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: 2JZ9R

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 OptH
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 -3028409.112671
FMO2-HF: Nuclear repulsion 2936852.808285
FMO2-HF: Total energy -91556.304386
FMO2-MP2: Total energy -91826.27953


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.
-5.260.1580.814-2.374-3.855-0.016
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 : -0.018 / q_NPA : -0.023
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].
3A12HIS0-0.0090.0123.045-2.4200.0590.163-1.190-1.453-0.004
4A13PHE00.0340.0224.7750.3620.453-0.001-0.009-0.0800.000
5A14VAL00.000-0.0107.995-0.046-0.0460.0000.0000.0000.000
6A15PHE00.006-0.00710.0930.0710.0710.0000.0000.0000.000
7A16VAL00.007-0.00514.0020.0020.0020.0000.0000.0000.000
8A17HIS0-0.0010.01217.5650.0110.0110.0000.0000.0000.000
9A18GLY00.1140.04720.3360.0050.0050.0000.0000.0000.000
10A19ALA00.0330.00823.861-0.005-0.0050.0000.0000.0000.000
11A20SER0-0.011-0.00227.2870.0030.0030.0000.0000.0000.000
12A21HIS0-0.033-0.01223.2000.0010.0010.0000.0000.0000.000
13A22GLY00.0470.00122.0480.0020.0020.0000.0000.0000.000
14A23ALA00.017-0.00816.945-0.003-0.0030.0000.0000.0000.000
15A24TRP00.0210.00017.742-0.017-0.0170.0000.0000.0000.000
16A25CYS0-0.049-0.01219.9970.0030.0030.0000.0000.0000.000
17A26TRP00.0420.01615.0010.0100.0100.0000.0000.0000.000
18A27TYR0-0.058-0.04915.495-0.027-0.0270.0000.0000.0000.000
19A28LYS10.8670.95216.3080.1080.1080.0000.0000.0000.000
20A29LEU00.0010.00213.1790.0010.0010.0000.0000.0000.000
21A30THR0-0.015-0.02210.826-0.013-0.0130.0000.0000.0000.000
22A31THR00.0540.03510.688-0.058-0.0580.0000.0000.0000.000
23A32LEU0-0.048-0.01911.9730.0020.0020.0000.0000.0000.000
24A33LEU0-0.015-0.0188.1180.0230.0230.0000.0000.0000.000
25A34ASP-1-0.885-0.9267.269-0.789-0.7890.0000.0000.0000.000
26A35ALA0-0.075-0.0347.655-0.027-0.0270.0000.0000.0000.000
27A36ALA0-0.073-0.0308.4330.0770.0770.0000.0000.0000.000
28A37GLY0-0.024-0.0025.0520.1360.197-0.001-0.008-0.0520.000
29A38PHE0-0.039-0.0262.780-3.096-1.2650.427-0.888-1.369-0.011
30A39LYS10.9891.0042.9250.5461.4740.226-0.276-0.877-0.001
31A40SER00.021-0.0024.251-0.0280.0000.000-0.003-0.0240.000
32A41THR0-0.040-0.0287.6630.0640.0640.0000.0000.0000.000
33A42SER0-0.0040.00410.4280.0420.0420.0000.0000.0000.000
34A43VAL0-0.015-0.00413.9390.0070.0070.0000.0000.0000.000
35A44ASP-1-0.799-0.89416.702-0.202-0.2020.0000.0000.0000.000
36A45LEU0-0.033-0.02420.361-0.003-0.0030.0000.0000.0000.000
37A46THR0-0.033-0.04022.3830.0020.0020.0000.0000.0000.000
38A47GLY00.015-0.00125.6640.0090.0090.0000.0000.0000.000
39A48ALA0-0.020-0.00523.8250.0090.0090.0000.0000.0000.000
