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: 6NJKZ

Calculation Name: 5HK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HK8

Chain ID: A

ChEMBL ID:

UniProt ID: O23512

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3029860.214318
FMO2-HF: Nuclear repulsion 2938303.137466
FMO2-HF: Total energy -91557.076852
FMO2-MP2: Total energy -91827.189085


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:10:VAL)


Summations of interaction energy for fragment #1(A:10: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.
-5.3140.0530.753-2.345-3.773-0.014
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.026
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].
3A12HIS00.0250.0243.136-2.2560.1480.114-1.139-1.378-0.002
4A13PHE00.0460.0274.8140.3140.406-0.001-0.009-0.0820.000
5A14VAL00.005-0.0128.048-0.046-0.0460.0000.0000.0000.000
6A15PHE0-0.002-0.00610.0250.0640.0640.0000.0000.0000.000
7A16VAL00.005-0.00614.0370.0000.0000.0000.0000.0000.000
8A17HIS0-0.0040.00917.5960.0100.0100.0000.0000.0000.000
9A18GLY00.1240.05520.3680.0060.0060.0000.0000.0000.000
10A19ALA00.0270.00723.899-0.005-0.0050.0000.0000.0000.000
11A20SER0-0.019-0.00927.3180.0030.0030.0000.0000.0000.000
12A21HIS0-0.023-0.00123.2480.0000.0000.0000.0000.0000.000
13A22GLY00.0520.00722.0570.0020.0020.0000.0000.0000.000
14A23ALA00.0260.00316.974-0.003-0.0030.0000.0000.0000.000
15A24TRP00.016-0.01017.753-0.016-0.0160.0000.0000.0000.000
16A25CYS0-0.071-0.02520.0800.0010.0010.0000.0000.0000.000
17A26TRP00.0310.00915.0590.0070.0070.0000.0000.0000.000
18A27TYR0-0.036-0.02915.528-0.023-0.0230.0000.0000.0000.000
19A28LYS10.8190.91216.3310.1030.1030.0000.0000.0000.000
20A29LEU00.0140.00813.385-0.002-0.0020.0000.0000.0000.000
21A30THR00.024-0.00610.8970.0030.0030.0000.0000.0000.000
22A31THR00.0040.01010.702-0.059-0.0590.0000.0000.0000.000
23A32LEU0-0.045-0.01611.924-0.005-0.0050.0000.0000.0000.000
24A33LEU0-0.010-0.0138.2000.0140.0140.0000.0000.0000.000
25A34ASP-1-0.897-0.9367.237-0.762-0.7620.0000.0000.0000.000
26A35ALA0-0.061-0.0257.612-0.049-0.0490.0000.0000.0000.000
27A36ALA0-0.066-0.0288.4280.0670.0670.0000.0000.0000.000
28A37GLY0-0.024-0.0035.0400.1150.177-0.001-0.008-0.0530.000
29A38PHE0-0.035-0.0232.780-3.241-1.3690.418-0.918-1.371-0.011
30A39LYS10.9210.9732.9540.3931.3090.223-0.267-0.872-0.001
31A40SER00.0320.0064.248-0.026-0.0050.000-0.004-0.0170.000
32A41THR0-0.053-0.0357.6740.0340.0340.0000.0000.0000.000
33A42SER00.0160.01410.4150.0180.0180.0000.0000.0000.000
34A43VAL0-0.0100.00013.9390.0050.0050.0000.0000.0000.000
35A44ASP-1-0.795-0.88216.692-0.177-0.1770.0000.0000.0000.000
36A45LEU0-0.026-0.01920.160-0.001-0.0010.0000.0000.0000.000
37A46THR0-0.032-0.04422.3780.0010.0010.0000.0000.0000.000
