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: G75L1

Calculation Name: 4V6X-A-Other547

Preferred Name: Elongation factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V6X

Chain ID: A

ChEMBL ID: CHEMBL1795108

UniProt ID: P13639

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 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2813365.11731
FMO2-HF: Nuclear repulsion 2719205.418285
FMO2-HF: Total energy -94159.699025
FMO2-MP2: Total energy -94435.533213


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:20:LYS)


Summations of interaction energy for fragment #1(A:20:LYS)
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.
710.443705.5955.5284.238-4.918-0.029
Interaction energy analysis for fragmet #1(A:20:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.779 / q_NPA : 1.895
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].
3A22ARG11.1141.0612.64359.93253.2950.0207.053-0.436-0.005
4A23ARG11.0140.9803.68837.03437.6790.006-0.268-0.383-0.002
5A24ASN00.010-0.0122.068-7.337-7.4243.361-1.634-1.640-0.015
6A25PHE0-0.0100.0013.911-7.842-7.2460.001-0.155-0.442-0.001
7A26ALA00.0840.0384.9914.0104.035-0.001-0.006-0.0180.000
9A28LEU0-0.048-0.0282.1342.1002.7102.141-0.752-1.999-0.006
8A27GLU-1-0.771-0.8805.074-68.304-68.3040.0000.0000.0000.000
10A29LYS10.9650.9905.54149.39849.3980.0000.0000.0000.000
11A30ILE00.0420.0168.8414.4854.4850.0000.0000.0000.000
12A31LYS10.9740.9896.29571.21171.2110.0000.0000.0000.000
13A32ARG10.9200.9615.87164.44064.4400.0000.0000.0000.000
14A33LEU00.0380.01911.1582.8822.8820.0000.0000.0000.000
15A34ARG10.9961.00012.44141.65841.6580.0000.0000.0000.000
16A35LYS10.9981.00312.64343.81143.8110.0000.0000.0000.000
17A36LYS10.9580.98615.69831.15831.1580.0000.0000.0000.000
18A37PHE00.0270.00617.6051.5401.5400.0000.0000.0000.000
19A38ALA00.0520.03118.8531.5311.5310.0000.0000.0000.000
20A39GLN00.0510.02220.0991.2771.2770.0000.0000.0000.000
21A40LYS10.8980.95121.72924.67424.6740.0000.0000.0000.000
22A41MET00.0560.02323.4360.8250.8250.0000.0000.0000.000
23A42LEU00.0360.03024.6491.1101.1100.0000.0000.0000.000
24A43ARG10.8890.92826.01922.05322.0530.0000.0000.0000.000
25A44LYS00.0150.00427.5610.6650.6650.0000.0000.0000.000
26A45ALA00.0320.02529.2860.7470.7470.0000.0000.0000.000
27A46ARG10.9150.95629.85120.51120.5110.0000.0000.0000.000
28A47ARG10.9490.96432.10318.31118.3110.0000.0000.0000.000
29A48LYS10.9931.00432.30718.80318.8030.0000.0000.0000.000
30A49LEU00.0530.03335.1360.4850.4850.0000.0000.0000.000
31A50ILE0-0.022-0.02335.1660.3880.3880.0000.0000.0000.000
32A51TYR00.0070.01338.3460.3790.3790.0000.0000.0000.000
33A52GLU-1-0.829-0.91239.880-14.490-14.4900.0000.0000.0000.000
34A53LYS10.8410.91339.20215.70115.7010.0000.0000.0000.000
