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: 6N14Z

Calculation Name: 2YT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YT4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYQ5

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2300856.925382
FMO2-HF: Nuclear repulsion 2218818.025321
FMO2-HF: Total energy -82038.900061
FMO2-MP2: Total energy -82275.200482


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:489:GLY)


Summations of interaction energy for fragment #1(A:489:GLY)
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.
-1.5560.5780.753-1.492-1.3950.002
Interaction energy analysis for fragmet #1(A:489:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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].
3A491HIS0-0.005-0.0113.775-2.047-1.296-0.003-0.537-0.2100.000
4A492MET00.0040.0095.9640.5490.5490.0000.0000.0000.000
5A493SER00.015-0.0068.812-0.130-0.1300.0000.0000.0000.000
6A494VAL0-0.027-0.00312.0230.0730.0730.0000.0000.0000.000
7A495GLN00.004-0.01714.270-0.007-0.0070.0000.0000.0000.000
8A496ASP-1-0.833-0.90817.992-0.089-0.0890.0000.0000.0000.000
9A497ALA0-0.028-0.04621.4850.0000.0000.0000.0000.0000.000
10A498PRO00.0480.04822.1100.0000.0000.0000.0000.0000.000
11A499THR00.0360.01323.387-0.001-0.0010.0000.0000.0000.000
12A500LYS10.8890.94523.7960.0560.0560.0000.0000.0000.000
13A501LYS10.7990.90921.1370.1070.1070.0000.0000.0000.000
14A502GLU-1-0.782-0.87616.221-0.115-0.1150.0000.0000.0000.000
15A503PHE0-0.028-0.01215.151-0.012-0.0120.0000.0000.0000.000
16A504VAL00.0580.04610.6550.0010.0010.0000.0000.0000.000
17A505ILE0-0.021-0.0088.8410.0240.0240.0000.0000.0000.000
18A506ASN00.0500.0236.010-0.689-0.6890.0000.0000.0000.000
19A507PRO00.0150.0112.9640.0700.4500.037-0.116-0.3010.000
20A508ASN0-0.006-0.0062.4031.1451.6560.705-0.569-0.6470.000
21A509GLY00.0490.0194.2610.2700.3360.001-0.039-0.0280.000
22A510LYS10.7730.8817.0871.1131.1130.0000.0000.0000.000
23A511SER00.012-0.0048.041-0.014-0.0140.0000.0000.0000.000
24A512GLU-1-0.738-0.8858.887-0.126-0.1260.0000.0000.0000.000
25A513VAL0-0.028-0.01910.6400.0110.0110.0000.0000.0000.000
26A514CYS0-0.058-0.01811.7030.0280.0280.0000.0000.0000.000
27A515ILE00.0420.0346.7230.0010.0010.0000.0000.0000.000
28A516LEU0-0.0020.00910.8380.0260.0260.0000.0000.0000.000
29A517HIS0-0.007-0.01713.7910.0340.0340.0000.0000.0000.000
30A518GLU-1-0.810-0.87912.081-0.612-0.6120.0000.0000.0000.000
31A519TYR00.0320.01012.7550.0240.0240.0000.0000.0000.000
32A520MET00.0060.01014.6170.0300.0300.0000.0000.0000.000
33A521GLN00.0240.01717.9950.0140.0140.0000.0000.0000.000
34A522ARG10.7680.84912.7820.4690.4690.0000.0000.0000.000
35A523VAL0-0.045-0.01615.9560.0140.0140.0000.0000.0000.000
36A524LEU0-0.035-0.01718.9770.0180.0180.0000.0000.0000.000
37A525LYS10.9160.97521.3470.1440.1440.0000.0000.0000.000
38A526VAL00.0240.02422.0290.0110.0110.0000.0000.0000.000
39A527ARG10.9550.96721.5210.0990.0990.0000.0000.0000.000
40A528PRO00.0060.00218.3540.0130.0130.0000.0000.0000.000
41A529VAL0-0.0180.00821.414-0.005-0.0050.0000.0000.0000.000
42A530TYR00.015-0.01216.8420.0080.0080.0000.0000.0000.000
43A531ASN00.0110.00423.2630.0050.0050.0000.0000.0000.000
44A532PHE0-0.034-0.04522.555-0.004-0.0040.0000.0000.0000.000
