Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 43R6N

Calculation Name: 3USY-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3USY

Chain ID: A

ChEMBL ID:

UniProt ID: O25119

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 228
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2319188.107032
FMO2-HF: Nuclear repulsion 2230649.523612
FMO2-HF: Total energy -88538.58342
FMO2-MP2: Total energy -88796.403266


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:110:GLY )


Summations of interaction energy for fragment #1(A:110:GLY )
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.
-105.536-108.914.5-6.424-4.71-0.066
Interaction energy analysis for fragmet #1(A:110:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.891
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].
3A112LEU 00.0920.0693.8371.2381.9720.000-0.306-0.4270.000
4A113GLY 0-0.047-0.0126.5463.6083.6080.0000.0000.0000.000
5A114SER 00.008-0.0429.5081.8321.8320.0000.0000.0000.000
6A115MET 0-0.052-0.03712.7180.9040.9040.0000.0000.0000.000
7A116GLN 00.0640.02516.2660.5000.5000.0000.0000.0000.000
8A117LYS 10.9480.97818.18513.24613.2460.0000.0000.0000.000
9A118ASN 0-0.047-0.03115.5061.7171.7170.0000.0000.0000.000
10A119PHE 00.026-0.00215.192-0.474-0.4740.0000.0000.0000.000
11A120ALA 00.0300.02919.2130.0790.0790.0000.0000.0000.000
12A121TYR 0-0.038-0.05221.2030.0630.0630.0000.0000.0000.000
13A122LEU 00.020-0.00118.1370.5740.5740.0000.0000.0000.000
14A123GLY 00.0090.02022.1140.0720.0720.0000.0000.0000.000
15A124LYS 10.9030.94323.09711.05911.0590.0000.0000.0000.000
16A125ILE 0-0.0060.01523.8550.5690.5690.0000.0000.0000.000
17A126LYS 10.9390.97725.0059.9889.9880.0000.0000.0000.000
18A127PRO 00.0880.04022.4080.0040.0040.0000.0000.0000.000
19A128GLN 00.0140.01423.875-0.149-0.1490.0000.0000.0000.000
20A129GLN 0-0.023-0.02426.454-0.089-0.0890.0000.0000.0000.000
21A130LEU 00.0220.01819.8390.0770.0770.0000.0000.0000.000
22A131ALA 00.0070.00022.195-0.368-0.3680.0000.0000.0000.000
23A132ASP -1-0.958-0.97723.231-11.214-11.2140.0000.0000.0000.000
24A133PHE 0-0.016-0.00424.3490.0890.0890.0000.0000.0000.000
25A134ILE 0-0.062-0.04618.637-0.146-0.1460.0000.0000.0000.000
26A135ILE 00.0120.01321.126-0.784-0.7840.0000.0000.0000.000
27A136ASN 0-0.012-0.01422.570-0.277-0.2770.0000.0000.0000.000
28A137GLU -1-0.986-0.97019.253-14.667-14.6670.0000.0000.0000.000
29A138HIS 00.0360.00614.546-0.959-0.9590.0000.0000.0000.000
30A139PRO 00.1020.03213.855-0.612-0.6120.0000.0000.0000.000
31A140GLN 0-0.031-0.0109.5760.6020.6020.0000.0000.0000.000
32A141THR 00.0020.00012.086-1.716-1.7160.0000.0000.0000.000
33A142ILE 00.0360.02414.844-0.333-0.3330.0000.0000.0000.000
34A143ALA 00.0050.0069.683-0.276-0.2760.0000.0000.0000.000
35A144LEU 0-0.052-0.02310.687-0.784-0.7840.0000.0000.0000.000
36A145ILE 00.0060.00311.8390.1970.1970.0000.0000.0000.000
37A146LEU 00.011-0.00713.1760.6030.6030.0000.0000.0000.000
