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: LZQR9

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216472.749404
FMO2-HF: Nuclear repulsion 2136029.150454
FMO2-HF: Total energy -80443.598949
FMO2-MP2: Total energy -80678.044989


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.
-28.675-30.91732.223-15.51-14.4690.008
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 : 0.008 / q_NPA : 0.018
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].
3C106VAL00.0350.0203.8411.2503.280-0.024-1.074-0.9320.003
4C107ILE0-0.016-0.0066.434-0.196-0.1960.0000.0000.0000.000
5C108ILE00.0150.02010.0170.2760.2760.0000.0000.0000.000
6C109SER0-0.0040.00213.629-0.005-0.0050.0000.0000.0000.000
7C110THR00.0640.01216.7670.0450.0450.0000.0000.0000.000
8C111LEU00.0650.02520.2210.0200.0200.0000.0000.0000.000
9C112ASP-1-0.878-0.94121.994-0.363-0.3630.0000.0000.0000.000
10C113GLY0-0.0030.00022.3690.0170.0170.0000.0000.0000.000
11C114ARG10.7370.86718.6990.4970.4970.0000.0000.0000.000
12C115ILE0-0.029-0.01212.7310.0170.0170.0000.0000.0000.000
13C116ALA0-0.013-0.02313.533-0.021-0.0210.0000.0000.0000.000
14C117ALA00.0040.0158.0750.0020.0020.0000.0000.0000.000
15C118LEU0-0.034-0.0379.0310.0560.0560.0000.0000.0000.000
16C119ASP-1-0.747-0.8626.267-4.482-4.4820.0000.0000.0000.000
17C120PRO0-0.045-0.0024.424-2.124-2.145-0.001-0.0340.0570.000
18C121GLU-1-0.930-0.9701.6060.001-0.0346.121-2.924-3.161-0.011
19C122ASN0-0.0120.0053.5932.5362.9350.004-0.139-0.265-0.001
20C123HIS00.0240.0157.3640.4290.4290.0000.0000.0000.000
21C124GLY00.0590.0418.4990.4220.4220.0000.0000.0000.000
22C125LYS10.8430.89310.1941.8621.8620.0000.0000.0000.000
23C126LYS10.8990.92810.4810.5290.5290.0000.0000.0000.000
24C127GLN00.0140.0095.7950.5090.5090.0000.0000.0000.000
25C128TRP0-0.013-0.0167.8770.4210.4210.0000.0000.0000.000
26C129ASP-1-0.831-0.89412.462-0.861-0.8610.0000.0000.0000.000
27C130LEU0-0.039-0.00314.8470.0620.0620.0000.0000.0000.000
28C131ASP-1-0.823-0.90017.367-0.383-0.3830.0000.0000.0000.000
29C132VAL00.0160.00719.9720.0190.0190.0000.0000.0000.000
30C133GLY0-0.0110.01422.5010.0070.0070.0000.0000.0000.000
31C134SER0-0.022-0.02125.3280.0090.0090.0000.0000.0000.000
32C135GLY00.040-0.00826.2870.0020.0020.0000.0000.0000.000
33C136SER00.0030.00125.127-0.012-0.0120.0000.0000.0000.000
34C137LEU0-0.0370.00220.8200.0170.0170.0000.0000.0000.000
35C138VAL00.0150.00825.3170.0230.0230.0000.0000.0000.000
36C139SER0-0.034-0.00128.782-0.013-0.0130.0000.0000.0000.000
37C140SER00.0100.00132.3300.0120.0120.0000.0000.0000.000
38C141SER0-0.048-0.01135.822-0.006-0.0060.0000.0000.0000.000
39C142LEU00.0530.03138.5350.0030.0030.0000.0000.0000.000
40C151LYS10.9850.98945.2230.0360.0360.0000.0000.0000.000
41C152MET0-0.047-0.02640.0230.0000.0000.0000.0000.0000.000
42C153ILE0-0.0110.00139.1040.0020.0020.0000.0000.0000.000
43C154ILE0-0.016-0.02234.647-0.008-0.0080.0000.0000.0000.000
44C155PRO0-0.031-0.00932.1200.0090.0090.0000.0000.0000.000
45C156SER00.012-0.01428.820-0.013-0.0130.0000.0000.0000.000
46C157LEU0-0.008-0.02423.660-0.004-0.0040.0000.0000.0000.000
47C158ASP-1-0.887-0.88827.199-0.010-0.0100.0000.0000.0000.000
