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: MVRZZ

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 OptHSide
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 -2261222.528737
FMO2-HF: Nuclear repulsion 2179447.807155
FMO2-HF: Total energy -81774.721582
FMO2-MP2: Total energy -82013.09204


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.
-91.674-88.57924.799-15.09-12.804-0.162
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 : 0.837 / q_NPA : 0.902
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].
3A105LEU0-0.014-0.0123.799-4.485-1.301-0.037-1.688-1.4590.006
4A106VAL00.0350.0166.9031.2601.2600.0000.0000.0000.000
5A107ILE0-0.050-0.0229.668-0.266-0.2660.0000.0000.0000.000
6A108ILE00.0180.00913.1100.6690.6690.0000.0000.0000.000
7A109SER0-0.0150.00416.6340.4590.4590.0000.0000.0000.000
8A110THR00.0530.01319.6720.0780.0780.0000.0000.0000.000
9A111LEU00.019-0.00522.5450.2440.2440.0000.0000.0000.000
10A112ASP-1-0.869-0.89624.826-12.095-12.0950.0000.0000.0000.000
11A113GLY0-0.026-0.00324.9790.0930.0930.0000.0000.0000.000
12A114ARG10.8080.88421.28512.15212.1520.0000.0000.0000.000
13A115ILE0-0.039-0.01715.431-0.354-0.3540.0000.0000.0000.000
14A116ALA00.0440.03115.5040.1370.1370.0000.0000.0000.000
15A117ALA0-0.024-0.0069.921-0.639-0.6390.0000.0000.0000.000
16A118LEU0-0.0080.02310.9360.2550.2550.0000.0000.0000.000
17A119ASP-1-0.747-0.8765.907-45.874-45.8740.0000.0000.0000.000
18A120PRO0-0.0110.0145.6543.5193.5190.0000.0000.0000.000
19A121GLU-1-0.779-0.8841.804-143.630-145.45224.103-12.707-9.575-0.161
20A122ASN0-0.019-0.0125.8451.3741.3740.0000.0000.0000.000
21A123HIS0-0.068-0.0406.9015.4855.4850.0000.0000.0000.000
22A124GLY00.1310.0779.4482.1262.1260.0000.0000.0000.000
23A125LYS10.7760.8627.12136.53936.5390.0000.0000.0000.000
24A126LYS10.8540.90110.45215.91915.9190.0000.0000.0000.000
25A127GLN0-0.084-0.0475.3523.2643.2640.0000.0000.0000.000
26A128TRP0-0.050-0.0399.5741.7981.7980.0000.0000.0000.000
27A129ASP-1-0.776-0.89013.159-17.659-17.6590.0000.0000.0000.000
28A130LEU0-0.044-0.00616.6230.6170.6170.0000.0000.0000.000
29A131ASP-1-0.781-0.88318.656-12.090-12.0900.0000.0000.0000.000
30A132VAL0-0.060-0.02121.6880.0680.0680.0000.0000.0000.000
31A133GLY00.0470.01824.1140.2260.2260.0000.0000.0000.000
32A134SER0-0.072-0.03426.8350.2850.2850.0000.0000.0000.000
33A135GLY00.0700.03827.592-0.242-0.2420.0000.0000.0000.000
34A136SER00.0060.00028.236-0.287-0.2870.0000.0000.0000.000
35A137LEU0-0.0220.00925.006-0.010-0.0100.0000.0000.0000.000
36A138VAL00.0580.02328.6430.1440.1440.0000.0000.0000.000
37A139SER0-0.070-0.04531.9190.0800.0800.0000.0000.0000.000
