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: 728KK

Calculation Name: 4Y98-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y98

Chain ID: A

ChEMBL ID:

UniProt ID: G2IN91

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2611709.477871
FMO2-HF: Nuclear repulsion 2525395.830644
FMO2-HF: Total energy -86313.647227
FMO2-MP2: Total energy -86565.637014


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:3:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
62.89466.56613.102-8.607-8.1670.077
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / q_NPA : -0.959
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].
3A5GLN0-0.015-0.0142.482-14.889-9.9070.816-2.741-3.0570.011
4A6ASP-1-0.917-0.9424.26423.42823.5640.000-0.030-0.1060.000
5A7GLN00.0330.0706.196-5.004-5.0040.0000.0000.0000.000
6A8VAL0-0.011-0.0018.627-0.470-0.4700.0000.0000.0000.000
7A9ALA00.0080.00311.0470.0510.0510.0000.0000.0000.000
8A10PHE00.0230.00313.105-1.116-1.1160.0000.0000.0000.000
9A11ILE00.005-0.00112.9110.0240.0240.0000.0000.0000.000
10A12THR00.0340.01817.237-0.954-0.9540.0000.0000.0000.000
11A13GLY0-0.017-0.01419.9320.3990.3990.0000.0000.0000.000
12A14GLY00.0130.01318.8150.3980.3980.0000.0000.0000.000
13A15ALA0-0.034-0.00419.3290.4680.4680.0000.0000.0000.000
14A16SER0-0.031-0.03021.139-0.534-0.5340.0000.0000.0000.000
15A17GLY00.0340.03120.4010.5640.5640.0000.0000.0000.000
16A18ALA00.0620.01817.5340.6820.6820.0000.0000.0000.000
17A19GLY00.0560.03016.1201.3691.3690.0000.0000.0000.000
18A20PHE0-0.031-0.00915.9121.3881.3880.0000.0000.0000.000
19A21GLY00.0230.00715.1680.9860.9860.0000.0000.0000.000
20A22GLN0-0.013-0.01911.8272.6352.6350.0000.0000.0000.000
21A23ALA00.0200.01711.1352.5512.5510.0000.0000.0000.000
22A24LYS10.8700.92211.706-19.545-19.5450.0000.0000.0000.000
23A25VAL0-0.042-0.0267.7131.9031.9030.0000.0000.0000.000
24A26PHE0-0.003-0.0156.3984.4304.4300.0000.0000.0000.000
25A27GLY00.0480.0296.8243.3993.3990.0000.0000.0000.000
26A28GLN0-0.038-0.0228.073-1.632-1.6320.0000.0000.0000.000
27A29ALA0-0.026-0.0042.9520.8401.7930.080-0.385-0.6480.003
28A30GLY0-0.023-0.0213.3499.26610.1240.079-0.602-0.335-0.003
29A31ALA0-0.045-0.0086.029-3.367-3.3670.0000.0000.0000.000
30A32LYS10.8660.9248.136-25.707-25.7070.0000.0000.0000.000
31A33ILE0-0.014-0.01010.5480.5270.5270.0000.0000.0000.000
32A34VAL00.0140.00113.846-1.270-1.2700.0000.0000.0000.000
33A35VAL0-0.035-0.01117.3680.2880.2880.0000.0000.0000.000
34A36ALA00.0640.04619.315-0.851-0.8510.0000.0000.0000.000
35A37ASP-1-0.834-0.94722.16813.32713.3270.0000.0000.0000.000
36A38VAL00.0320.02124.721-0.236-0.2360.0000.0000.0000.000