38A47GLY00.0180.00225.6490.0080.0080.0000.0000.0000.000
39A48ALA0-0.028-0.01123.9860.0080.0080.0000.0000.0000.000
40A49GLY00.0310.01423.063-0.008-0.0080.0000.0000.0000.000
41A50ILE0-0.068-0.03021.9300.0140.0140.0000.0000.0000.000
42A51SER00.0010.02024.7670.0050.0050.0000.0000.0000.000
43A52LEU00.019-0.00225.8400.0090.0090.0000.0000.0000.000
44A53ILE0-0.033-0.00427.8210.0080.0080.0000.0000.0000.000
45A54ASP-1-0.789-0.88930.039-0.079-0.0790.0000.0000.0000.000
46A55SER00.033-0.01830.1710.0010.0010.0000.0000.0000.000
47A56ASN0-0.042-0.02531.8120.0060.0060.0000.0000.0000.000
48A57ILE0-0.012-0.00333.6440.0040.0040.0000.0000.0000.000
49A58VAL0-0.063-0.02429.106-0.001-0.0010.0000.0000.0000.000
50A59PHE0-0.020-0.02432.4790.0010.0010.0000.0000.0000.000
51A60ASP-1-0.783-0.90430.922-0.074-0.0740.0000.0000.0000.000
52A61SER00.0410.02327.919-0.010-0.0100.0000.0000.0000.000
53A62ASP-1-0.818-0.91326.780-0.107-0.1070.0000.0000.0000.000
54A63GLN0-0.064-0.03026.487-0.007-0.0070.0000.0000.0000.000
55A64TYR00.0180.00724.640-0.010-0.0100.0000.0000.0000.000
56A65ASN00.0690.03722.637-0.020-0.0200.0000.0000.0000.000
57A66ARG10.8850.95721.6400.0990.0990.0000.0000.0000.000
58A67PRO00.0080.00520.046-0.012-0.0120.0000.0000.0000.000
59A68LEU00.0170.01515.914-0.028-0.0280.0000.0000.0000.000
60A69PHE00.005-0.02117.264-0.020-0.0200.0000.0000.0000.000
61A70SER00.0000.00719.0050.0030.0030.0000.0000.0000.000
62A71LEU0-0.0160.00411.687-0.016-0.0160.0000.0000.0000.000
63A72LEU00.005-0.00313.299-0.044-0.0440.0000.0000.0000.000
64A73SER00.009-0.00615.3380.0110.0110.0000.0000.0000.000
65A74ASP-1-0.946-0.96815.371-0.235-0.2350.0000.0000.0000.000
66A75LEU0-0.075-0.0199.734-0.062-0.0620.0000.0000.0000.000
67A76PRO00.014-0.0089.4090.0710.0710.0000.0000.0000.000
68A77PRO0-0.009-0.01011.809-0.005-0.0050.0000.0000.0000.000
69A78HIS00.0140.0099.7790.0540.0540.0000.0000.0000.000
70A79HIS0-0.038-0.0076.0290.1830.1830.0000.0000.0000.000
71A80LYS10.8980.9577.5290.0400.0400.0000.0000.0000.000
72A81VAL0-0.043-0.0187.696-0.293-0.2930.0000.0000.0000.000
73A82ILE00.0030.0178.4710.1830.1830.0000.0000.0000.000
74A83LEU00.0130.00910.610-0.076-0.0760.0000.0000.0000.000
75A84VAL00.0230.01112.2350.0510.0510.0000.0000.0000.000
76A85GLY00.0320.02214.996-0.021-0.0210.0000.0000.0000.000
77A86HIS0-0.028-0.01418.4960.0070.0070.0000.0000.0000.000
78A87SER00.0200.01821.157-0.001-0.0010.0000.0000.0000.000
79A88ILE00.0220.00024.6920.0010.0010.0000.0000.0000.000
80A89GLY00.0300.02221.7180.0010.0010.0000.0000.0000.000
81A90GLY0-0.045-0.02721.476-0.009-0.0090.0000.0000.0000.000
82A91GLY00.0700.03722.5120.0030.0030.0000.0000.0000.000
83A92SER0-0.048-0.04221.2720.0050.0050.0000.0000.0000.000
84A93VAL0-0.049-0.01917.514-0.009-0.0090.0000.0000.0000.000
