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: K3743

Calculation Name: 2YN7-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YN7

Chain ID: A

ChEMBL ID:

UniProt ID: O50955

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2717039.89512
FMO2-HF: Nuclear repulsion 2627240.058889
FMO2-HF: Total energy -89799.836231
FMO2-MP2: Total energy -90061.521498


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:192:ACE )


Summations of interaction energy for fragment #1(A:192:ACE )
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.
3.1793.889-0.008-0.312-0.3910
Interaction energy analysis for fragmet #1(A:192:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.025
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].
3A194LYS 10.9911.0133.7821.6442.354-0.008-0.312-0.3910.000
4A195LEU 00.0070.0186.7830.2330.2330.0000.0000.0000.000
5A196GLN 00.1000.0265.3390.2790.2790.0000.0000.0000.000
6A197THR 0-0.0010.0135.8970.3810.3810.0000.0000.0000.000
7A198LEU 0-0.022-0.0038.0510.1210.1210.0000.0000.0000.000
8A199LYS 10.8890.93510.8550.5010.5010.0000.0000.0000.000
9A200ASN 00.0180.0008.6180.0430.0430.0000.0000.0000.000
10A201GLU -1-0.959-0.98011.766-0.056-0.0560.0000.0000.0000.000
11A202LEU 0-0.039-0.01613.6700.0290.0290.0000.0000.0000.000
12A203ILE 00.0360.02213.8690.0180.0180.0000.0000.0000.000
13A204ARG 10.8600.93814.8460.0230.0230.0000.0000.0000.000
14A205ALA 0-0.003-0.00817.2550.0130.0130.0000.0000.0000.000
15A206ILE 00.0270.00619.5540.0080.0080.0000.0000.0000.000
16A207SER 00.0260.00419.8400.0090.0090.0000.0000.0000.000
17A208GLU -1-0.908-0.94219.498-0.001-0.0010.0000.0000.0000.000
18A209GLU -1-0.880-0.95723.229-0.028-0.0280.0000.0000.0000.000
19A210LYS 10.9340.95924.5220.0600.0600.0000.0000.0000.000
20A211ASN 00.0020.01223.8930.0010.0010.0000.0000.0000.000
21A212LYS 10.9220.97126.4470.0220.0220.0000.0000.0000.000
22A213THR 0-0.076-0.02329.4270.0020.0020.0000.0000.0000.000
23A214GLN 0-0.037-0.02928.9090.0010.0010.0000.0000.0000.000
24A215ASN 0-0.036-0.01230.6540.0030.0030.0000.0000.0000.000
25A216ASN 0-0.0100.00632.7130.0040.0040.0000.0000.0000.000
26A217PHE 0-0.038-0.03332.8090.0020.0020.0000.0000.0000.000
27A218GLY 00.0010.01136.4970.0020.0020.0000.0000.0000.000
28A219PHE 00.0050.01539.2050.0000.0000.0000.0000.0000.000
29A220ARG 10.9090.94140.8580.0040.0040.0000.0000.0000.000
30A221GLU -1-0.749-0.79844.281-0.010-0.0100.0000.0000.0000.000
31A222THR 0-0.0120.00746.1070.0010.0010.0000.0000.0000.000
32A223TYR 00.021-0.00749.451-0.001-0.0010.0000.0000.0000.000
33A224ASP -1-0.856-0.93852.629-0.006-0.0060.0000.0000.0000.000
34A225GLN 00.005-0.03349.210-0.001-0.0010.0000.0000.0000.000
35A226PHE 00.012-0.01745.123-0.001-0.0010.0000.0000.0000.000
36A227LYS 10.8720.93949.7350.0040.0040.0000.0000.0000.000
37A228MET 0-0.039-0.00546.549-0.001-0.0010.0000.0000.0000.000
