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: 94YN2

Calculation Name: 5H0J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H0J

Chain ID: A

ChEMBL ID:

UniProt ID: C6Y1J8

Base Structure: X-ray

Registration Date: 2023-06-21

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3165935.602981
FMO2-HF: Nuclear repulsion 3071081.162475
FMO2-HF: Total energy -94854.440506
FMO2-MP2: Total energy -95129.597748


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.161-4.2638.9-4.69-9.11-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.028
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].
3A3THR0-0.011-0.0103.798-0.6590.763-0.018-0.541-0.8630.001
4A4PHE0-0.006-0.0203.970-1.195-1.0480.001-0.077-0.0720.000
5A5ALA00.0480.0165.849-0.175-0.1750.0000.0000.0000.000
6A6ASP-1-0.803-0.8812.155-3.634-5.2966.073-1.775-2.636-0.004
7A7LYS10.8720.9472.851-1.8730.4751.011-1.089-2.271-0.012
8A8VAL0-0.028-0.0093.6840.6210.7250.0160.072-0.1920.000
9A9ILE0-0.0110.0004.8900.3730.3730.0000.0000.0000.000
10A10GLN0-0.028-0.0272.521-5.251-2.9511.819-1.265-2.854-0.014
11A11PHE0-0.001-0.0234.6600.6240.782-0.001-0.014-0.1430.000
12A12ASN0-0.009-0.0117.8320.2980.2980.0000.0000.0000.000
13A13LYS10.8610.9284.6483.1263.207-0.001-0.001-0.0790.000
14A14ASP-1-0.834-0.8946.627-0.344-0.3440.0000.0000.0000.000
15A15LEU0-0.099-0.0289.3390.1830.1830.0000.0000.0000.000
16A16SER00.002-0.01912.4840.0050.0050.0000.0000.0000.000
17A17TYR0-0.067-0.04915.6510.0220.0220.0000.0000.0000.000
18A18THR00.0340.01617.4580.0040.0040.0000.0000.0000.000
19A19GLY00.0040.00820.2540.0220.0220.0000.0000.0000.000
20A20SER0-0.0190.00523.5100.0100.0100.0000.0000.0000.000
21A21THR00.0210.00426.981-0.014-0.0140.0000.0000.0000.000
22A22LEU0-0.0140.00925.8480.0020.0020.0000.0000.0000.000
23A23PRO00.001-0.00829.6410.0060.0060.0000.0000.0000.000
24A24PRO00.0590.01732.528-0.007-0.0070.0000.0000.0000.000
25A25GLY00.0110.00934.121-0.002-0.0020.0000.0000.0000.000
26A26ILE0-0.067-0.02828.490-0.009-0.0090.0000.0000.0000.000
27A27ARG10.9010.94926.8730.1660.1660.0000.0000.0000.000
28A28ILE00.0250.00620.808-0.006-0.0060.0000.0000.0000.000
29A29MET0-0.0380.00922.083-0.007-0.0070.0000.0000.0000.000
30A30ASN00.0470.00515.124-0.051-0.0510.0000.0000.0000.000
31A31PRO00.0630.01617.243-0.005-0.0050.0000.0000.0000.000
32A32PHE00.002-0.00712.735-0.021-0.0210.0000.0000.0000.000
33A33LYS10.8170.90611.6350.5980.5980.0000.0000.0000.000
34A34GLU-1-0.883-0.89416.630-0.241-0.2410.0000.0000.0000.000
35A35HIS0-0.018-0.01218.7320.0120.0120.0000.0000.0000.000
36A36GLU-1-0.834-0.91916.701-0.428-0.4280.0000.0000.0000.000
37A37GLN0-0.007-0.00716.106-0.055-0.0550.0000.0000.0000.000
38A38THR0-0.012-0.00315.391-0.042-0.0420.0000.0000.0000.000
39A39MET00.010-0.0028.753-0.014-0.0140.0000.0000.0000.000
40A40HIS00.0730.04411.795-0.198-0.1980.0000.0000.0000.000
41A41ILE0-0.0080.00513.924-0.019-0.0190.0000.0000.0000.000
