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: 53Y8Z

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2482467.500249
FMO2-HF: Nuclear repulsion 2394318.91879
FMO2-HF: Total energy -88148.581459
FMO2-MP2: Total energy -88407.923355


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.
58.82561.706-0.009-1.579-1.2920.007
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 : -0.879 / q_NPA : -0.934
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].
3A527SER00.0170.0043.9111.5844.465-0.009-1.579-1.2920.007
4A528SER00.0360.0076.803-1.791-1.7910.0000.0000.0000.000
5A529THR00.0500.01810.017-0.782-0.7820.0000.0000.0000.000
6A530ALA00.0240.0187.871-1.695-1.6950.0000.0000.0000.000
7A531GLN0-0.012-0.0168.733-2.381-2.3810.0000.0000.0000.000
8A532ARG10.8700.91910.586-18.836-18.8360.0000.0000.0000.000
9A533LEU00.0240.01312.772-1.179-1.1790.0000.0000.0000.000
10A534LYS10.8760.91910.468-23.232-23.2320.0000.0000.0000.000
11A535PHE0-0.013-0.01113.351-0.577-0.5770.0000.0000.0000.000
12A536LEU00.0050.01616.533-0.904-0.9040.0000.0000.0000.000
13A537ASP-1-0.847-0.91715.98915.19315.1930.0000.0000.0000.000
14A538GLU-1-0.881-0.92615.43418.39218.3920.0000.0000.0000.000
15A539GLY00.0490.02918.948-0.718-0.7180.0000.0000.0000.000
16A540VAL0-0.009-0.02221.201-0.717-0.7170.0000.0000.0000.000
17A541GLU-1-0.790-0.87719.99113.13613.1360.0000.0000.0000.000
18A542GLU-1-0.984-0.98523.00111.74311.7430.0000.0000.0000.000
19A543ILE00.0100.01425.177-0.578-0.5780.0000.0000.0000.000
20A544ASP-1-0.800-0.86927.05710.35810.3580.0000.0000.0000.000
21A545ILE0-0.061-0.03326.420-0.440-0.4400.0000.0000.0000.000
22A546GLU-1-0.730-0.82529.4459.5039.5030.0000.0000.0000.000
23A547LEU0-0.018-0.01131.337-0.425-0.4250.0000.0000.0000.000
24A548ALA0-0.049-0.01832.410-0.336-0.3360.0000.0000.0000.000
25A549ARG10.7780.87629.236-10.342-10.3420.0000.0000.0000.000
26A550LEU0-0.001-0.00635.937-0.121-0.1210.0000.0000.0000.000
27A551ARG10.8610.94332.354-9.524-9.5240.0000.0000.0000.000
28A552PHE00.010-0.02134.5730.2610.2610.0000.0000.0000.000
29A553GLU-1-0.836-0.90135.2518.2928.2920.0000.0000.0000.000
30A554SER0-0.005-0.01631.5760.2320.2320.0000.0000.0000.000
31A555ALA00.0010.00630.5710.3470.3470.0000.0000.0000.000
32A556VAL00.0150.00630.5440.2680.2680.0000.0000.0000.000
33A557GLU-1-0.855-0.92131.5479.3289.3280.0000.0000.0000.000
34A558THR0-0.031-0.02425.9690.3800.3800.0000.0000.0000.000
35A559LEU0-0.034-0.01426.7460.4310.4310.0000.0000.0000.000
36A560LEU00.0000.00427.4120.2690.2690.0000.0000.0000.000
37A561ASP-1-0.926-0.94524.29013.00213.0020.0000.0000.0000.000
38A562ILE00.004-0.01321.8290.4870.4870.0000.0000.0000.000
39A563GLU-1-0.836-0.91923.54810.82610.8260.0000.0000.0000.000
40A564SER00.0350.01825.6200.0350.0350.0000.0000.0000.000
41A565GLN00.0030.00820.5311.1011.1010.0000.0000.0000.000
42A566LEU0-0.055-0.03519.7520.8860.8860.0000.0000.0000.000
43A567GLU-1-0.951-0.97021.74311.25811.2580.0000.0000.0000.000
44A568ASP-1-0.883-0.92021.88913.12713.1270.0000.0000.0000.000
45A569LEU0-0.155-0.07316.1200.8310.8310.0000.0000.0000.000
46A570SER0-0.114-0.07118.3820.6340.6340.0000.0000.0000.000
47A578LEU00.0390.01113.4410.2710.2710.0000.0000.0000.000
48A579MET00.012-0.00313.394-0.515-0.5150.0000.0000.0000.000
