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: 14J4Z

Calculation Name: 4EQ6-A-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2323209.392543
FMO2-HF: Nuclear repulsion 2243856.664173
FMO2-HF: Total energy -79352.72837
FMO2-MP2: Total energy -79585.640107


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:0:ACE )


Summations of interaction energy for fragment #1(A:0:ACE )
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.
-5.077-3.390.385-0.856-1.215-0.004
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.044
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].
3A2GLU -1-0.878-0.9233.8170.3491.226-0.006-0.360-0.511-0.001
4A3TYR 00.033-0.0186.8910.0240.0240.0000.0000.0000.000
5A4GLU -1-0.928-0.98310.227-0.356-0.3560.0000.0000.0000.000
6A5ASP -1-0.915-0.9408.476-0.986-0.9860.0000.0000.0000.000
7A6LEU 0-0.119-0.0497.482-0.052-0.0520.0000.0000.0000.000
8A7GLU -1-0.900-0.94210.619-0.406-0.4060.0000.0000.0000.000
9A8LEU 0-0.065-0.02513.5670.0110.0110.0000.0000.0000.000
10A9ILE 0-0.045-0.03114.9810.0290.0290.0000.0000.0000.000
11A10THR 00.0020.0169.130-0.049-0.0490.0000.0000.0000.000
12A11ILE 0-0.022-0.01212.2400.0520.0520.0000.0000.0000.000
13A12TRP 0-0.003-0.0014.598-0.157-0.1270.000-0.016-0.0150.000
14A13PRO 0-0.013-0.0139.9340.0830.0830.0000.0000.0000.000
15A14SER 0-0.036-0.02410.7020.0460.0460.0000.0000.0000.000
16A15PRO 00.0500.0697.8200.1100.1100.0000.0000.0000.000
17A16THR 00.005-0.0178.8030.0100.0100.0000.0000.0000.000
18A17LYS 11.0190.9899.280-0.156-0.1560.0000.0000.0000.000
19A18ASN 0-0.034-0.02210.164-0.010-0.0100.0000.0000.0000.000
20A19LYS 11.0181.0083.676-3.818-3.6930.001-0.044-0.0820.000
21A20LEU 00.0740.0665.3450.2260.2260.0000.0000.0000.000
22A21CYS 0-0.060-0.0307.598-0.126-0.1260.0000.0000.0000.000
23A22GLN 0-0.018-0.0145.3530.5610.5610.0000.0000.0000.000
24A23PHE 00.0500.0344.0790.0130.1210.001-0.034-0.0750.000
25A24ILE 00.0270.0125.413-0.331-0.3310.0000.0000.0000.000
26A25LYS 10.8850.9499.156-0.322-0.3220.0000.0000.0000.000
27A26GLN 0-0.026-0.0283.7810.2740.6030.006-0.115-0.218-0.001
28A27ASN 00.0110.0046.151-0.114-0.1140.0000.0000.0000.000
29A28LEU 0-0.053-0.0339.496-0.010-0.0100.0000.0000.0000.000
30A29SER 0-0.076-0.02611.3370.0120.0120.0000.0000.0000.000
31A30LYS 10.9771.01912.0680.2990.2990.0000.0000.0000.000
32A31DGL -1-0.870-0.93313.744-0.038-0.0380.0000.0000.0000.000
33A32HIS 0-0.032-0.02817.330-0.025-0.0250.0000.0000.0000.000
34A33VAL 00.0250.02615.459-0.011-0.0110.0000.0000.0000.000
35A34VAL 0-0.034-0.01418.5740.0210.0210.0000.0000.0000.000
36A35THR 00.0240.01512.701-0.011-0.0110.0000.0000.0000.000
37A36GLN 0-0.037-0.02616.1340.0320.0320.0000.0000.0000.000
38A37LEU 0-0.0160.00611.642-0.030-0.0300.0000.0000.0000.000
39A38PHE 0-0.006-0.00915.0440.0380.0380.0000.0000.0000.000
40A39PHE 00.0090.00013.189-0.017-0.0170.0000.0000.0000.000
41A40ILE 0-0.015-0.00916.6050.0160.0160.0000.0000.0000.000
42A41ASP -1-0.658-0.78318.0970.0340.0340.0000.0000.0000.000
43A42ALA 0-0.0070.00919.806-0.001-0.0010.0000.0000.0000.000
44A43THR 0-0.117-0.11120.6240.0010.0010.0000.0000.0000.000
