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: 39KGL

Calculation Name: 5SV7-C-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: C

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216109.019315
FMO2-HF: Nuclear repulsion 2135667.158733
FMO2-HF: Total energy -80441.860583
FMO2-MP2: Total energy -80676.455864


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(C:104:SER)


Summations of interaction energy for fragment #1(C: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.
-31.992-28.14921.805-11.749-13.8990.025
Interaction energy analysis for fragmet #1(C:104:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.022
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].
3C106VAL00.0720.0453.7820.1441.962-0.034-0.856-0.9290.003
4C107ILE0-0.033-0.0216.9080.0440.0440.0000.0000.0000.000
5C108ILE00.0180.01610.0310.1370.1370.0000.0000.0000.000
6C109SER00.0000.01113.649-0.007-0.0070.0000.0000.0000.000
7C110THR00.0220.00116.6240.0250.0250.0000.0000.0000.000
8C111LEU00.0350.00819.7460.0180.0180.0000.0000.0000.000
9C112ASP-1-0.892-0.97921.779-0.147-0.1470.0000.0000.0000.000
10C113GLY0-0.0160.00122.444-0.002-0.0020.0000.0000.0000.000
11C114ARG10.7800.89219.5020.2220.2220.0000.0000.0000.000
12C115ILE0-0.040-0.01513.2320.0120.0120.0000.0000.0000.000
13C116ALA00.007-0.00713.755-0.027-0.0270.0000.0000.0000.000
14C117ALA00.0150.0148.4280.0420.0420.0000.0000.0000.000
15C118LEU0-0.019-0.0198.7540.0430.0430.0000.0000.0000.000
16C119ASP-1-0.860-0.9284.855-3.851-3.811-0.001-0.008-0.0300.000
17C120PRO0-0.086-0.0214.163-2.991-3.037-0.001-0.0520.0990.000
18C121GLU-1-0.940-0.9782.3242.2523.6801.858-1.079-2.207-0.001
19C122ASN0-0.025-0.0173.4921.5001.8050.021-0.092-0.2340.000
20C123HIS0-0.060-0.0237.3070.0590.0590.0000.0000.0000.000
21C124GLY00.1960.1017.8780.2800.2800.0000.0000.0000.000
22C125LYS10.8840.9349.3261.3351.3350.0000.0000.0000.000
23C126LYS10.8890.92010.1170.2250.2250.0000.0000.0000.000
24C127GLN0-0.0050.0016.1960.5760.5760.0000.0000.0000.000
25C128TRP00.013-0.0028.6720.1800.1800.0000.0000.0000.000
26C129ASP-1-0.843-0.91613.096-0.417-0.4170.0000.0000.0000.000
27C130LEU0-0.0190.02115.6490.0300.0300.0000.0000.0000.000
28C131ASP-1-0.843-0.91917.929-0.136-0.1360.0000.0000.0000.000
29C132VAL0-0.0040.00120.8690.0130.0130.0000.0000.0000.000
30C133GLY0-0.0070.01023.2790.0010.0010.0000.0000.0000.000
31C134SER0-0.053-0.05126.4370.0080.0080.0000.0000.0000.000
32C135GLY00.0540.01727.0040.0030.0030.0000.0000.0000.000
33C136SER0-0.0060.01925.643-0.004-0.0040.0000.0000.0000.000
34C137LEU0-0.0030.00220.8420.0090.0090.0000.0000.0000.000
35C138VAL00.0200.00525.5510.0120.0120.0000.0000.0000.000
36C139SER0-0.087-0.02928.885-0.009-0.0090.0000.0000.0000.000
37C140SER00.044-0.00632.5580.0070.0070.0000.0000.0000.000
38C141SER0-0.079-0.02535.735-0.004-0.0040.0000.0000.0000.000
39C142LEU00.0610.04938.5290.0000.0000.0000.0000.0000.000
40C151LYS10.9860.98645.005-0.007-0.0070.0000.0000.0000.000
41C152MET0-0.058-0.02139.8150.0000.0000.0000.0000.0000.000
42C153ILE0-0.009-0.01638.9660.0030.0030.0000.0000.0000.000
43C154ILE0-0.020-0.02134.507-0.003-0.0030.0000.0000.0000.000
44C155PRO0-0.020-0.00531.8870.0050.0050.0000.0000.0000.000