49A580LEU00.0140.00710.946-0.562-0.5620.0000.0000.0000.000
50A581LEU00.0430.03914.303-0.388-0.3880.0000.0000.0000.000
51A582ASN0-0.001-0.01017.278-0.391-0.3910.0000.0000.0000.000
52A583LEU0-0.013-0.00415.216-0.585-0.5850.0000.0000.0000.000
53A584ILE00.0510.01915.250-0.520-0.5200.0000.0000.0000.000
54A585SER00.0290.01519.172-0.627-0.6270.0000.0000.0000.000
55A586LEU0-0.053-0.02021.483-0.588-0.5880.0000.0000.0000.000
56A587LYS10.7730.86118.171-15.270-15.2700.0000.0000.0000.000
57A588ILE00.0320.02022.182-0.311-0.3110.0000.0000.0000.000
58A589GLU-1-0.870-0.94124.9459.6399.6390.0000.0000.0000.000
59A590GLN0-0.086-0.04826.156-0.682-0.6820.0000.0000.0000.000
60A591ARG10.7420.83222.831-12.115-12.1150.0000.0000.0000.000
61A592ARG10.8430.91828.609-9.881-9.8810.0000.0000.0000.000
62A593GLU-1-0.911-0.94730.8868.1258.1250.0000.0000.0000.000
63A594ALA00.0180.01631.038-0.267-0.2670.0000.0000.0000.000
64A595ILE00.006-0.00630.454-0.299-0.2990.0000.0000.0000.000
65A596SER00.0320.00534.205-0.344-0.3440.0000.0000.0000.000
66A597SER0-0.0300.00336.273-0.391-0.3910.0000.0000.0000.000
67A598LYS10.8450.91635.956-8.356-8.3560.0000.0000.0000.000
68A599LEU00.0430.01537.228-0.228-0.2280.0000.0000.0000.000
69A600SER00.000-0.01940.237-0.261-0.2610.0000.0000.0000.000
70A601GLN0-0.0100.00039.687-0.122-0.1220.0000.0000.0000.000
71A602SER00.0090.01942.160-0.146-0.1460.0000.0000.0000.000
72A603ILE0-0.029-0.00643.336-0.150-0.1500.0000.0000.0000.000
73A604LEU0-0.0180.00646.206-0.167-0.1670.0000.0000.0000.000
74A605SER0-0.056-0.04246.449-0.144-0.1440.0000.0000.0000.000
75A606SER0-0.027-0.01748.011-0.091-0.0910.0000.0000.0000.000
76A607ASN0-0.051-0.02149.484-0.210-0.2100.0000.0000.0000.000
77A608GLU-1-0.883-0.94751.0066.1246.1240.0000.0000.0000.000
78A609ILE00.0270.00751.1180.1190.1190.0000.0000.0000.000
79A610VAL00.0270.01347.4570.1150.1150.0000.0000.0000.000
80A611HIS0-0.020-0.00546.4550.1740.1740.0000.0000.0000.000
81A612LEU00.0100.02246.1060.1440.1440.0000.0000.0000.000
82A613LYS10.7860.90747.020-6.512-6.5120.0000.0000.0000.000
83A614SER00.0330.01042.9680.1370.1370.0000.0000.0000.000
84A615GLY00.0420.02242.1190.2130.2130.0000.0000.0000.000
85A616THR0-0.017-0.04042.2530.1150.1150.0000.0000.0000.000
86A617GLU-1-0.822-0.91243.2667.0547.0540.0000.0000.0000.000
87A618ASN0-0.031-0.03338.0900.3690.3690.0000.0000.0000.000
88A619MET0-0.0130.01538.3410.2630.2630.0000.0000.0000.000
89A620ILE0-0.022-0.02539.8290.0660.0660.0000.0000.0000.000
90A621LYS10.7550.87536.243-8.417-8.4170.0000.0000.0000.000
91A622LEU00.0280.01633.5190.2080.2080.0000.0000.0000.000
92A623GLY00.0020.01635.3210.2070.2070.0000.0000.0000.000
93A624LEU0-0.027-0.00936.308-0.082-0.0820.0000.0000.0000.000
94A625PRO00.0370.00740.270-0.184-0.1840.0000.0000.0000.000
95A626GLU-1-0.797-0.88743.6466.4856.4850.0000.0000.0000.000
96A627GLN00.0190.01640.806-0.091-0.0910.0000.0000.0000.000
97A628ALA00.0000.00143.274-0.095-0.0950.0000.0000.0000.000
98A629LEU0-0.014-0.01245.015-0.124-0.1240.0000.0000.0000.000
99A630ASP-1-0.925-0.95847.7136.1776.1770.0000.0000.0000.000
100A631LEU00.0250.00844.256-0.121-0.1210.0000.0000.0000.000
101A632PHE00.0200.00848.376-0.121-0.1210.0000.0000.0000.000
102A633LEU00.006-0.01450.012-0.131-0.1310.0000.0000.0000.000
