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: 14Z2Z

Calculation Name: 3HD0-A-Xray372

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: 2023-06-20

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 OptHSide
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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2807775.463889
FMO2-HF: Nuclear repulsion 2721072.282603
FMO2-HF: Total energy -86703.181285
FMO2-MP2: Total energy -86959.479012


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-40.369-27.50120.791-10.82-22.84-0.087
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.078 / q_NPA : -0.032
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].
3A3TYR0-0.110-0.0763.263-3.857-1.3460.037-1.364-1.183-0.001
4A4ARG10.8650.9096.072-0.276-0.2760.0000.0000.0000.000
5A5GLN0-0.027-0.0319.691-0.272-0.2720.0000.0000.0000.000
6A6LEU0-0.057-0.03412.3800.0930.0930.0000.0000.0000.000
7A7HIS10.7890.89014.8470.3740.3740.0000.0000.0000.000
8A8ARG10.9010.94916.1720.1520.1520.0000.0000.0000.000
9A9TRP00.0950.03412.7030.0930.0930.0000.0000.0000.000
10A10ASP-1-0.835-0.88418.258-0.277-0.2770.0000.0000.0000.000
11A11LEU0-0.049-0.02321.4370.0460.0460.0000.0000.0000.000
12A12PRO00.0840.03423.744-0.019-0.0190.0000.0000.0000.000
13A13PRO00.0540.02026.0950.0010.0010.0000.0000.0000.000
14A14GLU-1-0.866-0.93927.007-0.151-0.1510.0000.0000.0000.000
15A15GLU-1-0.802-0.89826.079-0.085-0.0850.0000.0000.0000.000
16A16ALA0-0.0090.00222.8820.0080.0080.0000.0000.0000.000
17A17ILE00.010-0.01523.3140.0040.0040.0000.0000.0000.000
18A18LYS10.8130.89125.6180.0970.0970.0000.0000.0000.000
19A19VAL00.0210.01819.6480.0240.0240.0000.0000.0000.000
20A20GLN00.0080.01020.8660.0420.0420.0000.0000.0000.000
21A21ASN00.0380.01621.9450.0200.0200.0000.0000.0000.000
22A22GLU-1-0.821-0.89822.4790.0470.0470.0000.0000.0000.000
23A23LEU0-0.022-0.01716.5040.0350.0350.0000.0000.0000.000
24A24ARG10.9290.96819.3360.0730.0730.0000.0000.0000.000
25A25LYS10.8350.91421.486-0.019-0.0190.0000.0000.0000.000
26A26LYS10.9350.96116.836-0.106-0.1060.0000.0000.0000.000
27A27ILE00.0010.02016.5000.0550.0550.0000.0000.0000.000
28A28LYS10.8050.90417.353-0.235-0.2350.0000.0000.0000.000
29A29LEU0-0.0070.01118.1970.0210.0210.0000.0000.0000.000
30A30THR00.008-0.00618.068-0.003-0.0030.0000.0000.0000.000
31A31PRO00.0300.01919.0780.0130.0130.0000.0000.0000.000
32A32TYR00.0110.00413.3180.0610.0610.0000.0000.0000.000
33A33GLU-1-0.948-0.98318.4260.2760.2760.0000.0000.0000.000
34A34GLY00.0280.02918.7350.0550.0550.0000.0000.0000.000
35A35GLU-1-0.886-0.95017.8720.1680.1680.0000.0000.0000.000
36A36PRO0-0.050-0.01212.4950.0560.0560.0000.0000.0000.000
