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: 72Y4K

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2260780.489857
FMO2-HF: Nuclear repulsion 2179003.988881
FMO2-HF: Total energy -81776.500976
FMO2-MP2: Total energy -82014.673114


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.
-86.484-87.80729.321-15.315-12.683-0.149
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 : 0.851 / q_NPA : 0.906
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].
3A105LEU0-0.009-0.0213.850-4.244-1.580-0.028-1.418-1.2180.003
4A106VAL00.0090.0107.0851.4351.4350.0000.0000.0000.000
5A107ILE0-0.042-0.0179.459-0.401-0.4010.0000.0000.0000.000
6A108ILE00.0200.01213.2670.7460.7460.0000.0000.0000.000
7A109SER00.0210.01216.9100.0830.0830.0000.0000.0000.000
8A110THR00.0370.00120.0340.0210.0210.0000.0000.0000.000
9A111LEU00.0610.01923.3260.2410.2410.0000.0000.0000.000
10A112ASP-1-0.826-0.85825.304-12.155-12.1550.0000.0000.0000.000
11A113GLY0-0.036-0.01325.2190.1930.1930.0000.0000.0000.000
12A114ARG10.7840.87121.27012.11712.1170.0000.0000.0000.000
13A115ILE0-0.021-0.01615.452-0.272-0.2720.0000.0000.0000.000
14A116ALA00.0160.01716.0450.1000.1000.0000.0000.0000.000
15A117ALA0-0.0040.00010.469-0.480-0.4800.0000.0000.0000.000
16A118LEU00.0010.00210.9440.2690.2690.0000.0000.0000.000
17A119ASP-1-0.747-0.8645.748-45.600-45.6000.0000.0000.0000.000
18A120PRO0-0.0180.0026.3222.9762.9760.0000.0000.0000.000
19A121GLU-1-0.768-0.8441.757-137.322-143.68828.577-12.817-9.394-0.146
20A122ASN00.008-0.0085.8800.7120.7120.0000.0000.0000.000
21A123HIS0-0.086-0.0287.1255.1385.1380.0000.0000.0000.000
22A124GLY00.0880.0399.8632.3612.3610.0000.0000.0000.000
23A125LYS10.8080.8827.56535.08335.0830.0000.0000.0000.000
24A126LYS10.8610.91110.59016.16816.1680.0000.0000.0000.000
25A127GLN0-0.071-0.0375.4952.8022.8020.0000.0000.0000.000
26A128TRP0-0.056-0.0429.1561.4011.4010.0000.0000.0000.000
27A129ASP-1-0.756-0.86113.400-18.156-18.1560.0000.0000.0000.000
28A130LEU0-0.082-0.04416.6740.1010.1010.0000.0000.0000.000
29A131ASP-1-0.773-0.87118.475-12.095-12.0950.0000.0000.0000.000
30A132VAL0-0.040-0.02521.682-0.124-0.1240.0000.0000.0000.000
31A133GLY00.0200.01224.3560.2690.2690.0000.0000.0000.000
32A134SER0-0.068-0.03026.2910.2960.2960.0000.0000.0000.000
33A135GLY00.0850.04426.891-0.354-0.3540.0000.0000.0000.000
34A136SER00.0020.00028.153-0.345-0.3450.0000.0000.0000.000
35A137LEU0-0.0240.02124.9910.1660.1660.0000.0000.0000.000
36A138VAL00.0450.01728.3880.1850.1850.0000.0000.0000.000
37A139SER0-0.070-0.04731.8930.0600.0600.0000.0000.0000.000
