FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5J77Z

Calculation Name: 3EQ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EQ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I045

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 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 387
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5128960.880915
FMO2-HF: Nuclear repulsion 4980476.999763
FMO2-HF: Total energy -148483.881152
FMO2-MP2: Total energy -148920.661392


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:4:VAL)


Summations of interaction energy for fragment #1(A:4:VAL)
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.
0.9754.0080.05-1.439-1.6440.004
Interaction energy analysis for fragmet #1(A:4:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.041
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].
3A6ALA0-0.0060.0143.806-0.8961.235-0.037-1.086-1.0080.001
4A7THR0-0.0010.0046.9290.5110.5110.0000.0000.0000.000
5A8LEU0-0.059-0.0467.969-0.180-0.1800.0000.0000.0000.000
6A9LEU00.0000.00811.3690.0480.0480.0000.0000.0000.000
7A10ILE0-0.0230.00914.525-0.045-0.0450.0000.0000.0000.000
8A11ILE00.010-0.01517.147-0.002-0.0020.0000.0000.0000.000
9A12ASP-1-0.827-0.93020.7260.1400.1400.0000.0000.0000.000
10A13ASP-1-0.840-0.90423.2240.1260.1260.0000.0000.0000.000
11A14ASP-1-0.828-0.89525.6320.1330.1330.0000.0000.0000.000
12A15GLU-1-0.859-0.92923.4200.1990.1990.0000.0000.0000.000
13A16VAL0-0.012-0.00723.0740.0170.0170.0000.0000.0000.000
14A17VAL0-0.001-0.01022.6650.0150.0150.0000.0000.0000.000
15A18ARG10.7890.87719.031-0.205-0.2050.0000.0000.0000.000
16A19GLU-1-0.855-0.92018.5840.3560.3560.0000.0000.0000.000
17A20SER0-0.078-0.03118.2910.0450.0450.0000.0000.0000.000
18A21LEU00.017-0.01117.4530.0330.0330.0000.0000.0000.000
19A22ALA00.0070.01114.3720.0570.0570.0000.0000.0000.000
20A23ALA00.0200.01412.9490.1310.1310.0000.0000.0000.000
21A24TYR00.006-0.00312.8360.0750.0750.0000.0000.0000.000
22A25LEU0-0.005-0.00311.6150.0350.0350.0000.0000.0000.000
23A26GLU-1-0.849-0.9327.9191.5941.5940.0000.0000.0000.000
24A27ASP-1-0.959-0.9698.0021.1311.1310.0000.0000.0000.000
25A28SER0-0.090-0.0488.738-0.056-0.0560.0000.0000.0000.000
26A29ASN0-0.115-0.0673.325-0.6010.3100.088-0.336-0.6620.003
27A30PHE0-0.038-0.0144.7230.8110.802-0.001-0.0170.0260.000
28A31LYS10.8830.9465.659-1.681-1.6810.0000.0000.0000.000
29A32VAL00.0180.0347.245-0.329-0.3290.0000.0000.0000.000
30A33LEU0-0.0080.00311.034-0.024-0.0240.0000.0000.0000.000
31A34GLN00.0180.00313.566-0.079-0.0790.0000.0000.0000.000
32A35ALA0-0.031-0.01116.932-0.019-0.0190.0000.0000.0000.000
33A36LEU0-0.025-0.00320.188-0.008-0.0080.0000.0000.0000.000
34A37ASN0-0.001-0.00723.308-0.006-0.0060.0000.0000.0000.000