40A49GLY00.0330.01423.079-0.009-0.0090.0000.0000.0000.000
41A50ILE0-0.062-0.01921.8540.0160.0160.0000.0000.0000.000
42A51SER0-0.0130.01424.8030.0060.0060.0000.0000.0000.000
43A52LEU00.0340.00325.8690.0100.0100.0000.0000.0000.000
44A53ILE0-0.035-0.00427.6890.0090.0090.0000.0000.0000.000
45A54ASP-1-0.806-0.88830.060-0.091-0.0910.0000.0000.0000.000
46A55SER00.045-0.01930.1680.0010.0010.0000.0000.0000.000
47A56ASN0-0.048-0.04331.8190.0060.0060.0000.0000.0000.000
48A57ILE0-0.025-0.01133.6030.0050.0050.0000.0000.0000.000
49A58VAL0-0.069-0.02729.175-0.002-0.0020.0000.0000.0000.000
50A59PHE0-0.029-0.03332.4870.0010.0010.0000.0000.0000.000
51A60ASP-1-0.841-0.91831.320-0.084-0.0840.0000.0000.0000.000
52A61SER00.0370.01628.013-0.011-0.0110.0000.0000.0000.000
53A62ASP-1-0.861-0.94126.778-0.117-0.1170.0000.0000.0000.000
54A63GLN0-0.093-0.04626.499-0.009-0.0090.0000.0000.0000.000
55A64TYR00.0260.00724.996-0.011-0.0110.0000.0000.0000.000
56A65ASN00.1000.06422.531-0.022-0.0220.0000.0000.0000.000
57A66ARG10.9651.00521.6490.1250.1250.0000.0000.0000.000
58A67PRO0-0.002-0.00120.058-0.015-0.0150.0000.0000.0000.000
59A68LEU00.0230.01816.014-0.031-0.0310.0000.0000.0000.000
60A69PHE00.008-0.02317.278-0.025-0.0250.0000.0000.0000.000
61A70SER0-0.019-0.01119.0110.0000.0000.0000.0000.0000.000
62A71LEU0-0.0190.00311.720-0.015-0.0150.0000.0000.0000.000
63A72LEU00.009-0.00613.385-0.052-0.0520.0000.0000.0000.000
64A73SER0-0.020-0.01715.3500.0090.0090.0000.0000.0000.000
65A74ASP-1-0.948-0.96415.280-0.279-0.2790.0000.0000.0000.000
66A75LEU0-0.079-0.0249.705-0.070-0.0700.0000.0000.0000.000
67A76PRO0-0.020-0.0279.3420.0750.0750.0000.0000.0000.000
68A77PRO0-0.006-0.00811.796-0.013-0.0130.0000.0000.0000.000
69A78HIS00.0170.0079.6830.0480.0480.0000.0000.0000.000
70A79HIS0-0.043-0.0076.3240.1270.1270.0000.0000.0000.000
71A80LYS10.9670.9957.4590.1030.1030.0000.0000.0000.000
72A81VAL0-0.035-0.0127.629-0.344-0.3440.0000.0000.0000.000
73A82ILE0-0.0040.0058.4270.2040.2040.0000.0000.0000.000
74A83LEU00.0120.00710.543-0.075-0.0750.0000.0000.0000.000
75A84VAL00.0250.01512.2380.0580.0580.0000.0000.0000.000
76A85GLY00.0310.01814.931-0.021-0.0210.0000.0000.0000.000
77A86HIS0-0.031-0.01218.4390.0080.0080.0000.0000.0000.000
78A87SER00.0290.02621.0970.0000.0000.0000.0000.0000.000
79A88ILE00.018-0.00324.6340.0000.0000.0000.0000.0000.000
80A89GLY00.0310.02021.6750.0000.0000.0000.0000.0000.000
81A90GLY0-0.044-0.02621.432-0.012-0.0120.0000.0000.0000.000
82A91GLY00.0620.03322.4560.0020.0020.0000.0000.0000.000
83A92SER0-0.030-0.04621.3680.0050.0050.0000.0000.0000.000
84A93VAL0-0.052-0.01317.603-0.013-0.0130.0000.0000.0000.000
