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: 4LLKN

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 OptH
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 -2552296.049067
FMO2-HF: Nuclear repulsion 2467876.765227
FMO2-HF: Total energy -84419.28384
FMO2-MP2: Total energy -84666.973233


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.
-0.8970.147-0.005-0.536-0.5030.001
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 : 0.018 / 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].
3A2ALA00.0080.0103.789-1.084-0.040-0.005-0.536-0.5030.001
4A3ALA00.0600.0245.991-0.031-0.0310.0000.0000.0000.000
5A4GLY00.0320.0327.9510.1780.1780.0000.0000.0000.000
6A5THR0-0.079-0.03711.473-0.010-0.0100.0000.0000.0000.000
7A6LEU0-0.023-0.01115.1450.0240.0240.0000.0000.0000.000
8A7TYR0-0.0040.00317.2350.0070.0070.0000.0000.0000.000
9A8THR00.026-0.04320.8180.0120.0120.0000.0000.0000.000
10A9TYR00.0120.02623.4320.0000.0000.0000.0000.0000.000
11A10PRO00.038-0.01125.883-0.007-0.0070.0000.0000.0000.000
12A11GLU-1-0.885-0.93926.292-0.100-0.1000.0000.0000.0000.000
13A12ASN0-0.0270.00824.3780.0100.0100.0000.0000.0000.000
14A13TRP00.0750.02324.396-0.012-0.0120.0000.0000.0000.000
15A14ARG10.9370.95723.6410.0490.0490.0000.0000.0000.000
16A15ALA0-0.003-0.00820.516-0.006-0.0060.0000.0000.0000.000
17A16PHE00.0240.01019.579-0.022-0.0220.0000.0000.0000.000
18A17LYS10.8810.93419.4580.0660.0660.0000.0000.0000.000
19A18ALA00.007-0.00315.448-0.013-0.0130.0000.0000.0000.000
20A19LEU0-0.0100.00014.798-0.048-0.0480.0000.0000.0000.000
21A20ILE00.0160.00615.785-0.024-0.0240.0000.0000.0000.000
22A21ALA00.012-0.00413.384-0.009-0.0090.0000.0000.0000.000
23A22ALA00.0120.00810.975-0.033-0.0330.0000.0000.0000.000
24A23GLN0-0.048-0.01011.060-0.046-0.0460.0000.0000.0000.000
25A24TYR0-0.018-0.01712.3690.0200.0200.0000.0000.0000.000
26A25SER0-0.053-0.0367.499-0.006-0.0060.0000.0000.0000.000
27A26GLY00.0360.0216.894-0.071-0.0710.0000.0000.0000.000
28A27ALA0-0.033-0.0167.008-0.141-0.1410.0000.0000.0000.000
29A28GLN0-0.024-0.0145.3400.2320.2320.0000.0000.0000.000
30A29VAL0-0.005-0.0049.9630.0180.0180.0000.0000.0000.000
31A30ARG10.8780.93712.5350.3850.3850.0000.0000.0000.000
32A31VAL00.0350.01315.7830.0170.0170.0000.0000.0000.000
33A32LEU0-0.044-0.01219.1250.0120.0120.0000.0000.0000.000
34A33SER00.038-0.00521.7940.0080.0080.0000.0000.0000.000
35A34ALA00.0690.03325.0100.0100.0100.0000.0000.0000.000
36A35PRO0-0.060-0.02624.2650.0040.0040.0000.0000.0000.000
37A36PRO00.0160.01025.1570.0060.0060.0000.0000.0000.000
38A37HIS00.0080.00327.9540.0060.0060.0000.0000.0000.000
39A38PHE0-0.029-0.02131.1200.0030.0030.0000.0000.0000.000