48C159GLY00.0100.00128.3050.0030.0030.0000.0000.0000.000
49C160ALA00.0370.00631.1040.0030.0030.0000.0000.0000.000
50C161LEU0-0.038-0.00733.648-0.010-0.0100.0000.0000.0000.000
51C162PHE00.0350.01232.9400.0080.0080.0000.0000.0000.000
52C163GLN0-0.016-0.01137.812-0.004-0.0040.0000.0000.0000.000
53C164TRP00.0290.02438.6000.0030.0030.0000.0000.0000.000
54C165ASP-1-0.810-0.89742.192-0.037-0.0370.0000.0000.0000.000
55C166GLN00.0250.00343.7510.0020.0020.0000.0000.0000.000
56C167ASP-1-0.938-0.96445.762-0.036-0.0360.0000.0000.0000.000
57C168ARG10.6930.83145.3730.0280.0280.0000.0000.0000.000
58C169GLU-1-0.899-0.94444.057-0.025-0.0250.0000.0000.0000.000
59C170SER0-0.088-0.06642.0500.0000.0000.0000.0000.0000.000
60C171MET0-0.028-0.01836.461-0.005-0.0050.0000.0000.0000.000
61C172GLU-1-0.778-0.84839.202-0.008-0.0080.0000.0000.0000.000
62C173THR0-0.048-0.02337.216-0.004-0.0040.0000.0000.0000.000
63C174VAL0-0.018-0.01339.1580.0010.0010.0000.0000.0000.000
64C175PRO00.000-0.00940.1620.0020.0020.0000.0000.0000.000
65C176PHE0-0.036-0.01440.1290.0020.0020.0000.0000.0000.000
66C177THR00.0410.01534.666-0.002-0.0020.0000.0000.0000.000
67C178VAL0-0.025-0.02733.244-0.001-0.0010.0000.0000.0000.000
68C179GLU-1-0.759-0.85631.0240.0000.0000.0000.0000.0000.000
69C180SER00.0360.01935.725-0.001-0.0010.0000.0000.0000.000
70C181LEU00.0070.00438.9060.0000.0000.0000.0000.0000.000
71C182LEU0-0.092-0.03935.106-0.004-0.0040.0000.0000.0000.000
72C183GLU-1-0.943-0.96339.8020.0100.0100.0000.0000.0000.000
73C184SER0-0.049-0.02042.3660.0010.0010.0000.0000.0000.000
74C192VAL0-0.030-0.01346.733-0.001-0.0010.0000.0000.0000.000
75C193VAL0-0.029-0.01546.7550.0040.0040.0000.0000.0000.000
76C194LEU00.0130.01442.388-0.004-0.0040.0000.0000.0000.000
77C195VAL00.0200.00840.3950.0030.0030.0000.0000.0000.000
78C196GLY00.012-0.01137.380-0.005-0.0050.0000.0000.0000.000
79C197GLY0-0.0050.00934.9300.0040.0040.0000.0000.0000.000
80C198LYS10.8600.91129.521-0.020-0.0200.0000.0000.0000.000
81C199SER0-0.037-0.02128.2060.0040.0040.0000.0000.0000.000
82C200LEU00.0380.01123.221-0.001-0.0010.0000.0000.0000.000
83C201THR0-0.027-0.01622.2700.0130.0130.0000.0000.0000.000
84C202THR0-0.0100.01618.064-0.006-0.0060.0000.0000.0000.000
85C203TYR00.015-0.00817.2760.0030.0030.0000.0000.0000.000
86C204GLY00.0320.01715.187-0.011-0.0110.0000.0000.0000.000
87C205LEU0-0.047-0.01810.797-0.034-0.0340.0000.0000.0000.000
88C206SER00.0140.01310.8290.1790.1790.0000.0000.0000.000
89C207ALA00.008-0.0015.628-0.156-0.1560.0000.0000.0000.000
90C208TYR00.0330.0081.768-6.412-11.31713.690-5.456-3.3300.009
91C209SER0-0.084-0.0497.2600.4840.4840.0000.0000.0000.000
92C210GLY00.0730.0479.8600.1240.1240.0000.0000.0000.000
93C211LYS10.9200.93911.6770.7810.7810.0000.0000.0000.000
94C212VAL00.009-0.00315.0510.0380.0380.0000.0000.0000.000
95C213ARG10.9310.96313.5770.0860.0860.0000.0000.0000.000
96C214TYR0-0.009-0.01816.9010.0180.0180.0000.0000.0000.000
97C215ILE0-0.0010.00619.141-0.028-0.0280.0000.0000.0000.000
98C216CYS0-0.084-0.03321.7270.0130.0130.0000.0000.0000.000
99C217SER00.0810.03623.7560.0020.0020.0000.0000.0000.000
100C218ALA00.0400.01726.4690.0100.0100.0000.0000.0000.000