42A42VAL0-0.039-0.0229.723-0.022-0.0220.0000.0000.0000.000
43A43GLU-1-0.852-0.9257.454-2.108-2.1080.0000.0000.0000.000
44A44ALA00.0140.00910.574-0.009-0.0090.0000.0000.0000.000
45A45PHE00.003-0.01713.5380.0460.0460.0000.0000.0000.000
46A46TYR0-0.018-0.0239.1940.0750.0750.0000.0000.0000.000
47A47HIS00.0450.0216.5390.2220.2220.0000.0000.0000.000
48A48LYS10.8630.95510.8430.5690.5690.0000.0000.0000.000
49A49TYR00.002-0.01613.5080.0860.0860.0000.0000.0000.000
50A50TYR0-0.073-0.0749.7280.0770.0770.0000.0000.0000.000
51A51ASN0-0.0070.0119.062-0.266-0.2660.0000.0000.0000.000
52A52ASP-1-0.676-0.8329.345-0.494-0.4940.0000.0000.0000.000
53A53ASN0-0.016-0.0336.966-0.271-0.2710.0000.0000.0000.000
54A54GLN0-0.047-0.01110.0650.1720.1720.0000.0000.0000.000
55A55SER0-0.020-0.00412.049-0.107-0.1070.0000.0000.0000.000
56A56ARG10.7660.86912.2300.6600.6600.0000.0000.0000.000
57A57TYR00.0280.01715.3050.0350.0350.0000.0000.0000.000
58A58LEU00.0130.00915.386-0.039-0.0390.0000.0000.0000.000
59A59ILE0-0.007-0.00117.9840.0500.0500.0000.0000.0000.000
60A60LEU00.0110.00818.338-0.035-0.0350.0000.0000.0000.000
61A61GLY00.0220.00721.1820.0270.0270.0000.0000.0000.000
62A62ILE0-0.050-0.02423.2390.0130.0130.0000.0000.0000.000
63A63ASN00.011-0.01921.8370.0210.0210.0000.0000.0000.000
64A64PRO0-0.0020.01719.1170.0160.0160.0000.0000.0000.000
65A65GLY00.0170.01022.1630.0300.0300.0000.0000.0000.000
66A66ARG10.8260.86023.7490.2140.2140.0000.0000.0000.000
67A67PHE0-0.052-0.02024.905-0.008-0.0080.0000.0000.0000.000
68A68GLY00.0260.00825.111-0.012-0.0120.0000.0000.0000.000
69A69SER0-0.010-0.03520.861-0.014-0.0140.0000.0000.0000.000
70A70GLY0-0.032-0.00720.359-0.043-0.0430.0000.0000.0000.000
71A71LEU0-0.044-0.03820.878-0.008-0.0080.0000.0000.0000.000
72A72THR0-0.020-0.02319.167-0.022-0.0220.0000.0000.0000.000
73A73GLY0-0.0080.00115.983-0.060-0.0600.0000.0000.0000.000
74A74ILE0-0.0130.00514.659-0.065-0.0650.0000.0000.0000.000
75A75PRO00.005-0.00715.9910.0740.0740.0000.0000.0000.000
76A76PHE00.0050.00019.1230.0110.0110.0000.0000.0000.000
77A77THR00.0360.06620.0710.0260.0260.0000.0000.0000.000
78A78ASP-1-0.750-0.82221.735-0.290-0.2900.0000.0000.0000.000
79A79PRO00.0330.00923.777-0.007-0.0070.0000.0000.0000.000
80A80LYS10.9580.98824.7960.2010.2010.0000.0000.0000.000
81A81ARG10.8500.89324.6160.2550.2550.0000.0000.0000.000
82A82LEU00.0140.01118.665-0.008-0.0080.0000.0000.0000.000
83A83ILE0-0.015-0.00422.639-0.007-0.0070.0000.0000.0000.000
84A84THR0-0.096-0.08025.0980.0020.0020.0000.0000.0000.000
85A85GLU-1-0.856-0.89824.259-0.246-0.2460.0000.0000.0000.000
86A86CYS0-0.082-0.02819.805-0.018-0.0180.0000.0000.0000.000
87A87ASN0-0.0290.00721.122-0.007-0.0070.0000.0000.0000.000
88A88ILE0-0.0080.00716.901-0.017-0.0170.0000.0000.0000.000
89A89PRO00.011-0.00620.7400.0190.0190.0000.0000.0000.000
90A90TYR0-0.018-0.02421.315-0.038-0.0380.0000.0000.0000.000
