Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4N4VN

Calculation Name: 2D2S-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D2S

Chain ID: A

ChEMBL ID:

UniProt ID: P38261

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2489173.423586
FMO2-HF: Nuclear repulsion 2400706.839597
FMO2-HF: Total energy -88466.583989
FMO2-MP2: Total energy -88727.407501


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:524:ACE )


Summations of interaction energy for fragment #1(A:524: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.
1.782.449-0.005-0.348-0.3160
Interaction energy analysis for fragmet #1(A:524:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.035
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].
3A526MET 0-0.056-0.0213.8551.4952.164-0.005-0.348-0.3160.000
4A527SER 00.0010.0087.2130.0750.0750.0000.0000.0000.000
5A528SER 00.038-0.0039.8180.0390.0390.0000.0000.0000.000
6A529THR 00.0780.03113.4580.0100.0100.0000.0000.0000.000
7A530ALA 00.0120.0179.8600.0360.0360.0000.0000.0000.000
8A531GLN 0-0.0140.00611.8360.0390.0390.0000.0000.0000.000
9A532ARG 10.9460.96213.3700.1280.1280.0000.0000.0000.000
10A533LEU 00.0240.00013.7020.0180.0180.0000.0000.0000.000
11A534LYS 10.9940.9969.5380.0460.0460.0000.0000.0000.000
12A535PHE 00.0220.00014.6440.0030.0030.0000.0000.0000.000
13A536LEU 0-0.0190.01218.0110.0100.0100.0000.0000.0000.000
14A537ASP -1-0.889-0.92416.6130.0870.0870.0000.0000.0000.000
15A538GLU -1-0.942-0.95616.941-0.049-0.0490.0000.0000.0000.000
16A539GLY 00.027-0.00219.9880.0040.0040.0000.0000.0000.000
17A540VAL 00.020-0.01721.7970.0040.0040.0000.0000.0000.000
18A541GLU -1-0.847-0.91619.9510.0580.0580.0000.0000.0000.000
19A542GLU -1-0.940-0.96323.845-0.019-0.0190.0000.0000.0000.000
20A543ILE 0-0.0070.00326.0750.0000.0000.0000.0000.0000.000
21A544ASP -1-0.856-0.91926.6710.0360.0360.0000.0000.0000.000
22A545ILE 0-0.084-0.05126.679-0.001-0.0010.0000.0000.0000.000
23A546GLU -1-0.812-0.93830.286-0.010-0.0100.0000.0000.0000.000
24A547LEU 00.0000.00932.132-0.001-0.0010.0000.0000.0000.000
25A548ALA 0-0.078-0.02132.5500.0000.0000.0000.0000.0000.000
26A549ARG 10.8000.90730.8480.0060.0060.0000.0000.0000.000
27A550LEU 0-0.029-0.01936.532-0.002-0.0020.0000.0000.0000.000
28A551ARG 10.8970.97434.1450.0090.0090.0000.0000.0000.000
29A552PHE 00.033-0.01235.5530.0000.0000.0000.0000.0000.000
30A553GLU -1-0.911-0.94236.511-0.010-0.0100.0000.0000.0000.000
31A554SER 00.0050.00732.487-0.001-0.0010.0000.0000.0000.000
32A555ALA 0-0.0140.00131.9060.0000.0000.0000.0000.0000.000
33A556VAL 00.011-0.00231.6950.0010.0010.0000.0000.0000.000
34A557GLU -1-0.947-0.97632.572-0.016-0.0160.0000.0000.0000.000
35A558THR 00.009-0.00326.948-0.003-0.0030.0000.0000.0000.000
36A559LEU 0-0.043-0.01428.0740.0000.0000.0000.0000.0000.000
37A560LEU 00.0160.00828.5610.0020.0020.0000.0000.0000.000