45C156SER0-0.005-0.03328.611-0.005-0.0050.0000.0000.0000.000
46C157LEU00.006-0.00423.165-0.006-0.0060.0000.0000.0000.000
47C158ASP-1-0.852-0.86826.3550.0850.0850.0000.0000.0000.000
48C159GLY0-0.033-0.02628.2760.0050.0050.0000.0000.0000.000
49C160ALA00.0470.00431.009-0.003-0.0030.0000.0000.0000.000
50C161LEU0-0.0050.00233.493-0.005-0.0050.0000.0000.0000.000
51C162PHE00.0130.01932.6710.0030.0030.0000.0000.0000.000
52C163GLN0-0.0050.00237.613-0.004-0.0040.0000.0000.0000.000
53C164TRP00.0240.01438.7860.0020.0020.0000.0000.0000.000
54C165ASP-1-0.821-0.91041.3360.0070.0070.0000.0000.0000.000
55C166GLN00.0010.00342.5210.0030.0030.0000.0000.0000.000
56C167ASP-1-0.929-0.95644.9640.0050.0050.0000.0000.0000.000
57C168ARG10.7580.86645.230-0.016-0.0160.0000.0000.0000.000
58C169GLU-1-0.894-0.94543.4210.0160.0160.0000.0000.0000.000
59C170SER0-0.098-0.06741.6360.0010.0010.0000.0000.0000.000
60C171MET0-0.036-0.01535.919-0.003-0.0030.0000.0000.0000.000
61C172GLU-1-0.826-0.87839.4310.0360.0360.0000.0000.0000.000
62C173THR0-0.039-0.02436.850-0.001-0.0010.0000.0000.0000.000
63C174VAL0-0.019-0.01938.994-0.002-0.0020.0000.0000.0000.000
64C175PRO0-0.014-0.01639.7180.0030.0030.0000.0000.0000.000
65C176PHE0-0.012-0.00539.9330.0010.0010.0000.0000.0000.000
66C177THR00.0520.01934.373-0.001-0.0010.0000.0000.0000.000
67C178VAL0-0.036-0.03233.279-0.002-0.0020.0000.0000.0000.000
68C179GLU-1-0.788-0.88231.2600.0680.0680.0000.0000.0000.000
69C180SER00.0850.04736.032-0.001-0.0010.0000.0000.0000.000
70C181LEU0-0.012-0.00438.474-0.002-0.0020.0000.0000.0000.000
71C182LEU0-0.082-0.02235.367-0.003-0.0030.0000.0000.0000.000
72C183GLU-1-0.980-0.97139.8780.0450.0450.0000.0000.0000.000
73C184SER0-0.037-0.01342.455-0.001-0.0010.0000.0000.0000.000
74C192VAL0-0.060-0.04046.344-0.001-0.0010.0000.0000.0000.000
75C193VAL00.0200.01946.9240.0020.0020.0000.0000.0000.000
76C194LEU00.0140.02042.329-0.002-0.0020.0000.0000.0000.000
77C195VAL0-0.0020.00640.5120.0020.0020.0000.0000.0000.000
78C196GLY00.028-0.00737.609-0.001-0.0010.0000.0000.0000.000
79C197GLY00.0050.00635.2540.0000.0000.0000.0000.0000.000
80C198LYS10.8310.90329.331-0.081-0.0810.0000.0000.0000.000
81C199SER0-0.036-0.01428.3710.0010.0010.0000.0000.0000.000
82C200LEU00.028-0.00924.2620.0050.0050.0000.0000.0000.000
83C201THR0-0.0130.00623.621-0.002-0.0020.0000.0000.0000.000
84C202THR0-0.0150.00419.3800.0160.0160.0000.0000.0000.000
85C203TYR00.013-0.00618.341-0.024-0.0240.0000.0000.0000.000
86C204GLY00.0240.02316.4290.0390.0390.0000.0000.0000.000
87C205LEU00.0310.03811.693-0.068-0.0680.0000.0000.0000.000
88C206SER00.0090.00511.7880.1150.1150.0000.0000.0000.000
89C207ALA00.012-0.0056.589-0.181-0.1810.0000.0000.0000.000
90C208TYR00.0110.0152.511-8.819-6.5921.741-1.884-2.0840.017
91C209SER0-0.096-0.0457.7270.0540.0540.0000.0000.0000.000
92C210GLY00.0760.03810.538-0.021-0.0210.0000.0000.0000.000
93C211LYS10.9440.95512.3860.2960.2960.0000.0000.0000.000
94C212VAL00.010-0.00315.6670.0440.0440.0000.0000.0000.000
95C213ARG10.9100.94514.796-0.079-0.0790.0000.0000.0000.000
96C214TYR0-0.002-0.00818.090-0.015-0.0150.0000.0000.0000.000
97C215ILE00.011-0.00120.5110.0010.0010.0000.0000.0000.000
98C216CYS0-0.045-0.00423.071-0.001-0.0010.0000.0000.0000.000