45A44SER 0-0.056-0.01421.6730.0060.0060.0000.0000.0000.000
46A45SER 0-0.038-0.04818.3890.0060.0060.0000.0000.0000.000
47A46PHE 0-0.0010.01613.9910.0270.0270.0000.0000.0000.000
48A47PRO 0-0.0140.00712.9970.0010.0010.0000.0000.0000.000
49A48LEU 00.0550.00715.9250.0310.0310.0000.0000.0000.000
50A49SER 00.0160.00918.3750.0150.0150.0000.0000.0000.000
51A50GLN 0-0.006-0.02514.5550.0020.0020.0000.0000.0000.000
52A51PHE 00.0660.01912.1440.0370.0370.0000.0000.0000.000
53A52GLN 00.0180.01115.1640.0000.0000.0000.0000.0000.000
54A53LYS 10.9010.96815.851-0.344-0.3440.0000.0000.0000.000
55A54LEU 0-0.069-0.05411.1550.0030.0030.0000.0000.0000.000
56A55VAL 0-0.0220.00312.8620.0190.0190.0000.0000.0000.000
57A56PRO 00.0480.03915.720-0.033-0.0330.0000.0000.0000.000
58A57PRO 00.0090.00619.548-0.008-0.0080.0000.0000.0000.000
59A58THR 0-0.020-0.01221.517-0.009-0.0090.0000.0000.0000.000
60A59LEU 0-0.0260.00519.077-0.006-0.0060.0000.0000.0000.000
61A60PRO 00.0710.02821.593-0.002-0.0020.0000.0000.0000.000
62A61GLU -1-0.903-0.95717.6080.1060.1060.0000.0000.0000.000
63A62ASN 0-0.007-0.02416.4700.0070.0070.0000.0000.0000.000
64A63VAL 00.0020.01118.592-0.003-0.0030.0000.0000.0000.000
65A64ARG 10.9080.92716.4280.0440.0440.0000.0000.0000.000
66A65ILE 0-0.0020.00313.526-0.007-0.0070.0000.0000.0000.000
67A66TYR 0-0.059-0.05417.159-0.008-0.0080.0000.0000.0000.000
68A67GLU -1-0.915-0.94519.292-0.005-0.0050.0000.0000.0000.000
69A68ASN 0-0.055-0.00717.821-0.023-0.0230.0000.0000.0000.000
70A69ILE 00.0180.02414.645-0.017-0.0170.0000.0000.0000.000
71A70ARG 10.8220.88917.7190.0390.0390.0000.0000.0000.000
72A71ILE 00.0110.00918.056-0.004-0.0040.0000.0000.0000.000
73A72ASN 0-0.016-0.02720.637-0.005-0.0050.0000.0000.0000.000
74A73THR 0-0.0020.01621.5680.0050.0050.0000.0000.0000.000
75A74CYS 0-0.0180.00023.046-0.006-0.0060.0000.0000.0000.000
76A75LEU 00.0360.00224.5630.0020.0020.0000.0000.0000.000
77A76ASP -1-0.851-0.91427.278-0.025-0.0250.0000.0000.0000.000
78A77LEU 00.011-0.00925.553-0.005-0.0050.0000.0000.0000.000
79A78GLU -1-0.859-0.92727.668-0.042-0.0420.0000.0000.0000.000
80A79GLU -1-0.862-0.92727.410-0.023-0.0230.0000.0000.0000.000
81A80LEU 00.0460.01121.243-0.004-0.0040.0000.0000.0000.000
82A81SER 0-0.0290.00125.065-0.011-0.0110.0000.0000.0000.000
83A82ALA 00.016-0.00327.504-0.004-0.0040.0000.0000.0000.000
84A83ILE 0-0.045-0.02622.348-0.002-0.0020.0000.0000.0000.000
85A84THR 00.0120.00523.726-0.010-0.0100.0000.0000.0000.000
86A85VAL 0-0.054-0.02624.734-0.006-0.0060.0000.0000.0000.000
87A86LYS 10.9670.99125.4550.0430.0430.0000.0000.0000.000
88A87LEU 00.0270.00820.2190.0000.0000.0000.0000.0000.000
89A88LEU 00.0070.00424.089-0.005-0.0050.0000.0000.0000.000
90A89GLN 0-0.034-0.02526.1830.0020.0020.0000.0000.0000.000
91A90ILE 0-0.0040.00023.6380.0020.0020.0000.0000.0000.000
92A91LEU 00.0090.00421.1000.0020.0020.0000.0000.0000.000
93A92SER 0-0.007-0.00525.2390.0000.0000.0000.0000.0000.000
94A93MET 0-0.033-0.01828.7860.0050.0050.0000.0000.0000.000
95A94ASN 0-0.0230.00025.208-0.001-0.0010.0000.0000.0000.000
96A95LYS 10.8740.91224.5200.1410.1410.0000.0000.0000.000