37A37GLU-1-0.837-0.88611.0820.3830.3830.0000.0000.0000.000
38A38TYR0-0.079-0.0797.832-0.387-0.3870.0000.0000.0000.000
39A39VAL00.0010.0079.8520.1840.1840.0000.0000.0000.000
40A40ALA00.0150.0037.449-0.196-0.1960.0000.0000.0000.000
41A41GLY0-0.031-0.0149.5530.2190.2190.0000.0000.0000.000
42A42VAL0-0.044-0.0249.643-0.244-0.2440.0000.0000.0000.000
43A43ASP-1-0.815-0.89012.345-0.546-0.5460.0000.0000.0000.000
44A44LEU0-0.046-0.00912.157-0.143-0.1430.0000.0000.0000.000
45A45SER00.0170.00715.9390.1260.1260.0000.0000.0000.000
46A46PHE00.017-0.01518.307-0.049-0.0490.0000.0000.0000.000
47A47PRO0-0.0010.01120.3140.0590.0590.0000.0000.0000.000
48A48GLY0-0.012-0.00723.2980.0500.0500.0000.0000.0000.000
49A49LYS10.8630.93825.0990.3680.3680.0000.0000.0000.000
50A50GLU-1-0.871-0.94423.881-0.353-0.3530.0000.0000.0000.000
51A51GLU-1-0.849-0.89519.617-0.740-0.7400.0000.0000.0000.000
52A52GLY00.019-0.01317.9200.0320.0320.0000.0000.0000.000
53A53LEU0-0.029-0.01115.176-0.031-0.0310.0000.0000.0000.000
54A54ALA0-0.0230.00711.1620.0670.0670.0000.0000.0000.000
55A55VAL00.0230.00812.149-0.183-0.1830.0000.0000.0000.000
56A56ILE0-0.017-0.0036.5210.1680.1680.0000.0000.0000.000
57A57VAL0-0.018-0.00610.153-0.088-0.0880.0000.0000.0000.000
58A58VAL00.0270.0145.6880.1120.1120.0000.0000.0000.000
59A59LEU0-0.033-0.0189.1290.0640.0640.0000.0000.0000.000
60A60GLU-1-0.758-0.86011.104-0.115-0.1150.0000.0000.0000.000
61A61TYR0-0.0460.00613.194-0.038-0.0380.0000.0000.0000.000
62A62PRO00.0360.00015.7630.0430.0430.0000.0000.0000.000
63A63SER0-0.062-0.06517.044-0.049-0.0490.0000.0000.0000.000
64A64PHE0-0.031-0.03316.113-0.020-0.0200.0000.0000.0000.000
65A65LYS10.8360.93615.1330.1900.1900.0000.0000.0000.000
66A66ILE00.011-0.00313.107-0.016-0.0160.0000.0000.0000.000
67A67LEU0-0.034-0.0019.6090.0340.0340.0000.0000.0000.000
68A68GLU-1-0.769-0.8675.695-3.701-3.7010.0000.0000.0000.000
69A69VAL0-0.021-0.0189.7090.1010.1010.0000.0000.0000.000
70A70VAL0-0.0170.0136.6030.1310.1310.0000.0000.0000.000
71A71SER0-0.002-0.0229.8560.1610.1610.0000.0000.0000.000
72A72GLU-1-0.832-0.88710.104-1.664-1.6640.0000.0000.0000.000
73A73ARG10.9010.93612.2260.8540.8540.0000.0000.0000.000
74A74GLY00.018-0.00514.595-0.079-0.0790.0000.0000.0000.000
75A75GLU-1-0.903-0.94016.337-0.429-0.4290.0000.0000.0000.000
76A76ILE0-0.107-0.06117.539-0.041-0.0410.0000.0000.0000.000
77A77THR00.0370.01620.3500.0510.0510.0000.0000.0000.000
78A78PHE00.0130.01021.2580.0410.0410.0000.0000.0000.000
79A79PRO00.0770.03323.031-0.020-0.0200.0000.0000.0000.000
80A80TYR0-0.027-0.03023.9290.0030.0030.0000.0000.0000.000
81A81ILE00.0670.02325.1210.0280.0280.0000.0000.0000.000
82A82PRO00.0490.02525.384-0.017-0.0170.0000.0000.0000.000