38A561ASP -1-0.911-0.93026.914-0.034-0.0340.0000.0000.0000.000
39A562ILE 0-0.044-0.03922.763-0.002-0.0020.0000.0000.0000.000
40A563GLU -1-0.833-0.94424.3700.0190.0190.0000.0000.0000.000
41A564SER 0-0.025-0.01026.9590.0000.0000.0000.0000.0000.000
42A565GLN 0-0.058-0.03022.513-0.012-0.0120.0000.0000.0000.000
43A566LEU 0-0.075-0.03620.759-0.002-0.0020.0000.0000.0000.000
44A567GLU -1-0.943-0.96123.1220.0110.0110.0000.0000.0000.000
45A568ASP -1-0.895-0.92924.051-0.028-0.0280.0000.0000.0000.000
46A569LEU 0-0.162-0.08518.136-0.005-0.0050.0000.0000.0000.000
47A570SER 0-0.083-0.03919.6290.0120.0120.0000.0000.0000.000
48A571NME 0-0.0010.00121.912-0.007-0.0070.0000.0000.0000.000
49A577ACE 0-0.018-0.02112.5880.0030.0030.0000.0000.0000.000
50A578LEU 00.0330.01413.173-0.022-0.0220.0000.0000.0000.000
51A579MET 00.0130.01112.9510.0140.0140.0000.0000.0000.000
52A580LEU 00.0240.01211.483-0.006-0.0060.0000.0000.0000.000
53A581LEU 00.0790.05014.509-0.015-0.0150.0000.0000.0000.000
54A582ASN 00.008-0.01117.7110.0050.0050.0000.0000.0000.000
55A583LEU 0-0.013-0.00914.861-0.002-0.0020.0000.0000.0000.000
56A584ILE 00.0410.01516.130-0.006-0.0060.0000.0000.0000.000
57A585SER 00.001-0.00719.616-0.012-0.0120.0000.0000.0000.000
58A586LEU 0-0.0050.00221.907-0.005-0.0050.0000.0000.0000.000
59A587LYS 10.7010.82718.552-0.087-0.0870.0000.0000.0000.000
60A588ILE 00.0700.02622.990-0.006-0.0060.0000.0000.0000.000
61A589GLU -1-0.866-0.92225.7590.0330.0330.0000.0000.0000.000
62A590GLN 0-0.085-0.04025.947-0.004-0.0040.0000.0000.0000.000
63A591ARG 10.8490.92223.446-0.051-0.0510.0000.0000.0000.000
64A592ARG 10.8920.96629.118-0.022-0.0220.0000.0000.0000.000
65A593GLU -1-0.969-0.99631.3270.0290.0290.0000.0000.0000.000
66A594ALA 00.009-0.00331.726-0.003-0.0030.0000.0000.0000.000
67A595ILE 0-0.009-0.00931.313-0.003-0.0030.0000.0000.0000.000
68A596SER 00.0470.02934.940-0.003-0.0030.0000.0000.0000.000
69A597SER 0-0.0360.00437.004-0.003-0.0030.0000.0000.0000.000
70A598LYS 10.9550.97435.969-0.022-0.0220.0000.0000.0000.000
71A599LEU 00.0520.03238.047-0.002-0.0020.0000.0000.0000.000
72A600SER 00.002-0.01541.049-0.001-0.0010.0000.0000.0000.000
73A601GLN 0-0.041-0.01440.920-0.002-0.0020.0000.0000.0000.000
74A602SER 0-0.041-0.01442.723-0.001-0.0010.0000.0000.0000.000
75A603ILE 00.0110.01144.587-0.001-0.0010.0000.0000.0000.000
76A604LEU 0-0.044-0.04746.695-0.001-0.0010.0000.0000.0000.000
77A605SER 0-0.111-0.04847.4280.0000.0000.0000.0000.0000.000
78A606SER 0-0.0330.00549.020-0.001-0.0010.0000.0000.0000.000
79A607ASN 0-0.016-0.00450.4900.0010.0010.0000.0000.0000.000
80A608GLU -1-0.938-0.97551.479-0.001-0.0010.0000.0000.0000.000
81A609ILE 00.0310.00452.2750.0000.0000.0000.0000.0000.000
82A610VAL 00.0580.02149.0380.0000.0000.0000.0000.0000.000
83A611HIS 00.0200.00846.7390.0000.0000.0000.0000.0000.000
84A612LEU 00.0160.01547.3370.0000.0000.0000.0000.0000.000