40A39HIS00.016-0.00825.8030.0060.0060.0000.0000.0000.000
41A40PHE0-0.019-0.03624.780-0.008-0.0080.0000.0000.0000.000
42A41GLY00.0550.01327.8110.0040.0040.0000.0000.0000.000
43A42GLN0-0.015-0.01130.1770.0020.0020.0000.0000.0000.000
44A43THR0-0.0080.05025.9850.0050.0050.0000.0000.0000.000
45A44ASN00.0310.01026.6750.0010.0010.0000.0000.0000.000
46A45ARG10.8400.91127.6820.0360.0360.0000.0000.0000.000
47A46THR00.0030.02327.2840.0050.0050.0000.0000.0000.000
48A47PRO00.0810.01228.5570.0000.0000.0000.0000.0000.000
49A48GLU-1-0.798-0.89623.683-0.014-0.0140.0000.0000.0000.000
50A49PHE0-0.084-0.02922.7300.0020.0020.0000.0000.0000.000
51A50LEU00.0190.01324.3130.0020.0020.0000.0000.0000.000
52A51ARG10.8650.96421.204-0.005-0.0050.0000.0000.0000.000
53A52LYS10.8520.92619.2090.0500.0500.0000.0000.0000.000
54A53PHE00.002-0.02417.9810.0040.0040.0000.0000.0000.000
55A54PRO00.0380.03622.939-0.005-0.0050.0000.0000.0000.000
56A55ALA0-0.019-0.00725.427-0.001-0.0010.0000.0000.0000.000
57A56GLY0-0.0100.00626.379-0.002-0.0020.0000.0000.0000.000
58A57LYS10.8840.95022.7050.0480.0480.0000.0000.0000.000
59A58VAL00.0190.06323.193-0.004-0.0040.0000.0000.0000.000
60A59PRO0-0.099-0.07020.0750.0080.0080.0000.0000.0000.000
61A60ALA0-0.025-0.01719.5440.0120.0120.0000.0000.0000.000
62A61PHE00.003-0.00410.171-0.013-0.0130.0000.0000.0000.000
63A62GLU-1-0.816-0.91914.808-0.031-0.0310.0000.0000.0000.000
64A63GLY00.0070.00210.554-0.062-0.0620.0000.0000.0000.000
65A64ASP-1-0.829-0.9349.338-0.373-0.3730.0000.0000.0000.000
66A65ASP-1-0.924-0.9608.1710.2750.2750.0000.0000.0000.000
67A66GLY0-0.0080.00210.8260.0650.0650.0000.0000.0000.000
68A67PHE0-0.0390.00311.0440.0190.0190.0000.0000.0000.000
69A68CYS0-0.042-0.01913.086-0.076-0.0760.0000.0000.0000.000
70A69VAL0-0.0050.00414.3390.0260.0260.0000.0000.0000.000
71A70PHE00.0390.00616.798-0.029-0.0290.0000.0000.0000.000
72A71GLU-1-0.843-0.93619.501-0.027-0.0270.0000.0000.0000.000
73A72SER0-0.041-0.01819.278-0.008-0.0080.0000.0000.0000.000
74A73ASN00.0410.00618.746-0.031-0.0310.0000.0000.0000.000
75A74ALA00.0230.02016.876-0.010-0.0100.0000.0000.0000.000
76A75ILE00.0010.00314.705-0.006-0.0060.0000.0000.0000.000
77A76ALA00.0360.01613.664-0.054-0.0540.0000.0000.0000.000
78A77TYR00.0610.06711.918-0.063-0.0630.0000.0000.0000.000
79A78TYR0-0.007-0.0028.157-0.147-0.1470.0000.0000.0000.000
80A79VAL0-0.0120.0018.950-0.106-0.1060.0000.0000.0000.000
81A80SER0-0.022-0.0359.625-0.088-0.0880.0000.0000.0000.000
82A81ASN00.0570.0217.771-0.115-0.1150.0000.0000.0000.000
83A82GLU-1-0.943-0.9808.9300.1630.1630.0000.0000.0000.000
84A83GLU-1-0.926-0.96310.819-0.109-0.1090.0000.0000.0000.000
