Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YNN72

Calculation Name: 5DQS-A-Xray372

Preferred Name: Elongation factor 1-beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DQS

Chain ID: A

ChEMBL ID: CHEMBL4295731

UniProt ID: P24534

Base Structure: X-ray

Registration Date: 2023-09-27

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

DOI:


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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2560916.796413
FMO2-HF: Nuclear repulsion 2476495.715572
FMO2-HF: Total energy -84421.080841
FMO2-MP2: Total energy -84668.808912


3D Structure
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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-1.9450.0780.004-1.212-0.8150.004
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.020
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].
3A2ALA00.0010.0043.493-2.246-0.2230.004-1.212-0.8150.004
4A3ALA00.0360.0235.9240.3720.3720.0000.0000.0000.000
5A4GLY00.0530.0287.8580.0390.0390.0000.0000.0000.000
6A5THR0-0.042-0.00811.4570.0540.0540.0000.0000.0000.000
7A6LEU0-0.0070.00415.214-0.018-0.0180.0000.0000.0000.000
8A7TYR0-0.045-0.04617.0770.0570.0570.0000.0000.0000.000
9A8THR00.005-0.04120.716-0.008-0.0080.0000.0000.0000.000
10A9TYR00.0180.02723.3340.0080.0080.0000.0000.0000.000
11A10PRO00.0400.00325.496-0.019-0.0190.0000.0000.0000.000
12A11GLU-1-0.888-0.94626.383-0.192-0.1920.0000.0000.0000.000
13A12ASN0-0.022-0.00624.3440.0130.0130.0000.0000.0000.000
14A13TRP00.0760.02924.124-0.028-0.0280.0000.0000.0000.000
15A14ARG10.8510.91323.4830.2030.2030.0000.0000.0000.000
16A15ALA00.0020.00220.334-0.033-0.0330.0000.0000.0000.000
17A16PHE00.0170.00419.356-0.044-0.0440.0000.0000.0000.000
18A17LYS10.8480.93619.5940.2830.2830.0000.0000.0000.000
19A18ALA00.0160.00915.417-0.034-0.0340.0000.0000.0000.000
20A19LEU00.001-0.00315.012-0.071-0.0710.0000.0000.0000.000
21A20ILE00.0290.00615.728-0.021-0.0210.0000.0000.0000.000
22A21ALA00.003-0.00813.5750.0060.0060.0000.0000.0000.000
23A22ALA00.0030.00011.213-0.058-0.0580.0000.0000.0000.000
24A23GLN0-0.048-0.01111.3190.0110.0110.0000.0000.0000.000
25A24TYR0-0.015-0.01712.6150.0750.0750.0000.0000.0000.000
26A25SER0-0.036-0.0317.4960.0930.0930.0000.0000.0000.000
27A26GLY00.0300.0257.197-0.050-0.0500.0000.0000.0000.000
28A27ALA0-0.0140.0087.215-0.093-0.0930.0000.0000.0000.000
29A28GLN0-0.027-0.0255.6550.4020.4020.0000.0000.0000.000
30A29VAL0-0.037-0.0279.7230.0370.0370.0000.0000.0000.000
31A30ARG10.8340.90312.4330.6040.6040.0000.0000.0000.000
32A31VAL00.013-0.00215.113-0.023-0.0230.0000.0000.0000.000
33A32LEU0-0.045-0.02018.5510.0400.0400.0000.0000.0000.000
34A33SER00.027-0.00921.529-0.001-0.0010.0000.0000.0000.000