38A140SER00.0560.00335.3270.0910.0910.0000.0000.0000.000
39A141SER0-0.0520.01138.881-0.060-0.0600.0000.0000.0000.000
40A142LEU0-0.0190.01241.8360.1850.1850.0000.0000.0000.000
41A152MET0-0.038-0.01342.9780.0170.0170.0000.0000.0000.000
42A153ILE00.024-0.00241.658-0.077-0.0770.0000.0000.0000.000
43A154ILE0-0.006-0.00237.257-0.092-0.0920.0000.0000.0000.000
44A155PRO0-0.057-0.02235.787-0.017-0.0170.0000.0000.0000.000
45A156SER00.007-0.03932.976-0.300-0.3000.0000.0000.0000.000
46A157LEU00.0510.00227.0900.0570.0570.0000.0000.0000.000
47A158ASP-1-0.856-0.88230.764-9.709-9.7090.0000.0000.0000.000
48A159GLY0-0.0170.00731.616-0.113-0.1130.0000.0000.0000.000
49A160ALA00.004-0.01234.0250.2820.2820.0000.0000.0000.000
50A161LEU00.0000.00236.938-0.106-0.1060.0000.0000.0000.000
51A162PHE00.0420.02936.6890.0790.0790.0000.0000.0000.000
52A163GLN00.0090.01641.6580.0890.0890.0000.0000.0000.000
53A164TRP00.014-0.00443.371-0.096-0.0960.0000.0000.0000.000
54A165ASP-1-0.833-0.91945.424-6.186-6.1860.0000.0000.0000.000
55A166GLN0-0.029-0.00547.888-0.077-0.0770.0000.0000.0000.000
56A167ASP-1-0.893-0.93449.236-5.842-5.8420.0000.0000.0000.000
57A168ARG10.7310.85249.9666.3256.3250.0000.0000.0000.000
58A169GLU-1-0.894-0.95146.795-6.649-6.6490.0000.0000.0000.000
59A170SER0-0.080-0.05045.884-0.143-0.1430.0000.0000.0000.000
60A171MET00.0160.03640.362-0.012-0.0120.0000.0000.0000.000
61A172GLU-1-0.931-0.97043.388-6.580-6.5800.0000.0000.0000.000
62A173THR0-0.0020.00339.886-0.165-0.1650.0000.0000.0000.000
63A174VAL0-0.021-0.02242.5620.1990.1990.0000.0000.0000.000
64A175PRO0-0.009-0.01543.501-0.140-0.1400.0000.0000.0000.000
65A176PHE0-0.024-0.01143.6660.0750.0750.0000.0000.0000.000
66A177THR00.0190.00238.013-0.196-0.1960.0000.0000.0000.000
67A178VAL00.028-0.00236.1880.1190.1190.0000.0000.0000.000
68A179GLU-1-0.815-0.88434.542-8.874-8.8740.0000.0000.0000.000
69A180SER00.0260.01138.2340.0770.0770.0000.0000.0000.000
70A181LEU00.0080.01241.4900.1730.1730.0000.0000.0000.000
71A182LEU0-0.034-0.01038.0500.1100.1100.0000.0000.0000.000
72A183GLU-1-0.920-0.93442.332-6.933-6.9330.0000.0000.0000.000
73A184SER00.028-0.00844.5500.0520.0520.0000.0000.0000.000
74A185SER00.0380.02747.3140.0650.0650.0000.0000.0000.000
75A186TYR0-0.082-0.07950.0550.0390.0390.0000.0000.0000.000
76A187LYS10.7700.89845.4916.7846.7840.0000.0000.0000.000
77A188PHE0-0.041-0.00650.4460.0440.0440.0000.0000.0000.000
78A189GLY00.0060.00050.281-0.160-0.1600.0000.0000.0000.000
79A190ASP-1-0.849-0.93751.645-5.643-5.6430.0000.0000.0000.000
80A191ASP-1-0.867-0.92854.088-5.824-5.8240.0000.0000.0000.000