85A613LYS 10.8380.95748.2850.0030.0030.0000.0000.0000.000
86A614SER 00.0530.02843.9820.0000.0000.0000.0000.0000.000
87A615GLY 0-0.0090.01443.1600.0000.0000.0000.0000.0000.000
88A616THR 00.008-0.04943.3120.0010.0010.0000.0000.0000.000
89A617GLU -1-0.854-0.94543.990-0.003-0.0030.0000.0000.0000.000
90A618ASN 0-0.036-0.01539.214-0.001-0.0010.0000.0000.0000.000
91A619MET 00.0080.00939.3320.0010.0010.0000.0000.0000.000
92A620ILE 00.001-0.00940.6620.0010.0010.0000.0000.0000.000
93A621LYS 10.9140.96737.2640.0080.0080.0000.0000.0000.000
94A622LEU 00.0150.00634.4690.0000.0000.0000.0000.0000.000
95A623GLY 0-0.007-0.00636.5470.0010.0010.0000.0000.0000.000
96A624LEU 0-0.061-0.02637.4260.0020.0020.0000.0000.0000.000
97A625PRO 00.0400.00641.3440.0000.0000.0000.0000.0000.000
98A626GLU -1-0.911-0.96344.7790.0110.0110.0000.0000.0000.000
99A627GLN 00.0450.03541.1810.0000.0000.0000.0000.0000.000
100A628ALA 00.0180.00544.2960.0000.0000.0000.0000.0000.000
101A629LEU 0-0.029-0.02445.894-0.001-0.0010.0000.0000.0000.000
102A630ASP -1-0.973-0.99148.2380.0130.0130.0000.0000.0000.000
103A631LEU 0-0.0180.00044.4760.0000.0000.0000.0000.0000.000
104A632PHE 00.009-0.00648.9370.0000.0000.0000.0000.0000.000
105A633LEU 00.009-0.00650.658-0.001-0.0010.0000.0000.0000.000
106A634GLN 00.0330.03750.2610.0000.0000.0000.0000.0000.000
107A635ASN 0-0.0100.01551.350-0.001-0.0010.0000.0000.0000.000
108A636ARG 10.8810.94453.539-0.005-0.0050.0000.0000.0000.000
109A637SER 00.023-0.00256.5220.0000.0000.0000.0000.0000.000
110A638ASN 00.0220.00553.8220.0000.0000.0000.0000.0000.000
111A639PHE 0-0.0090.00057.307-0.001-0.0010.0000.0000.0000.000
112A640ILE 0-0.045-0.03858.9120.0000.0000.0000.0000.0000.000
113A641GLN 0-0.026-0.01360.3300.0000.0000.0000.0000.0000.000
114A642ASP -1-0.873-0.93558.4550.0090.0090.0000.0000.0000.000
115A643LEU 0-0.060-0.03961.9160.0000.0000.0000.0000.0000.000
116A644ILE 0-0.047-0.03364.4720.0000.0000.0000.0000.0000.000
117A645LEU 0-0.009-0.00563.3150.0000.0000.0000.0000.0000.000
118A646GLN 0-0.0650.00264.4230.0000.0000.0000.0000.0000.000
119A647ILE 0-0.095-0.04967.566-0.001-0.0010.0000.0000.0000.000
120A648GLY 00.007-0.00571.2280.0000.0000.0000.0000.0000.000
121A649SER 0-0.018-0.00573.9270.0000.0000.0000.0000.0000.000
122A650VAL 0-0.011-0.01075.2290.0000.0000.0000.0000.0000.000
123A651ASP -1-0.946-0.94876.9070.0050.0050.0000.0000.0000.000
124A652ASN 00.017-0.02979.2180.0000.0000.0000.0000.0000.000
125A653PRO 00.0820.04680.0470.0000.0000.0000.0000.0000.000
126A654THR 00.0280.01079.8820.0000.0000.0000.0000.0000.000
127A655ASN 0-0.066-0.04278.7020.0000.0000.0000.0000.0000.000
128A656TYR 00.0510.04571.8290.0000.0000.0000.0000.0000.000
129A657LEU 00.0620.02674.7540.0000.0000.0000.0000.0000.000
130A658THR 0-0.022-0.01474.6960.0000.0000.0000.0000.0000.000
131A659GLN 00.0090.01970.1960.0000.0000.0000.0000.0000.000