37A39ARG10.8560.93325.129-12.466-12.4660.0000.0000.0000.000
38A40ALA00.0520.01527.8120.3790.3790.0000.0000.0000.000
39A41GLU-1-0.826-0.92328.17410.79910.7990.0000.0000.0000.000
40A42ALA0-0.044-0.02326.1180.2640.2640.0000.0000.0000.000
41A43VAL00.0100.00422.9620.6360.6360.0000.0000.0000.000
42A44GLU-1-0.932-0.95723.23411.32111.3210.0000.0000.0000.000
43A45LYS10.8550.92323.964-12.719-12.7190.0000.0000.0000.000
44A46ALA0-0.020-0.01020.3810.3810.3810.0000.0000.0000.000
45A47VAL00.0420.00318.9940.8630.8630.0000.0000.0000.000
46A48ALA00.0540.04819.4310.5080.5080.0000.0000.0000.000
47A49GLU-1-0.930-0.96219.43414.93414.9340.0000.0000.0000.000
48A50LEU0-0.034-0.01814.1910.7780.7780.0000.0000.0000.000
49A51GLU-1-0.900-0.94615.84415.47515.4750.0000.0000.0000.000
50A52GLY0-0.081-0.03917.9120.0070.0070.0000.0000.0000.000
51A53LEU0-0.092-0.05614.169-0.076-0.0760.0000.0000.0000.000
52A54GLY0-0.043-0.01513.6471.3561.3560.0000.0000.0000.000
53A55ILE0-0.068-0.01511.0261.3111.3110.0000.0000.0000.000
54A56THR0-0.026-0.01112.837-1.247-1.2470.0000.0000.0000.000
55A57ALA00.005-0.01314.0351.3121.3120.0000.0000.0000.000
56A58HIS0-0.012-0.00916.576-0.618-0.6180.0000.0000.0000.000
57A59GLY00.0080.00719.5660.5780.5780.0000.0000.0000.000
58A60ILE0-0.019-0.01822.171-0.362-0.3620.0000.0000.0000.000
59A61VAL0-0.013-0.00424.4150.1890.1890.0000.0000.0000.000
60A62LEU0-0.015-0.01824.759-0.228-0.2280.0000.0000.0000.000
61A63ASP-1-0.845-0.91827.51010.61410.6140.0000.0000.0000.000
62A64ILE0-0.0030.00324.583-0.147-0.1470.0000.0000.0000.000
63A65MET0-0.051-0.01727.920-0.066-0.0660.0000.0000.0000.000
64A66ASP-1-0.840-0.90831.1299.4039.4030.0000.0000.0000.000
65A67ARG10.9190.91930.743-9.515-9.5150.0000.0000.0000.000
66A68GLU-1-0.854-0.88930.9529.1799.1790.0000.0000.0000.000
67A69ALA0-0.024-0.01530.6140.1720.1720.0000.0000.0000.000
68A70TYR0-0.035-0.01522.9820.6460.6460.0000.0000.0000.000
69A71ALA00.005-0.00426.4800.5030.5030.0000.0000.0000.000
70A72ARG10.8400.90527.715-9.541-9.5410.0000.0000.0000.000
71A73ALA00.0470.02924.3680.2180.2180.0000.0000.0000.000
72A74ALA0-0.011-0.00722.8060.5010.5010.0000.0000.0000.000
73A75ASP-1-0.821-0.88523.02211.80311.8030.0000.0000.0000.000
74A76GLU-1-0.884-0.93824.16312.52112.5210.0000.0000.0000.000
75A77VAL0-0.041-0.03118.2720.3940.3940.0000.0000.0000.000
76A78GLU-1-0.890-0.93119.51514.17414.1740.0000.0000.0000.000
77A79ALA0-0.080-0.02821.104-0.054-0.0540.0000.0000.0000.000
78A80VAL0-0.048-0.01618.937-0.050-0.0500.0000.0000.0000.000
79A81PHE0-0.026-0.02915.4840.3890.3890.0000.0000.0000.000
80A82GLY0-0.0020.00616.5230.6900.6900.0000.0000.0000.000
81A83GLN0-0.026-0.01112.302-0.017-0.0170.0000.0000.0000.000
