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: 2JKZR

Calculation Name: 2D4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4X

Chain ID: A

ChEMBL ID:

UniProt ID: P16326

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 OptAll
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2165645.102256
FMO2-HF: Nuclear repulsion 2086244.135934
FMO2-HF: Total energy -79400.966322
FMO2-MP2: Total energy -79634.543626


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:50:VAL)


Summations of interaction energy for fragment #1(A:50: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.
-3.7980.2870.357-1.687-2.755-0.001
Interaction energy analysis for fragmet #1(A:50:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.015
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].
3A52LEU00.0100.0203.460-2.843-0.905-0.002-0.837-1.0990.001
4A53SER00.0230.0012.669-1.0490.0960.325-0.512-0.959-0.002
5A54GLN0-0.059-0.0253.121-0.4510.4510.035-0.333-0.6040.000
6A55ALA00.0500.0215.1830.2720.372-0.001-0.005-0.0930.000
7A56GLN00.008-0.0037.944-0.052-0.0520.0000.0000.0000.000
8A57ALA00.0210.0278.1490.1240.1240.0000.0000.0000.000
9A58GLN0-0.016-0.0098.2130.0420.0420.0000.0000.0000.000
10A59ASN00.0350.00211.0390.0710.0710.0000.0000.0000.000
11A60SER0-0.024-0.01512.7390.0520.0520.0000.0000.0000.000
12A61GLN0-0.018-0.01513.0670.0350.0350.0000.0000.0000.000
13A62TYR0-0.001-0.00813.4210.0130.0130.0000.0000.0000.000
14A63ALA00.0330.02917.2680.0250.0250.0000.0000.0000.000
15A64LEU0-0.0080.00917.1700.0220.0220.0000.0000.0000.000
16A65ALA0-0.008-0.00619.3960.0190.0190.0000.0000.0000.000
17A66ARG10.8520.90920.8240.1290.1290.0000.0000.0000.000
18A67THR0-0.035-0.01522.7550.0130.0130.0000.0000.0000.000
19A68PHE0-0.017-0.00924.4120.0090.0090.0000.0000.0000.000
20A69ALA00.0260.01225.5030.0100.0100.0000.0000.0000.000
21A70THR00.0500.01727.2400.0080.0080.0000.0000.0000.000
22A71GLN0-0.0200.00729.1490.0080.0080.0000.0000.0000.000
23A72LYS10.7920.90530.0330.0700.0700.0000.0000.0000.000
24A73VAL00.0870.04030.4530.0040.0040.0000.0000.0000.000
25A74SER0-0.011-0.01732.9320.0060.0060.0000.0000.0000.000
26A75LEU0-0.036-0.00735.1190.0040.0040.0000.0000.0000.000
27A76GLU-1-0.829-0.91733.946-0.052-0.0520.0000.0000.0000.000
28A77GLU-1-0.755-0.86037.260-0.027-0.0270.0000.0000.0000.000
29A78SER0-0.012-0.00839.1510.0030.0030.0000.0000.0000.000
30A79VAL0-0.014-0.00340.8640.0020.0020.0000.0000.0000.000
31A80LEU00.0380.01140.4060.0030.0030.0000.0000.0000.000
32A81SER0-0.0050.01643.2750.0040.0040.0000.0000.0000.000
33A82GLN00.0030.00345.1890.0010.0010.0000.0000.0000.000
34A83VAL00.0050.00645.3240.0020.0020.0000.0000.0000.000
35A84THR0-0.020-0.02146.2420.0020.0020.0000.0000.0000.000
