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: YQK52

Calculation Name: 2HLY-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLY

Chain ID: A

ChEMBL ID:

UniProt ID: A9CI22

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 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2329774.636993
FMO2-HF: Nuclear repulsion 2249059.222984
FMO2-HF: Total energy -80715.414008
FMO2-MP2: Total energy -80947.97948


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:0:GLY )


Summations of interaction energy for fragment #1(A:0: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.
-0.7921.658-0.015-1.205-1.23-0.002
Interaction energy analysis for fragmet #1(A:0:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.001
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].
3A2PHE 00.0090.0043.806-2.0120.371-0.015-1.197-1.171-0.002
4A3GLU -1-0.951-0.9764.8261.7551.8220.000-0.008-0.0590.000
5A4GLY 00.002-0.0017.082-0.156-0.1560.0000.0000.0000.000
6A5MET 0-0.084-0.0328.692-0.278-0.2780.0000.0000.0000.000
7A6LEU 00.0220.03811.011-0.036-0.0360.0000.0000.0000.000
8A7ILE 00.0060.00013.642-0.061-0.0610.0000.0000.0000.000
9A8LYS 10.9890.9979.049-0.095-0.0950.0000.0000.0000.000
10A9GLN 00.0780.03110.365-0.113-0.1130.0000.0000.0000.000
11A10THR 0-0.017-0.01111.836-0.051-0.0510.0000.0000.0000.000
12A11ASP -1-0.778-0.90113.6990.1200.1200.0000.0000.0000.000
13A12TYR 00.023-0.01214.977-0.018-0.0180.0000.0000.0000.000
14A13PHE 00.0210.00215.216-0.018-0.0180.0000.0000.0000.000
15A14ARG 10.7840.89117.717-0.068-0.0680.0000.0000.0000.000
16A15ILE 0-0.0080.00218.942-0.013-0.0130.0000.0000.0000.000
17A16TYR 00.0640.03920.968-0.009-0.0090.0000.0000.0000.000
18A17ARG 10.8450.91220.879-0.059-0.0590.0000.0000.0000.000
19A18VAL 0-0.0400.00024.008-0.009-0.0090.0000.0000.0000.000
20A19ILE 0-0.001-0.00124.961-0.006-0.0060.0000.0000.0000.000
21A20ASN 00.0570.01826.799-0.005-0.0050.0000.0000.0000.000
22A21SER 0-0.059-0.04727.674-0.008-0.0080.0000.0000.0000.000
23A22LEU 0-0.067-0.03429.820-0.005-0.0050.0000.0000.0000.000
24A23LEU 0-0.008-0.00830.343-0.003-0.0030.0000.0000.0000.000
25A24ILE 00.0080.03432.366-0.003-0.0030.0000.0000.0000.000
26A25SER 0-0.072-0.04234.154-0.002-0.0020.0000.0000.0000.000
27A26GLN 0-0.025-0.01936.8360.0000.0000.0000.0000.0000.000
28A27ASN 0-0.036-0.01237.4020.0000.0000.0000.0000.0000.000
29A28ALA 0-0.027-0.00435.2270.0000.0000.0000.0000.0000.000
30A29ASP -1-0.715-0.83236.3390.0530.0530.0000.0000.0000.000
31A30PRO 00.0650.01633.5850.0040.0040.0000.0000.0000.000
32A31ALA 00.0040.02233.1770.0060.0060.0000.0000.0000.000
33A32SER 0-0.012-0.03334.2490.0050.0050.0000.0000.0000.000
