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: 2JZMR

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2616050.191139
FMO2-HF: Nuclear repulsion 2529736.218265
FMO2-HF: Total energy -86313.972874
FMO2-MP2: Total energy -86565.901089


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.
45.25748.29118.178-11.704-9.5080.112
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 : -0.857 / q_NPA : -0.930
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].
3A5GLN0-0.008-0.0062.954-13.995-9.5890.251-2.267-2.3910.011
4A6ASP-1-0.919-0.9444.68924.14724.251-0.001-0.018-0.0840.000
5A7GLN00.0160.0536.155-6.437-6.4370.0000.0000.0000.000
6A8VAL0-0.011-0.0048.736-0.750-0.7500.0000.0000.0000.000
7A9ALA00.0110.00311.029-0.183-0.1830.0000.0000.0000.000
8A10PHE00.0210.01113.185-0.950-0.9500.0000.0000.0000.000
9A11ILE00.000-0.01012.6760.2420.2420.0000.0000.0000.000
10A12THR00.014-0.00217.115-1.004-1.0040.0000.0000.0000.000
11A13GLY0-0.005-0.00719.9950.3380.3380.0000.0000.0000.000
12A14GLY0-0.016-0.00318.2640.3340.3340.0000.0000.0000.000
13A15ALA00.0230.02018.8400.5490.5490.0000.0000.0000.000
14A16SER0-0.023-0.02220.892-0.779-0.7790.0000.0000.0000.000
15A17GLY00.0350.02620.1010.6600.6600.0000.0000.0000.000
16A18ALA00.0560.01917.2800.7380.7380.0000.0000.0000.000
17A19GLY00.0320.03915.9061.4401.4400.0000.0000.0000.000
18A20PHE0-0.009-0.00315.6761.3411.3410.0000.0000.0000.000
19A21GLY00.0170.01114.7610.9420.9420.0000.0000.0000.000
20A22GLN0-0.010-0.01711.5142.6302.6300.0000.0000.0000.000
21A23ALA00.0050.00910.8752.6242.6240.0000.0000.0000.000
22A24LYS10.8610.92311.659-21.236-21.2360.0000.0000.0000.000
23A25VAL0-0.048-0.0317.3312.1602.1600.0000.0000.0000.000
24A26PHE00.008-0.0106.3525.1005.1000.0000.0000.0000.000
25A27GLY00.0360.0207.0043.6023.6020.0000.0000.0000.000
26A28GLN0-0.058-0.0418.010-1.733-1.7330.0000.0000.0000.000
27A29ALA0-0.0220.0032.778-0.0361.8070.468-0.993-1.3190.012
28A30GLY0-0.010-0.0143.1737.0658.0940.089-0.742-0.376-0.006
29A31ALA0-0.030-0.0095.915-3.726-3.7260.0000.0000.0000.000
30A32LYS10.8590.9308.254-25.911-25.9110.0000.0000.0000.000
31A33ILE0-0.022-0.01110.708-0.034-0.0340.0000.0000.0000.000
32A34VAL00.0260.00713.977-1.346-1.3460.0000.0000.0000.000
33A35VAL0-0.027-0.00617.5370.2900.2900.0000.0000.0000.000
34A36ALA00.0500.03419.262-0.797-0.7970.0000.0000.0000.000
35A37ASP-1-0.806-0.93622.01013.47913.4790.0000.0000.0000.000
36A38VAL00.0310.03024.619-0.254-0.2540.0000.0000.0000.000
37A39ARG10.8130.90024.465-12.906-12.9060.0000.0000.0000.000
38A40ALA00.0490.02227.3520.4140.4140.0000.0000.0000.000
39A41GLU-1-0.820-0.92127.92911.16211.1620.0000.0000.0000.000
40A42ALA0-0.043-0.01825.3100.2490.2490.0000.0000.0000.000
41A43VAL0-0.014-0.00623.2000.7110.7110.0000.0000.0000.000
42A44GLU-1-0.943-0.96323.32611.44511.4450.0000.0000.0000.000
43A45LYS10.8010.88623.207-13.293-13.2930.0000.0000.0000.000