35A38GLY00.008-0.01124.3120.0060.0060.0000.0000.0000.000
36A39LEU00.0430.03324.7670.0010.0010.0000.0000.0000.000
37A40GLN00.009-0.00421.355-0.006-0.0060.0000.0000.0000.000
38A41GLY00.0430.01320.2760.0070.0070.0000.0000.0000.000
39A42LEU0-0.008-0.00420.371-0.001-0.0010.0000.0000.0000.000
40A43GLN0-0.079-0.04122.225-0.008-0.0080.0000.0000.0000.000
41A44ILE0-0.003-0.00616.366-0.005-0.0050.0000.0000.0000.000
42A45PHE00.0090.01217.3620.0000.0000.0000.0000.0000.000
43A46GLU-1-0.886-0.93518.6230.0480.0480.0000.0000.0000.000
44A47SER0-0.078-0.05617.469-0.015-0.0150.0000.0000.0000.000
45A48GLU-1-0.908-0.93213.0860.1770.1770.0000.0000.0000.000
46A49GLN0-0.039-0.02714.517-0.003-0.0030.0000.0000.0000.000
47A50PRO0-0.037-0.02111.865-0.016-0.0160.0000.0000.0000.000
48A51ASP-1-0.839-0.9188.801-0.177-0.1770.0000.0000.0000.000
49A52LEU0-0.088-0.05212.319-0.034-0.0340.0000.0000.0000.000
50A53VAL00.0140.00614.3740.0470.0470.0000.0000.0000.000
51A54ILE0-0.023-0.01815.283-0.026-0.0260.0000.0000.0000.000
52A55CYS00.0170.01618.6270.0070.0070.0000.0000.0000.000
53A56ASP-1-0.719-0.82921.8830.1030.1030.0000.0000.0000.000
54A57LEU0-0.0660.00025.192-0.001-0.0010.0000.0000.0000.000
55A58ARG10.8290.88327.892-0.122-0.1220.0000.0000.0000.000
56A59MET00.0190.03630.371-0.003-0.0030.0000.0000.0000.000
57A60PRO0-0.034-0.04733.1000.0020.0020.0000.0000.0000.000
58A61GLN0-0.032-0.03429.105-0.006-0.0060.0000.0000.0000.000
59A62ILE0-0.040-0.01625.4500.0000.0000.0000.0000.0000.000
60A63ASP-1-0.828-0.90827.6420.0830.0830.0000.0000.0000.000
61A64GLY00.010-0.00327.890-0.007-0.0070.0000.0000.0000.000
62A65LEU00.000-0.02327.9860.0000.0000.0000.0000.0000.000
63A66GLU-1-0.925-0.97029.7840.0440.0440.0000.0000.0000.000
64A67LEU00.0310.01922.417-0.004-0.0040.0000.0000.0000.000
65A68ILE0-0.013-0.00625.261-0.003-0.0030.0000.0000.0000.000
66A69ARG10.9330.97426.313-0.043-0.0430.0000.0000.0000.000
67A70ARG10.8970.95426.912-0.060-0.0600.0000.0000.0000.000
68A71ILE00.0060.00621.272-0.006-0.0060.0000.0000.0000.000
69A72ARG10.7730.87521.348-0.028-0.0280.0000.0000.0000.000
70A73GLN0-0.072-0.03626.206-0.005-0.0050.0000.0000.0000.000
71A74THR0-0.083-0.02523.371-0.003-0.0030.0000.0000.0000.000
72A75ALA0-0.036-0.02624.762-0.002-0.0020.0000.0000.0000.000
73A76SER0-0.0110.01120.027-0.008-0.0080.0000.0000.0000.000
74A77GLU-1-0.872-0.92220.6320.0070.0070.0000.0000.0000.000
75A78THR00.0360.01716.134-0.016-0.0160.0000.0000.0000.000
76A79PRO0-0.0060.00016.1590.0110.0110.0000.0000.0000.000
77A80ILE00.0540.02218.1490.0170.0170.0000.0000.0000.000
78A81ILE0-0.0260.00917.845-0.013-0.0130.0000.0000.0000.000
79A82VAL00.004-0.00421.0440.0140.0140.0000.0000.0000.000
80A83LEU00.0160.00221.260-0.005-0.0050.0000.0000.0000.000