82A84ALA00.0430.03117.9670.0640.0640.0000.0000.0000.000
83A85PRO0-0.018-0.01615.3060.8310.8310.0000.0000.0000.000
84A86THR00.011-0.01510.310-0.919-0.9190.0000.0000.0000.000
85A87LEU0-0.026-0.0078.9341.1181.1180.0000.0000.0000.000
86A88LEU0-0.0100.01112.967-1.020-1.0200.0000.0000.0000.000
87A89SER00.007-0.01514.294-0.071-0.0710.0000.0000.0000.000
88A90ASN0-0.006-0.01216.307-1.194-1.1940.0000.0000.0000.000
89A91THR00.0250.00117.2780.1170.1170.0000.0000.0000.000
90A92ALA0-0.0200.00519.912-0.473-0.4730.0000.0000.0000.000
91A93GLY00.0080.00123.313-0.048-0.0480.0000.0000.0000.000
92A94VAL0-0.039-0.00325.952-0.068-0.0680.0000.0000.0000.000
93A95ASN00.013-0.01129.458-0.132-0.1320.0000.0000.0000.000
94A96SER00.0210.01932.051-0.055-0.0550.0000.0000.0000.000
95A97PHE0-0.0100.00432.2060.0310.0310.0000.0000.0000.000
96A98GLY00.0220.00537.409-0.181-0.1810.0000.0000.0000.000
97A99PRO0-0.045-0.02140.4560.1200.1200.0000.0000.0000.000
98A100ILE00.0700.04939.571-0.049-0.0490.0000.0000.0000.000
99A101GLU-1-0.855-0.92542.0817.1107.1100.0000.0000.0000.000
100A102LYS10.7820.87944.958-6.909-6.9090.0000.0000.0000.000
101A103THR0-0.051-0.01440.1810.0660.0660.0000.0000.0000.000
102A104THR0-0.035-0.04442.591-0.164-0.1640.0000.0000.0000.000
103A105TYR00.022-0.00941.9080.1680.1680.0000.0000.0000.000
104A106ASP-1-0.856-0.91240.8627.7067.7060.0000.0000.0000.000
105A107ASP-1-0.842-0.89438.8518.2008.2000.0000.0000.0000.000
106A108PHE0-0.032-0.03637.2140.3470.3470.0000.0000.0000.000
107A109ASP-1-0.891-0.94436.2918.5448.5440.0000.0000.0000.000
108A110TRP0-0.0140.00232.9200.3380.3380.0000.0000.0000.000
109A111ILE0-0.005-0.00432.2320.4200.4200.0000.0000.0000.000
110A112ILE00.002-0.01231.5930.4560.4560.0000.0000.0000.000
111A113GLY00.0200.01431.5720.3350.3350.0000.0000.0000.000
112A114VAL00.000-0.00627.4140.3430.3430.0000.0000.0000.000
113A115ASN0-0.100-0.07527.0280.8940.8940.0000.0000.0000.000
114A116LEU00.0080.00827.0010.3710.3710.0000.0000.0000.000
115A117ASN00.003-0.00828.1560.3560.3560.0000.0000.0000.000
116A118GLY00.0450.03327.3710.0890.0890.0000.0000.0000.000
117A119VAL00.006-0.00322.8550.4040.4040.0000.0000.0000.000
118A120ILE0-0.016-0.00524.7530.3240.3240.0000.0000.0000.000
119A121ASN0-0.016-0.00827.039-0.088-0.0880.0000.0000.0000.000
120A122GLY00.0640.04923.4100.0400.0400.0000.0000.0000.000
121A123MET0-0.048-0.01620.6500.5860.5860.0000.0000.0000.000
122A124VAL0-0.057-0.04423.9530.0120.0120.0000.0000.0000.000
123A125THR0-0.043-0.02124.488-0.293-0.2930.0000.0000.0000.000
124A126PHE00.0390.00720.3780.0650.0650.0000.0000.0000.000
125A127VAL00.0040.01821.4710.2950.2950.0000.0000.0000.000
126A128PRO0-0.003-0.00422.4090.2240.2240.0000.0000.0000.000