99C217SER00.0680.03425.2000.0090.0090.0000.0000.0000.000
100C218ALA00.0530.02227.4730.0030.0030.0000.0000.0000.000
101C219LEU0-0.027-0.00330.791-0.002-0.0020.0000.0000.0000.000
102C220GLY00.0430.02830.692-0.004-0.0040.0000.0000.0000.000
103C222ARG10.8740.92625.405-0.025-0.0250.0000.0000.0000.000
104C223GLN00.016-0.01123.4390.0090.0090.0000.0000.0000.000
105C224TRP00.0100.02520.959-0.003-0.0030.0000.0000.0000.000
106C236LEU0-0.015-0.0138.2010.0720.0720.0000.0000.0000.000
107C237LEU0-0.063-0.03311.703-0.119-0.1190.0000.0000.0000.000
108C238LEU00.0210.00112.5420.0300.0300.0000.0000.0000.000
109C239GLN0-0.037-0.02316.179-0.039-0.0390.0000.0000.0000.000
110C240ARG10.8760.94719.2670.0030.0030.0000.0000.0000.000
111C241THR0-0.0160.00421.628-0.004-0.0040.0000.0000.0000.000
112C242GLN00.0380.01224.697-0.011-0.0110.0000.0000.0000.000
113C243LYS10.8140.90827.563-0.067-0.0670.0000.0000.0000.000
114C244THR0-0.020-0.01731.020-0.007-0.0070.0000.0000.0000.000
115C245VAL00.0590.02133.8250.0030.0030.0000.0000.0000.000
116C246ARG10.8870.93635.8190.0000.0000.0000.0000.0000.000
117C247ALA00.0560.03640.3660.0030.0030.0000.0000.0000.000
118C248VAL00.017-0.00743.859-0.003-0.0030.0000.0000.0000.000
119C249GLY0-0.054-0.03646.6390.0020.0020.0000.0000.0000.000
120C250PRO00.005-0.00350.3350.0000.0000.0000.0000.0000.000
121C251ARG10.9570.97752.144-0.002-0.0020.0000.0000.0000.000
122C252SER00.0030.00952.245-0.001-0.0010.0000.0000.0000.000
123C253GLY00.0420.03849.3330.0010.0010.0000.0000.0000.000
124C254ASN0-0.066-0.04947.5690.0000.0000.0000.0000.0000.000
125C255GLU-1-0.851-0.90743.579-0.007-0.0070.0000.0000.0000.000
126C256LYS10.8800.93545.612-0.003-0.0030.0000.0000.0000.000
127C257TRP00.0720.03339.960-0.001-0.0010.0000.0000.0000.000
128C258ASN0-0.039-0.03136.7290.0010.0010.0000.0000.0000.000
129C259PHE00.0780.02834.719-0.001-0.0010.0000.0000.0000.000
130C260SER0-0.027-0.00430.9500.0060.0060.0000.0000.0000.000
131C261VAL00.0160.02028.552-0.007-0.0070.0000.0000.0000.000
132C262GLY00.0270.00725.7500.0050.0050.0000.0000.0000.000
133C263HIS0-0.0080.01221.225-0.007-0.0070.0000.0000.0000.000
134C264PHE00.014-0.00516.8900.0010.0010.0000.0000.0000.000
135C265GLU-1-0.855-0.91216.3690.2330.2330.0000.0000.0000.000
136C266LEU00.0270.01010.368-0.015-0.0150.0000.0000.0000.000
137C267ARG10.8550.92512.016-0.341-0.3410.0000.0000.0000.000
138C268TYR00.006-0.0065.468-0.121-0.1210.0000.0000.0000.000
139C269ILE00.0110.0329.932-0.069-0.0690.0000.0000.0000.000
140C309VAL0-0.037-0.0318.8990.0270.0270.0000.0000.0000.000
141C310ILE00.0490.0297.012-0.181-0.1810.0000.0000.0000.000
142C311LYS10.9700.9729.757-0.139-0.1390.0000.0000.0000.000
143C312VAL00.0320.02813.223-0.098-0.0980.0000.0000.0000.000
144C313SER00.0020.01715.6200.0440.0440.0000.0000.0000.000
145C314VAL00.0400.01619.301-0.014-0.0140.0000.0000.0000.000
146C315ALA0-0.0020.00820.495-0.013-0.0130.0000.0000.0000.000
147C316ASP-1-0.842-0.91921.010-0.131-0.1310.0000.0000.0000.000
148C317TRP0-0.038-0.00819.886-0.015-0.0150.0000.0000.0000.000
149C318LYS10.8430.91216.6050.1310.1310.0000.0000.0000.000
150C319VAL0-0.069-0.02510.6260.0480.0480.0000.0000.0000.000
151C320MET00.002-0.01513.161-0.024-0.0240.0000.0000.0000.000
152C321ALA00.0210.0179.812-0.027-0.0270.0000.0000.0000.000