81A84SER0-0.044-0.03725.138-0.009-0.0090.0000.0000.0000.000
82A85GLY00.0230.00928.444-0.008-0.0080.0000.0000.0000.000
83A86ALA0-0.048-0.03629.8090.0020.0020.0000.0000.0000.000
84A87GLY0-0.006-0.00131.608-0.005-0.0050.0000.0000.0000.000
85A88VAL00.000-0.00632.397-0.006-0.0060.0000.0000.0000.000
86A89MET00.0290.00033.2760.0000.0000.0000.0000.0000.000
87A90SER0-0.043-0.02835.056-0.003-0.0030.0000.0000.0000.000
88A91ASP-1-0.845-0.91631.9490.0520.0520.0000.0000.0000.000
89A92ALA0-0.024-0.00730.0900.0010.0010.0000.0000.0000.000
90A93VAL0-0.035-0.03130.680-0.003-0.0030.0000.0000.0000.000
91A94GLU-1-0.831-0.89632.8290.0250.0250.0000.0000.0000.000
92A95ALA00.0130.01827.372-0.003-0.0030.0000.0000.0000.000
93A96LEU00.0310.00327.504-0.003-0.0030.0000.0000.0000.000
94A97ARG10.7890.89529.268-0.027-0.0270.0000.0000.0000.000
95A98LEU0-0.076-0.04429.355-0.004-0.0040.0000.0000.0000.000
96A99GLY00.0340.02526.897-0.004-0.0040.0000.0000.0000.000
97A100ALA0-0.033-0.00224.1990.0010.0010.0000.0000.0000.000
98A101ALA0-0.096-0.05121.130-0.008-0.0080.0000.0000.0000.000
99A102ASP-1-0.893-0.95923.1330.0350.0350.0000.0000.0000.000
100A103TYR0-0.036-0.01924.1170.0110.0110.0000.0000.0000.000
101A104LEU0-0.0040.00321.387-0.003-0.0030.0000.0000.0000.000
102A105ILE0-0.023-0.01125.8660.0030.0030.0000.0000.0000.000
103A106LYS10.8140.91325.212-0.129-0.1290.0000.0000.0000.000
104A107PRO0-0.034-0.02127.811-0.008-0.0080.0000.0000.0000.000
105A108LEU0-0.004-0.02021.972-0.009-0.0090.0000.0000.0000.000
106A109GLU-1-0.901-0.95525.1450.1260.1260.0000.0000.0000.000
107A110ASP-1-0.913-0.95822.1960.1230.1230.0000.0000.0000.000
108A111LEU00.0360.01018.572-0.002-0.0020.0000.0000.0000.000
109A112ALA00.0030.00117.9750.0210.0210.0000.0000.0000.000
110A113VAL0-0.030-0.01818.813-0.009-0.0090.0000.0000.0000.000
111A114LEU00.0170.01717.292-0.017-0.0170.0000.0000.0000.000
112A115GLU-1-0.706-0.82512.8690.3820.3820.0000.0000.0000.000
113A116HIS00.0160.01815.969-0.037-0.0370.0000.0000.0000.000
114A117SER0-0.027-0.02618.130-0.023-0.0230.0000.0000.0000.000
115A118VAL00.0560.02213.379-0.022-0.0220.0000.0000.0000.000
116A119ARG10.8720.91210.172-0.189-0.1890.0000.0000.0000.000
117A120ARG10.8890.95115.116-0.041-0.0410.0000.0000.0000.000
118A121ALA0-0.025-0.01117.193-0.023-0.0230.0000.0000.0000.000
119A122LEU00.0510.02610.847-0.023-0.0230.0000.0000.0000.000
120A123ASP-1-0.890-0.93714.235-0.215-0.2150.0000.0000.0000.000
121A124ARG10.8600.91015.6810.0330.0330.0000.0000.0000.000
122A125ALA00.0000.01115.2240.0120.0120.0000.0000.0000.000
123A126TYR0-0.018-0.04611.418-0.022-0.0220.0000.0000.0000.000
124A127LEU0-0.0100.00514.472-0.006-0.0060.0000.0000.0000.000
125A128ARG10.9030.93717.7800.0650.0650.0000.0000.0000.000
