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: G6871

Calculation Name: 5SV7-D-Xray372

Preferred Name: Eukaryotic translation initiation factor 2-alpha kinase 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5SV7

Chain ID: D

ChEMBL ID: CHEMBL6030

UniProt ID: Q9NZJ5

Base Structure: X-ray

Registration Date: 2023-06-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2319766.019569
FMO2-HF: Nuclear repulsion 2236149.369022
FMO2-HF: Total energy -83616.650547
FMO2-MP2: Total energy -83860.847543


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(D:104:SER)


Summations of interaction energy for fragment #1(D:104:SER)
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.
-15.554-13.9779.864-5.5-5.941-0.023
Interaction energy analysis for fragmet #1(D:104:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.031
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].
3D106VAL0-0.028-0.0113.8320.3161.253-0.008-0.557-0.3710.002
4D107ILE0-0.060-0.0127.0100.4180.4180.0000.0000.0000.000
5D108ILE00.025-0.0109.735-0.071-0.0710.0000.0000.0000.000
6D109SER0-0.053-0.00313.4150.0730.0730.0000.0000.0000.000
7D110THR00.0360.01116.296-0.057-0.0570.0000.0000.0000.000
8D111LEU00.0300.01519.2080.0440.0440.0000.0000.0000.000
9D112ASP-1-0.897-0.96921.905-0.079-0.0790.0000.0000.0000.000
10D113GLY0-0.036-0.01721.8770.0130.0130.0000.0000.0000.000
11D114ARG10.8420.91216.6120.1120.1120.0000.0000.0000.000
12D115ILE0-0.026-0.01612.5210.0060.0060.0000.0000.0000.000
13D116ALA0-0.055-0.04013.0370.0100.0100.0000.0000.0000.000
14D117ALA00.0160.0097.710-0.028-0.0280.0000.0000.0000.000
15D118LEU0-0.018-0.0098.5020.1350.1350.0000.0000.0000.000
16D119ASP-1-0.845-0.9294.126-3.299-3.202-0.001-0.020-0.0760.000
17D120PRO0-0.024-0.0063.8390.7200.9300.001-0.044-0.1680.000
18D121GLU-1-0.976-0.9863.683-7.689-6.8230.011-0.362-0.515-0.002
19D122ASN00.0040.0026.8190.6700.6700.0000.0000.0000.000
20D123HIS00.0400.0279.5230.2620.2620.0000.0000.0000.000
21D124GLY0-0.049-0.03410.5760.0580.0580.0000.0000.0000.000
22D125LYS10.9280.9699.6430.6750.6750.0000.0000.0000.000
23D126LYS10.8140.9069.1890.1100.1100.0000.0000.0000.000
24D127GLN00.010-0.0075.5760.3810.3810.0000.0000.0000.000
25D128TRP0-0.047-0.0107.278-0.095-0.0950.0000.0000.0000.000
26D129ASP-1-0.811-0.90911.511-0.173-0.1730.0000.0000.0000.000
27D130LEU00.0030.02514.1280.0310.0310.0000.0000.0000.000
28D131ASP-1-0.797-0.88316.088-0.012-0.0120.0000.0000.0000.000
29D132VAL0-0.052-0.02319.8160.0180.0180.0000.0000.0000.000
30D133GLY00.0760.02421.269-0.023-0.0230.0000.0000.0000.000
31D134SER0-0.098-0.05524.061-0.009-0.0090.0000.0000.0000.000
32D135GLY00.0250.01725.460-0.007-0.0070.0000.0000.0000.000
33D136SER00.0010.00225.164-0.010-0.0100.0000.0000.0000.000
