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: 3JRJL

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 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 190
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1913955.213059
FMO2-HF: Nuclear repulsion 1842020.519295
FMO2-HF: Total energy -71934.693764
FMO2-MP2: Total energy -72137.149713


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.
-16.803-12.740.079-2.134-2.007-0.001
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 : -0.031 / q_NPA : -0.018
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].
3A8THR0-0.023-0.0022.887-8.683-4.6510.080-2.132-1.980-0.001
4A9VAL00.0210.0035.3501.4541.485-0.001-0.002-0.0270.000
5A10ALA0-0.017-0.0088.3180.2530.2530.0000.0000.0000.000
6A11LEU0-0.0110.00511.8650.0790.0790.0000.0000.0000.000
7A12ALA00.0060.00514.9760.0650.0650.0000.0000.0000.000
8A13ILE0-0.030-0.01118.3510.0500.0500.0000.0000.0000.000
9A14ILE00.003-0.01521.4130.0180.0180.0000.0000.0000.000
10A15ASP-1-0.727-0.85924.325-0.421-0.4210.0000.0000.0000.000
11A16MET0-0.051-0.00525.7730.0370.0370.0000.0000.0000.000
12A17GLN0-0.033-0.03828.288-0.016-0.0160.0000.0000.0000.000
13A18ASN00.0520.00431.3580.0100.0100.0000.0000.0000.000
14A19ASP-1-0.839-0.93334.854-0.252-0.2520.0000.0000.0000.000
15A20PHE0-0.050-0.02331.6900.0140.0140.0000.0000.0000.000
16A21VAL0-0.020-0.00530.8570.0030.0030.0000.0000.0000.000
17A22LEU0-0.0180.00333.9310.0120.0120.0000.0000.0000.000
18A23PRO00.056-0.00737.0650.0060.0060.0000.0000.0000.000
19A24GLY0-0.043-0.01339.6210.0040.0040.0000.0000.0000.000
20A25ALA00.0060.02338.6600.0060.0060.0000.0000.0000.000
21A26PRO00.003-0.00140.5800.0020.0020.0000.0000.0000.000
22A27ALA0-0.050-0.03537.0890.0050.0050.0000.0000.0000.000
23A28CYS0-0.0490.00836.262-0.014-0.0140.0000.0000.0000.000
24A29VAL0-0.030-0.01431.6540.0110.0110.0000.0000.0000.000
25A30GLU-1-0.766-0.85734.076-0.222-0.2220.0000.0000.0000.000
26A31GLY0-0.052-0.02932.0020.0030.0030.0000.0000.0000.000
27A32ALA00.0350.02429.867-0.011-0.0110.0000.0000.0000.000
28A33MET00.0110.01129.911-0.012-0.0120.0000.0000.0000.000
29A34GLY0-0.005-0.00731.321-0.002-0.0020.0000.0000.0000.000
30A35THR0-0.037-0.02725.879-0.009-0.0090.0000.0000.0000.000
31A36VAL00.0140.01525.910-0.032-0.0320.0000.0000.0000.000
32A37PRO00.0190.00025.896-0.033-0.0330.0000.0000.0000.000
33A38VAL00.0260.03321.370-0.023-0.0230.0000.0000.0000.000
34A39ILE00.007-0.00621.524-0.060-0.0600.0000.0000.0000.000
35A40ALA00.0240.01421.330-0.066-0.0660.0000.0000.0000.000
36A41GLY0-0.008-0.00320.986-0.031-0.0310.0000.0000.0000.000
37A42LEU0-0.003-0.00515.320-0.050-0.0500.0000.0000.0000.000
38A43LEU0-0.027-0.00916.690-0.126-0.1260.0000.0000.0000.000
39A44ALA0-0.037-0.02317.588-0.075-0.0750.0000.0000.0000.000
40A45LYS10.7860.87811.6120.8810.8810.0000.0000.0000.000
41A46ALA00.0340.00712.931-0.133-0.1330.0000.0000.0000.000
42A47ARG10.7790.85512.8940.5610.5610.0000.0000.0000.000