44A46ALA0-0.020-0.01719.9660.4540.4540.0000.0000.0000.000
45A47VAL00.0100.00119.1980.9310.9310.0000.0000.0000.000
46A48ALA00.0850.05119.2810.6190.6190.0000.0000.0000.000
47A49GLU-1-0.890-0.92919.47214.67014.6700.0000.0000.0000.000
48A50LEU0-0.042-0.02214.0910.8690.8690.0000.0000.0000.000
49A51GLU-1-0.894-0.94815.64215.89815.8980.0000.0000.0000.000
50A52GLY0-0.051-0.02317.6680.0340.0340.0000.0000.0000.000
51A53LEU0-0.090-0.04914.099-0.108-0.1080.0000.0000.0000.000
52A54GLY0-0.030-0.01413.5551.4701.4700.0000.0000.0000.000
53A55ILE0-0.071-0.01010.9081.0741.0740.0000.0000.0000.000
54A56THR0-0.035-0.02212.685-1.193-1.1930.0000.0000.0000.000
55A57ALA00.009-0.00113.7921.4341.4340.0000.0000.0000.000
56A58HIS00.002-0.00816.299-0.617-0.6170.0000.0000.0000.000
57A59GLY0-0.015-0.01919.2990.7490.7490.0000.0000.0000.000
58A60ILE0-0.034-0.00622.072-0.512-0.5120.0000.0000.0000.000
59A61VAL0-0.007-0.01124.6640.1990.1990.0000.0000.0000.000
60A62LEU0-0.020-0.01924.518-0.270-0.2700.0000.0000.0000.000
61A63ASP-1-0.852-0.92427.09810.75310.7530.0000.0000.0000.000
62A64ILE0-0.014-0.00624.416-0.154-0.1540.0000.0000.0000.000
63A65MET0-0.026-0.00527.795-0.066-0.0660.0000.0000.0000.000
64A66ASP-1-0.820-0.91331.2539.5229.5220.0000.0000.0000.000
65A67ARG10.9120.93130.663-9.556-9.5560.0000.0000.0000.000
66A68GLU-1-0.843-0.88930.8319.2289.2280.0000.0000.0000.000
67A69ALA0-0.028-0.00630.2710.1450.1450.0000.0000.0000.000
68A70TYR00.0010.00822.7450.6670.6670.0000.0000.0000.000
69A71ALA0-0.018-0.01026.4750.4670.4670.0000.0000.0000.000
70A72ARG10.8290.89027.460-9.504-9.5040.0000.0000.0000.000
71A73ALA00.0460.02524.5810.1840.1840.0000.0000.0000.000
72A74ALA0-0.032-0.01922.8750.6230.6230.0000.0000.0000.000
73A75ASP-1-0.834-0.90023.04011.84511.8450.0000.0000.0000.000
74A76GLU-1-0.875-0.92624.36112.63212.6320.0000.0000.0000.000
75A77VAL0-0.008-0.01118.3500.3990.3990.0000.0000.0000.000
76A78GLU-1-0.885-0.92819.88514.03314.0330.0000.0000.0000.000
77A79ALA0-0.065-0.02721.355-0.027-0.0270.0000.0000.0000.000
78A80VAL0-0.057-0.01919.489-0.100-0.1000.0000.0000.0000.000
79A81PHE0-0.035-0.03715.7060.5380.5380.0000.0000.0000.000
80A82GLY0-0.0140.00416.5280.7300.7300.0000.0000.0000.000
81A83GLN0-0.0130.00212.098-0.491-0.4910.0000.0000.0000.000
82A84ALA00.0540.03017.9130.0830.0830.0000.0000.0000.000
83A85PRO0-0.034-0.02215.2750.7970.7970.0000.0000.0000.000
84A86THR00.018-0.00110.258-0.979-0.9790.0000.0000.0000.000
85A87LEU0-0.026-0.0089.0200.9910.9910.0000.0000.0000.000
86A88LEU0-0.0020.01212.830-1.089-1.0890.0000.0000.0000.000
87A89SER00.003-0.02014.435-0.003-0.0030.0000.0000.0000.000
88A90ASN00.0030.00016.444-1.410-1.4100.0000.0000.0000.000
89A91THR00.0220.00017.3320.0610.0610.0000.0000.0000.000
90A92ALA0-0.0130.01020.001-0.484-0.4840.0000.0000.0000.000
91A93GLY00.004-0.00923.390-0.039-0.0390.0000.0000.0000.000
92A94VAL0-0.0340.00226.305-0.008-0.0080.0000.0000.0000.000