36A85THR00.0180.00748.7870.0020.0020.0000.0000.0000.000
37A86ALA00.0070.02350.9300.0010.0010.0000.0000.0000.000
38A87ILE00.0240.00449.2740.0010.0010.0000.0000.0000.000
39A88GLN0-0.005-0.01252.0890.0000.0000.0000.0000.0000.000
40A89THR0-0.028-0.02154.9150.0010.0010.0000.0000.0000.000
41A90ALA00.0200.00256.1780.0010.0010.0000.0000.0000.000
42A91GLN0-0.021-0.02055.6920.0010.0010.0000.0000.0000.000
43A92GLU-1-0.810-0.87958.653-0.014-0.0140.0000.0000.0000.000
44A93LYS10.8350.92160.9520.0170.0170.0000.0000.0000.000
45A94ILE0-0.005-0.00360.0560.0010.0010.0000.0000.0000.000
46A95VAL0-0.049-0.01962.0480.0010.0010.0000.0000.0000.000
47A96TYR0-0.088-0.06664.5120.0010.0010.0000.0000.0000.000
48A97ALA0-0.003-0.00465.7180.0000.0000.0000.0000.0000.000
49A98GLY00.0080.01767.3330.0000.0000.0000.0000.0000.000
50A99ASN00.0090.02268.7100.0010.0010.0000.0000.0000.000
51A100GLY00.0350.01272.0250.0000.0000.0000.0000.0000.000
52A101THR0-0.117-0.08774.6710.0000.0000.0000.0000.0000.000
53A102LEU0-0.043-0.00370.7790.0000.0000.0000.0000.0000.000
54A103SER00.0080.00175.2890.0000.0000.0000.0000.0000.000
55A104ASP-1-0.705-0.86374.453-0.011-0.0110.0000.0000.0000.000
56A105ASP-1-0.862-0.91373.408-0.012-0.0120.0000.0000.0000.000
57A106ASP-1-0.852-0.90972.274-0.012-0.0120.0000.0000.0000.000
58A107ARG10.7980.88169.9730.0110.0110.0000.0000.0000.000
59A108ALA00.0540.02068.670-0.001-0.0010.0000.0000.0000.000
60A109SER0-0.034-0.02368.133-0.001-0.0010.0000.0000.0000.000
61A110LEU0-0.011-0.00865.863-0.001-0.0010.0000.0000.0000.000
62A111ALA0-0.007-0.00464.246-0.001-0.0010.0000.0000.0000.000
63A112THR0-0.043-0.02563.497-0.001-0.0010.0000.0000.0000.000
64A113ASP-1-0.862-0.93462.389-0.018-0.0180.0000.0000.0000.000
65A114LEU0-0.053-0.02759.445-0.001-0.0010.0000.0000.0000.000
66A115GLN0-0.046-0.03458.6520.0000.0000.0000.0000.0000.000
67A116GLY00.0240.01358.125-0.001-0.0010.0000.0000.0000.000
68A117ILE0-0.006-0.00855.108-0.001-0.0010.0000.0000.0000.000
69A118ARG10.7310.82754.3090.0220.0220.0000.0000.0000.000
70A119ASP-1-0.762-0.86353.539-0.026-0.0260.0000.0000.0000.000
71A120GLN0-0.047-0.01552.389-0.001-0.0010.0000.0000.0000.000
72A121LEU0-0.001-0.00549.620-0.002-0.0020.0000.0000.0000.000
73A122MET0-0.0230.00948.880-0.002-0.0020.0000.0000.0000.000
74A123ASN0-0.070-0.04948.396-0.003-0.0030.0000.0000.0000.000
75A124LEU0-0.0050.00646.023-0.002-0.0020.0000.0000.0000.000
76A125ALA00.0180.01644.394-0.002-0.0020.0000.0000.0000.000
77A126ASN0-0.081-0.05243.676-0.003-0.0030.0000.0000.0000.000
78A127SER00.0380.00241.799-0.002-0.0020.0000.0000.0000.000
79A128THR0-0.019-0.00939.245-0.001-0.0010.0000.0000.0000.000
80A129ASP-1-0.827-0.91434.044-0.074-0.0740.0000.0000.0000.000