38A147ALA 00.0030.0079.5130.1370.1370.0000.0000.0000.000
39A148HIS 0-0.0500.00811.337-0.178-0.1780.0000.0000.0000.000
40A149MET 0-0.060-0.01314.3231.7341.7340.0000.0000.0000.000
41A150GLU -1-0.925-0.96115.025-17.405-17.4050.0000.0000.0000.000
42A151ALA 00.024-0.00314.9420.3650.3650.0000.0000.0000.000
43A152PRO 00.0150.01316.1520.1390.1390.0000.0000.0000.000
44A153ASN 00.0770.02919.7380.6590.6590.0000.0000.0000.000
45A154ALA 00.0140.01614.9430.2950.2950.0000.0000.0000.000
46A155ALA 00.002-0.00717.069-0.053-0.0530.0000.0000.0000.000
47A156GLU -1-0.911-0.96117.885-12.395-12.3950.0000.0000.0000.000
48A157THR 00.0100.02518.7350.6950.6950.0000.0000.0000.000
49A158LEU 00.000-0.01614.8320.3870.3870.0000.0000.0000.000
50A159SER 0-0.086-0.06918.4210.4110.4110.0000.0000.0000.000
51A160TYR 0-0.001-0.00321.4540.8870.8870.0000.0000.0000.000
52A161PHE 00.0020.01319.4360.2630.2630.0000.0000.0000.000
53A162PRO 00.0600.02321.569-0.043-0.0430.0000.0000.0000.000
54A163ASP -1-0.884-0.95520.002-15.168-15.1680.0000.0000.0000.000
55A164GLU -1-0.929-0.95318.562-15.374-15.3740.0000.0000.0000.000
56A165MET 00.0090.00817.605-0.858-0.8580.0000.0000.0000.000
57A166LYS 10.8120.91315.77313.53213.5320.0000.0000.0000.000
58A167ALA 00.0150.02614.313-1.599-1.5990.0000.0000.0000.000
59A168GLU -1-0.894-0.95212.612-26.086-26.0860.0000.0000.0000.000
60A169ILE 0-0.026-0.02511.870-2.441-2.4410.0000.0000.0000.000
61A170SER 0-0.023-0.02210.113-2.966-2.9660.0000.0000.0000.000
62A171ILE 0-0.010-0.0028.085-5.324-5.3240.0000.0000.0000.000
63A172ARG 10.9040.9457.00221.81121.8110.0000.0000.0000.000
64A173MET 00.0090.0016.707-3.329-3.3290.0000.0000.0000.000
65A174ALA 0-0.0110.0193.957-7.365-7.0310.000-0.263-0.071-0.001
66A175ASN 0-0.093-0.0601.803-61.744-66.13314.489-5.997-4.103-0.064
67A176LEU 00.0460.0523.20815.81015.8120.0110.165-0.178-0.001
68A177GLY 00.0540.0395.5822.6982.6980.0000.0000.0000.000
69A178GLU -1-0.960-1.0294.463-55.479-55.5240.000-0.0230.0690.000
70A179ILE 0-0.072-0.0088.0614.2644.2640.0000.0000.0000.000
71A180SER 00.0210.01011.1580.0230.0230.0000.0000.0000.000
72A181PRO 00.1170.04013.5060.0600.0600.0000.0000.0000.000
73A182GLN 0-0.008-0.01415.3690.0970.0970.0000.0000.0000.000
74A183VAL 0-0.033-0.01215.3090.9290.9290.0000.0000.0000.000
75A184VAL 00.0560.03512.4940.7550.7550.0000.0000.0000.000
76A185LYS 10.9800.99715.48414.71214.7120.0000.0000.0000.000
77A186ARG 10.9520.97718.93016.09516.0950.0000.0000.0000.000
78A187VAL 00.0100.00616.4980.7860.7860.0000.0000.0000.000
79A188SER 00.0250.02518.5220.7270.7270.0000.0000.0000.000
80A189THR 00.0160.01519.8380.7370.7370.0000.0000.0000.000
81A190VAL 0-0.038-0.01622.4930.5840.5840.0000.0000.0000.000
82A191LEU 00.0020.00119.5860.5100.5100.0000.0000.0000.000
83A192GLU -1-0.949-0.98023.052-12.317-12.3170.0000.0000.0000.000
84A193ASN 00.0330.00725.1580.4740.4740.0000.0000.0000.000
85A194LYS 10.8790.96024.24512.96712.9670.0000.0000.0000.000