85A94THR00.0610.03419.769-0.003-0.0030.0000.0000.0000.000
86A95GLU-1-0.878-0.93222.402-0.099-0.0990.0000.0000.0000.000
87A96ALA0-0.046-0.04118.4000.0020.0020.0000.0000.0000.000
88A97LEU0-0.023-0.00517.976-0.010-0.0100.0000.0000.0000.000
89A98CYS0-0.049-0.01719.8350.0200.0200.0000.0000.0000.000
90A99LYS10.8970.96222.0940.1170.1170.0000.0000.0000.000
91A100PHE0-0.012-0.01217.255-0.007-0.0070.0000.0000.0000.000
92A101THR00.0290.02417.007-0.022-0.0220.0000.0000.0000.000
93A102ASP-1-0.898-0.94316.213-0.044-0.0440.0000.0000.0000.000
94A103LYS10.8300.91513.0060.2810.2810.0000.0000.0000.000
95A104ILE0-0.033-0.01212.409-0.101-0.1010.0000.0000.0000.000
96A105SER0-0.083-0.04610.3200.0870.0870.0000.0000.0000.000
97A106MET00.0130.00612.0080.0800.0800.0000.0000.0000.000
98A107ALA00.0130.02713.691-0.074-0.0740.0000.0000.0000.000
99A108ILE0-0.030-0.02713.2090.0370.0370.0000.0000.0000.000
100A109TYR0-0.015-0.03216.816-0.025-0.0250.0000.0000.0000.000
101A110LEU0-0.016-0.00518.7350.0170.0170.0000.0000.0000.000
102A111ALA00.0320.00620.707-0.008-0.0080.0000.0000.0000.000
103A112ALA0-0.046-0.01922.115-0.003-0.0030.0000.0000.0000.000
104A113SER00.002-0.00524.1450.0130.0130.0000.0000.0000.000
105A114MET0-0.034-0.01123.692-0.010-0.0100.0000.0000.0000.000
106A115VAL00.0140.01025.4600.0110.0110.0000.0000.0000.000
107A116GLN0-0.029-0.02927.296-0.006-0.0060.0000.0000.0000.000
108A117PRO0-0.006-0.01826.0890.0000.0000.0000.0000.0000.000
109A118GLY00.0100.00629.0100.0070.0070.0000.0000.0000.000
110A119SER0-0.072-0.01832.0300.0050.0050.0000.0000.0000.000
111A135ILE00.0000.00137.7910.0010.0010.0000.0000.0000.000
112A136TRP00.0310.00233.030-0.004-0.0040.0000.0000.0000.000
113A137GLU-1-0.947-0.97738.469-0.057-0.0570.0000.0000.0000.000
114A138TYR0-0.006-0.02238.526-0.002-0.0020.0000.0000.0000.000
115A139THR0-0.0140.00338.3730.0010.0010.0000.0000.0000.000
116A140TYR00.013-0.00540.353-0.001-0.0010.0000.0000.0000.000
117A141GLY00.0130.00540.5570.0020.0020.0000.0000.0000.000
118A142GLU-1-0.927-0.96541.584-0.058-0.0580.0000.0000.0000.000
119A143GLY00.0160.01444.0710.0030.0030.0000.0000.0000.000
120A144THR0-0.010-0.03246.141-0.001-0.0010.0000.0000.0000.000
121A145ASP-1-0.936-0.95548.004-0.040-0.0400.0000.0000.0000.000
122A146LYS10.9220.97944.7620.0460.0460.0000.0000.0000.000
123A147PRO00.0140.00241.9780.0000.0000.0000.0000.0000.000
124A148PRO00.0010.01139.806-0.001-0.0010.0000.0000.0000.000
125A149THR0-0.013-0.02137.5640.0010.0010.0000.0000.0000.000
126A150GLY00.0080.01335.230-0.005-0.0050.0000.0000.0000.000
127A151VAL0-0.048-0.02133.7220.0050.0050.0000.0000.0000.000
128A152LEU00.0500.02632.707-0.007-0.0070.0000.0000.0000.000
129A153MET0-0.0230.02533.4170.0050.0050.0000.0000.0000.000