38A229LYS 10.8670.95551.8500.0070.0070.0000.0000.0000.000
39A230ASP -1-0.862-0.92353.365-0.008-0.0080.0000.0000.0000.000
40A231SER 00.0660.01154.0000.0000.0000.0000.0000.0000.000
41A232ALA 0-0.022-0.01550.036-0.001-0.0010.0000.0000.0000.000
42A233PHE 0-0.043-0.02645.730-0.001-0.0010.0000.0000.0000.000
43A234GLU -1-0.863-0.91250.781-0.011-0.0110.0000.0000.0000.000
44A235LEU 0-0.083-0.02252.693-0.001-0.0010.0000.0000.0000.000
45A236LEU 0-0.034-0.02847.107-0.001-0.0010.0000.0000.0000.000
46A237ASP -1-0.856-0.91150.111-0.017-0.0170.0000.0000.0000.000
47A238VAL 0-0.076-0.03544.239-0.001-0.0010.0000.0000.0000.000
48A239ILE 00.0450.01641.969-0.001-0.0010.0000.0000.0000.000
49A240SER 0-0.138-0.07539.675-0.002-0.0020.0000.0000.0000.000
50A241SER 0-0.113-0.09341.692-0.001-0.0010.0000.0000.0000.000
51A242ALA 00.0650.05742.4670.0010.0010.0000.0000.0000.000
52A243LYS 10.8490.92538.8670.0290.0290.0000.0000.0000.000
53A244VAL 00.0430.02342.1130.0010.0010.0000.0000.0000.000
54A245TYR 0-0.064-0.03745.627-0.002-0.0020.0000.0000.0000.000
55A246ASP -1-0.818-0.91947.629-0.021-0.0210.0000.0000.0000.000
56A247ARG 10.9710.97847.4280.0270.0270.0000.0000.0000.000
57A248SER 0-0.022-0.01550.1210.0010.0010.0000.0000.0000.000
58A249TYR 0-0.058-0.02250.6690.0010.0010.0000.0000.0000.000
59A250ALA 0-0.027-0.00148.5160.0000.0000.0000.0000.0000.000
60A251PRO 00.0300.02148.2050.0010.0010.0000.0000.0000.000
61A252GLN 00.0500.02450.039-0.001-0.0010.0000.0000.0000.000
62A253LEU 0-0.0110.01745.3820.0000.0000.0000.0000.0000.000
63A254ASN 00.0540.03248.7030.0000.0000.0000.0000.0000.000
64A255SER 0-0.039-0.02951.0670.0010.0010.0000.0000.0000.000
65A256ASN 0-0.026-0.02250.3610.0000.0000.0000.0000.0000.000
66A257THR 00.0060.01049.3120.0000.0000.0000.0000.0000.000
67A258PRO 00.0400.00445.2070.0000.0000.0000.0000.0000.000
68A259GLU -1-0.894-0.95343.845-0.019-0.0190.0000.0000.0000.000
69A260ALA 00.0190.01344.186-0.001-0.0010.0000.0000.0000.000
70A261GLU -1-0.925-0.94944.278-0.010-0.0100.0000.0000.0000.000
71A262ASN 0-0.065-0.03437.927-0.002-0.0020.0000.0000.0000.000
72A263GLU -1-0.705-0.84840.297-0.026-0.0260.0000.0000.0000.000
73A264ARG 10.7990.86441.7370.0120.0120.0000.0000.0000.000
74A265ASN 0-0.022-0.03239.1810.0010.0010.0000.0000.0000.000
75A266LYS 10.8830.96735.7210.0280.0280.0000.0000.0000.000
76A267PHE 00.0340.00938.299-0.001-0.0010.0000.0000.0000.000
77A268TYR 0-0.028-0.06040.1320.0000.0000.0000.0000.0000.000
78A269ALA 00.0460.03334.6350.0010.0010.0000.0000.0000.000
79A270LEU 0-0.086-0.01735.402-0.001-0.0010.0000.0000.0000.000
80A271MET 0-0.085-0.02836.8440.0000.0000.0000.0000.0000.000
81A272ASP -1-0.891-0.94333.815-0.011-0.0110.0000.0000.0000.000
82A273PHE 0-0.082-0.05234.2190.0020.0020.0000.0000.0000.000
83A274ASP -1-0.871-0.91438.3720.0000.0000.0000.0000.0000.000
