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: YZL52

Calculation Name: 2HLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLC

Chain ID: A

ChEMBL ID:

UniProt ID: P08897

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2864891.076977
FMO2-HF: Nuclear repulsion 2775899.519631
FMO2-HF: Total energy -88991.557346
FMO2-MP2: Total energy -89250.384891


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:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
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.
-30.932-28.37346.403-18.661-30.301-0.125
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.045
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].
3A18ASN0-0.084-0.0653.1030.0342.1220.231-0.976-1.3430.001
4A19GLY00.0270.0112.372-0.2740.4121.646-1.011-1.321-0.001
5A20TYR0-0.090-0.0393.0000.245-1.0060.1181.412-0.2790.000
6A21GLU-1-0.850-0.9255.6770.8590.8590.0000.0000.0000.000
7A22ALA0-0.025-0.0147.298-0.085-0.0850.0000.0000.0000.000
8A23TYR00.0120.0088.935-0.078-0.0780.0000.0000.0000.000
9A24THR00.012-0.01712.1760.0330.0330.0000.0000.0000.000
10A25GLY00.0770.03813.983-0.016-0.0160.0000.0000.0000.000
11A26LEU0-0.093-0.0069.567-0.008-0.0080.0000.0000.0000.000
12A27PHE0-0.007-0.0177.2850.0330.0330.0000.0000.0000.000
13A28PRO00.0080.00611.261-0.031-0.0310.0000.0000.0000.000
14A29TYR00.0590.0388.911-0.042-0.0420.0000.0000.0000.000
15A30GLN0-0.0160.0016.8720.0870.0870.0000.0000.0000.000
16A31ALA00.0010.00110.615-0.014-0.0140.0000.0000.0000.000
17A32GLY00.0260.00410.445-0.040-0.0400.0000.0000.0000.000
18A33LEU0-0.066-0.03211.5850.0500.0500.0000.0000.0000.000
19A34ASP-1-0.753-0.84713.083-0.275-0.2750.0000.0000.0000.000
20A35ILE0-0.010-0.00513.8070.0490.0490.0000.0000.0000.000
21A36THR00.0040.01117.113-0.022-0.0220.0000.0000.0000.000
22A37LEU0-0.011-0.00217.6550.0160.0160.0000.0000.0000.000
23A37GLN00.010-0.01221.2620.0110.0110.0000.0000.0000.000
24A37ASP-1-0.883-0.93121.915-0.223-0.2230.0000.0000.0000.000
25A37GLN0-0.067-0.04723.776-0.003-0.0030.0000.0000.0000.000
26A38ARG10.8570.94118.6590.2790.2790.0000.0000.0000.000
27A39ARG10.8350.88816.6240.2170.2170.0000.0000.0000.000
28A40VAL00.0060.00112.635-0.048-0.0480.0000.0000.0000.000
29A41TRP00.0140.0247.8870.1540.1540.0000.0000.0000.000
30A42CYS0-0.091-0.0269.210-0.200-0.2000.0000.0000.0000.000
31A43GLY00.0600.0398.0110.0780.0780.0000.0000.0000.000
32A44GLY00.0220.0009.0570.0000.0000.0000.0000.0000.000
33A45SER0-0.0210.00010.4630.0810.0810.0000.0000.0000.000
34A46LEU00.0070.01312.425-0.034-0.0340.0000.0000.0000.000
35A47ILE0-0.034-0.02815.7710.0250.0250.0000.0000.0000.000