130A154LYS10.9430.97935.6700.0450.0450.0000.0000.0000.000
131A155PRO00.0610.02336.494-0.001-0.0010.0000.0000.0000.000
132A156GLU-1-0.926-0.96837.281-0.051-0.0510.0000.0000.0000.000
133A157PHE0-0.028-0.02237.8860.0030.0030.0000.0000.0000.000
134A158ILE00.0230.00832.1760.0000.0000.0000.0000.0000.000
135A159ARG10.9640.98332.8180.0490.0490.0000.0000.0000.000
136A160HIS0-0.022-0.01333.5150.0010.0010.0000.0000.0000.000
137A161TYR00.0250.00133.6910.0020.0020.0000.0000.0000.000
138A162TYR00.0320.01728.886-0.001-0.0010.0000.0000.0000.000
139A163TYR0-0.029-0.01526.511-0.001-0.0010.0000.0000.0000.000
140A164SER0-0.0190.01230.0140.0000.0000.0000.0000.0000.000
141A165GLN0-0.048-0.03628.9480.0060.0060.0000.0000.0000.000
142A166SER0-0.046-0.03827.296-0.005-0.0050.0000.0000.0000.000
143A167PRO0-0.013-0.00226.1760.0060.0060.0000.0000.0000.000
144A168LEU00.039-0.00429.325-0.003-0.0030.0000.0000.0000.000
145A169GLU-1-0.921-0.95726.905-0.095-0.0950.0000.0000.0000.000
146A170ASP-1-0.706-0.84425.044-0.122-0.1220.0000.0000.0000.000
147A171VAL0-0.037-0.00627.498-0.003-0.0030.0000.0000.0000.000
148A172THR0-0.047-0.02230.5110.0010.0010.0000.0000.0000.000
149A173LEU00.0060.00623.7700.0000.0000.0000.0000.0000.000
150A174SER00.0460.00927.079-0.006-0.0060.0000.0000.0000.000
151A175SER0-0.090-0.03828.3740.0010.0010.0000.0000.0000.000
152A176LYS10.8700.93630.3800.0850.0850.0000.0000.0000.000
153A177LEU0-0.006-0.00924.694-0.004-0.0040.0000.0000.0000.000
154A178LEU0-0.063-0.01027.916-0.004-0.0040.0000.0000.0000.000
155A179ARG10.8270.91927.3970.1320.1320.0000.0000.0000.000
156A180PRO00.0210.00630.573-0.001-0.0010.0000.0000.0000.000
157A181ALA00.0050.01830.051-0.007-0.0070.0000.0000.0000.000
158A182PRO00.0480.03229.2040.0070.0070.0000.0000.0000.000
159A183MET0-0.023-0.00631.9890.0010.0010.0000.0000.0000.000
160A184ARG10.8210.90734.2590.0620.0620.0000.0000.0000.000
161A185ALA00.0630.04829.8710.0020.0020.0000.0000.0000.000
162A186PHE0-0.010-0.02727.764-0.001-0.0010.0000.0000.0000.000
163A187GLN0-0.059-0.02331.3780.0030.0030.0000.0000.0000.000
164A188ASP-1-0.904-0.95931.920-0.064-0.0640.0000.0000.0000.000
165A189LEU0-0.060-0.01826.289-0.002-0.0020.0000.0000.0000.000
166A190ASP-1-0.855-0.93626.853-0.074-0.0740.0000.0000.0000.000
167A191LYS10.8630.95729.2600.0630.0630.0000.0000.0000.000
168A192LEU00.004-0.00726.211-0.001-0.0010.0000.0000.0000.000
169A193PRO0-0.009-0.00130.2780.0060.0060.0000.0000.0000.000
170A194PRO00.0410.01130.012-0.003-0.0030.0000.0000.0000.000
171A195ASN00.0250.00724.7620.0060.0060.0000.0000.0000.000
172A196PRO00.0260.00926.1090.0010.0010.0000.0000.0000.000
173A197GLU-1-0.866-0.94721.5090.0290.0290.0000.0000.0000.000