43A48ALA0-0.061-0.02214.517-0.022-0.0220.0000.0000.0000.000
44A49GLU-1-0.876-0.9289.238-1.323-1.3230.0000.0000.0000.000
45A50GLY0-0.0360.0049.136-0.468-0.4680.0000.0000.0000.000
46A51TRP0-0.009-0.0247.754-0.164-0.1640.0000.0000.0000.000
47A52MET0-0.039-0.00610.4220.2950.2950.0000.0000.0000.000
48A53VAL00.0370.01812.6890.0030.0030.0000.0000.0000.000
49A54LEU0-0.030-0.02215.2300.0830.0830.0000.0000.0000.000
50A55HIS10.8270.91118.6550.7410.7410.0000.0000.0000.000
51A56VAL00.0130.00321.1670.0180.0180.0000.0000.0000.000
52A57VAL00.0200.00923.8440.0250.0250.0000.0000.0000.000
53A58ARG10.7950.87127.6140.3610.3610.0000.0000.0000.000
54A59ALA00.0350.00131.0440.0010.0010.0000.0000.0000.000
55A60HIS0-0.062-0.01633.320-0.008-0.0080.0000.0000.0000.000
56A61ARG10.9110.93334.7540.3000.3000.0000.0000.0000.000
57A62ALA00.016-0.00838.8660.0050.0050.0000.0000.0000.000
58A63ASP-1-0.828-0.88942.058-0.215-0.2150.0000.0000.0000.000
59A64GLY00.0480.02541.4100.0080.0080.0000.0000.0000.000
60A65SER0-0.103-0.06840.906-0.007-0.0070.0000.0000.0000.000
61A66ASP-1-0.788-0.88035.750-0.301-0.3010.0000.0000.0000.000
62A67ALA00.0480.04836.286-0.020-0.0200.0000.0000.0000.000
63A68GLU-1-0.788-0.88133.771-0.314-0.3140.0000.0000.0000.000
64A69LYS11.0431.01237.9890.1900.1900.0000.0000.0000.000
65A70SER0-0.070-0.04038.6690.0060.0060.0000.0000.0000.000
66A71ARG10.8660.90134.2490.2900.2900.0000.0000.0000.000
67A72GLU-1-0.904-0.93241.464-0.193-0.1930.0000.0000.0000.000
68A73HIS0-0.003-0.00843.2310.0010.0010.0000.0000.0000.000
69A74LEU0-0.045-0.02541.3890.0050.0050.0000.0000.0000.000
70A75PHE0-0.033-0.00138.703-0.003-0.0030.0000.0000.0000.000
71A76LEU0-0.053-0.00544.8750.0050.0050.0000.0000.0000.000
72A77GLU-1-0.975-0.96548.660-0.150-0.1500.0000.0000.0000.000
73A78GLY0-0.0020.01146.7210.0030.0030.0000.0000.0000.000
74A79GLY0-0.002-0.04143.8810.0020.0020.0000.0000.0000.000
75A80GLY00.0430.02441.8950.0010.0010.0000.0000.0000.000
76A81LEU0-0.055-0.02435.8790.0020.0020.0000.0000.0000.000
77A82CYS0-0.048-0.02733.916-0.011-0.0110.0000.0000.0000.000
78A83VAL00.0210.02735.673-0.012-0.0120.0000.0000.0000.000
79A84ALA00.003-0.00535.378-0.006-0.0060.0000.0000.0000.000
80A85GLY0-0.0080.00335.4770.0140.0140.0000.0000.0000.000
81A86THR0-0.054-0.03636.9930.0100.0100.0000.0000.0000.000
82A87PRO00.0890.02336.834-0.012-0.0120.0000.0000.0000.000
83A88GLY00.0250.03136.575-0.010-0.0100.0000.0000.0000.000
84A89ALA0-0.031-0.01633.943-0.014-0.0140.0000.0000.0000.000
85A90GLU-1-0.922-0.93232.358-0.314-0.3140.0000.0000.0000.000
86A91ILE0-0.060-0.03525.760-0.001-0.0010.0000.0000.0000.000
87A92VAL00.0120.00429.1200.0170.0170.0000.0000.0000.000
88A93ALA00.0190.01029.423-0.023-0.0230.0000.0000.0000.000
89A94GLY0-0.065-0.02628.6920.0100.0100.0000.0000.0000.000
90A95LEU0-0.046-0.03323.936-0.034-0.0340.0000.0000.0000.000
91A96GLU-1-0.834-0.91025.117-0.433-0.4330.0000.0000.0000.000
92A97PRO0-0.030-0.02922.890-0.039-0.0390.0000.0000.0000.000
93A98ALA0-0.0100.01020.7770.0540.0540.0000.0000.0000.000