35A34ALA00.011-0.00924.6490.0110.0110.0000.0000.0000.000
36A35PRO00.0040.01824.0090.0090.0090.0000.0000.0000.000
37A36PRO00.0250.02024.7240.0090.0090.0000.0000.0000.000
38A37HIS00.0120.00327.5800.0030.0030.0000.0000.0000.000
39A38PHE0-0.007-0.01030.6400.0060.0060.0000.0000.0000.000
40A39HIS0-0.003-0.00125.5520.0060.0060.0000.0000.0000.000
41A40PHE0-0.016-0.02124.032-0.020-0.0200.0000.0000.0000.000
42A41GLY00.0370.03527.9050.0120.0120.0000.0000.0000.000
43A42GLN0-0.002-0.01430.1060.0010.0010.0000.0000.0000.000
44A43THR00.0640.04026.5770.0040.0040.0000.0000.0000.000
45A44ASN00.0080.01226.4060.0100.0100.0000.0000.0000.000
46A45ARG10.8410.90927.5380.1570.1570.0000.0000.0000.000
47A46THR0-0.020-0.01127.5330.0070.0070.0000.0000.0000.000
48A47PRO00.0470.00628.224-0.010-0.0100.0000.0000.0000.000
49A48GLU-1-0.753-0.83522.173-0.191-0.1910.0000.0000.0000.000
50A49PHE00.0060.01822.699-0.017-0.0170.0000.0000.0000.000
51A50LEU00.003-0.00924.145-0.014-0.0140.0000.0000.0000.000
52A51ARG10.8260.89021.0450.1730.1730.0000.0000.0000.000
53A52LYS10.7720.89218.3040.2650.2650.0000.0000.0000.000
54A53PHE0-0.024-0.02017.608-0.028-0.0280.0000.0000.0000.000
55A54PRO00.0370.02322.5490.0130.0130.0000.0000.0000.000
56A55ALA0-0.0150.00224.9460.0140.0140.0000.0000.0000.000
57A56GLY0-0.0030.01226.2530.0080.0080.0000.0000.0000.000
58A57LYS10.8150.90323.3830.2750.2750.0000.0000.0000.000
59A58VAL0-0.0220.00723.458-0.010-0.0100.0000.0000.0000.000
60A59PRO0-0.064-0.04020.0080.0200.0200.0000.0000.0000.000
61A60ALA0-0.023-0.01119.2340.0030.0030.0000.0000.0000.000
62A61PHE0-0.002-0.00410.2390.0200.0200.0000.0000.0000.000
63A62GLU-1-0.742-0.86714.491-0.298-0.2980.0000.0000.0000.000
64A63GLY00.0110.01410.231-0.020-0.0200.0000.0000.0000.000
65A64ASP-1-0.836-0.9229.177-0.500-0.5000.0000.0000.0000.000
66A65ASP-1-0.866-0.9308.121-0.897-0.8970.0000.0000.0000.000
67A66GLY00.0010.00310.2130.1070.1070.0000.0000.0000.000
68A67PHE0-0.055-0.00810.5140.0590.0590.0000.0000.0000.000
69A68CYS0-0.053-0.02912.444-0.034-0.0340.0000.0000.0000.000
70A69VAL0-0.009-0.00213.8490.0310.0310.0000.0000.0000.000
71A70PHE00.0290.00216.643-0.006-0.0060.0000.0000.0000.000
72A71GLU-1-0.742-0.84719.040-0.248-0.2480.0000.0000.0000.000
73A72SER0-0.005-0.02318.735-0.044-0.0440.0000.0000.0000.000
74A73ASN00.0260.01318.357-0.055-0.0550.0000.0000.0000.000
75A74ALA00.0220.01816.629-0.040-0.0400.0000.0000.0000.000
76A75ILE0-0.017-0.00314.364-0.093-0.0930.0000.0000.0000.000
77A76ALA00.0320.01113.405-0.132-0.1320.0000.0000.0000.000
78A77TYR00.0370.03212.085-0.110-0.1100.0000.0000.0000.000
79A78TYR0-0.0070.0037.913-0.201-0.2010.0000.0000.0000.000
80A79VAL0-0.014-0.0118.696-0.401-0.4010.0000.0000.0000.000