34D137LEU0-0.049-0.00721.8990.0160.0160.0000.0000.0000.000
35D138VAL00.0060.01525.9300.0070.0070.0000.0000.0000.000
36D139SER0-0.060-0.02129.064-0.005-0.0050.0000.0000.0000.000
37D140SER0-0.152-0.17232.1980.0040.0040.0000.0000.0000.000
38D141SER0-0.0380.10335.572-0.008-0.0080.0000.0000.0000.000
39D142LEU00.1650.09836.7650.0050.0050.0000.0000.0000.000
40D151LYS10.8760.92744.3750.0340.0340.0000.0000.0000.000
41D152MET0-0.022-0.02038.663-0.001-0.0010.0000.0000.0000.000
42D153ILE0-0.0250.01538.710-0.002-0.0020.0000.0000.0000.000
43D154ILE00.007-0.00633.5870.0010.0010.0000.0000.0000.000
44D155PRO0-0.0190.01132.1400.0030.0030.0000.0000.0000.000
45D156SER00.0230.00728.061-0.016-0.0160.0000.0000.0000.000
46D157LEU0-0.012-0.02423.3310.0120.0120.0000.0000.0000.000
47D158ASP-1-0.881-0.94325.3600.0520.0520.0000.0000.0000.000
48D159GLY0-0.052-0.03926.7680.0180.0180.0000.0000.0000.000
49D160ALA00.0580.05830.5570.0010.0010.0000.0000.0000.000
50D161LEU0-0.012-0.01933.028-0.002-0.0020.0000.0000.0000.000
51D162PHE00.027-0.00332.0300.0010.0010.0000.0000.0000.000
52D163GLN0-0.0400.00037.202-0.003-0.0030.0000.0000.0000.000
53D164TRP00.0410.00539.218-0.001-0.0010.0000.0000.0000.000
54D165ASP-1-0.843-0.92941.126-0.025-0.0250.0000.0000.0000.000
55D166GLN0-0.010-0.00244.340-0.002-0.0020.0000.0000.0000.000
56D167ASP-1-0.923-0.95045.210-0.034-0.0340.0000.0000.0000.000
57D168ARG10.8450.91046.2120.0210.0210.0000.0000.0000.000
58D169GLU-1-0.958-0.98041.835-0.064-0.0640.0000.0000.0000.000
59D170SER00.0360.04841.750-0.003-0.0030.0000.0000.0000.000
60D171MET0-0.057-0.02835.5300.0020.0020.0000.0000.0000.000
61D172GLU-1-0.850-0.93639.251-0.024-0.0240.0000.0000.0000.000
62D173THR00.0220.00138.4440.0010.0010.0000.0000.0000.000
63D174VAL0-0.0310.00238.6440.0010.0010.0000.0000.0000.000
64D175PRO0-0.035-0.01339.8610.0020.0020.0000.0000.0000.000
65D176PHE00.026-0.00639.5810.0040.0040.0000.0000.0000.000
66D177THR0-0.027-0.02033.549-0.002-0.0020.0000.0000.0000.000
67D178VAL00.0140.00833.3040.0020.0020.0000.0000.0000.000
68D179GLU-1-0.875-0.96132.0170.1030.1030.0000.0000.0000.000
69D180SER00.0100.00735.339-0.003-0.0030.0000.0000.0000.000
70D181LEU00.0130.00638.216-0.001-0.0010.0000.0000.0000.000
71D182LEU0-0.065-0.00735.8220.0000.0000.0000.0000.0000.000
72D183GLU-1-0.958-0.95839.0460.0720.0720.0000.0000.0000.000
73D184SER0-0.005-0.00341.921-0.004-0.0040.0000.0000.0000.000
74D185SER0-0.063-0.03943.096-0.007-0.0070.0000.0000.0000.000
75D186TYR0-0.041-0.01943.1830.0020.0020.0000.0000.0000.000
76D187LYS10.8500.93247.712-0.022-0.0220.0000.0000.0000.000
77D188PHE00.029-0.00846.7520.0030.0030.0000.0000.0000.000
78D189GLY0-0.0250.00050.0580.0000.0000.0000.0000.0000.000