97A96ILE 0-0.027-0.01728.7360.0040.0040.0000.0000.0000.000
98A97ASN 0-0.075-0.04731.1390.0050.0050.0000.0000.0000.000
99A98ALA 00.0020.02528.8200.0040.0040.0000.0000.0000.000
100A99GLN 0-0.0270.00230.4130.0020.0020.0000.0000.0000.000
101A100NME 0-0.043-0.02133.7100.0040.0040.0000.0000.0000.000
102A107ACE 0-0.006-0.02422.2680.0000.0000.0000.0000.0000.000
103A108GLU -1-0.942-0.95322.593-0.099-0.0990.0000.0000.0000.000
104A109PRO 00.0620.05720.3240.0000.0000.0000.0000.0000.000
105A110LEU 0-0.041-0.01620.028-0.003-0.0030.0000.0000.0000.000
106A111LYS 10.8480.93215.3330.2550.2550.0000.0000.0000.000
107A112ILE 00.004-0.00416.2860.0160.0160.0000.0000.0000.000
108A113ILE 00.0320.0159.873-0.035-0.0350.0000.0000.0000.000
109A114LEU 0-0.032-0.01013.7550.0610.0610.0000.0000.0000.000
110A115TYR 0-0.048-0.0489.021-0.036-0.0360.0000.0000.0000.000
111A116ILE 0-0.002-0.00813.8400.0400.0400.0000.0000.0000.000
112A117ASN 00.0290.01715.180-0.019-0.0190.0000.0000.0000.000
113A118GLY 00.0770.03616.6450.0020.0020.0000.0000.0000.000
114A119LEU 00.0560.01719.2260.0000.0000.0000.0000.0000.000
115A120GLU -1-0.829-0.93720.485-0.011-0.0110.0000.0000.0000.000
116A121VAL 0-0.055-0.02022.9390.0040.0040.0000.0000.0000.000
117A122MET 0-0.0270.00720.909-0.004-0.0040.0000.0000.0000.000
118A123PHE 00.0240.00225.2250.0000.0000.0000.0000.0000.000
119A124ARG 10.9200.95926.0420.0120.0120.0000.0000.0000.000
120A125ASN 0-0.009-0.01228.4770.0030.0030.0000.0000.0000.000
121A126SER 00.0420.01229.7310.0000.0000.0000.0000.0000.000
122A127GLN 0-0.071-0.03031.224-0.002-0.0020.0000.0000.0000.000
123A128PHE 0-0.040-0.01232.6890.0020.0020.0000.0000.0000.000
124A129LYS 10.8360.91332.7040.0180.0180.0000.0000.0000.000
125A130SER 0-0.040-0.01034.844-0.002-0.0020.0000.0000.0000.000
126A131SER 00.0430.01836.5070.0000.0000.0000.0000.0000.000
127A132PRO 00.0760.02733.931-0.002-0.0020.0000.0000.0000.000
128A133GLN 00.0140.02033.500-0.003-0.0030.0000.0000.0000.000
129A134ARG 10.9590.99234.3500.0400.0400.0000.0000.0000.000
130A135SER 00.0410.01430.415-0.005-0.0050.0000.0000.0000.000
131A136HIS 0-0.046-0.04629.600-0.007-0.0070.0000.0000.0000.000
132A137GLU -1-0.882-0.93629.752-0.055-0.0550.0000.0000.0000.000
133A138LEU 00.0030.01129.221-0.005-0.0050.0000.0000.0000.000
134A139LEU 0-0.013-0.00723.256-0.006-0.0060.0000.0000.0000.000
135A140ARG 10.8800.94325.6550.0620.0620.0000.0000.0000.000
136A141ASP -1-0.844-0.92626.830-0.083-0.0830.0000.0000.0000.000
137A142THR 0-0.063-0.03523.349-0.005-0.0050.0000.0000.0000.000
138A143LEU 00.0020.00120.385-0.012-0.0120.0000.0000.0000.000
139A144LEU 00.016-0.00222.713-0.017-0.0170.0000.0000.0000.000
140A145LYS 10.9310.98224.9920.0810.0810.0000.0000.0000.000
141A146LEU 00.014-0.01419.457-0.005-0.0050.0000.0000.0000.000
142A147ARG 10.7810.87918.6660.2200.2200.0000.0000.0000.000
143A148VAL 00.005-0.00121.533-0.010-0.0100.0000.0000.0000.000
144A149MET 0-0.085-0.03422.2430.0030.0030.0000.0000.0000.000
145A150GLY 00.002-0.00319.052-0.004-0.0040.0000.0000.0000.000
146A151ASN 0-0.047-0.03419.767-0.035-0.0350.0000.0000.0000.000
147A152ASP -1-0.872-0.89721.914-0.131-0.1310.0000.0000.0000.000
