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: GN2Y1

Calculation Name: 3USY-A-Xray372

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: 2023-06-19

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 OptH
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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2316556.083295
FMO2-HF: Nuclear repulsion 2228037.090494
FMO2-HF: Total energy -88518.992801
FMO2-MP2: Total energy -88776.726579


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.
-4.436-13.5521.277-7.852-4.313-0.035
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 : 0 / q_Mulliken : 0.014 / q_NPA : 0.009
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].
3A112LEU00.0760.0573.837-0.2901.259-0.006-0.865-0.6780.005
4A113GLY0-0.054-0.0176.5620.5370.5370.0000.0000.0000.000
5A114SER00.008-0.0449.5180.0860.0860.0000.0000.0000.000
6A115MET0-0.057-0.03812.7310.1280.1280.0000.0000.0000.000
7A116GLN00.0630.02516.266-0.008-0.0080.0000.0000.0000.000
8A117LYS10.9440.97618.1850.3010.3010.0000.0000.0000.000
9A118ASN0-0.047-0.03115.5060.1020.1020.0000.0000.0000.000
10A119PHE00.0290.00115.251-0.030-0.0300.0000.0000.0000.000
11A120ALA00.0270.02719.2130.0060.0060.0000.0000.0000.000
12A121TYR0-0.037-0.05121.2030.0060.0060.0000.0000.0000.000
13A122LEU00.020-0.00118.0280.0320.0320.0000.0000.0000.000
14A123GLY00.0100.02122.0120.0080.0080.0000.0000.0000.000
15A124LYS10.9000.94123.0160.2320.2320.0000.0000.0000.000
16A125ILE0-0.0050.01523.7430.0240.0240.0000.0000.0000.000
17A126LYS10.9380.97624.9180.1870.1870.0000.0000.0000.000
18A127PRO00.0880.04022.330-0.006-0.0060.0000.0000.0000.000
19A128GLN00.0150.01423.781-0.012-0.0120.0000.0000.0000.000
20A129GLN0-0.027-0.02526.365-0.004-0.0040.0000.0000.0000.000
21A130LEU00.0240.01919.7290.0030.0030.0000.0000.0000.000
22A131ALA00.0090.00122.088-0.021-0.0210.0000.0000.0000.000
23A132ASP-1-0.958-0.97923.124-0.232-0.2320.0000.0000.0000.000
24A133PHE0-0.022-0.00724.2890.0040.0040.0000.0000.0000.000
25A134ILE0-0.060-0.04518.514-0.008-0.0080.0000.0000.0000.000
26A135ILE00.0120.01420.998-0.034-0.0340.0000.0000.0000.000
27A136ASN0-0.014-0.01622.4490.0030.0030.0000.0000.0000.000
28A137GLU-1-0.989-0.97019.320-0.395-0.3950.0000.0000.0000.000
29A138HIS00.0360.00614.587-0.054-0.0540.0000.0000.0000.000
30A139PRO00.1020.03213.879-0.060-0.0600.0000.0000.0000.000
31A140GLN0-0.026-0.0069.6080.0500.0500.0000.0000.0000.000
32A141THR0-0.002-0.00112.152-0.179-0.1790.0000.0000.0000.000
33A142ILE00.0290.02014.909-0.049-0.0490.0000.0000.0000.000
34A143ALA00.0110.0099.553-0.020-0.0200.0000.0000.0000.000
35A144LEU0-0.042-0.01810.747-0.091-0.0910.0000.0000.0000.000
36A145ILE00.000-0.00111.9020.0100.0100.0000.0000.0000.000