91A91SER00.0080.01223.2000.0390.0390.0000.0000.0000.000
92A92GLY00.0470.02424.735-0.011-0.0110.0000.0000.0000.000
93A93LYS10.9420.97727.4150.2280.2280.0000.0000.0000.000
94A94LEU00.0690.03127.865-0.017-0.0170.0000.0000.0000.000
95A95SER0-0.018-0.01527.2020.0100.0100.0000.0000.0000.000
96A96HIS00.0410.02228.175-0.020-0.0200.0000.0000.0000.000
97A97GLU-1-0.774-0.87725.022-0.291-0.2910.0000.0000.0000.000
98A98PRO0-0.029-0.02829.060-0.005-0.0050.0000.0000.0000.000
99A99SER00.010-0.01127.2460.0100.0100.0000.0000.0000.000
100A100SER00.0270.00424.796-0.005-0.0050.0000.0000.0000.000
101A101VAL0-0.032-0.01926.916-0.003-0.0030.0000.0000.0000.000
102A102PHE00.0010.00328.7480.0010.0010.0000.0000.0000.000
103A103ILE00.0070.00123.3070.0050.0050.0000.0000.0000.000
104A104TYR00.0800.00820.761-0.008-0.0080.0000.0000.0000.000
105A105GLU-1-0.816-0.88126.699-0.167-0.1670.0000.0000.0000.000
106A106MET0-0.067-0.01324.6130.0100.0100.0000.0000.0000.000
107A107ILE00.0100.00422.0160.0040.0040.0000.0000.0000.000
108A108ASN0-0.041-0.03625.920-0.002-0.0020.0000.0000.0000.000
109A109ALA0-0.0180.00028.3930.0080.0080.0000.0000.0000.000
110A110PHE0-0.064-0.03423.5660.0090.0090.0000.0000.0000.000
111A111GLY00.0200.01627.0760.0060.0060.0000.0000.0000.000
112A112GLY00.0090.01525.243-0.003-0.0030.0000.0000.0000.000
113A113ALA0-0.009-0.02420.665-0.009-0.0090.0000.0000.0000.000
114A114GLU-1-0.930-0.96218.808-0.380-0.3800.0000.0000.0000.000
115A115ALA00.0460.02319.180-0.020-0.0200.0000.0000.0000.000
116A116PHE0-0.003-0.00620.459-0.007-0.0070.0000.0000.0000.000
117A117TYR0-0.012-0.03315.954-0.001-0.0010.0000.0000.0000.000
118A118LYS10.8380.95714.2800.4400.4400.0000.0000.0000.000
119A119GLN0-0.017-0.01216.5540.0060.0060.0000.0000.0000.000
120A120PHE0-0.027-0.01417.8230.0170.0170.0000.0000.0000.000
121A121TYR00.0080.01111.927-0.076-0.0760.0000.0000.0000.000
122A122ILE0-0.013-0.00315.4560.0620.0620.0000.0000.0000.000
123A123SER00.0530.02414.706-0.038-0.0380.0000.0000.0000.000
124A124SER0-0.030-0.04016.9770.0300.0300.0000.0000.0000.000
125A125PRO0-0.0030.01218.364-0.015-0.0150.0000.0000.0000.000
126A126CYS0-0.0050.02019.4420.0090.0090.0000.0000.0000.000
127A127PRO00.0200.02415.768-0.009-0.0090.0000.0000.0000.000
128A128LEU0-0.0080.00016.847-0.035-0.0350.0000.0000.0000.000
129A129GLY00.0570.02619.9190.0200.0200.0000.0000.0000.000
130A130PHE00.000-0.01223.3700.0090.0090.0000.0000.0000.000
131A131THR00.0190.01526.4950.0050.0050.0000.0000.0000.000
132A132SER00.0110.00229.1110.0060.0060.0000.0000.0000.000
133A133ILE0-0.005-0.00631.814-0.007-0.0070.0000.0000.0000.000
134A134ALA0-0.0160.00134.9380.0070.0070.0000.0000.0000.000
135A135ALA00.0670.03038.643-0.002-0.0020.0000.0000.0000.000
136A136ASN00.000-0.00540.683-0.004-0.0040.0000.0000.0000.000
137A137GLY00.0690.04038.201-0.001-0.0010.0000.0000.0000.000
138A138LYS10.8760.93935.1990.1310.1310.0000.0000.0000.000
