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: 43R2N

Calculation Name: 3HD0-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2H9

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 222
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2815992.247837
FMO2-HF: Nuclear repulsion 2729119.889824
FMO2-HF: Total energy -86872.358013
FMO2-MP2: Total energy -87129.204092


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:ACE )


Summations of interaction energy for fragment #1(A:0:ACE )
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.
-1.161-0.1393.674-2.711-1.986-0.021
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.014
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].
3A2ASP -1-0.831-0.9223.8410.3261.142-0.005-0.329-0.4830.000
4A3TYR 0-0.082-0.0366.5860.1300.1300.0000.0000.0000.000
5A4ARG 10.9480.9959.8600.3520.3520.0000.0000.0000.000
6A5GLN 0-0.018-0.03513.2270.0120.0120.0000.0000.0000.000
7A6LEU 0-0.064-0.04014.7860.0420.0420.0000.0000.0000.000
8A7HIS 10.8060.91317.9900.1390.1390.0000.0000.0000.000
9A8ARG 10.9841.00718.2100.0150.0150.0000.0000.0000.000
10A9TRP 00.0710.02315.1370.0060.0060.0000.0000.0000.000
11A10ASP -1-0.914-0.93720.187-0.006-0.0060.0000.0000.0000.000
12A11LEU 0-0.052-0.03022.8920.0030.0030.0000.0000.0000.000
13A12PRO 00.0900.03725.6710.0000.0000.0000.0000.0000.000
14A13PRO 00.0560.02328.934-0.006-0.0060.0000.0000.0000.000
15A14GLU -1-0.876-0.94529.921-0.034-0.0340.0000.0000.0000.000
16A15GLU -1-0.893-0.95928.399-0.042-0.0420.0000.0000.0000.000
17A16ALA 0-0.022-0.00426.038-0.007-0.0070.0000.0000.0000.000
18A17ILE 0-0.002-0.01826.955-0.010-0.0100.0000.0000.0000.000
19A18LYS 10.9300.96929.6710.0350.0350.0000.0000.0000.000
20A19VAL 00.0280.02123.115-0.005-0.0050.0000.0000.0000.000
21A20GLN 00.0120.00125.437-0.003-0.0030.0000.0000.0000.000
22A21ASN 00.0280.01626.581-0.009-0.0090.0000.0000.0000.000
23A22GLU -1-0.868-0.93226.618-0.077-0.0770.0000.0000.0000.000
24A23LEU 0-0.043-0.03421.345-0.007-0.0070.0000.0000.0000.000
25A24ARG 10.9300.97024.7790.0720.0720.0000.0000.0000.000
26A25LYS 10.8870.95527.1660.0790.0790.0000.0000.0000.000
27A26LYS 10.9230.95321.5790.1400.1400.0000.0000.0000.000
28A27ILE 00.0030.01822.892-0.014-0.0140.0000.0000.0000.000
29A28LYS 10.8510.93224.1000.1490.1490.0000.0000.0000.000
30A29LEU 0-0.0110.00825.030-0.012-0.0120.0000.0000.0000.000
31A30THR 0-0.003-0.01725.1460.0070.0070.0000.0000.0000.000
32A31PRO 00.0340.02725.930-0.011-0.0110.0000.0000.0000.000
33A32TYR 00.008-0.00820.072-0.016-0.0160.0000.0000.0000.000
34A33GLU -1-0.957-0.99125.247-0.113-0.1130.0000.0000.0000.000
35A34GLY 00.0250.02725.220-0.009-0.0090.0000.0000.0000.000
36A35GLU -1-0.896-0.96324.142-0.131-0.1310.0000.0000.0000.000
37A36PRO 0-0.067-0.02018.739-0.004-0.0040.0000.0000.0000.000
