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: 4368N

Calculation Name: 2D2S-A-Xray372

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: 2023-03-13

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2479399.930753
FMO2-HF: Nuclear repulsion 2391252.860762
FMO2-HF: Total energy -88147.069991
FMO2-MP2: Total energy -88406.714904


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:525:ASP)


Summations of interaction energy for fragment #1(A:525:ASP)
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.
59.0461.447-0.023-1.219-1.1640.002
Interaction energy analysis for fragmet #1(A:525:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.932 / q_NPA : -0.976
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].
3A527SER00.0120.0083.8200.2952.702-0.023-1.219-1.1640.002
4A528SER00.0370.0016.255-1.271-1.2710.0000.0000.0000.000
5A529THR00.0550.0179.915-0.630-0.6300.0000.0000.0000.000
6A530ALA00.0220.0247.877-1.693-1.6930.0000.0000.0000.000
7A531GLN0-0.0120.0018.625-1.860-1.8600.0000.0000.0000.000
8A532ARG10.9310.94810.883-18.832-18.8320.0000.0000.0000.000
9A533LEU00.001-0.00712.373-0.894-0.8940.0000.0000.0000.000
10A534LYS10.9200.95010.213-23.022-23.0220.0000.0000.0000.000
11A535PHE00.0030.00113.213-0.646-0.6460.0000.0000.0000.000
12A536LEU0-0.0050.01816.402-0.997-0.9970.0000.0000.0000.000
13A537ASP-1-0.863-0.92515.55115.39715.3970.0000.0000.0000.000
14A538GLU-1-0.908-0.94215.05618.43018.4300.0000.0000.0000.000
15A539GLY00.0440.01318.785-0.747-0.7470.0000.0000.0000.000
16A540VAL00.012-0.02121.026-0.709-0.7090.0000.0000.0000.000
17A541GLU-1-0.761-0.85719.65413.26613.2660.0000.0000.0000.000
18A542GLU-1-0.955-0.96522.98011.63911.6390.0000.0000.0000.000
19A543ILE0-0.016-0.00424.982-0.621-0.6210.0000.0000.0000.000
20A544ASP-1-0.805-0.86326.43510.55210.5520.0000.0000.0000.000
21A545ILE0-0.073-0.04926.067-0.459-0.4590.0000.0000.0000.000
22A546GLU-1-0.717-0.82429.1159.4989.4980.0000.0000.0000.000
23A547LEU00.0130.01531.157-0.420-0.4200.0000.0000.0000.000
24A548ALA0-0.044-0.00632.061-0.336-0.3360.0000.0000.0000.000
25A549ARG10.7350.85429.198-10.332-10.3320.0000.0000.0000.000
26A550LEU0-0.034-0.02335.570-0.184-0.1840.0000.0000.0000.000
27A551ARG10.8690.93232.158-9.561-9.5610.0000.0000.0000.000
28A552PHE00.043-0.00534.3280.2610.2610.0000.0000.0000.000
29A553GLU-1-0.881-0.92235.2448.4318.4310.0000.0000.0000.000
30A554SER0-0.025-0.02731.4330.2560.2560.0000.0000.0000.000
31A555ALA0-0.0120.00530.6540.3220.3220.0000.0000.0000.000
32A556VAL00.0200.00530.4070.2940.2940.0000.0000.0000.000
33A557GLU-1-0.858-0.92331.1699.4289.4280.0000.0000.0000.000
34A558THR0-0.026-0.02125.5030.3890.3890.0000.0000.0000.000