93A95ASN00.024-0.00629.692-0.119-0.1190.0000.0000.0000.000
94A96SER00.0300.02132.331-0.042-0.0420.0000.0000.0000.000
95A97PHE0-0.017-0.00231.773-0.009-0.0090.0000.0000.0000.000
96A98GLY00.0310.00937.212-0.205-0.2050.0000.0000.0000.000
97A99PRO0-0.039-0.01940.4130.1210.1210.0000.0000.0000.000
98A100ILE00.0600.04639.569-0.053-0.0530.0000.0000.0000.000
99A101GLU-1-0.853-0.92142.1047.1397.1390.0000.0000.0000.000
100A102LYS10.7860.87544.759-6.980-6.9800.0000.0000.0000.000
101A103THR0-0.065-0.02340.1500.0720.0720.0000.0000.0000.000
102A104THR0-0.025-0.03742.729-0.143-0.1430.0000.0000.0000.000
103A105TYR00.010-0.01542.0940.1440.1440.0000.0000.0000.000
104A106ASP-1-0.855-0.91740.9227.7377.7370.0000.0000.0000.000
105A107ASP-1-0.852-0.89538.5928.3208.3200.0000.0000.0000.000
106A108PHE0-0.027-0.03037.1110.3560.3560.0000.0000.0000.000
107A109ASP-1-0.888-0.94936.3878.5478.5470.0000.0000.0000.000
108A110TRP0-0.0070.00032.9740.2990.2990.0000.0000.0000.000
109A111ILE0-0.035-0.01032.2240.4280.4280.0000.0000.0000.000
110A112ILE00.005-0.00731.6490.4610.4610.0000.0000.0000.000
111A113GLY00.0540.04032.0690.2380.2380.0000.0000.0000.000
112A114VAL00.003-0.01027.1440.3440.3440.0000.0000.0000.000
113A115ASN0-0.124-0.08827.1450.8880.8880.0000.0000.0000.000
114A116LEU0-0.0050.00427.4050.2990.2990.0000.0000.0000.000
115A117ASN0-0.026-0.02128.6800.1560.1560.0000.0000.0000.000
116A118GLY00.0390.03027.4310.1020.1020.0000.0000.0000.000
117A119VAL00.0170.01623.0140.3440.3440.0000.0000.0000.000
118A120ILE0-0.012-0.00925.0490.2600.2600.0000.0000.0000.000
119A121ASN0-0.032-0.01327.397-0.166-0.1660.0000.0000.0000.000
120A122GLY00.0680.03923.692-0.019-0.0190.0000.0000.0000.000
121A123MET0-0.049-0.01120.7470.6040.6040.0000.0000.0000.000
122A124VAL0-0.027-0.02323.9210.0380.0380.0000.0000.0000.000
123A125THR0-0.052-0.02424.684-0.301-0.3010.0000.0000.0000.000
124A126PHE00.0490.00520.4180.0460.0460.0000.0000.0000.000
125A127VAL0-0.0040.01321.2880.3830.3830.0000.0000.0000.000
126A128PRO0-0.024-0.01122.3610.1920.1920.0000.0000.0000.000
127A129ARG10.7860.86321.821-12.650-12.6500.0000.0000.0000.000
128A130MET0-0.0010.00115.612-0.043-0.0430.0000.0000.0000.000
129A131ILE0-0.0230.00618.9300.2940.2940.0000.0000.0000.000
130A132ALA0-0.040-0.02121.225-0.021-0.0210.0000.0000.0000.000
131A133SER0-0.046-0.02617.2420.0620.0620.0000.0000.0000.000
132A134GLY0-0.007-0.00418.2730.0870.0870.0000.0000.0000.000
133A135ARG10.8070.89712.209-18.345-18.3450.0000.0000.0000.000
134A136PRO0-0.008-0.00411.404-0.362-0.3620.0000.0000.0000.000
135A137GLY00.0330.01711.9590.6050.6050.0000.0000.0000.000
136A138HIS0-0.043-0.02210.8570.7780.7780.0000.0000.0000.000
137A139ILE00.0070.00312.882-0.474-0.4740.0000.0000.0000.000
138A140VAL00.0160.00612.823-0.037-0.0370.0000.0000.0000.000
139A141THR00.025-0.01416.003-0.961-0.9610.0000.0000.0000.000
140A142VAL0-0.025-0.00317.2050.2880.2880.0000.0000.0000.000
