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: MVKLZ

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2611265.943404
FMO2-HF: Nuclear repulsion 2524953.362239
FMO2-HF: Total energy -86312.581165
FMO2-MP2: Total energy -86564.574962


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.
125.744133.9421.446-4.326-5.3180.017
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 : -0.968 / q_NPA : -0.984
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].
3A5GLN0-0.020-0.0192.700-16.071-10.9520.814-2.882-3.0510.018
4A6ASP-1-0.976-0.9744.64925.55025.7030.000-0.043-0.1100.000
5A7GLN00.0130.0506.019-4.633-4.6330.0000.0000.0000.000
6A8VAL00.0020.0068.827-0.854-0.8540.0000.0000.0000.000
7A9ALA00.0100.00410.8480.0490.0490.0000.0000.0000.000
8A10PHE00.0160.00112.882-1.084-1.0840.0000.0000.0000.000
9A11ILE00.001-0.00312.9280.0340.0340.0000.0000.0000.000
10A12THR00.0560.03817.259-0.633-0.6330.0000.0000.0000.000
11A13GLY0-0.005-0.01020.2220.3490.3490.0000.0000.0000.000
12A14GLY00.0070.00918.8950.3330.3330.0000.0000.0000.000
13A15ALA0-0.0240.00019.2800.4030.4030.0000.0000.0000.000
14A16SER0-0.022-0.03121.291-0.604-0.6040.0000.0000.0000.000
15A17GLY00.0150.02720.7380.5040.5040.0000.0000.0000.000
16A18ALA00.0590.01618.1120.5730.5730.0000.0000.0000.000
17A19GLY00.0490.02716.7151.1841.1840.0000.0000.0000.000
18A20PHE0-0.018-0.00516.1541.2171.2170.0000.0000.0000.000
19A21GLY00.0170.00415.4770.8370.8370.0000.0000.0000.000
20A22GLN0-0.010-0.02412.3402.4862.4860.0000.0000.0000.000
21A23ALA00.0270.02111.2672.1072.1070.0000.0000.0000.000
22A24LYS10.9360.98511.671-17.945-17.9450.0000.0000.0000.000
23A25VAL0-0.039-0.0268.4531.6191.6190.0000.0000.0000.000
24A26PHE0-0.003-0.0176.8283.3653.3650.0000.0000.0000.000
25A27GLY00.0400.0256.7952.8012.8010.0000.0000.0000.000
26A28GLN0-0.035-0.0268.199-1.588-1.5880.0000.0000.0000.000
27A29ALA0-0.041-0.0082.8741.0011.5530.086-0.152-0.4860.001
28A30GLY0-0.022-0.0233.2006.2447.0300.071-0.589-0.268-0.004
29A31ALA0-0.0320.0015.528-2.075-2.0750.0000.0000.0000.000
30A32LYS10.9240.9628.071-23.849-23.8490.0000.0000.0000.000
31A33ILE0-0.014-0.00910.3540.4590.4590.0000.0000.0000.000
32A34VAL00.0250.00613.801-1.116-1.1160.0000.0000.0000.000
33A35VAL0-0.036-0.01417.2710.2310.2310.0000.0000.0000.000
34A36ALA00.0590.04319.202-0.759-0.7590.0000.0000.0000.000
35A37ASP-1-0.858-0.95821.99212.78412.7840.0000.0000.0000.000
36A38VAL00.0210.01324.609-0.222-0.2220.0000.0000.0000.000
37A39ARG10.8970.94825.994-11.675-11.6750.0000.0000.0000.000
38A40ALA00.0600.02127.7200.3580.3580.0000.0000.0000.000
39A41GLU-1-0.827-0.91828.14610.25610.2560.0000.0000.0000.000