174A198ALA00.015-0.00321.4800.0050.0050.0000.0000.0000.000
175A199GLU-1-0.865-0.91221.996-0.005-0.0050.0000.0000.0000.000
176A200LYS10.8050.92020.866-0.022-0.0220.0000.0000.0000.000
177A201VAL0-0.0340.00416.2010.0240.0240.0000.0000.0000.000
178A202PRO00.0000.01515.843-0.009-0.0090.0000.0000.0000.000
179A203ARG10.9230.96017.486-0.012-0.0120.0000.0000.0000.000
180A204VAL0-0.006-0.01117.0310.0250.0250.0000.0000.0000.000
181A205TYR00.0230.01019.365-0.026-0.0260.0000.0000.0000.000
182A206ILE0-0.039-0.03317.3230.0140.0140.0000.0000.0000.000
183A207LYS10.8900.92021.8360.0040.0040.0000.0000.0000.000
184A208THR0-0.062-0.02124.3140.0030.0030.0000.0000.0000.000
185A209ALA00.0090.00926.6030.0010.0010.0000.0000.0000.000
186A210LYS10.8840.95529.6610.0310.0310.0000.0000.0000.000
187A211ASP-1-0.723-0.84128.280-0.069-0.0690.0000.0000.0000.000
188A212ASN0-0.044-0.02730.8530.0050.0050.0000.0000.0000.000
189A213LEU0-0.064-0.03030.1360.0010.0010.0000.0000.0000.000
190A214PHE0-0.089-0.03027.5570.0030.0030.0000.0000.0000.000
191A215ASP-1-0.820-0.93231.112-0.027-0.0270.0000.0000.0000.000
192A216SER00.0590.01831.5650.0000.0000.0000.0000.0000.000
193A217VAL00.0130.01532.2620.0020.0020.0000.0000.0000.000
194A218ARG10.9420.96332.8690.0360.0360.0000.0000.0000.000
195A219GLN00.0160.00927.192-0.002-0.0020.0000.0000.0000.000
196A220ASP-1-0.814-0.88529.431-0.011-0.0110.0000.0000.0000.000
197A221LEU0-0.002-0.00231.4880.0030.0030.0000.0000.0000.000
198A222LEU0-0.049-0.01927.5040.0010.0010.0000.0000.0000.000
199A223VAL0-0.033-0.01426.4570.0020.0020.0000.0000.0000.000
200A224GLU-1-0.960-0.98528.6350.0030.0030.0000.0000.0000.000
201A225ASN0-0.036-0.02031.9330.0060.0060.0000.0000.0000.000
202A226TRP0-0.043-0.01724.043-0.004-0.0040.0000.0000.0000.000
203A227PRO00.0260.01726.906-0.003-0.0030.0000.0000.0000.000
204A228PRO0-0.044-0.00222.4170.0020.0020.0000.0000.0000.000
205A229SER0-0.014-0.01219.8850.0070.0070.0000.0000.0000.000
206A230GLN00.0100.04516.2940.0060.0060.0000.0000.0000.000
207A231LEU00.0470.02321.762-0.015-0.0150.0000.0000.0000.000
208A232TYR0-0.108-0.08317.9860.0110.0110.0000.0000.0000.000
209A233VAL00.0530.01722.976-0.010-0.0100.0000.0000.0000.000
210A234LEU0-0.042-0.02520.9580.0040.0040.0000.0000.0000.000
211A235GLU-1-0.885-0.96425.023-0.009-0.0090.0000.0000.0000.000
212A236ASP-1-0.932-0.97127.366-0.024-0.0240.0000.0000.0000.000
213A237SER0-0.057-0.04324.774-0.008-0.0080.0000.0000.0000.000
214A238ASP-1-0.733-0.82826.804-0.071-0.0710.0000.0000.0000.000
215A239HIS0-0.041-0.03726.719-0.009-0.0090.0000.0000.0000.000
216A240SER0-0.008-0.01824.139-0.011-0.0110.0000.0000.0000.000
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