FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JQGQ9

Calculation Name: 3HU5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HU5

Chain ID: A

ChEMBL ID:

UniProt ID: Q72G28

Base Structure: X-ray

Registration Date: 2023-09-23

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 190
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1913731.564892
FMO2-HF: Nuclear repulsion 1841797.602285
FMO2-HF: Total energy -71933.962607
FMO2-MP2: Total energy -72136.528047


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:6:ASN)


Summations of interaction energy for fragment #1(A:6:ASN)
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.
-2.567-0.913-0.019-0.669-0.9660.003
Interaction energy analysis for fragmet #1(A:6:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.050
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].
3A8THR0-0.0270.0003.701-5.440-3.786-0.019-0.669-0.9660.003
4A9VAL00.0180.0066.2001.2411.2410.0000.0000.0000.000
5A10ALA0-0.014-0.0048.940-0.114-0.1140.0000.0000.0000.000
6A11LEU0-0.010-0.00312.6020.1560.1560.0000.0000.0000.000
7A12ALA00.0010.01315.396-0.009-0.0090.0000.0000.0000.000
8A13ILE0-0.044-0.02718.7770.0410.0410.0000.0000.0000.000
9A14ILE00.004-0.01321.574-0.003-0.0030.0000.0000.0000.000
10A15ASP-1-0.732-0.88424.526-0.151-0.1510.0000.0000.0000.000
11A16MET0-0.072-0.01925.8220.0240.0240.0000.0000.0000.000
12A17GLN0-0.033-0.03728.512-0.014-0.0140.0000.0000.0000.000
13A18ASN00.0510.00531.8400.0120.0120.0000.0000.0000.000
14A19ASP-1-0.819-0.92335.260-0.114-0.1140.0000.0000.0000.000
15A20PHE0-0.054-0.02632.0460.0150.0150.0000.0000.0000.000
16A21VAL0-0.015-0.00130.9360.0080.0080.0000.0000.0000.000
17A22LEU0-0.019-0.00333.9320.0060.0060.0000.0000.0000.000
18A23PRO00.052-0.00337.0310.0080.0080.0000.0000.0000.000
19A24GLY0-0.036-0.01239.622-0.002-0.0020.0000.0000.0000.000
20A25ALA00.0160.03038.6200.0020.0020.0000.0000.0000.000
21A26PRO0-0.0050.00239.9650.0060.0060.0000.0000.0000.000
22A27ALA0-0.070-0.05137.0670.0080.0080.0000.0000.0000.000
23A28CYS0-0.0420.01136.275-0.002-0.0020.0000.0000.0000.000
24A29VAL0-0.040-0.01931.6480.0130.0130.0000.0000.0000.000
25A30GLU-1-0.760-0.87534.087-0.063-0.0630.0000.0000.0000.000
26A31GLY0-0.062-0.03432.017-0.004-0.0040.0000.0000.0000.000
27A32ALA00.0410.02529.872-0.006-0.0060.0000.0000.0000.000
28A33MET00.0060.01529.911-0.012-0.0120.0000.0000.0000.000
29A34GLY0-0.005-0.00831.320-0.009-0.0090.0000.0000.0000.000
30A35THR0-0.035-0.02625.840-0.006-0.0060.0000.0000.0000.000
31A36VAL00.0150.00925.904-0.020-0.0200.0000.0000.0000.000
32A37PRO00.015-0.00225.879-0.030-0.0300.0000.0000.0000.000
33A38VAL00.0370.04121.496-0.030-0.0300.0000.0000.0000.000
34A39ILE00.005-0.00921.510-0.041-0.0410.0000.0000.0000.000
35A40ALA00.0200.01121.327-0.056-0.0560.0000.0000.0000.000
36A41GLY0-0.005-0.00221.042-0.049-0.0490.0000.0000.0000.000
37A42LEU0-0.008-0.00315.280-0.056-0.0560.0000.0000.0000.000
38A43LEU0-0.011-0.01016.711-0.103-0.1030.0000.0000.0000.000
39A44ALA0-0.047-0.02317.661-0.093-0.0930.0000.0000.0000.000