40A42ALA0-0.069-0.03926.0310.2200.2200.0000.0000.0000.000
41A43VAL00.0240.01322.9700.5560.5560.0000.0000.0000.000
42A44GLU-1-0.912-0.95423.23710.89910.8990.0000.0000.0000.000
43A45LYS10.9060.95624.317-11.441-11.4410.0000.0000.0000.000
44A46ALA0-0.006-0.00220.3220.3200.3200.0000.0000.0000.000
45A47VAL00.0560.01219.1290.7500.7500.0000.0000.0000.000
46A48ALA00.0370.03619.4780.4620.4620.0000.0000.0000.000
47A49GLU-1-0.985-0.99519.06314.61314.6130.0000.0000.0000.000
48A50LEU0-0.048-0.02414.5190.6900.6900.0000.0000.0000.000
49A51GLU-1-0.906-0.95015.80214.82514.8250.0000.0000.0000.000
50A52GLY0-0.078-0.03917.5400.0340.0340.0000.0000.0000.000
51A53LEU0-0.096-0.05514.298-0.087-0.0870.0000.0000.0000.000
52A54GLY0-0.042-0.01413.4731.1771.1770.0000.0000.0000.000
53A55ILE0-0.057-0.00811.1241.2401.2400.0000.0000.0000.000
54A56THR0-0.046-0.02612.344-1.010-1.0100.0000.0000.0000.000
55A57ALA00.0220.00013.7321.2011.2010.0000.0000.0000.000
56A58HIS0-0.010-0.00616.397-0.511-0.5110.0000.0000.0000.000
57A59GLY0-0.0010.00519.5140.5080.5080.0000.0000.0000.000
58A60ILE0-0.010-0.01322.148-0.311-0.3110.0000.0000.0000.000
59A61VAL0-0.020-0.00824.3230.1530.1530.0000.0000.0000.000
60A62LEU0-0.018-0.02024.652-0.212-0.2120.0000.0000.0000.000
61A63ASP-1-0.851-0.92027.41210.28510.2850.0000.0000.0000.000
62A64ILE0-0.0090.00124.762-0.108-0.1080.0000.0000.0000.000
63A65MET0-0.050-0.01628.010-0.038-0.0380.0000.0000.0000.000
64A66ASP-1-0.840-0.89931.1699.2049.2040.0000.0000.0000.000
65A67ARG10.9260.93030.694-9.301-9.3010.0000.0000.0000.000
66A68GLU-1-0.874-0.90130.8049.0719.0710.0000.0000.0000.000
67A69ALA0-0.027-0.02230.4880.1800.1800.0000.0000.0000.000
68A70TYR0-0.032-0.01522.8880.6210.6210.0000.0000.0000.000
69A71ALA0-0.001-0.00826.3090.5020.5020.0000.0000.0000.000
70A72ARG10.8700.92127.715-9.447-9.4470.0000.0000.0000.000
71A73ALA00.0500.03324.1270.2130.2130.0000.0000.0000.000
72A74ALA0-0.016-0.01022.8050.4850.4850.0000.0000.0000.000
73A75ASP-1-0.853-0.92523.13811.72911.7290.0000.0000.0000.000
74A76GLU-1-0.898-0.94023.84012.30012.3000.0000.0000.0000.000
75A77VAL0-0.050-0.03618.4470.3870.3870.0000.0000.0000.000
76A78GLU-1-0.888-0.92319.79414.02914.0290.0000.0000.0000.000
77A79ALA0-0.078-0.02621.463-0.011-0.0110.0000.0000.0000.000
78A80VAL0-0.042-0.01518.934-0.027-0.0270.0000.0000.0000.000
79A81PHE0-0.030-0.03015.3940.4190.4190.0000.0000.0000.000
80A82GLY0-0.0010.00516.9960.7550.7550.0000.0000.0000.000
81A83GLN0-0.081-0.05213.2340.4560.4560.0000.0000.0000.000
82A84ALA00.0490.02918.324-0.024-0.0240.0000.0000.0000.000
83A85PRO0-0.030-0.02015.3100.8450.8450.0000.0000.0000.000