35A559LEU0-0.027-0.01226.8320.3810.3810.0000.0000.0000.000
36A560LEU00.0120.01427.2200.1960.1960.0000.0000.0000.000
37A561ASP-1-0.907-0.92324.54612.90312.9030.0000.0000.0000.000
38A562ILE0-0.039-0.04621.2910.5330.5330.0000.0000.0000.000
39A563GLU-1-0.800-0.90622.92911.07711.0770.0000.0000.0000.000
40A564SER0-0.020-0.00825.569-0.109-0.1090.0000.0000.0000.000
41A565GLN0-0.028-0.02320.4561.1771.1770.0000.0000.0000.000
42A566LEU0-0.075-0.03019.4170.6400.6400.0000.0000.0000.000
43A567GLU-1-0.934-0.96421.84911.27411.2740.0000.0000.0000.000
44A568ASP-1-0.897-0.93121.58113.22913.2290.0000.0000.0000.000
45A569LEU0-0.157-0.08516.0470.7260.7260.0000.0000.0000.000
46A570SER0-0.081-0.03418.0530.5410.5410.0000.0000.0000.000
47A578LEU00.0380.01013.9460.3610.3610.0000.0000.0000.000
48A579MET00.0080.00313.118-0.651-0.6510.0000.0000.0000.000
49A580LEU00.0250.00910.517-0.571-0.5710.0000.0000.0000.000
50A581LEU00.0550.03913.873-0.466-0.4660.0000.0000.0000.000
51A582ASN00.011-0.00716.892-0.343-0.3430.0000.0000.0000.000
52A583LEU0-0.015-0.00715.049-0.619-0.6190.0000.0000.0000.000
53A584ILE00.0330.01114.786-0.451-0.4510.0000.0000.0000.000
54A585SER00.009-0.00118.821-0.633-0.6330.0000.0000.0000.000
55A586LEU0-0.026-0.01021.492-0.600-0.6000.0000.0000.0000.000
56A587LYS10.7460.85918.013-15.379-15.3790.0000.0000.0000.000
57A588ILE00.0470.02621.985-0.348-0.3480.0000.0000.0000.000
58A589GLU-1-0.877-0.93124.8899.7529.7520.0000.0000.0000.000
59A590GLN0-0.070-0.03425.802-0.680-0.6800.0000.0000.0000.000
60A591ARG10.7330.81922.495-12.265-12.2650.0000.0000.0000.000
61A592ARG10.8450.92428.361-10.026-10.0260.0000.0000.0000.000
62A593GLU-1-0.946-0.98730.4428.2198.2190.0000.0000.0000.000
63A594ALA00.009-0.00131.052-0.302-0.3020.0000.0000.0000.000
64A595ILE0-0.003-0.00830.340-0.314-0.3140.0000.0000.0000.000
65A596SER00.0390.02534.059-0.321-0.3210.0000.0000.0000.000
66A597SER0-0.0260.01236.368-0.373-0.3730.0000.0000.0000.000
67A598LYS10.8850.94035.770-8.334-8.3340.0000.0000.0000.000
68A599LEU00.0620.03337.215-0.253-0.2530.0000.0000.0000.000
69A600SER0-0.001-0.01040.119-0.254-0.2540.0000.0000.0000.000
70A601GLN0-0.021-0.00239.716-0.136-0.1360.0000.0000.0000.000
71A602SER0-0.047-0.01741.843-0.146-0.1460.0000.0000.0000.000
72A603ILE00.0120.00243.360-0.174-0.1740.0000.0000.0000.000
73A604LEU0-0.063-0.03845.897-0.173-0.1730.0000.0000.0000.000
74A605SER0-0.085-0.03946.575-0.133-0.1330.0000.0000.0000.000
75A606SER0-0.021-0.00348.021-0.053-0.0530.0000.0000.0000.000
76A607ASN0-0.043-0.01449.538-0.184-0.1840.0000.0000.0000.000
77A608GLU-1-0.925-0.97450.6356.1376.1370.0000.0000.0000.000
