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: R5Z18

Calculation Name: 4EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2023-06-20

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 192
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301785.558167
FMO2-HF: Nuclear repulsion 2222925.294008
FMO2-HF: Total energy -78860.264159
FMO2-MP2: Total energy -79091.675902


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.
-14.115-3.1845.262-5.104-11.09-0.028
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 : -0.022 / q_NPA : -0.005
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].
3A3TYR00.025-0.0183.810-0.2002.7920.179-1.430-1.741-0.001
4A4GLU-1-0.882-0.9465.834-0.250-0.2500.0000.0000.0000.000
5A5ASP-1-0.929-0.9522.503-1.192-0.4501.835-0.787-1.790-0.007
6A6LEU0-0.112-0.0502.509-6.713-3.8922.308-1.674-3.456-0.015
7A7GLU-1-0.899-0.9464.254-2.384-2.2300.0060.037-0.1980.000
8A8LEU0-0.052-0.0226.1720.3070.3070.0000.0000.0000.000
9A9ILE0-0.043-0.0329.2590.1310.1310.0000.0000.0000.000
10A10THR00.0030.0114.094-0.297-0.144-0.001-0.014-0.1380.000
11A11ILE0-0.004-0.0017.2950.1730.1730.0000.0000.0000.000
12A12TRP0-0.002-0.0065.2640.1850.1850.0000.0000.0000.000
13A13PRO0-0.015-0.0088.242-0.059-0.0590.0000.0000.0000.000
14A14SER0-0.040-0.03210.9550.1240.1240.0000.0000.0000.000
15A15PRO00.0250.0558.3520.1050.1050.0000.0000.0000.000
16A16THR00.016-0.01010.327-0.139-0.1390.0000.0000.0000.000
17A17LYS11.0050.98510.868-0.153-0.1530.0000.0000.0000.000
18A18ASN0-0.025-0.01711.739-0.068-0.0680.0000.0000.0000.000
19A19LYS10.9700.9796.051-2.593-2.5930.0000.0000.0000.000
20A20LEU00.0550.0576.549-0.024-0.0240.0000.0000.0000.000
21A21CYS0-0.039-0.0238.139-0.223-0.2230.0000.0000.0000.000
22A22GLN0-0.0130.0026.2480.3150.3150.0000.0000.0000.000
23A23PHE00.0500.0292.592-0.8370.4770.287-0.410-1.1920.000
24A24ILE00.0440.0215.079-0.368-0.371-0.001-0.0010.0060.000
25A25LYS10.8680.9358.4020.0840.0840.0000.0000.0000.000
26A26GLN0-0.022-0.0083.5090.1320.4760.005-0.090-0.2590.000
27A27ASN00.001-0.0093.9540.3470.610-0.001-0.124-0.1380.000
28A28LEU0-0.049-0.0347.9100.1710.1710.0000.0000.0000.000
29A29SER0-0.086-0.04910.9110.0950.0950.0000.0000.0000.000
30A30LYS10.8710.9469.8260.5490.5490.0000.0000.0000.000
31A31DGL-1-0.861-0.93212.500-0.135-0.1350.0000.0000.0000.000
32A32HIS0-0.058-0.04115.600-0.020-0.0200.0000.0000.0000.000
33A33VAL00.0300.03712.7910.0000.0000.0000.0000.0000.000
34A34VAL0-0.035-0.01916.2620.0050.0050.0000.0000.0000.000
35A35THR00.0180.0139.9010.0200.0200.0000.0000.0000.000
36A36GLN0-0.051-0.03913.1050.0360.0360.0000.0000.0000.000
37A37LEU0-0.0180.0049.866-0.035-0.0350.0000.0000.0000.000
38A38PHE0-0.008-0.00912.7930.0520.0520.0000.0000.0000.000
39A39PHE00.0110.00012.699-0.009-0.0090.0000.0000.0000.000
40A40ILE0-0.017-0.00915.1060.0150.0150.0000.0000.0000.000
41A41ASP-1-0.716-0.83716.6450.0430.0430.0000.0000.0000.000
42A42ALA00.0070.01918.725-0.007-0.0070.0000.0000.0000.000
43A43THR0-0.026-0.03820.5470.0010.0010.0000.0000.0000.000