85A94THR00.0780.04919.8120.0010.0010.0000.0000.0000.000
86A95GLU-1-0.828-0.90422.450-0.077-0.0770.0000.0000.0000.000
87A96ALA0-0.030-0.02518.3000.0020.0020.0000.0000.0000.000
88A97LEU0-0.014-0.00617.928-0.006-0.0060.0000.0000.0000.000
89A98CYS0-0.068-0.02219.8730.0200.0200.0000.0000.0000.000
90A99LYS10.8030.91022.0610.0990.0990.0000.0000.0000.000
91A100PHE0-0.003-0.00717.328-0.007-0.0070.0000.0000.0000.000
92A101THR00.0250.01117.074-0.014-0.0140.0000.0000.0000.000
93A102ASP-1-0.899-0.94516.2960.0050.0050.0000.0000.0000.000
94A103LYS10.7700.87713.0680.2500.2500.0000.0000.0000.000
95A104ILE0-0.017-0.00512.477-0.081-0.0810.0000.0000.0000.000
96A105SER0-0.072-0.03610.3900.0740.0740.0000.0000.0000.000
97A106MET00.010-0.00112.0070.0690.0690.0000.0000.0000.000
98A107ALA00.0100.02513.762-0.066-0.0660.0000.0000.0000.000
99A108ILE0-0.026-0.02713.3010.0300.0300.0000.0000.0000.000
100A109TYR0-0.024-0.03916.901-0.024-0.0240.0000.0000.0000.000
101A110LEU0-0.019-0.00718.3280.0140.0140.0000.0000.0000.000
102A111ALA00.0280.00420.788-0.007-0.0070.0000.0000.0000.000
103A112ALA0-0.053-0.02022.206-0.003-0.0030.0000.0000.0000.000
104A113SER00.001-0.00424.2160.0120.0120.0000.0000.0000.000
105A114MET0-0.032-0.00623.849-0.008-0.0080.0000.0000.0000.000
106A115VAL00.0160.01025.5310.0080.0080.0000.0000.0000.000
107A116GLN0-0.018-0.00727.357-0.005-0.0050.0000.0000.0000.000
108A117PRO00.003-0.01526.096-0.001-0.0010.0000.0000.0000.000
109A118GLY00.0020.00529.0630.0060.0060.0000.0000.0000.000
110A119SER0-0.067-0.01831.9250.0030.0030.0000.0000.0000.000
111A135ILE00.0000.01538.0280.0000.0000.0000.0000.0000.000
112A136TRP00.0320.01033.162-0.004-0.0040.0000.0000.0000.000
113A137GLU-1-0.940-0.97738.508-0.049-0.0490.0000.0000.0000.000
114A138TYR0-0.001-0.02038.548-0.002-0.0020.0000.0000.0000.000
115A139THR0-0.022-0.00238.4060.0010.0010.0000.0000.0000.000
116A140TYR00.015-0.00440.362-0.001-0.0010.0000.0000.0000.000
117A141GLY00.0170.00640.5510.0010.0010.0000.0000.0000.000
118A142GLU-1-0.846-0.90341.485-0.048-0.0480.0000.0000.0000.000
119A143GLY00.0130.00944.0660.0020.0020.0000.0000.0000.000
120A144THR00.003-0.02746.144-0.001-0.0010.0000.0000.0000.000
121A145ASP-1-0.882-0.91948.011-0.034-0.0340.0000.0000.0000.000
122A146LYS10.8460.93644.8500.0370.0370.0000.0000.0000.000
123A147PRO00.0220.00542.0370.0000.0000.0000.0000.0000.000
124A148PRO0-0.0050.00739.924-0.001-0.0010.0000.0000.0000.000
125A149THR0-0.016-0.02437.5680.0010.0010.0000.0000.0000.000
126A150GLY00.0080.01235.242-0.004-0.0040.0000.0000.0000.000
127A151VAL0-0.042-0.02133.8340.0050.0050.0000.0000.0000.000
128A152LEU00.0480.02832.623-0.006-0.0060.0000.0000.0000.000
129A153MET0-0.0260.01833.4010.0040.0040.0000.0000.0000.000
