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: 94LQ2

Calculation Name: 5SV7-A-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: A

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2261196.554578
FMO2-HF: Nuclear repulsion 2179424.03267
FMO2-HF: Total energy -81772.521908
FMO2-MP2: Total energy -82011.10748


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:103:ARG)


Summations of interaction energy for fragment #1(A:103:ARG)
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.
-2.891.7391.29-2.479-3.439-0.004
Interaction energy analysis for fragmet #1(A:103:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.975
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].
3A105LEU0-0.029-0.0223.799-2.9310.038-0.037-1.577-1.3540.006
4A106VAL00.0520.0296.8571.0821.0820.0000.0000.0000.000
5A107ILE0-0.059-0.0259.711-0.337-0.3370.0000.0000.0000.000
6A108ILE00.0100.00613.0580.6130.6130.0000.0000.0000.000
7A109SER0-0.0220.00016.5860.4000.4000.0000.0000.0000.000
8A110THR00.042-0.02019.6200.1200.1200.0000.0000.0000.000
9A111LEU00.013-0.01622.4970.2330.2330.0000.0000.0000.000
10A112ASP-1-0.873-0.88924.239-11.910-11.9100.0000.0000.0000.000
11A113GLY0-0.027-0.00524.9940.0800.0800.0000.0000.0000.000
12A114ARG10.8470.93421.22811.93711.9370.0000.0000.0000.000
13A115ILE0-0.043-0.01715.402-0.359-0.3590.0000.0000.0000.000
14A116ALA00.0350.01915.4580.0290.0290.0000.0000.0000.000
15A117ALA0-0.0250.0029.856-0.511-0.5110.0000.0000.0000.000
16A118LEU0-0.0090.00610.9980.2750.2750.0000.0000.0000.000
17A119ASP-1-0.795-0.9266.337-43.470-43.4700.0000.0000.0000.000
18A120PRO0-0.057-0.0045.7282.9142.9140.0000.0000.0000.000
19A121GLU-1-0.879-0.9503.728-52.502-52.1800.002-0.083-0.2420.000
20A122ASN0-0.024-0.0126.7681.0591.0590.0000.0000.0000.000
21A123HIS0-0.117-0.0566.7174.3984.3980.0000.0000.0000.000
22A124GLY00.1360.07910.3781.8861.8860.0000.0000.0000.000
23A125LYS10.8830.9186.78034.86034.8600.0000.0000.0000.000
24A126LYS10.9010.95211.11515.90515.9050.0000.0000.0000.000
25A127GLN0-0.088-0.0446.7531.8821.8820.0000.0000.0000.000
26A128TRP0-0.055-0.0409.4641.4891.4890.0000.0000.0000.000
27A129ASP-1-0.848-0.95513.493-16.448-16.4480.0000.0000.0000.000
28A130LEU0-0.047-0.00416.7020.5010.5010.0000.0000.0000.000
29A131ASP-1-0.807-0.91918.679-11.769-11.7690.0000.0000.0000.000
30A132VAL0-0.067-0.02721.7270.0200.0200.0000.0000.0000.000
31A133GLY00.0490.02224.1280.2250.2250.0000.0000.0000.000
32A134SER0-0.082-0.04326.9830.2570.2570.0000.0000.0000.000
33A135GLY00.0720.03827.602-0.233-0.2330.0000.0000.0000.000
34A136SER00.002-0.00728.244-0.343-0.3430.0000.0000.0000.000