85A84LEU0-0.054-0.02112.3660.0220.0220.0000.0000.0000.000
86A85ARG10.8670.9267.4780.1970.1970.0000.0000.0000.000
87A86GLY00.0130.00914.4080.0190.0190.0000.0000.0000.000
88A87SER00.0160.00514.4810.0160.0160.0000.0000.0000.000
89A88THR00.0390.02915.5010.0200.0200.0000.0000.0000.000
90A89PRO00.0630.01618.638-0.007-0.0070.0000.0000.0000.000
91A90GLU-1-0.897-0.94820.2710.0410.0410.0000.0000.0000.000
92A91ALA0-0.011-0.00219.079-0.008-0.0080.0000.0000.0000.000
93A92ALA00.0290.01017.270-0.012-0.0120.0000.0000.0000.000
94A93ALA0-0.012-0.00519.003-0.005-0.0050.0000.0000.0000.000
95A94GLN0-0.011-0.01822.476-0.009-0.0090.0000.0000.0000.000
96A95VAL0-0.0010.00517.934-0.008-0.0080.0000.0000.0000.000
97A96VAL00.001-0.00120.113-0.007-0.0070.0000.0000.0000.000
98A97GLN0-0.0160.00422.1830.0010.0010.0000.0000.0000.000
99A98TRP00.012-0.00624.244-0.002-0.0020.0000.0000.0000.000
100A99VAL0-0.030-0.00820.450-0.005-0.0050.0000.0000.0000.000
101A100SER00.000-0.00823.8950.0000.0000.0000.0000.0000.000
102A101PHE00.0040.01626.489-0.001-0.0010.0000.0000.0000.000
103A102ALA0-0.015-0.01926.222-0.001-0.0010.0000.0000.0000.000
104A103ASP-1-0.867-0.93025.293-0.037-0.0370.0000.0000.0000.000
105A104SER0-0.055-0.05728.5100.0010.0010.0000.0000.0000.000
106A105ASP-1-0.846-0.90631.655-0.011-0.0110.0000.0000.0000.000
107A106ILE0-0.041-0.01929.820-0.001-0.0010.0000.0000.0000.000
108A107VAL00.000-0.00129.048-0.001-0.0010.0000.0000.0000.000
109A108PRO00.0150.06432.227-0.001-0.0010.0000.0000.0000.000
110A109PRO00.0310.02735.4070.0000.0000.0000.0000.0000.000
111A110ALA00.0490.01134.1320.0000.0000.0000.0000.0000.000
112A111SER0-0.059-0.07434.487-0.002-0.0020.0000.0000.0000.000
113A112THR0-0.057-0.02636.5640.0010.0010.0000.0000.0000.000
114A113TRP0-0.010-0.00539.5680.0000.0000.0000.0000.0000.000
115A114VAL00.023-0.00436.2320.0000.0000.0000.0000.0000.000
116A115PHE00.0220.00834.058-0.001-0.0010.0000.0000.0000.000
117A116PRO00.0000.02539.4730.0000.0000.0000.0000.0000.000
118A117THR0-0.105-0.05240.284-0.001-0.0010.0000.0000.0000.000
119A118LEU0-0.032-0.02236.056-0.001-0.0010.0000.0000.0000.000
120A119GLY00.0280.02740.6140.0000.0000.0000.0000.0000.000
121A120ILE0-0.085-0.03937.0880.0010.0010.0000.0000.0000.000
122A121MET0-0.024-0.02340.1500.0020.0020.0000.0000.0000.000
123A122HIS00.0220.02442.538-0.001-0.0010.0000.0000.0000.000
124A123HIS00.0520.02145.8990.0000.0000.0000.0000.0000.000
125A124ASN00.0560.03447.2050.0010.0010.0000.0000.0000.000
126A125LYS10.8640.90548.4450.0160.0160.0000.0000.0000.000
127A126GLN00.0320.02049.847-0.001-0.0010.0000.0000.0000.000
128A127ALA00.0440.02945.2650.0000.0000.0000.0000.0000.000