35A54ALA00.0100.00742.5780.3650.3650.0000.0000.0000.000
36A55LYS10.8680.92644.02614.31514.3150.0000.0000.0000.000
37A56HIS0-0.049-0.02745.6880.2210.2210.0000.0000.0000.000
38A57TYR0-0.002-0.05042.9840.2570.2570.0000.0000.0000.000
39A58HIS00.0080.01948.6140.2580.2580.0000.0000.0000.000
40A59LYS10.9390.97250.43512.13412.1340.0000.0000.0000.000
41A60GLU-1-0.854-0.91750.793-12.115-12.1150.0000.0000.0000.000
42A61TYR00.012-0.03049.3680.2550.2550.0000.0000.0000.000
43A62ARG10.9470.98654.70111.40211.4020.0000.0000.0000.000
44A63GLN0-0.019-0.01356.0730.0960.0960.0000.0000.0000.000
45A64MET00.013-0.00355.6590.1420.1420.0000.0000.0000.000
46A65TYR00.0100.00458.7890.1690.1690.0000.0000.0000.000
47A66ARG10.9370.95760.36710.46410.4640.0000.0000.0000.000
48A67THR00.0170.01761.6080.2250.2250.0000.0000.0000.000
49A68GLU-1-0.795-0.89162.999-9.758-9.7580.0000.0000.0000.000
50A69ILE0-0.025-0.00564.6280.1950.1950.0000.0000.0000.000
51A70ARG10.8530.93265.9399.3849.3840.0000.0000.0000.000
52A71MET00.0420.02765.0580.1980.1980.0000.0000.0000.000
53A72ALA00.0420.02569.6280.1520.1520.0000.0000.0000.000
54A73ARG10.9020.93269.8869.1389.1380.0000.0000.0000.000
55A74MET0-0.0150.00271.8660.0990.0990.0000.0000.0000.000
56A75ALA00.0270.01573.7080.1050.1050.0000.0000.0000.000
57A76ARG10.9950.99175.5988.5158.5150.0000.0000.0000.000
58A77LYS10.9140.96177.1558.1968.1960.0000.0000.0000.000
59A78ALA0-0.0090.00277.8880.0800.0800.0000.0000.0000.000
60A79GLY00.0330.03479.7020.0780.0780.0000.0000.0000.000
61A80ASN0-0.019-0.00277.6140.1020.1020.0000.0000.0000.000
62A81PHE00.006-0.01276.537-0.073-0.0730.0000.0000.0000.000
63A82TYR0-0.071-0.04966.2260.0080.0080.0000.0000.0000.000
64A83VAL00.0250.01570.9620.0010.0010.0000.0000.0000.000
65A84PRO0-0.006-0.01166.591-0.112-0.1120.0000.0000.0000.000
66A85ALA0-0.023-0.00863.5700.0260.0260.0000.0000.0000.000
67A86GLU-1-0.849-0.92264.940-9.453-9.4530.0000.0000.0000.000
68A87PRO0-0.024-0.00561.883-0.237-0.2370.0000.0000.0000.000
69A88LYS10.9630.97057.84110.41310.4130.0000.0000.0000.000
70A89LEU0-0.054-0.01954.014-0.180-0.1800.0000.0000.0000.000
71A90ALA00.0530.03457.8240.1640.1640.0000.0000.0000.000
72A91PHE0-0.039-0.02652.343-0.260-0.2600.0000.0000.0000.000
73A92VAL00.011-0.00156.5650.2550.2550.0000.0000.0000.000
74A93ILE00.0290.01256.608-0.275-0.2750.0000.0000.0000.000
75A94ARG10.8520.91857.80110.93210.9320.0000.0000.0000.000
76A95ILE0-0.016-0.00959.585-0.129-0.1290.0000.0000.0000.000
77A96ARG10.9380.98162.3949.4369.4360.0000.0000.0000.000
78A97GLY00.0370.02261.145-0.200-0.2000.0000.0000.0000.000
79A98ILE0-0.041-0.03258.3900.1050.1050.0000.0000.0000.000
80A99ASN00.0050.00061.908-0.077-0.0770.0000.0000.0000.000