36A48ASP-1-0.849-0.95118.0050.0510.0510.0000.0000.0000.000
37A49ASN0-0.023-0.01220.656-0.003-0.0030.0000.0000.0000.000
38A50LYS10.8900.94823.016-0.036-0.0360.0000.0000.0000.000
39A51TRP0-0.005-0.00720.528-0.017-0.0170.0000.0000.0000.000
40A52ILE00.0450.03914.5350.0180.0180.0000.0000.0000.000
41A53LEU0-0.041-0.01514.670-0.015-0.0150.0000.0000.0000.000
42A54THR00.019-0.01012.098-0.002-0.0020.0000.0000.0000.000
43A55ALA00.0410.02512.2220.0330.0330.0000.0000.0000.000
44A56ALA0-0.022-0.01314.120-0.017-0.0170.0000.0000.0000.000
45A57HIS0-0.056-0.04311.297-0.106-0.1060.0000.0000.0000.000
46A59VAL00.009-0.01814.8740.0090.0090.0000.0000.0000.000
47A59HIS0-0.0300.00218.2710.0440.0440.0000.0000.0000.000
48A60ASP-1-0.880-0.93219.945-0.210-0.2100.0000.0000.0000.000
49A61ALA0-0.007-0.00719.334-0.005-0.0050.0000.0000.0000.000
50A62VAL0-0.090-0.03421.3040.0200.0200.0000.0000.0000.000
51A63SER0-0.069-0.05022.2300.0160.0160.0000.0000.0000.000
52A64VAL00.0470.01917.157-0.021-0.0210.0000.0000.0000.000
53A65VAL0-0.0140.00618.4760.0250.0250.0000.0000.0000.000
54A66VAL0-0.010-0.01916.011-0.021-0.0210.0000.0000.0000.000
55A67TYR0-0.020-0.00513.9830.0180.0180.0000.0000.0000.000
56A68LEU00.043-0.00114.3400.0080.0080.0000.0000.0000.000
57A69GLY00.0790.03215.161-0.011-0.0110.0000.0000.0000.000
58A70SER0-0.022-0.01114.1890.0160.0160.0000.0000.0000.000
59A71ALA00.0240.01510.243-0.004-0.0040.0000.0000.0000.000
60A72VAL00.0030.01310.1730.0750.0750.0000.0000.0000.000
61A73GLN00.0120.0049.5440.0160.0160.0000.0000.0000.000
62A74TYR0-0.085-0.04911.701-0.028-0.0280.0000.0000.0000.000
63A75GLU-1-0.915-0.95014.5290.0740.0740.0000.0000.0000.000
64A76GLY0-0.022-0.03315.2440.0100.0100.0000.0000.0000.000
65A80GLU-1-0.899-0.91917.4840.1110.1110.0000.0000.0000.000
66A81ALA0-0.024-0.01419.292-0.011-0.0110.0000.0000.0000.000
67A82VAL00.0040.00518.8350.0000.0000.0000.0000.0000.000
68A83VAL0-0.029-0.00520.241-0.001-0.0010.0000.0000.0000.000
69A84ASN00.0110.00220.801-0.007-0.0070.0000.0000.0000.000
70A85SER00.0000.00421.0470.0040.0040.0000.0000.0000.000
71A86GLU-1-0.946-0.98822.840-0.012-0.0120.0000.0000.0000.000
72A87ARG10.9110.94024.5370.0290.0290.0000.0000.0000.000
73A88ILE00.0470.04320.7730.0050.0050.0000.0000.0000.000
74A89ILE0-0.072-0.04022.0730.0020.0020.0000.0000.0000.000
75A90SER00.0940.03820.930-0.002-0.0020.0000.0000.0000.000
76A91HIS0-0.0090.00121.0640.0020.0020.0000.0000.0000.000
77A92SER0-0.010-0.01722.872-0.009-0.0090.0000.0000.0000.000
78A93MET0-0.042-0.01725.244-0.003-0.0030.0000.0000.0000.000
79A94PHE00.0540.04317.8060.0010.0010.0000.0000.0000.000
80A95ASN0-0.024-0.00621.500-0.011-0.0110.0000.0000.0000.000