126A129VAL00.0170.01814.4000.0110.0110.0000.0000.0000.000
127A130GLU-1-0.788-0.87713.404-0.308-0.3080.0000.0000.0000.000
128A131ASN0-0.047-0.02017.2290.0120.0120.0000.0000.0000.000
129A132GLN0-0.0010.00520.4820.0160.0160.0000.0000.0000.000
130A133ARG10.9350.96813.8540.2510.2510.0000.0000.0000.000
131A134TYR00.0200.00717.7700.0020.0020.0000.0000.0000.000
132A135ARG10.8630.92622.3150.0860.0860.0000.0000.0000.000
133A136ASP-1-0.893-0.93922.482-0.104-0.1040.0000.0000.0000.000
134A137LYN00.0400.02119.139-0.004-0.0040.0000.0000.0000.000
135A138LEU0-0.0110.00123.6690.0040.0040.0000.0000.0000.000
136A139GLU-1-0.878-0.92526.484-0.063-0.0630.0000.0000.0000.000
137A140ALA00.001-0.00425.7160.0060.0060.0000.0000.0000.000
138A141ALA00.0370.03226.7610.0030.0030.0000.0000.0000.000
139A142ASN00.034-0.00328.5500.0040.0040.0000.0000.0000.000
140A143ARG10.7620.86930.4800.0740.0740.0000.0000.0000.000
141A144GLU-1-0.921-0.95428.558-0.089-0.0890.0000.0000.0000.000
142A145LEU0-0.040-0.00132.3290.0020.0020.0000.0000.0000.000
143A146GLN00.000-0.01734.0110.0020.0020.0000.0000.0000.000
144A147ALA0-0.0060.00035.5600.0040.0040.0000.0000.0000.000
145A148SER0-0.029-0.02735.8760.0020.0020.0000.0000.0000.000
146A149LEU00.0020.00037.6930.0020.0020.0000.0000.0000.000
147A150ASN00.003-0.00639.9650.0020.0020.0000.0000.0000.000
148A151LEU0-0.0130.01138.9730.0020.0020.0000.0000.0000.000
149A152LEU00.0240.00840.0160.0020.0020.0000.0000.0000.000
150A153GLN00.0090.01643.3380.0020.0020.0000.0000.0000.000
151A154GLU-1-0.889-0.93845.565-0.034-0.0340.0000.0000.0000.000
152A155ASP-1-0.902-0.96145.350-0.042-0.0420.0000.0000.0000.000
153A156GLN0-0.030-0.02545.8970.0020.0020.0000.0000.0000.000
154A157ASN0-0.030-0.02549.2400.0020.0020.0000.0000.0000.000
155A158ALA0-0.029-0.01050.1790.0020.0020.0000.0000.0000.000
156A159GLY00.016-0.00751.0960.0010.0010.0000.0000.0000.000
157A160ARG10.9050.96652.5590.0340.0340.0000.0000.0000.000
158A161GLN0-0.0200.00355.1790.0020.0020.0000.0000.0000.000
159A162VAL0-0.005-0.01254.7760.0010.0010.0000.0000.0000.000
160A163GLN00.0170.00556.3790.0010.0010.0000.0000.0000.000
161A164MET00.003-0.00158.3180.0010.0010.0000.0000.0000.000
162A165ASN0-0.068-0.04560.4730.0010.0010.0000.0000.0000.000
163A166MET0-0.0620.00658.2610.0010.0010.0000.0000.0000.000
164A167LEU00.0020.02062.9220.0010.0010.0000.0000.0000.000
165A168PRO0-0.0170.02365.4010.0000.0000.0000.0000.0000.000
166A169VAL0-0.034-0.01869.1760.0000.0000.0000.0000.0000.000
167A170THR0-0.0380.01370.9520.0000.0000.0000.0000.0000.000
168A171PRO00.001-0.00372.8140.0000.0000.0000.0000.0000.000
169A172TRP0-0.006-0.01374.7460.0010.0010.0000.0000.0000.000
170A173SER00.023-0.00576.4410.0000.0000.0000.0000.0000.000
171A174ILE0-0.040-0.00979.4620.0000.0000.0000.0000.0000.000