81A100GLY00.0910.05064.6610.0700.0700.0000.0000.0000.000
82A101VAL0-0.079-0.01962.6650.0700.0700.0000.0000.0000.000
83A102SER00.0990.04266.027-0.060-0.0600.0000.0000.0000.000
84A103PRO00.0570.01564.684-0.151-0.1510.0000.0000.0000.000
85A104LYS11.0071.00064.0149.0869.0860.0000.0000.0000.000
86A105VAL00.0340.02963.824-0.097-0.0970.0000.0000.0000.000
87A106ARG10.9490.98060.21110.13610.1360.0000.0000.0000.000
88A107LYS10.9310.96257.50110.74810.7480.0000.0000.0000.000
89A108VAL00.0520.03058.877-0.222-0.2220.0000.0000.0000.000
90A109LEU00.0040.00258.630-0.193-0.1930.0000.0000.0000.000
91A110GLN0-0.0180.00154.272-0.064-0.0640.0000.0000.0000.000
92A111LEU0-0.012-0.00854.298-0.274-0.2740.0000.0000.0000.000
93A112LEU00.0070.00954.210-0.211-0.2110.0000.0000.0000.000
94A113ARG10.8460.91448.15312.52012.5200.0000.0000.0000.000
95A114LEU0-0.0080.01752.635-0.174-0.1740.0000.0000.0000.000
96A115ARG10.9090.94447.35413.04013.0400.0000.0000.0000.000
97A116GLN00.0370.02151.571-0.008-0.0080.0000.0000.0000.000
98A117ILE00.0290.01955.9120.0100.0100.0000.0000.0000.000
99A118PHE00.025-0.00456.192-0.137-0.1370.0000.0000.0000.000
100A119ASN0-0.0030.00751.836-0.263-0.2630.0000.0000.0000.000
101A120GLY00.0550.02352.9810.2680.2680.0000.0000.0000.000
102A121THR0-0.087-0.04451.184-0.279-0.2790.0000.0000.0000.000
103A122PHE00.0790.04449.9420.2210.2210.0000.0000.0000.000
104A123VAL0-0.012-0.00353.480-0.145-0.1450.0000.0000.0000.000
105A124LYS10.9661.00253.94611.73411.7340.0000.0000.0000.000
106A125LEU0-0.038-0.01156.3850.0650.0650.0000.0000.0000.000
107A126ASN00.0610.01258.9790.1060.1060.0000.0000.0000.000
108A127LYS11.0101.01561.6039.2819.2810.0000.0000.0000.000
109A128ALA00.0170.00460.7770.0770.0770.0000.0000.0000.000
110A129SER0-0.009-0.02958.6320.0290.0290.0000.0000.0000.000
111A130ILE00.0210.01561.1060.0070.0070.0000.0000.0000.000
112A131ASN00.0320.01464.5150.2040.2040.0000.0000.0000.000
113A132MET0-0.032-0.00660.4230.0020.0020.0000.0000.0000.000
114A133LEU00.008-0.01360.3160.0250.0250.0000.0000.0000.000
115A134ARG10.9781.00463.9098.9048.9040.0000.0000.0000.000
116A135ILE0-0.042-0.01764.5810.1120.1120.0000.0000.0000.000
117A136VAL0-0.025-0.02561.8600.0220.0220.0000.0000.0000.000
118A137GLU-1-0.828-0.90065.098-9.178-9.1780.0000.0000.0000.000
119A138PRO00.0690.02467.095-0.060-0.0600.0000.0000.0000.000
120A139TYR0-0.013-0.03263.553-0.058-0.0580.0000.0000.0000.000
121A140ILE0-0.047-0.02260.718-0.235-0.2350.0000.0000.0000.000
122A141ALA00.0150.02862.2380.1760.1760.0000.0000.0000.000
123A142TRP0-0.012-0.02561.271-0.284-0.2840.0000.0000.0000.000
124A143GLY00.0820.04761.1540.1930.1930.0000.0000.0000.000
125A144TYR00.0470.01860.349-0.281-0.2810.0000.0000.0000.000
126A145PRO0-0.068-0.00955.5700.0360.0360.0000.0000.0000.000