86A195LEU 00.002-0.00723.2880.2560.2560.0000.0000.0000.000
87A196GLU -1-0.902-0.93627.688-10.318-10.3180.0000.0000.0000.000
88A197SER 0-0.072-0.03531.0080.4060.4060.0000.0000.0000.000
89A198LEU 0-0.032-0.02727.4340.2110.2110.0000.0000.0000.000
90A199THR 0-0.011-0.00127.186-0.011-0.0110.0000.0000.0000.000
91A200SER 0-0.0050.01430.1470.2910.2910.0000.0000.0000.000
92A201TYR 0-0.027-0.01533.3350.1620.1620.0000.0000.0000.000
93A202LYS 10.9270.96035.2227.9977.9970.0000.0000.0000.000
94A203ILE 0-0.0050.00935.158-0.079-0.0790.0000.0000.0000.000
95A204GLU -1-0.962-0.97838.567-7.318-7.3180.0000.0000.0000.000
96A205VAL 0-0.006-0.01337.673-0.230-0.2300.0000.0000.0000.000
97A206GLY 0-0.0030.00340.6490.1910.1910.0000.0000.0000.000
98A207GLY 00.0580.02043.1120.0390.0390.0000.0000.0000.000
99A208LEU 00.015-0.01045.876-0.115-0.1150.0000.0000.0000.000
100A209ARG 11.0140.99943.6887.0537.0530.0000.0000.0000.000
101A210ALA 00.0190.02741.656-0.109-0.1090.0000.0000.0000.000
102A211VAL 00.0150.00742.236-0.144-0.1440.0000.0000.0000.000
103A212ALA 00.0200.01244.613-0.024-0.0240.0000.0000.0000.000
104A213GLU -1-0.948-0.98540.191-7.964-7.9640.0000.0000.0000.000
105A214ILE 0-0.035-0.01639.442-0.131-0.1310.0000.0000.0000.000
106A215PHE 0-0.027-0.03941.386-0.007-0.0070.0000.0000.0000.000
107A216ASN 00.0090.00242.4960.1360.1360.0000.0000.0000.000
108A217ARG 10.9090.96934.7678.7388.7380.0000.0000.0000.000
109A218LEU 0-0.0400.00539.689-0.103-0.1030.0000.0000.0000.000
110A219GLY 00.0300.01942.0260.0560.0560.0000.0000.0000.000
111A220GLN 00.0810.02543.8180.2230.2230.0000.0000.0000.000
112A221LYS 10.9420.96747.0986.3866.3860.0000.0000.0000.000
113A222SER 00.0240.00544.4770.1590.1590.0000.0000.0000.000
114A223ALA 00.0860.05846.3130.0960.0960.0000.0000.0000.000
115A224LYS 10.9790.98947.9256.2606.2600.0000.0000.0000.000
116A225THR 0-0.076-0.03849.9080.1050.1050.0000.0000.0000.000
117A226THR 0-0.002-0.01947.5900.0760.0760.0000.0000.0000.000
118A227LEU 00.0130.00250.4860.0660.0660.0000.0000.0000.000
119A228ALA 00.0190.02452.5300.1030.1030.0000.0000.0000.000
120A229ARG 10.9360.96452.1556.1016.1010.0000.0000.0000.000
121A230ILE 00.0070.01049.9830.0590.0590.0000.0000.0000.000
122A231GLU -1-0.906-0.95554.581-5.385-5.3850.0000.0000.0000.000
123A232SER 0-0.119-0.05357.7590.0940.0940.0000.0000.0000.000
124A233VAL 0-0.059-0.02756.9180.0600.0600.0000.0000.0000.000
125A234ASP -1-0.889-0.96056.609-5.598-5.5980.0000.0000.0000.000
126A235ASN 00.0530.02157.379-0.097-0.0970.0000.0000.0000.000
127A236LYS 10.9380.96458.8285.1285.1280.0000.0000.0000.000
128A237LEU 00.0440.03551.435-0.074-0.0740.0000.0000.0000.000
129A238ALA 00.0260.01753.707-0.122-0.1220.0000.0000.0000.000
130A239GLY 0-0.024-0.01354.247-0.062-0.0620.0000.0000.0000.000
131A240ALA 00.0410.01653.694-0.043-0.0430.0000.0000.0000.000
132A241ILE 0-0.046-0.03148.666-0.114-0.1140.0000.0000.0000.000
133A242LYS 10.9470.96350.1615.6065.6060.0000.0000.0000.000