34A33ALA 00.0100.00531.5410.0030.0030.0000.0000.0000.000
35A34SER 0-0.029-0.02929.6360.0070.0070.0000.0000.0000.000
36A35MET 0-0.031-0.00629.8910.0070.0070.0000.0000.0000.000
37A36TYR 00.0310.02131.3200.0030.0030.0000.0000.0000.000
38A37PHE 0-0.009-0.00925.7130.0060.0060.0000.0000.0000.000
39A38SER 0-0.011-0.00226.3170.0130.0130.0000.0000.0000.000
40A39THR 0-0.023-0.03527.2680.0060.0060.0000.0000.0000.000
41A40PHE 00.0060.00028.0570.0010.0010.0000.0000.0000.000
42A41GLY 00.0360.02024.1400.0030.0030.0000.0000.0000.000
43A42ALA 0-0.002-0.00223.8130.0110.0110.0000.0000.0000.000
44A43PHE 0-0.0120.00125.5000.0040.0040.0000.0000.0000.000
45A44ILE 00.0350.00821.828-0.001-0.0010.0000.0000.0000.000
46A45LEU 0-0.003-0.00719.0730.0040.0040.0000.0000.0000.000
47A46GLN 0-0.063-0.03522.238-0.003-0.0030.0000.0000.0000.000
48A47GLN 0-0.068-0.03725.044-0.004-0.0040.0000.0000.0000.000
49A48HIS 0-0.093-0.05020.818-0.001-0.0010.0000.0000.0000.000
50A49TYR 0-0.030-0.03515.161-0.014-0.0140.0000.0000.0000.000
51A50LYS 10.8930.97320.093-0.094-0.0940.0000.0000.0000.000
52A51VAL 00.0640.05219.2870.0010.0010.0000.0000.0000.000
53A52LYS 10.9250.94922.587-0.142-0.1420.0000.0000.0000.000
54A53ALA 00.0200.01423.4020.0170.0170.0000.0000.0000.000
55A54VAL 0-0.010-0.01425.019-0.016-0.0160.0000.0000.0000.000
56A55PRO 00.0110.01827.0920.0080.0080.0000.0000.0000.000
57A56LYS 10.8330.91428.225-0.137-0.1370.0000.0000.0000.000
58A57GLY 00.0930.03929.9860.0020.0020.0000.0000.0000.000
59A58GLY 0-0.017-0.00732.164-0.001-0.0010.0000.0000.0000.000
60A59LEU 0-0.0220.01331.470-0.002-0.0020.0000.0000.0000.000
61A60ALA 0-0.032-0.02027.8270.0080.0080.0000.0000.0000.000
62A61ALA 00.0150.01527.961-0.008-0.0080.0000.0000.0000.000
63A62TYR 00.003-0.02022.5640.0160.0160.0000.0000.0000.000
64A63ASN 00.0130.01423.517-0.012-0.0120.0000.0000.0000.000
65A64LEU 00.005-0.01421.9600.0150.0150.0000.0000.0000.000
66A65GLY 00.008-0.00921.906-0.010-0.0100.0000.0000.0000.000
67A66GLY 0-0.029-0.01122.897-0.010-0.0100.0000.0000.0000.000
68A67THR 0-0.0310.00325.849-0.004-0.0040.0000.0000.0000.000
69A68VAL 00.017-0.00126.8630.0080.0080.0000.0000.0000.000
70A69LEU 0-0.0110.01827.237-0.006-0.0060.0000.0000.0000.000
71A70LEU 0-0.004-0.02029.1600.0080.0080.0000.0000.0000.000
72A71PHE 0-0.037-0.01228.028-0.005-0.0050.0000.0000.0000.000
73A72ALA 00.008-0.02232.9350.0030.0030.0000.0000.0000.000
74A73ASP -1-0.808-0.89436.0970.0490.0490.0000.0000.0000.000
75A74HIS 0-0.036-0.00539.8130.0000.0000.0000.0000.0000.000
76A75ARG 10.9130.94541.495-0.047-0.0470.0000.0000.0000.000
77A76GLU -1-0.950-0.96744.1470.0410.0410.0000.0000.0000.000
78A77ASP -1-0.871-0.95441.9900.0460.0460.0000.0000.0000.000