38A37GLU -1-0.888-0.94217.383-0.219-0.2190.0000.0000.0000.000
39A38TYR 0-0.020-0.01913.5570.0090.0090.0000.0000.0000.000
40A39VAL 00.0020.00416.004-0.021-0.0210.0000.0000.0000.000
41A40ALA 00.0210.01012.6020.0040.0040.0000.0000.0000.000
42A41GLY 0-0.045-0.02214.6380.0290.0290.0000.0000.0000.000
43A42VAL 0-0.034-0.02013.997-0.018-0.0180.0000.0000.0000.000
44A43ASP -1-0.810-0.87916.193-0.063-0.0630.0000.0000.0000.000
45A44LEU 0-0.036-0.00515.4980.0000.0000.0000.0000.0000.000
46A45SER 00.0140.00518.7470.0120.0120.0000.0000.0000.000
47A46PHE 00.029-0.01320.4910.0060.0060.0000.0000.0000.000
48A47PRO 0-0.0060.01221.3830.0030.0030.0000.0000.0000.000
49A48GLY 0-0.021-0.02124.3600.0040.0040.0000.0000.0000.000
50A49LYS 10.9000.95026.069-0.015-0.0150.0000.0000.0000.000
51A50GLU -1-0.902-0.95525.0060.0080.0080.0000.0000.0000.000
52A51GLU -1-0.883-0.91620.3230.0540.0540.0000.0000.0000.000
53A52GLY 00.018-0.02019.534-0.011-0.0110.0000.0000.0000.000
54A53LEU 0-0.035-0.02315.6950.0190.0190.0000.0000.0000.000
55A54ALA 0-0.0280.00813.224-0.022-0.0220.0000.0000.0000.000
56A55VAL 00.0260.01213.4390.0180.0180.0000.0000.0000.000
57A56ILE 0-0.017-0.0029.472-0.024-0.0240.0000.0000.0000.000
58A57VAL 0-0.041-0.01512.0500.0240.0240.0000.0000.0000.000
59A58VAL 00.0340.01310.016-0.023-0.0230.0000.0000.0000.000
60A59LEU 0-0.039-0.02113.3150.0450.0450.0000.0000.0000.000
61A60GLU -1-0.877-0.94016.311-0.196-0.1960.0000.0000.0000.000
62A61TYR 0-0.045-0.00418.3370.0290.0290.0000.0000.0000.000
63A62PRO 00.0540.00821.396-0.001-0.0010.0000.0000.0000.000
64A63SER 0-0.044-0.02621.7020.0090.0090.0000.0000.0000.000
65A64PHE 0-0.006-0.02520.8740.0100.0100.0000.0000.0000.000
66A65LYS 10.8980.96518.3410.1270.1270.0000.0000.0000.000
67A66ILE 00.0170.00115.504-0.023-0.0230.0000.0000.0000.000
68A67LEU 0-0.055-0.01213.0870.0320.0320.0000.0000.0000.000
69A68GLU -1-0.811-0.9176.963-0.444-0.4440.0000.0000.0000.000
70A69VAL 0-0.019-0.01211.109-0.028-0.0280.0000.0000.0000.000
71A70VAL 0-0.0110.0176.4970.0920.0920.0000.0000.0000.000
72A71SER 0-0.033-0.0409.851-0.028-0.0280.0000.0000.0000.000
73A72GLU -1-0.847-0.92510.1910.3510.3510.0000.0000.0000.000
74A73ARG 10.9450.97112.361-0.102-0.1020.0000.0000.0000.000
75A74GLY 00.017-0.00314.9560.0220.0220.0000.0000.0000.000
76A75GLU -1-0.888-0.92917.0440.0320.0320.0000.0000.0000.000
77A76ILE 0-0.127-0.07019.424-0.014-0.0140.0000.0000.0000.000
78A77THR 00.0380.02221.458-0.002-0.0020.0000.0000.0000.000
79A78PHE 00.0200.01023.388-0.003-0.0030.0000.0000.0000.000
80A79PRO 00.0860.03525.115-0.002-0.0020.0000.0000.0000.000
81A80TYR 0-0.031-0.02327.391-0.006-0.0060.0000.0000.0000.000
82A81ILE 00.0510.01928.5030.0030.0030.0000.0000.0000.000
83A82PRO 00.0560.02829.141-0.007-0.0070.0000.0000.0000.000
84A83GLY 00.0030.00129.2710.0010.0010.0000.0000.0000.000