81A130GLY0-0.005-0.01336.2820.0010.0010.0000.0000.0000.000
82A131ASN0-0.110-0.06132.196-0.004-0.0040.0000.0000.0000.000
83A132GLY00.0040.00535.7110.0000.0000.0000.0000.0000.000
84A133ARG10.7880.88032.5260.0830.0830.0000.0000.0000.000
85A134TYR00.028-0.00136.6320.0010.0010.0000.0000.0000.000
86A135ILE0-0.028-0.02236.127-0.002-0.0020.0000.0000.0000.000
87A136PHE00.0350.02636.4690.0000.0000.0000.0000.0000.000
88A137ALA00.0210.01037.7110.0030.0030.0000.0000.0000.000
89A138GLY00.0470.03134.5730.0000.0000.0000.0000.0000.000
90A139TYR0-0.034-0.03628.129-0.005-0.0050.0000.0000.0000.000
91A140LYS10.7840.90233.0980.0400.0400.0000.0000.0000.000
92A141THR0-0.002-0.02733.3260.0010.0010.0000.0000.0000.000
93A142GLU-1-0.767-0.83134.911-0.075-0.0750.0000.0000.0000.000
94A143ALA0-0.052-0.02438.2720.0020.0020.0000.0000.0000.000
95A144ALA00.0190.02241.2540.0000.0000.0000.0000.0000.000
96A145PRO0-0.033-0.00641.3770.0010.0010.0000.0000.0000.000
97A146PHE00.0140.01043.2610.0020.0020.0000.0000.0000.000
98A147ASP-1-0.767-0.84247.060-0.028-0.0280.0000.0000.0000.000
99A148GLN00.050-0.00250.2300.0000.0000.0000.0000.0000.000
100A149ALA0-0.029-0.01152.9420.0010.0010.0000.0000.0000.000
101A150THR0-0.052-0.04953.4100.0010.0010.0000.0000.0000.000
102A151GLY00.0470.03850.5260.0010.0010.0000.0000.0000.000
103A152GLY00.0230.01949.6960.0000.0000.0000.0000.0000.000
104A153TYR0-0.020-0.01938.893-0.002-0.0020.0000.0000.0000.000
105A154HIS10.7770.85844.2470.0320.0320.0000.0000.0000.000
106A155GLY00.0820.04340.275-0.002-0.0020.0000.0000.0000.000
107A156GLY0-0.044-0.01336.6040.0020.0020.0000.0000.0000.000
108A157GLU-1-0.857-0.93237.647-0.031-0.0310.0000.0000.0000.000
109A158LYS10.8670.91532.8400.0360.0360.0000.0000.0000.000
110A159SER00.0560.04431.658-0.001-0.0010.0000.0000.0000.000
111A160VAL0-0.0050.00528.379-0.002-0.0020.0000.0000.0000.000
112A161THR0-0.047-0.01525.8670.0040.0040.0000.0000.0000.000
113A162GLN00.0210.00421.621-0.014-0.0140.0000.0000.0000.000
114A163GLN00.0350.04218.2000.0200.0200.0000.0000.0000.000
115A164VAL00.001-0.00119.348-0.020-0.0200.0000.0000.0000.000
116A165ASP-1-0.783-0.89517.806-0.045-0.0450.0000.0000.0000.000
117A166SER0-0.0230.00214.400-0.008-0.0080.0000.0000.0000.000
118A167ALA0-0.040-0.00816.5420.0100.0100.0000.0000.0000.000
119A168ARG10.7990.87619.8540.0320.0320.0000.0000.0000.000
120A169THR0-0.015-0.02721.739-0.010-0.0100.0000.0000.0000.000
121A170MET0-0.0220.00523.4180.0080.0080.0000.0000.0000.000
122A171VAL00.006-0.00526.089-0.007-0.0070.0000.0000.0000.000
123A172ILE0-0.007-0.00726.748-0.002-0.0020.0000.0000.0000.000
124A173GLY00.0340.01830.3440.0010.0010.0000.0000.0000.000
125A174HIS00.0200.00933.2670.0000.0000.0000.0000.0000.000