79A78GLY 00.0520.04640.4440.0020.0020.0000.0000.0000.000
80A79TYR 0-0.060-0.04937.1200.0040.0040.0000.0000.0000.000
81A80VAL 0-0.051-0.02238.8950.0020.0020.0000.0000.0000.000
82A81THR 0-0.017-0.02536.1520.0020.0020.0000.0000.0000.000
83A82GLY 00.0300.04037.055-0.003-0.0030.0000.0000.0000.000
84A83ALA 0-0.018-0.02338.8080.0010.0010.0000.0000.0000.000
85A84GLY 0-0.007-0.01240.970-0.002-0.0020.0000.0000.0000.000
86A85GLU -1-0.896-0.96838.4230.0490.0490.0000.0000.0000.000
87A86ASN 00.0000.00735.9790.0030.0030.0000.0000.0000.000
88A87PHE 0-0.078-0.02934.8450.0050.0050.0000.0000.0000.000
89A88HIS 10.8530.90926.931-0.101-0.1010.0000.0000.0000.000
90A89CYS 0-0.020-0.01330.1320.0000.0000.0000.0000.0000.000
91A90TRP 0-0.007-0.00824.750-0.002-0.0020.0000.0000.0000.000
92A91VAL 0-0.016-0.01623.095-0.008-0.0080.0000.0000.0000.000
93A92GLU -1-0.806-0.88422.9010.1680.1680.0000.0000.0000.000
94A93ALA 0-0.005-0.02820.642-0.018-0.0180.0000.0000.0000.000
95A94ASP -1-0.901-0.94118.5150.3240.3240.0000.0000.0000.000
96A95GLY 0-0.0130.00218.7480.0340.0340.0000.0000.0000.000
97A96TRP 0-0.002-0.00211.6580.0120.0120.0000.0000.0000.000
98A97ALA 00.0340.02818.500-0.034-0.0340.0000.0000.0000.000
99A98ILE 0-0.026-0.02817.8660.0270.0270.0000.0000.0000.000
100A99ASP -1-0.685-0.79320.3010.1050.1050.0000.0000.0000.000
101A100PHE 0-0.019-0.01119.2380.0030.0030.0000.0000.0000.000
102A101MET 00.0200.03222.661-0.007-0.0070.0000.0000.0000.000
103A102ALA 00.0240.01821.275-0.008-0.0080.0000.0000.0000.000
104A103PRO 0-0.075-0.04820.659-0.008-0.0080.0000.0000.0000.000
105A104ALA 00.0560.02323.216-0.008-0.0080.0000.0000.0000.000
106A105PHE 0-0.042-0.02624.447-0.004-0.0040.0000.0000.0000.000
107A106SER 00.010-0.00926.785-0.002-0.0020.0000.0000.0000.000
108A107GLU -1-1.000-0.98328.8380.0460.0460.0000.0000.0000.000
109A108GLY 0-0.026-0.01831.9910.0030.0030.0000.0000.0000.000
110A109THR 0-0.009-0.01130.143-0.001-0.0010.0000.0000.0000.000
111A110ASP -1-0.868-0.91133.0220.0380.0380.0000.0000.0000.000
112A111ALA 0-0.047-0.04733.5080.0000.0000.0000.0000.0000.000
113A112LEU 0-0.055-0.03130.2280.0000.0000.0000.0000.0000.000
114A113ALA 0-0.0330.00029.4670.0020.0020.0000.0000.0000.000
115A114VAL 00.0280.02125.1350.0030.0030.0000.0000.0000.000
116A115PRO 0-0.033-0.01122.140-0.001-0.0010.0000.0000.0000.000
117A116ALA 00.0750.05322.6880.0090.0090.0000.0000.0000.000
118A117LYS 10.8610.93517.410-0.101-0.1010.0000.0000.0000.000
119A118MET 0-0.017-0.00412.0100.0070.0070.0000.0000.0000.000
120A119PHE 00.0150.01717.0700.0120.0120.0000.0000.0000.000
121A120GLN 00.000-0.04213.3410.0180.0180.0000.0000.0000.000
