FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YV7K2

Calculation Name: 1D5F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D5F

Chain ID: A

ChEMBL ID:

UniProt ID: Q05086

Base Structure: X-ray

Registration Date: 2023-09-23

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 350
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5540065.683968
FMO2-HF: Nuclear repulsion 5397208.308005
FMO2-HF: Total energy -142857.375963
FMO2-MP2: Total energy -143273.571921


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:497:ASN)


Summations of interaction energy for fragment #1(A:497:ASN)
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.
-6.74-2.8280.374-1.469-2.8150.003
Interaction energy analysis for fragmet #1(A:497:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / 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].
3A499TYR0-0.011-0.0323.1662.0984.1610.319-0.925-1.4560.001
4A500LEU00.0210.0483.9490.9181.0430.004-0.051-0.0780.000
5A501ARG10.8950.9363.381-6.684-5.7820.024-0.325-0.6010.002
6A502LEU00.0070.0146.355-0.801-0.8010.0000.0000.0000.000
7A503LYS10.9230.9749.510-0.359-0.3590.0000.0000.0000.000
8A504VAL00.003-0.00311.061-0.167-0.1670.0000.0000.0000.000
9A505ARG10.8410.94414.6080.0220.0220.0000.0000.0000.000
10A506ARG10.8500.90318.076-0.311-0.3110.0000.0000.0000.000
11A507ASP-1-0.930-0.95221.2150.1050.1050.0000.0000.0000.000
12A508HIS0-0.006-0.01620.051-0.029-0.0290.0000.0000.0000.000
13A509ILE00.0570.04418.2570.0060.0060.0000.0000.0000.000
14A510ILE00.004-0.00218.033-0.013-0.0130.0000.0000.0000.000
15A511ASP-1-0.895-0.94318.810-0.036-0.0360.0000.0000.0000.000
16A512ASP-1-0.797-0.90615.290-0.006-0.0060.0000.0000.0000.000
17A513ALA00.006-0.01413.643-0.048-0.0480.0000.0000.0000.000
18A514LEU0-0.0330.00113.875-0.054-0.0540.0000.0000.0000.000
19A515VAL00.002-0.01214.003-0.083-0.0830.0000.0000.0000.000
20A516ARG10.8460.9344.1550.8490.922-0.001-0.001-0.0700.000
21A517LEU00.015-0.02010.430-0.194-0.1940.0000.0000.0000.000
22A518GLU-1-0.925-0.94611.764-0.446-0.4460.0000.0000.0000.000
23A519MET00.0070.0019.746-0.125-0.1250.0000.0000.0000.000
24A520ILE0-0.109-0.0456.963-0.190-0.1900.0000.0000.0000.000
25A521ALA00.037-0.0039.021-0.057-0.0570.0000.0000.0000.000
26A522MET0-0.148-0.05911.8920.0940.0940.0000.0000.0000.000
27A523GLU-1-0.940-0.9875.360-4.775-4.7750.0000.0000.0000.000
28A524ASN00.0180.0056.2410.7950.7950.0000.0000.0000.000
29A525PRO00.0230.0388.066-0.096-0.0960.0000.0000.0000.000
30A526ALA0-0.054-0.0247.6000.2300.2300.0000.0000.0000.000
31A527ASP-1-0.881-0.9574.407-3.685-3.3880.000-0.076-0.2210.000
32A528LEU00.0010.0056.7250.5920.5920.0000.0000.0000.000
33A529LYS10.8310.9159.9060.1360.1360.0000.0000.0000.000