153C330GLU-1-0.988-0.99211.627-0.264-0.2640.0000.0000.0000.000
154C331TRP00.0180.0047.5940.0040.0040.0000.0000.0000.000
155C332GLU-1-0.812-0.92013.457-0.178-0.1780.0000.0000.0000.000
156C333TYR0-0.046-0.01913.267-0.052-0.0520.0000.0000.0000.000
157C334GLN0-0.018-0.02515.1150.0110.0110.0000.0000.0000.000
158C335PHE0-0.040-0.03113.232-0.019-0.0190.0000.0000.0000.000
159C336CYS0-0.028-0.01119.0980.0300.0300.0000.0000.0000.000
160C337THR0-0.028-0.01022.573-0.009-0.0090.0000.0000.0000.000
161C338PRO00.0330.02421.543-0.017-0.0170.0000.0000.0000.000
162C339ILE00.004-0.01215.6050.0050.0050.0000.0000.0000.000
163C340ALA0-0.0010.00218.6610.0200.0200.0000.0000.0000.000
164C341SER0-0.039-0.01615.6700.0300.0300.0000.0000.0000.000
165C342ALA00.0350.00412.376-0.065-0.0650.0000.0000.0000.000
166C343TRP00.002-0.0059.8740.1400.1400.0000.0000.0000.000
167C344LEU00.0130.0185.593-0.293-0.2930.0000.0000.0000.000
168C345LEU0-0.066-0.0403.140-1.0180.5190.124-0.767-0.8940.003
169C346LYS10.9690.9521.851-21.387-24.62218.052-7.509-7.3070.004
170C347ASP-1-0.845-0.8863.0981.5681.2350.0460.502-0.216-0.001
171C348GLY0-0.011-0.0074.8600.6530.755-0.001-0.004-0.0970.000
172C349LYS10.8560.9186.529-1.729-1.7290.0000.0000.0000.000
173C350VAL00.0030.0006.2740.4370.4370.0000.0000.0000.000
174C351ILE0-0.0080.0007.328-0.173-0.1730.0000.0000.0000.000
175C352PRO00.0110.0119.551-0.022-0.0220.0000.0000.0000.000
176C353ILE0-0.042-0.02311.5250.0370.0370.0000.0000.0000.000
177C354SER00.0350.02914.123-0.082-0.0820.0000.0000.0000.000
178C374ILE00.0660.03534.7810.0000.0000.0000.0000.0000.000
179C375VAL00.033-0.01535.3070.0040.0040.0000.0000.0000.000
180C376GLU-1-0.789-0.88436.2380.0560.0560.0000.0000.0000.000
181C377ALA0-0.003-0.00131.740-0.001-0.0010.0000.0000.0000.000
182C378ALA0-0.051-0.02431.5810.0050.0050.0000.0000.0000.000
183C379ARG10.8120.88932.499-0.053-0.0530.0000.0000.0000.000
184C380GLY00.0550.03931.577-0.003-0.0030.0000.0000.0000.000
185C381ALA0-0.061-0.03228.0030.0000.0000.0000.0000.0000.000
186C382THR0-0.037-0.00628.4900.0030.0030.0000.0000.0000.000
187C383GLU-1-0.852-0.92430.6470.0520.0520.0000.0000.0000.000
188C384ASN0-0.015-0.00424.625-0.013-0.0130.0000.0000.0000.000
189C385SER0-0.035-0.02825.7470.0110.0110.0000.0000.0000.000
190C386VAL0-0.024-0.00926.0520.0030.0030.0000.0000.0000.000
191C387TYR0-0.0030.00725.645-0.006-0.0060.0000.0000.0000.000
192C388LEU0-0.010-0.00427.6350.0020.0020.0000.0000.0000.000
193C389GLY00.0310.02027.883-0.006-0.0060.0000.0000.0000.000
194C390MET0-0.023-0.02328.3880.0050.0050.0000.0000.0000.000
195C391TYR00.0230.04327.422-0.015-0.0150.0000.0000.0000.000
196C392ARG10.8800.94728.5290.0910.0910.0000.0000.0000.000
197C393GLY00.026-0.01031.173-0.006-0.0060.0000.0000.0000.000
198C394GLN0-0.012-0.01932.5130.0040.0040.0000.0000.0000.000
199C395LEU00.0950.04432.109-0.005-0.0050.0000.0000.0000.000
200C396TYR0-0.058-0.02925.4800.0020.0020.0000.0000.0000.000
201C397LEU00.0480.02329.601-0.001-0.0010.0000.0000.0000.000
202C398GLN00.011-0.00722.0030.0030.0030.0000.0000.0000.000
203C399SER00.0190.00624.9540.0020.0020.0000.0000.0000.000
204C400SER0-0.019-0.01522.7030.0080.0080.0000.0000.0000.000
205C401VAL0-0.0470.00320.5560.0240.0240.0000.0000.0000.000