79D190ASP-1-0.903-0.95750.7710.0240.0240.0000.0000.0000.000
80D191ASP-1-0.879-0.92451.8580.0150.0150.0000.0000.0000.000
81D192VAL0-0.061-0.04047.5720.0010.0010.0000.0000.0000.000
82D193VAL0-0.028-0.01345.9830.0020.0020.0000.0000.0000.000
83D194LEU00.0250.00342.222-0.002-0.0020.0000.0000.0000.000
84D195VAL0-0.030-0.01439.5710.0040.0040.0000.0000.0000.000
85D196GLY00.046-0.01136.963-0.004-0.0040.0000.0000.0000.000
86D197GLY00.0350.00534.7160.0030.0030.0000.0000.0000.000
87D198LYS10.8980.98928.397-0.154-0.1540.0000.0000.0000.000
88D199SER0-0.011-0.00728.1800.0160.0160.0000.0000.0000.000
89D200LEU00.012-0.02124.688-0.008-0.0080.0000.0000.0000.000
90D201THR0-0.0260.02522.7420.0160.0160.0000.0000.0000.000
91D202THR00.0650.01718.011-0.007-0.0070.0000.0000.0000.000
92D203TYR0-0.015-0.01316.995-0.038-0.0380.0000.0000.0000.000
93D204GLY00.0200.02515.4110.0740.0740.0000.0000.0000.000
94D205LEU0-0.001-0.01811.555-0.101-0.1010.0000.0000.0000.000
95D206SER00.006-0.02411.0050.0450.0450.0000.0000.0000.000
96D207ALA0-0.0070.0295.7580.2700.2700.0000.0000.0000.000
97D208TYR00.0080.0203.2340.3740.8100.037-0.109-0.365-0.001
98D209SER00.0110.0057.6180.1160.1160.0000.0000.0000.000
99D210GLY00.053-0.0139.9930.0260.0260.0000.0000.0000.000
100D211LYS11.0170.97210.899-0.394-0.3940.0000.0000.0000.000
101D212VAL0-0.0290.02014.3230.0980.0980.0000.0000.0000.000
102D213ARG10.9741.00814.806-0.783-0.7830.0000.0000.0000.000
103D214TYR00.0510.02417.420-0.066-0.0660.0000.0000.0000.000
104D215ILE0-0.046-0.04719.1920.0170.0170.0000.0000.0000.000
105D216CYS0-0.0620.00321.640-0.040-0.0400.0000.0000.0000.000
106D217SER0-0.0010.00223.5950.0070.0070.0000.0000.0000.000
107D218ALA00.0320.01726.6990.0060.0060.0000.0000.0000.000
108D219LEU0-0.002-0.00429.714-0.006-0.0060.0000.0000.0000.000
109D220GLY00.0310.00829.820-0.006-0.0060.0000.0000.0000.000
110D221CYS00.011-0.02025.7970.0170.0170.0000.0000.0000.000
111D222ARG10.9150.97824.567-0.239-0.2390.0000.0000.0000.000
112D223GLN00.008-0.00421.0510.0290.0290.0000.0000.0000.000
113D224TRP0-0.029-0.02620.549-0.028-0.0280.0000.0000.0000.000
114D225ASP-1-0.957-0.96921.0610.3870.3870.0000.0000.0000.000
115D235ILE0-0.012-0.0088.224-0.124-0.1240.0000.0000.0000.000
116D236LEU0-0.011-0.0077.6910.3620.3620.0000.0000.0000.000
117D237LEU0-0.103-0.05210.382-0.209-0.2090.0000.0000.0000.000
118D238LEU00.0410.01512.593-0.019-0.0190.0000.0000.0000.000
119D239GLN00.0420.02815.208-0.044-0.0440.0000.0000.0000.000
120D240ARG10.8690.96418.739-0.144-0.1440.0000.0000.0000.000
121D241THR00.023-0.00421.2540.0090.0090.0000.0000.0000.000
122D242GLN00.001-0.00124.491-0.013-0.0130.0000.0000.0000.000
123D243LYS10.8760.94827.486-0.070-0.0700.0000.0000.0000.000
124D244THR0-0.046-0.01530.899-0.007-0.0070.0000.0000.0000.000