81A192VAL0-0.092-0.05449.922-0.007-0.0070.0000.0000.0000.000
82A193VAL00.0140.03449.055-0.054-0.0540.0000.0000.0000.000
83A194LEU0-0.013-0.00445.150-0.087-0.0870.0000.0000.0000.000
84A195VAL00.0060.00142.0770.0090.0090.0000.0000.0000.000
85A196GLY00.045-0.00239.578-0.070-0.0700.0000.0000.0000.000
86A197GLY0-0.004-0.00536.8300.0950.0950.0000.0000.0000.000
87A198LYS10.8160.91231.4348.9548.9540.0000.0000.0000.000
88A199SER0-0.0320.00029.9150.1030.1030.0000.0000.0000.000
89A200LEU00.006-0.01226.274-0.079-0.0790.0000.0000.0000.000
90A201THR0-0.0330.00424.9280.1800.1800.0000.0000.0000.000
91A202THR0-0.021-0.00420.707-0.530-0.5300.0000.0000.0000.000
92A203TYR00.0720.04018.7630.3570.3570.0000.0000.0000.000
93A204GLY00.0050.01816.809-0.434-0.4340.0000.0000.0000.000
94A205LEU00.020-0.00113.1590.1150.1150.0000.0000.0000.000
95A206SER0-0.038-0.02611.101-0.063-0.0630.0000.0000.0000.000
96A207ALA0-0.006-0.0086.381-0.526-0.5260.0000.0000.0000.000
97A208TYR00.1100.0602.698-1.855-0.3370.735-0.654-1.599-0.007
98A209SER0-0.054-0.0158.1891.7291.7290.0000.0000.0000.000
99A210GLY00.0210.00611.2391.3481.3480.0000.0000.0000.000
100A211LYS10.9540.96813.05819.34919.3490.0000.0000.0000.000
101A212VAL00.008-0.00715.581-0.348-0.3480.0000.0000.0000.000
102A213ARG10.9140.96811.56219.45419.4540.0000.0000.0000.000
103A214TYR00.0200.01417.9350.2420.2420.0000.0000.0000.000
104A215ILE00.0340.00720.279-0.493-0.4930.0000.0000.0000.000
105A216CYS0-0.066-0.03123.1000.3180.3180.0000.0000.0000.000
106A217SER00.001-0.00325.538-0.107-0.1070.0000.0000.0000.000
107A218ALA00.0890.04328.063-0.002-0.0020.0000.0000.0000.000
108A219LEU0-0.007-0.00231.2020.1770.1770.0000.0000.0000.000
109A220GLY00.0320.01030.8000.1430.1430.0000.0000.0000.000
110A221CYS0-0.048-0.03526.856-0.361-0.3610.0000.0000.0000.000
111A222ARG10.9480.99825.52610.52810.5280.0000.0000.0000.000
112A223GLN00.0660.03221.735-0.375-0.3750.0000.0000.0000.000
113A235ILE0-0.049-0.0398.1290.5400.5400.0000.0000.0000.000
114A236LEU0-0.026-0.0139.463-1.616-1.6160.0000.0000.0000.000
115A237LEU0-0.062-0.02611.9730.5170.5170.0000.0000.0000.000
116A238LEU00.0400.02113.9890.1310.1310.0000.0000.0000.000
117A239GLN00.0140.00017.5210.8260.8260.0000.0000.0000.000
118A240ARG10.8310.92921.11011.50811.5080.0000.0000.0000.000
119A241THR0-0.010-0.01223.8720.4360.4360.0000.0000.0000.000
120A242GLN00.030-0.00127.080-0.499-0.4990.0000.0000.0000.000
121A243LYS10.8430.91130.0479.6169.6160.0000.0000.0000.000
122A244THR0-0.022-0.01433.5350.0380.0380.0000.0000.0000.000
123A245VAL00.0850.03036.5650.0530.0530.0000.0000.0000.000
