.8180.0000.0000.0000.000
44A53CYS0-0.036-0.00411.663-1.979-1.9790.0000.0000.0000.000
45A54LEU0-0.014-0.00810.6831.5611.5610.0000.0000.0000.000
46A55GLU-1-0.913-0.9529.062-32.866-32.8660.0000.0000.0000.000
47A56THR0-0.024-0.0328.4803.2663.2660.0000.0000.0000.000
48A57GLU-1-0.929-0.9618.973-26.283-26.2830.0000.0000.0000.000
49A58GLU-1-0.913-0.9416.649-35.956-35.9560.0000.0000.0000.000
51A60ARG10.8310.9094.86339.73639.7360.0000.0000.0000.000
53A62GLU-1-0.853-0.9257.626-21.106-21.1060.0000.0000.0000.000
54A63LEU00.010-0.0019.5930.0800.0800.0000.0000.0000.000
55A64SER00.0090.01212.5931.3121.3120.0000.0000.0000.000
56A65LEU00.011-0.00314.8360.3240.3240.0000.0000.0000.000
57A66TRP00.004-0.00417.3741.1721.1720.0000.0000.0000.000
58A67ASP-1-0.750-0.86521.150-11.261-11.2610.0000.0000.0000.000
59A68THR0-0.011-0.03824.5990.3600.3600.0000.0000.0000.000
60A69SER00.0190.01827.6150.2420.2420.0000.0000.0000.000
61A70GLY0-0.0020.00031.387-0.045-0.0450.0000.0000.0000.000
62A71SER0-0.022-0.01832.9450.2740.2740.0000.0000.0000.000
63A72PRO00.0680.01235.239-0.151-0.1510.0000.0000.0000.000
64A73TYR0-0.055-0.00836.9740.0820.0820.0000.0000.0000.000
65A74TYR00.014-0.00732.4610.0460.0460.0000.0000.0000.000
66A75ASP-1-0.746-0.85432.764-8.993-8.9930.0000.0000.0000.000
67A76ASN0-0.038-0.02133.201-0.156-0.1560.0000.0000.0000.000
68A77VAL0-0.037-0.01730.167-0.035-0.0350.0000.0000.0000.000
69A78ARG10.7740.86627.6829.3329.3320.0000.0000.0000.000
70A79PRO00.0830.03126.870-0.444-0.4440.0000.0000.0000.000
71A80LEU0-0.0170.00925.888-0.321-0.3210.0000.0000.0000.000
72A81CYS0-0.088-0.04222.726-0.414-0.4140.0000.0000.0000.000
73A82TYR00.005-0.01621.440-0.687-0.6870.0000.0000.0000.000
74A83SER0-0.0040.02320.894-0.563-0.5630.0000.0000.0000.000
75A84ASP-1-0.921-0.96315.907-15.407-15.4070.0000.0000.0000.000
76A85SER0-0.052-0.03215.613-0.793-0.7930.0000.0000.0000.000
77A86ASP-1-0.778-0.87012.467-21.180-21.1800.0000.0000.0000.000
78A87ALA00.009-0.00715.2540.2820.2820.0000.0000.0000.000
79A88VAL0-0.0170.00118.084-0.007-0.0070.0000.0000.0000.000
80A89LEU0-0.010-0.00918.3430.1920.1920.0000.0000.0000.000
81A90LEU00.0040.00122.2920.3900.3900.0000.0000.0000.000
82A91CYS0-0.053-0.02125.421-0.095-0.0950.0000.0000.0000.000
83A92PHE00.0460.00927.7650.3190.3190.0000.0000.0000.000
84A93ASP-1-0.713-0.82330.904-9.020-9.0200.0000.0000.0000.000
85A94ILE0-0.026-0.00630.9550.2430.2430.0000.0000.0000.000
86A95SER0-0.034-0.03834.7920.2770.2770.0000.0000.0000.000
87A96ARG10.8540.90835.7908.6338.6330.0000.0000.0000.000
88A97PRO00.0480.03137.692-0.212-0.2120.0000.0000.0000.000
89A98GLU-1-0.899-0.96138.714-7.442-7.4420.0000.0000.0000.000
90A99THR0-0.016-0.02334.554-0.219-0.2190.0000.0000.0000.000