139A139GLU-1-0.820-0.90729.542-0.193-0.1930.0000.0000.0000.000
140A140LYS10.8910.94833.2840.1140.1140.0000.0000.0000.000
141A141ASN00.0220.01227.635-0.019-0.0190.0000.0000.0000.000
142A142TYR0-0.0050.00928.9020.0110.0110.0000.0000.0000.000
143A143ASN0-0.011-0.01927.755-0.026-0.0260.0000.0000.0000.000
144A144TYR00.046-0.00225.0540.0210.0210.0000.0000.0000.000
145A145TYR00.0040.00227.5080.0140.0140.0000.0000.0000.000
146A146ASP-1-0.841-0.91930.476-0.124-0.1240.0000.0000.0000.000
147A147SER0-0.027-0.01532.7720.0090.0090.0000.0000.0000.000
148A148LYS10.9010.93932.4930.0660.0660.0000.0000.0000.000
149A149ALA00.0270.01933.1670.0020.0020.0000.0000.0000.000
150A150LEU00.0100.01327.9930.0030.0030.0000.0000.0000.000
151A151GLU-1-0.787-0.89928.535-0.082-0.0820.0000.0000.0000.000
152A152LYS10.9370.96228.2380.0370.0370.0000.0000.0000.000
153A153ALA0-0.031-0.00428.4550.0070.0070.0000.0000.0000.000
154A154VAL00.013-0.00623.9390.0010.0010.0000.0000.0000.000
155A155TYR0-0.037-0.01223.663-0.017-0.0170.0000.0000.0000.000
156A156GLU-1-0.824-0.93622.989-0.021-0.0210.0000.0000.0000.000
157A157PHE00.0000.00017.316-0.006-0.0060.0000.0000.0000.000
158A158ILE0-0.030-0.01418.917-0.022-0.0220.0000.0000.0000.000
159A159ILE0-0.0060.00119.314-0.021-0.0210.0000.0000.0000.000
160A160GLU-1-0.821-0.89816.5640.0580.0580.0000.0000.0000.000
161A161ASN0-0.032-0.01214.687-0.056-0.0560.0000.0000.0000.000
162A162ILE0-0.016-0.01014.706-0.049-0.0490.0000.0000.0000.000
163A163ARG10.8900.93014.706-0.141-0.1410.0000.0000.0000.000
164A164LYS10.9420.9849.5600.4290.4290.0000.0000.0000.000
165A165GLN00.0060.00910.607-0.176-0.1760.0000.0000.0000.000
166A166LEU0-0.001-0.00111.917-0.073-0.0730.0000.0000.0000.000
167A167THR0-0.084-0.0478.790-0.014-0.0140.0000.0000.0000.000
168A168LEU0-0.0010.0027.072-0.059-0.0590.0000.0000.0000.000
169A169GLY0-0.0040.0138.941-0.144-0.1440.0000.0000.0000.000
170A170ILE0-0.020-0.01111.300-0.026-0.0260.0000.0000.0000.000
171A171THR00.0150.00714.7850.0620.0620.0000.0000.0000.000
172A172THR00.0140.00517.563-0.014-0.0140.0000.0000.0000.000
173A173ASP-1-0.791-0.86520.010-0.068-0.0680.0000.0000.0000.000
174A174THR00.024-0.01222.8240.0160.0160.0000.0000.0000.000
175A175CYS0-0.0680.00120.765-0.022-0.0220.0000.0000.0000.000
176A176PHE00.0570.01422.3780.0200.0200.0000.0000.0000.000
177A177CYS0-0.0060.01123.294-0.018-0.0180.0000.0000.0000.000
178A178LEU00.0150.01824.1780.0130.0130.0000.0000.0000.000
179A179GLY0-0.017-0.03026.912-0.004-0.0040.0000.0000.0000.000
180A180THR00.0470.02030.0040.0010.0010.0000.0000.0000.000
181A181GLY00.0150.01632.7620.0100.0100.0000.0000.0000.000
182A182LYS10.9280.94432.0140.1020.1020.0000.0000.0000.000
183A183ASN0-0.0110.00025.1680.0090.0090.0000.0000.0000.000
184A184GLU-1-0.759-0.86828.246-0.099-0.0990.0000.0000.0000.000
185A185LYS10.7830.88230.1510.0970.0970.0000.0000.0000.000
186A186PHE0-0.020-0.00424.3570.0110.0110.0000.0000.0000.000