40A45LYS10.8620.91611.9090.5870.5870.0000.0000.0000.000
41A46ALA00.0320.00312.963-0.158-0.1580.0000.0000.0000.000
42A47ARG10.7670.84713.0900.4040.4040.0000.0000.0000.000
43A48ALA0-0.062-0.02214.501-0.082-0.0820.0000.0000.0000.000
44A49GLU-1-0.932-0.9669.204-1.775-1.7750.0000.0000.0000.000
45A50GLY0-0.052-0.0049.111-0.545-0.5450.0000.0000.0000.000
46A51TRP0-0.014-0.0187.5540.0920.0920.0000.0000.0000.000
47A52MET0-0.039-0.01110.7960.1970.1970.0000.0000.0000.000
48A53VAL00.0410.01813.1750.0840.0840.0000.0000.0000.000
49A54LEU0-0.023-0.01416.1910.0360.0360.0000.0000.0000.000
50A55HIS10.8410.92119.2890.5260.5260.0000.0000.0000.000
51A56VAL00.0110.00521.9730.0070.0070.0000.0000.0000.000
52A57VAL00.0350.02224.5650.0150.0150.0000.0000.0000.000
53A58ARG10.7600.86328.3200.1200.1200.0000.0000.0000.000
54A59ALA00.0440.00131.780-0.009-0.0090.0000.0000.0000.000
55A60HIS0-0.053-0.00234.0080.0000.0000.0000.0000.0000.000
56A61ARG10.9070.93435.4770.1280.1280.0000.0000.0000.000
57A62ALA00.020-0.00539.5830.0050.0050.0000.0000.0000.000
58A63ASP-1-0.846-0.91942.759-0.086-0.0860.0000.0000.0000.000
59A64GLY00.0420.02242.1970.0060.0060.0000.0000.0000.000
60A65SER0-0.076-0.02941.7300.0020.0020.0000.0000.0000.000
61A66ASP-1-0.814-0.89936.529-0.120-0.1200.0000.0000.0000.000
62A67ALA00.0450.04037.113-0.005-0.0050.0000.0000.0000.000
63A68GLU-1-0.799-0.90734.008-0.075-0.0750.0000.0000.0000.000
64A69LYS11.0451.00438.3220.0240.0240.0000.0000.0000.000
65A70SER0-0.091-0.04638.914-0.001-0.0010.0000.0000.0000.000
66A71ARG10.9140.93934.4540.0770.0770.0000.0000.0000.000
67A72GLU-1-0.907-0.93241.639-0.057-0.0570.0000.0000.0000.000
68A73HIS0-0.004-0.00943.697-0.002-0.0020.0000.0000.0000.000
69A74LEU0-0.039-0.02541.6160.0000.0000.0000.0000.0000.000
70A75PHE0-0.042-0.00139.455-0.004-0.0040.0000.0000.0000.000
71A76LEU0-0.046-0.01345.6100.0000.0000.0000.0000.0000.000
72A77GLU-1-0.977-0.96049.401-0.068-0.0680.0000.0000.0000.000
73A78GLY0-0.0030.01247.4110.0000.0000.0000.0000.0000.000
74A79GLY0-0.003-0.04044.5630.0030.0030.0000.0000.0000.000
75A80GLY00.0420.02142.5970.0020.0020.0000.0000.0000.000
76A81LEU0-0.051-0.02035.7430.0000.0000.0000.0000.0000.000
77A82CYS0-0.066-0.03434.607-0.004-0.0040.0000.0000.0000.000
78A83VAL00.0270.03136.369-0.006-0.0060.0000.0000.0000.000
79A84ALA00.000-0.01136.009-0.009-0.0090.0000.0000.0000.000
80A85GLY0-0.0090.00136.0570.0070.0070.0000.0000.0000.000
81A86THR0-0.054-0.03737.5480.0020.0020.0000.0000.0000.000
82A87PRO00.0770.02137.394-0.006-0.0060.0000.0000.0000.000
83A88GLY00.0280.03237.124-0.006-0.0060.0000.0000.0000.000
84A89ALA0-0.039-0.01634.435-0.002-0.0020.0000.0000.0000.000
85A90GLU-1-0.907-0.93232.956-0.204-0.2040.0000.0000.0000.000
86A91ILE0-0.062-0.03426.2390.0070.0070.0000.0000.0000.000
87A92VAL00.0140.00429.4330.0040.0040.0000.0000.0000.000
88A93ALA00.0270.01329.769-0.021-0.0210.0000.0000.0000.000
89A94GLY0-0.075-0.03228.7940.0130.0130.0000.0000.0000.000
90A95LEU0-0.049-0.03524.010-0.025-0.0250.0000.0000.0000.000