129A128THR00.005-0.01044.390-0.001-0.0010.0000.0000.0000.000
130A129GLU-1-0.811-0.90044.739-0.020-0.0200.0000.0000.0000.000
131A130ASN00.003-0.01445.6130.0000.0000.0000.0000.0000.000
132A131ALA00.0220.01541.0020.0000.0000.0000.0000.0000.000
133A132LYS10.8570.93941.0390.0200.0200.0000.0000.0000.000
134A133GLU-1-0.923-0.96542.106-0.015-0.0150.0000.0000.0000.000
135A134GLU-1-0.789-0.87538.976-0.015-0.0150.0000.0000.0000.000
136A135VAL0-0.036-0.02536.719-0.001-0.0010.0000.0000.0000.000
137A136ARG10.9050.96138.0760.0190.0190.0000.0000.0000.000
138A137ARG10.8280.91236.8610.0130.0130.0000.0000.0000.000
139A138ILE00.0130.01033.6470.0000.0000.0000.0000.0000.000
140A139LEU0-0.027-0.01134.587-0.001-0.0010.0000.0000.0000.000
141A140GLY00.028-0.00236.266-0.001-0.0010.0000.0000.0000.000
142A141LEU0-0.037-0.00733.2130.0010.0010.0000.0000.0000.000
143A142LEU0-0.003-0.00830.2710.0000.0000.0000.0000.0000.000
144A143ASP-1-0.824-0.91333.174-0.026-0.0260.0000.0000.0000.000
145A144ALA00.000-0.01135.6160.0000.0000.0000.0000.0000.000
146A145TYR0-0.042-0.00528.0850.0030.0030.0000.0000.0000.000
147A146LEU00.0130.00028.3670.0010.0010.0000.0000.0000.000
148A147LYS10.9410.98832.1160.0140.0140.0000.0000.0000.000
149A148THR0-0.042-0.02633.420-0.001-0.0010.0000.0000.0000.000
150A149ARG10.9320.97628.2420.0160.0160.0000.0000.0000.000
151A150THR00.0360.02126.197-0.001-0.0010.0000.0000.0000.000
152A151PHE0-0.015-0.02523.153-0.007-0.0070.0000.0000.0000.000
153A152LEU0-0.033-0.02324.2180.0070.0070.0000.0000.0000.000
154A153VAL0-0.019-0.01121.2750.0080.0080.0000.0000.0000.000
155A154GLY00.0050.01321.776-0.006-0.0060.0000.0000.0000.000
156A155GLU-1-0.910-0.96522.109-0.032-0.0320.0000.0000.0000.000
157A156ARG10.8630.92418.0640.0500.0500.0000.0000.0000.000
158A157VAL00.0160.03017.7320.0050.0050.0000.0000.0000.000
159A158THR00.0150.01516.971-0.007-0.0070.0000.0000.0000.000
160A159LEU00.020-0.01214.657-0.004-0.0040.0000.0000.0000.000
161A160ALA00.0150.04218.1350.0050.0050.0000.0000.0000.000
162A161ASP-1-0.716-0.87121.531-0.065-0.0650.0000.0000.0000.000
163A162ILE00.0180.01816.6790.0030.0030.0000.0000.0000.000
164A163THR0-0.025-0.03720.570-0.002-0.0020.0000.0000.0000.000
165A164VAL00.0150.02222.5270.0050.0050.0000.0000.0000.000
166A165VAL00.0040.00824.1860.0040.0040.0000.0000.0000.000
167A166CYS0-0.045-0.02722.4220.0000.0000.0000.0000.0000.000
168A167THR0-0.050-0.03725.4150.0040.0040.0000.0000.0000.000
169A168LEU0-0.031-0.01027.9530.0050.0050.0000.0000.0000.000
170A169LEU0-0.0070.01026.6840.0030.0030.0000.0000.0000.000
171A170TRP00.032-0.00529.8100.0030.0030.0000.0000.0000.000
172A171LEU00.0200.02132.8040.0020.0020.0000.0000.0000.000