45A533PHE00.0320.02424.9930.0000.0000.0000.0000.0000.000
46A534GLU-1-0.916-0.94027.9590.0050.0050.0000.0000.0000.000
47A535CYS0-0.044-0.03327.7290.0050.0050.0000.0000.0000.000
48A536GLU-1-0.874-0.92129.9090.0250.0250.0000.0000.0000.000
49A537ASN0-0.002-0.01526.5530.0030.0030.0000.0000.0000.000
50A538PRO00.027-0.00428.8930.0000.0000.0000.0000.0000.000
51A539SER00.0010.01425.1410.0000.0000.0000.0000.0000.000
52A540GLU-1-0.929-0.97320.7980.0890.0890.0000.0000.0000.000
53A541PRO00.0380.04925.1790.0000.0000.0000.0000.0000.000
54A542PHE0-0.018-0.01024.039-0.008-0.0080.0000.0000.0000.000
55A543GLY00.0750.03023.8570.0060.0060.0000.0000.0000.000
56A544ALA0-0.087-0.06121.131-0.012-0.0120.0000.0000.0000.000
57A545SER00.0500.02222.2120.0090.0090.0000.0000.0000.000
58A546VAL00.002-0.00218.314-0.016-0.0160.0000.0000.0000.000
59A547THR0-0.017-0.00221.7880.0100.0100.0000.0000.0000.000
60A548ILE0-0.010-0.02221.246-0.013-0.0130.0000.0000.0000.000
61A549ASP-1-0.864-0.92925.500-0.025-0.0250.0000.0000.0000.000
62A550GLY00.0030.00828.8570.0040.0040.0000.0000.0000.000
63A551VAL0-0.0190.00926.7590.0050.0050.0000.0000.0000.000
64A552THR00.003-0.02024.603-0.009-0.0090.0000.0000.0000.000
65A553TYR0-0.044-0.03420.6880.0030.0030.0000.0000.0000.000
66A554GLY00.0570.04518.6750.0110.0110.0000.0000.0000.000
67A555SER0-0.058-0.05819.730-0.015-0.0150.0000.0000.0000.000
68A556GLY00.007-0.00519.5110.0150.0150.0000.0000.0000.000
69A557THR00.0330.02320.497-0.013-0.0130.0000.0000.0000.000
70A558ALA0-0.006-0.00819.4950.0130.0130.0000.0000.0000.000
71A559SER00.0900.05821.285-0.010-0.0100.0000.0000.0000.000
72A560SER00.017-0.00120.332-0.013-0.0130.0000.0000.0000.000
73A561LYS10.9841.00321.0410.0350.0350.0000.0000.0000.000
74A562LYS10.9620.98216.3710.0900.0900.0000.0000.0000.000
75A563LEU00.0370.01715.898-0.019-0.0190.0000.0000.0000.000
76A564ALA00.0360.03716.8960.0050.0050.0000.0000.0000.000
77A565LYS10.8930.95918.2780.1050.1050.0000.0000.0000.000
78A566ASN0-0.028-0.03613.099-0.050-0.0500.0000.0000.0000.000
79A567LYS10.8260.91014.027-0.091-0.0910.0000.0000.0000.000
80A568ALA00.0260.03115.8190.0120.0120.0000.0000.0000.000
81A569ALA0-0.017-0.01014.1260.0010.0010.0000.0000.0000.000
82A570ARG10.8250.9007.696-0.371-0.3710.0000.0000.0000.000
83A571ALA00.0120.02112.7280.0230.0230.0000.0000.0000.000
84A572THR00.009-0.01615.7930.0090.0090.0000.0000.0000.000
85A573LEU0-0.038-0.01110.528-0.012-0.0120.0000.0000.0000.000
86A574GLU-1-0.804-0.89712.3060.3330.3330.0000.0000.0000.000
87A575ILE0-0.0200.00514.0270.0160.0160.0000.0000.0000.000
88A576LEU0-0.0110.00616.148-0.011-0.0110.0000.0000.0000.000
89A577ILE0-0.043-0.01810.982-0.014-0.0140.0000.0000.0000.000
90A578PRO0-0.025-0.01213.9320.0400.0400.0000.0000.0000.000
91A579ASP-1-0.836-0.91112.3400.3160.3160.0000.0000.0000.000
92A580PHE00.0140.0187.9970.1050.1050.0000.0000.0000.000
93A581VAL00.015-0.0028.4690.1250.1250.0000.0000.0000.000
94A582LYS10.8540.9063.791-2.905-2.4360.014-0.218-0.2650.002
95A583GLN00.0170.0234.4560.0950.052-0.001-0.0130.0560.000
96A592SER0-0.061-0.03919.2970.0020.0020.0000.0000.0000.000
97A593GLU-1-0.909-0.97420.2130.1540.1540.0000.0000.0000.000
98A594GLU-1-0.912-0.94621.9850.0900.0900.0000.0000.0000.000