81A96PRO00.001-0.01720.014-0.006-0.0060.0000.0000.0000.000
82A97ASP-1-0.925-0.95119.882-0.169-0.1690.0000.0000.0000.000
83A98THR0-0.050-0.03520.573-0.006-0.0060.0000.0000.0000.000
84A99TYR00.0120.01614.846-0.001-0.0010.0000.0000.0000.000
85A100LEU00.0050.01617.7270.0190.0190.0000.0000.0000.000
86A101ASN0-0.032-0.03819.9830.0030.0030.0000.0000.0000.000
87A102ASP-1-0.687-0.79714.092-0.222-0.2220.0000.0000.0000.000
88A103VAL0-0.051-0.00715.4220.0060.0060.0000.0000.0000.000
89A104ALA00.012-0.00716.758-0.007-0.0070.0000.0000.0000.000
90A105LEU0-0.0160.00217.3300.0130.0130.0000.0000.0000.000
91A106ILE00.0180.01717.346-0.013-0.0130.0000.0000.0000.000
92A107LYS10.8800.95520.1190.0170.0170.0000.0000.0000.000
93A108ILE00.0090.00619.575-0.013-0.0130.0000.0000.0000.000
94A109PRO00.0250.00923.2030.0070.0070.0000.0000.0000.000
95A111HIS0-0.121-0.08724.352-0.001-0.0010.0000.0000.0000.000
96A112VAL00.0260.02820.954-0.002-0.0020.0000.0000.0000.000
97A113GLU-1-0.903-0.93523.8590.0670.0670.0000.0000.0000.000
98A114TYR00.001-0.00120.8300.0040.0040.0000.0000.0000.000
99A115THR0-0.025-0.03621.155-0.002-0.0020.0000.0000.0000.000
100A116ASP-1-0.911-0.94621.0950.1480.1480.0000.0000.0000.000
101A117ASN0-0.069-0.04616.8860.0430.0430.0000.0000.0000.000
102A118ILE0-0.0350.00516.3140.0130.0130.0000.0000.0000.000
103A119GLN0-0.020-0.03216.910-0.016-0.0160.0000.0000.0000.000
104A120PRO0-0.0070.01716.4550.0100.0100.0000.0000.0000.000
105A121ILE0-0.0060.00112.9190.0190.0190.0000.0000.0000.000
106A122ARG10.7630.86415.799-0.202-0.2020.0000.0000.0000.000
107A123LEU00.0360.01016.6680.0180.0180.0000.0000.0000.000
108A124PRO0-0.0050.00317.828-0.004-0.0040.0000.0000.0000.000
109A125SER00.000-0.02020.700-0.018-0.0180.0000.0000.0000.000
110A125GLY00.0230.00124.4710.0070.0070.0000.0000.0000.000
111A125GLU-1-0.843-0.94426.7600.0820.0820.0000.0000.0000.000
112A126GLU-1-0.841-0.88921.2910.1620.1620.0000.0000.0000.000
113A127LEU0-0.028-0.01822.0640.0080.0080.0000.0000.0000.000
114A128ASN00.0020.00523.843-0.010-0.0100.0000.0000.0000.000
115A129ASN0-0.041-0.00521.3380.0020.0020.0000.0000.0000.000
116A130LYS10.9430.97020.344-0.091-0.0910.0000.0000.0000.000
117A131PHE0-0.005-0.02216.5540.0120.0120.0000.0000.0000.000
118A132GLU-1-0.867-0.94416.8600.1470.1470.0000.0000.0000.000
119A133ASN0-0.059-0.03517.023-0.002-0.0020.0000.0000.0000.000
120A134ILE0-0.0140.01714.787-0.002-0.0020.0000.0000.0000.000
121A135TRP00.0070.00210.1450.0260.0260.0000.0000.0000.000
122A136ALA0-0.019-0.00410.128-0.054-0.0540.0000.0000.0000.000
123A137THR0-0.022-0.0276.6800.1500.1500.0000.0000.0000.000
124A138VAL0-0.0200.0132.511-1.182-0.4930.846-0.275-1.2610.003