81A80SER0-0.0030.0059.355-0.015-0.0150.0000.0000.0000.000
82A81ASN00.003-0.0187.469-0.391-0.3910.0000.0000.0000.000
83A82GLU-1-0.945-0.9828.417-0.180-0.1800.0000.0000.0000.000
84A83GLU-1-0.878-0.93210.263-0.230-0.2300.0000.0000.0000.000
85A84LEU0-0.040-0.00912.3600.0430.0430.0000.0000.0000.000
86A85ARG10.8470.9247.1061.5231.5230.0000.0000.0000.000
87A86GLY00.0120.01114.3240.0450.0450.0000.0000.0000.000
88A87SER0-0.008-0.00313.931-0.009-0.0090.0000.0000.0000.000
89A88THR0-0.025-0.02515.0810.0310.0310.0000.0000.0000.000
90A89PRO00.0410.01918.544-0.027-0.0270.0000.0000.0000.000
91A90GLU-1-0.823-0.89920.448-0.121-0.1210.0000.0000.0000.000
92A91ALA0-0.0060.00418.893-0.007-0.0070.0000.0000.0000.000
93A92ALA00.0350.01717.501-0.016-0.0160.0000.0000.0000.000
94A93ALA0-0.010-0.00219.207-0.011-0.0110.0000.0000.0000.000
95A94GLN00.009-0.00422.798-0.003-0.0030.0000.0000.0000.000
96A95VAL0-0.003-0.00117.8840.0030.0030.0000.0000.0000.000
97A96VAL00.0130.00420.160-0.003-0.0030.0000.0000.0000.000
98A97GLN0-0.0200.01522.3860.0120.0120.0000.0000.0000.000
99A98TRP0-0.016-0.01824.0780.0090.0090.0000.0000.0000.000
100A99VAL0-0.024-0.01720.2810.0020.0020.0000.0000.0000.000
101A100SER0-0.052-0.03823.7350.0030.0030.0000.0000.0000.000
102A101PHE00.0210.01126.4460.0080.0080.0000.0000.0000.000
103A102ALA0-0.002-0.00126.0700.0100.0100.0000.0000.0000.000
104A103ASP-1-0.767-0.90625.159-0.238-0.2380.0000.0000.0000.000
105A104SER0-0.046-0.02528.3680.0050.0050.0000.0000.0000.000
106A105ASP-1-0.812-0.88931.373-0.116-0.1160.0000.0000.0000.000
107A106ILE0-0.009-0.00929.7060.0070.0070.0000.0000.0000.000
108A107VAL0-0.0130.00029.0660.0050.0050.0000.0000.0000.000
109A108PRO00.0220.03532.2270.0050.0050.0000.0000.0000.000
110A109PRO00.0270.03535.4250.0060.0060.0000.0000.0000.000
111A110ALA00.0470.00933.7180.0050.0050.0000.0000.0000.000
112A111SER0-0.053-0.03334.1890.0010.0010.0000.0000.0000.000
113A112THR0-0.066-0.04436.3030.0060.0060.0000.0000.0000.000
114A113TRP00.0100.00239.3260.0060.0060.0000.0000.0000.000
115A114VAL00.017-0.00535.7330.0040.0040.0000.0000.0000.000
116A115PHE00.0260.01633.6230.0010.0010.0000.0000.0000.000
117A116PRO0-0.0150.00439.2120.0020.0020.0000.0000.0000.000
118A117THR0-0.098-0.05940.2340.0020.0020.0000.0000.0000.000
119A118LEU0-0.031-0.01536.2000.0000.0000.0000.0000.0000.000
120A119GLY0-0.0040.00440.5680.0000.0000.0000.0000.0000.000
121A120ILE0-0.038-0.01136.8600.0010.0010.0000.0000.0000.000
122A121MET0-0.008-0.01339.955-0.002-0.0020.0000.0000.0000.000
123A122HIS00.0410.02342.4310.0010.0010.0000.0000.0000.000
124A123HIS00.0640.04045.726-0.004-0.0040.0000.0000.0000.000
125A124ASN00.0020.00247.1610.0050.0050.0000.0000.0000.000