85A84LEU 0-0.012-0.02626.660-0.007-0.0070.0000.0000.0000.000
86A85LEU 00.0200.02624.613-0.001-0.0010.0000.0000.0000.000
87A86ALA 00.0370.01620.6850.0000.0000.0000.0000.0000.000
88A87PHE 0-0.044-0.02920.173-0.012-0.0120.0000.0000.0000.000
89A88ARG 10.9010.96921.2890.0390.0390.0000.0000.0000.000
90A89GLU -1-0.927-0.96919.015-0.082-0.0820.0000.0000.0000.000
91A90GLY 0-0.002-0.00416.740-0.015-0.0150.0000.0000.0000.000
92A91PRO 0-0.011-0.00814.781-0.030-0.0300.0000.0000.0000.000
93A92LEU 00.0230.04213.357-0.008-0.0080.0000.0000.0000.000
94A93PHE 00.0620.02012.1680.0000.0000.0000.0000.0000.000
95A94LEU 0-0.047-0.01810.470-0.060-0.0600.0000.0000.0000.000
96A95LYS 10.8830.9538.647-0.025-0.0250.0000.0000.0000.000
97A96ALA 00.0050.0037.7260.0800.0800.0000.0000.0000.000
98A97TRP 0-0.011-0.0356.864-0.064-0.0640.0000.0000.0000.000
99A98GLU -1-0.902-0.9604.269-0.768-0.6830.001-0.042-0.0440.000
100A99LYS 10.8260.9272.5930.5840.4163.524-1.936-1.421-0.018
101A100LEU 0-0.058-0.0173.6680.0220.2900.020-0.066-0.2220.000
102A101ARG 10.9410.9663.245-1.945-1.9270.134-0.3350.183-0.003
103A102THR 0-0.045-0.0105.253-0.075-0.0720.000-0.0030.0010.000
104A103LYS 10.9670.9798.3870.7260.7260.0000.0000.0000.000
105A104PRO 0-0.031-0.0229.3010.1800.1800.0000.0000.0000.000
106A105ASP -1-0.738-0.86412.512-0.396-0.3960.0000.0000.0000.000
107A106VAL 0-0.040-0.03215.9020.0360.0360.0000.0000.0000.000
108A107VAL 0-0.052-0.02613.222-0.015-0.0150.0000.0000.0000.000
109A108VAL 0-0.015-0.00116.3320.0370.0370.0000.0000.0000.000
110A109PHE 00.011-0.01815.0110.0000.0000.0000.0000.0000.000
111A110ASP -1-0.898-0.94919.497-0.084-0.0840.0000.0000.0000.000
112A111GLY 00.0440.01422.2510.0060.0060.0000.0000.0000.000
113A112GLN 0-0.112-0.06924.3210.0080.0080.0000.0000.0000.000
114A113GLY 00.0420.01323.875-0.013-0.0130.0000.0000.0000.000
115A114LEU 00.0120.02125.2760.0100.0100.0000.0000.0000.000
116A115ALA 0-0.013-0.00628.4220.0090.0090.0000.0000.0000.000
117A116HIS 00.0040.00927.560-0.001-0.0010.0000.0000.0000.000
118A117PRO 00.0120.01630.3530.0010.0010.0000.0000.0000.000
119A118ARG 10.8420.91629.6210.0680.0680.0000.0000.0000.000
120A119LYS 10.9040.94629.5010.0730.0730.0000.0000.0000.000
121A120LEU 00.002-0.02023.314-0.010-0.0100.0000.0000.0000.000
122A121GLY 0-0.018-0.00224.7040.0000.0000.0000.0000.0000.000
123A122ILE 00.0220.00418.739-0.009-0.0090.0000.0000.0000.000
124A123ALA 00.0580.03219.715-0.020-0.0200.0000.0000.0000.000
125A124SER 00.0190.03019.890-0.021-0.0210.0000.0000.0000.000
126A125HIS 0-0.0070.00619.042-0.015-0.0150.0000.0000.0000.000
127A126MET 00.0090.02215.506-0.014-0.0140.0000.0000.0000.000
128A127GLY 00.0570.04015.565-0.047-0.0470.0000.0000.0000.000
129A128LEU 0-0.069-0.04316.910-0.021-0.0210.0000.0000.0000.000
130A129PHE 0-0.032-0.01713.4010.0150.0150.0000.0000.0000.000