127A129ARG10.8060.87321.905-12.663-12.6630.0000.0000.0000.000
128A130MET0-0.022-0.01115.6870.0280.0280.0000.0000.0000.000
129A131ILE0-0.0180.00818.8670.4310.4310.0000.0000.0000.000
130A132ALA0-0.049-0.02121.317-0.041-0.0410.0000.0000.0000.000
131A133SER0-0.069-0.03517.6420.0910.0910.0000.0000.0000.000
132A134GLY0-0.020-0.01018.6940.0760.0760.0000.0000.0000.000
133A135ARG10.8490.92112.675-18.413-18.4130.0000.0000.0000.000
134A136PRO0-0.002-0.00111.239-0.370-0.3700.0000.0000.0000.000
135A137GLY00.0430.01912.3480.2470.2470.0000.0000.0000.000
136A138HIS0-0.041-0.02511.1980.8680.8680.0000.0000.0000.000
137A139ILE00.002-0.00213.226-0.459-0.4590.0000.0000.0000.000
138A140VAL00.0090.01512.524-0.310-0.3100.0000.0000.0000.000
139A141THR00.021-0.01815.741-0.821-0.8210.0000.0000.0000.000
140A142VAL0-0.0220.00417.0890.1990.1990.0000.0000.0000.000
141A143SER00.0200.00619.508-0.926-0.9260.0000.0000.0000.000
142A144SER0-0.007-0.03822.911-0.169-0.1690.0000.0000.0000.000
143A145LEU00.0580.02624.696-0.059-0.0590.0000.0000.0000.000
144A146GLY00.0070.00726.207-0.360-0.3600.0000.0000.0000.000
145A147GLY0-0.007-0.00527.663-0.357-0.3570.0000.0000.0000.000
146A148PHE0-0.020-0.02324.033-0.196-0.1960.0000.0000.0000.000
147A149MET0-0.054-0.03129.580-0.367-0.3670.0000.0000.0000.000
148A150GLY00.0280.03332.8520.0530.0530.0000.0000.0000.000
149A151SER0-0.005-0.01534.321-0.220-0.2200.0000.0000.0000.000
150A152ALA00.0290.00036.834-0.036-0.0360.0000.0000.0000.000
151A153LEU0-0.006-0.00637.752-0.131-0.1310.0000.0000.0000.000
152A154ALA00.0780.03433.3620.0560.0560.0000.0000.0000.000
153A155GLY00.0380.05134.3780.2720.2720.0000.0000.0000.000
154A156PRO00.0410.01135.3990.2060.2060.0000.0000.0000.000
155A157TYR00.0510.02526.4900.3370.3370.0000.0000.0000.000
156A158SER0-0.025-0.04330.6760.3900.3900.0000.0000.0000.000
157A159ALA00.0080.01530.9930.2510.2510.0000.0000.0000.000
158A160ALA00.0180.01030.1150.1360.1360.0000.0000.0000.000
159A161LYS10.8290.92323.754-12.808-12.8080.0000.0000.0000.000
160A162ALA00.0430.02426.8940.4430.4430.0000.0000.0000.000
161A163ALA0-0.0170.00428.7910.1350.1350.0000.0000.0000.000
162A164SER0-0.0020.00424.1490.3870.3870.0000.0000.0000.000
163A165ILE0-0.037-0.00823.6690.5700.5700.0000.0000.0000.000
164A166ASN0-0.027-0.00824.4290.1100.1100.0000.0000.0000.000
165A167LEU00.0210.00925.5270.0980.0980.0000.0000.0000.000
166A168MET0-0.0140.01520.4500.5420.5420.0000.0000.0000.000
167A169GLU-1-0.821-0.88622.22412.92112.9210.0000.0000.0000.000
168A170GLY0-0.0220.00124.053-0.002-0.0020.0000.0000.0000.000
169A171TYR00.010-0.02421.748-0.135-0.1350.0000.0000.0000.000
170A172ARG10.8670.93415.379-19.054-19.0540.0000.0000.0000.000