173A172TYR0-0.019-0.06431.9770.0030.0030.0000.0000.0000.000
174A173LYS10.9680.99730.5430.0740.0740.0000.0000.0000.000
175A174GLN0-0.023-0.01434.958-0.002-0.0020.0000.0000.0000.000
176A175VAL00.033-0.00637.8570.0030.0030.0000.0000.0000.000
177A176LEU0-0.0170.01635.3270.0030.0030.0000.0000.0000.000
178A177GLU-1-0.705-0.84339.170-0.029-0.0290.0000.0000.0000.000
179A178PRO0-0.018-0.01141.5850.0010.0010.0000.0000.0000.000
180A179SER0-0.017-0.01842.5870.0010.0010.0000.0000.0000.000
181A180PHE0-0.020-0.00640.1600.0020.0020.0000.0000.0000.000
182A181ARG10.9170.95837.4970.0400.0400.0000.0000.0000.000
183A182GLN0-0.0120.00139.733-0.001-0.0010.0000.0000.0000.000
184A183ALA0-0.051-0.01842.2890.0010.0010.0000.0000.0000.000
185A184PHE0-0.016-0.00137.4380.0010.0010.0000.0000.0000.000
186A185PRO00.0230.01937.215-0.003-0.0030.0000.0000.0000.000
187A186ASN0-0.023-0.02134.411-0.004-0.0040.0000.0000.0000.000
188A187THR00.0190.01132.136-0.003-0.0030.0000.0000.0000.000
189A188ASN00.0340.04931.937-0.006-0.0060.0000.0000.0000.000
190A189ARG10.9010.97430.0110.0340.0340.0000.0000.0000.000
191A190TRP0-0.050-0.01125.432-0.003-0.0030.0000.0000.0000.000
192A191PHE00.0220.00927.849-0.007-0.0070.0000.0000.0000.000
193A192LEU0-0.007-0.01528.211-0.006-0.0060.0000.0000.0000.000
194A193THR0-0.005-0.02025.656-0.004-0.0040.0000.0000.0000.000
195A194CYS0-0.0210.00023.965-0.007-0.0070.0000.0000.0000.000
196A195ILE0-0.036-0.01923.528-0.011-0.0110.0000.0000.0000.000
197A196ASN0-0.058-0.03425.382-0.006-0.0060.0000.0000.0000.000
198A197GLN0-0.095-0.02720.606-0.004-0.0040.0000.0000.0000.000
199A198PRO00.0190.00119.188-0.004-0.0040.0000.0000.0000.000
200A199GLN00.0700.02515.4360.0120.0120.0000.0000.0000.000
201A200PHE00.0260.00818.155-0.009-0.0090.0000.0000.0000.000
202A201ARG10.9040.94820.9490.0950.0950.0000.0000.0000.000
203A202ALA0-0.018-0.00418.9850.0060.0060.0000.0000.0000.000
204A203VAL0-0.044-0.01418.634-0.007-0.0070.0000.0000.0000.000
205A204LEU0-0.066-0.03621.5750.0110.0110.0000.0000.0000.000
206A205GLY00.0230.03224.7160.0080.0080.0000.0000.0000.000
207A206GLU-1-0.917-0.96026.693-0.072-0.0720.0000.0000.0000.000
208A207VAL0-0.032-0.01128.1590.0020.0020.0000.0000.0000.000
209A208LYS10.9410.97630.9170.0490.0490.0000.0000.0000.000
210A209LEU0-0.020-0.02333.1570.0010.0010.0000.0000.0000.000
211A210CYS0-0.0370.00936.0700.0020.0020.0000.0000.0000.000
212A211GLU-1-0.879-0.95538.976-0.039-0.0390.0000.0000.0000.000
213A212LYS10.8170.88942.1400.0290.0290.0000.0000.0000.000
214A213MET0-0.045-0.03442.969-0.001-0.0010.0000.0000.0000.000
215A214ALA0-0.0140.01541.6720.0020.0020.0000.0000.0000.000