126A175THR0-0.027-0.02035.9670.0000.0000.0000.0000.0000.000
127A176GLY00.0820.02238.1350.0020.0020.0000.0000.0000.000
128A177ALA0-0.004-0.00441.4730.0020.0020.0000.0000.0000.000
129A178GLN00.0250.02135.6260.0000.0000.0000.0000.0000.000
130A179ILE0-0.0010.03239.1520.0020.0020.0000.0000.0000.000
131A180PHE00.007-0.00642.9360.0020.0020.0000.0000.0000.000
132A181ASN0-0.0060.00045.4610.0010.0010.0000.0000.0000.000
133A182SER0-0.030-0.01943.9920.0010.0010.0000.0000.0000.000
134A183ILE0-0.024-0.01146.2380.0000.0000.0000.0000.0000.000
135A184THR00.0130.00244.8330.0000.0000.0000.0000.0000.000
136A185SER0-0.011-0.01646.2260.0000.0000.0000.0000.0000.000
137A186ASN0-0.064-0.04546.5060.0020.0020.0000.0000.0000.000
138A187ALA0-0.049-0.00450.3350.0000.0000.0000.0000.0000.000
139A188VAL00.005-0.00752.3250.0010.0010.0000.0000.0000.000
140A189PRO00.0310.02656.160-0.001-0.0010.0000.0000.0000.000
141A190GLU-1-0.744-0.84557.345-0.010-0.0100.0000.0000.0000.000
142A191PRO0-0.013-0.01460.3440.0010.0010.0000.0000.0000.000
143A192ASP-1-0.828-0.87362.553-0.008-0.0080.0000.0000.0000.000
144A193GLY0-0.022-0.00761.1390.0000.0000.0000.0000.0000.000
145A194SER0-0.094-0.07759.9890.0000.0000.0000.0000.0000.000
146A195ASP-1-0.920-0.97354.613-0.010-0.0100.0000.0000.0000.000
147A196SER0-0.022-0.02254.1930.0000.0000.0000.0000.0000.000
148A197GLU-1-0.815-0.89553.112-0.017-0.0170.0000.0000.0000.000
149A198LYS10.8010.86648.9350.0160.0160.0000.0000.0000.000
150A199ASN0-0.045-0.02449.582-0.001-0.0010.0000.0000.0000.000
151A200LEU00.0430.00549.5180.0010.0010.0000.0000.0000.000
152A201PHE00.0120.00748.4690.0000.0000.0000.0000.0000.000
153A202VAL00.0240.02453.6550.0010.0010.0000.0000.0000.000
154A203MET0-0.0540.02252.1100.0010.0010.0000.0000.0000.000
155A204LEU00.0100.02754.3870.0010.0010.0000.0000.0000.000
156A205ASP-1-0.754-0.85457.096-0.020-0.0200.0000.0000.0000.000
157A206THR0-0.043-0.03659.4090.0010.0010.0000.0000.0000.000
158A207ALA00.0280.02361.2220.0010.0010.0000.0000.0000.000
159A208ILE00.0010.00059.4880.0010.0010.0000.0000.0000.000
160A209ALA0-0.037-0.02563.4860.0000.0000.0000.0000.0000.000
161A210ALA00.0110.01265.4540.0000.0000.0000.0000.0000.000
162A211LEU0-0.041-0.02065.0390.0010.0010.0000.0000.0000.000
163A212LYS10.9060.95364.9050.0170.0170.0000.0000.0000.000
164A213THR0-0.061-0.01269.3160.0000.0000.0000.0000.0000.000
165A214PRO0-0.0110.01371.6360.0000.0000.0000.0000.0000.000
166A215VAL0-0.047-0.04873.6690.0000.0000.0000.0000.0000.000
167A216GLU-1-0.924-0.95276.651-0.009-0.0090.0000.0000.0000.000
168A217GLY0-0.048-0.02880.0210.0000.0000.0000.0000.0000.000
169A218ASN0-0.023-0.00978.2210.0010.0010.0000.0000.0000.000
170A219ASN00.0590.00577.8350.0000.0000.0000.0000.0000.000