122A121ARG 10.9170.95814.515-0.203-0.2030.0000.0000.0000.000
123A122PRO 00.0220.01614.273-0.022-0.0220.0000.0000.0000.000
124A123LEU 00.0650.01717.015-0.028-0.0280.0000.0000.0000.000
125A124SER 0-0.070-0.03418.148-0.014-0.0140.0000.0000.0000.000
126A125ALA 0-0.039-0.02217.404-0.008-0.0080.0000.0000.0000.000
127A126MET 0-0.0910.00219.567-0.014-0.0140.0000.0000.0000.000
128A127ALA 00.0410.03122.839-0.004-0.0040.0000.0000.0000.000
129A128ALA 0-0.012-0.02625.143-0.002-0.0020.0000.0000.0000.000
130A129SER 0-0.044-0.02928.681-0.008-0.0080.0000.0000.0000.000
131A130ILE 00.025-0.00229.2710.0050.0050.0000.0000.0000.000
132A131ASN 0-0.011-0.01031.138-0.003-0.0030.0000.0000.0000.000
133A132ASP -1-0.918-0.94026.8290.1040.1040.0000.0000.0000.000
134A133LEU 0-0.0040.00725.4100.0100.0100.0000.0000.0000.000
135A134GLY 00.0410.03225.719-0.006-0.0060.0000.0000.0000.000
136A135GLN 0-0.052-0.02518.798-0.016-0.0160.0000.0000.0000.000
137A136SER 00.0000.00119.2820.0020.0020.0000.0000.0000.000
138A137GLY 00.0240.00518.2590.0140.0140.0000.0000.0000.000
139A138ASP -1-0.878-0.91719.2980.1610.1610.0000.0000.0000.000
140A139PHE 0-0.032-0.02719.574-0.006-0.0060.0000.0000.0000.000
141A140PHE 0-0.0050.00623.7380.0010.0010.0000.0000.0000.000
142A141TYR 0-0.011-0.04023.4680.0020.0020.0000.0000.0000.000
143A142ARG 10.9040.94728.365-0.075-0.0750.0000.0000.0000.000
144A143SER 00.001-0.01130.978-0.002-0.0020.0000.0000.0000.000
145A144GLU -1-0.841-0.92232.5220.0670.0670.0000.0000.0000.000
146A145PRO 00.0000.00835.364-0.001-0.0010.0000.0000.0000.000
147A146GLU -1-0.875-0.94536.7800.0650.0650.0000.0000.0000.000
148A147ALA 0-0.014-0.00938.255-0.003-0.0030.0000.0000.0000.000
149A148THR 00.024-0.00133.935-0.001-0.0010.0000.0000.0000.000
150A149ALA 0-0.016-0.00637.007-0.001-0.0010.0000.0000.0000.000
151A150ARG 10.9370.95139.401-0.053-0.0530.0000.0000.0000.000
152A151ARG 10.8700.95737.962-0.061-0.0610.0000.0000.0000.000
153A152PHE 00.0070.00533.126-0.001-0.0010.0000.0000.0000.000
154A153ALA 0-0.0040.01539.088-0.001-0.0010.0000.0000.0000.000
155A154ASP -1-0.864-0.95042.5950.0410.0410.0000.0000.0000.000
156A155TRP 00.008-0.01034.048-0.001-0.0010.0000.0000.0000.000
157A156HIS 0-0.039-0.01640.499-0.003-0.0030.0000.0000.0000.000
158A157LYS 10.8930.96141.602-0.041-0.0410.0000.0000.0000.000
159A158GLN 0-0.025-0.01341.330-0.003-0.0030.0000.0000.0000.000
160A159ALA 00.0250.00540.8580.0020.0020.0000.0000.0000.000
161A160MET 00.0180.00937.2530.0010.0010.0000.0000.0000.000
162A161ILE 00.0430.02735.6720.0010.0010.0000.0000.0000.000
163A162GLY 00.0220.00835.5060.0030.0030.0000.0000.0000.000
164A163ASP -1-0.793-0.86535.4580.0410.0410.0000.0000.0000.000