134A243GLU -1-0.894-0.94151.548-5.923-5.9230.0000.0000.0000.000
135A244MET 0-0.120-0.04147.329-0.097-0.0970.0000.0000.0000.000
136A245MET 0-0.052-0.02646.658-0.115-0.1150.0000.0000.0000.000
137A246PHE 00.0300.03747.107-0.102-0.1020.0000.0000.0000.000
138A247THR 0-0.039-0.02843.467-0.050-0.0500.0000.0000.0000.000
139A248PHE 00.0450.00345.1630.1360.1360.0000.0000.0000.000
140A249GLU -1-0.808-0.91141.302-7.578-7.5780.0000.0000.0000.000
141A250ASP -1-0.833-0.91644.660-7.015-7.0150.0000.0000.0000.000
142A251ILE 0-0.009-0.00347.1520.1670.1670.0000.0000.0000.000
143A252VAL 0-0.0020.00945.1010.1520.1520.0000.0000.0000.000
144A253LYS 10.8600.93145.8266.9556.9550.0000.0000.0000.000
145A254LEU 00.0090.02849.9740.1320.1320.0000.0000.0000.000
146A255ASP -1-0.813-0.91353.280-5.642-5.6420.0000.0000.0000.000
147A256ASN 00.020-0.02554.567-0.083-0.0830.0000.0000.0000.000
148A257PHE 0-0.021-0.00856.8030.0340.0340.0000.0000.0000.000
149A258ALA 00.0740.04356.5560.0490.0490.0000.0000.0000.000
150A259ILE 0-0.020-0.00152.5680.0160.0160.0000.0000.0000.000
151A260ARG 10.8990.94156.1475.4535.4530.0000.0000.0000.000
152A261GLU -1-0.878-0.93259.254-5.038-5.0380.0000.0000.0000.000
153A262ILE 0-0.008-0.00254.2790.0220.0220.0000.0000.0000.000
154A263LEU 0-0.088-0.04455.108-0.001-0.0010.0000.0000.0000.000
155A264LYS 10.8420.93058.2945.1105.1100.0000.0000.0000.000
156A265VAL 0-0.0170.00560.3080.0610.0610.0000.0000.0000.000
157A266ALA 0-0.002-0.00555.753-0.002-0.0020.0000.0000.0000.000
158A267ASP -1-0.825-0.91956.972-5.560-5.5600.0000.0000.0000.000
159A268LYS 10.8610.92255.0175.5785.5780.0000.0000.0000.000
160A269LYS 10.9600.99753.3175.5515.5510.0000.0000.0000.000
161A270ASP -1-0.859-0.92451.905-6.133-6.1330.0000.0000.0000.000
162A271LEU 0-0.036-0.02250.491-0.155-0.1550.0000.0000.0000.000
163A272SER 0-0.012-0.03549.405-0.170-0.1700.0000.0000.0000.000
164A273LEU 00.0220.00245.714-0.199-0.1990.0000.0000.0000.000
165A274ALA 0-0.031-0.02245.761-0.203-0.2030.0000.0000.0000.000
166A275LEU 00.001-0.00545.240-0.155-0.1550.0000.0000.0000.000
167A276LYS 10.8770.95741.7217.4617.4610.0000.0000.0000.000
168A277THR 0-0.053-0.02638.715-0.148-0.1480.0000.0000.0000.000
169A278SER 00.0330.02639.885-0.058-0.0580.0000.0000.0000.000
170A279THR 0-0.032-0.02538.776-0.107-0.1070.0000.0000.0000.000
171A280LYS 10.9490.97140.3297.6657.6650.0000.0000.0000.000
172A281ASP -1-0.881-0.94142.075-7.270-7.2700.0000.0000.0000.000
173A282LEU 0-0.0080.00544.0050.2340.2340.0000.0000.0000.000
174A283THR 0-0.001-0.01244.0370.2020.2020.0000.0000.0000.000
175A284ASP -1-0.844-0.94445.535-6.925-6.9250.0000.0000.0000.000
176A285LYS 10.8150.94248.0716.4636.4630.0000.0000.0000.000
177A286PHE 00.0350.00449.4120.2140.2140.0000.0000.0000.000
178A287LEU 00.0020.00048.3060.1620.1620.0000.0000.0000.000
179A288ASN 0-0.024-0.02450.0010.1420.1420.0000.0000.0000.000
180A289ASN 0-0.094-0.05753.4840.2500.2500.0000.0000.0000.000
181A290MET 0-0.052-0.00152.9850.1350.1350.0000.0000.0000.000