78A609ILE00.0340.00551.1440.1080.1080.0000.0000.0000.000
79A610VAL00.0710.02647.6800.1220.1220.0000.0000.0000.000
80A611HIS0-0.027-0.00846.4500.1430.1430.0000.0000.0000.000
81A612LEU00.0280.02646.1670.1370.1370.0000.0000.0000.000
82A613LYS10.7880.92547.102-6.550-6.5500.0000.0000.0000.000
83A614SER00.0630.02842.6720.1240.1240.0000.0000.0000.000
84A615GLY00.0060.02141.9990.1710.1710.0000.0000.0000.000
85A616THR00.001-0.03642.1500.1180.1180.0000.0000.0000.000
86A617GLU-1-0.805-0.91142.6617.0997.0990.0000.0000.0000.000
87A618ASN0-0.033-0.01637.9510.3220.3220.0000.0000.0000.000
88A619MET00.0040.01538.0920.2570.2570.0000.0000.0000.000
89A620ILE00.003-0.01139.5050.0660.0660.0000.0000.0000.000
90A621LYS10.7820.88835.845-8.497-8.4970.0000.0000.0000.000
91A622LEU00.0280.01333.3690.2220.2220.0000.0000.0000.000
92A623GLY0-0.011-0.00435.3340.1920.1920.0000.0000.0000.000
93A624LEU0-0.057-0.02836.331-0.059-0.0590.0000.0000.0000.000
94A625PRO00.0430.00840.258-0.161-0.1610.0000.0000.0000.000
95A626GLU-1-0.829-0.90243.6086.5246.5240.0000.0000.0000.000
96A627GLN00.0390.02540.680-0.066-0.0660.0000.0000.0000.000
97A628ALA00.0340.02443.100-0.089-0.0890.0000.0000.0000.000
98A629LEU0-0.031-0.02144.847-0.133-0.1330.0000.0000.0000.000
99A630ASP-1-0.969-0.99447.3536.2346.2340.0000.0000.0000.000
100A631LEU0-0.002-0.00143.851-0.112-0.1120.0000.0000.0000.000
101A632PHE00.009-0.00848.063-0.155-0.1550.0000.0000.0000.000
102A633LEU00.015-0.00349.652-0.131-0.1310.0000.0000.0000.000
103A634GLN00.0310.04249.617-0.167-0.1670.0000.0000.0000.000
104A635ASN0-0.0140.01050.611-0.188-0.1880.0000.0000.0000.000
105A636ARG10.8110.89752.661-5.948-5.9480.0000.0000.0000.000
106A637SER0-0.004-0.02155.623-0.138-0.1380.0000.0000.0000.000
107A638ASN00.0140.00453.136-0.175-0.1750.0000.0000.0000.000
108A639PHE00.0120.01056.463-0.117-0.1170.0000.0000.0000.000
109A640ILE0-0.038-0.03458.049-0.117-0.1170.0000.0000.0000.000
110A641GLN0-0.044-0.01759.680-0.157-0.1570.0000.0000.0000.000
111A642ASP-1-0.874-0.94157.7745.3005.3000.0000.0000.0000.000
112A643LEU0-0.052-0.03460.890-0.097-0.0970.0000.0000.0000.000
113A644ILE0-0.061-0.03563.662-0.107-0.1070.0000.0000.0000.000
114A645LEU0-0.017-0.00762.842-0.088-0.0880.0000.0000.0000.000
115A646GLN0-0.0650.00163.501-0.116-0.1160.0000.0000.0000.000
116A647ILE0-0.081-0.05066.860-0.041-0.0410.0000.0000.0000.000
117A648GLY0-0.012-0.01170.502-0.027-0.0270.0000.0000.0000.000
118A649SER0-0.046-0.03673.711-0.002-0.0020.0000.0000.0000.000
119A650VAL0-0.023-0.00374.418-0.010-0.0100.0000.0000.0000.000
120A651ASP-1-0.905-0.92475.7674.1634.1630.0000.0000.0000.000
121A652ASN00.027-0.01878.512-0.080-0.0800.0000.0000.0000.000