38A140SER00.030-0.00135.3460.0700.0700.0000.0000.0000.000
39A141SER0-0.074-0.01939.045-0.076-0.0760.0000.0000.0000.000
40A142LEU0-0.0360.00742.1580.2290.2290.0000.0000.0000.000
41A152MET0-0.031-0.01543.4940.0160.0160.0000.0000.0000.000
42A153ILE00.0070.00041.923-0.097-0.0970.0000.0000.0000.000
43A154ILE0-0.0020.00037.888-0.084-0.0840.0000.0000.0000.000
44A155PRO0-0.038-0.01035.7830.0020.0020.0000.0000.0000.000
45A156SER00.029-0.00933.269-0.227-0.2270.0000.0000.0000.000
46A157LEU00.038-0.00627.0890.0820.0820.0000.0000.0000.000
47A158ASP-1-0.816-0.85130.728-9.774-9.7740.0000.0000.0000.000
48A159GLY0-0.0330.00131.904-0.064-0.0640.0000.0000.0000.000
49A160ALA00.010-0.00434.1620.3060.3060.0000.0000.0000.000
50A161LEU0-0.024-0.01136.893-0.118-0.1180.0000.0000.0000.000
51A162PHE00.0350.01736.6790.0770.0770.0000.0000.0000.000
52A163GLN0-0.017-0.01241.6050.1330.1330.0000.0000.0000.000
53A164TRP0-0.0040.00643.953-0.109-0.1090.0000.0000.0000.000
54A165ASP-1-0.791-0.90745.779-6.179-6.1790.0000.0000.0000.000
55A166GLN0-0.018-0.00148.495-0.115-0.1150.0000.0000.0000.000
56A167ASP-1-0.917-0.94249.857-5.857-5.8570.0000.0000.0000.000
57A168ARG10.6870.81950.3256.3826.3820.0000.0000.0000.000
58A169GLU-1-0.912-0.95947.356-6.658-6.6580.0000.0000.0000.000
59A170SER0-0.079-0.06446.099-0.147-0.1470.0000.0000.0000.000
60A171MET0-0.0060.02640.496-0.038-0.0380.0000.0000.0000.000
61A172GLU-1-0.808-0.88843.190-6.573-6.5730.0000.0000.0000.000
62A173THR0-0.005-0.00440.366-0.112-0.1120.0000.0000.0000.000
63A174VAL0-0.019-0.00843.0230.1990.1990.0000.0000.0000.000
64A175PRO00.003-0.00643.811-0.134-0.1340.0000.0000.0000.000
65A176PHE0-0.035-0.01643.5970.0480.0480.0000.0000.0000.000
66A177THR00.0200.00237.966-0.194-0.1940.0000.0000.0000.000
67A178VAL00.005-0.01635.8390.1410.1410.0000.0000.0000.000
68A179GLU-1-0.816-0.88034.474-9.001-9.0010.0000.0000.0000.000
69A180SER00.0250.00538.0480.0750.0750.0000.0000.0000.000
70A181LEU00.0200.01641.3950.1730.1730.0000.0000.0000.000
71A182LEU0-0.043-0.01738.0280.1270.1270.0000.0000.0000.000
72A183GLU-1-0.904-0.93442.317-6.904-6.9040.0000.0000.0000.000
73A184SER0-0.003-0.02944.5810.1460.1460.0000.0000.0000.000
74A185SER00.0360.02147.2010.0370.0370.0000.0000.0000.000
75A186TYR0-0.083-0.08150.2590.0490.0490.0000.0000.0000.000
76A187LYS10.7940.91046.0606.7556.7550.0000.0000.0000.000
77A188PHE0-0.029-0.00350.4170.0400.0400.0000.0000.0000.000
78A189GLY00.0100.01650.400-0.167-0.1670.0000.0000.0000.000
79A190ASP-1-0.884-0.94051.922-5.687-5.6870.0000.0000.0000.000
80A191ASP-1-0.826-0.89853.887-5.777-5.7770.0000.0000.0000.000
81A192VAL0-0.118-0.09050.1070.0160.0160.0000.0000.0000.000