35A137LEU00.0040.02924.808-0.019-0.0190.0000.0000.0000.000
36A138VAL00.0350.01128.5890.1390.1390.0000.0000.0000.000
37A139SER0-0.081-0.04631.8660.0930.0930.0000.0000.0000.000
38A140SER00.036-0.00335.2740.0760.0760.0000.0000.0000.000
39A141SER0-0.0080.02338.828-0.046-0.0460.0000.0000.0000.000
40A142LEU0-0.0300.00641.7950.1940.1940.0000.0000.0000.000
41A152MET0-0.015-0.00642.7420.0090.0090.0000.0000.0000.000
42A153ILE00.0230.00041.749-0.076-0.0760.0000.0000.0000.000
43A154ILE0-0.003-0.00237.247-0.094-0.0940.0000.0000.0000.000
44A155PRO0-0.061-0.02535.750-0.022-0.0220.0000.0000.0000.000
45A156SER00.011-0.00833.017-0.304-0.3040.0000.0000.0000.000
46A157LEU00.0550.00027.6430.0410.0410.0000.0000.0000.000
47A158ASP-1-0.893-0.91830.787-9.555-9.5550.0000.0000.0000.000
48A159GLY0-0.057-0.03031.589-0.124-0.1240.0000.0000.0000.000
49A160ALA00.002-0.01534.0020.2590.2590.0000.0000.0000.000
50A161LEU00.0090.00536.912-0.103-0.1030.0000.0000.0000.000
51A162PHE00.0230.01836.7160.0680.0680.0000.0000.0000.000
52A163GLN0-0.0100.00441.6100.1170.1170.0000.0000.0000.000
53A164TRP00.018-0.00143.114-0.090-0.0900.0000.0000.0000.000
54A165ASP-1-0.900-0.96145.376-6.157-6.1570.0000.0000.0000.000
55A166GLN0-0.046-0.01148.114-0.033-0.0330.0000.0000.0000.000
56A167ASP-1-0.893-0.93949.192-5.763-5.7630.0000.0000.0000.000
57A168ARG10.8430.92249.7316.1146.1140.0000.0000.0000.000
58A169GLU-1-0.892-0.95146.790-6.504-6.5040.0000.0000.0000.000
59A170SER0-0.075-0.04745.835-0.114-0.1140.0000.0000.0000.000
60A171MET00.0150.03539.6210.0280.0280.0000.0000.0000.000
61A172GLU-1-0.948-0.97343.388-6.474-6.4740.0000.0000.0000.000
62A173THR00.018-0.00340.327-0.158-0.1580.0000.0000.0000.000
63A174VAL0-0.048-0.02142.5620.1870.1870.0000.0000.0000.000
64A175PRO0-0.013-0.02043.472-0.138-0.1380.0000.0000.0000.000
65A176PHE0-0.019-0.00843.6400.0810.0810.0000.0000.0000.000
66A177THR00.0320.01337.983-0.122-0.1220.0000.0000.0000.000
67A178VAL00.010-0.01036.4530.1040.1040.0000.0000.0000.000
68A179GLU-1-0.987-0.98035.390-8.397-8.3970.0000.0000.0000.000
69A180SER00.0280.00838.2090.1000.1000.0000.0000.0000.000
70A181LEU00.0120.00741.4780.1700.1700.0000.0000.0000.000
71A182LEU0-0.033-0.00538.2150.1050.1050.0000.0000.0000.000
72A183GLU-1-1.006-0.98442.305-7.045-7.0450.0000.0000.0000.000
73A184SER00.037-0.01244.5250.0490.0490.0000.0000.0000.000
74A185SER00.0370.03147.2920.0630.0630.0000.0000.0000.000
75A186TYR0-0.077-0.07550.1430.0350.0350.0000.0000.0000.000
76A187LYS10.8360.94745.1216.7236.7230.0000.0000.0000.000
77A188PHE0-0.047-0.01150.3550.0400.0400.0000.0000.0000.000
78A189GLY00.009-0.00850.349-0.159-0.1590.0000.0000.0000.000