37A146LEU00.005-0.01013.0760.0540.0540.0000.0000.0000.000
38A147ALA00.0120.0129.4070.0490.0490.0000.0000.0000.000
39A148HIS0-0.0490.00811.2420.0400.0400.0000.0000.0000.000
40A149MET0-0.064-0.01614.2750.1400.1400.0000.0000.0000.000
41A150GLU-1-0.927-0.96214.965-0.428-0.4280.0000.0000.0000.000
42A151ALA00.027-0.00214.9320.0090.0090.0000.0000.0000.000
43A152PRO00.0120.01116.1250.0030.0030.0000.0000.0000.000
44A153ASN00.0740.02819.7080.0270.0270.0000.0000.0000.000
45A154ALA00.0170.01814.8740.0090.0090.0000.0000.0000.000
46A155ALA00.002-0.00617.002-0.003-0.0030.0000.0000.0000.000
47A156GLU-1-0.913-0.96317.840-0.234-0.2340.0000.0000.0000.000
48A157THR00.0050.02318.6510.0280.0280.0000.0000.0000.000
49A158LEU00.008-0.01314.7760.0210.0210.0000.0000.0000.000
50A159SER0-0.087-0.07018.3470.0330.0330.0000.0000.0000.000
51A160TYR0-0.002-0.00521.3950.0420.0420.0000.0000.0000.000
52A161PHE00.0010.01419.3540.0050.0050.0000.0000.0000.000
53A162PRO00.0560.02121.4850.0150.0150.0000.0000.0000.000
54A163ASP-1-0.885-0.95719.951-0.225-0.2250.0000.0000.0000.000
55A164GLU-1-0.931-0.95418.509-0.213-0.2130.0000.0000.0000.000
56A165MET00.0100.00917.531-0.021-0.0210.0000.0000.0000.000
57A166LYS10.8110.91215.6880.1910.1910.0000.0000.0000.000
58A167ALA00.0130.02514.271-0.061-0.0610.0000.0000.0000.000
59A168GLU-1-0.894-0.95312.553-0.584-0.5840.0000.0000.0000.000
60A169ILE0-0.033-0.02811.773-0.151-0.1510.0000.0000.0000.000
61A170SER0-0.023-0.02310.045-0.281-0.2810.0000.0000.0000.000
62A171ILE0-0.013-0.0038.022-0.314-0.3140.0000.0000.0000.000
63A172ARG10.9050.9446.9160.5020.5020.0000.0000.0000.000
64A173MET0-0.005-0.0086.776-0.437-0.4370.0000.0000.0000.000
65A174ALA0-0.0240.0093.907-1.529-1.0710.000-0.345-0.114-0.001
66A175ASN0-0.029-0.0131.717-2.126-13.07421.276-6.925-3.404-0.039
67A176LEU00.0220.0403.2562.8542.7260.0080.301-0.1810.000
68A177GLY00.0550.0385.6380.3910.3910.0000.0000.0000.000
69A178GLU-1-0.958-1.0274.455-4.005-4.050-0.001-0.0180.0640.000
70A179ILE0-0.079-0.0138.0540.4590.4590.0000.0000.0000.000
71A180SER00.0160.00711.1660.0010.0010.0000.0000.0000.000
72A181PRO00.1160.03913.523-0.050-0.0500.0000.0000.0000.000
73A182GLN0-0.013-0.01715.387-0.019-0.0190.0000.0000.0000.000
74A183VAL0-0.035-0.01215.3270.0380.0380.0000.0000.0000.000
75A184VAL00.0630.03812.5140.0360.0360.0000.0000.0000.000
76A185LYS10.9760.99515.5230.3710.3710.0000.0000.0000.000
77A186ARG10.9480.97418.9500.4340.4340.0000.0000.0000.000
78A187VAL00.0110.00716.5430.0440.0440.0000.0000.0000.000
79A188SER00.0270.02518.5740.0420.0420.0000.0000.0000.000
80A189THR00.0130.01319.8960.0420.0420.0000.0000.0000.000
81A190VAL0-0.039-0.01722.5460.0290.0290.0000.0000.0000.000
82A191LEU00.0020.00219.6580.0270.0270.0000.0000.0000.000
83A192GLU-1-0.951-0.98023.118-0.300-0.3000.0000.0000.0000.000