141A143SER00.0470.01919.710-0.921-0.9210.0000.0000.0000.000
142A144SER0-0.012-0.03523.132-0.167-0.1670.0000.0000.0000.000
143A145LEU00.0490.02125.048-0.059-0.0590.0000.0000.0000.000
144A146GLY00.0170.01126.598-0.357-0.3570.0000.0000.0000.000
145A147GLY0-0.027-0.01827.787-0.358-0.3580.0000.0000.0000.000
146A148PHE00.007-0.01124.242-0.127-0.1270.0000.0000.0000.000
147A149MET0-0.064-0.03229.791-0.372-0.3720.0000.0000.0000.000
148A150GLY00.0370.03232.9290.0790.0790.0000.0000.0000.000
149A151SER0-0.004-0.01334.700-0.199-0.1990.0000.0000.0000.000
150A152ALA00.027-0.00436.979-0.032-0.0320.0000.0000.0000.000
151A153LEU0-0.0020.00137.890-0.166-0.1660.0000.0000.0000.000
152A154ALA00.0780.03733.4460.0670.0670.0000.0000.0000.000
153A155GLY00.0210.04234.3370.2840.2840.0000.0000.0000.000
154A156PRO00.0460.01735.2300.2170.2170.0000.0000.0000.000
155A157TYR00.0390.01926.3160.3220.3220.0000.0000.0000.000
156A158SER0-0.034-0.04030.6210.3470.3470.0000.0000.0000.000
157A159ALA00.0150.01031.1390.2520.2520.0000.0000.0000.000
158A160ALA00.0090.00730.2880.1400.1400.0000.0000.0000.000
159A161LYS10.8630.94423.775-12.973-12.9730.0000.0000.0000.000
160A162ALA00.0460.03227.0320.4740.4740.0000.0000.0000.000
161A163ALA0-0.033-0.00928.6080.2020.2020.0000.0000.0000.000
162A164SER0-0.062-0.04324.9090.4150.4150.0000.0000.0000.000
163A165ILE0-0.026-0.00323.8990.6130.6130.0000.0000.0000.000
164A166ASN0-0.030-0.01824.4740.0740.0740.0000.0000.0000.000
165A167LEU00.0050.00925.3380.0160.0160.0000.0000.0000.000
166A168MET0-0.0080.02020.5280.5280.5280.0000.0000.0000.000
167A169GLU-1-0.798-0.87122.02612.90312.9030.0000.0000.0000.000
168A170GLY0-0.0110.01023.921-0.082-0.0820.0000.0000.0000.000
169A171TYR00.011-0.02521.820-0.062-0.0620.0000.0000.0000.000
170A172ARG10.8090.89915.456-18.654-18.6540.0000.0000.0000.000
171A173GLN0-0.043-0.02720.921-0.147-0.1470.0000.0000.0000.000
172A174GLY0-0.034-0.00323.792-0.294-0.2940.0000.0000.0000.000
173A175LEU0-0.034-0.02619.516-0.372-0.3720.0000.0000.0000.000
174A176GLU-1-0.802-0.89017.79716.98316.9830.0000.0000.0000.000
175A177LYS10.8370.91618.914-12.213-12.2130.0000.0000.0000.000
176A178TYR0-0.042-0.03319.898-0.823-0.8230.0000.0000.0000.000
177A179GLY00.0140.01915.9410.3420.3420.0000.0000.0000.000
178A180ILE0-0.028-0.01014.5001.4171.4170.0000.0000.0000.000
179A181GLY00.0320.02213.648-1.110-1.1100.0000.0000.0000.000
180A182VAL0-0.036-0.02314.642-0.276-0.2760.0000.0000.0000.000
181A183SER00.000-0.00914.3630.2950.2950.0000.0000.0000.000
182A184VAL0-0.048-0.02316.655-0.352-0.3520.0000.0000.0000.000
183A185CYS0-0.047-0.01116.5960.0540.0540.0000.0000.0000.000
184A186THR00.014-0.00718.612-0.670-0.6700.0000.0000.0000.000
185A187PRO00.0210.00520.090-0.296-0.2960.0000.0000.0000.000
186A188ALA00.0320.03322.343-0.600-0.6000.0000.0000.0000.000
187A189ASN0-0.030-0.00325.186-0.217-0.2170.0000.0000.0000.000
188A190ILE00.0030.01027.013-0.385-0.3850.0000.0000.0000.000