125A139SER0-0.020-0.0322.804-0.2490.8240.416-0.484-1.004-0.001
126A140GLY0-0.011-0.0102.917-1.368-0.6040.268-0.034-0.998-0.002
127A141TRP0-0.024-0.0173.2430.2181.1260.101-0.317-0.692-0.003
128A142GLY0-0.0160.0033.0670.1100.6470.071-0.202-0.4060.000
129A143GLN0-0.014-0.0303.0090.6221.8910.455-0.724-1.001-0.005
130A144SER00.0380.0291.920-8.015-9.6307.542-3.169-2.757-0.026
131A145ASN0-0.006-0.0263.9200.1870.4090.002-0.059-0.1660.000
132A146THR0-0.039-0.0157.0310.2200.2200.0000.0000.0000.000
133A147ASP-1-0.915-0.9357.848-0.433-0.4330.0000.0000.0000.000
134A152THR0-0.038-0.0336.8490.0350.0350.0000.0000.0000.000
135A153VAL00.0190.0168.767-0.016-0.0160.0000.0000.0000.000
136A154ILE0-0.039-0.0208.743-0.064-0.0640.0000.0000.0000.000
137A155LEU0-0.060-0.0065.4330.2510.2510.0000.0000.0000.000
138A156GLN00.0890.0322.256-1.664-0.7991.913-0.803-1.975-0.001
139A157TYR0-0.023-0.0272.723-2.392-0.5941.025-0.823-2.000-0.009
140A158THR00.0190.0002.500-1.492-0.3331.609-0.300-2.468-0.001
141A159TYR0-0.021-0.0063.866-0.463-0.3220.0040.006-0.1510.000
142A160ASN0-0.017-0.0155.4990.3150.3150.0000.0000.0000.000
143A161LEU00.0090.0128.447-0.056-0.0560.0000.0000.0000.000
144A162VAL00.0090.01012.162-0.020-0.0200.0000.0000.0000.000
145A163ILE0-0.026-0.00413.673-0.031-0.0310.0000.0000.0000.000
146A164ASP-1-0.836-0.92416.3620.0970.0970.0000.0000.0000.000
147A165ASN00.020-0.02318.7560.0130.0130.0000.0000.0000.000
148A166ASP-1-0.913-0.93620.1330.0300.0300.0000.0000.0000.000
149A167ARG10.8960.95917.708-0.144-0.1440.0000.0000.0000.000
150A168CYS0-0.023-0.02712.671-0.032-0.0320.0000.0000.0000.000
151A169ALA00.0540.01018.298-0.024-0.0240.0000.0000.0000.000
152A170GLN0-0.073-0.02120.982-0.010-0.0100.0000.0000.0000.000
153A170GLU-1-0.897-0.93317.239-0.037-0.0370.0000.0000.0000.000
154A171TYR0-0.038-0.04012.930-0.058-0.0580.0000.0000.0000.000
155A172PRO0-0.022-0.00319.7540.0120.0120.0000.0000.0000.000
156A173PRO00.024-0.01722.4180.0050.0050.0000.0000.0000.000
157A174GLY0-0.015-0.00924.322-0.008-0.0080.0000.0000.0000.000
158A175ILE00.0000.02117.7490.0000.0000.0000.0000.0000.000
159A176ILE0-0.038-0.00116.5090.0040.0040.0000.0000.0000.000
160A177VAL00.0410.02019.7760.0020.0020.0000.0000.0000.000
161A178GLU-1-0.902-0.97320.4360.0210.0210.0000.0000.0000.000
162A179SER0-0.040-0.01720.0360.0170.0170.0000.0000.0000.000
163A180THR00.0120.02615.413-0.003-0.0030.0000.0000.0000.000
164A181ILE0-0.016-0.01712.8310.0080.0080.0000.0000.0000.000
165A183GLY00.0240.0229.6470.0330.0330.0000.0000.0000.000
166A184ASP-1-0.867-0.93110.6480.2010.2010.0000.0000.0000.000
167A185THR0-0.013-0.0237.3900.1280.1280.0000.0000.0000.000