91A96GLU-1-0.824-0.90425.553-0.316-0.3160.0000.0000.0000.000
92A97PRO0-0.051-0.03723.244-0.039-0.0390.0000.0000.0000.000
93A98ALA00.0000.01120.9920.0290.0290.0000.0000.0000.000
94A99SER00.012-0.01522.282-0.010-0.0100.0000.0000.0000.000
95A100GLY0-0.014-0.00219.660-0.053-0.0530.0000.0000.0000.000
96A101GLU-1-0.773-0.83718.186-0.737-0.7370.0000.0000.0000.000
97A102THR0-0.0030.00418.9810.0430.0430.0000.0000.0000.000
98A103VAL0-0.011-0.01220.8600.0000.0000.0000.0000.0000.000
99A104LEU0-0.0010.00822.7750.0040.0040.0000.0000.0000.000
100A105VAL0-0.009-0.00424.7990.0120.0120.0000.0000.0000.000
101A106LYS10.8440.92126.3900.1550.1550.0000.0000.0000.000
102A107THR00.004-0.01029.1780.0080.0080.0000.0000.0000.000
103A108ARG10.8370.91430.7690.0930.0930.0000.0000.0000.000
104A109PHE00.002-0.02629.048-0.011-0.0110.0000.0000.0000.000
105A110SER0-0.030-0.04325.065-0.026-0.0260.0000.0000.0000.000
106A111ALA00.0460.00322.593-0.005-0.0050.0000.0000.0000.000
107A112PHE00.0170.01918.416-0.031-0.0310.0000.0000.0000.000
108A113MET0-0.029-0.01024.4590.0080.0080.0000.0000.0000.000
109A114GLY0-0.048-0.01828.218-0.004-0.0040.0000.0000.0000.000
110A115THR0-0.030-0.02024.931-0.014-0.0140.0000.0000.0000.000
111A116GLU-1-0.871-0.94623.056-0.264-0.2640.0000.0000.0000.000
112A117CYS0-0.028-0.02520.656-0.062-0.0620.0000.0000.0000.000
113A118ASP-1-0.770-0.87518.449-0.214-0.2140.0000.0000.0000.000
114A119MET0-0.072-0.04317.904-0.031-0.0310.0000.0000.0000.000
115A120LEU0-0.021-0.00618.130-0.056-0.0560.0000.0000.0000.000
116A121LEU0-0.001-0.01814.537-0.146-0.1460.0000.0000.0000.000
117A122ARG11.0111.02113.1970.0190.0190.0000.0000.0000.000
118A123ARG10.8690.94613.3740.4680.4680.0000.0000.0000.000
119A124ARG10.8890.95510.2341.8021.8020.0000.0000.0000.000
120A125GLY00.0070.0019.160-0.412-0.4120.0000.0000.0000.000
121A126VAL0-0.073-0.0448.422-0.226-0.2260.0000.0000.0000.000
122A127ASP-1-0.757-0.8646.176-0.643-0.6430.0000.0000.0000.000
123A128THR0-0.0120.0027.4140.6260.6260.0000.0000.0000.000
124A129LEU0-0.006-0.0069.817-0.323-0.3230.0000.0000.0000.000
125A130LEU0-0.031-0.01210.8580.1680.1680.0000.0000.0000.000
126A131VAL00.009-0.00214.493-0.046-0.0460.0000.0000.0000.000
127A132SER00.002-0.02918.2620.0320.0320.0000.0000.0000.000
128A133GLY00.0500.01720.874-0.014-0.0140.0000.0000.0000.000
129A134THR0-0.033-0.02224.5110.0340.0340.0000.0000.0000.000
130A135GLN00.0460.02027.6370.0030.0030.0000.0000.0000.000
131A136TYR0-0.019-0.07323.6790.0080.0080.0000.0000.0000.000
132A137PRO0-0.030-0.00827.2000.0070.0070.0000.0000.0000.000
133A138ASN0-0.0180.00629.3330.0150.0150.0000.0000.0000.000
134A139CYM-1-0.774-0.85526.794-0.105-0.1050.0000.0000.0000.000
135A140ILE0-0.0450.01322.541-0.006-0.0060.0000.0000.0000.000
136A141ARG10.8920.92223.104-0.063-0.0630.0000.0000.0000.000
137A142GLY0-0.031-0.01824.2000.0200.0200.0000.0000.0000.000
138A143THR00.0210.00720.400-0.001-0.0010.0000.0000.0000.000
139A144ALA0-0.026-0.01419.458-0.003-0.0030.0000.0000.0000.000
140A145VAL00.007-0.00719.7390.0360.0360.0000.0000.0000.000