171A173GLN0-0.035-0.02320.746-0.187-0.1870.0000.0000.0000.000
172A174GLY0-0.042-0.00923.514-0.186-0.1860.0000.0000.0000.000
173A175LEU00.010-0.00819.535-0.426-0.4260.0000.0000.0000.000
174A176GLU-1-0.863-0.90418.15316.90316.9030.0000.0000.0000.000
175A177LYS10.8200.90319.091-12.352-12.3520.0000.0000.0000.000
176A178TYR0-0.070-0.05619.867-0.679-0.6790.0000.0000.0000.000
177A179GLY00.0090.01716.0940.4440.4440.0000.0000.0000.000
178A180ILE0-0.044-0.01314.3711.5541.5540.0000.0000.0000.000
179A181GLY00.0290.02613.953-1.151-1.1510.0000.0000.0000.000
180A182VAL0-0.028-0.02314.904-0.298-0.2980.0000.0000.0000.000
181A183SER0-0.018-0.01714.1800.6340.6340.0000.0000.0000.000
182A184VAL0-0.027-0.01916.499-0.569-0.5690.0000.0000.0000.000
183A185CYS0-0.058-0.01916.2620.1910.1910.0000.0000.0000.000
184A186THR00.007-0.00518.286-0.671-0.6710.0000.0000.0000.000
185A187PRO00.0180.00319.734-0.202-0.2020.0000.0000.0000.000
186A188ALA00.0120.01221.951-0.608-0.6080.0000.0000.0000.000
187A189ASN0-0.025-0.00525.221-0.072-0.0720.0000.0000.0000.000
188A190ILE00.0220.02227.199-0.375-0.3750.0000.0000.0000.000
189A226HIS00.0090.00726.504-0.276-0.2760.0000.0000.0000.000
190A227GLY0-0.010-0.01325.211-0.169-0.1690.0000.0000.0000.000
191A228LEU0-0.035-0.02117.5230.0910.0910.0000.0000.0000.000
192A229GLU-1-0.866-0.94519.15914.94114.9410.0000.0000.0000.000
193A230PRO0-0.007-0.00118.1131.0031.0030.0000.0000.0000.000
194A231GLU-1-0.802-0.88313.42922.78522.7850.0000.0000.0000.000
195A232LYS10.8180.89413.560-19.708-19.7080.0000.0000.0000.000
196A233LEU00.001-0.00414.0451.1421.1420.0000.0000.0000.000
197A234ALA00.0120.01412.1050.8030.8030.0000.0000.0000.000
198A235GLU-1-0.798-0.8939.38626.62926.6290.0000.0000.0000.000
199A236ALA0-0.038-0.0159.5892.4022.4020.0000.0000.0000.000
200A237ILE0-0.008-0.00611.1230.3000.3000.0000.0000.0000.000
201A238LYS10.8050.9031.786-113.462-117.15612.125-4.763-3.6680.066
202A239LYS10.8030.8996.767-34.900-34.9000.0000.0000.0000.000
203A240GLY00.0280.0058.342-0.060-0.0600.0000.0000.0000.000
204A241VAL0-0.027-0.0217.747-1.324-1.3240.0000.0000.0000.000
205A242GLU-1-0.833-0.8964.16263.42463.8610.002-0.086-0.3530.000
206A243ASP-1-0.891-0.9386.98829.86229.8620.0000.0000.0000.000
207A244ASN00.0020.00710.264-3.756-3.7560.0000.0000.0000.000
208A245ALA00.0160.02312.155-2.427-2.4270.0000.0000.0000.000
209A246LEU00.0060.02214.8750.2400.2400.0000.0000.0000.000
210A247TYR0-0.036-0.05918.0800.0050.0050.0000.0000.0000.000
211A248ILE00.0170.01613.0530.5860.5860.0000.0000.0000.000
212A249ILE00.022-0.00216.859-0.526-0.5260.0000.0000.0000.000
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