82A193VAL00.0210.04349.303-0.087-0.0870.0000.0000.0000.000
83A194LEU00.0090.01145.555-0.092-0.0920.0000.0000.0000.000
84A195VAL0-0.002-0.00542.5850.0040.0040.0000.0000.0000.000
85A196GLY00.004-0.01139.893-0.082-0.0820.0000.0000.0000.000
86A197GLY0-0.0020.00737.0820.0950.0950.0000.0000.0000.000
87A198LYS10.8700.92931.7599.0299.0290.0000.0000.0000.000
88A199SER0-0.013-0.00429.9640.0280.0280.0000.0000.0000.000
89A200LEU00.002-0.00726.161-0.148-0.1480.0000.0000.0000.000
90A201THR0-0.036-0.01725.5050.0630.0630.0000.0000.0000.000
91A202THR0-0.027-0.01720.851-0.540-0.5400.0000.0000.0000.000
92A203TYR00.0790.04418.5550.3450.3450.0000.0000.0000.000
93A204GLY00.1050.03816.396-0.218-0.2180.0000.0000.0000.000
94A205LEU0-0.0500.00012.7600.0600.0600.0000.0000.0000.000
95A206SER0-0.062-0.03910.294-0.112-0.1120.0000.0000.0000.000
96A207ALA0-0.004-0.0096.586-0.213-0.2130.0000.0000.0000.000
97A208TYR00.0170.0062.763-0.5491.6270.774-1.048-1.902-0.006
98A209SER00.007-0.0067.2941.8331.8330.0000.0000.0000.000
99A210GLY00.0370.02811.0611.4791.4790.0000.0000.0000.000
100A211LYS10.9410.97213.06119.94019.9400.0000.0000.0000.000
101A212VAL0-0.007-0.00815.000-0.606-0.6060.0000.0000.0000.000
102A213ARG10.9200.95011.07820.18720.1870.0000.0000.0000.000
103A214TYR0-0.0120.02217.5370.3380.3380.0000.0000.0000.000
104A215ILE00.0140.00120.106-0.474-0.4740.0000.0000.0000.000
105A216CYS0-0.034-0.01222.8660.3140.3140.0000.0000.0000.000
106A217SER00.025-0.00125.389-0.199-0.1990.0000.0000.0000.000
107A218ALA00.0500.02128.2300.0710.0710.0000.0000.0000.000
108A219LEU0-0.0010.00631.5240.2390.2390.0000.0000.0000.000
109A220GLY00.0190.01830.8980.1710.1710.0000.0000.0000.000
110A221CYS0-0.044-0.02526.316-0.448-0.4480.0000.0000.0000.000
111A222ARG10.9430.98925.38510.69710.6970.0000.0000.0000.000
112A223GLN00.0610.00921.301-0.433-0.4330.0000.0000.0000.000
113A235ILE0-0.005-0.0117.7780.0660.0660.0000.0000.0000.000
114A236LEU0-0.0070.0049.750-1.810-1.8100.0000.0000.0000.000
115A237LEU0-0.050-0.00711.7700.6390.6390.0000.0000.0000.000
116A238LEU00.0440.01314.160-0.345-0.3450.0000.0000.0000.000
117A239GLN00.008-0.01017.5480.6860.6860.0000.0000.0000.000
118A240ARG10.7820.89221.17911.53611.5360.0000.0000.0000.000
119A241THR0-0.003-0.00723.7360.4240.4240.0000.0000.0000.000
120A242GLN0-0.002-0.01127.018-0.513-0.5130.0000.0000.0000.000
121A243LYS10.7990.88530.1279.7499.7490.0000.0000.0000.000
122A244THR0-0.052-0.02833.5270.0300.0300.0000.0000.0000.000
123A245VAL00.0730.02736.4400.0910.0910.0000.0000.0000.000
124A246ARG10.8780.92438.6067.6667.6660.0000.0000.0000.000