132A660LEU 00.016-0.00770.5000.0000.0000.0000.0000.0000.000
133A661ALA 0-0.010-0.00569.8150.0000.0000.0000.0000.0000.000
134A662VAL 00.002-0.01469.1400.0000.0000.0000.0000.0000.000
135A663ILE 00.0210.03065.4330.0000.0000.0000.0000.0000.000
136A664ARG 10.9170.96364.059-0.007-0.0070.0000.0000.0000.000
137A665PHE 00.0280.00665.1420.0000.0000.0000.0000.0000.000
138A666GLN 0-0.0010.00965.955-0.001-0.0010.0000.0000.0000.000
139A667THR 0-0.081-0.04960.0920.0000.0000.0000.0000.0000.000
140A668ILE 0-0.0110.00461.0460.0000.0000.0000.0000.0000.000
141A669LYS 10.9180.96461.8310.0000.0000.0000.0000.0000.000
142A670LYS 10.9740.99559.274-0.003-0.0030.0000.0000.0000.000
143A671THR 0-0.043-0.02356.2180.0000.0000.0000.0000.0000.000
144A672VAL 00.0000.01057.0220.0000.0000.0000.0000.0000.000
145A673GLU -1-0.878-0.97058.2140.0000.0000.0000.0000.0000.000
146A674ASP -1-0.889-0.94954.5230.0000.0000.0000.0000.0000.000
147A675PHE 0-0.029-0.01652.7630.0000.0000.0000.0000.0000.000
148A676GLN 0-0.048-0.02453.8100.0000.0000.0000.0000.0000.000
149A677ASP -1-0.935-0.97553.438-0.004-0.0040.0000.0000.0000.000
150A678ILE 0-0.028-0.00448.494-0.001-0.0010.0000.0000.0000.000
151A679PHE 0-0.0060.00848.0280.0000.0000.0000.0000.0000.000
152A680LYS 10.9490.97950.0170.0050.0050.0000.0000.0000.000
153A681GLU -1-0.977-1.00149.099-0.006-0.0060.0000.0000.0000.000
154A682LEU 00.0040.02246.4480.0000.0000.0000.0000.0000.000
155A683GLY 00.0010.00848.9860.0010.0010.0000.0000.0000.000
156A684ALA 0-0.035-0.02751.4680.0000.0000.0000.0000.0000.000
157A685LYS 11.0060.99549.805-0.010-0.0100.0000.0000.0000.000
158A686ILE 00.0910.04947.6890.0000.0000.0000.0000.0000.000
159A687SER 00.015-0.00451.7630.0000.0000.0000.0000.0000.000
160A688SER 0-0.093-0.03655.1300.0000.0000.0000.0000.0000.000
161A689ILE 00.0530.02052.0870.0000.0000.0000.0000.0000.000
162A690LEU 0-0.0090.00655.3380.0000.0000.0000.0000.0000.000
163A691VAL 0-0.013-0.02456.5150.0000.0000.0000.0000.0000.000
164A692ASP -1-0.872-0.92857.7900.0080.0080.0000.0000.0000.000
165A693TRP 00.0400.02656.9410.0000.0000.0000.0000.0000.000
166A694CYS 0-0.065-0.03159.0650.0000.0000.0000.0000.0000.000
167A695SER 0-0.034-0.02361.9290.0000.0000.0000.0000.0000.000
168A696ASP -1-0.852-0.92660.5440.0090.0090.0000.0000.0000.000
169A697GLU -1-0.845-0.91360.6280.0080.0080.0000.0000.0000.000
170A698VAL 0-0.065-0.03163.8970.0000.0000.0000.0000.0000.000
171A699ASP -1-0.861-0.94066.0440.0070.0070.0000.0000.0000.000
172A700ASN 0-0.105-0.06962.6720.0000.0000.0000.0000.0000.000
173A701HIS 0-0.0130.00167.0490.0000.0000.0000.0000.0000.000
174A702PHE 00.0440.01269.6470.0000.0000.0000.0000.0000.000
175A703LYS 10.9560.99265.558-0.009-0.0090.0000.0000.0000.000
176A704LEU 0-0.040-0.02867.7210.0000.0000.0000.0000.0000.000
177A705ILE 0-0.047-0.01571.7690.0000.0000.0000.0000.0000.000
178A706ASP -1-0.882-0.96074.0320.0070.0070.0000.0000.0000.000