126A125LYS10.8790.92948.1420.0620.0620.0000.0000.0000.000
127A126GLN00.0260.03049.545-0.001-0.0010.0000.0000.0000.000
128A127ALA00.0550.03045.217-0.001-0.0010.0000.0000.0000.000
129A128THR0-0.001-0.02344.157-0.004-0.0040.0000.0000.0000.000
130A129GLU-1-0.769-0.87244.642-0.070-0.0700.0000.0000.0000.000
131A130ASN0-0.039-0.04045.440-0.001-0.0010.0000.0000.0000.000
132A131ALA00.0170.01540.745-0.002-0.0020.0000.0000.0000.000
133A132LYS10.8260.90940.8910.0690.0690.0000.0000.0000.000
134A133GLU-1-0.865-0.93942.018-0.073-0.0730.0000.0000.0000.000
135A134GLU-1-0.800-0.86339.167-0.099-0.0990.0000.0000.0000.000
136A135VAL0-0.010-0.00936.942-0.004-0.0040.0000.0000.0000.000
137A136ARG10.8150.91338.1190.0740.0740.0000.0000.0000.000
138A137ARG10.7540.83936.3130.1040.1040.0000.0000.0000.000
139A138ILE0-0.016-0.00333.313-0.001-0.0010.0000.0000.0000.000
140A139LEU00.0160.00134.267-0.003-0.0030.0000.0000.0000.000
141A140GLY00.0430.01836.1680.0010.0010.0000.0000.0000.000
142A141LEU0-0.044-0.00832.9240.0030.0030.0000.0000.0000.000
143A142LEU00.0190.00429.896-0.001-0.0010.0000.0000.0000.000
144A143ASP-1-0.792-0.87533.129-0.081-0.0810.0000.0000.0000.000
145A144ALA0-0.018-0.01935.6090.0040.0040.0000.0000.0000.000
146A145TYR0-0.046-0.01526.8930.0080.0080.0000.0000.0000.000
147A146LEU00.0230.00228.3580.0020.0020.0000.0000.0000.000
148A147LYS10.8160.92731.8780.0770.0770.0000.0000.0000.000
149A148THR0-0.049-0.02433.4450.0030.0030.0000.0000.0000.000
150A149ARG10.9320.97628.1300.1010.1010.0000.0000.0000.000
151A150THR0-0.047-0.04225.9720.0020.0020.0000.0000.0000.000
152A151PHE0-0.043-0.03623.192-0.007-0.0070.0000.0000.0000.000
153A152LEU0-0.004-0.01624.0960.0110.0110.0000.0000.0000.000
154A153VAL0-0.0110.00020.6160.0090.0090.0000.0000.0000.000
155A154GLY00.0130.01721.654-0.007-0.0070.0000.0000.0000.000
156A155GLU-1-0.799-0.87522.144-0.101-0.1010.0000.0000.0000.000
157A156ARG10.8780.92918.1090.1250.1250.0000.0000.0000.000
158A157VAL00.0250.03217.932-0.001-0.0010.0000.0000.0000.000
159A158THR00.0120.00717.000-0.022-0.0220.0000.0000.0000.000
160A159LEU00.027-0.01014.6580.0130.0130.0000.0000.0000.000
161A160ALA00.0080.02518.1620.0150.0150.0000.0000.0000.000
162A161ASP-1-0.734-0.86721.201-0.200-0.2000.0000.0000.0000.000
163A162ILE00.0340.02316.8200.0160.0160.0000.0000.0000.000
164A163THR00.0080.00120.6390.0040.0040.0000.0000.0000.000
165A164VAL00.0110.01322.8100.0170.0170.0000.0000.0000.000
166A165VAL0-0.014-0.00224.3140.0160.0160.0000.0000.0000.000
167A166CYS0-0.056-0.03322.7680.0090.0090.0000.0000.0000.000
168A167THR0-0.050-0.03925.6850.0090.0090.0000.0000.0000.000
169A168LEU0-0.006-0.00528.2310.0150.0150.0000.0000.0000.000
170A169LEU0-0.0060.01826.9140.0140.0140.0000.0000.0000.000