182A291SER 00.0150.00657.457-0.018-0.0180.0000.0000.0000.000
183A292SER 00.0580.01056.717-0.051-0.0510.0000.0000.0000.000
184A293ARG 10.9971.00456.4275.3505.3500.0000.0000.0000.000
185A294ALA 0-0.018-0.01357.399-0.052-0.0520.0000.0000.0000.000
186A295ALA 00.0380.00753.140-0.081-0.0810.0000.0000.0000.000
187A296GLU -1-0.919-0.96152.561-5.954-5.9540.0000.0000.0000.000
188A297GLN 0-0.024-0.01452.871-0.018-0.0180.0000.0000.0000.000
189A298PHE 00.0000.00749.643-0.047-0.0470.0000.0000.0000.000
190A299VAL 00.0120.00647.159-0.140-0.1400.0000.0000.0000.000
191A300GLU -1-0.916-0.95748.237-6.241-6.2410.0000.0000.0000.000
192A301GLU -1-0.891-0.93549.562-6.257-6.2570.0000.0000.0000.000
193A302MET 0-0.033-0.01144.915-0.065-0.0650.0000.0000.0000.000
194A303GLN 0-0.049-0.01744.637-0.081-0.0810.0000.0000.0000.000
195A304TYR 0-0.041-0.03845.436-0.118-0.1180.0000.0000.0000.000
196A305LEU 0-0.0560.00346.024-0.009-0.0090.0000.0000.0000.000
197A306GLY 0-0.0030.01543.159-0.079-0.0790.0000.0000.0000.000
198A307ALA 0-0.053-0.03938.984-0.092-0.0920.0000.0000.0000.000
199A308VAL 00.0450.02740.6130.1490.1490.0000.0000.0000.000
200A309LYS 10.9060.94840.0717.6357.6350.0000.0000.0000.000
201A310ILE 00.0820.03235.7320.1460.1460.0000.0000.0000.000
202A311LYS 10.9680.98640.3037.3037.3030.0000.0000.0000.000
203A312ASP -1-0.883-0.94942.880-7.019-7.0190.0000.0000.0000.000
204A313VAL 00.0110.01141.9530.1780.1780.0000.0000.0000.000
205A314ASP -1-0.858-0.93541.925-7.640-7.6400.0000.0000.0000.000
206A315VAL 0-0.099-0.05345.1290.1750.1750.0000.0000.0000.000
207A316ALA 00.0100.00947.9940.1720.1720.0000.0000.0000.000
208A317GLN 00.012-0.00542.8700.1370.1370.0000.0000.0000.000
209A318ARG 10.9120.96447.4276.7086.7080.0000.0000.0000.000
210A319LYS 10.9921.00450.4246.2076.2070.0000.0000.0000.000
211A320ILE 0-0.0010.01051.1480.1300.1300.0000.0000.0000.000
212A321ILE 0-0.050-0.03547.9510.0860.0860.0000.0000.0000.000
213A322GLU -1-0.940-0.97052.510-5.769-5.7690.0000.0000.0000.000
214A323ILE 0-0.0230.01055.6880.1340.1340.0000.0000.0000.000
215A324VAL 0-0.022-0.01553.1900.1090.1090.0000.0000.0000.000
216A325GLN 00.012-0.00953.0890.1000.1000.0000.0000.0000.000
217A326SER 00.0020.01057.4600.1310.1310.0000.0000.0000.000
218A327LEU 0-0.019-0.02758.6530.1040.1040.0000.0000.0000.000
219A328GLN 00.000-0.01057.8750.1310.1310.0000.0000.0000.000
220A329GLU -1-0.965-0.97460.518-5.098-5.0980.0000.0000.0000.000
221A330LYS 10.8480.92963.0545.1095.1090.0000.0000.0000.000
222A331GLY 0-0.0050.01263.9850.0800.0800.0000.0000.0000.000
223A332VAL 0-0.050-0.01962.7690.0270.0270.0000.0000.0000.000
224A333ILE 0-0.032-0.01156.790-0.043-0.0430.0000.0000.0000.000
225A334GLN 00.0650.04058.414-0.047-0.0470.0000.0000.0000.000
226A335THR 0-0.009-0.00854.025-0.063-0.0630.0000.0000.0000.000
227A336GLY 0-0.028-0.00454.183-0.113-0.1130.0000.0000.0000.000
228A1NME 0-0.034-0.01955.6710.0410.0410.0000.0000.0000.000