44A44SER0-0.082-0.01921.3670.0030.0030.0000.0000.0000.000
45A45SER0-0.027-0.04118.8910.0080.0080.0000.0000.0000.000
46A46PHE00.0080.02013.5810.0300.0300.0000.0000.0000.000
47A47PRO0-0.021-0.00113.8050.0060.0060.0000.0000.0000.000
48A48LEU00.0610.00916.6330.0040.0040.0000.0000.0000.000
49A49SER00.0430.02418.8700.0020.0020.0000.0000.0000.000
50A50GLN0-0.015-0.02515.7820.0000.0000.0000.0000.0000.000
51A51PHE00.0690.02211.9400.0160.0160.0000.0000.0000.000
52A52GLN00.0220.01515.745-0.006-0.0060.0000.0000.0000.000
53A53LYS10.9010.96417.095-0.172-0.1720.0000.0000.0000.000
54A54LEU0-0.087-0.06012.5140.0120.0120.0000.0000.0000.000
55A55VAL0-0.0030.01112.808-0.015-0.0150.0000.0000.0000.000
56A56PRO00.0460.03715.965-0.012-0.0120.0000.0000.0000.000
57A57PRO00.011-0.00319.793-0.012-0.0120.0000.0000.0000.000
58A58THR0-0.033-0.01521.379-0.005-0.0050.0000.0000.0000.000
59A59LEU0-0.0410.00019.6570.0040.0040.0000.0000.0000.000
60A60PRO00.0780.02621.436-0.011-0.0110.0000.0000.0000.000
61A61GLU-1-0.874-0.93717.271-0.061-0.0610.0000.0000.0000.000
62A62ASN00.0170.00116.287-0.052-0.0520.0000.0000.0000.000
63A63VAL0-0.0100.00418.170-0.010-0.0100.0000.0000.0000.000
64A64ARG10.9570.96715.4990.2530.2530.0000.0000.0000.000
65A65ILE0-0.0060.00713.043-0.011-0.0110.0000.0000.0000.000
66A66TYR0-0.052-0.04616.107-0.001-0.0010.0000.0000.0000.000
67A67GLU-1-0.893-0.94018.482-0.110-0.1100.0000.0000.0000.000
68A68ASN0-0.054-0.01716.0080.0010.0010.0000.0000.0000.000
69A69ILE00.0190.02913.875-0.027-0.0270.0000.0000.0000.000
70A70ARG10.8020.88616.3990.1650.1650.0000.0000.0000.000
71A71ILE00.0120.00317.302-0.004-0.0040.0000.0000.0000.000
72A72ASN0-0.025-0.02819.3360.0000.0000.0000.0000.0000.000
73A73THR00.0020.01220.3420.0030.0030.0000.0000.0000.000
74A74CYS0-0.0070.00721.228-0.007-0.0070.0000.0000.0000.000
75A75LEU00.021-0.00623.0970.0070.0070.0000.0000.0000.000
76A76ASP-1-0.839-0.90525.543-0.038-0.0380.0000.0000.0000.000
77A77LEU00.0310.00122.658-0.007-0.0070.0000.0000.0000.000
78A78GLU-1-0.788-0.89624.888-0.067-0.0670.0000.0000.0000.000
79A79GLU-1-0.856-0.91725.234-0.049-0.0490.0000.0000.0000.000
80A80LEU00.0450.01118.287-0.008-0.0080.0000.0000.0000.000
81A81SER0-0.0080.00921.784-0.016-0.0160.0000.0000.0000.000
82A82ALA0-0.001-0.00724.087-0.009-0.0090.0000.0000.0000.000
83A83ILE0-0.041-0.02319.388-0.006-0.0060.0000.0000.0000.000
84A84THR00.008-0.00119.496-0.016-0.0160.0000.0000.0000.000
85A85VAL0-0.053-0.02820.935-0.011-0.0110.0000.0000.0000.000
86A86LYS10.9720.99522.4360.0980.0980.0000.0000.0000.000
87A87LEU00.0120.00416.521-0.002-0.0020.0000.0000.0000.000
88A88LEU00.0340.01520.155-0.008-0.0080.0000.0000.0000.000
89A89GLN0-0.027-0.01121.7820.0010.0010.0000.0000.0000.000
90A90ILE0-0.002-0.00220.0590.0020.0020.0000.0000.0000.000
91A91LEU00.0200.01016.5390.0020.0020.0000.0000.0000.000
92A92SER0-0.008-0.01420.7720.0000.0000.0000.0000.0000.000
93A93MET0-0.029-0.01624.1460.0080.0080.0000.0000.0000.000
94A94ASN0-0.0160.00721.0370.0020.0020.0000.0000.0000.000