94A99SER00.013-0.01722.018-0.037-0.0370.0000.0000.0000.000
95A100GLY0-0.0060.00019.492-0.038-0.0380.0000.0000.0000.000
96A101GLU-1-0.763-0.82717.937-0.934-0.9340.0000.0000.0000.000
97A102THR0-0.0060.00218.5550.0560.0560.0000.0000.0000.000
98A103VAL0-0.010-0.01420.356-0.015-0.0150.0000.0000.0000.000
99A104LEU0-0.0010.00921.5100.0070.0070.0000.0000.0000.000
100A105VAL0-0.009-0.00624.1210.0100.0100.0000.0000.0000.000
101A106LYS10.8350.89725.8290.4620.4620.0000.0000.0000.000
102A107THR00.005-0.00728.3790.0190.0190.0000.0000.0000.000
103A108ARG10.7990.88030.1500.3350.3350.0000.0000.0000.000
104A109PHE00.026-0.02129.121-0.018-0.0180.0000.0000.0000.000
105A110SER0-0.044-0.05224.909-0.041-0.0410.0000.0000.0000.000
106A111ALA00.0480.00422.0570.0200.0200.0000.0000.0000.000
107A112PHE00.0190.01618.039-0.023-0.0230.0000.0000.0000.000
108A113MET0-0.033-0.00923.8130.0340.0340.0000.0000.0000.000
109A114GLY0-0.049-0.01827.6320.0200.0200.0000.0000.0000.000
110A115THR0-0.023-0.02424.298-0.001-0.0010.0000.0000.0000.000
111A116GLU-1-0.888-0.94922.603-0.584-0.5840.0000.0000.0000.000
112A117CYS00.015-0.01318.875-0.080-0.0800.0000.0000.0000.000
113A118ASP-1-0.769-0.85018.102-1.019-1.0190.0000.0000.0000.000
114A119MET0-0.040-0.03017.607-0.069-0.0690.0000.0000.0000.000
115A120LEU0-0.023-0.00717.740-0.051-0.0510.0000.0000.0000.000
116A121LEU00.000-0.01713.788-0.144-0.1440.0000.0000.0000.000
117A122ARG10.9330.97112.8710.6010.6010.0000.0000.0000.000
118A123ARG10.8780.95413.3470.7770.7770.0000.0000.0000.000
119A124ARG10.8910.9519.4232.4572.4570.0000.0000.0000.000
120A125GLY00.0040.0019.133-0.438-0.4380.0000.0000.0000.000
121A126VAL0-0.073-0.0448.277-0.626-0.6260.0000.0000.0000.000
122A127ASP-1-0.765-0.8576.119-6.327-6.3270.0000.0000.0000.000
123A128THR0-0.001-0.0087.2870.5440.5440.0000.0000.0000.000
124A129LEU0-0.013-0.0049.778-0.080-0.0800.0000.0000.0000.000
125A130LEU0-0.026-0.01110.8930.2150.2150.0000.0000.0000.000
126A131VAL00.003-0.00214.4740.0400.0400.0000.0000.0000.000
127A132SER00.008-0.03018.2400.0680.0680.0000.0000.0000.000
128A133GLY00.0450.01420.862-0.014-0.0140.0000.0000.0000.000
129A134THR0-0.041-0.03124.5010.0400.0400.0000.0000.0000.000
130A135GLN00.0290.01527.6200.0040.0040.0000.0000.0000.000
131A136TYR0-0.002-0.06623.723-0.013-0.0130.0000.0000.0000.000
132A137PRO0-0.040-0.01227.161-0.015-0.0150.0000.0000.0000.000
133A138ASN0-0.0150.00829.2720.0100.0100.0000.0000.0000.000
134A139CYM-1-0.800-0.84427.071-0.423-0.4230.0000.0000.0000.000
135A140ILE0-0.0390.02722.589-0.046-0.0460.0000.0000.0000.000
136A141ARG10.8640.89723.0650.2580.2580.0000.0000.0000.000
137A142GLY0-0.032-0.01524.152-0.017-0.0170.0000.0000.0000.000
138A143THR00.020-0.00620.481-0.017-0.0170.0000.0000.0000.000
139A144ALA0-0.035-0.01419.405-0.063-0.0630.0000.0000.0000.000
140A145VAL00.0140.00019.589-0.031-0.0310.0000.0000.0000.000
141A146ASP-1-0.825-0.87121.331-0.505-0.5050.0000.0000.0000.000
