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

tag_button

FMODB ID: G5911

Calculation Name: 4YO2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO2

Chain ID: A

ChEMBL ID:

UniProt ID: A0AVK6

Base Structure: X-ray

Registration Date: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063453.830276
FMO2-HF: Nuclear repulsion 1987665.684199
FMO2-HF: Total energy -75788.146077
FMO2-MP2: Total energy -76008.951077


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:GLN)


Summations of interaction energy for fragment #1(A:110:GLN)
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.
-10.419-11.82515.153-7.382-6.365-0.064
Interaction energy analysis for fragmet #1(A:110:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.005
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].
3A112SER00.0100.0152.9280.3612.4130.007-0.984-1.0750.002
4A113ARG10.9960.9794.8030.0190.118-0.001-0.006-0.0920.000
5A114LYS10.9410.9617.4951.1601.1600.0000.0000.0000.000
6A115GLU-1-0.768-0.8671.814-16.692-20.87514.993-6.128-4.682-0.068
7A116LYS10.8680.9342.7544.0894.7150.154-0.264-0.5160.002
8A117SER0-0.036-0.0098.7590.2890.2890.0000.0000.0000.000
9A118LEU00.0220.00711.9630.0240.0240.0000.0000.0000.000
10A119GLY00.0870.04115.2690.0320.0320.0000.0000.0000.000
11A120LEU0-0.0310.0049.7190.0180.0180.0000.0000.0000.000
12A121LEU00.0370.01313.4120.0440.0440.0000.0000.0000.000
13A122CYS0-0.075-0.02115.2870.0650.0650.0000.0000.0000.000
14A123HIS0-0.016-0.02416.5680.0390.0390.0000.0000.0000.000
15A124LYS10.7670.88715.7900.1130.1130.0000.0000.0000.000
16A125PHE00.003-0.01017.8990.0350.0350.0000.0000.0000.000
17A126LEU0-0.056-0.04720.7440.0220.0220.0000.0000.0000.000
18A127ALA0-0.036-0.00220.1300.0060.0060.0000.0000.0000.000
19A128ARG10.7380.85120.3780.0300.0300.0000.0000.0000.000
20A129TYR0-0.016-0.01823.4460.0190.0190.0000.0000.0000.000
21A130PRO00.0320.03426.882-0.011-0.0110.0000.0000.0000.000
22A131ASN0-0.001-0.02626.7710.0030.0030.0000.0000.0000.000
23A132TYR0-0.022-0.01530.2680.0010.0010.0000.0000.0000.000
24A133PRO00.0260.04232.6430.0010.0010.0000.0000.0000.000
25A134ASN0-0.002-0.01434.8000.0030.0030.0000.0000.0000.000
26A135PRO00.008-0.01537.3870.0010.0010.0000.0000.0000.000
27A136ALA00.0780.05536.5650.0010.0010.0000.0000.0000.000
28A137VAL0-0.0070.00834.4180.0020.0020.0000.0000.0000.000
29A138ASN0-0.029-0.01431.815-0.001-0.0010.0000.0000.0000.000
30A139ASN0-0.015-0.02630.7540.0100.0100.0000.0000.0000.000
31A140ASP-1-0.753-0.85426.981-0.014-0.0140.0000.0000.0000.000
32A141ILE0-0.013-0.00626.1030.0070.0070.0000.0000.0000.000
33A142CYS0-0.082-0.04023.3040.0080.0080.0000.0000.0000.000
34A143LEU0-0.002-0.02021.8880.0110.0110.0000.0000.0000.000
35A144ASP-1-0.793-0.89621.6980.1230.1230.0000.0000.0000.000
36A145GLU-1-0.819-0.88220.048-0.029-0.0290.0000.0000.0000.000
37A146VAL0-0.113-0.05116.707-0.014-0.0140.0000.0000.0000.000
38A147ALA0-0.024-0.01017.8000.0570.0570.0000.0000.0000.000