84A86THR00.006-0.00910.187-0.841-0.8410.0000.0000.0000.000
85A87LEU0-0.0020.0029.1421.0111.0110.0000.0000.0000.000
86A88LEU0-0.0140.01112.961-1.046-1.0460.0000.0000.0000.000
87A89SER00.004-0.00414.819-0.060-0.0600.0000.0000.0000.000
88A90ASN0-0.013-0.01816.752-1.237-1.2370.0000.0000.0000.000
89A91THR00.0260.00117.8980.1560.1560.0000.0000.0000.000
90A92ALA0-0.028-0.00620.428-0.475-0.4750.0000.0000.0000.000
91A93GLY00.0040.00023.814-0.033-0.0330.0000.0000.0000.000
92A94VAL0-0.037-0.00126.482-0.079-0.0790.0000.0000.0000.000
93A95ASN00.035-0.00330.010-0.108-0.1080.0000.0000.0000.000
94A96SER00.0280.01932.564-0.078-0.0780.0000.0000.0000.000
95A97PHE0-0.0260.00232.8640.0270.0270.0000.0000.0000.000
96A98GLY00.0160.00137.880-0.174-0.1740.0000.0000.0000.000
97A99PRO0-0.034-0.01840.8530.1130.1130.0000.0000.0000.000
98A100ILE00.0720.04539.876-0.043-0.0430.0000.0000.0000.000
99A101GLU-1-0.904-0.96542.4157.0027.0020.0000.0000.0000.000
100A102LYS10.8160.91345.317-6.780-6.7800.0000.0000.0000.000
101A103THR0-0.0320.00340.5530.0500.0500.0000.0000.0000.000
102A104THR0-0.0120.00542.993-0.136-0.1360.0000.0000.0000.000
103A105TYR00.023-0.00842.3330.1560.1560.0000.0000.0000.000
104A106ASP-1-0.832-0.89841.3047.5887.5880.0000.0000.0000.000
105A107ASP-1-0.899-0.95739.3558.0328.0320.0000.0000.0000.000
106A108PHE0-0.045-0.04537.6750.3310.3310.0000.0000.0000.000
107A109ASP-1-0.884-0.94136.7078.3408.3400.0000.0000.0000.000
108A110TRP0-0.0100.00333.4530.3170.3170.0000.0000.0000.000
109A111ILE0-0.005-0.00332.6440.4080.4080.0000.0000.0000.000
110A112ILE0-0.006-0.01932.0190.4300.4300.0000.0000.0000.000
111A113GLY00.0270.00831.9530.3290.3290.0000.0000.0000.000
112A114VAL0-0.006-0.00827.8420.3350.3350.0000.0000.0000.000
113A115ASN0-0.116-0.08427.4440.8920.8920.0000.0000.0000.000
114A116LEU00.0240.01727.3420.3650.3650.0000.0000.0000.000
115A117ASN00.009-0.00428.4750.3750.3750.0000.0000.0000.000
116A118GLY00.0320.02627.8060.0990.0990.0000.0000.0000.000
117A119VAL00.0140.00623.7920.3850.3850.0000.0000.0000.000
118A120ILE0-0.017-0.00825.0410.3350.3350.0000.0000.0000.000
119A121ASN0-0.001-0.01127.303-0.020-0.0200.0000.0000.0000.000
120A122GLY00.0580.07723.6740.0460.0460.0000.0000.0000.000
121A123MET0-0.044-0.01820.5900.5580.5580.0000.0000.0000.000
122A124VAL0-0.052-0.04124.1710.0450.0450.0000.0000.0000.000
123A125THR0-0.050-0.05724.751-0.278-0.2780.0000.0000.0000.000
124A126PHE00.0400.00620.3850.0520.0520.0000.0000.0000.000
125A127VAL00.0100.02321.6160.3320.3320.0000.0000.0000.000
126A128PRO0-0.007-0.00522.4090.2680.2680.0000.0000.0000.000
127A129ARG10.8390.90421.886-12.592-12.5920.0000.0000.0000.000