79A190ASP-1-0.865-0.93551.797-5.544-5.5440.0000.0000.0000.000
80A191ASP-1-0.873-0.93454.456-5.734-5.7340.0000.0000.0000.000
81A192VAL0-0.075-0.05349.745-0.005-0.0050.0000.0000.0000.000
82A193VAL00.0110.03648.919-0.052-0.0520.0000.0000.0000.000
83A194LEU0-0.010-0.00445.009-0.077-0.0770.0000.0000.0000.000
84A195VAL00.0170.00941.9760.0080.0080.0000.0000.0000.000
85A196GLY00.054-0.00139.585-0.065-0.0650.0000.0000.0000.000
86A197GLY0-0.001-0.00636.8170.0830.0830.0000.0000.0000.000
87A198LYS10.9320.98830.7829.0859.0850.0000.0000.0000.000
88A199SER0-0.038-0.00429.8420.0780.0780.0000.0000.0000.000
89A200LEU00.000-0.01726.261-0.055-0.0550.0000.0000.0000.000
90A201THR0-0.0260.00424.8630.1440.1440.0000.0000.0000.000
91A202THR00.0020.00420.559-0.292-0.2920.0000.0000.0000.000
92A203TYR00.0650.04318.7310.3180.3180.0000.0000.0000.000
93A204GLY0-0.0010.01716.745-0.398-0.3980.0000.0000.0000.000
94A205LEU00.0450.00713.0100.1110.1110.0000.0000.0000.000
95A206SER0-0.068-0.03211.069-0.100-0.1000.0000.0000.0000.000
96A207ALA00.0030.0096.351-0.434-0.4340.0000.0000.0000.000
97A208TYR00.1120.0582.463-3.843-2.5861.326-0.796-1.787-0.010
98A209SER0-0.052-0.0158.2281.4751.4750.0000.0000.0000.000
99A210GLY00.0280.00811.2631.3341.3340.0000.0000.0000.000
100A211LYS10.9310.96213.08719.56219.5620.0000.0000.0000.000
101A212VAL00.015-0.00515.603-0.394-0.3940.0000.0000.0000.000
102A213ARG10.9210.96211.55019.38019.3800.0000.0000.0000.000
103A214TYR00.0200.01418.0220.4660.4660.0000.0000.0000.000
104A215ILE00.0330.00720.281-0.480-0.4800.0000.0000.0000.000
105A216CYS0-0.056-0.02323.1010.3240.3240.0000.0000.0000.000
106A217SER0-0.005-0.00725.532-0.070-0.0700.0000.0000.0000.000
107A218ALA00.0860.04528.054-0.009-0.0090.0000.0000.0000.000
108A219LEU0-0.009-0.00431.1890.1760.1760.0000.0000.0000.000
109A220GLY00.0200.00530.7990.1350.1350.0000.0000.0000.000
110A221CYS0-0.041-0.03326.854-0.344-0.3440.0000.0000.0000.000
111A222ARG10.9440.99625.50810.39110.3910.0000.0000.0000.000
112A223GLN00.0580.02521.617-0.418-0.4180.0000.0000.0000.000
113A235ILE0-0.046-0.0367.8960.5710.5710.0000.0000.0000.000
114A236LEU0-0.028-0.0149.918-1.567-1.5670.0000.0000.0000.000
115A237LEU0-0.077-0.03311.9550.5170.5170.0000.0000.0000.000
116A238LEU00.0360.01713.9490.1610.1610.0000.0000.0000.000
117A239GLN00.0310.00217.5070.8690.8690.0000.0000.0000.000
118A240ARG10.8650.96121.09211.26811.2680.0000.0000.0000.000
119A241THR0-0.013-0.01823.8600.4360.4360.0000.0000.0000.000
120A242GLN00.014-0.00227.062-0.477-0.4770.0000.0000.0000.000
121A243LYS10.9330.96630.0349.5599.5590.0000.0000.0000.000
122A244THR0-0.023-0.00933.5200.0350.0350.0000.0000.0000.000