124A246ARG10.8170.90038.5257.6637.6630.0000.0000.0000.000
125A247ALA00.0880.05143.1940.0670.0670.0000.0000.0000.000
126A248VAL0-0.0100.01446.9230.0200.0200.0000.0000.0000.000
127A249GLY0-0.032-0.01349.3630.0930.0930.0000.0000.0000.000
128A250PRO00.0100.03453.004-0.019-0.0190.0000.0000.0000.000
129A251ARG10.9440.96254.4315.2045.2040.0000.0000.0000.000
130A252SER0-0.039-0.01553.9480.0020.0020.0000.0000.0000.000
131A253GLY00.0490.02951.270-0.014-0.0140.0000.0000.0000.000
132A254ASN0-0.010-0.01549.197-0.062-0.0620.0000.0000.0000.000
133A255GLU-1-0.799-0.89443.370-7.194-7.1940.0000.0000.0000.000
134A256LYS10.9140.94447.8195.9465.9460.0000.0000.0000.000
135A257TRP00.0550.02943.590-0.065-0.0650.0000.0000.0000.000
136A258ASN0-0.087-0.06640.160-0.161-0.1610.0000.0000.0000.000
137A259PHE00.0760.02937.982-0.052-0.0520.0000.0000.0000.000
138A260SER0-0.055-0.01433.532-0.051-0.0510.0000.0000.0000.000
139A261VAL00.0170.02131.246-0.078-0.0780.0000.0000.0000.000
140A262GLY00.0170.01328.6390.1020.1020.0000.0000.0000.000
141A263HIS00.0270.01324.1070.1410.1410.0000.0000.0000.000
142A264PHE00.001-0.01219.8810.0310.0310.0000.0000.0000.000
143A265GLU-1-0.832-0.91219.376-14.962-14.9620.0000.0000.0000.000
144A266LEU0-0.0150.00513.3240.0010.0010.0000.0000.0000.000
145A267ARG10.9140.96114.44216.51516.5150.0000.0000.0000.000
146A268TYR00.1090.04710.185-0.970-0.9700.0000.0000.0000.000
147A309VAL00.002-0.01114.069-0.417-0.4170.0000.0000.0000.000
148A310ILE0-0.003-0.01610.583-0.469-0.4690.0000.0000.0000.000
149A311LYS10.8960.94714.56216.27616.2760.0000.0000.0000.000
150A312VAL00.0400.02918.387-0.528-0.5280.0000.0000.0000.000
151A313SER0-0.0040.00620.0930.5790.5790.0000.0000.0000.000
152A314VAL00.0250.00423.670-0.261-0.2610.0000.0000.0000.000
153A315ALA00.0200.00625.6830.1580.1580.0000.0000.0000.000
154A316ASP-1-0.931-0.95426.058-11.005-11.0050.0000.0000.0000.000
155A317TRP0-0.016-0.03024.147-0.604-0.6040.0000.0000.0000.000
156A318LYS10.8550.95420.81013.11713.1170.0000.0000.0000.000
157A319VAL0-0.042-0.01014.786-0.049-0.0490.0000.0000.0000.000
158A320MET0-0.0040.00215.683-0.276-0.2760.0000.0000.0000.000
159A330GLU-1-0.935-0.97715.404-16.349-16.3490.0000.0000.0000.000
160A331TRP00.0080.02710.9470.4460.4460.0000.0000.0000.000
161A332GLU-1-0.813-0.91815.235-13.969-13.9690.0000.0000.0000.000
162A333TYR0-0.046-0.02314.971-0.349-0.3490.0000.0000.0000.000
163A334GLN0-0.009-0.01517.6340.2490.2490.0000.0000.0000.000
164A335PHE0-0.007-0.00816.603-0.215-0.2150.0000.0000.0000.000
165A336CYS00.0450.03222.0200.7350.7350.0000.0000.0000.000
166A337THR0-0.120-0.06324.830-0.089-0.0890.0000.0000.0000.000