39A148GLU-1-0.845-0.89419.4640.0440.0440.0000.0000.0000.000
40A149GLU-1-0.817-0.90014.448-0.120-0.1200.0000.0000.0000.000
41A150LEU0-0.0010.0038.8310.0470.0470.0000.0000.0000.000
42A151ASN0-0.101-0.05410.9090.0440.0440.0000.0000.0000.000
43A152VAL00.0690.03011.693-0.045-0.0450.0000.0000.0000.000
44A153GLU-1-0.798-0.88613.9830.2320.2320.0000.0000.0000.000
45A154ARG11.0150.97915.944-0.263-0.2630.0000.0000.0000.000
46A155ARG10.8500.92418.944-0.105-0.1050.0000.0000.0000.000
47A156ARG10.8240.89014.526-0.089-0.0890.0000.0000.0000.000
48A157ILE00.0790.05817.902-0.039-0.0390.0000.0000.0000.000
49A158TYR0-0.008-0.00920.406-0.003-0.0030.0000.0000.0000.000
50A159ASP-1-0.848-0.91220.184-0.031-0.0310.0000.0000.0000.000
51A160ILE00.0560.02517.958-0.007-0.0070.0000.0000.0000.000
52A161VAL00.0340.02222.507-0.005-0.0050.0000.0000.0000.000
53A162ASN0-0.085-0.06325.5720.0050.0050.0000.0000.0000.000
54A163VAL00.0130.00324.2450.0010.0010.0000.0000.0000.000
55A164LEU00.0420.03624.726-0.001-0.0010.0000.0000.0000.000
56A165GLU-1-0.727-0.82628.0320.0090.0090.0000.0000.0000.000
57A166SER0-0.124-0.04230.0280.0010.0010.0000.0000.0000.000
58A167LEU00.0420.01729.3180.0010.0010.0000.0000.0000.000
59A168HIS0-0.087-0.04432.8470.0000.0000.0000.0000.0000.000
60A169MET00.0010.00827.979-0.002-0.0020.0000.0000.0000.000
61A170VAL00.0230.03728.3880.0010.0010.0000.0000.0000.000
62A171SER0-0.019-0.02431.7610.0000.0000.0000.0000.0000.000
63A172ARG10.8500.91530.946-0.019-0.0190.0000.0000.0000.000
64A173LEU0-0.0010.02333.607-0.004-0.0040.0000.0000.0000.000
65A174ALA00.0430.00933.9990.0020.0020.0000.0000.0000.000
66A175LYS10.9710.98131.332-0.107-0.1070.0000.0000.0000.000
67A176ASN0-0.008-0.01826.901-0.001-0.0010.0000.0000.0000.000
68A177ARG10.9340.98029.466-0.042-0.0420.0000.0000.0000.000
69A178TYR0-0.026-0.05028.8590.0020.0020.0000.0000.0000.000
70A179THR00.0150.01131.0090.0040.0040.0000.0000.0000.000
71A180TRP0-0.001-0.03126.367-0.006-0.0060.0000.0000.0000.000
72A181HIS0-0.070-0.04030.600-0.010-0.0100.0000.0000.0000.000
73A182GLY00.0530.04531.993-0.001-0.0010.0000.0000.0000.000
74A183ARG10.7960.87527.3950.1110.1110.0000.0000.0000.000
75A184HIS00.0190.00833.500-0.004-0.0040.0000.0000.0000.000
76A185ASN00.0310.01836.6200.0030.0030.0000.0000.0000.000
77A186LEU00.0020.02832.2420.0000.0000.0000.0000.0000.000
78A187ASN00.000-0.02735.7490.0000.0000.0000.0000.0000.000
79A188LYS10.9901.00238.5760.0280.0280.0000.0000.0000.000
80A189THR0-0.016-0.01435.7230.0040.0040.0000.0000.0000.000
81A190LEU0-0.0060.00835.2050.0010.0010.0000.0000.0000.000
82A191GLY00.0170.01538.2970.0010.0010.0000.0000.0000.000
83A192THR0-0.037-0.03741.2650.0020.0020.0000.0000.0000.000
84A193LEU00.005-0.01135.9040.0020.0020.0000.0000.0000.000
85A194LYS10.8910.94440.3900.0520.0520.0000.0000.0000.000
86A195SER0-0.012-0.01242.5220.0020.0020.0000.0000.0000.000
87A196ILE0-0.087-0.02742.0830.0030.0030.0000.0000.0000.000
88A197GLY00.018-0.00442.675-0.001-0.0010.0000.0000.0000.000