101C219LEU0-0.027-0.00229.4960.0040.0040.0000.0000.0000.000
102C220GLY00.0510.03829.439-0.006-0.0060.0000.0000.0000.000
103C222ARG10.8900.94224.3690.0650.0650.0000.0000.0000.000
104C223GLN00.0580.01622.5290.0000.0000.0000.0000.0000.000
105C224TRP0-0.0020.01720.056-0.012-0.0120.0000.0000.0000.000
106C236LEU00.0020.0167.2170.1040.1040.0000.0000.0000.000
107C237LEU0-0.063-0.02310.676-0.116-0.1160.0000.0000.0000.000
108C238LEU00.0370.00111.5920.0160.0160.0000.0000.0000.000
109C239GLN0-0.033-0.01115.3040.0050.0050.0000.0000.0000.000
110C240ARG10.8220.91818.6740.1830.1830.0000.0000.0000.000
111C241THR0-0.050-0.02420.8730.0260.0260.0000.0000.0000.000
112C242GLN00.0110.01124.212-0.029-0.0290.0000.0000.0000.000
113C243LYS10.8080.89727.1670.0380.0380.0000.0000.0000.000
114C244THR0-0.056-0.03730.879-0.012-0.0120.0000.0000.0000.000
115C245VAL00.0510.03033.7700.0060.0060.0000.0000.0000.000
116C246ARG10.8980.94034.9780.0740.0740.0000.0000.0000.000
117C247ALA00.0500.03940.3440.0060.0060.0000.0000.0000.000
118C248VAL00.0210.01043.983-0.004-0.0040.0000.0000.0000.000
119C249GLY0-0.031-0.02446.6920.0040.0040.0000.0000.0000.000
120C250PRO00.0080.00450.523-0.001-0.0010.0000.0000.0000.000
121C251ARG10.9540.97451.9770.0270.0270.0000.0000.0000.000
122C252SER0-0.019-0.01752.2990.0000.0000.0000.0000.0000.000
123C253GLY00.0250.02648.4460.0000.0000.0000.0000.0000.000
124C254ASN0-0.030-0.01646.7600.0000.0000.0000.0000.0000.000
125C255GLU-1-0.885-0.93043.096-0.062-0.0620.0000.0000.0000.000
126C256LYS10.8960.93845.5190.0410.0410.0000.0000.0000.000
127C257TRP00.0710.03440.440-0.003-0.0030.0000.0000.0000.000
128C258ASN0-0.042-0.03536.958-0.002-0.0020.0000.0000.0000.000
129C259PHE00.0750.03334.500-0.002-0.0020.0000.0000.0000.000
130C260SER0-0.0120.00430.4080.0080.0080.0000.0000.0000.000
131C261VAL00.0110.01528.713-0.009-0.0090.0000.0000.0000.000
132C262GLY00.0630.02025.6250.0130.0130.0000.0000.0000.000
133C263HIS0-0.0100.00721.050-0.031-0.0310.0000.0000.0000.000
134C264PHE00.0500.00516.552-0.007-0.0070.0000.0000.0000.000
135C265GLU-1-0.804-0.87516.5310.1030.1030.0000.0000.0000.000
136C266LEU0-0.016-0.0139.902-0.042-0.0420.0000.0000.0000.000
137C267ARG10.8320.90411.943-0.116-0.1160.0000.0000.0000.000
138C268TYR0-0.015-0.0395.740-0.498-0.4980.0000.0000.0000.000
139C269ILE00.0150.0249.2990.0090.0090.0000.0000.0000.000
140C309VAL0-0.004-0.0189.1220.0720.0720.0000.0000.0000.000
141C310ILE00.0040.0197.680-0.159-0.1590.0000.0000.0000.000
142C311LYS10.9170.95210.3910.1260.1260.0000.0000.0000.000
143C312VAL00.0240.01513.876-0.143-0.1430.0000.0000.0000.000
144C313SER00.002-0.00216.3890.0530.0530.0000.0000.0000.000
145C314VAL00.002-0.00119.7390.0230.0230.0000.0000.0000.000
146C315ALA00.0110.01721.534-0.013-0.0130.0000.0000.0000.000
147C316ASP-1-0.836-0.91522.530-0.318-0.3180.0000.0000.0000.000
148C317TRP0-0.0380.00321.037-0.024-0.0240.0000.0000.0000.000
149C318LYS10.8270.90117.0950.3340.3340.0000.0000.0000.000
150C319VAL0-0.038-0.01511.3640.0560.0560.0000.0000.0000.000
151C320MET00.006-0.01113.433-0.041-0.0410.0000.0000.0000.000
152C321ALA00.0490.0279.5150.0650.0650.0000.0000.0000.000
153C330GLU-1-1.001-0.99811.454-0.658-0.6580.0000.0000.0000.000