84A193ASN00.0360.00825.2240.0220.0220.0000.0000.0000.000
85A194LYS10.8760.95924.3110.3280.3280.0000.0000.0000.000
86A195LEU00.004-0.00623.2000.0120.0120.0000.0000.0000.000
87A196GLU-1-0.906-0.93827.681-0.217-0.2170.0000.0000.0000.000
88A197SER0-0.074-0.03631.0140.0170.0170.0000.0000.0000.000
89A198LEU0-0.031-0.02727.3130.0100.0100.0000.0000.0000.000
90A199THR0-0.0080.00127.0680.0010.0010.0000.0000.0000.000
91A200SER0-0.0060.01330.0330.0130.0130.0000.0000.0000.000
92A201TYR0-0.027-0.01433.2320.0070.0070.0000.0000.0000.000
93A202LYS10.9260.95935.1180.1260.1260.0000.0000.0000.000
94A203ILE0-0.0050.00935.158-0.001-0.0010.0000.0000.0000.000
95A204GLU-1-0.962-0.97838.506-0.098-0.0980.0000.0000.0000.000
96A205VAL0-0.007-0.01337.673-0.005-0.0050.0000.0000.0000.000
97A206GLY0-0.0030.00440.6490.0040.0040.0000.0000.0000.000
98A207GLY00.0570.01943.1120.0000.0000.0000.0000.0000.000
99A208LEU00.014-0.01045.910-0.002-0.0020.0000.0000.0000.000
100A209ARG11.0161.00043.7190.0810.0810.0000.0000.0000.000
101A210ALA00.0170.02641.690-0.001-0.0010.0000.0000.0000.000
102A211VAL00.0170.00842.271-0.002-0.0020.0000.0000.0000.000
103A212ALA00.0160.01044.6490.0020.0020.0000.0000.0000.000
104A213GLU-1-0.947-0.98440.223-0.089-0.0890.0000.0000.0000.000
105A214ILE0-0.032-0.01539.4790.0000.0000.0000.0000.0000.000
106A215PHE0-0.028-0.03941.4220.0030.0030.0000.0000.0000.000
107A216ASN00.0070.00142.5290.0060.0060.0000.0000.0000.000
108A217ARG10.9140.97234.7990.0950.0950.0000.0000.0000.000
109A218LEU0-0.0400.00539.7260.0010.0010.0000.0000.0000.000
110A219GLY00.0290.01942.0640.0030.0030.0000.0000.0000.000
111A220GLN00.0800.02443.8560.0000.0000.0000.0000.0000.000
112A221LYS10.9400.96647.1350.0350.0350.0000.0000.0000.000
113A222SER00.0250.00644.5180.0010.0010.0000.0000.0000.000
114A223ALA00.0840.05646.3500.0000.0000.0000.0000.0000.000
115A224LYS10.9780.98947.9640.0380.0380.0000.0000.0000.000
116A225THR0-0.072-0.03749.9510.0010.0010.0000.0000.0000.000
117A226THR0-0.004-0.02047.6300.0000.0000.0000.0000.0000.000
118A227LEU00.0140.00350.5260.0000.0000.0000.0000.0000.000
119A228ALA00.0180.02452.5690.0010.0010.0000.0000.0000.000
120A229ARG10.9350.96452.1970.0450.0450.0000.0000.0000.000
121A230ILE00.0060.01050.0230.0000.0000.0000.0000.0000.000
122A231GLU-1-0.902-0.95354.621-0.039-0.0390.0000.0000.0000.000
123A232SER0-0.120-0.05557.7970.0010.0010.0000.0000.0000.000
124A233VAL0-0.061-0.02856.9590.0010.0010.0000.0000.0000.000
125A234ASP-1-0.888-0.95956.647-0.050-0.0500.0000.0000.0000.000
126A235ASN00.0510.02157.416-0.002-0.0020.0000.0000.0000.000
127A236LYS10.9370.96358.8640.0430.0430.0000.0000.0000.000
128A237LEU00.0470.03751.471-0.001-0.0010.0000.0000.0000.000
129A238ALA00.0270.01653.743-0.002-0.0020.0000.0000.0000.000