172A175GLU-1-0.830-0.88481.464-0.014-0.0140.0000.0000.0000.000
173A176GLY00.0050.00484.6390.0000.0000.0000.0000.0000.000
174A177LEU0-0.0220.00180.2540.0000.0000.0000.0000.0000.000
175A178GLU-1-0.925-0.98177.376-0.018-0.0180.0000.0000.0000.000
176A179PHE00.0190.01673.8070.0000.0000.0000.0000.0000.000
177A180SER00.0080.00173.0280.0000.0000.0000.0000.0000.000
178A181HIS00.0650.05266.7790.0000.0000.0000.0000.0000.000
179A182ARG10.8700.93366.8760.0220.0220.0000.0000.0000.000
180A183ILE00.0260.01260.7990.0000.0000.0000.0000.0000.000
181A184ILE0-0.063-0.05361.2730.0000.0000.0000.0000.0000.000
182A185PRO0-0.0050.01858.0750.0000.0000.0000.0000.0000.000
183A186SER0-0.052-0.04854.7500.0000.0000.0000.0000.0000.000
184A187LEU00.0810.08950.315-0.001-0.0010.0000.0000.0000.000
185A188TYR0-0.066-0.04945.4580.0000.0000.0000.0000.0000.000
186A189LEU0-0.085-0.01250.0120.0010.0010.0000.0000.0000.000
187A190SER00.0090.02152.168-0.001-0.0010.0000.0000.0000.000
188A191GLY00.0140.01054.8120.0000.0000.0000.0000.0000.000
189A192ASP-1-0.861-0.92255.332-0.029-0.0290.0000.0000.0000.000
190A193PHE0-0.005-0.01758.9860.0000.0000.0000.0000.0000.000
191A194VAL00.000-0.00661.5830.0000.0000.0000.0000.0000.000
192A195ASP-1-0.805-0.91965.359-0.022-0.0220.0000.0000.0000.000
193A196TYR0-0.007-0.04167.4810.0000.0000.0000.0000.0000.000
194A197PHE0-0.0400.00567.5720.0000.0000.0000.0000.0000.000
195A198ARG10.8190.88172.5960.0160.0160.0000.0000.0000.000
196A199VAL0-0.010-0.01474.3300.0000.0000.0000.0000.0000.000
197A200ASP-1-0.832-0.91676.940-0.016-0.0160.0000.0000.0000.000
198A201GLU-1-0.868-0.89979.582-0.015-0.0150.0000.0000.0000.000
199A202ARG10.7630.83081.4200.0140.0140.0000.0000.0000.000
200A203ARG10.7880.88078.6800.0160.0160.0000.0000.0000.000
201A204VAL00.0280.01576.0240.0000.0000.0000.0000.0000.000
202A205ALA0-0.0040.00972.4070.0000.0000.0000.0000.0000.000
203A206PHE0-0.007-0.00771.0710.0000.0000.0000.0000.0000.000
204A207TYR0-0.005-0.01363.5520.0000.0000.0000.0000.0000.000
205A208LEU00.001-0.01063.8420.0000.0000.0000.0000.0000.000
206A209ALA0-0.044-0.02460.8730.0000.0000.0000.0000.0000.000
207A210ASP-1-0.750-0.87059.657-0.030-0.0300.0000.0000.0000.000
208A211VAL0-0.091-0.05153.744-0.001-0.0010.0000.0000.0000.000
209A212SER00.0510.02452.632-0.001-0.0010.0000.0000.0000.000
210A213GLY0-0.038-0.02550.267-0.001-0.0010.0000.0000.0000.000
211A214HIS00.0500.02546.7430.0020.0020.0000.0000.0000.000
212A215GLY00.010-0.01548.349-0.002-0.0020.0000.0000.0000.000
213A216ALA00.034-0.00147.3970.0020.0020.0000.0000.0000.000
214A217SER0-0.016-0.00346.3890.0010.0010.0000.0000.0000.000
215A218SER00.0380.02448.4990.0000.0000.0000.0000.0000.000
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