128A130MET0-0.023-0.01215.8180.0300.0300.0000.0000.0000.000
129A131ILE0-0.0090.00618.8210.4940.4940.0000.0000.0000.000
130A132ALA0-0.054-0.02621.2730.0090.0090.0000.0000.0000.000
131A133SER0-0.076-0.03017.5550.1480.1480.0000.0000.0000.000
132A134GLY0-0.014-0.00318.8060.1210.1210.0000.0000.0000.000
133A135ARG10.9110.95813.113-18.840-18.8400.0000.0000.0000.000
134A136PRO0-0.008-0.00211.206-0.452-0.4520.0000.0000.0000.000
135A137GLY00.0480.02512.3740.2120.2120.0000.0000.0000.000
136A138HIS0-0.038-0.03011.4960.9300.9300.0000.0000.0000.000
137A139ILE0-0.0040.00113.438-0.566-0.5660.0000.0000.0000.000
138A140VAL00.0160.01212.809-0.287-0.2870.0000.0000.0000.000
139A141THR00.001-0.03215.949-0.786-0.7860.0000.0000.0000.000
140A142VAL0-0.0220.00217.6090.2230.2230.0000.0000.0000.000
141A143SER00.010-0.00719.853-0.887-0.8870.0000.0000.0000.000
142A144SER0-0.020-0.04723.189-0.169-0.1690.0000.0000.0000.000
143A145LEU00.0600.02724.954-0.030-0.0300.0000.0000.0000.000
144A146GLY00.0020.00626.374-0.329-0.3290.0000.0000.0000.000
145A147GLY0-0.012-0.00927.849-0.330-0.3300.0000.0000.0000.000
146A148PHE0-0.024-0.02524.100-0.148-0.1480.0000.0000.0000.000
147A149MET0-0.059-0.02829.628-0.311-0.3110.0000.0000.0000.000
148A150GLY00.0290.03332.9450.0380.0380.0000.0000.0000.000
149A151SER0-0.011-0.01334.802-0.223-0.2230.0000.0000.0000.000
150A152ALA00.0420.00437.064-0.033-0.0330.0000.0000.0000.000
151A153LEU0-0.005-0.00438.097-0.128-0.1280.0000.0000.0000.000
152A154ALA00.0630.02633.7310.0530.0530.0000.0000.0000.000
153A155GLY00.0330.03034.6930.2510.2510.0000.0000.0000.000
154A156PRO00.0490.01335.6770.2010.2010.0000.0000.0000.000
155A157TYR00.0520.02326.6460.3360.3360.0000.0000.0000.000
156A158SER0-0.013-0.02330.9860.3780.3780.0000.0000.0000.000
157A159ALA00.0130.01631.2030.2490.2490.0000.0000.0000.000
158A160ALA00.0180.00930.4490.1430.1430.0000.0000.0000.000
159A161LYS10.8440.94924.667-12.106-12.1060.0000.0000.0000.000
160A162ALA00.0590.02527.0580.4500.4500.0000.0000.0000.000
161A163ALA0-0.0210.00328.8650.1450.1450.0000.0000.0000.000
162A164SER0-0.037-0.00824.5370.4460.4460.0000.0000.0000.000
163A165ILE0-0.018-0.00323.7290.5400.5400.0000.0000.0000.000
164A166ASN0-0.0070.01324.4150.3200.3200.0000.0000.0000.000
165A167LEU00.0300.01125.6790.1250.1250.0000.0000.0000.000
166A168MET0-0.0230.01820.5380.5530.5530.0000.0000.0000.000
167A169GLU-1-0.859-0.91222.14212.71212.7120.0000.0000.0000.000
168A170GLY0-0.025-0.00823.9160.0440.0440.0000.0000.0000.000
169A171TYR00.002-0.02721.847-0.130-0.1300.0000.0000.0000.000
170A172ARG10.8460.92215.540-18.786-18.7860.0000.0000.0000.000