171A220VAL00.0060.01176.8820.0000.0000.0000.0000.0000.000
172A221GLU-1-0.824-0.89373.362-0.010-0.0100.0000.0000.0000.000
173A222LYS10.9030.95772.9400.0080.0080.0000.0000.0000.000
174A223GLU-1-0.931-0.96072.414-0.008-0.0080.0000.0000.0000.000
175A224LYS10.8120.88569.5380.0090.0090.0000.0000.0000.000
176A225ALA00.009-0.00168.6770.0000.0000.0000.0000.0000.000
177A226ALA00.0110.01067.8000.0000.0000.0000.0000.0000.000
178A227ALA00.0360.01267.3580.0000.0000.0000.0000.0000.000
179A228ALA0-0.018-0.00664.3400.0000.0000.0000.0000.0000.000
180A229ILE0-0.001-0.00263.083-0.001-0.0010.0000.0000.0000.000
181A230ASP-1-0.845-0.90662.987-0.009-0.0090.0000.0000.0000.000
182A231LYS10.8130.89659.8000.0100.0100.0000.0000.0000.000
183A232THR0-0.002-0.01858.4150.0000.0000.0000.0000.0000.000
184A233ASN0-0.049-0.01858.2580.0000.0000.0000.0000.0000.000
185A234ARG10.7790.87057.6370.0090.0090.0000.0000.0000.000
186A235GLY00.0510.01755.0020.0000.0000.0000.0000.0000.000
187A236LEU00.038-0.00753.622-0.001-0.0010.0000.0000.0000.000
188A237LYS10.8810.95153.2490.0090.0090.0000.0000.0000.000
189A238ASN00.0080.00351.7250.0000.0000.0000.0000.0000.000
190A239SER00.0210.01249.279-0.001-0.0010.0000.0000.0000.000
191A240LEU0-0.006-0.00448.285-0.001-0.0010.0000.0000.0000.000
192A241ASN00.0270.03847.9710.0000.0000.0000.0000.0000.000
193A242ASN0-0.040-0.01243.7300.0010.0010.0000.0000.0000.000
194A243VAL00.0330.01043.809-0.001-0.0010.0000.0000.0000.000
195A244LEU0-0.013-0.00743.254-0.001-0.0010.0000.0000.0000.000
196A245THR0-0.004-0.01741.0650.0000.0000.0000.0000.0000.000
197A246VAL0-0.015-0.01338.246-0.001-0.0010.0000.0000.0000.000
198A247ARG10.8040.87438.4880.0240.0240.0000.0000.0000.000
199A248ALA0-0.0210.00638.960-0.001-0.0010.0000.0000.0000.000
200A249GLU-1-0.856-0.91735.285-0.017-0.0170.0000.0000.0000.000
201A250LEU0-0.035-0.01134.368-0.003-0.0030.0000.0000.0000.000
202A251GLY00.0070.00834.327-0.003-0.0030.0000.0000.0000.000
203A252THR0-0.031-0.03732.255-0.001-0.0010.0000.0000.0000.000
204A253GLN00.000-0.01730.278-0.005-0.0050.0000.0000.0000.000
205A254LEU0-0.016-0.01329.666-0.005-0.0050.0000.0000.0000.000
206A255SER00.0230.02030.803-0.002-0.0020.0000.0000.0000.000
207A256GLU-1-0.909-0.93126.798-0.026-0.0260.0000.0000.0000.000
208A257LEU0-0.023-0.01825.148-0.005-0.0050.0000.0000.0000.000
209A258SER0-0.025-0.00726.178-0.005-0.0050.0000.0000.0000.000
210A259THR0-0.033-0.03626.3040.0000.0000.0000.0000.0000.000
211A260LEU0-0.045-0.03821.3660.0010.0010.0000.0000.0000.000
212A261ASP-1-0.898-0.92422.440-0.114-0.1140.0000.0000.0000.000
213A262SER0-0.025-0.01324.029-0.004-0.0040.0000.0000.0000.000
214A263LEU0-0.113-0.04120.4170.0050.0050.0000.0000.0000.000