141A146ASP-1-0.829-0.87321.8200.0190.0190.0000.0000.0000.000
142A147ALA0-0.017-0.00916.8320.0060.0060.0000.0000.0000.000
143A148PHE0-0.007-0.01717.2330.0270.0270.0000.0000.0000.000
144A149ALA0-0.037-0.01418.3440.0540.0540.0000.0000.0000.000
145A150LEU0-0.094-0.05018.7730.0170.0170.0000.0000.0000.000
146A151ASP-1-0.927-0.94114.4650.4110.4110.0000.0000.0000.000
147A152TYR0-0.129-0.07212.7230.0380.0380.0000.0000.0000.000
148A153ASP-1-0.822-0.8919.3101.5141.5140.0000.0000.0000.000
149A154VAL0-0.037-0.02911.973-0.225-0.2250.0000.0000.0000.000
150A155VAL0-0.046-0.02911.5520.1180.1180.0000.0000.0000.000
151A156VAL0-0.013-0.02514.510-0.110-0.1100.0000.0000.0000.000
152A157VAL00.0490.01515.9350.0410.0410.0000.0000.0000.000
153A158THR00.004-0.01418.446-0.009-0.0090.0000.0000.0000.000
154A159ASP-1-0.862-0.92421.221-0.107-0.1070.0000.0000.0000.000
155A160ALA0-0.007-0.00320.519-0.018-0.0180.0000.0000.0000.000
156A161CYS0-0.0160.02821.647-0.022-0.0220.0000.0000.0000.000
157A162SER00.0270.02624.4790.0170.0170.0000.0000.0000.000
158A163ALA00.0220.01628.2350.0020.0020.0000.0000.0000.000
159A164ARG10.8930.92031.1640.0420.0420.0000.0000.0000.000
160A165THR00.0100.00434.1230.0020.0020.0000.0000.0000.000
161A166PRO00.0850.02532.1510.0020.0020.0000.0000.0000.000
162A167GLY00.0650.04131.8730.0080.0080.0000.0000.0000.000
163A168VAL0-0.015-0.00331.5260.0100.0100.0000.0000.0000.000
164A169ALA00.0190.02528.1400.0050.0050.0000.0000.0000.000
165A170GLU-1-0.940-0.97727.9310.0580.0580.0000.0000.0000.000
166A171SER0-0.062-0.02628.5430.0170.0170.0000.0000.0000.000
167A172ASN00.023-0.01127.1540.0120.0120.0000.0000.0000.000
168A173ILE00.0310.02523.0910.0140.0140.0000.0000.0000.000
169A174ASN0-0.040-0.02524.2670.0370.0370.0000.0000.0000.000
170A175ASP-1-0.834-0.89925.8890.1260.1260.0000.0000.0000.000
171A176MET0-0.023-0.02221.6800.0100.0100.0000.0000.0000.000
172A177ARG10.8800.94020.661-0.147-0.1470.0000.0000.0000.000
173A178ALA0-0.0380.00021.8570.0440.0440.0000.0000.0000.000
174A179MET0-0.070-0.03422.5020.0080.0080.0000.0000.0000.000
175A180GLY00.0020.01419.3900.0270.0270.0000.0000.0000.000
176A181ILE00.0080.01017.1670.0540.0540.0000.0000.0000.000
177A182THR0-0.025-0.00713.8860.0370.0370.0000.0000.0000.000
178A183CYS0-0.0060.01216.430-0.082-0.0820.0000.0000.0000.000
179A184VAL0-0.019-0.01115.0470.0390.0390.0000.0000.0000.000
180A185PRO00.0320.02318.370-0.041-0.0410.0000.0000.0000.000
181A186LEU00.0590.02316.2260.0120.0120.0000.0000.0000.000
182A187THR0-0.056-0.04816.317-0.018-0.0180.0000.0000.0000.000
183A188ALA00.0280.02316.1310.0140.0140.0000.0000.0000.000
184A189LEU0-0.019-0.00711.6680.0980.0980.0000.0000.0000.000
185A190ASP-1-0.803-0.89110.262-0.397-0.3970.0000.0000.0000.000
186A191ASP-1-0.896-0.9459.4990.4470.4470.0000.0000.0000.000
187A192VAL0-0.103-0.05410.5310.2570.2570.0000.0000.0000.000
188A193LEU0-0.029-0.0266.4830.3600.3600.0000.0000.0000.000
189A194ALA00.0160.0265.3840.7100.7100.0000.0000.0000.000
190A195ARG10.9020.9746.623-0.025-0.0250.0000.0000.0000.000