122A653PRO00.0770.03979.2530.0660.0660.0000.0000.0000.000
123A654THR00.018-0.00479.0620.0600.0600.0000.0000.0000.000
124A655ASN0-0.055-0.02777.9190.0030.0030.0000.0000.0000.000
125A656TYR00.0620.04770.7660.0440.0440.0000.0000.0000.000
126A657LEU00.0620.02273.8980.0670.0670.0000.0000.0000.000
127A658THR0-0.028-0.01473.7780.0520.0520.0000.0000.0000.000
128A659GLN00.0150.02369.3550.0120.0120.0000.0000.0000.000
129A660LEU00.000-0.00869.1120.0740.0740.0000.0000.0000.000
130A661ALA00.001-0.00968.8840.0740.0740.0000.0000.0000.000
131A662VAL0-0.024-0.02068.3370.0660.0660.0000.0000.0000.000
132A663ILE00.0130.02264.4580.0720.0720.0000.0000.0000.000
133A664ARG10.9150.94062.914-4.857-4.8570.0000.0000.0000.000
134A665PHE00.0440.01064.1000.0710.0710.0000.0000.0000.000
135A666GLN00.0020.01364.8380.0600.0600.0000.0000.0000.000
136A667THR0-0.059-0.03259.1710.0950.0950.0000.0000.0000.000
137A668ILE0-0.0010.02159.9240.0980.0980.0000.0000.0000.000
138A669LYS10.8040.88560.652-4.975-4.9750.0000.0000.0000.000
139A670LYS10.9440.98258.089-5.258-5.2580.0000.0000.0000.000
140A671THR0-0.011-0.02155.1320.1200.1200.0000.0000.0000.000
141A672VAL0-0.0040.00255.7900.1090.1090.0000.0000.0000.000
142A673GLU-1-0.806-0.90256.8715.2445.2440.0000.0000.0000.000
143A674ASP-1-0.808-0.89253.2185.8835.8830.0000.0000.0000.000
144A675PHE00.002-0.01051.4670.1310.1310.0000.0000.0000.000
145A676GLN0-0.027-0.01352.4360.0670.0670.0000.0000.0000.000
146A677ASP-1-0.872-0.93051.5176.3846.3840.0000.0000.0000.000
147A678ILE0-0.023-0.00547.1010.1270.1270.0000.0000.0000.000
148A679PHE0-0.0060.00746.7830.1450.1450.0000.0000.0000.000
149A680LYS10.8570.92248.680-6.516-6.5160.0000.0000.0000.000
150A681GLU-1-0.977-0.99747.7736.8186.8180.0000.0000.0000.000
151A682LEU00.0210.02244.7710.1210.1210.0000.0000.0000.000
152A683GLY0-0.0140.00147.6290.0840.0840.0000.0000.0000.000
153A684ALA0-0.037-0.02850.099-0.089-0.0890.0000.0000.0000.000
154A685LYS10.8930.92348.240-6.545-6.5450.0000.0000.0000.000
155A686ILE00.0660.04046.706-0.096-0.0960.0000.0000.0000.000
156A687SER00.018-0.00150.585-0.064-0.0640.0000.0000.0000.000
157A688SER0-0.036-0.02153.888-0.079-0.0790.0000.0000.0000.000
158A689ILE00.0170.01051.140-0.075-0.0750.0000.0000.0000.000
159A690LEU0-0.0060.01454.214-0.082-0.0820.0000.0000.0000.000
160A691VAL00.004-0.01055.399-0.093-0.0930.0000.0000.0000.000
161A692ASP-1-0.857-0.92256.7535.4155.4150.0000.0000.0000.000
162A693TRP00.0380.01756.038-0.103-0.1030.0000.0000.0000.000
163A694CYS0-0.085-0.04858.119-0.097-0.0970.0000.0000.0000.000
164A695SER0-0.0120.00160.895-0.144-0.1440.0000.0000.0000.000
165A696ASP-1-0.871-0.93659.7395.1205.1200.0000.0000.0000.000