130A154LYS10.9130.95935.7030.0390.0390.0000.0000.0000.000
131A155PRO00.0470.01436.518-0.001-0.0010.0000.0000.0000.000
132A156GLU-1-0.891-0.95737.316-0.046-0.0460.0000.0000.0000.000
133A157PHE0-0.021-0.02137.8520.0020.0020.0000.0000.0000.000
134A158ILE00.0180.00832.2170.0000.0000.0000.0000.0000.000
135A159ARG10.9630.98132.8670.0450.0450.0000.0000.0000.000
136A160HIS0-0.019-0.01033.5720.0010.0010.0000.0000.0000.000
137A161TYR00.0320.00733.7140.0020.0020.0000.0000.0000.000
138A162TYR00.0340.01428.858-0.001-0.0010.0000.0000.0000.000
139A163TYR0-0.020-0.02026.546-0.001-0.0010.0000.0000.0000.000
140A164SER00.0030.02130.0710.0000.0000.0000.0000.0000.000
141A165GLN0-0.072-0.04529.1940.0090.0090.0000.0000.0000.000
142A166SER0-0.014-0.02627.328-0.005-0.0050.0000.0000.0000.000
143A167PRO00.0060.01226.2230.0060.0060.0000.0000.0000.000
144A168LEU00.033-0.00629.377-0.003-0.0030.0000.0000.0000.000
145A169GLU-1-0.885-0.93526.424-0.095-0.0950.0000.0000.0000.000
146A170ASP-1-0.698-0.83924.734-0.114-0.1140.0000.0000.0000.000
147A171VAL0-0.0290.00627.532-0.003-0.0030.0000.0000.0000.000
148A172THR0-0.051-0.02630.5470.0010.0010.0000.0000.0000.000
149A173LEU00.0090.01623.7650.0010.0010.0000.0000.0000.000
150A174SER00.0490.00427.202-0.005-0.0050.0000.0000.0000.000
151A175SER0-0.088-0.04228.3960.0020.0020.0000.0000.0000.000
152A176LYS10.8540.92630.3560.0780.0780.0000.0000.0000.000
153A177LEU0-0.006-0.00824.740-0.004-0.0040.0000.0000.0000.000
154A178LEU0-0.060-0.00828.045-0.003-0.0030.0000.0000.0000.000
155A179ARG10.8130.91327.5870.1180.1180.0000.0000.0000.000
156A180PRO00.0240.00730.5860.0000.0000.0000.0000.0000.000
157A181ALA0-0.0030.01130.228-0.006-0.0060.0000.0000.0000.000
158A182PRO00.0450.02829.1980.0060.0060.0000.0000.0000.000
159A183MET0-0.0150.00032.0050.0010.0010.0000.0000.0000.000
160A184ARG10.7560.84734.2820.0510.0510.0000.0000.0000.000
161A185ALA00.0540.04329.8880.0020.0020.0000.0000.0000.000
162A186PHE00.005-0.02727.868-0.001-0.0010.0000.0000.0000.000
163A187GLN0-0.051-0.01331.4050.0040.0040.0000.0000.0000.000
164A188ASP-1-0.859-0.92432.254-0.047-0.0470.0000.0000.0000.000
165A189LEU0-0.063-0.01026.188-0.001-0.0010.0000.0000.0000.000
166A190ASP-1-0.857-0.94326.793-0.054-0.0540.0000.0000.0000.000
167A191LYS10.8100.91429.3030.0500.0500.0000.0000.0000.000
168A192LEU0-0.008-0.00926.302-0.001-0.0010.0000.0000.0000.000
169A193PRO00.0020.00130.2580.0050.0050.0000.0000.0000.000
170A194PRO00.0340.01030.052-0.002-0.0020.0000.0000.0000.000
171A195ASN00.0340.01124.4230.0080.0080.0000.0000.0000.000
172A196PRO00.0250.00626.2020.0020.0020.0000.0000.0000.000
173A197GLU-1-0.821-0.90421.6990.0580.0580.0000.0000.0000.000
174A198ALA00.004-0.00921.5700.0070.0070.0000.0000.0000.000