123A245VAL00.0860.03536.5540.0490.0490.0000.0000.0000.000
124A246ARG10.8210.90538.1167.6017.6010.0000.0000.0000.000
125A247ALA00.1060.05643.1860.0650.0650.0000.0000.0000.000
126A248VAL0-0.0140.01846.9140.0240.0240.0000.0000.0000.000
127A249GLY0-0.034-0.02249.3580.0930.0930.0000.0000.0000.000
128A250PRO00.0030.02953.000-0.013-0.0130.0000.0000.0000.000
129A251ARG10.9600.97154.4245.1615.1610.0000.0000.0000.000
130A252SER0-0.087-0.03554.1130.0080.0080.0000.0000.0000.000
131A253GLY00.0590.04051.267-0.013-0.0130.0000.0000.0000.000
132A254ASN00.017-0.00249.205-0.080-0.0800.0000.0000.0000.000
133A255GLU-1-0.759-0.90343.533-7.092-7.0920.0000.0000.0000.000
134A256LYS10.8920.94047.8185.8755.8750.0000.0000.0000.000
135A257TRP00.0480.02943.278-0.055-0.0550.0000.0000.0000.000
136A258ASN0-0.111-0.06240.687-0.120-0.1200.0000.0000.0000.000
137A259PHE00.0690.02738.006-0.042-0.0420.0000.0000.0000.000
138A260SER0-0.036-0.01833.3650.0350.0350.0000.0000.0000.000
139A261VAL00.0240.02331.268-0.088-0.0880.0000.0000.0000.000
140A262GLY0-0.004-0.00728.6200.1060.1060.0000.0000.0000.000
141A263HIS00.0150.00924.8870.0550.0550.0000.0000.0000.000
142A264PHE00.012-0.00919.846-0.010-0.0100.0000.0000.0000.000
143A265GLU-1-0.865-0.92719.385-14.068-14.0680.0000.0000.0000.000
144A266LEU0-0.030-0.00713.663-0.038-0.0380.0000.0000.0000.000
145A267ARG10.9300.98014.36815.95215.9520.0000.0000.0000.000
146A268TYR00.0770.02910.089-0.868-0.8680.0000.0000.0000.000
147A309VAL00.009-0.00913.889-0.317-0.3170.0000.0000.0000.000
148A310ILE0-0.002-0.01510.590-0.388-0.3880.0000.0000.0000.000
149A311LYS10.9670.98214.50715.78015.7800.0000.0000.0000.000
150A312VAL00.0410.03518.333-0.450-0.4500.0000.0000.0000.000
151A313SER0-0.020-0.00120.0510.5620.5620.0000.0000.0000.000
152A314VAL00.0390.01123.634-0.250-0.2500.0000.0000.0000.000
153A315ALA00.012-0.00325.6460.1430.1430.0000.0000.0000.000
154A316ASP-1-0.897-0.93826.023-10.705-10.7050.0000.0000.0000.000
155A317TRP0-0.031-0.04624.101-0.582-0.5820.0000.0000.0000.000
156A318LYS10.9191.00621.13312.35712.3570.0000.0000.0000.000
157A319VAL0-0.043-0.01114.760-0.019-0.0190.0000.0000.0000.000
158A320MET0-0.001-0.00615.663-0.263-0.2630.0000.0000.0000.000
159A330GLU-1-0.998-1.01015.832-15.346-15.3460.0000.0000.0000.000
160A331TRP0-0.0040.02110.7030.4670.4670.0000.0000.0000.000
161A332GLU-1-0.881-0.96416.106-13.656-13.6560.0000.0000.0000.000
162A333TYR0-0.053-0.02815.350-0.348-0.3480.0000.0000.0000.000
163A334GLN0-0.036-0.03218.4750.1690.1690.0000.0000.0000.000
164A335PHE00.0120.00316.651-0.245-0.2450.0000.0000.0000.000
165A336CYS00.0150.03422.2970.6480.6480.0000.0000.0000.000
166A337THR0-0.043-0.02124.953-0.276-0.2760.0000.0000.0000.000