165A164MET 0-0.036-0.01233.363-0.001-0.0010.0000.0000.0000.000
166A165ALA 00.0410.02931.2660.0030.0030.0000.0000.0000.000
167A166SER 0-0.025-0.00930.5800.0040.0040.0000.0000.0000.000
168A167VAL 00.0090.00631.2080.0000.0000.0000.0000.0000.000
169A168ALA 00.0280.00527.7590.0000.0000.0000.0000.0000.000
170A169ALA 0-0.028-0.01326.4970.0040.0040.0000.0000.0000.000
171A170ASN 0-0.036-0.01926.6350.0000.0000.0000.0000.0000.000
172A171TRP 0-0.079-0.03526.999-0.003-0.0030.0000.0000.0000.000
173A172PHE 0-0.007-0.01218.193-0.004-0.0040.0000.0000.0000.000
174A173ARG 10.9190.95721.618-0.035-0.0350.0000.0000.0000.000
175A174LYS 10.9420.99516.184-0.166-0.1660.0000.0000.0000.000
176A175SER 0-0.023-0.00514.139-0.036-0.0360.0000.0000.0000.000
177A176PRO 0-0.004-0.00615.0660.0070.0070.0000.0000.0000.000
178A177LYS 10.9340.95416.982-0.042-0.0420.0000.0000.0000.000
179A178GLN 00.0440.06120.4630.0150.0150.0000.0000.0000.000
180A179MET 0-0.045-0.04022.2290.0050.0050.0000.0000.0000.000
181A180ALA 00.0160.01824.766-0.005-0.0050.0000.0000.0000.000
182A181ALA 00.0680.03727.8390.0040.0040.0000.0000.0000.000
183A182SER 0-0.033-0.01229.1100.0020.0020.0000.0000.0000.000
184A183LEU 00.0100.00830.460-0.002-0.0020.0000.0000.0000.000
185A184SER 00.0120.01833.7080.0000.0000.0000.0000.0000.000
186A185VAL 0-0.009-0.01335.1210.0020.0020.0000.0000.0000.000
187A186THR 00.0000.00037.878-0.002-0.0020.0000.0000.0000.000
188A187ASP -1-0.831-0.91340.8490.0280.0280.0000.0000.0000.000
189A188ARG 10.8310.85341.201-0.037-0.0370.0000.0000.0000.000
190A189ASP -1-0.867-0.90845.3050.0230.0230.0000.0000.0000.000
191A190GLY 0-0.032-0.01046.199-0.001-0.0010.0000.0000.0000.000
192A191LYS 10.7800.88646.053-0.024-0.0240.0000.0000.0000.000
193A192ALA 0-0.0010.00341.4850.0020.0020.0000.0000.0000.000
194A193ARG 10.9650.98637.092-0.034-0.0340.0000.0000.0000.000
195A194THR 0-0.001-0.00236.2030.0010.0010.0000.0000.0000.000
196A195VAL 0-0.019-0.01132.6380.0000.0000.0000.0000.0000.000
197A196PRO 00.0200.00532.1750.0000.0000.0000.0000.0000.000
198A197LEU 0-0.014-0.01425.1460.0040.0040.0000.0000.0000.000
199A198THR 00.0020.00227.741-0.003-0.0030.0000.0000.0000.000
200A199GLY 00.026-0.00426.7960.0010.0010.0000.0000.0000.000
201A200GLU -1-0.904-0.92524.3090.0500.0500.0000.0000.0000.000
202A201MET 0-0.012-0.00620.8100.0010.0010.0000.0000.0000.000
203A202LEU 00.0110.00419.2680.0040.0040.0000.0000.0000.000
204A203THR 0-0.041-0.02116.078-0.003-0.0030.0000.0000.0000.000
205A204GLY 00.0620.02814.774-0.003-0.0030.0000.0000.0000.000
206A205ALA 0-0.066-0.05012.6600.0160.0160.0000.0000.0000.000
207A206TRP -1-0.859-0.92514.7770.2350.2350.0000.0000.0000.000