130A239GLY0-0.026-0.01554.2820.0000.0000.0000.0000.0000.000
131A240ALA00.0390.01653.7260.0000.0000.0000.0000.0000.000
132A241ILE0-0.046-0.03248.701-0.002-0.0020.0000.0000.0000.000
133A242LYS10.9470.96350.1950.0420.0420.0000.0000.0000.000
134A243GLU-1-0.892-0.94151.580-0.047-0.0470.0000.0000.0000.000
135A244MET0-0.117-0.04047.359-0.002-0.0020.0000.0000.0000.000
136A245MET0-0.055-0.02846.693-0.002-0.0020.0000.0000.0000.000
137A246PHE00.0300.03747.1370.0000.0000.0000.0000.0000.000
138A247THR0-0.037-0.02643.496-0.002-0.0020.0000.0000.0000.000
139A248PHE00.0490.00445.1840.0030.0030.0000.0000.0000.000
140A249GLU-1-0.812-0.91241.325-0.063-0.0630.0000.0000.0000.000
141A250ASP-1-0.836-0.91744.684-0.054-0.0540.0000.0000.0000.000
142A251ILE0-0.007-0.00247.1780.0040.0040.0000.0000.0000.000
143A252VAL0-0.0040.00845.1230.0030.0030.0000.0000.0000.000
144A253LYS10.8600.93145.8540.0510.0510.0000.0000.0000.000
145A254LEU00.0080.02949.9990.0020.0020.0000.0000.0000.000
146A255ASP-1-0.811-0.91253.303-0.029-0.0290.0000.0000.0000.000
147A256ASN00.019-0.02554.586-0.003-0.0030.0000.0000.0000.000
148A257PHE0-0.022-0.00956.8230.0000.0000.0000.0000.0000.000
149A258ALA00.0740.04456.5780.0000.0000.0000.0000.0000.000
150A259ILE0-0.019-0.00152.589-0.001-0.0010.0000.0000.0000.000
151A260ARG10.8990.94056.1670.0250.0250.0000.0000.0000.000
152A261GLU-1-0.879-0.93359.272-0.029-0.0290.0000.0000.0000.000
153A262ILE0-0.0050.00054.300-0.001-0.0010.0000.0000.0000.000
154A263LEU0-0.092-0.04555.108-0.001-0.0010.0000.0000.0000.000
155A264LYS10.8430.92958.3110.0270.0270.0000.0000.0000.000
156A265VAL0-0.0170.00560.3270.0000.0000.0000.0000.0000.000
157A266ALA0-0.003-0.00455.734-0.001-0.0010.0000.0000.0000.000
158A267ASP-1-0.824-0.91956.943-0.042-0.0420.0000.0000.0000.000
159A268LYS10.8620.92455.0000.0370.0370.0000.0000.0000.000
160A269LYS10.9580.99553.2970.0420.0420.0000.0000.0000.000
161A270ASP-1-0.860-0.92351.876-0.055-0.0550.0000.0000.0000.000
162A271LEU0-0.031-0.02050.464-0.003-0.0030.0000.0000.0000.000
163A272SER0-0.018-0.03749.389-0.002-0.0020.0000.0000.0000.000
164A273LEU00.0220.00245.681-0.003-0.0030.0000.0000.0000.000
165A274ALA0-0.034-0.02345.734-0.004-0.0040.0000.0000.0000.000
166A275LEU00.005-0.00445.219-0.003-0.0030.0000.0000.0000.000
167A276LYS10.8760.95641.7030.0720.0720.0000.0000.0000.000
168A277THR0-0.053-0.02638.694-0.002-0.0020.0000.0000.0000.000
169A278SER00.0350.02839.870-0.003-0.0030.0000.0000.0000.000
170A279THR0-0.031-0.02338.7950.0010.0010.0000.0000.0000.000
171A280LYS10.9460.97040.3440.0420.0420.0000.0000.0000.000
172A281ASP-1-0.879-0.94142.091-0.040-0.0400.0000.0000.0000.000
173A282LEU0-0.0110.00544.0230.0040.0040.0000.0000.0000.000