171A170TRP00.0540.00629.3390.0160.0160.0000.0000.0000.000
172A171LEU00.0510.03032.9890.0090.0090.0000.0000.0000.000
173A172TYR00.008-0.02431.9860.0090.0090.0000.0000.0000.000
174A173LYS10.8910.97830.9680.1550.1550.0000.0000.0000.000
175A174GLN0-0.019-0.01035.2240.0010.0010.0000.0000.0000.000
176A175VAL00.0190.00338.1180.0060.0060.0000.0000.0000.000
177A176LEU00.0110.01435.4060.0060.0060.0000.0000.0000.000
178A177GLU-1-0.744-0.81639.337-0.068-0.0680.0000.0000.0000.000
179A178PRO0-0.003-0.01042.0010.0000.0000.0000.0000.0000.000
180A179SER0-0.036-0.03943.0160.0000.0000.0000.0000.0000.000
181A180PHE00.0280.02640.4720.0020.0020.0000.0000.0000.000
182A181ARG10.8960.91937.6970.0880.0880.0000.0000.0000.000
183A182GLN0-0.034-0.01139.9810.0000.0000.0000.0000.0000.000
184A183ALA0-0.023-0.00842.1790.0020.0020.0000.0000.0000.000
185A184PHE0-0.0040.01537.1830.0000.0000.0000.0000.0000.000
186A185PRO00.0200.01136.806-0.006-0.0060.0000.0000.0000.000
187A186ASN0-0.010-0.01733.959-0.001-0.0010.0000.0000.0000.000
188A187THR00.0280.00932.186-0.006-0.0060.0000.0000.0000.000
189A188ASN00.006-0.00332.072-0.012-0.0120.0000.0000.0000.000
190A189ARG10.8600.91530.2000.0920.0920.0000.0000.0000.000
191A190TRP0-0.0210.00425.3370.0010.0010.0000.0000.0000.000
192A191PHE00.0410.02527.803-0.011-0.0110.0000.0000.0000.000
193A192LEU0-0.008-0.01528.171-0.008-0.0080.0000.0000.0000.000
194A193THR0-0.012-0.01125.6800.0020.0020.0000.0000.0000.000
195A194CYS0-0.038-0.01523.943-0.008-0.0080.0000.0000.0000.000
196A195ILE0-0.035-0.02123.678-0.013-0.0130.0000.0000.0000.000
197A196ASN0-0.037-0.02425.415-0.002-0.0020.0000.0000.0000.000
198A197GLN0-0.048-0.01320.7160.0100.0100.0000.0000.0000.000
199A198PRO00.006-0.00619.344-0.013-0.0130.0000.0000.0000.000
200A199GLN00.0550.02215.2410.0230.0230.0000.0000.0000.000
201A200PHE00.0220.00718.368-0.030-0.0300.0000.0000.0000.000
202A201ARG10.8480.89721.3650.1240.1240.0000.0000.0000.000
203A202ALA0-0.028-0.00919.2480.0110.0110.0000.0000.0000.000
204A203VAL0-0.069-0.03318.699-0.016-0.0160.0000.0000.0000.000
205A204LEU0-0.049-0.03221.7780.0100.0100.0000.0000.0000.000
206A205GLY00.0200.03224.9700.0150.0150.0000.0000.0000.000
207A206GLU-1-0.835-0.89426.973-0.112-0.1120.0000.0000.0000.000
208A207VAL0-0.033-0.01628.043-0.001-0.0010.0000.0000.0000.000
209A208LYS10.8310.88931.1150.0880.0880.0000.0000.0000.000
210A209LEU0-0.008-0.00932.881-0.002-0.0020.0000.0000.0000.000
211A210CYS0-0.0410.01836.0600.0070.0070.0000.0000.0000.000
212A211GLU-1-0.790-0.88239.189-0.075-0.0750.0000.0000.0000.000
213A212LYS10.8330.87542.5540.0680.0680.0000.0000.0000.000
214A213MET0-0.021-0.00843.134-0.003-0.0030.0000.0000.0000.000
215A214ALA0-0.039-0.00341.8850.0030.0030.0000.0000.0000.000