127A146ASN00.050-0.00157.138-0.205-0.2050.0000.0000.0000.000
128A147LEU00.0700.04450.810-0.140-0.1400.0000.0000.0000.000
129A148LYS10.9800.97952.53511.17611.1760.0000.0000.0000.000
130A149SER0-0.028-0.01452.717-0.168-0.1680.0000.0000.0000.000
131A150VAL00.0090.01449.431-0.134-0.1340.0000.0000.0000.000
132A151ASN0-0.0020.00646.799-0.211-0.2110.0000.0000.0000.000
133A152GLU-1-0.888-0.94948.009-12.577-12.5770.0000.0000.0000.000
134A153LEU0-0.025-0.00748.841-0.208-0.2080.0000.0000.0000.000
135A154ILE0-0.048-0.03444.208-0.277-0.2770.0000.0000.0000.000
136A155TYR0-0.056-0.06643.953-0.393-0.3930.0000.0000.0000.000
137A156LYS10.8750.94043.98012.20312.2030.0000.0000.0000.000
138A157ARG10.7990.88645.73312.41012.4100.0000.0000.0000.000
139A158GLY00.0560.04343.6600.0740.0740.0000.0000.0000.000
140A159TYR0-0.038-0.03440.961-0.426-0.4260.0000.0000.0000.000
141A160GLY00.0350.02739.4530.3150.3150.0000.0000.0000.000
142A161LYS10.7900.89739.87814.02414.0240.0000.0000.0000.000
143A162ILE00.0170.00033.983-0.181-0.1810.0000.0000.0000.000
144A163ASN00.0280.00833.056-0.215-0.2150.0000.0000.0000.000
145A164LYS10.9600.98036.59114.97714.9770.0000.0000.0000.000
146A165LYS10.9830.99934.05517.83317.8330.0000.0000.0000.000
147A166ARG10.9190.97738.99114.28614.2860.0000.0000.0000.000
148A167ILE00.0090.00333.943-0.090-0.0900.0000.0000.0000.000
149A168ALA00.0600.03037.8580.2770.2770.0000.0000.0000.000
150A169LEU0-0.045-0.02036.974-0.508-0.5080.0000.0000.0000.000
151A170THR00.0470.01334.4630.1070.1070.0000.0000.0000.000
152A171ASP-1-0.858-0.91831.395-19.667-19.6670.0000.0000.0000.000
153A172ASN00.0060.00332.579-0.255-0.2550.0000.0000.0000.000
154A173ALA0-0.025-0.01829.4110.0630.0630.0000.0000.0000.000
155A174LEU0-0.029-0.00731.452-0.163-0.1630.0000.0000.0000.000
156A175ILE0-0.0020.00833.5290.1510.1510.0000.0000.0000.000
157A176ALA00.0130.00132.6140.0360.0360.0000.0000.0000.000
158A177ARG10.9200.97029.08919.56919.5690.0000.0000.0000.000
159A178SER0-0.068-0.02132.295-0.057-0.0570.0000.0000.0000.000
160A179LEU0-0.005-0.02535.6790.2400.2400.0000.0000.0000.000
161A180GLY00.0560.03234.8170.2580.2580.0000.0000.0000.000
162A181LYS10.8450.92335.90416.28616.2860.0000.0000.0000.000
163A182TYR-1-0.902-0.95137.175-15.068-15.0680.0000.0000.0000.000
164A183GLY00.0160.02538.9400.4410.4410.0000.0000.0000.000
165A184ILE0-0.044-0.04438.358-0.356-0.3560.0000.0000.0000.000
166A185ILE00.0380.01434.113-0.417-0.4170.0000.0000.0000.000
167A186CYS0-0.083-0.01935.971-0.306-0.3060.0000.0000.0000.000
168A187MET00.0620.03038.4690.2190.2190.0000.0000.0000.000
169A188GLU-1-0.767-0.87441.169-13.781-13.7810.0000.0000.0000.000
170A189ASP-1-0.745-0.85240.433-15.088-15.0880.0000.0000.0000.000