91A100VAL0-0.015-0.01633.857-0.282-0.2820.0000.0000.0000.000
92A101ASP-1-0.948-0.94735.521-7.724-7.7240.0000.0000.0000.000
93A102SER00.0810.02837.670-0.085-0.0850.0000.0000.0000.000
94A103ALA0-0.0310.00635.564-0.116-0.1160.0000.0000.0000.000
95A104LEU0-0.017-0.00830.633-0.237-0.2370.0000.0000.0000.000
96A105LYS10.8710.94532.6008.1908.1900.0000.0000.0000.000
97A106LYS10.8640.95433.9638.7548.7540.0000.0000.0000.000
98A107TRP0-0.040-0.04129.939-0.239-0.2390.0000.0000.0000.000
99A108ARG10.8990.95326.13210.70310.7030.0000.0000.0000.000
100A109THR0-0.032-0.02129.641-0.227-0.2270.0000.0000.0000.000
101A110GLU-1-0.767-0.86730.251-9.808-9.8080.0000.0000.0000.000
102A111ILE0-0.013-0.00724.665-0.176-0.1760.0000.0000.0000.000
103A112LEU0-0.073-0.03326.900-0.304-0.3040.0000.0000.0000.000
104A113ASP-1-0.894-0.95829.013-9.104-9.1040.0000.0000.0000.000
105A114TYR0-0.065-0.01522.895-0.077-0.0770.0000.0000.0000.000
106A115CYS0-0.007-0.01322.489-0.117-0.1170.0000.0000.0000.000
107A116PRO00.0300.02524.963-0.331-0.3310.0000.0000.0000.000
108A117SER0-0.034-0.02821.2220.1200.1200.0000.0000.0000.000
109A118THR0-0.042-0.01320.374-0.767-0.7670.0000.0000.0000.000
110A119ARG10.8730.93814.35818.47418.4740.0000.0000.0000.000
111A120VAL0-0.005-0.00420.487-0.007-0.0070.0000.0000.0000.000
112A121LEU00.0050.01417.5050.0060.0060.0000.0000.0000.000
113A122LEU0-0.034-0.00422.1840.2060.2060.0000.0000.0000.000
114A123ILE00.005-0.02021.729-0.201-0.2010.0000.0000.0000.000
115A124GLY00.0350.02425.8130.3850.3850.0000.0000.0000.000
116A125CYS0-0.046-0.03328.343-0.378-0.3780.0000.0000.0000.000
117A126LYS10.8490.90429.8529.2839.2830.0000.0000.0000.000
118A127THR00.003-0.01629.7800.3020.3020.0000.0000.0000.000
119A128ASP-1-0.815-0.87432.693-9.138-9.1380.0000.0000.0000.000
120A129LEU00.0340.00035.1450.2690.2690.0000.0000.0000.000
121A130ARG10.7370.82132.1069.5599.5590.0000.0000.0000.000
122A131THR0-0.074-0.04437.9150.1760.1760.0000.0000.0000.000
123A132ASP-1-0.778-0.85440.190-7.295-7.2950.0000.0000.0000.000
124A133LEU00.0240.00341.8410.0720.0720.0000.0000.0000.000
125A134SER0-0.011-0.00344.6050.2040.2040.0000.0000.0000.000
126A135THR00.009-0.01740.1130.0510.0510.0000.0000.0000.000
127A136LEU0-0.041-0.02042.6030.0790.0790.0000.0000.0000.000
128A137MET0-0.070-0.03644.9870.1680.1680.0000.0000.0000.000
129A138GLU-1-0.931-0.95945.416-6.856-6.8560.0000.0000.0000.000
130A139LEU0-0.021-0.01741.1840.0710.0710.0000.0000.0000.000
131A140SER00.0050.02145.8700.1200.1200.0000.0000.0000.000
132A141HIS0-0.065-0.03748.6450.1590.1590.0000.0000.0000.000
133A142GLN0-0.038-0.01344.8860.0300.0300.0000.0000.0000.000
134A143LYS10.8720.93848.5306.1736.1730.0000.0000.0000.000
135A144GLN00.0040.00643.186-0.123-0.1230.0000.0000.0000.000