89A198GLU-1-0.792-0.87642.789-0.022-0.0220.0000.0000.0000.000
90A199GLU-1-0.872-0.92842.298-0.039-0.0390.0000.0000.0000.000
91A200ASN0-0.031-0.03343.290-0.002-0.0020.0000.0000.0000.000
92A201LYS10.9100.93944.5310.0230.0230.0000.0000.0000.000
93A202TYR0-0.043-0.03239.7320.0000.0000.0000.0000.0000.000
94A203ALA00.0080.00041.433-0.003-0.0030.0000.0000.0000.000
95A204GLU-1-0.885-0.94543.326-0.031-0.0310.0000.0000.0000.000
96A205GLN00.007-0.00740.228-0.001-0.0010.0000.0000.0000.000
97A206ILE0-0.009-0.01438.398-0.001-0.0010.0000.0000.0000.000
98A207MET00.0190.03241.103-0.004-0.0040.0000.0000.0000.000
99A208MET00.0080.02543.4940.0000.0000.0000.0000.0000.000
100A209ILE0-0.004-0.00837.523-0.001-0.0010.0000.0000.0000.000
101A210LYS10.7850.89040.5260.0530.0530.0000.0000.0000.000
102A211LYS10.8840.92541.7200.0510.0510.0000.0000.0000.000
103A212LYS11.0071.02844.1720.0420.0420.0000.0000.0000.000
104A259ASN00.0710.03841.455-0.002-0.0020.0000.0000.0000.000
105A260SER0-0.010-0.01539.9950.0010.0010.0000.0000.0000.000
106A261ARG11.0161.00240.132-0.019-0.0190.0000.0000.0000.000
107A262LYS10.9190.94035.234-0.046-0.0460.0000.0000.0000.000
108A263ASP-1-0.801-0.86735.4130.0110.0110.0000.0000.0000.000
109A264LYS10.8620.95133.594-0.005-0.0050.0000.0000.0000.000
110A265SER00.040-0.01831.568-0.002-0.0020.0000.0000.0000.000
111A266LEU0-0.0260.00725.507-0.005-0.0050.0000.0000.0000.000
112A267ARG10.9180.94829.511-0.017-0.0170.0000.0000.0000.000
113A268VAL00.0750.04731.543-0.007-0.0070.0000.0000.0000.000
114A269MET0-0.043-0.01728.126-0.004-0.0040.0000.0000.0000.000
115A270SER00.021-0.01228.594-0.005-0.0050.0000.0000.0000.000
116A271GLN00.002-0.00230.566-0.003-0.0030.0000.0000.0000.000
117A272LYS10.9590.97234.1240.0260.0260.0000.0000.0000.000
118A273PHE0-0.054-0.01427.633-0.002-0.0020.0000.0000.0000.000
119A274VAL00.018-0.00731.098-0.003-0.0030.0000.0000.0000.000
120A275MET0-0.0440.02233.4860.0000.0000.0000.0000.0000.000
121A276LEU0-0.007-0.01633.8280.0000.0000.0000.0000.0000.000
122A277PHE0-0.038-0.01429.474-0.004-0.0040.0000.0000.0000.000
123A278LEU0-0.063-0.01435.292-0.002-0.0020.0000.0000.0000.000
124A279VAL00.0280.01138.1650.0060.0060.0000.0000.0000.000
125A280SER00.010-0.01139.978-0.004-0.0040.0000.0000.0000.000
126A281THR0-0.024-0.01140.4520.0000.0000.0000.0000.0000.000
127A282PRO0-0.0070.00235.1620.0010.0010.0000.0000.0000.000
128A283GLN0-0.009-0.00335.553-0.001-0.0010.0000.0000.0000.000
129A284ILE00.0200.02831.1050.0040.0040.0000.0000.0000.000
130A285VAL00.0170.00027.538-0.001-0.0010.0000.0000.0000.000
131A286SER00.011-0.01929.8650.0040.0040.0000.0000.0000.000
132A287LEU00.0240.02431.5860.0080.0080.0000.0000.0000.000
133A288GLU-1-0.703-0.85631.781-0.077-0.0770.0000.0000.0000.000
134A289VAL0-0.068-0.03229.7080.0070.0070.0000.0000.0000.000
135A290ALA00.0410.02833.0530.0070.0070.0000.0000.0000.000
136A291ALA00.0800.04336.4580.0060.0060.0000.0000.0000.000
137A292LYS10.8090.88831.9370.0670.0670.0000.0000.0000.000
