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: 6G6RZ

Calculation Name: 3HD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W2Q0

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1800429.457512
FMO2-HF: Nuclear repulsion 1729658.119696
FMO2-HF: Total energy -70771.337816
FMO2-MP2: Total energy -70976.863254


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:28:GLN)


Summations of interaction energy for fragment #1(A:28:GLN)
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.
-5.06-0.0510.227-2.28-2.9560.002
Interaction energy analysis for fragmet #1(A:28:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.009
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].
3A30ALA00.0060.0163.027-4.566-1.4330.131-1.542-1.7230.006
4A31GLN00.0210.0024.7191.3131.444-0.001-0.010-0.1200.000
5A32GLN00.0010.0115.5080.2930.2930.0000.0000.0000.000
6A33TYR0-0.094-0.0378.302-0.552-0.5520.0000.0000.0000.000
7A34VAL00.0270.02912.0340.1350.1350.0000.0000.0000.000
8A35ASN00.002-0.01814.9550.0070.0070.0000.0000.0000.000
9A36ILE0-0.0040.01818.360-0.034-0.0340.0000.0000.0000.000
10A37ASN0-0.068-0.03021.6760.0410.0410.0000.0000.0000.000
11A38PRO00.0210.00124.660-0.019-0.0190.0000.0000.0000.000
12A39PRO00.0050.00724.4660.0030.0030.0000.0000.0000.000
13A40MET0-0.027-0.00624.839-0.029-0.0290.0000.0000.0000.000
14A41PRO0-0.029-0.01227.2750.0190.0190.0000.0000.0000.000
15A42SER0-0.009-0.01028.797-0.006-0.0060.0000.0000.0000.000
16A43ASP-1-0.841-0.90729.9220.2580.2580.0000.0000.0000.000
17A44THR0-0.048-0.03531.181-0.028-0.0280.0000.0000.0000.000
18A45PRO0-0.010-0.00932.2770.0180.0180.0000.0000.0000.000
19A46GLY0-0.013-0.01433.295-0.009-0.0090.0000.0000.0000.000
20A47LYS10.8540.92729.311-0.284-0.2840.0000.0000.0000.000
21A48ILE0-0.0050.00723.3180.0070.0070.0000.0000.0000.000
22A49GLU-1-0.700-0.83825.6220.3220.3220.0000.0000.0000.000
23A50VAL0-0.018-0.00620.4930.0550.0550.0000.0000.0000.000
24A51LEU0-0.031-0.01622.367-0.053-0.0530.0000.0000.0000.000
25A52GLU-1-0.788-0.90021.3670.3200.3200.0000.0000.0000.000
26A53PHE00.010-0.00221.420-0.047-0.0470.0000.0000.0000.000
27A54PHE00.034-0.00921.6850.0000.0000.0000.0000.0000.000
28A55ALA00.0580.00623.953-0.007-0.0070.0000.0000.0000.000
29A56TYR00.010-0.02125.917-0.011-0.0110.0000.0000.0000.000
30A57THR00.005-0.00328.240-0.009-0.0090.0000.0000.0000.000
31A58CYS0-0.0300.00921.581-0.029-0.0290.0000.0000.0000.000
32A59PRO00.0220.00022.4310.0100.0100.0000.0000.0000.000
33A60HIS00.0540.01718.095-0.004-0.0040.0000.0000.0000.000
34A61CYS0-0.051-0.00119.7930.0390.0390.0000.0000.0000.000
35A62ALA00.0180.01022.0690.0080.0080.0000.0000.0000.000
36A63ALA0-0.042-0.01719.919-0.005-0.0050.0000.0000.0000.000
37A64ILE0-0.0040.00616.0610.0000.0000.0000.0000.0000.000
38A65GLU-1-0.745-0.85120.1320.1910.1910.0000.0000.0000.000
39A66PRO00.0170.00523.3920.0160.0160.0000.0000.0000.000