166A697GLU-1-0.826-0.88860.2865.0595.0590.0000.0000.0000.000
167A698VAL0-0.048-0.02662.998-0.099-0.0990.0000.0000.0000.000
168A699ASP-1-0.859-0.94765.3644.6794.6790.0000.0000.0000.000
169A700ASN0-0.071-0.04961.885-0.134-0.1340.0000.0000.0000.000
170A701HIS00.0150.01666.277-0.030-0.0300.0000.0000.0000.000
171A702PHE00.0470.01268.814-0.084-0.0840.0000.0000.0000.000
172A703LYS10.8930.94564.545-4.921-4.9210.0000.0000.0000.000
173A704LEU0-0.028-0.01767.025-0.036-0.0360.0000.0000.0000.000
174A705ILE0-0.034-0.00171.070-0.064-0.0640.0000.0000.0000.000
175A706ASP-1-0.825-0.94073.4994.1764.1760.0000.0000.0000.000
176A707LYS10.8890.95870.733-4.473-4.4730.0000.0000.0000.000
177A708GLN00.0920.03273.888-0.095-0.0950.0000.0000.0000.000
178A709LEU0-0.105-0.04077.152-0.062-0.0620.0000.0000.0000.000
179A710LEU0-0.063-0.03276.357-0.043-0.0430.0000.0000.0000.000
180A711ASN0-0.077-0.05879.381-0.017-0.0170.0000.0000.0000.000
181A712ASP-1-0.874-0.94382.2413.6683.6680.0000.0000.0000.000
182A713GLU-1-0.947-0.96983.6433.7703.7700.0000.0000.0000.000
183A714MET0-0.0500.01481.8620.0210.0210.0000.0000.0000.000
184A715LEU0-0.0160.00678.5160.0700.0700.0000.0000.0000.000
185A716SER00.0610.02482.032-0.074-0.0740.0000.0000.0000.000
186A717PRO00.0390.00982.6080.0570.0570.0000.0000.0000.000
187A718GLY0-0.050-0.02283.5580.0040.0040.0000.0000.0000.000
188A719SER0-0.010-0.00878.8730.0220.0220.0000.0000.0000.000
189A720ILE00.0220.02078.2970.0630.0630.0000.0000.0000.000
190A721LYS10.9630.97878.522-3.759-3.7590.0000.0000.0000.000
191A722SER0-0.0350.00176.6380.0560.0560.0000.0000.0000.000
192A723SER00.0730.01474.1870.0650.0650.0000.0000.0000.000
193A724ARG10.8620.89973.870-4.063-4.0630.0000.0000.0000.000
194A725LYS10.9801.00574.349-4.199-4.1990.0000.0000.0000.000
195A726GLN0-0.059-0.03170.0670.0720.0720.0000.0000.0000.000
196A727ILE00.0120.00270.1480.0670.0670.0000.0000.0000.000
197A728ASP-1-0.896-0.96170.4354.3504.3500.0000.0000.0000.000
198A729GLY0-0.046-0.02670.4170.0410.0410.0000.0000.0000.000
199A730LEU00.0130.01165.2000.0680.0680.0000.0000.0000.000
200A731LYS10.8270.92265.972-4.403-4.4030.0000.0000.0000.000
201A732ALA0-0.075-0.02666.7140.0320.0320.0000.0000.0000.000
202A733VAL0-0.047-0.01961.4530.0470.0470.0000.0000.0000.000
203A734GLY00.0120.01062.0960.0740.0740.0000.0000.0000.000
204A735LEU0-0.010-0.00561.3100.0170.0170.0000.0000.0000.000
205A736ASP-1-0.836-0.92865.3754.4504.4500.0000.0000.0000.000
206A737PHE00.0610.01663.378-0.001-0.0010.0000.0000.0000.000
207A738VAL0-0.018-0.01169.359-0.042-0.0420.0000.0000.0000.000
208A739TYR00.0390.01167.345-0.036-0.0360.0000.0000.0000.000
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