99A595LEU0-0.053-0.03222.978-0.017-0.0170.0000.0000.0000.000
100A596GLU-1-0.833-0.90719.4250.1640.1640.0000.0000.0000.000
101A597TYR00.0350.01421.821-0.015-0.0150.0000.0000.0000.000
102A598PHE0-0.011-0.02424.479-0.019-0.0190.0000.0000.0000.000
103A599ASN0-0.014-0.01119.591-0.019-0.0190.0000.0000.0000.000
104A600HIS0-0.031-0.01820.064-0.003-0.0030.0000.0000.0000.000
105A601ILE0-0.049-0.00524.117-0.011-0.0110.0000.0000.0000.000
106A602SER0-0.004-0.02426.707-0.001-0.0010.0000.0000.0000.000
107A603ILE00.0390.03426.3570.0060.0060.0000.0000.0000.000
108A604GLU-1-0.883-0.95329.775-0.004-0.0040.0000.0000.0000.000
109A605ASP-1-0.832-0.87331.7960.0110.0110.0000.0000.0000.000
110A606SER00.014-0.01033.6240.0030.0030.0000.0000.0000.000
111A607ARG10.8650.90632.288-0.014-0.0140.0000.0000.0000.000
112A608VAL00.0300.02930.5220.0040.0040.0000.0000.0000.000
113A609TYR00.0500.04533.1030.0030.0030.0000.0000.0000.000
114A610GLU-1-0.943-0.96236.0460.0280.0280.0000.0000.0000.000
115A611LEU00.0180.00530.5770.0030.0030.0000.0000.0000.000
116A612THR0-0.012-0.02530.6980.0040.0040.0000.0000.0000.000
117A613SER0-0.058-0.04132.8820.0030.0030.0000.0000.0000.000
118A614LYS10.9030.95335.167-0.041-0.0410.0000.0000.0000.000
119A615ALA00.0060.00930.4800.0020.0020.0000.0000.0000.000
120A616GLY00.0150.02531.9970.0050.0050.0000.0000.0000.000
121A617LEU0-0.010-0.01027.7550.0020.0020.0000.0000.0000.000
122A618LEU0-0.0030.00230.724-0.006-0.0060.0000.0000.0000.000
123A619SER0-0.029-0.02532.128-0.001-0.0010.0000.0000.0000.000
124A620PRO00.010-0.01433.2160.0000.0000.0000.0000.0000.000
125A621TYR00.010-0.01134.283-0.001-0.0010.0000.0000.0000.000
126A622GLN00.0060.01434.5190.0010.0010.0000.0000.0000.000
127A623ILE00.0630.02828.6100.0000.0000.0000.0000.0000.000
128A624LEU0-0.018-0.00331.406-0.002-0.0020.0000.0000.0000.000
129A625HIS0-0.017-0.02233.8710.0000.0000.0000.0000.0000.000
130A626GLU-1-0.832-0.89830.0580.0410.0410.0000.0000.0000.000
131A627CYS0-0.026-0.00729.880-0.002-0.0020.0000.0000.0000.000
132A628LEU0-0.026-0.00830.881-0.003-0.0030.0000.0000.0000.000
133A629LYS10.8620.91633.063-0.038-0.0380.0000.0000.0000.000
134A630ARG10.8120.89123.657-0.049-0.0490.0000.0000.0000.000
135A631ASN0-0.019-0.01228.457-0.006-0.0060.0000.0000.0000.000
136A632HIS00.0690.03331.7270.0000.0000.0000.0000.0000.000
137A633GLY0-0.003-0.00434.175-0.002-0.0020.0000.0000.0000.000
138A634MET0-0.045-0.01232.400-0.002-0.0020.0000.0000.0000.000
139A635GLY00.0200.01536.319-0.002-0.0020.0000.0000.0000.000
140A636ASP-1-0.889-0.93539.9850.0030.0030.0000.0000.0000.000
141A637THR0-0.003-0.01239.220-0.001-0.0010.0000.0000.0000.000
142A638SER0-0.060-0.01341.8980.0010.0010.0000.0000.0000.000
143A639ILE0-0.027-0.03243.0940.0000.0000.0000.0000.0000.000
144A640LYS10.8620.91245.801-0.001-0.0010.0000.0000.0000.000
145A641PHE0-0.030-0.03448.2290.0000.0000.0000.0000.0000.000
146A642GLU-1-0.771-0.85450.5450.0020.0020.0000.0000.0000.000
147A643VAL0-0.048-0.03153.2720.0000.0000.0000.0000.0000.000
148A644VAL00.1200.06055.4470.0000.0000.0000.0000.0000.000
149A645PRO00.0190.01858.2530.0010.0010.0000.0000.0000.000
150A646GLY00.020-0.00854.9720.0000.0000.0000.0000.0000.000
151A647LYS10.9190.96554.375-0.007-0.0070.0000.0000.0000.000