136A145ALA0-0.004-0.00942.5420.0990.0990.0000.0000.0000.000
137A146PRO00.0280.01238.567-0.104-0.1040.0000.0000.0000.000
138A147ILE0-0.0170.02033.9680.0130.0130.0000.0000.0000.000
139A148SER00.0210.00835.361-0.262-0.2620.0000.0000.0000.000
140A149TYR00.0800.02626.2420.0020.0020.0000.0000.0000.000
141A150GLU-1-0.913-0.95531.559-8.652-8.6520.0000.0000.0000.000
142A151GLN00.0160.01033.696-0.139-0.1390.0000.0000.0000.000
143A152GLY00.0570.02930.993-0.026-0.0260.0000.0000.0000.000
144A153CYS0-0.021-0.01129.283-0.323-0.3230.0000.0000.0000.000
145A154ALA0-0.037-0.02030.322-0.074-0.0740.0000.0000.0000.000
146A155ILE0-0.024-0.01531.6270.1070.1070.0000.0000.0000.000
147A156ALA00.0500.01427.018-0.033-0.0330.0000.0000.0000.000
148A157LYS10.9440.97628.8758.9308.9300.0000.0000.0000.000
149A158GLN0-0.078-0.04230.5530.1260.1260.0000.0000.0000.000
150A159LEU00.0080.00829.5500.1960.1960.0000.0000.0000.000
151A160GLY0-0.0160.00128.099-0.168-0.1680.0000.0000.0000.000
152A161ALA0-0.027-0.00824.652-0.319-0.3190.0000.0000.0000.000
153A162GLU-1-0.852-0.92318.473-15.350-15.3500.0000.0000.0000.000
154A163ILE0-0.034-0.01620.3230.0110.0110.0000.0000.0000.000
155A164TYR0-0.044-0.04623.3000.2690.2690.0000.0000.0000.000
156A165LEU0-0.017-0.00219.691-0.215-0.2150.0000.0000.0000.000
157A166GLU-1-0.749-0.81824.287-9.752-9.7520.0000.0000.0000.000
158A167GLY00.0300.00725.798-0.373-0.3730.0000.0000.0000.000
159A168SER0-0.069-0.04427.2710.3870.3870.0000.0000.0000.000
160A169ALA00.002-0.00927.465-0.166-0.1660.0000.0000.0000.000
161A170PHE0-0.0040.02628.465-0.065-0.0650.0000.0000.0000.000
162A171THR00.000-0.01131.4350.0650.0650.0000.0000.0000.000
163A172SER0-0.006-0.00727.789-0.193-0.1930.0000.0000.0000.000
164A173GLU-1-0.796-0.88124.978-12.390-12.3900.0000.0000.0000.000
165A174LYS10.8510.91620.76114.35114.3510.0000.0000.0000.000
166A175SER0-0.003-0.01422.270-0.500-0.5000.0000.0000.0000.000
167A176ILE00.0420.02421.743-0.468-0.4680.0000.0000.0000.000
168A177HIS00.0580.01018.903-1.269-1.2690.0000.0000.0000.000
169A178SER0-0.030-0.01417.681-1.376-1.3760.0000.0000.0000.000
170A179ILE0-0.0060.01918.427-0.552-0.5520.0000.0000.0000.000
171A180PHE00.0560.01716.265-0.358-0.3580.0000.0000.0000.000
172A181ARG10.9320.99213.68117.25317.2530.0000.0000.0000.000
173A182THR0-0.011-0.01413.698-1.047-1.0470.0000.0000.0000.000
174A183ALA00.001-0.01515.523-0.183-0.1830.0000.0000.0000.000
175A184SER00.006-0.02310.724-0.356-0.3560.0000.0000.0000.000
176A185MET0-0.045-0.01210.641-1.381-1.3810.0000.0000.0000.000
177A186LEU00.005-0.00211.722-0.163-0.1630.0000.0000.0000.000
178A187CYS0-0.120-0.06411.8661.1221.1220.0000.0000.0000.000
179A188LEU-1-0.955-0.9455.691-26.413-26.4130.0000.0000.0000.000