148A153GLU -1-0.908-0.94922.915-0.156-0.1560.0000.0000.0000.000
149A154ASN 0-0.097-0.05724.558-0.004-0.0040.0000.0000.0000.000
150A155GLU -1-0.829-0.91220.463-0.232-0.2320.0000.0000.0000.000
151A156ASN 0-0.082-0.05422.163-0.009-0.0090.0000.0000.0000.000
152A157ALA 0-0.0010.00321.8460.0060.0060.0000.0000.0000.000
153A158SER 0-0.0050.01118.218-0.021-0.0210.0000.0000.0000.000
154A159ILE 0-0.017-0.01417.2200.0130.0130.0000.0000.0000.000
155A160ARG 10.9360.98712.9650.4050.4050.0000.0000.0000.000
156A161THR 00.0110.00214.3560.0430.0430.0000.0000.0000.000
157A162LEU 0-0.0110.0017.988-0.038-0.0380.0000.0000.0000.000
158A163LEU 0-0.033-0.02112.1500.0770.0770.0000.0000.0000.000
159A164GLU -1-0.838-0.90512.1840.0780.0780.0000.0000.0000.000
160A165PHE 0-0.019-0.02713.2820.0040.0040.0000.0000.0000.000
161A166PRO 00.0290.03314.5290.0180.0180.0000.0000.0000.000
162A167LYS 11.0141.00214.398-0.153-0.1530.0000.0000.0000.000
163A168GLU -1-0.906-0.96316.5980.0550.0550.0000.0000.0000.000
164A169GLN 0-0.091-0.04719.286-0.020-0.0200.0000.0000.0000.000
165A170LEU 00.0320.01615.301-0.015-0.0150.0000.0000.0000.000
166A171LEU 00.0260.00719.177-0.005-0.0050.0000.0000.0000.000
167A172ASP -1-0.809-0.90021.515-0.048-0.0480.0000.0000.0000.000
168A173TYR 0-0.067-0.02012.827-0.019-0.0190.0000.0000.0000.000
169A174TYR 0-0.056-0.04713.1860.0030.0030.0000.0000.0000.000
170A175LEU 0-0.0130.00218.9680.0070.0070.0000.0000.0000.000
171A176LYS 10.9260.98017.6910.1210.1210.0000.0000.0000.000
172A177LYS 10.8270.90014.2830.0270.0270.0000.0000.0000.000
173A178ASN 00.0030.00220.9010.0180.0180.0000.0000.0000.000
174A179NME 00.0170.03920.860-0.009-0.0090.0000.0000.0000.000
175A191ACE 00.0220.00229.2670.0000.0000.0000.0000.0000.000
176A192ARG 10.8330.90724.7800.0240.0240.0000.0000.0000.000
177A193ILE 00.0300.03430.816-0.004-0.0040.0000.0000.0000.000
178A194LYS 10.7550.86425.9620.0480.0480.0000.0000.0000.000
179A195ASN 0-0.014-0.00931.3220.0000.0000.0000.0000.0000.000
180A196GLY 00.0260.01330.868-0.001-0.0010.0000.0000.0000.000
181A197ASP -1-0.837-0.89325.531-0.059-0.0590.0000.0000.0000.000
182A198SER 0-0.017-0.01122.3030.0000.0000.0000.0000.0000.000
183A199LEU 00.0340.00920.988-0.007-0.0070.0000.0000.0000.000
184A200ALA 00.0420.02418.328-0.012-0.0120.0000.0000.0000.000
185A201GLU -1-0.742-0.87319.669-0.061-0.0610.0000.0000.0000.000
186A202TYR 0-0.021-0.00821.709-0.012-0.0120.0000.0000.0000.000
187A203ILE 00.026-0.00118.383-0.007-0.0070.0000.0000.0000.000
188A204TRP 0-0.005-0.00416.690-0.001-0.0010.0000.0000.0000.000
189A205LYS 10.7950.89019.1900.0650.0650.0000.0000.0000.000
190A206TYR 0-0.050-0.02422.5100.0020.0020.0000.0000.0000.000
191A207TYR 0-0.021-0.02021.2280.0070.0070.0000.0000.0000.000
192A208ALA 0-0.0010.00615.906-0.010-0.0100.0000.0000.0000.000
193A209ASP -1-0.749-0.84915.432-0.294-0.2940.0000.0000.0000.000
194A210SER 00.0040.00112.172-0.009-0.0090.0000.0000.0000.000
195A211LEU 0-0.043-0.02411.3040.0260.0260.0000.0000.0000.000
196A212PHE 0-0.025-0.0112.678-0.630-0.4120.383-0.287-0.314-0.002
197A213GLU -2-1.746-1.9016.1260.3280.3280.0000.0000.0000.000