83A83GLY00.0050.00124.8580.0220.0220.0000.0000.0000.000
84A84LEU0-0.020-0.02122.8310.0100.0100.0000.0000.0000.000
85A85LEU00.0100.02020.895-0.022-0.0220.0000.0000.0000.000
86A86ALA00.0450.01716.609-0.046-0.0460.0000.0000.0000.000
87A87PHE0-0.035-0.02516.645-0.072-0.0720.0000.0000.0000.000
88A88ARG10.8850.97018.6370.4390.4390.0000.0000.0000.000
89A89GLU-1-0.940-0.97416.037-0.653-0.6530.0000.0000.0000.000
90A90GLY00.007-0.00312.962-0.151-0.1510.0000.0000.0000.000
91A91PRO0-0.015-0.01611.586-0.238-0.2380.0000.0000.0000.000
92A92LEU00.0070.02311.353-0.220-0.2200.0000.0000.0000.000
93A93PHE00.0590.0167.172-0.313-0.3130.0000.0000.0000.000
94A94LEU0-0.0220.0006.697-0.535-0.5350.0000.0000.0000.000
95A95LYS10.7970.9046.5241.1211.1210.0000.0000.0000.000
96A96ALA00.0230.0106.855-0.417-0.4170.0000.0000.0000.000
97A97TRP0-0.002-0.0352.631-4.159-1.3941.971-1.018-3.719-0.009
98A98GLU-1-0.779-0.8672.377-8.317-6.5952.342-1.541-2.523-0.016
99A99LYS10.7890.8792.1950.4560.6603.831-1.849-2.186-0.025
100A100LEU0-0.064-0.0142.1170.3711.5662.513-1.120-2.5880.000
101A101ARG10.8770.9162.371-7.726-4.0772.305-2.552-3.402-0.034
102A102THR0-0.045-0.0223.005-0.7220.5990.368-0.632-1.057-0.006
103A103LYS10.9620.9702.492-15.569-14.9597.270-2.379-5.5010.005
104A104PRO0-0.034-0.0203.2600.434-0.6750.1541.635-0.681-0.001
105A105ASP-1-0.769-0.8806.2662.2162.2160.0000.0000.0000.000
106A106VAL0-0.048-0.0279.420-0.064-0.0640.0000.0000.0000.000
107A107VAL0-0.041-0.0126.831-0.217-0.2170.0000.0000.0000.000
108A108VAL0-0.029-0.0089.9290.1080.1080.0000.0000.0000.000
109A109PHE00.021-0.0119.421-0.128-0.1280.0000.0000.0000.000
110A110ASP-1-0.812-0.90114.300-0.365-0.3650.0000.0000.0000.000
111A111GLY00.0360.01117.658-0.023-0.0230.0000.0000.0000.000
112A112GLN0-0.092-0.06519.4120.0700.0700.0000.0000.0000.000
113A113GLY00.0290.01418.254-0.049-0.0490.0000.0000.0000.000
114A114LEU00.0180.02219.338-0.002-0.0020.0000.0000.0000.000
115A115ALA0-0.001-0.00222.2160.0070.0070.0000.0000.0000.000
116A116HIS0-0.005-0.00222.781-0.010-0.0100.0000.0000.0000.000
117A117PRO0-0.0070.01624.9240.0190.0190.0000.0000.0000.000
118A118ARG10.8530.91725.0060.1780.1780.0000.0000.0000.000
119A119LYS10.8280.89623.6440.0500.0500.0000.0000.0000.000
120A120LEU0-0.002-0.01317.7970.0180.0180.0000.0000.0000.000
121A121GLY0-0.0040.00519.604-0.044-0.0440.0000.0000.0000.000
122A122ILE00.0220.00114.3620.0350.0350.0000.0000.0000.000
123A123ALA00.0570.03313.959-0.062-0.0620.0000.0000.0000.000
124A124SER00.0270.02513.8030.0240.0240.0000.0000.0000.000
125A125HIS00.0100.01714.3990.0310.0310.0000.0000.0000.000
126A126MET0-0.0170.00810.304-0.037-0.0370.0000.0000.0000.000