40A67MET0-0.017-0.01017.0120.0170.0170.0000.0000.0000.000
41A68VAL0-0.007-0.00619.4980.0360.0360.0000.0000.0000.000
42A69GLU-1-0.917-0.96421.7610.1440.1440.0000.0000.0000.000
43A70ASP-1-0.879-0.93823.1800.1500.1500.0000.0000.0000.000
44A71TRP0-0.005-0.00118.8180.0120.0120.0000.0000.0000.000
45A72ALA0-0.004-0.00822.1580.0160.0160.0000.0000.0000.000
46A73LYS10.7560.87425.155-0.148-0.1480.0000.0000.0000.000
47A74THR0-0.070-0.03723.388-0.002-0.0020.0000.0000.0000.000
48A75ALA00.0130.03523.2500.0280.0280.0000.0000.0000.000
49A76PRO00.010-0.00622.267-0.025-0.0250.0000.0000.0000.000
50A77GLN00.0180.01425.219-0.024-0.0240.0000.0000.0000.000
51A78ASP-1-0.915-0.95525.8030.4090.4090.0000.0000.0000.000
52A79VAL0-0.025-0.01022.9370.0110.0110.0000.0000.0000.000
53A80VAL0-0.022-0.00926.184-0.033-0.0330.0000.0000.0000.000
54A81LEU00.0090.00822.9070.0320.0320.0000.0000.0000.000
55A82LYS10.7830.89125.941-0.330-0.3300.0000.0000.0000.000
56A83GLN0-0.031-0.02725.0880.0110.0110.0000.0000.0000.000
57A84VAL0-0.026-0.01226.012-0.019-0.0190.0000.0000.0000.000
58A85PRO0-0.0200.02126.4060.0080.0080.0000.0000.0000.000
59A86ILE00.0110.00924.422-0.002-0.0020.0000.0000.0000.000
60A87ALA0-0.017-0.03927.803-0.021-0.0210.0000.0000.0000.000
61A88PHE00.0440.02222.619-0.009-0.0090.0000.0000.0000.000
62A89ASN00.012-0.00228.501-0.014-0.0140.0000.0000.0000.000
63A90ALA00.0540.01532.1310.0030.0030.0000.0000.0000.000
64A91GLY00.0070.00734.814-0.001-0.0010.0000.0000.0000.000
65A92MET0-0.0460.00426.645-0.006-0.0060.0000.0000.0000.000
66A93LYS10.9490.98132.383-0.099-0.0990.0000.0000.0000.000
67A94PRO0-0.020-0.01234.6820.0050.0050.0000.0000.0000.000
68A95LEU00.0070.00531.3110.0000.0000.0000.0000.0000.000
69A96GLN0-0.007-0.02730.740-0.006-0.0060.0000.0000.0000.000
70A97GLN00.003-0.00133.1440.0050.0050.0000.0000.0000.000
71A98LEU00.0170.02034.4690.0000.0000.0000.0000.0000.000
72A99TYR0-0.0020.01129.906-0.002-0.0020.0000.0000.0000.000
73A100TYR00.020-0.00930.8870.0000.0000.0000.0000.0000.000
74A101THR0-0.005-0.01836.212-0.004-0.0040.0000.0000.0000.000
75A102LEU0-0.026-0.01935.107-0.005-0.0050.0000.0000.0000.000
76A103GLN0-0.0140.00033.233-0.004-0.0040.0000.0000.0000.000
77A104ALA00.0050.00637.561-0.002-0.0020.0000.0000.0000.000
78A105LEU0-0.117-0.06140.788-0.007-0.0070.0000.0000.0000.000
79A106GLU-1-0.946-0.96140.4830.0940.0940.0000.0000.0000.000
80A107ARG10.7770.86439.681-0.069-0.0690.0000.0000.0000.000
81A108PRO00.0720.03834.786-0.002-0.0020.0000.0000.0000.000
82A109ASP-1-0.773-0.87634.3700.0710.0710.0000.0000.0000.000
83A110LEU0-0.046-0.01935.358-0.008-0.0080.0000.0000.0000.000
84A111HIS00.0280.03027.834-0.020-0.0200.0000.0000.0000.000
85A112PRO00.0670.03229.485-0.004-0.0040.0000.0000.0000.000
86A113LYS10.8540.91630.626-0.069-0.0690.0000.0000.0000.000
87A114VAL00.0020.01432.019-0.013-0.0130.0000.0000.0000.000