189A226HIS00.0010.00126.578-0.320-0.3200.0000.0000.0000.000
190A227GLY0-0.004-0.02124.829-0.293-0.2930.0000.0000.0000.000
191A228LEU0-0.030-0.00317.1630.0670.0670.0000.0000.0000.000
192A229GLU-1-0.870-0.94318.49015.52915.5290.0000.0000.0000.000
193A230PRO00.0030.00117.5841.1171.1170.0000.0000.0000.000
194A231GLU-1-0.753-0.86012.37124.74324.7430.0000.0000.0000.000
195A232LYS10.8150.87712.955-20.478-20.4780.0000.0000.0000.000
196A233LEU0-0.030-0.01114.0510.8290.8290.0000.0000.0000.000
197A234ALA00.0250.01311.7280.7160.7160.0000.0000.0000.000
198A235GLU-1-0.793-0.8699.19227.63927.6390.0000.0000.0000.000
199A236ALA0-0.017-0.0049.4912.6792.6790.0000.0000.0000.000
200A237ILE0-0.038-0.01711.3090.2790.2790.0000.0000.0000.000
201A238LYS10.7850.8701.703-124.252-128.94717.370-7.625-5.0500.095
202A239LYS10.7760.8707.272-35.858-35.8580.0000.0000.0000.000
203A240GLY00.016-0.0078.776-0.631-0.6310.0000.0000.0000.000
204A241VAL0-0.018-0.0067.543-1.606-1.6060.0000.0000.0000.000
205A242GLU-1-0.838-0.8974.05461.39361.7400.001-0.059-0.2880.000
206A243ASP-1-0.865-0.9176.81729.63829.6380.0000.0000.0000.000
207A244ASN0-0.014-0.01510.067-3.651-3.6510.0000.0000.0000.000
208A245ALA00.0380.03612.046-2.420-2.4200.0000.0000.0000.000
209A246LEU0-0.0060.01814.6940.2560.2560.0000.0000.0000.000
210A247TYR0-0.043-0.05317.892-0.183-0.1830.0000.0000.0000.000
211A248ILE00.0190.01413.3940.5940.5940.0000.0000.0000.000
212A249ILE00.0290.00717.042-0.501-0.5010.0000.0000.0000.000
213A250PRO0-0.0260.00216.320-0.378-0.3780.0000.0000.0000.000
214A251TYR00.0310.00318.452-0.306-0.3060.0000.0000.0000.000
215A252PRO00.0110.00721.289-0.524-0.5240.0000.0000.0000.000
216A253GLU-1-0.857-0.94623.96012.91112.9110.0000.0000.0000.000
217A254VAL0-0.030-0.01725.235-0.509-0.5090.0000.0000.0000.000
218A255ARG10.8000.89026.331-12.134-12.1340.0000.0000.0000.000
219A256GLU-1-0.897-0.94328.3989.1449.1440.0000.0000.0000.000
220A257GLY00.007-0.00531.820-0.305-0.3050.0000.0000.0000.000
221A258LEU0-0.015-0.00626.497-0.220-0.2200.0000.0000.0000.000
222A259GLU-1-0.796-0.87929.88610.78410.7840.0000.0000.0000.000
223A260LYS10.9500.97732.186-8.654-8.6540.0000.0000.0000.000
224A261HIS0-0.055-0.02433.043-0.555-0.5550.0000.0000.0000.000
225A262PHE00.022-0.00928.156-0.158-0.1580.0000.0000.0000.000
226A263GLN0-0.057-0.03434.1600.0430.0430.0000.0000.0000.000
227A264ALA00.0280.01936.983-0.225-0.2250.0000.0000.0000.000
228A265ILE0-0.030-0.00134.709-0.222-0.2220.0000.0000.0000.000
229A266ILE0-0.020-0.01435.269-0.147-0.1470.0000.0000.0000.000
230A267ASP-1-0.871-0.93439.0107.7877.7870.0000.0000.0000.000
231A268SER0-0.086-0.04341.647-0.275-0.2750.0000.0000.0000.000
232A269VAL0-0.079-0.02740.199-0.109-0.1090.0000.0000.0000.000
233A270ALA0-0.0070.00043.325-0.123-0.1230.0000.0000.0000.000
234A271PRO0-0.007-0.00146.4260.0680.0680.0000.0000.0000.000
235A272MET0-0.024-0.01245.795-0.145-0.1450.0000.0000.0000.000