95A95LYS10.8660.92518.5190.2470.2470.0000.0000.0000.000
96A96ILE0-0.022-0.01524.0880.0070.0070.0000.0000.0000.000
97A97ASN0-0.113-0.07127.0330.0120.0120.0000.0000.0000.000
98A98ALA0-0.0030.02524.5640.0050.0050.0000.0000.0000.000
99A99GLN0-0.101-0.03625.2370.0060.0060.0000.0000.0000.000
100A108GLU-1-0.868-0.93119.812-0.177-0.1770.0000.0000.0000.000
101A109PRO0-0.0180.00116.677-0.002-0.0020.0000.0000.0000.000
102A110LEU0-0.045-0.01716.390-0.015-0.0150.0000.0000.0000.000
103A111LYS10.7970.87511.2060.3620.3620.0000.0000.0000.000
104A112ILE0-0.002-0.00612.609-0.008-0.0080.0000.0000.0000.000
105A113ILE00.0330.0156.808-0.024-0.0240.0000.0000.0000.000
106A114LEU0-0.027-0.00910.0570.0490.0490.0000.0000.0000.000
107A115TYR0-0.052-0.0657.8570.0000.0000.0000.0000.0000.000
108A116ILE0-0.003-0.00811.4860.0220.0220.0000.0000.0000.000
109A117ASN00.000-0.01113.7280.0360.0360.0000.0000.0000.000
110A118GLY00.0590.02915.428-0.014-0.0140.0000.0000.0000.000
111A119LEU00.0520.01416.678-0.009-0.0090.0000.0000.0000.000
112A120GLU-1-0.807-0.91018.9790.0370.0370.0000.0000.0000.000
113A121VAL0-0.059-0.02421.120-0.001-0.0010.0000.0000.0000.000
114A122MET0-0.0250.01019.159-0.009-0.0090.0000.0000.0000.000
115A123PHE00.0280.00222.687-0.003-0.0030.0000.0000.0000.000
116A124ARG10.9140.95824.434-0.017-0.0170.0000.0000.0000.000
117A125ASN0-0.006-0.01426.9220.0040.0040.0000.0000.0000.000
118A126SER00.0510.01627.1210.0000.0000.0000.0000.0000.000
119A127GLN0-0.065-0.02628.798-0.006-0.0060.0000.0000.0000.000
120A128PHE0-0.051-0.01930.5670.0040.0040.0000.0000.0000.000
121A129LYS10.8420.91130.8680.0300.0300.0000.0000.0000.000
122A130SER0-0.043-0.01131.868-0.003-0.0030.0000.0000.0000.000
123A131SER00.0430.02133.6310.0010.0010.0000.0000.0000.000
124A132PRO00.0790.02630.675-0.003-0.0030.0000.0000.0000.000
125A133GLN00.0140.01229.831-0.004-0.0040.0000.0000.0000.000
126A134ARG10.8700.93830.2070.0590.0590.0000.0000.0000.000
127A135SER00.0540.02327.208-0.007-0.0070.0000.0000.0000.000
128A136HIS0-0.048-0.04225.308-0.007-0.0070.0000.0000.0000.000
129A137GLU-1-0.894-0.93425.264-0.080-0.0800.0000.0000.0000.000
130A138LEU0-0.0120.00925.373-0.009-0.0090.0000.0000.0000.000
131A139LEU0-0.021-0.00519.593-0.010-0.0100.0000.0000.0000.000
132A140ARG10.8630.90821.2230.0880.0880.0000.0000.0000.000
133A141ASP-1-0.818-0.88721.566-0.128-0.1280.0000.0000.0000.000
134A142THR0-0.069-0.04519.655-0.011-0.0110.0000.0000.0000.000
135A143LEU00.0000.00115.801-0.018-0.0180.0000.0000.0000.000
136A144LEU00.012-0.00317.174-0.032-0.0320.0000.0000.0000.000
137A145LYS10.9320.98118.9220.1260.1260.0000.0000.0000.000
138A146LEU00.017-0.00915.280-0.010-0.0100.0000.0000.0000.000
139A147ARG10.7930.87811.7220.4300.4300.0000.0000.0000.000
140A148VAL00.003-0.00415.309-0.024-0.0240.0000.0000.0000.000
141A149MET0-0.074-0.02917.2550.0040.0040.0000.0000.0000.000
142A150GLY00.0070.00613.211-0.002-0.0020.0000.0000.0000.000
143A151ASN0-0.038-0.02813.564-0.077-0.0770.0000.0000.0000.000