125A247ALA00.0670.04943.2800.0610.0610.0000.0000.0000.000
126A248VAL0-0.008-0.00746.7990.0080.0080.0000.0000.0000.000
127A249GLY00.0140.00149.3750.1050.1050.0000.0000.0000.000
128A250PRO00.0060.01753.119-0.012-0.0120.0000.0000.0000.000
129A251ARG10.9260.96954.6805.2405.2400.0000.0000.0000.000
130A252SER0-0.034-0.02454.0020.0740.0740.0000.0000.0000.000
131A253GLY00.0140.02350.859-0.027-0.0270.0000.0000.0000.000
132A254ASN0-0.024-0.01348.853-0.062-0.0620.0000.0000.0000.000
133A255GLU-1-0.783-0.88143.310-7.256-7.2560.0000.0000.0000.000
134A256LYS10.9180.95347.6856.0326.0320.0000.0000.0000.000
135A257TRP00.0640.03643.967-0.057-0.0570.0000.0000.0000.000
136A258ASN0-0.061-0.05739.720-0.180-0.1800.0000.0000.0000.000
137A259PHE00.0580.03537.708-0.056-0.0560.0000.0000.0000.000
138A260SER0-0.027-0.01433.767-0.054-0.0540.0000.0000.0000.000
139A261VAL00.0270.02031.491-0.121-0.1210.0000.0000.0000.000
140A262GLY00.0160.01328.5790.1310.1310.0000.0000.0000.000
141A263HIS00.0190.01023.7500.1650.1650.0000.0000.0000.000
142A264PHE00.0240.00519.8310.0340.0340.0000.0000.0000.000
143A265GLU-1-0.810-0.89819.201-15.307-15.3070.0000.0000.0000.000
144A266LEU0-0.0340.00113.479-0.139-0.1390.0000.0000.0000.000
145A267ARG10.8790.93314.72117.23117.2310.0000.0000.0000.000
146A268TYR00.0880.04610.044-1.466-1.4660.0000.0000.0000.000
147A309VAL00.017-0.00414.465-0.524-0.5240.0000.0000.0000.000
148A310ILE00.0000.00710.6660.0820.0820.0000.0000.0000.000
149A311LYS10.8290.88714.81316.31116.3110.0000.0000.0000.000
150A312VAL0-0.004-0.00718.473-0.699-0.6990.0000.0000.0000.000
151A313SER0-0.033-0.03520.7240.5450.5450.0000.0000.0000.000
152A314VAL00.0190.00424.415-0.218-0.2180.0000.0000.0000.000
153A315ALA00.0060.00825.9460.2360.2360.0000.0000.0000.000
154A316ASP-1-0.857-0.89525.791-11.238-11.2380.0000.0000.0000.000
155A317TRP0-0.024-0.01424.663-0.325-0.3250.0000.0000.0000.000
156A318LYS10.8970.94321.29513.11213.1120.0000.0000.0000.000
157A319VAL0-0.026-0.00415.752-0.038-0.0380.0000.0000.0000.000
158A320MET0-0.027-0.01915.505-0.386-0.3860.0000.0000.0000.000
159A330GLU-1-0.852-0.91314.890-16.338-16.3380.0000.0000.0000.000
160A331TRP0-0.0070.03710.7840.8130.8130.0000.0000.0000.000
161A332GLU-1-0.819-0.91915.416-14.058-14.0580.0000.0000.0000.000
162A333TYR0-0.027-0.02315.210-0.570-0.5700.0000.0000.0000.000
163A334GLN0-0.027-0.02317.8390.2480.2480.0000.0000.0000.000
164A335PHE0-0.028-0.01816.825-0.392-0.3920.0000.0000.0000.000
165A336CYS00.0490.02422.2770.7600.7600.0000.0000.0000.000
166A337THR0-0.115-0.06424.837-0.169-0.1690.0000.0000.0000.000