138A293ILE0-0.056-0.02533.9580.0070.0070.0000.0000.0000.000
139A294LEU00.0900.05336.7120.0040.0040.0000.0000.0000.000
140A295ILE00.009-0.01036.7110.0030.0030.0000.0000.0000.000
141A296GLY0-0.087-0.04237.0630.0020.0020.0000.0000.0000.000
142A297GLU-1-0.917-0.97636.7370.0070.0070.0000.0000.0000.000
143A298ASP-1-0.961-0.96740.288-0.008-0.0080.0000.0000.0000.000
144A299HIS0-0.013-0.00243.5070.0020.0020.0000.0000.0000.000
145A300VAL00.0060.02344.665-0.003-0.0030.0000.0000.0000.000
146A301GLU-1-0.890-0.93541.9080.0050.0050.0000.0000.0000.000
147A302ASP-1-0.866-0.95039.608-0.009-0.0090.0000.0000.0000.000
148A303LEU00.007-0.00436.6400.0030.0030.0000.0000.0000.000
149A304ASP-1-0.794-0.86736.001-0.024-0.0240.0000.0000.0000.000
150A305LYS10.8100.90833.5440.0160.0160.0000.0000.0000.000
151A306SER0-0.071-0.04430.847-0.005-0.0050.0000.0000.0000.000
152A307LYS10.9360.97931.040-0.017-0.0170.0000.0000.0000.000
153A308PHE00.0880.04030.215-0.004-0.0040.0000.0000.0000.000
154A309LYS10.9280.92726.4420.0080.0080.0000.0000.0000.000
155A310THR0-0.057-0.04025.264-0.010-0.0100.0000.0000.0000.000
156A311LYS10.8590.92626.3730.0120.0120.0000.0000.0000.000
157A312ILE00.0430.02525.083-0.005-0.0050.0000.0000.0000.000
158A313ARG10.9130.97021.8240.0240.0240.0000.0000.0000.000
159A314ARG10.8640.91420.1170.0100.0100.0000.0000.0000.000
160A315LEU00.0260.02424.678-0.002-0.0020.0000.0000.0000.000
161A316TYR00.008-0.00421.057-0.009-0.0090.0000.0000.0000.000
162A317ASP-1-0.854-0.90719.509-0.127-0.1270.0000.0000.0000.000
163A318ILE0-0.013-0.01621.344-0.014-0.0140.0000.0000.0000.000
164A319ALA00.0060.00723.111-0.004-0.0040.0000.0000.0000.000
165A320ASN0-0.041-0.04017.386-0.046-0.0460.0000.0000.0000.000
166A321VAL0-0.0020.00919.772-0.019-0.0190.0000.0000.0000.000
167A322LEU0-0.0150.00021.0370.0000.0000.0000.0000.0000.000
168A323SER0-0.028-0.02420.5260.0070.0070.0000.0000.0000.000
169A324SER0-0.012-0.01319.884-0.048-0.0480.0000.0000.0000.000
170A325LEU00.0220.02121.5370.0220.0220.0000.0000.0000.000
171A326ASP-1-0.786-0.89824.223-0.148-0.1480.0000.0000.0000.000
172A327LEU0-0.060-0.03126.9180.0040.0040.0000.0000.0000.000
173A328ILE00.0830.06324.5170.0070.0070.0000.0000.0000.000
174A329LYS10.8310.90426.1280.1320.1320.0000.0000.0000.000
175A330LYS10.8390.90920.2650.2430.2430.0000.0000.0000.000
176A331VAL0-0.041-0.03323.9160.0030.0030.0000.0000.0000.000
177A332HIS00.0630.03625.046-0.001-0.0010.0000.0000.0000.000
178A333VAL00.0300.01323.648-0.021-0.0210.0000.0000.0000.000
179A334THR0-0.066-0.02625.9580.0160.0160.0000.0000.0000.000
180A335GLU-1-0.768-0.86823.689-0.216-0.2160.0000.0000.0000.000
181A336GLU-1-0.786-0.91128.419-0.089-0.0890.0000.0000.0000.000
182A337ARG10.7920.89227.5000.1410.1410.0000.0000.0000.000
183A338GLY00.1540.08431.235-0.001-0.0010.0000.0000.0000.000
184A339ARG10.8440.93730.4970.1200.1200.0000.0000.0000.000
185A340LYS10.9560.97032.9450.0770.0770.0000.0000.0000.000
186A341PRO00.0700.05935.6080.0030.0030.0000.0000.0000.000