144A152ASP-1-0.874-0.91415.133-0.225-0.2250.0000.0000.0000.000
145A153GLU-1-0.912-0.95316.561-0.266-0.2660.0000.0000.0000.000
146A154ASN0-0.101-0.05518.208-0.004-0.0040.0000.0000.0000.000
147A155GLU-1-0.797-0.89115.727-0.338-0.3380.0000.0000.0000.000
148A156ASN0-0.050-0.02917.695-0.010-0.0100.0000.0000.0000.000
149A157ALA00.0300.01417.3530.0040.0040.0000.0000.0000.000
150A158SER00.0090.02613.349-0.018-0.0180.0000.0000.0000.000
151A159ILE0-0.006-0.00812.5640.0160.0160.0000.0000.0000.000
152A160ARG10.9090.9737.8250.5670.5670.0000.0000.0000.000
153A161THR00.011-0.0019.9090.0590.0590.0000.0000.0000.000
154A162LEU0-0.025-0.0034.667-0.168-0.055-0.001-0.003-0.1080.000
155A163LEU0-0.020-0.0148.8520.0440.0440.0000.0000.0000.000
156A164GLU-1-0.824-0.88910.5520.2580.2580.0000.0000.0000.000
157A165PHE0-0.002-0.02111.983-0.051-0.0510.0000.0000.0000.000
158A166PRO00.0410.03514.0290.0690.0690.0000.0000.0000.000
159A167LYS10.9980.99414.996-0.481-0.4810.0000.0000.0000.000
160A168GLU-1-0.902-0.95616.3520.1760.1760.0000.0000.0000.000
161A169GLN0-0.103-0.06417.923-0.039-0.0390.0000.0000.0000.000
162A170LEU00.0270.01313.273-0.030-0.0300.0000.0000.0000.000
163A171LEU00.0360.01417.4480.0100.0100.0000.0000.0000.000
164A172ASP-1-0.803-0.88119.7330.0240.0240.0000.0000.0000.000
165A173TYR0-0.084-0.06012.033-0.051-0.0510.0000.0000.0000.000
166A174TYR0-0.099-0.08712.763-0.006-0.0060.0000.0000.0000.000
167A175LEU00.0040.01318.0720.0050.0050.0000.0000.0000.000
168A176LYS10.8910.96814.723-0.042-0.0420.0000.0000.0000.000
169A177LYS10.8230.89713.964-0.331-0.3310.0000.0000.0000.000
170A178ASN00.0120.03619.5190.0120.0120.0000.0000.0000.000
171A192ARG10.8630.91622.597-0.051-0.0510.0000.0000.0000.000
172A193ILE0-0.008-0.00529.510-0.005-0.0050.0000.0000.0000.000
173A194LYS10.7390.84023.1840.0010.0010.0000.0000.0000.000
174A195ASN0-0.017-0.01129.205-0.003-0.0030.0000.0000.0000.000
175A196GLY00.0410.02027.791-0.003-0.0030.0000.0000.0000.000
176A197ASP-1-0.820-0.89122.080-0.029-0.0290.0000.0000.0000.000
177A198SER0-0.027-0.01419.969-0.008-0.0080.0000.0000.0000.000
178A199LEU00.0520.01418.189-0.008-0.0080.0000.0000.0000.000
179A200ALA00.0430.02415.911-0.020-0.0200.0000.0000.0000.000
180A201GLU-1-0.761-0.87316.3270.0130.0130.0000.0000.0000.000
181A202TYR0-0.008-0.00218.063-0.026-0.0260.0000.0000.0000.000
182A203ILE00.0310.00314.086-0.020-0.0200.0000.0000.0000.000
183A204TRP00.004-0.00712.044-0.003-0.0030.0000.0000.0000.000
184A205LYS10.7800.88814.3280.0250.0250.0000.0000.0000.000
185A206TYR0-0.043-0.02317.064-0.005-0.0050.0000.0000.0000.000
186A207TYR0-0.023-0.01315.6190.0020.0020.0000.0000.0000.000
187A208ALA0-0.0050.00310.445-0.024-0.0240.0000.0000.0000.000
188A209ASP-1-0.741-0.8288.039-0.600-0.6000.0000.0000.0000.000
189A210SER00.0080.0104.8540.0730.0730.0000.0000.0000.000
190A211LEU0-0.038-0.0147.6280.0990.0990.0000.0000.0000.000
191A212PHE00.0130.0093.104-1.8020.2360.646-0.608-2.076-0.005
192A213GLU-1-0.759-0.8605.9401.2181.2180.0000.0000.0000.000