187A187LEU00.0700.01722.8780.0070.0070.0000.0000.0000.000
188A188MET0-0.0030.00826.7540.0080.0080.0000.0000.0000.000
189A189LYS10.8910.96029.4010.0770.0770.0000.0000.0000.000
190A190VAL00.0080.00223.3070.0100.0100.0000.0000.0000.000
191A191ASN00.003-0.00524.6170.0090.0090.0000.0000.0000.000
192A192ALA0-0.0020.00426.2990.0110.0110.0000.0000.0000.000
193A193GLN0-0.029-0.00327.3030.0110.0110.0000.0000.0000.000
194A194TYR0-0.002-0.01522.7320.0070.0070.0000.0000.0000.000
195A195LYS10.8610.94023.5690.0120.0120.0000.0000.0000.000
196A196PHE00.0270.02019.2190.0020.0020.0000.0000.0000.000
197A197PHE00.002-0.01118.779-0.010-0.0100.0000.0000.0000.000
198A198LYS10.8750.94923.0730.0590.0590.0000.0000.0000.000
199A199ARG10.8560.91325.7540.0900.0900.0000.0000.0000.000
200A200ILE00.004-0.00324.882-0.014-0.0140.0000.0000.0000.000
201A201VAL00.0130.01526.8410.0110.0110.0000.0000.0000.000
202A202ALA0-0.0070.00427.558-0.016-0.0160.0000.0000.0000.000
203A203LEU0-0.0020.00327.3480.0080.0080.0000.0000.0000.000
204A204GLU-1-0.794-0.89430.125-0.129-0.1290.0000.0000.0000.000
205A205HIS00.0530.03726.3300.0000.0000.0000.0000.0000.000
206A206PRO00.0880.04126.7070.0120.0120.0000.0000.0000.000
207A207ARG10.8930.95130.0260.1810.1810.0000.0000.0000.000
208A208PHE0-0.005-0.00731.7520.0090.0090.0000.0000.0000.000
209A209ILE00.0140.01531.5430.0090.0090.0000.0000.0000.000
210A210MET0-0.016-0.01232.4060.0080.0080.0000.0000.0000.000
211A211GLN0-0.0300.00935.256-0.001-0.0010.0000.0000.0000.000
212A212TYR0-0.001-0.00737.4360.0040.0040.0000.0000.0000.000
213A213LYS10.8970.96137.5570.1070.1070.0000.0000.0000.000
214A214THR00.0400.02137.9520.0010.0010.0000.0000.0000.000
215A215ALA00.0130.00139.260-0.003-0.0030.0000.0000.0000.000
216A216SER0-0.037-0.01839.7890.0030.0030.0000.0000.0000.000
217A217LYS10.8540.90134.6040.1590.1590.0000.0000.0000.000
218A218GLN00.0210.00135.440-0.009-0.0090.0000.0000.0000.000
219A219PHE00.0520.03436.237-0.002-0.0020.0000.0000.0000.000
220A220TYR0-0.022-0.02033.5450.0010.0010.0000.0000.0000.000
221A221ILE0-0.0030.00831.361-0.007-0.0070.0000.0000.0000.000
222A222ASP-1-0.797-0.88731.846-0.132-0.1320.0000.0000.0000.000
223A223LYS10.8240.91033.2580.1180.1180.0000.0000.0000.000
224A224TYR0-0.015-0.04526.500-0.006-0.0060.0000.0000.0000.000
225A225ILE00.0370.02128.748-0.004-0.0040.0000.0000.0000.000
226A226SER0-0.073-0.03929.9850.0050.0050.0000.0000.0000.000
227A227ALA0-0.014-0.01228.9170.0070.0070.0000.0000.0000.000
228A228PHE0-0.018-0.02224.122-0.001-0.0010.0000.0000.0000.000
229A229LYS10.9210.96027.0650.1440.1440.0000.0000.0000.000
230A230ALA00.0330.01929.5930.0080.0080.0000.0000.0000.000
231A231LEU0-0.029-0.01323.1660.0070.0070.0000.0000.0000.000
232A232ASN0-0.023-0.00625.9120.0010.0010.0000.0000.0000.000
233A233ASN0-0.045-0.01927.2650.0030.0030.0000.0000.0000.000
234A234SER0-0.037-0.00728.7770.0070.0070.0000.0000.0000.000