154C331TRP0-0.002-0.0038.2100.0320.0320.0000.0000.0000.000
155C332GLU-1-0.810-0.91013.607-0.433-0.4330.0000.0000.0000.000
156C333TYR0-0.042-0.02913.985-0.087-0.0870.0000.0000.0000.000
157C334GLN0-0.001-0.00615.7980.0030.0030.0000.0000.0000.000
158C335PHE0-0.032-0.02613.846-0.049-0.0490.0000.0000.0000.000
159C336CYS0-0.022-0.02019.7980.0560.0560.0000.0000.0000.000
160C337THR0-0.018-0.01222.892-0.018-0.0180.0000.0000.0000.000
161C338PRO00.0150.01422.229-0.042-0.0420.0000.0000.0000.000
162C339ILE00.0150.00416.7910.0010.0010.0000.0000.0000.000
163C340ALA00.0120.00119.3500.0400.0400.0000.0000.0000.000
164C341SER0-0.056-0.03615.9920.0730.0730.0000.0000.0000.000
165C342ALA00.0260.01912.641-0.112-0.1120.0000.0000.0000.000
166C343TRP00.0420.01310.3630.2290.2290.0000.0000.0000.000
167C344LEU00.0110.0166.258-0.418-0.4180.0000.0000.0000.000
168C345LEU0-0.013-0.0092.669-0.4890.2930.135-0.269-0.647-0.002
169C346LYS10.9240.9231.901-22.068-22.68312.292-5.638-6.0380.010
170C347ASP-1-0.806-0.8773.5512.7302.8530.0060.024-0.1530.000
171C348GLY00.0000.0145.7720.1510.1510.0000.0000.0000.000
172C349LYS10.8410.9056.880-3.393-3.3930.0000.0000.0000.000
173C350VAL00.0050.0016.4890.3210.3210.0000.0000.0000.000
174C351ILE0-0.022-0.0137.8220.0200.0200.0000.0000.0000.000
175C352PRO0-0.0040.01210.248-0.129-0.1290.0000.0000.0000.000
176C353ILE0-0.031-0.02211.8530.0930.0930.0000.0000.0000.000
177C354SER00.0180.01714.450-0.139-0.1390.0000.0000.0000.000
178C374ILE00.0610.03035.2230.0010.0010.0000.0000.0000.000
179C375VAL0-0.001-0.03135.7680.0010.0010.0000.0000.0000.000
180C376GLU-1-0.804-0.87836.7140.0230.0230.0000.0000.0000.000
181C377ALA0-0.0080.00032.042-0.005-0.0050.0000.0000.0000.000
182C378ALA0-0.024-0.00931.9930.0010.0010.0000.0000.0000.000
183C379ARG10.8150.86732.792-0.018-0.0180.0000.0000.0000.000
184C380GLY00.0770.05232.496-0.005-0.0050.0000.0000.0000.000
185C381ALA0-0.032-0.02128.588-0.006-0.0060.0000.0000.0000.000
186C382THR0-0.078-0.03628.986-0.004-0.0040.0000.0000.0000.000
187C383GLU-1-0.827-0.89430.9460.0010.0010.0000.0000.0000.000
188C384ASN0-0.0280.00124.820-0.026-0.0260.0000.0000.0000.000
189C385SER0-0.023-0.02826.1660.0100.0100.0000.0000.0000.000
190C386VAL0-0.016-0.00826.9260.0010.0010.0000.0000.0000.000
191C387TYR0-0.0080.00226.133-0.013-0.0130.0000.0000.0000.000
192C388LEU00.0140.00928.2090.0040.0040.0000.0000.0000.000
193C389GLY00.0240.01928.555-0.008-0.0080.0000.0000.0000.000
194C390MET0-0.029-0.01129.4040.0140.0140.0000.0000.0000.000
195C391TYR00.0280.03327.471-0.027-0.0270.0000.0000.0000.000
196C392ARG10.8980.95328.8410.2340.2340.0000.0000.0000.000
197C393GLY00.007-0.00731.987-0.010-0.0100.0000.0000.0000.000
198C394GLN0-0.002-0.01433.2040.0040.0040.0000.0000.0000.000
199C395LEU00.0810.02832.717-0.010-0.0100.0000.0000.0000.000
200C396TYR0-0.050-0.02026.1330.0010.0010.0000.0000.0000.000
201C397LEU00.0370.01729.981-0.002-0.0020.0000.0000.0000.000
202C398GLN00.014-0.00422.0000.0060.0060.0000.0000.0000.000
203C399SER00.0230.00725.0900.0100.0100.0000.0000.0000.000
204C400SER0-0.007-0.00622.7250.0030.0030.0000.0000.0000.000
205C401VAL0-0.062-0.01721.0040.0170.0170.0000.0000.0000.000