84A275GLN 00.014-0.01740.263-0.001-0.0010.0000.0000.0000.000
85A276TYR 0-0.007-0.01343.6910.0000.0000.0000.0000.0000.000
86A277LYS 10.9080.97539.3720.0100.0100.0000.0000.0000.000
87A278ILE 0-0.041-0.02441.037-0.001-0.0010.0000.0000.0000.000
88A279GLU -1-0.865-0.91744.889-0.005-0.0050.0000.0000.0000.000
89A280GLN 00.0390.01046.499-0.001-0.0010.0000.0000.0000.000
90A281PHE 00.005-0.01945.818-0.001-0.0010.0000.0000.0000.000
91A282GLY 00.032-0.00647.941-0.001-0.0010.0000.0000.0000.000
92A283SER 0-0.025-0.00150.0670.0000.0000.0000.0000.0000.000
93A284ILE 0-0.0030.00149.7490.0000.0000.0000.0000.0000.000
94A285MET 0-0.083-0.03949.501-0.001-0.0010.0000.0000.0000.000
95A286GLU -1-0.887-0.95152.859-0.006-0.0060.0000.0000.0000.000
96A287ALA 0-0.020-0.00255.8030.0000.0000.0000.0000.0000.000
97A288LEU 0-0.042-0.03053.2610.0000.0000.0000.0000.0000.000
98A289TYR 0-0.018-0.03156.451-0.001-0.0010.0000.0000.0000.000
99A290ASN 0-0.0100.01558.2690.0000.0000.0000.0000.0000.000
100A291GLU -1-0.934-0.95461.219-0.008-0.0080.0000.0000.0000.000
101A292ASN 00.0460.00160.8110.0000.0000.0000.0000.0000.000
102A293GLN 0-0.0190.00260.6660.0000.0000.0000.0000.0000.000
103A294ASN 0-0.062-0.04756.993-0.001-0.0010.0000.0000.0000.000
104A295HIS 0-0.016-0.01055.952-0.001-0.0010.0000.0000.0000.000
105A296SER 0-0.026-0.02454.686-0.001-0.0010.0000.0000.0000.000
106A297LEU 00.0360.03351.635-0.001-0.0010.0000.0000.0000.000
107A298ILE 00.0310.03351.121-0.001-0.0010.0000.0000.0000.000
108A299ARG 10.9260.95250.0590.0160.0160.0000.0000.0000.000
109A300GLU -1-0.897-0.93548.224-0.024-0.0240.0000.0000.0000.000
110A301LEU 0-0.030-0.03346.910-0.001-0.0010.0000.0000.0000.000
111A302MET 00.0130.01545.364-0.001-0.0010.0000.0000.0000.000
112A303ILE 00.0150.02144.408-0.001-0.0010.0000.0000.0000.000
113A304SER 0-0.048-0.01542.684-0.002-0.0020.0000.0000.0000.000
114A305GLY 00.0700.03640.612-0.002-0.0020.0000.0000.0000.000
115A306LEU 00.0290.00939.481-0.002-0.0020.0000.0000.0000.000
116A307GLY 0-0.021-0.01239.329-0.002-0.0020.0000.0000.0000.000
117A308THR 0-0.059-0.06435.682-0.004-0.0040.0000.0000.0000.000
118A309GLN 0-0.013-0.01933.009-0.003-0.0030.0000.0000.0000.000
119A310ILE 00.0240.01434.446-0.003-0.0030.0000.0000.0000.000
120A311SER 00.0030.00134.286-0.004-0.0040.0000.0000.0000.000
121A312PHE 0-0.025-0.01028.228-0.006-0.0060.0000.0000.0000.000
122A313GLU -1-0.801-0.90429.874-0.036-0.0360.0000.0000.0000.000
123A314LEU 0-0.021-0.00830.014-0.004-0.0040.0000.0000.0000.000
124A315ALA 00.0330.01828.667-0.006-0.0060.0000.0000.0000.000
125A316LEU 0-0.030-0.01424.972-0.010-0.0100.0000.0000.0000.000
126A317GLU -1-0.880-0.94624.925-0.075-0.0750.0000.0000.0000.000
127A318GLU -1-0.910-0.96726.083-0.090-0.0900.0000.0000.0000.000
128A319ILE 0-0.046-0.03221.260-0.013-0.0130.0000.0000.0000.000