167A338PRO00.0390.01724.512-0.450-0.4500.0000.0000.0000.000
168A339ILE0-0.003-0.00120.009-0.219-0.2190.0000.0000.0000.000
169A340ALA0-0.040-0.02422.1030.4140.4140.0000.0000.0000.000
170A341SER0-0.012-0.00919.5160.4010.4010.0000.0000.0000.000
171A342ALA00.0370.01316.555-0.355-0.3550.0000.0000.0000.000
172A343TRP0-0.027-0.01913.499-0.136-0.1360.0000.0000.0000.000
173A344LEU00.0370.0459.265-1.311-1.3110.0000.0000.0000.000
174A345LEU0-0.065-0.0365.9351.6861.6860.0000.0000.0000.000
175A346LYS11.0280.9884.56833.15733.238-0.001-0.023-0.0560.000
176A347ASP-1-0.887-0.9214.809-33.627-33.6270.0000.0000.0000.000
177A348GLY0-0.002-0.0046.2020.9430.9430.0000.0000.0000.000
178A349LYS10.7780.9017.35028.62328.6230.0000.0000.0000.000
179A350VAL0-0.004-0.0219.4421.1961.1960.0000.0000.0000.000
180A351ILE00.0600.04312.6591.0331.0330.0000.0000.0000.000
181A352PRO0-0.005-0.00914.488-1.052-1.0520.0000.0000.0000.000
182A353ILE0-0.040-0.00615.669-0.112-0.1120.0000.0000.0000.000
183A354SER00.0490.02718.5950.5980.5980.0000.0000.0000.000
184A375VAL00.014-0.01740.2970.0490.0490.0000.0000.0000.000
185A376GLU-1-0.889-0.95338.767-7.671-7.6710.0000.0000.0000.000
186A377ALA00.0400.03834.591-0.083-0.0830.0000.0000.0000.000
187A378ALA0-0.022-0.01335.092-0.210-0.2100.0000.0000.0000.000
188A379ARG10.9350.94936.4606.9686.9680.0000.0000.0000.000
189A380GLY00.0380.03936.1070.0090.0090.0000.0000.0000.000
190A381ALA0-0.055-0.02731.681-0.193-0.1930.0000.0000.0000.000
191A382THR0-0.019-0.00432.206-0.175-0.1750.0000.0000.0000.000
192A383GLU-1-0.851-0.88733.777-8.534-8.5340.0000.0000.0000.000
193A384ASN0-0.027-0.01327.540-0.030-0.0300.0000.0000.0000.000
194A385SER0-0.138-0.10929.421-0.269-0.2690.0000.0000.0000.000
195A386VAL00.0040.00930.104-0.149-0.1490.0000.0000.0000.000
196A387TYR00.0320.01329.385-0.125-0.1250.0000.0000.0000.000
197A388LEU00.005-0.00731.8880.0450.0450.0000.0000.0000.000
198A389GLY00.0190.01231.501-0.143-0.1430.0000.0000.0000.000
199A390MET0-0.044-0.02932.3310.3320.3320.0000.0000.0000.000
200A391TYR0-0.0180.01530.094-0.248-0.2480.0000.0000.0000.000
201A392ARG10.9250.98433.0508.3358.3350.0000.0000.0000.000
202A393GLY0-0.002-0.04234.511-0.112-0.1120.0000.0000.0000.000
203A394GLN0-0.004-0.00234.7350.4440.4440.0000.0000.0000.000
204A395LEU00.0910.02835.692-0.259-0.2590.0000.0000.0000.000
205A396TYR0-0.026-0.00128.7630.0390.0390.0000.0000.0000.000
206A397LEU00.0560.02133.3780.0240.0240.0000.0000.0000.000
207A398GLN0-0.050-0.04425.572-0.146-0.1460.0000.0000.0000.000
208A399SER00.0100.02928.5730.1800.1800.0000.0000.0000.000
209A400SER00.0030.00327.801-0.353-0.3530.0000.0000.0000.000