103A634GLN0-0.0250.01449.601-0.150-0.1500.0000.0000.0000.000
104A635ASN0-0.022-0.01050.679-0.162-0.1620.0000.0000.0000.000
105A636ARG10.7970.88252.698-5.956-5.9560.0000.0000.0000.000
106A637SER0-0.012-0.02455.877-0.149-0.1490.0000.0000.0000.000
107A638ASN0-0.0060.00053.076-0.175-0.1750.0000.0000.0000.000
108A639PHE00.0510.02956.582-0.119-0.1190.0000.0000.0000.000
109A640ILE0-0.037-0.02458.277-0.111-0.1110.0000.0000.0000.000
110A641GLN0-0.014-0.01360.047-0.156-0.1560.0000.0000.0000.000
111A642ASP-1-0.874-0.93458.0035.2925.2920.0000.0000.0000.000
112A643LEU0-0.064-0.04860.978-0.098-0.0980.0000.0000.0000.000
113A644ILE0-0.062-0.03463.923-0.107-0.1070.0000.0000.0000.000
114A645LEU0-0.020-0.01262.941-0.089-0.0890.0000.0000.0000.000
115A646GLN0-0.065-0.00863.834-0.105-0.1050.0000.0000.0000.000
116A647ILE0-0.098-0.05167.057-0.046-0.0460.0000.0000.0000.000
117A648GLY00.007-0.00270.687-0.027-0.0270.0000.0000.0000.000
118A649SER0-0.038-0.02273.5060.0060.0060.0000.0000.0000.000
119A650VAL0-0.048-0.01274.767-0.018-0.0180.0000.0000.0000.000
120A651ASP-1-0.882-0.93175.7084.1654.1650.0000.0000.0000.000
121A652ASN00.027-0.00378.620-0.086-0.0860.0000.0000.0000.000
122A653PRO00.0680.04179.3780.0660.0660.0000.0000.0000.000
123A654THR0-0.013-0.01778.7760.0590.0590.0000.0000.0000.000
124A655ASN0-0.014-0.01077.9690.0050.0050.0000.0000.0000.000
125A656TYR00.0670.04770.6480.0460.0460.0000.0000.0000.000
126A657LEU00.0440.00873.9470.0650.0650.0000.0000.0000.000
127A658THR0-0.031-0.01174.0300.0460.0460.0000.0000.0000.000
128A659GLN00.0200.01769.4590.0100.0100.0000.0000.0000.000
129A660LEU0-0.0080.00369.1380.0750.0750.0000.0000.0000.000
130A661ALA00.013-0.00169.0210.0720.0720.0000.0000.0000.000
131A662VAL0-0.050-0.02868.7920.0620.0620.0000.0000.0000.000
132A663ILE00.0110.00664.5850.0710.0710.0000.0000.0000.000
133A664ARG10.8790.94162.970-4.853-4.8530.0000.0000.0000.000
134A665PHE00.029-0.00264.3350.0650.0650.0000.0000.0000.000
135A666GLN00.0000.00165.1220.0800.0800.0000.0000.0000.000
136A667THR0-0.029-0.01459.6000.0950.0950.0000.0000.0000.000
137A668ILE00.0140.03460.2260.0970.0970.0000.0000.0000.000
138A669LYS10.7910.87360.627-4.971-4.9710.0000.0000.0000.000
139A670LYS10.9370.96958.313-5.228-5.2280.0000.0000.0000.000
140A671THR0-0.014-0.01455.3580.1240.1240.0000.0000.0000.000
141A672VAL0-0.0010.00256.0260.1150.1150.0000.0000.0000.000
142A673GLU-1-0.808-0.89057.0255.2535.2530.0000.0000.0000.000
143A674ASP-1-0.786-0.88553.5095.8875.8870.0000.0000.0000.000
144A675PHE0-0.005-0.00452.0540.1320.1320.0000.0000.0000.000
145A676GLN0-0.018-0.00852.3910.1030.1030.0000.0000.0000.000
146A677ASP-1-0.839-0.90451.2986.3886.3880.0000.0000.0000.000
147A678ILE0-0.047-0.00747.2290.1410.1410.0000.0000.0000.000
148A679PHE0-0.004-0.01247.0470.1520.1520.0000.0000.0000.000
149A680LYS10.8410.91348.484-6.547-6.5470.0000.0000.0000.000
150A681GLU-1-0.961-0.99547.8996.8096.8090.0000.0000.0000.000
151A682LEU0-0.0070.00944.4510.0780.0780.0000.0000.0000.000
152A683GLY00.0050.01447.8990.0400.0400.0000.0000.0000.000
153A684ALA0-0.029-0.02950.463-0.062-0.0620.0000.0000.0000.000
154A685LYS10.8300.88447.950-6.564-6.5640.0000.0000.0000.000
155A686ILE00.0620.03846.984-0.070-0.0700.0000.0000.0000.000