171A173GLN0-0.014-0.00520.908-0.109-0.1090.0000.0000.0000.000
172A174GLY0-0.060-0.02023.671-0.161-0.1610.0000.0000.0000.000
173A175LEU00.018-0.02219.670-0.356-0.3560.0000.0000.0000.000
174A176GLU-1-0.857-0.89918.47616.49816.4980.0000.0000.0000.000
175A177LYS10.8400.92519.041-12.216-12.2160.0000.0000.0000.000
176A178TYR0-0.079-0.05219.819-0.643-0.6430.0000.0000.0000.000
177A179GLY00.0110.01615.9850.4850.4850.0000.0000.0000.000
178A180ILE0-0.048-0.01614.3551.5961.5960.0000.0000.0000.000
179A181GLY00.0270.02614.119-1.175-1.1750.0000.0000.0000.000
180A182VAL0-0.024-0.02015.097-0.381-0.3810.0000.0000.0000.000
181A183SER0-0.012-0.00814.0930.5890.5890.0000.0000.0000.000
182A184VAL0-0.013-0.00716.451-0.594-0.5940.0000.0000.0000.000
183A185CYS0-0.047-0.01216.5190.1560.1560.0000.0000.0000.000
184A186THR0-0.003-0.02518.454-0.660-0.6600.0000.0000.0000.000
185A187PRO00.0080.01020.094-0.190-0.1900.0000.0000.0000.000
186A188ALA00.0200.01822.230-0.540-0.5400.0000.0000.0000.000
187A189ASN0-0.0100.00925.486-0.134-0.1340.0000.0000.0000.000
188A190ILE00.0110.01227.568-0.368-0.3680.0000.0000.0000.000
189A226HIS00.009-0.02026.898-0.276-0.2760.0000.0000.0000.000
190A227GLY0-0.0090.01425.598-0.166-0.1660.0000.0000.0000.000
191A228LEU0-0.024-0.01918.1300.0620.0620.0000.0000.0000.000
192A229GLU-1-0.890-0.95619.80014.10714.1070.0000.0000.0000.000
193A230PRO0-0.0040.00018.6530.8890.8890.0000.0000.0000.000
194A231GLU-1-0.831-0.93013.87221.01721.0170.0000.0000.0000.000
195A232LYS10.9390.97214.148-15.674-15.6740.0000.0000.0000.000
196A233LEU0-0.006-0.00914.4561.0081.0080.0000.0000.0000.000
197A234ALA00.0080.01412.7280.7210.7210.0000.0000.0000.000
198A235GLU-1-0.924-0.9639.88027.18027.1800.0000.0000.0000.000
199A236ALA0-0.056-0.0239.8622.1942.1940.0000.0000.0000.000
200A237ILE0-0.010-0.01011.4520.4260.4260.0000.0000.0000.000
201A238LYS10.8750.9553.761-63.827-63.2740.003-0.259-0.2970.002
202A239LYS10.9160.9746.818-30.105-30.1050.0000.0000.0000.000
203A240GLY0-0.011-0.0108.2770.3290.3290.0000.0000.0000.000
204A241VAL0-0.021-0.0177.493-1.198-1.1980.0000.0000.0000.000
205A242GLU-1-0.840-0.9223.07671.64772.6820.472-0.401-1.1060.000
206A243ASP-1-0.918-0.9696.82129.38329.3830.0000.0000.0000.000
207A244ASN00.0070.00810.128-3.402-3.4020.0000.0000.0000.000
208A245ALA0-0.0040.01112.186-2.412-2.4120.0000.0000.0000.000
209A246LEU0-0.0030.01514.6030.1510.1510.0000.0000.0000.000
210A247TYR0-0.034-0.05917.842-0.054-0.0540.0000.0000.0000.000
211A248ILE00.0230.02013.1010.5750.5750.0000.0000.0000.000
212A249ILE00.016-0.00716.842-0.525-0.5250.0000.0000.0000.000
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