34A530LYS10.8280.9372.9860.7271.1790.028-0.091-0.3890.000
35A531GLN0-0.007-0.0098.5620.0530.0530.0000.0000.0000.000
36A532LEU00.0400.0348.0380.5560.5560.0000.0000.0000.000
37A533TYR00.0080.0367.0950.1310.1310.0000.0000.0000.000
38A534VAL0-0.0030.0038.8800.1810.1810.0000.0000.0000.000
39A535GLU-1-0.914-0.9748.8021.8961.8960.0000.0000.0000.000
40A536PHE00.0510.01712.512-0.085-0.0850.0000.0000.0000.000
41A537GLU-1-0.954-0.99415.7460.1790.1790.0000.0000.0000.000
42A538GLY0-0.026-0.00316.583-0.044-0.0440.0000.0000.0000.000
43A539GLU-1-0.879-0.93617.8700.3400.3400.0000.0000.0000.000
44A540GLN0-0.036-0.01416.4590.0730.0730.0000.0000.0000.000
45A541GLY00.028-0.00315.553-0.069-0.0690.0000.0000.0000.000
46A542VAL0-0.045-0.01712.5080.0990.0990.0000.0000.0000.000
47A543ASP-1-0.699-0.82311.5700.8170.8170.0000.0000.0000.000
48A544GLU-1-1.004-0.99812.6940.6550.6550.0000.0000.0000.000
49A545GLY0-0.001-0.00814.674-0.079-0.0790.0000.0000.0000.000
50A546GLY00.015-0.00715.929-0.057-0.0570.0000.0000.0000.000
51A547VAL00.0500.02714.629-0.059-0.0590.0000.0000.0000.000
52A548SER0-0.061-0.09613.036-0.035-0.0350.0000.0000.0000.000
53A549LYS10.7840.90815.302-0.337-0.3370.0000.0000.0000.000
54A550GLU-1-0.850-0.92718.8910.2780.2780.0000.0000.0000.000
55A551PHE0-0.0020.00515.196-0.038-0.0380.0000.0000.0000.000
56A552PHE0-0.010-0.02515.384-0.046-0.0460.0000.0000.0000.000
57A553GLN0-0.051-0.04919.627-0.027-0.0270.0000.0000.0000.000
58A554LEU00.0490.01820.660-0.025-0.0250.0000.0000.0000.000
59A555VAL00.0030.01118.612-0.029-0.0290.0000.0000.0000.000
60A556VAL0-0.081-0.05321.925-0.027-0.0270.0000.0000.0000.000
61A557GLU-1-0.955-0.96924.4300.0830.0830.0000.0000.0000.000
62A558GLU-1-0.826-0.91924.0720.0790.0790.0000.0000.0000.000
63A559ILE0-0.042-0.02723.333-0.017-0.0170.0000.0000.0000.000
64A560PHE0-0.086-0.05825.987-0.015-0.0150.0000.0000.0000.000
65A561ASN00.0230.02029.588-0.009-0.0090.0000.0000.0000.000
66A562PRO0-0.028-0.03331.535-0.008-0.0080.0000.0000.0000.000
67A563ASP-1-0.892-0.92932.2040.0310.0310.0000.0000.0000.000
68A564ILE0-0.073-0.03026.539-0.010-0.0100.0000.0000.0000.000
69A565GLY00.0170.00230.901-0.008-0.0080.0000.0000.0000.000
70A566MET0-0.058-0.01625.660-0.004-0.0040.0000.0000.0000.000
71A567PHE0-0.022-0.03527.981-0.004-0.0040.0000.0000.0000.000
72A568THR0-0.0160.00033.107-0.001-0.0010.0000.0000.0000.000
73A569TYR00.0130.00835.6420.0030.0030.0000.0000.0000.000
74A570ASP-1-0.868-0.92537.4100.0230.0230.0000.0000.0000.000
75A571GLU-1-0.896-0.97340.3310.0410.0410.0000.0000.0000.000
76A572SER0-0.079-0.03042.2050.0040.0040.0000.0000.0000.000
77A573THR0-0.047-0.02639.9680.0030.0030.0000.0000.0000.000
78A574LYS10.9110.95737.671-0.048-0.0480.0000.0000.0000.000