129A320ASN 0-0.005-0.00521.321-0.023-0.0230.0000.0000.0000.000
130A321LYS 10.9880.99521.4970.0620.0620.0000.0000.0000.000
131A322LYS 10.8430.94222.6120.0980.0980.0000.0000.0000.000
132A323ILE 0-0.027-0.01416.418-0.027-0.0270.0000.0000.0000.000
133A324GLU -1-0.968-0.97318.187-0.149-0.1490.0000.0000.0000.000
134A325ILE 00.0110.00419.890-0.011-0.0110.0000.0000.0000.000
135A326PHE 00.0300.00118.573-0.012-0.0120.0000.0000.0000.000
136A327ASN 00.0440.01213.842-0.095-0.0950.0000.0000.0000.000
137A328GLN 00.0200.00816.689-0.021-0.0210.0000.0000.0000.000
138A329ASP -1-0.890-0.93319.339-0.178-0.1780.0000.0000.0000.000
139A330TYR 0-0.073-0.04310.246-0.029-0.0290.0000.0000.0000.000
140A331LEU 0-0.048-0.02213.866-0.018-0.0180.0000.0000.0000.000
141A332ASN 0-0.076-0.03716.7720.0140.0140.0000.0000.0000.000
142A333ALA 0-0.034-0.01718.1810.0160.0160.0000.0000.0000.000
143A334LYS 10.9480.97819.0780.1510.1510.0000.0000.0000.000
144A335ILE 0-0.035-0.00917.6520.0090.0090.0000.0000.0000.000
145A336ASN 00.0970.06116.354-0.053-0.0530.0000.0000.0000.000
146A337SER 00.036-0.01411.4470.0310.0310.0000.0000.0000.000
147A338PHE 00.0110.01513.580-0.023-0.0230.0000.0000.0000.000
148A339ASP -1-0.853-0.93515.760-0.218-0.2180.0000.0000.0000.000
149A340PHE 00.0360.00812.7770.0140.0140.0000.0000.0000.000
150A341THR 0-0.040-0.03312.872-0.015-0.0150.0000.0000.0000.000
151A342MET 0-0.049-0.02414.9480.0290.0290.0000.0000.0000.000
152A343LYS 10.9871.00918.6010.2140.2140.0000.0000.0000.000
153A344LEU 00.0070.00913.4540.0180.0180.0000.0000.0000.000
154A345LYS 10.9100.95415.4030.2950.2950.0000.0000.0000.000
155A346GLU -1-0.923-0.96218.422-0.113-0.1130.0000.0000.0000.000
156A347LEU 00.0150.00819.3250.0160.0160.0000.0000.0000.000
157A348LYS 10.9460.97316.7470.1490.1490.0000.0000.0000.000
158A349SER 0-0.078-0.03920.2910.0210.0210.0000.0000.0000.000
159A350LYS 10.9630.97723.2840.1090.1090.0000.0000.0000.000
160A351LEU 00.0170.01221.0190.0090.0090.0000.0000.0000.000
161A352ASN 0-0.009-0.02521.4880.0150.0150.0000.0000.0000.000
162A353GLN 00.0270.03225.2230.0030.0030.0000.0000.0000.000
163A354ILE 0-0.012-0.00927.0440.0070.0070.0000.0000.0000.000
164A355LEU 0-0.027-0.00124.2010.0070.0070.0000.0000.0000.000
165A356ASP -1-0.914-0.95428.694-0.036-0.0360.0000.0000.0000.000
166A357LYS 10.9040.95830.6440.0440.0440.0000.0000.0000.000
167A358ARG 10.8570.92731.4320.0270.0270.0000.0000.0000.000
168A359LYS 10.8810.93828.1980.0290.0290.0000.0000.0000.000
169A360GLU -1-0.928-0.98033.959-0.020-0.0200.0000.0000.0000.000
170A361TRP 0-0.003-0.00336.4920.0020.0020.0000.0000.0000.000
171A362SER 00.0310.00736.5110.0030.0030.0000.0000.0000.000
172A363ARG 10.9650.99031.9670.0220.0220.0000.0000.0000.000
173A364GLN 0-0.0040.01139.5490.0020.0020.0000.0000.0000.000
174A365ALA 0-0.007-0.00141.7880.0010.0010.0000.0000.0000.000