131A130ILE 0-0.008-0.01410.949-0.021-0.0210.0000.0000.0000.000
132A131GLU -1-0.914-0.94412.558-0.417-0.4170.0000.0000.0000.000
133A132ILE 0-0.0050.00712.548-0.012-0.0120.0000.0000.0000.000
134A133PRO 00.0030.00915.8030.0290.0290.0000.0000.0000.000
135A134THR 0-0.022-0.02016.761-0.014-0.0140.0000.0000.0000.000
136A135ILE 0-0.038-0.02919.3210.0320.0320.0000.0000.0000.000
137A136GLY 0-0.0040.00521.097-0.011-0.0110.0000.0000.0000.000
138A137VAL 0-0.022-0.01423.4460.0130.0130.0000.0000.0000.000
139A138ALA 00.0790.04324.8630.0000.0000.0000.0000.0000.000
140A139LYS 10.9160.94426.7730.0700.0700.0000.0000.0000.000
141A140SER 00.0250.00029.8260.0070.0070.0000.0000.0000.000
142A141ARG 10.9230.97530.9940.0480.0480.0000.0000.0000.000
143A142LEU 0-0.022-0.00227.2540.0030.0030.0000.0000.0000.000
144A143TYR 0-0.039-0.03831.8970.0050.0050.0000.0000.0000.000
145A144GLY 00.0760.03733.604-0.002-0.0020.0000.0000.0000.000
146A145THR 0-0.055-0.03136.2610.0020.0020.0000.0000.0000.000
147A146PHE 00.0830.02538.069-0.003-0.0030.0000.0000.0000.000
148A147LYS 10.9930.99840.1950.0420.0420.0000.0000.0000.000
149A148MET 0-0.0070.00739.387-0.003-0.0030.0000.0000.0000.000
150A149PRO 00.0240.03638.1290.0020.0020.0000.0000.0000.000
151A150GLU -1-0.857-0.93541.458-0.041-0.0410.0000.0000.0000.000
152A151ASP -1-0.872-0.91841.774-0.042-0.0420.0000.0000.0000.000
153A152LYS 11.0000.99941.8580.0450.0450.0000.0000.0000.000
154A153ARG 10.9150.94736.1260.0480.0480.0000.0000.0000.000
155A154CYS 0-0.050-0.04135.391-0.001-0.0010.0000.0000.0000.000
156A155SER 00.0330.02837.257-0.002-0.0020.0000.0000.0000.000
157A156TRP 0-0.047-0.03836.192-0.005-0.0050.0000.0000.0000.000
158A157SER 00.0110.00137.3810.0030.0030.0000.0000.0000.000
159A158TYR 00.0020.00035.652-0.003-0.0030.0000.0000.0000.000
160A159LEU 0-0.082-0.03232.5170.0040.0040.0000.0000.0000.000
161A160TYR 00.0230.00336.183-0.003-0.0030.0000.0000.0000.000
162A161ASP -1-0.866-0.92536.032-0.060-0.0600.0000.0000.0000.000
163A162GLY 0-0.0110.00138.0610.0000.0000.0000.0000.0000.000
164A163GLU -1-0.919-0.96841.664-0.046-0.0460.0000.0000.0000.000
165A164GLU -1-0.918-0.94537.200-0.062-0.0620.0000.0000.0000.000
166A165ILE 0-0.009-0.00434.570-0.001-0.0010.0000.0000.0000.000
167A166ILE 0-0.062-0.03832.486-0.005-0.0050.0000.0000.0000.000
168A167GLY 00.0370.00231.214-0.008-0.0080.0000.0000.0000.000
169A168CYS 0-0.066-0.02131.3610.0060.0060.0000.0000.0000.000
170A169VAL 00.0180.01732.439-0.003-0.0030.0000.0000.0000.000
171A170ILE 00.0410.00931.0690.0040.0040.0000.0000.0000.000
172A171ARG 10.8210.89634.3640.0460.0460.0000.0000.0000.000
173A172THR 0-0.0370.00031.8350.0000.0000.0000.0000.0000.000
174A173LYS 10.9150.95734.1650.0440.0440.0000.0000.0000.000
175A174GLU -1-0.816-0.89436.187-0.047-0.0470.0000.0000.0000.000
176A175GLY 00.010-0.00239.9250.0010.0010.0000.0000.0000.000