168A186SER0-0.050-0.0369.240-0.085-0.0850.0000.0000.0000.000
169A186ASP-1-0.948-0.9729.8040.3150.3150.0000.0000.0000.000
170A187GLY0-0.022-0.0178.8770.0160.0160.0000.0000.0000.000
171A188LYS10.9080.9804.700-1.010-0.933-0.001-0.009-0.0660.000
172A189SER00.025-0.0113.547-0.2900.1810.005-0.131-0.3450.000
173A190PRO0-0.0070.0301.930-2.020-1.1387.472-4.372-3.982-0.014
174A191CYS0-0.054-0.0132.9220.8130.8400.1641.291-1.4830.004
175A192PHE00.049-0.0214.452-0.341-0.168-0.001-0.014-0.1580.000
176A193GLY00.0310.0335.309-0.600-0.6000.0000.0000.0000.000
177A194ASP-1-0.718-0.8501.716-13.658-22.11622.518-7.657-6.404-0.070
178A195SER0-0.054-0.0534.8860.6690.723-0.001-0.010-0.0410.000
179A196GLY0-0.001-0.0178.2260.0120.0120.0000.0000.0000.000
180A197GLY0-0.0090.0096.0900.0880.0880.0000.0000.0000.000
181A198PRO0-0.030-0.0136.1670.0470.0470.0000.0000.0000.000
182A199PHE00.0580.0426.2270.1940.1940.0000.0000.0000.000
183A200VAL00.010-0.0258.258-0.147-0.1470.0000.0000.0000.000
184A201LEU00.0110.02510.6810.0720.0720.0000.0000.0000.000
185A202SER00.034-0.01411.707-0.018-0.0180.0000.0000.0000.000
186A203ASP-1-0.888-0.92313.8370.2980.2980.0000.0000.0000.000
187A206LYS10.8070.90016.967-0.222-0.2220.0000.0000.0000.000
188A207ASN00.0340.01615.2420.0050.0050.0000.0000.0000.000
189A208LEU0-0.065-0.03015.437-0.031-0.0310.0000.0000.0000.000
190A209LEU00.0390.02911.0050.0450.0450.0000.0000.0000.000
191A210ILE0-0.039-0.03212.418-0.047-0.0470.0000.0000.0000.000
192A211GLY0-0.008-0.02111.568-0.041-0.0410.0000.0000.0000.000
193A212VAL0-0.0130.0149.9550.0470.0470.0000.0000.0000.000
194A213VAL0-0.023-0.0025.0590.0120.0120.0000.0000.0000.000
195A214SER0-0.051-0.0438.324-0.115-0.1150.0000.0000.0000.000
196A215PHE00.0300.00310.706-0.078-0.0780.0000.0000.0000.000
197A216VAL00.0560.0377.2760.1000.1000.0000.0000.0000.000
198A217SER00.0610.03010.3280.0190.0190.0000.0000.0000.000
199A217GLY00.0160.00712.759-0.086-0.0860.0000.0000.0000.000
200A218ALA0-0.071-0.04014.481-0.024-0.0240.0000.0000.0000.000
201A219GLY00.0150.00611.193-0.017-0.0170.0000.0000.0000.000
202A221GLU-1-0.923-0.9517.554-0.759-0.7590.0000.0000.0000.000
203A222SER0-0.070-0.0409.7900.1480.1480.0000.0000.0000.000
204A223GLY00.0160.01911.0660.0460.0460.0000.0000.0000.000
205A224LYS10.7490.87212.2690.1480.1480.0000.0000.0000.000
206A225PRO00.0360.02511.2640.0140.0140.0000.0000.0000.000
207A226VAL0-0.0010.0296.936-0.097-0.0970.0000.0000.0000.000
208A227GLY00.0280.01510.0210.0940.0940.0000.0000.0000.000
209A228PHE0-0.009-0.0136.593-0.063-0.0630.0000.0000.0000.000
210A229SER0-0.016-0.02011.665-0.014-0.0140.0000.0000.0000.000
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