174A283THR00.003-0.01044.0570.0020.0020.0000.0000.0000.000
175A284ASP-1-0.847-0.94545.547-0.037-0.0370.0000.0000.0000.000
176A285LYS10.8140.94148.0850.0370.0370.0000.0000.0000.000
177A286PHE00.0330.00349.4290.0020.0020.0000.0000.0000.000
178A287LEU00.0040.00048.3210.0020.0020.0000.0000.0000.000
179A288ASN0-0.025-0.02450.0150.0020.0020.0000.0000.0000.000
180A289ASN0-0.095-0.05853.4970.0040.0040.0000.0000.0000.000
181A290MET0-0.0500.00152.9850.0000.0000.0000.0000.0000.000
182A291SER00.0140.00657.4700.0010.0010.0000.0000.0000.000
183A292SER00.0590.01056.741-0.001-0.0010.0000.0000.0000.000
184A293ARG10.9971.00356.4470.0240.0240.0000.0000.0000.000
185A294ALA0-0.019-0.01457.410-0.001-0.0010.0000.0000.0000.000
186A295ALA00.0380.00753.157-0.002-0.0020.0000.0000.0000.000
187A296GLU-1-0.920-0.96152.572-0.028-0.0280.0000.0000.0000.000
188A297GLN0-0.025-0.01552.8790.0000.0000.0000.0000.0000.000
189A298PHE00.0010.00749.638-0.002-0.0020.0000.0000.0000.000
190A299VAL00.0140.00747.168-0.003-0.0030.0000.0000.0000.000
191A300GLU-1-0.917-0.95848.236-0.039-0.0390.0000.0000.0000.000
192A301GLU-1-0.895-0.93649.554-0.051-0.0510.0000.0000.0000.000
193A302MET0-0.028-0.00944.908-0.002-0.0020.0000.0000.0000.000
194A303GLN0-0.050-0.01744.632-0.002-0.0020.0000.0000.0000.000
195A304TYR0-0.042-0.03945.419-0.003-0.0030.0000.0000.0000.000
196A305LEU0-0.0530.00446.001-0.002-0.0020.0000.0000.0000.000
197A306GLY0-0.0050.01443.136-0.003-0.0030.0000.0000.0000.000
198A307ALA0-0.051-0.03838.945-0.001-0.0010.0000.0000.0000.000
199A308VAL00.0430.02640.5770.0010.0010.0000.0000.0000.000
200A309LYS10.9080.94940.0200.1000.1000.0000.0000.0000.000
201A310ILE00.0820.03235.6890.0040.0040.0000.0000.0000.000
202A311LYS10.9680.98540.2560.0930.0930.0000.0000.0000.000
203A312ASP-1-0.884-0.95042.824-0.081-0.0810.0000.0000.0000.000
204A313VAL00.0100.01141.9190.0040.0040.0000.0000.0000.000
205A314ASP-1-0.858-0.93541.878-0.089-0.0890.0000.0000.0000.000
206A315VAL0-0.099-0.05345.0870.0040.0040.0000.0000.0000.000
207A316ALA00.0120.00947.9520.0040.0040.0000.0000.0000.000
208A317GLN00.013-0.00442.8450.0030.0030.0000.0000.0000.000
209A318ARG10.9090.96247.4530.0680.0680.0000.0000.0000.000
210A319LYS10.9901.00350.4080.0600.0600.0000.0000.0000.000
211A320ILE0-0.0030.00951.1690.0030.0030.0000.0000.0000.000
212A321ILE0-0.047-0.03447.9750.0020.0020.0000.0000.0000.000
213A322GLU-1-0.940-0.97052.534-0.051-0.0510.0000.0000.0000.000
214A323ILE0-0.0260.00855.7120.0020.0020.0000.0000.0000.000
215A324VAL0-0.017-0.01353.2130.0020.0020.0000.0000.0000.000
216A325GLN00.014-0.00853.1180.0010.0010.0000.0000.0000.000
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218A327LEU0-0.018-0.02758.6750.0020.0020.0000.0000.0000.000
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