156A687SER00.005-0.00350.904-0.073-0.0730.0000.0000.0000.000
157A688SER0-0.075-0.03254.386-0.074-0.0740.0000.0000.0000.000
158A689ILE00.0560.02951.465-0.090-0.0900.0000.0000.0000.000
159A690LEU00.0200.02454.529-0.066-0.0660.0000.0000.0000.000
160A691VAL00.0220.01055.887-0.106-0.1060.0000.0000.0000.000
161A692ASP-1-0.858-0.93856.9305.4125.4120.0000.0000.0000.000
162A693TRP00.001-0.01656.433-0.099-0.0990.0000.0000.0000.000
163A694CYS0-0.076-0.03958.515-0.091-0.0910.0000.0000.0000.000
164A695SER0-0.0240.00361.295-0.134-0.1340.0000.0000.0000.000
165A696ASP-1-0.839-0.92660.9395.0035.0030.0000.0000.0000.000
166A697GLU-1-0.759-0.85460.5105.0515.0510.0000.0000.0000.000
167A698VAL0-0.052-0.03563.313-0.092-0.0920.0000.0000.0000.000
168A699ASP-1-0.863-0.94965.8214.6724.6720.0000.0000.0000.000
169A700ASN0-0.030-0.03062.244-0.135-0.1350.0000.0000.0000.000
170A701HIS0-0.0130.01266.540-0.013-0.0130.0000.0000.0000.000
171A702PHE00.0190.00369.285-0.083-0.0830.0000.0000.0000.000
172A703LYS10.8820.94064.089-4.963-4.9630.0000.0000.0000.000
173A704LEU00.0220.01967.328-0.039-0.0390.0000.0000.0000.000
174A705ILE00.0290.02071.188-0.071-0.0710.0000.0000.0000.000
175A706ASP-1-0.843-0.92673.5404.1484.1480.0000.0000.0000.000
176A707LYS10.7850.89071.019-4.378-4.3780.0000.0000.0000.000
177A708GLN00.0780.03474.214-0.087-0.0870.0000.0000.0000.000
178A709LEU0-0.080-0.04677.725-0.063-0.0630.0000.0000.0000.000
179A710LEU0-0.055-0.01176.484-0.035-0.0350.0000.0000.0000.000
180A711ASN0-0.057-0.03579.545-0.019-0.0190.0000.0000.0000.000
181A712ASP-1-0.861-0.93882.6763.6573.6570.0000.0000.0000.000
182A713GLU-1-0.966-0.98383.8713.7643.7640.0000.0000.0000.000
183A714MET0-0.0530.00281.7700.0250.0250.0000.0000.0000.000
184A715LEU00.0040.00378.7100.0700.0700.0000.0000.0000.000
185A716SER00.0290.01082.475-0.074-0.0740.0000.0000.0000.000
186A717PRO00.0210.00582.9680.0550.0550.0000.0000.0000.000
187A718GLY0-0.017-0.00783.4910.0250.0250.0000.0000.0000.000
188A719SER00.0790.02978.9200.0240.0240.0000.0000.0000.000
189A720ILE00.0120.03078.3900.0620.0620.0000.0000.0000.000
190A721LYS10.9450.96778.852-3.754-3.7540.0000.0000.0000.000
191A722SER0-0.046-0.01576.8920.0600.0600.0000.0000.0000.000
192A723SER00.0440.00074.4290.0690.0690.0000.0000.0000.000
193A724ARG10.8360.89774.063-4.045-4.0450.0000.0000.0000.000
194A725LYS10.9540.98174.804-4.209-4.2090.0000.0000.0000.000
195A726GLN0-0.021-0.00770.1970.0520.0520.0000.0000.0000.000
196A727ILE00.0080.01570.2230.0620.0620.0000.0000.0000.000
197A728ASP-1-0.844-0.95070.4874.3544.3540.0000.0000.0000.000
198A729GLY0-0.025-0.00970.6260.0340.0340.0000.0000.0000.000
199A730LEU0-0.006-0.00365.2680.0620.0620.0000.0000.0000.000
200A731LYS10.8310.92466.213-4.399-4.3990.0000.0000.0000.000
201A732ALA0-0.074-0.02767.2710.0330.0330.0000.0000.0000.000
202A733VAL0-0.030-0.01261.8550.0470.0470.0000.0000.0000.000
203A734GLY00.0010.00562.3240.0820.0820.0000.0000.0000.000
204A735LEU0-0.020-0.00761.3350.0110.0110.0000.0000.0000.000
205A736ASP-1-0.833-0.93365.3524.4354.4350.0000.0000.0000.000
206A737PHE00.0570.01763.4370.0080.0080.0000.0000.0000.000
207A738VAL0-0.022-0.01169.525-0.040-0.0400.0000.0000.0000.000
208A739TYR00.0270.01067.880-0.035-0.0350.0000.0000.0000.000
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