125D245VAL00.0510.02033.8750.0040.0040.0000.0000.0000.000
126D246ARG10.8780.93835.640-0.044-0.0440.0000.0000.0000.000
127D247ALA00.0760.05440.0940.0030.0030.0000.0000.0000.000
128D248VAL0-0.020-0.00643.718-0.003-0.0030.0000.0000.0000.000
129D249GLY00.0760.04346.2840.0000.0000.0000.0000.0000.000
130D250PRO0-0.0330.00449.992-0.001-0.0010.0000.0000.0000.000
131D251ARG10.9820.98952.910-0.021-0.0210.0000.0000.0000.000
132D252SER0-0.037-0.03152.0740.0020.0020.0000.0000.0000.000
133D253GLY00.0400.02648.451-0.001-0.0010.0000.0000.0000.000
134D254ASN0-0.048-0.02047.3310.0020.0020.0000.0000.0000.000
135D255GLU-1-0.874-0.94141.0640.0140.0140.0000.0000.0000.000
136D256LYS10.9020.94644.769-0.014-0.0140.0000.0000.0000.000
137D257TRP00.0480.01340.065-0.003-0.0030.0000.0000.0000.000
138D258ASN0-0.045-0.06236.9520.0090.0090.0000.0000.0000.000
139D259PHE00.0780.03234.761-0.006-0.0060.0000.0000.0000.000
140D260SER0-0.040-0.03130.5880.0140.0140.0000.0000.0000.000
141D261VAL00.0310.03528.220-0.011-0.0110.0000.0000.0000.000
142D262GLY00.011-0.00425.1770.0160.0160.0000.0000.0000.000
143D263HIS0-0.001-0.01021.436-0.009-0.0090.0000.0000.0000.000
144D264PHE00.016-0.03217.0220.0140.0140.0000.0000.0000.000
145D265GLU-1-0.900-0.91116.5950.2350.2350.0000.0000.0000.000
146D266LEU0-0.007-0.0199.8270.0700.0700.0000.0000.0000.000
147D267ARG10.9630.97412.381-0.822-0.8220.0000.0000.0000.000
148D268TYR0-0.031-0.0028.811-0.054-0.0540.0000.0000.0000.000
149D269ILE0-0.0200.00110.952-0.183-0.1830.0000.0000.0000.000
150D270PRO00.0470.0309.9950.0220.0220.0000.0000.0000.000
151D310ILE0-0.017-0.0208.1110.0560.0560.0000.0000.0000.000
152D311LYS10.9060.94011.3890.8720.8720.0000.0000.0000.000
153D312VAL0-0.034-0.01212.7170.0110.0110.0000.0000.0000.000
154D313SER0-0.0120.01115.3570.0650.0650.0000.0000.0000.000
155D314VAL00.067-0.00218.7220.0010.0010.0000.0000.0000.000
156D315ALA00.0120.02221.1960.0240.0240.0000.0000.0000.000
157D316ASP-1-0.872-0.93922.476-0.300-0.3000.0000.0000.0000.000
158D317TRP0-0.0250.00220.742-0.006-0.0060.0000.0000.0000.000
159D318LYS10.9030.96418.7940.4160.4160.0000.0000.0000.000
160D319VAL00.0430.01512.429-0.004-0.0040.0000.0000.0000.000
161D320MET00.0890.05711.2330.0610.0610.0000.0000.0000.000
162D333TYR00.0290.00113.6950.0410.0410.0000.0000.0000.000
163D334GLN0-0.013-0.02016.461-0.037-0.0370.0000.0000.0000.000
164D335PHE00.0210.01615.4360.0140.0140.0000.0000.0000.000
165D336CYS0-0.030-0.02019.9460.0230.0230.0000.0000.0000.000
166D337THR0-0.016-0.00922.9640.0290.0290.0000.0000.0000.000
167D338PRO0-0.0260.00222.225-0.024-0.0240.0000.0000.0000.000
168D339ILE00.0190.01017.4000.0170.0170.0000.0000.0000.000
169D340ALA00.0370.01318.8750.0210.0210.0000.0000.0000.000