88A115PHE00.0040.01125.962-0.014-0.0140.0000.0000.0000.000
89A116THR00.0260.01029.782-0.012-0.0120.0000.0000.0000.000
90A117ALA00.0150.01331.615-0.013-0.0130.0000.0000.0000.000
91A118ILE0-0.022-0.01030.204-0.010-0.0100.0000.0000.0000.000
92A119HIS0-0.063-0.04726.947-0.028-0.0280.0000.0000.0000.000
93A120THR0-0.018-0.00629.879-0.015-0.0150.0000.0000.0000.000
94A121GLU-1-0.838-0.91831.941-0.002-0.0020.0000.0000.0000.000
95A122ARG10.8340.93328.8530.0410.0410.0000.0000.0000.000
96A123LYS10.8500.92434.756-0.005-0.0050.0000.0000.0000.000
97A124ARG10.9590.97535.5660.0290.0290.0000.0000.0000.000
98A125LEU0-0.0030.00635.2760.0020.0020.0000.0000.0000.000
99A126PHE00.001-0.02732.5110.0050.0050.0000.0000.0000.000
100A127ASP-1-0.796-0.89236.3330.0370.0370.0000.0000.0000.000
101A128LYS10.8210.90839.817-0.063-0.0630.0000.0000.0000.000
102A129LYS10.8250.90842.151-0.021-0.0210.0000.0000.0000.000
103A130ALA0-0.002-0.00640.251-0.001-0.0010.0000.0000.0000.000
104A131MET0-0.053-0.01335.9750.0010.0010.0000.0000.0000.000
105A132GLY00.0850.04740.4040.0020.0020.0000.0000.0000.000
106A133GLU-1-0.820-0.90743.9630.0220.0220.0000.0000.0000.000
107A134TRP0-0.031-0.00236.125-0.001-0.0010.0000.0000.0000.000
108A135ALA00.0430.03041.8150.0000.0000.0000.0000.0000.000
109A136ALA00.0140.00842.6230.0000.0000.0000.0000.0000.000
110A137SER0-0.109-0.07742.555-0.002-0.0020.0000.0000.0000.000
111A138GLN0-0.0160.00139.5100.0010.0010.0000.0000.0000.000
112A139GLY00.0100.02242.8040.0040.0040.0000.0000.0000.000
113A140VAL0-0.042-0.02642.4980.0050.0050.0000.0000.0000.000
114A141ASP-1-0.811-0.91145.9150.0440.0440.0000.0000.0000.000
115A142ARG10.8190.90246.758-0.034-0.0340.0000.0000.0000.000
116A143ALA00.0250.01848.4380.0020.0020.0000.0000.0000.000
117A144LYS10.9480.96445.863-0.074-0.0740.0000.0000.0000.000
118A145PHE00.0140.00340.4700.0050.0050.0000.0000.0000.000
119A146ASP-1-0.822-0.92544.7970.0530.0530.0000.0000.0000.000
120A147SER0-0.044-0.00146.6940.0030.0030.0000.0000.0000.000
121A148VAL00.012-0.00342.2190.0040.0040.0000.0000.0000.000
122A149PHE00.0230.01938.8520.0060.0060.0000.0000.0000.000
123A150ASP-1-0.847-0.91242.0390.0730.0730.0000.0000.0000.000
124A151SER0-0.037-0.01843.2110.0040.0040.0000.0000.0000.000
125A152PHE00.0490.00643.1140.0050.0050.0000.0000.0000.000
126A153SER0-0.0190.00340.8480.0070.0070.0000.0000.0000.000
127A154VAL00.0500.03238.2640.0100.0100.0000.0000.0000.000
128A155GLN0-0.051-0.03238.2670.0010.0010.0000.0000.0000.000
129A156THR00.002-0.01138.5670.0080.0080.0000.0000.0000.000
130A157GLN0-0.0070.00335.6950.0040.0040.0000.0000.0000.000
131A158VAL00.0350.02134.0640.0120.0120.0000.0000.0000.000
132A159GLN0-0.0150.00633.7780.0000.0000.0000.0000.0000.000
133A160ARG10.8420.89632.139-0.250-0.2500.0000.0000.0000.000
134A161ALA00.0270.00330.2510.0190.0190.0000.0000.0000.000
135A162SER00.015-0.01329.1450.0150.0150.0000.0000.0000.000