175A199GLU-1-0.844-0.90222.0940.0170.0170.0000.0000.0000.000
176A200LYS10.7600.88120.965-0.046-0.0460.0000.0000.0000.000
177A201VAL0-0.044-0.00316.2610.0250.0250.0000.0000.0000.000
178A202PRO0-0.0020.01315.863-0.012-0.0120.0000.0000.0000.000
179A203ARG10.9280.96917.559-0.033-0.0330.0000.0000.0000.000
180A204VAL0-0.017-0.01616.9040.0210.0210.0000.0000.0000.000
181A205TYR00.0160.00419.464-0.023-0.0230.0000.0000.0000.000
182A206ILE0-0.047-0.03817.3640.0110.0110.0000.0000.0000.000
183A207LYS10.8720.91121.934-0.002-0.0020.0000.0000.0000.000
184A208THR0-0.062-0.02324.3960.0020.0020.0000.0000.0000.000
185A209ALA00.0090.01126.6940.0010.0010.0000.0000.0000.000
186A210LYS10.7630.88329.7490.0290.0290.0000.0000.0000.000
187A211ASP-1-0.724-0.84428.359-0.057-0.0570.0000.0000.0000.000
188A212ASN0-0.058-0.03730.9320.0050.0050.0000.0000.0000.000
189A213LEU0-0.064-0.02930.1020.0010.0010.0000.0000.0000.000
190A214PHE0-0.075-0.02627.8060.0020.0020.0000.0000.0000.000
191A215ASP-1-0.789-0.91531.192-0.019-0.0190.0000.0000.0000.000
192A216SER00.0640.02931.6550.0010.0010.0000.0000.0000.000
193A217VAL00.008-0.00232.3540.0020.0020.0000.0000.0000.000
194A218ARG10.9390.97033.1310.0270.0270.0000.0000.0000.000
195A219GLN00.0140.01027.2710.0000.0000.0000.0000.0000.000
196A220ASP-1-0.812-0.88929.523-0.002-0.0020.0000.0000.0000.000
197A221LEU00.0110.01031.5840.0030.0030.0000.0000.0000.000
198A222LEU0-0.0180.00227.6340.0010.0010.0000.0000.0000.000
199A223VAL0-0.026-0.01726.3980.0030.0030.0000.0000.0000.000
200A224GLU-1-0.961-0.98228.7290.0120.0120.0000.0000.0000.000
201A225ASN0-0.097-0.06231.9900.0040.0040.0000.0000.0000.000
202A226TRP0-0.043-0.03123.893-0.003-0.0030.0000.0000.0000.000
203A227PRO00.0290.02026.994-0.002-0.0020.0000.0000.0000.000
204A228PRO0-0.051-0.00722.4330.0040.0040.0000.0000.0000.000
205A229SER0-0.006-0.01119.8470.0060.0060.0000.0000.0000.000
206A230GLN0-0.0100.00116.1890.0020.0020.0000.0000.0000.000
207A231LEU00.0440.02621.753-0.014-0.0140.0000.0000.0000.000
208A232TYR0-0.070-0.03717.9900.0060.0060.0000.0000.0000.000
209A233VAL00.0540.02123.085-0.009-0.0090.0000.0000.0000.000
210A234LEU0-0.035-0.01420.9770.0030.0030.0000.0000.0000.000
211A235GLU-1-0.858-0.95525.123-0.005-0.0050.0000.0000.0000.000
212A236ASP-1-0.863-0.92927.406-0.022-0.0220.0000.0000.0000.000
213A237SER0-0.032-0.02024.998-0.007-0.0070.0000.0000.0000.000
214A238ASP-1-0.748-0.82426.890-0.063-0.0630.0000.0000.0000.000
215A239HIS0-0.032-0.03326.797-0.008-0.0080.0000.0000.0000.000
216A240SER0-0.012-0.01124.203-0.009-0.0090.0000.0000.0000.000
217A241ALA00.0680.04321.294-0.004-0.0040.0000.0000.0000.000
218A242PHE0-0.026-0.02318.635-0.001-0.0010.0000.0000.0000.000
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