79A575LEU0-0.029-0.00335.2610.0060.0060.0000.0000.0000.000
80A576PHE00.0450.02032.349-0.004-0.0040.0000.0000.0000.000
81A577TRP0-0.040-0.02633.998-0.001-0.0010.0000.0000.0000.000
82A578PHE00.020-0.00928.6620.0010.0010.0000.0000.0000.000
83A579ASN00.0800.05033.279-0.005-0.0050.0000.0000.0000.000
84A580PRO0-0.052-0.04534.552-0.005-0.0050.0000.0000.0000.000
85A581SER0-0.008-0.01536.572-0.005-0.0050.0000.0000.0000.000
86A582SER0-0.0250.01030.968-0.001-0.0010.0000.0000.0000.000
87A583PHE0-0.057-0.01832.139-0.002-0.0020.0000.0000.0000.000
88A584GLU-1-0.864-0.93629.492-0.081-0.0810.0000.0000.0000.000
89A585THR00.0620.03227.0290.0000.0000.0000.0000.0000.000
90A586GLU-1-1.006-1.01726.237-0.084-0.0840.0000.0000.0000.000
91A587GLY0-0.029-0.01322.251-0.021-0.0210.0000.0000.0000.000
92A588GLN00.1290.04921.391-0.012-0.0120.0000.0000.0000.000
93A589PHE0-0.0010.00223.2730.0180.0180.0000.0000.0000.000
94A590THR0-0.053-0.03919.2980.0130.0130.0000.0000.0000.000
95A591LEU00.0720.05017.365-0.005-0.0050.0000.0000.0000.000
96A592ILE00.0640.04219.2530.0260.0260.0000.0000.0000.000
97A593GLY0-0.018-0.00221.3880.0160.0160.0000.0000.0000.000
98A594ILE00.0160.00214.8490.0100.0100.0000.0000.0000.000
99A595VAL0-0.048-0.00917.1880.0400.0400.0000.0000.0000.000
100A596LEU0-0.014-0.02118.3740.0300.0300.0000.0000.0000.000
101A597GLY0-0.007-0.00218.1890.0090.0090.0000.0000.0000.000
102A598LEU00.027-0.01212.2580.0240.0240.0000.0000.0000.000
103A599ALA0-0.018-0.00715.8290.0440.0440.0000.0000.0000.000
104A600ILE0-0.0160.00118.582-0.002-0.0020.0000.0000.0000.000
105A601TYR0-0.057-0.02814.720-0.029-0.0290.0000.0000.0000.000
106A602ASN0-0.0140.01413.3330.0520.0520.0000.0000.0000.000
107A603ASN0-0.0120.00616.694-0.055-0.0550.0000.0000.0000.000
108A604CYS0-0.026-0.01518.797-0.002-0.0020.0000.0000.0000.000
109A605ILE0-0.040-0.00520.531-0.012-0.0120.0000.0000.0000.000
110A606LEU0-0.008-0.01120.8160.0100.0100.0000.0000.0000.000
111A607ASP-1-0.834-0.90724.4610.1110.1110.0000.0000.0000.000
112A608VAL0-0.0150.00125.371-0.012-0.0120.0000.0000.0000.000
113A609HIS10.8450.91028.264-0.090-0.0900.0000.0000.0000.000
114A610PHE00.0410.01327.270-0.007-0.0070.0000.0000.0000.000
115A611PRO00.0210.04632.5410.0020.0020.0000.0000.0000.000
116A612MET00.0830.02034.527-0.005-0.0050.0000.0000.0000.000
117A613VAL0-0.012-0.01134.362-0.003-0.0030.0000.0000.0000.000
118A614VAL00.0190.03429.553-0.008-0.0080.0000.0000.0000.000
119A615TYR00.0960.03827.584-0.008-0.0080.0000.0000.0000.000
120A616ARG10.9410.97530.921-0.012-0.0120.0000.0000.0000.000
121A617LYS10.8650.91832.3270.0170.0170.0000.0000.0000.000
122A618LEU0-0.0140.00225.780-0.012-0.0120.0000.0000.0000.000
123A619MET0-0.084-0.01928.118-0.007-0.0070.0000.0000.0000.000