171A190LEU0-0.028-0.00740.9630.2220.2220.0000.0000.0000.000
172A191ILE00.0100.00343.9650.3280.3280.0000.0000.0000.000
173A192HIS00.0390.04546.3880.3270.3270.0000.0000.0000.000
174A193GLU-1-0.794-0.88546.106-12.915-12.9150.0000.0000.0000.000
175A194ILE0-0.053-0.03747.5500.2820.2820.0000.0000.0000.000
176A195TYR0-0.015-0.01749.9890.3120.3120.0000.0000.0000.000
177A196THR0-0.036-0.03650.5480.2510.2510.0000.0000.0000.000
178A197VAL0-0.051-0.01852.3850.2130.2130.0000.0000.0000.000
179A198GLY00.0550.04250.920-0.240-0.2400.0000.0000.0000.000
180A199LYS10.9310.93848.27612.73012.7300.0000.0000.0000.000
181A200ARG10.8630.94443.35114.07614.0760.0000.0000.0000.000
182A201PHE0-0.0140.00346.739-0.124-0.1240.0000.0000.0000.000
183A202LYS10.9550.98348.25412.79812.7980.0000.0000.0000.000
184A203GLU-1-0.792-0.89943.431-13.517-13.5170.0000.0000.0000.000
185A204ALA00.0270.01043.684-0.243-0.2430.0000.0000.0000.000
186A205ASN0-0.008-0.01544.759-0.211-0.2110.0000.0000.0000.000
187A206ASN00.0060.01645.4950.1130.1130.0000.0000.0000.000
188A207PHE00.0120.00537.707-0.174-0.1740.0000.0000.0000.000
189A208LEU00.0210.02242.632-0.238-0.2380.0000.0000.0000.000
190A209TRP0-0.024-0.03042.4540.2220.2220.0000.0000.0000.000
191A210PRO0-0.042-0.02545.6490.0810.0810.0000.0000.0000.000
192A211PHE00.0300.01547.236-0.145-0.1450.0000.0000.0000.000
193A212LYS10.8970.94548.33012.59212.5920.0000.0000.0000.000
194A213LEU0-0.036-0.01150.401-0.210-0.2100.0000.0000.0000.000
195A214SER00.0150.00753.206-0.017-0.0170.0000.0000.0000.000
196A215SER00.0280.00355.2830.1600.1600.0000.0000.0000.000
197A216PRO0-0.044-0.00959.031-0.072-0.0720.0000.0000.0000.000
198A217ARG10.9850.98859.22410.51510.5150.0000.0000.0000.000
199A218GLY00.0660.04662.7820.0880.0880.0000.0000.0000.000
200A219GLY0-0.040-0.02065.236-0.120-0.1200.0000.0000.0000.000
201A220MET00.0660.02966.2340.0500.0500.0000.0000.0000.000
202A221LYS10.9710.98469.9088.4638.4630.0000.0000.0000.000
203A222LYS10.9890.98772.6198.3718.3710.0000.0000.0000.000
204A223LYS10.9770.99364.9709.7389.7380.0000.0000.0000.000
205A224THR0-0.083-0.05968.560-0.155-0.1550.0000.0000.0000.000
206A225THR00.0140.04570.5770.0290.0290.0000.0000.0000.000
207A226HIS00.0510.02071.125-0.135-0.1350.0000.0000.0000.000
208A227PHE0-0.021-0.02068.5290.0270.0270.0000.0000.0000.000
209A228VAL00.024-0.00571.2770.0090.0090.0000.0000.0000.000
210A229GLU-1-0.902-0.93174.704-8.094-8.0940.0000.0000.0000.000
211A230GLY00.0240.01275.1090.0700.0700.0000.0000.0000.000
212A231GLY0-0.058-0.02771.220-0.050-0.0500.0000.0000.0000.000
213A232ASP-1-0.945-0.99666.521-9.630-9.6300.0000.0000.0000.000
214A233ALA00.0040.00666.5620.0730.0730.0000.0000.0000.000
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