177A176SER 0-0.091-0.04036.0060.0010.0010.0000.0000.0000.000
178A177ALA 00.0220.01635.850-0.001-0.0010.0000.0000.0000.000
179A178PRO 00.0030.01035.081-0.002-0.0020.0000.0000.0000.000
180A179ILE 0-0.026-0.00728.3790.0010.0010.0000.0000.0000.000
181A180PHE 0-0.005-0.00830.1740.0030.0030.0000.0000.0000.000
182A181VAL 00.0360.02726.856-0.006-0.0060.0000.0000.0000.000
183A182SER 00.0100.00026.9520.0050.0050.0000.0000.0000.000
184A183PRO 00.0160.02825.308-0.011-0.0110.0000.0000.0000.000
185A184GLY 00.0240.00922.0710.0100.0100.0000.0000.0000.000
186A185HIS 00.0050.00418.9270.0340.0340.0000.0000.0000.000
187A186LEU 0-0.0050.00618.799-0.019-0.0190.0000.0000.0000.000
188A187MET 00.0100.01822.2250.0020.0020.0000.0000.0000.000
189A188ASP -1-0.779-0.88824.851-0.114-0.1140.0000.0000.0000.000
190A189VAL 00.052-0.00328.204-0.005-0.0050.0000.0000.0000.000
191A190GLU -1-0.863-0.92430.435-0.084-0.0840.0000.0000.0000.000
192A191SER 00.0280.01926.8170.0000.0000.0000.0000.0000.000
193A192SER 0-0.029-0.01426.105-0.003-0.0030.0000.0000.0000.000
194A193LYS 10.9130.95827.0830.0800.0800.0000.0000.0000.000
195A194ARG 10.7950.89826.8480.1320.1320.0000.0000.0000.000
196A195LEU 00.0710.03023.0010.0040.0040.0000.0000.0000.000
197A196ILE 00.0200.01223.7250.0010.0010.0000.0000.0000.000
198A197LYS 10.8140.91526.5380.0830.0830.0000.0000.0000.000
199A198ALA 0-0.0010.01226.4290.0050.0050.0000.0000.0000.000
200A199PHE 00.0230.00921.539-0.002-0.0020.0000.0000.0000.000
201A200THR 0-0.021-0.01125.2530.0020.0020.0000.0000.0000.000
202A201LEU 00.0050.02027.2400.0040.0040.0000.0000.0000.000
203A202PRO 0-0.0010.03229.8550.0030.0030.0000.0000.0000.000
204A203GLY 00.024-0.01333.5850.0030.0030.0000.0000.0000.000
205A204ARG 10.8550.91427.4640.0690.0690.0000.0000.0000.000
206A205ARG 10.8630.90431.4130.0570.0570.0000.0000.0000.000
207A206ILE 0-0.028-0.02825.1930.0000.0000.0000.0000.0000.000
208A207PRO 00.0500.03023.8620.0030.0030.0000.0000.0000.000
209A208GLU -1-0.709-0.85722.636-0.087-0.0870.0000.0000.0000.000
210A209PRO 00.0340.03018.4860.0060.0060.0000.0000.0000.000
211A210THR 00.0640.01519.2390.0010.0010.0000.0000.0000.000
212A211ARG 10.7770.88321.1860.0870.0870.0000.0000.0000.000
213A212LEU 0-0.010-0.00919.6500.0130.0130.0000.0000.0000.000
214A213ALA 00.0450.02517.0550.0120.0120.0000.0000.0000.000
215A214HIS 0-0.049-0.01618.4590.0230.0230.0000.0000.0000.000
216A215ILE 0-0.052-0.02121.5670.0130.0130.0000.0000.0000.000
217A216TYR 0-0.028-0.03016.9650.0160.0160.0000.0000.0000.000
218A217THR 0-0.008-0.03919.0270.0130.0130.0000.0000.0000.000
219A218GLN 00.010-0.00219.7920.0140.0140.0000.0000.0000.000
220A219ARG 10.8160.93219.7200.0220.0220.0000.0000.0000.000
221A220LEU 0-0.050-0.03116.4670.0150.0150.0000.0000.0000.000
222A221NME 00.0060.01820.954-0.004-0.0040.0000.0000.0000.000