127A127GLY00.0720.0439.623-0.073-0.0730.0000.0000.0000.000
128A128LEU0-0.079-0.04210.4390.1840.1840.0000.0000.0000.000
129A129PHE0-0.018-0.0168.9200.1830.1830.0000.0000.0000.000
130A130ILE00.002-0.0065.1450.0940.0940.0000.0000.0000.000
131A131GLU-1-0.837-0.8655.9411.6031.6030.0000.0000.0000.000
132A132ILE0-0.0050.0026.0240.4670.4670.0000.0000.0000.000
133A133PRO00.0110.0128.951-0.386-0.3860.0000.0000.0000.000
134A134THR0-0.008-0.00610.102-0.059-0.0590.0000.0000.0000.000
135A135ILE0-0.027-0.02612.5550.0490.0490.0000.0000.0000.000
136A136GLY0-0.0190.00115.007-0.100-0.1000.0000.0000.0000.000
137A137VAL0-0.014-0.01217.5660.0620.0620.0000.0000.0000.000
138A138ALA00.0510.03219.799-0.048-0.0480.0000.0000.0000.000
139A139LYS10.8280.89121.7110.4750.4750.0000.0000.0000.000
140A140SER00.0240.00625.2330.0290.0290.0000.0000.0000.000
141A141ARG10.9140.97526.1300.1350.1350.0000.0000.0000.000
142A142LEU00.0000.00422.673-0.004-0.0040.0000.0000.0000.000
143A143TYR0-0.049-0.06126.565-0.001-0.0010.0000.0000.0000.000
144A144GLY00.0710.03828.2780.0020.0020.0000.0000.0000.000
145A145THR0-0.072-0.03930.532-0.008-0.0080.0000.0000.0000.000
146A146PHE00.0810.02332.0600.0020.0020.0000.0000.0000.000
147A147LYS10.9830.99734.2110.0560.0560.0000.0000.0000.000
148A148MET00.0160.01533.961-0.002-0.0020.0000.0000.0000.000
149A149PRO00.0170.03332.2130.0060.0060.0000.0000.0000.000
150A150GLU-1-0.764-0.85935.548-0.056-0.0560.0000.0000.0000.000
151A151ASP-1-0.833-0.91736.145-0.114-0.1140.0000.0000.0000.000
152A152LYS10.9040.94536.2760.0480.0480.0000.0000.0000.000
153A153ARG10.9000.94630.7460.1000.1000.0000.0000.0000.000
154A154CYS0-0.015-0.01729.3620.0130.0130.0000.0000.0000.000
155A155SER0-0.017-0.01831.4400.0120.0120.0000.0000.0000.000
156A156TRP0-0.038-0.03229.906-0.012-0.0120.0000.0000.0000.000
157A157SER00.0090.00331.1530.0100.0100.0000.0000.0000.000
158A158TYR0-0.018-0.02528.583-0.011-0.0110.0000.0000.0000.000
159A159LEU0-0.073-0.02926.461-0.007-0.0070.0000.0000.0000.000
160A160TYR00.0250.00929.7730.0070.0070.0000.0000.0000.000
161A161ASP-1-0.813-0.87229.955-0.078-0.0780.0000.0000.0000.000
162A162GLY00.0130.01231.9800.0090.0090.0000.0000.0000.000
163A163GLU-1-0.913-0.97135.386-0.008-0.0080.0000.0000.0000.000
164A164GLU-1-0.923-0.94030.4990.0220.0220.0000.0000.0000.000
165A165ILE0-0.012-0.01128.070-0.016-0.0160.0000.0000.0000.000
166A166ILE0-0.056-0.03426.2100.0060.0060.0000.0000.0000.000
167A167GLY00.0490.00724.807-0.014-0.0140.0000.0000.0000.000
168A168CYS0-0.072-0.02124.9270.0140.0140.0000.0000.0000.000
169A169VAL00.0080.01426.287-0.020-0.0200.0000.0000.0000.000
170A170ILE00.0320.01024.9310.0160.0160.0000.0000.0000.000