136A163GLN0-0.0020.01229.6370.0160.0160.0000.0000.0000.000
137A164LEU0-0.024-0.01827.4420.0180.0180.0000.0000.0000.000
138A165ALA00.0160.00325.1790.0310.0310.0000.0000.0000.000
139A166GLU-1-0.937-0.96625.0170.2700.2700.0000.0000.0000.000
140A167ALA0-0.055-0.02026.2550.0230.0230.0000.0000.0000.000
141A168ALA0-0.026-0.02522.0370.0350.0350.0000.0000.0000.000
142A169HIS0-0.037-0.01721.3740.0430.0430.0000.0000.0000.000
143A170ILE0-0.053-0.01820.2980.0220.0220.0000.0000.0000.000
144A171ASP-1-0.878-0.93917.8360.3830.3830.0000.0000.0000.000
145A172GLY0-0.012-0.00818.863-0.057-0.0570.0000.0000.0000.000
146A173THR0-0.068-0.01719.6130.0180.0180.0000.0000.0000.000
147A174PRO00.004-0.01817.042-0.046-0.0460.0000.0000.0000.000
148A175ALA0-0.005-0.01317.0090.0390.0390.0000.0000.0000.000
149A176PHE0-0.0010.00216.054-0.048-0.0480.0000.0000.0000.000
150A177ALA00.0320.03217.7200.0910.0910.0000.0000.0000.000
151A178VAL0-0.016-0.02117.267-0.046-0.0460.0000.0000.0000.000
152A179GLY00.0250.00120.2270.0420.0420.0000.0000.0000.000
153A180GLY0-0.0080.00522.997-0.008-0.0080.0000.0000.0000.000
154A181ARG10.9110.95620.950-0.700-0.7000.0000.0000.0000.000
155A182TYR00.0140.01216.4590.0170.0170.0000.0000.0000.000
156A183MET00.0270.02516.879-0.066-0.0660.0000.0000.0000.000
157A184THR00.030-0.01111.4540.0990.0990.0000.0000.0000.000
158A185SER00.0750.02912.527-0.145-0.1450.0000.0000.0000.000
159A186PRO00.0470.02411.3870.1720.1720.0000.0000.0000.000
160A187VAL00.0200.0099.6780.0440.0440.0000.0000.0000.000
161A188LEU0-0.0010.0148.8920.0680.0680.0000.0000.0000.000
162A189ALA0-0.009-0.0047.2320.7190.7190.0000.0000.0000.000
163A190GLY00.0270.0164.9100.1460.1460.0000.0000.0000.000
164A191ASN0-0.057-0.0425.954-0.712-0.7120.0000.0000.0000.000
165A192ASP-1-0.853-0.9269.160-0.557-0.5570.0000.0000.0000.000
166A193TYR0-0.025-0.0203.141-1.773-0.0280.097-0.728-1.113-0.004
167A194ALA0-0.035-0.0187.725-0.027-0.0270.0000.0000.0000.000
168A195GLY0-0.0040.00210.7310.0980.0980.0000.0000.0000.000
169A196ALA00.0380.01412.977-0.110-0.1100.0000.0000.0000.000
170A197LEU00.0080.0037.1080.0140.0140.0000.0000.0000.000
171A198LYS10.9370.97910.5820.8860.8860.0000.0000.0000.000
172A199VAL0-0.004-0.00511.5550.0690.0690.0000.0000.0000.000
173A200VAL00.0030.00412.8520.0790.0790.0000.0000.0000.000
174A201ASP-1-0.880-0.9399.654-2.364-2.3640.0000.0000.0000.000
175A202GLN0-0.059-0.04513.1880.0920.0920.0000.0000.0000.000
176A203LEU00.0100.01216.3940.0900.0900.0000.0000.0000.000
177A204ILE00.0070.02713.5070.0850.0850.0000.0000.0000.000
178A205VAL0-0.053-0.01915.9650.0150.0150.0000.0000.0000.000
179A206GLN00.0430.02118.4560.0440.0440.0000.0000.0000.000
180A207SER0-0.093-0.06920.0040.0470.0470.0000.0000.0000.000
181A208ARG10.8610.94116.9780.9720.9720.0000.0000.0000.000
182A209GLU-1-1.014-1.00422.593-0.534-0.5340.0000.0000.0000.000