152A648ASN0-0.026-0.01955.5770.0010.0010.0000.0000.0000.000
153A649GLN00.0070.00655.473-0.001-0.0010.0000.0000.0000.000
154A650LYS10.9150.97446.3130.0000.0000.0000.0000.0000.000
155A651SER00.0710.03950.039-0.001-0.0010.0000.0000.0000.000
156A652GLU-1-0.810-0.88349.096-0.003-0.0030.0000.0000.0000.000
157A653TYR0-0.011-0.01742.1530.0010.0010.0000.0000.0000.000
158A654VAL00.009-0.00445.746-0.001-0.0010.0000.0000.0000.000
159A655MET0-0.030-0.01438.6800.0020.0020.0000.0000.0000.000
160A656ALA00.0150.01842.389-0.002-0.0020.0000.0000.0000.000
161A657CYS0-0.015-0.02737.3060.0030.0030.0000.0000.0000.000
162A658GLY00.1090.06638.650-0.002-0.0020.0000.0000.0000.000
163A659LYS10.8090.90433.0060.0230.0230.0000.0000.0000.000
164A660HIS0-0.0230.00034.457-0.002-0.0020.0000.0000.0000.000
165A661THR00.013-0.00239.4420.0030.0030.0000.0000.0000.000
166A662VAL00.0050.01238.618-0.002-0.0020.0000.0000.0000.000
167A663ARG10.8790.91042.0010.0060.0060.0000.0000.0000.000
168A664GLY0-0.015-0.00743.326-0.001-0.0010.0000.0000.0000.000
169A665TRP00.0520.03745.2540.0010.0010.0000.0000.0000.000
170A666CYS0-0.132-0.04445.4520.0010.0010.0000.0000.0000.000
171A667LYS11.0300.99346.932-0.008-0.0080.0000.0000.0000.000
172A668ASN00.0510.02546.9040.0010.0010.0000.0000.0000.000
173A669LYS11.0271.01747.001-0.011-0.0110.0000.0000.0000.000
174A670ARG10.9290.96942.205-0.025-0.0250.0000.0000.0000.000
175A671VAL00.0340.00441.9010.0010.0010.0000.0000.0000.000
176A672GLY00.0130.00242.0020.0000.0000.0000.0000.0000.000
177A673LYS10.9370.98541.181-0.018-0.0180.0000.0000.0000.000
178A674GLN00.0370.04937.8600.0010.0010.0000.0000.0000.000
179A675LEU00.0440.02037.5710.0000.0000.0000.0000.0000.000
180A676ALA0-0.016-0.00138.175-0.002-0.0020.0000.0000.0000.000
181A677SER00.009-0.02236.261-0.001-0.0010.0000.0000.0000.000
182A678GLN0-0.071-0.05333.4550.0010.0010.0000.0000.0000.000
183A679LYS10.9160.96633.4550.0020.0020.0000.0000.0000.000
184A680ILE00.0080.00534.632-0.003-0.0030.0000.0000.0000.000
185A681LEU0-0.008-0.00229.796-0.002-0.0020.0000.0000.0000.000
186A682GLN0-0.012-0.00527.8140.0000.0000.0000.0000.0000.000
187A683LEU0-0.022-0.02930.362-0.005-0.0050.0000.0000.0000.000
188A684LEU0-0.0010.01030.761-0.003-0.0030.0000.0000.0000.000
189A685HIS10.7930.88125.492-0.002-0.0020.0000.0000.0000.000
190A686PRO00.0300.02227.079-0.001-0.0010.0000.0000.0000.000
191A687HIS0-0.012-0.00423.457-0.007-0.0070.0000.0000.0000.000
192A688VAL00.0310.01422.304-0.005-0.0050.0000.0000.0000.000
193A689LYS10.9150.96823.4860.0170.0170.0000.0000.0000.000
194A690ASN0-0.0040.01920.2920.0120.0120.0000.0000.0000.000
195A691TRP00.0980.03824.577-0.003-0.0030.0000.0000.0000.000
196A692GLY00.0610.02622.3000.0050.0050.0000.0000.0000.000
197A693SER0-0.006-0.01920.4860.0110.0110.0000.0000.0000.000
198A694LEU0-0.037-0.01921.4610.0030.0030.0000.0000.0000.000
199A695LEU00.0270.01024.0680.0030.0030.0000.0000.0000.000
200A696ARG10.8060.90016.037-0.082-0.0820.0000.0000.0000.000
201A697MET0-0.016-0.00121.4860.0030.0030.0000.0000.0000.000
202A698TYR0-0.010-0.01623.198-0.005-0.0050.0000.0000.0000.000
203A699GLY00.0240.01225.148-0.005-0.0050.0000.0000.0000.000
204A700ARG10.8430.93815.928-0.201-0.2010.0000.0000.0000.000
205A701GLU-1-0.882-0.90620.4720.0690.0690.0000.0000.0000.000