171A171ARG10.7900.90128.6950.0870.0870.0000.0000.0000.000
172A172THR0-0.036-0.01926.0340.0150.0150.0000.0000.0000.000
173A173LYS10.9450.96528.8130.1500.1500.0000.0000.0000.000
174A174GLU-1-0.830-0.89731.300-0.115-0.1150.0000.0000.0000.000
175A175GLY00.0310.00735.026-0.006-0.0060.0000.0000.0000.000
176A176SER0-0.074-0.03231.647-0.013-0.0130.0000.0000.0000.000
177A177ALA00.0400.02231.1750.0090.0090.0000.0000.0000.000
178A178PRO00.0090.01329.690-0.009-0.0090.0000.0000.0000.000
179A179ILE0-0.0200.00422.870-0.018-0.0180.0000.0000.0000.000
180A180PHE00.004-0.00824.7610.0290.0290.0000.0000.0000.000
181A181VAL00.0420.03420.588-0.036-0.0360.0000.0000.0000.000
182A182SER00.006-0.00220.7840.0280.0280.0000.0000.0000.000
183A183PRO00.0040.02418.603-0.036-0.0360.0000.0000.0000.000
184A184GLY00.0380.01115.559-0.042-0.0420.0000.0000.0000.000
185A185HIS00.0210.00712.186-0.056-0.0560.0000.0000.0000.000
186A186LEU0-0.0050.00212.1270.0480.0480.0000.0000.0000.000
187A187MET0-0.0010.01515.262-0.004-0.0040.0000.0000.0000.000
188A188ASP-1-0.776-0.86117.9240.1240.1240.0000.0000.0000.000
189A189VAL00.0630.00021.242-0.015-0.0150.0000.0000.0000.000
190A190GLU-1-0.770-0.84323.5780.0180.0180.0000.0000.0000.000
191A191SER00.019-0.01419.932-0.002-0.0020.0000.0000.0000.000
192A192SER0-0.040-0.02319.315-0.022-0.0220.0000.0000.0000.000
193A193LYS10.8160.89120.294-0.040-0.0400.0000.0000.0000.000
194A194ARG10.7810.87820.058-0.212-0.2120.0000.0000.0000.000
195A195LEU00.0520.02516.288-0.022-0.0220.0000.0000.0000.000
196A196ILE00.0220.00817.558-0.038-0.0380.0000.0000.0000.000
197A197LYS10.8140.90420.4100.0190.0190.0000.0000.0000.000
198A198ALA00.0050.01620.404-0.017-0.0170.0000.0000.0000.000
199A199PHE00.0320.00615.415-0.028-0.0280.0000.0000.0000.000
200A200THR0-0.042-0.02719.789-0.064-0.0640.0000.0000.0000.000
201A201LEU00.0160.02322.2100.0250.0250.0000.0000.0000.000
202A202PRO0-0.0120.03325.027-0.004-0.0040.0000.0000.0000.000
203A203GLY00.031-0.02128.7000.0000.0000.0000.0000.0000.000
204A204ARG10.8060.88223.2850.2450.2450.0000.0000.0000.000
205A205ARG10.8530.90227.0380.2310.2310.0000.0000.0000.000
206A206ILE0-0.040-0.03320.8830.0130.0130.0000.0000.0000.000
207A207PRO00.0480.03318.730-0.002-0.0020.0000.0000.0000.000
208A208GLU-1-0.707-0.84518.417-0.366-0.3660.0000.0000.0000.000
209A209PRO00.0450.03213.545-0.056-0.0560.0000.0000.0000.000
210A210THR00.0580.01515.377-0.083-0.0830.0000.0000.0000.000
211A211ARG10.8080.90617.0160.3430.3430.0000.0000.0000.000
212A212LEU00.008-0.00516.523-0.008-0.0080.0000.0000.0000.000
213A213ALA00.0440.02414.113-0.033-0.0330.0000.0000.0000.000
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