124A620GLY0-0.056-0.02229.989-0.005-0.0050.0000.0000.0000.000
125A621LYS10.8570.93331.5060.0080.0080.0000.0000.0000.000
126A622LYS10.9740.98435.0660.0390.0390.0000.0000.0000.000
127A623GLY0-0.006-0.00237.6890.0040.0040.0000.0000.0000.000
128A624THR0-0.070-0.06339.180-0.003-0.0030.0000.0000.0000.000
129A625PHE00.1340.03942.8700.0020.0020.0000.0000.0000.000
130A626ARG10.9550.96444.379-0.006-0.0060.0000.0000.0000.000
131A627ASP-1-0.807-0.88439.8200.0070.0070.0000.0000.0000.000
132A628LEU0-0.029-0.01441.2330.0030.0030.0000.0000.0000.000
133A629GLY0-0.0250.00643.2990.0010.0010.0000.0000.0000.000
134A630ASP-1-0.865-0.93039.6390.0310.0310.0000.0000.0000.000
135A631SER0-0.051-0.03438.4900.0000.0000.0000.0000.0000.000
136A632HIS10.8300.90739.390-0.006-0.0060.0000.0000.0000.000
137A633PRO00.1120.07242.694-0.003-0.0030.0000.0000.0000.000
138A634VAL00.0580.01745.774-0.002-0.0020.0000.0000.0000.000
139A635LEU0-0.0010.00145.117-0.001-0.0010.0000.0000.0000.000
140A636TYR00.022-0.00446.264-0.001-0.0010.0000.0000.0000.000
141A637GLN00.0220.00648.1950.0010.0010.0000.0000.0000.000
142A638SER00.0320.04151.285-0.001-0.0010.0000.0000.0000.000
143A639LEU0-0.032-0.02148.163-0.001-0.0010.0000.0000.0000.000
144A640LYS10.8110.89751.541-0.012-0.0120.0000.0000.0000.000
145A641ASP-1-0.876-0.94453.1330.0080.0080.0000.0000.0000.000
146A642LEU0-0.036-0.00855.023-0.001-0.0010.0000.0000.0000.000
147A643LEU0-0.097-0.06052.334-0.001-0.0010.0000.0000.0000.000
148A644GLU-1-0.907-0.94655.8990.0090.0090.0000.0000.0000.000
149A645TYR0-0.147-0.11758.8570.0010.0010.0000.0000.0000.000
150A646GLU-1-0.935-0.98561.5460.0040.0040.0000.0000.0000.000
151A647GLY0-0.0270.00564.8610.0000.0000.0000.0000.0000.000
152A648ASN0-0.012-0.01366.042-0.001-0.0010.0000.0000.0000.000
153A649VAL00.015-0.01960.5500.0000.0000.0000.0000.0000.000
154A650GLU-1-0.985-0.98563.806-0.009-0.0090.0000.0000.0000.000
155A651ASP-1-0.969-0.98465.063-0.005-0.0050.0000.0000.0000.000
156A652ASP-1-0.797-0.81465.6060.0000.0000.0000.0000.0000.000
157A653MET0-0.105-0.05558.5170.0010.0010.0000.0000.0000.000
158A654MET00.0040.01162.739-0.001-0.0010.0000.0000.0000.000
159A655ILE0-0.009-0.00156.9820.0000.0000.0000.0000.0000.000
160A656THR00.0390.01757.4800.0000.0000.0000.0000.0000.000
161A657PHE0-0.038-0.02252.9390.0010.0010.0000.0000.0000.000
162A658GLN0-0.056-0.02052.8160.0000.0000.0000.0000.0000.000
163A659ILE0-0.017-0.00447.5290.0020.0020.0000.0000.0000.000
164A660SER00.0210.00450.397-0.002-0.0020.0000.0000.0000.000
165A661GLN0-0.0240.00543.4480.0000.0000.0000.0000.0000.000
166A662THR0-0.032-0.03146.946-0.002-0.0020.0000.0000.0000.000
167A663ASP-1-0.840-0.90245.148-0.014-0.0140.0000.0000.0000.000