167A338PRO00.0600.01624.553-0.484-0.4840.0000.0000.0000.000
168A339ILE00.0020.00620.206-0.218-0.2180.0000.0000.0000.000
169A340ALA0-0.039-0.02822.1380.4520.4520.0000.0000.0000.000
170A341SER0-0.004-0.00219.7690.4250.4250.0000.0000.0000.000
171A342ALA00.0400.01316.718-0.382-0.3820.0000.0000.0000.000
172A343TRP0-0.049-0.03913.553-0.130-0.1300.0000.0000.0000.000
173A344LEU00.0160.0399.772-1.481-1.4810.0000.0000.0000.000
174A345LEU0-0.038-0.0365.6361.5771.5770.0000.0000.0000.000
175A346LYS10.9550.9354.37736.28536.364-0.001-0.022-0.0550.000
176A347ASP-1-0.834-0.8804.691-35.846-35.710-0.001-0.019-0.1160.000
177A348GLY00.0090.0066.3061.1001.1000.0000.0000.0000.000
178A349LYS10.7380.8837.11529.02329.0230.0000.0000.0000.000
179A350VAL0-0.009-0.0149.5321.1221.1220.0000.0000.0000.000
180A351ILE00.0620.04912.7191.1451.1450.0000.0000.0000.000
181A352PRO0-0.003-0.00514.488-1.164-1.1640.0000.0000.0000.000
182A353ILE0-0.0130.00515.728-0.066-0.0660.0000.0000.0000.000
183A354SER00.0120.00418.6710.9620.9620.0000.0000.0000.000
184A375VAL00.016-0.02340.3790.0560.0560.0000.0000.0000.000
185A376GLU-1-0.887-0.94738.866-7.807-7.8070.0000.0000.0000.000
186A377ALA00.0390.03434.712-0.091-0.0910.0000.0000.0000.000
187A378ALA0-0.026-0.01735.185-0.224-0.2240.0000.0000.0000.000
188A379ARG10.9410.96136.5537.1517.1510.0000.0000.0000.000
189A380GLY00.0310.03236.1870.0050.0050.0000.0000.0000.000
190A381ALA0-0.072-0.03831.810-0.203-0.2030.0000.0000.0000.000
191A382THR0-0.010-0.02032.294-0.240-0.2400.0000.0000.0000.000
192A383GLU-1-0.857-0.90433.858-8.619-8.6190.0000.0000.0000.000
193A384ASN0-0.058-0.02727.675-0.044-0.0440.0000.0000.0000.000
194A385SER0-0.098-0.05529.493-0.359-0.3590.0000.0000.0000.000
195A386VAL00.0130.01330.178-0.163-0.1630.0000.0000.0000.000
196A387TYR00.0270.00729.399-0.137-0.1370.0000.0000.0000.000
197A388LEU00.0080.00031.9300.0480.0480.0000.0000.0000.000
198A389GLY00.0260.02331.553-0.147-0.1470.0000.0000.0000.000
199A390MET0-0.049-0.02832.3760.3460.3460.0000.0000.0000.000
200A391TYR0-0.0220.01029.658-0.244-0.2440.0000.0000.0000.000
201A392ARG10.8900.95933.0968.4498.4490.0000.0000.0000.000
202A393GLY0-0.006-0.04234.556-0.118-0.1180.0000.0000.0000.000
203A394GLN00.0360.02034.9050.4250.4250.0000.0000.0000.000
204A395LEU00.0920.02735.739-0.272-0.2720.0000.0000.0000.000
205A396TYR0-0.055-0.02528.7860.0660.0660.0000.0000.0000.000
206A397LEU00.0610.03233.4260.0230.0230.0000.0000.0000.000
207A398GLN0-0.048-0.04325.712-0.125-0.1250.0000.0000.0000.000
208A399SER0-0.0040.00128.5420.2260.2260.0000.0000.0000.000
209A400SER00.0020.01127.576-0.421-0.4210.0000.0000.0000.000