179A707LYS 10.8530.93471.046-0.009-0.0090.0000.0000.0000.000
180A708GLN 00.0960.03974.6050.0000.0000.0000.0000.0000.000
181A709LEU 0-0.114-0.03277.7930.0000.0000.0000.0000.0000.000
182A710LEU 0-0.079-0.04276.9410.0000.0000.0000.0000.0000.000
183A711ASN 0-0.090-0.07280.4050.0000.0000.0000.0000.0000.000
184A712ASP -1-0.864-0.90182.8490.0060.0060.0000.0000.0000.000
185A713GLU -1-0.949-0.96384.5120.0040.0040.0000.0000.0000.000
186A714MET 0-0.053-0.02784.3340.0000.0000.0000.0000.0000.000
187A715LEU 00.0000.03080.0630.0000.0000.0000.0000.0000.000
188A716SER 00.0490.01382.8440.0000.0000.0000.0000.0000.000
189A717PRO 00.0700.01483.5350.0000.0000.0000.0000.0000.000
190A718GLY 0-0.055-0.02084.5640.0000.0000.0000.0000.0000.000
191A719SER 0-0.014-0.00979.9020.0000.0000.0000.0000.0000.000
192A720ILE 00.0190.02279.2980.0000.0000.0000.0000.0000.000
193A721LYS 10.9680.97779.585-0.002-0.0020.0000.0000.0000.000
194A722SER 0-0.0420.00177.4440.0000.0000.0000.0000.0000.000
195A723SER 00.0880.01875.2360.0000.0000.0000.0000.0000.000
196A724ARG 10.8870.90274.968-0.003-0.0030.0000.0000.0000.000
197A725LYS 10.9801.00475.513-0.001-0.0010.0000.0000.0000.000
198A726GLN 0-0.074-0.03971.0080.0000.0000.0000.0000.0000.000
199A727ILE 00.0150.00971.3150.0000.0000.0000.0000.0000.000
200A728ASP -1-0.924-0.96871.6360.0020.0020.0000.0000.0000.000
201A729GLY 0-0.047-0.03071.7080.0000.0000.0000.0000.0000.000
202A730LEU 00.0250.01266.1250.0000.0000.0000.0000.0000.000
203A731LYS 10.8710.94967.266-0.002-0.0020.0000.0000.0000.000
204A732ALA 0-0.090-0.03368.0930.0000.0000.0000.0000.0000.000
205A733VAL 0-0.030-0.00762.6510.0000.0000.0000.0000.0000.000
206A734GLY 00.0030.00563.4330.0000.0000.0000.0000.0000.000
207A735LEU 0-0.013-0.01362.5550.0000.0000.0000.0000.0000.000
208A736ASP -1-0.883-0.95566.6260.0020.0020.0000.0000.0000.000
209A737PHE 00.0620.01364.6440.0000.0000.0000.0000.0000.000
210A738VAL 0-0.011-0.01270.4690.0000.0000.0000.0000.0000.000
211A739TYR 00.0310.01267.8930.0000.0000.0000.0000.0000.000
212A740LYS 10.9270.98466.915-0.006-0.0060.0000.0000.0000.000
213A741LEU 0-0.0350.02473.1470.0000.0000.0000.0000.0000.000
214A742ASP -1-0.829-0.91775.6790.0030.0030.0000.0000.0000.000
215A743GLU -1-0.957-0.97573.8140.0050.0050.0000.0000.0000.000
216A744PHE 00.000-0.00375.4470.0000.0000.0000.0000.0000.000
217A745ILE 0-0.029-0.00277.4310.0000.0000.0000.0000.0000.000
218A746LYS 10.9530.98080.600-0.005-0.0050.0000.0000.0000.000
219A747LYS 10.9280.96376.336-0.007-0.0070.0000.0000.0000.000
220A748ASN 0-0.031-0.02478.6430.0000.0000.0000.0000.0000.000
221A749SER 00.0080.00082.8480.0000.0000.0000.0000.0000.000
222A750ASP -1-0.953-0.98685.9910.0050.0050.0000.0000.0000.000
223A751LYS 10.8730.94581.311-0.006-0.0060.0000.0000.0000.000
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225A753ARG 00.0530.02986.0060.0000.0000.0000.0000.0000.000