168A664LEU00.0360.02141.6950.0020.0020.0000.0000.0000.000
169A665PHE0-0.059-0.05345.2260.0020.0020.0000.0000.0000.000
170A666GLY0-0.0080.00948.4790.0000.0000.0000.0000.0000.000
171A667ASN0-0.069-0.03948.7280.0000.0000.0000.0000.0000.000
172A668PRO0-0.0010.02248.774-0.001-0.0010.0000.0000.0000.000
173A669MET00.0280.01044.475-0.002-0.0020.0000.0000.0000.000
174A670MET0-0.048-0.02449.0280.0010.0010.0000.0000.0000.000
175A671TYR00.0310.00444.336-0.003-0.0030.0000.0000.0000.000
176A672ASP-1-0.844-0.92249.029-0.022-0.0220.0000.0000.0000.000
177A673LEU0-0.098-0.03847.490-0.002-0.0020.0000.0000.0000.000
178A674LYS10.8190.88149.7210.0210.0210.0000.0000.0000.000
179A675GLU-1-0.988-0.99651.972-0.031-0.0310.0000.0000.0000.000
180A676ASN00.0520.02953.732-0.002-0.0020.0000.0000.0000.000
181A677GLY0-0.006-0.02854.6320.0010.0010.0000.0000.0000.000
182A678ASP-1-0.822-0.89655.834-0.020-0.0200.0000.0000.0000.000
183A679LYS10.8980.94858.2010.0150.0150.0000.0000.0000.000
184A680ILE0-0.029-0.01056.9150.0000.0000.0000.0000.0000.000
185A681PRO00.041-0.00659.0910.0000.0000.0000.0000.0000.000
186A682ILE0-0.0180.00755.5710.0000.0000.0000.0000.0000.000
187A683THR00.0690.03159.6490.0010.0010.0000.0000.0000.000
188A684ASN00.018-0.01160.4230.0000.0000.0000.0000.0000.000
189A685GLU-1-0.935-0.97060.599-0.008-0.0080.0000.0000.0000.000
190A686ASN00.0380.03657.3930.0000.0000.0000.0000.0000.000
191A687ARG10.8680.94855.7630.0010.0010.0000.0000.0000.000
192A688LYS10.9991.00353.7110.0040.0040.0000.0000.0000.000
193A689GLU-1-0.855-0.90552.099-0.019-0.0190.0000.0000.0000.000
194A690PHE00.0240.01051.172-0.001-0.0010.0000.0000.0000.000
195A691VAL00.0330.01349.534-0.001-0.0010.0000.0000.0000.000
196A692ASN0-0.045-0.03747.7520.0020.0020.0000.0000.0000.000
197A693LEU0-0.031-0.01546.487-0.001-0.0010.0000.0000.0000.000
198A694TYR0-0.006-0.00946.239-0.001-0.0010.0000.0000.0000.000
199A695SER00.003-0.00644.4250.0020.0020.0000.0000.0000.000
200A696ASP-1-0.897-0.94941.732-0.028-0.0280.0000.0000.0000.000
201A697TYR0-0.048-0.04841.193-0.005-0.0050.0000.0000.0000.000
202A698ILE00.0390.01540.9130.0020.0020.0000.0000.0000.000
203A699LEU0-0.037-0.00638.4200.0020.0020.0000.0000.0000.000
204A700ASN0-0.122-0.05536.667-0.001-0.0010.0000.0000.0000.000
205A701LYS10.9660.99736.5430.0290.0290.0000.0000.0000.000
206A702SER00.0130.00037.545-0.002-0.0020.0000.0000.0000.000
207A703VAL00.0310.04833.9970.0000.0000.0000.0000.0000.000
208A704GLU-1-0.959-0.97832.897-0.072-0.0720.0000.0000.0000.000
209A705LYS10.9470.96630.9000.0890.0890.0000.0000.0000.000
210A706GLN00.0970.05829.174-0.014-0.0140.0000.0000.0000.000
211A707PHE00.0020.00028.265-0.001-0.0010.0000.0000.0000.000
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