142A147ALA0-0.014-0.01216.763-0.030-0.0300.0000.0000.0000.000
143A148PHE0-0.003-0.01316.267-0.057-0.0570.0000.0000.0000.000
144A149ALA0-0.028-0.01117.5930.0160.0160.0000.0000.0000.000
145A150LEU0-0.102-0.05018.2740.0480.0480.0000.0000.0000.000
146A151ASP-1-0.935-0.94614.198-0.711-0.7110.0000.0000.0000.000
147A152TYR0-0.123-0.07212.404-0.227-0.2270.0000.0000.0000.000
148A153ASP-1-0.787-0.8638.626-1.252-1.2520.0000.0000.0000.000
149A154VAL0-0.049-0.02911.517-0.170-0.1700.0000.0000.0000.000
150A155VAL0-0.047-0.03211.3710.1540.1540.0000.0000.0000.000
151A156VAL0-0.006-0.01314.468-0.050-0.0500.0000.0000.0000.000
152A157VAL00.0610.02115.8810.0520.0520.0000.0000.0000.000
153A158THR00.009-0.00918.4260.0350.0350.0000.0000.0000.000
154A159ASP-1-0.854-0.92421.171-0.386-0.3860.0000.0000.0000.000
155A160ALA0-0.003-0.00520.5420.0140.0140.0000.0000.0000.000
156A161CYS0-0.0310.01821.574-0.044-0.0440.0000.0000.0000.000
157A162SER00.0420.03824.4610.0410.0410.0000.0000.0000.000
158A163ALA00.0130.00728.216-0.014-0.0140.0000.0000.0000.000
159A164ARG10.8880.89731.1380.2160.2160.0000.0000.0000.000
160A165THR00.0080.00134.1030.0110.0110.0000.0000.0000.000
161A166PRO00.0890.02932.123-0.013-0.0130.0000.0000.0000.000
162A167GLY00.0700.04631.838-0.006-0.0060.0000.0000.0000.000
163A168VAL0-0.0060.00231.633-0.002-0.0020.0000.0000.0000.000
164A169ALA00.0240.03028.108-0.014-0.0140.0000.0000.0000.000
165A170GLU-1-0.939-0.97627.890-0.189-0.1890.0000.0000.0000.000
166A171SER0-0.052-0.03228.494-0.006-0.0060.0000.0000.0000.000
167A172ASN00.003-0.01827.018-0.015-0.0150.0000.0000.0000.000
168A173ILE00.0230.02823.006-0.021-0.0210.0000.0000.0000.000
169A174ASN0-0.039-0.02824.213-0.008-0.0080.0000.0000.0000.000
170A175ASP-1-0.801-0.87425.774-0.228-0.2280.0000.0000.0000.000
171A176MET0-0.025-0.02021.616-0.019-0.0190.0000.0000.0000.000
172A177ARG10.8890.93620.7080.2520.2520.0000.0000.0000.000
173A178ALA0-0.041-0.00321.4500.0120.0120.0000.0000.0000.000
174A179MET0-0.073-0.03321.9650.0070.0070.0000.0000.0000.000
175A180GLY00.0050.01518.601-0.005-0.0050.0000.0000.0000.000
176A181ILE00.0100.01216.749-0.061-0.0610.0000.0000.0000.000
177A182THR0-0.0050.00713.9790.1190.1190.0000.0000.0000.000
178A183CYS0-0.0190.00016.373-0.074-0.0740.0000.0000.0000.000
179A184VAL0-0.006-0.00215.0770.0860.0860.0000.0000.0000.000
180A185PRO00.0160.01918.337-0.059-0.0590.0000.0000.0000.000
181A186LEU00.0550.02216.265-0.021-0.0210.0000.0000.0000.000
182A187THR0-0.048-0.04316.320-0.044-0.0440.0000.0000.0000.000
183A188ALA00.0200.01416.1170.0470.0470.0000.0000.0000.000
184A189LEU0-0.0160.00211.6380.0290.0290.0000.0000.0000.000
185A190ASP-1-0.798-0.90510.245-0.817-0.8170.0000.0000.0000.000
186A191ASP-1-0.897-0.9419.4930.1340.1340.0000.0000.0000.000
187A192VAL0-0.101-0.05610.4710.1320.1320.0000.0000.0000.000
188A193LEU0-0.037-0.0316.511-0.053-0.0530.0000.0000.0000.000
189A194ALA00.0050.0195.348-0.088-0.0880.0000.0000.0000.000
190A195ARG10.8820.9616.1260.6120.6120.0000.0000.0000.000