170D341SER0-0.042-0.03615.9410.0280.0280.0000.0000.0000.000
171D342ALA00.0230.00911.930-0.026-0.0260.0000.0000.0000.000
172D343TRP00.014-0.0039.1800.1140.1140.0000.0000.0000.000
173D344LEU00.0220.0044.370-0.477-0.408-0.001-0.010-0.0580.000
174D345LEU0-0.0020.0233.167-0.0481.5920.469-0.813-1.2960.004
175D346LYS11.0260.9891.953-6.597-9.3509.343-3.641-2.948-0.026
176D347ASP-1-0.970-0.9823.5821.4871.5620.0130.056-0.1440.000
177D348GLY00.0320.0205.274-0.356-0.3560.0000.0000.0000.000
178D349LYS10.9340.9546.201-1.314-1.3140.0000.0000.0000.000
179D350VAL00.0140.0057.039-0.169-0.1690.0000.0000.0000.000
180D351ILE0-0.0330.0157.031-0.158-0.1580.0000.0000.0000.000
181D352PRO00.014-0.0059.139-0.170-0.1700.0000.0000.0000.000
182D353ILE0-0.025-0.0029.930-0.129-0.1290.0000.0000.0000.000
183D354SER00.013-0.00412.7870.1090.1090.0000.0000.0000.000
184D355LEU00.0140.02116.483-0.048-0.0480.0000.0000.0000.000
185D371GLU-1-0.923-0.98339.346-0.074-0.0740.0000.0000.0000.000
186D372GLU-1-1.033-1.01439.646-0.070-0.0700.0000.0000.0000.000
187D373ASP-1-0.814-0.91837.710-0.095-0.0950.0000.0000.0000.000
188D374ILE0-0.007-0.00135.162-0.006-0.0060.0000.0000.0000.000
189D375VAL0-0.040-0.02934.649-0.002-0.0020.0000.0000.0000.000
190D376GLU-1-0.951-0.97135.175-0.117-0.1170.0000.0000.0000.000
191D377ALA00.0620.03531.356-0.007-0.0070.0000.0000.0000.000
192D378ALA0-0.073-0.02830.578-0.008-0.0080.0000.0000.0000.000
193D379ARG10.8660.91031.7520.0700.0700.0000.0000.0000.000
194D380GLY00.0960.07731.3030.0000.0000.0000.0000.0000.000
195D381ALA0-0.036-0.01327.207-0.011-0.0110.0000.0000.0000.000
196D382THR0-0.038-0.02828.1800.0040.0040.0000.0000.0000.000
197D383GLU-1-0.836-0.91230.503-0.108-0.1080.0000.0000.0000.000
198D384ASN0-0.124-0.06925.705-0.027-0.0270.0000.0000.0000.000
199D385SER0-0.096-0.02925.270-0.009-0.0090.0000.0000.0000.000
200D386VAL0-0.016-0.03225.7150.0010.0010.0000.0000.0000.000
201D387TYR0-0.022-0.00225.273-0.015-0.0150.0000.0000.0000.000
202D388LEU00.0180.01627.6400.0140.0140.0000.0000.0000.000
203D389GLY00.0160.00028.508-0.013-0.0130.0000.0000.0000.000
204D390MET0-0.025-0.01829.2400.0140.0140.0000.0000.0000.000
205D391TYR0-0.020-0.01026.743-0.019-0.0190.0000.0000.0000.000
206D392ARG10.8800.94126.9870.1080.1080.0000.0000.0000.000
207D393GLY00.0420.02132.2760.0100.0100.0000.0000.0000.000
208D394GLN00.0220.00632.5840.0080.0080.0000.0000.0000.000
209D395LEU00.0660.03932.420-0.008-0.0080.0000.0000.0000.000
210D396TYR0-0.047-0.04624.3560.0080.0080.0000.0000.0000.000
211D397LEU00.0560.03129.379-0.013-0.0130.0000.0000.0000.000
212D398GLN0-0.019-0.01121.3670.0030.0030.0000.0000.0000.000
213D399SER00.0320.02925.284-0.007-0.0070.0000.0000.0000.000
214D400SER00.0320.03523.0300.0060.0060.0000.0000.0000.000