167A338PRO00.0400.01525.070-0.486-0.4860.0000.0000.0000.000
168A339ILE00.0090.01120.564-0.218-0.2180.0000.0000.0000.000
169A340ALA0-0.020-0.00323.1220.4790.4790.0000.0000.0000.000
170A341SER0-0.011-0.00920.4340.4680.4680.0000.0000.0000.000
171A342ALA00.0340.01517.342-0.395-0.3950.0000.0000.0000.000
172A343TRP0-0.044-0.04114.0330.2010.2010.0000.0000.0000.000
173A344LEU00.0020.0229.897-1.339-1.3390.0000.0000.0000.000
174A345LEU0-0.048-0.0295.3921.9161.9160.0000.0000.0000.000
175A346LYS10.9550.9314.67435.20635.257-0.001-0.020-0.0300.000
176A347ASP-1-0.849-0.8974.755-34.868-34.716-0.001-0.012-0.1390.000
177A348GLY00.0210.0236.2910.7890.7890.0000.0000.0000.000
178A349LYS10.7800.8917.06828.50328.5030.0000.0000.0000.000
179A350VAL0-0.007-0.0059.5281.4451.4450.0000.0000.0000.000
180A351ILE00.0500.03912.5151.5151.5150.0000.0000.0000.000
181A352PRO00.0230.00414.775-1.030-1.0300.0000.0000.0000.000
182A353ILE0-0.0080.00615.849-0.088-0.0880.0000.0000.0000.000
183A354SER0-0.001-0.00218.8160.9060.9060.0000.0000.0000.000
184A375VAL00.037-0.00640.6310.0450.0450.0000.0000.0000.000
185A376GLU-1-0.835-0.89939.363-7.621-7.6210.0000.0000.0000.000
186A377ALA00.0120.00334.960-0.093-0.0930.0000.0000.0000.000
187A378ALA0-0.023-0.01435.312-0.236-0.2360.0000.0000.0000.000
188A379ARG10.8760.92836.4767.1677.1670.0000.0000.0000.000
189A380GLY00.0370.02035.992-0.081-0.0810.0000.0000.0000.000
190A381ALA0-0.046-0.02332.082-0.237-0.2370.0000.0000.0000.000
191A382THR0-0.028-0.02832.608-0.212-0.2120.0000.0000.0000.000
192A383GLU-1-0.848-0.89134.344-8.503-8.5030.0000.0000.0000.000
193A384ASN0-0.062-0.03528.198-0.077-0.0770.0000.0000.0000.000
194A385SER0-0.094-0.04929.862-0.395-0.3950.0000.0000.0000.000
195A386VAL00.0100.00430.834-0.113-0.1130.0000.0000.0000.000
196A387TYR00.0130.00730.159-0.071-0.0710.0000.0000.0000.000
197A388LEU00.0140.00632.3510.0460.0460.0000.0000.0000.000
198A389GLY00.0330.02432.205-0.137-0.1370.0000.0000.0000.000
199A390MET0-0.049-0.02733.0950.3230.3230.0000.0000.0000.000
200A391TYR00.0210.01130.787-0.307-0.3070.0000.0000.0000.000
201A392ARG10.8630.93533.5258.4278.4270.0000.0000.0000.000
202A393GLY0-0.007-0.01535.069-0.121-0.1210.0000.0000.0000.000
203A394GLN00.0500.02435.0680.4420.4420.0000.0000.0000.000
204A395LEU00.0830.02736.250-0.273-0.2730.0000.0000.0000.000
205A396TYR0-0.081-0.04329.1380.0600.0600.0000.0000.0000.000
206A397LEU00.0520.03033.834-0.035-0.0350.0000.0000.0000.000
207A398GLN0-0.059-0.05126.186-0.068-0.0680.0000.0000.0000.000
208A399SER00.007-0.00728.9640.2560.2560.0000.0000.0000.000
209A400SER0-0.0160.00127.703-0.467-0.4670.0000.0000.0000.000