175A366ASP -1-0.831-0.90639.679-0.008-0.0080.0000.0000.0000.000
176A367GLY 0-0.037-0.01143.1290.0010.0010.0000.0000.0000.000
177A368LEU 0-0.014-0.01245.3770.0010.0010.0000.0000.0000.000
178A369ILE 00.0180.01244.5640.0010.0010.0000.0000.0000.000
179A370ALA 0-0.0120.00046.4200.0010.0010.0000.0000.0000.000
180A371ASN 0-0.132-0.05948.3250.0000.0000.0000.0000.0000.000
181A372ALA 00.0670.01751.0600.0000.0000.0000.0000.0000.000
182A373SER 0-0.051-0.02550.0280.0000.0000.0000.0000.0000.000
183A374SER 0-0.018-0.00352.1750.0000.0000.0000.0000.0000.000
184A375ASN 00.010-0.00754.8220.0000.0000.0000.0000.0000.000
185A376SER 00.0910.05854.9980.0000.0000.0000.0000.0000.000
186A377SER 0-0.009-0.00957.1210.0000.0000.0000.0000.0000.000
187A378LEU 0-0.043-0.01259.9910.0000.0000.0000.0000.0000.000
188A379SER 0-0.090-0.04459.3700.0000.0000.0000.0000.0000.000
189A380ASP -1-0.806-0.88561.579-0.008-0.0080.0000.0000.0000.000
190A381SER 00.0850.03760.3120.0000.0000.0000.0000.0000.000
191A382LYS 10.9961.00959.6010.0090.0090.0000.0000.0000.000
192A383SER 0-0.089-0.09059.633-0.001-0.0010.0000.0000.0000.000
193A384LEU 00.0400.03954.2740.0000.0000.0000.0000.0000.000
194A385ALA 00.0670.03155.211-0.001-0.0010.0000.0000.0000.000
195A386GLU -1-0.908-0.96354.971-0.013-0.0130.0000.0000.0000.000
196A387TYR 00.0330.02450.596-0.001-0.0010.0000.0000.0000.000
197A388ILE 00.0550.03049.679-0.001-0.0010.0000.0000.0000.000
198A389LYS 10.8310.89850.3720.0130.0130.0000.0000.0000.000
199A390LYS 10.8460.94451.4120.0130.0130.0000.0000.0000.000
200A391ARG 10.8730.92749.0740.0120.0120.0000.0000.0000.000
201A392TYR 00.000-0.00345.4960.0000.0000.0000.0000.0000.000
202A393LEU 00.0230.02845.768-0.001-0.0010.0000.0000.0000.000
203A394ASP -1-0.856-0.92445.832-0.022-0.0220.0000.0000.0000.000
204A395ASN 0-0.051-0.03141.918-0.003-0.0030.0000.0000.0000.000
205A396MET 0-0.046-0.01441.184-0.002-0.0020.0000.0000.0000.000
206A397GLN 0-0.009-0.03341.387-0.002-0.0020.0000.0000.0000.000
207A398ASN 00.0040.00240.396-0.003-0.0030.0000.0000.0000.000
208A399ALA 0-0.0210.00137.231-0.003-0.0030.0000.0000.0000.000
209A400ARG 10.9780.99436.7990.0290.0290.0000.0000.0000.000
210A401GLN 00.002-0.01037.818-0.001-0.0010.0000.0000.0000.000
211A402SER 0-0.034-0.00634.505-0.003-0.0030.0000.0000.0000.000
212A403VAL 0-0.021-0.00232.103-0.004-0.0040.0000.0000.0000.000
213A404LEU 0-0.0210.00333.205-0.004-0.0040.0000.0000.0000.000
214A405GLU -1-0.900-0.96634.905-0.051-0.0510.0000.0000.0000.000
215A406ALA 0-0.029-0.00529.741-0.005-0.0050.0000.0000.0000.000
216A407TYR 00.017-0.00230.292-0.005-0.0050.0000.0000.0000.000
217A408ILE 00.0180.00431.323-0.004-0.0040.0000.0000.0000.000
218A409SER 0-0.097-0.04530.268-0.005-0.0050.0000.0000.0000.000
219A410ILE 0-0.047-0.02425.710-0.008-0.0080.0000.0000.0000.000
220A411MET -1-0.904-0.93127.750-0.100-0.1000.0000.0000.0000.000