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: N9RQQ

Calculation Name: 5WQN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WQN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HWU9

Base Structure: X-ray

Registration Date: 2023-09-20

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2404027.227051
FMO2-HF: Nuclear repulsion 2323039.107463
FMO2-HF: Total energy -80988.119588
FMO2-MP2: Total energy -81224.088657


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.
-9.634-1.2744.035-3.943-8.454-0.019
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 : -0.006 / q_NPA : 0.002
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].
3A3ASN0-0.007-0.0042.941-1.6311.5320.252-1.568-1.847-0.001
4A4VAL00.002-0.0065.0360.4530.548-0.001-0.008-0.0860.000
5A5LEU0-0.0060.0087.7780.2340.2340.0000.0000.0000.000
6A6ILE00.0020.00510.9160.0660.0660.0000.0000.0000.000
7A7VAL00.017-0.00413.7110.0530.0530.0000.0000.0000.000
8A8GLY00.0050.01316.9860.0280.0280.0000.0000.0000.000
9A9ALA00.030-0.00315.5900.0190.0190.0000.0000.0000.000
10A10SER00.0130.01017.5590.0330.0330.0000.0000.0000.000
11A11ARG11.0091.00420.4240.1070.1070.0000.0000.0000.000
12A12GLY0-0.0090.00521.163-0.022-0.0220.0000.0000.0000.000
13A13ILE00.0890.02619.1490.0130.0130.0000.0000.0000.000
14A14GLY00.0500.03317.713-0.014-0.0140.0000.0000.0000.000
15A15LEU0-0.042-0.00616.147-0.023-0.0230.0000.0000.0000.000
16A16GLY00.0370.00915.9980.0320.0320.0000.0000.0000.000
17A17LEU0-0.0050.00314.2420.0310.0310.0000.0000.0000.000
18A18ALA00.004-0.00111.744-0.026-0.0260.0000.0000.0000.000
19A19ASP-1-0.804-0.86411.2550.3590.3590.0000.0000.0000.000
20A20ALA00.0590.02112.1290.1120.1120.0000.0000.0000.000
21A21PHE00.017-0.0138.2600.0370.0370.0000.0000.0000.000
22A22LEU0-0.0130.0027.3180.1480.1480.0000.0000.0000.000
23A23GLN0-0.049-0.0388.1340.4370.4370.0000.0000.0000.000
24A24ARG10.9110.9668.2230.1960.1960.0000.0000.0000.000
25A25GLY0-0.0100.0055.269-0.071-0.0710.0000.0000.0000.000
26A26ALA0-0.045-0.0152.999-1.7860.3280.373-0.962-1.526-0.010
27A27GLN00.0000.0002.1890.1642.3683.227-1.322-4.108-0.009
28A28VAL0-0.046-0.0263.785-1.364-1.3750.0250.112-0.1270.000
29A29PHE00.0210.0136.0440.2270.2270.0000.0000.0000.000
30A30ALA00.0200.01010.064-0.008-0.0080.0000.0000.0000.000
31A31VAL00.0120.01313.3690.0380.0380.0000.0000.0000.000
32A32ALA0-0.012-0.01616.5950.0340.0340.0000.0000.0000.000
33A33ARG10.9920.99919.9130.1520.1520.0000.0000.0000.000
34A34ARG10.9190.95022.8410.1320.1320.0000.0000.0000.000
35A35PRO00.0480.04017.9340.0260.0260.0000.0000.0000.000
36A36GLN00.0760.03920.0910.0150.0150.0000.0000.0000.000
37A37GLY0-0.0150.00121.9890.0170.0170.0000.0000.0000.000
38A38SER0-0.070-0.04520.8490.0120.0120.0000.0000.0000.000
39A39PRO00.034-0.00121.2120.0090.0090.0000.0000.0000.000
40A40GLY00.0140.00820.5240.0200.0200.0000.0000.0000.000
41A41LEU00.030-0.00315.5490.0230.0230.0000.0000.0000.000
42A42GLN0-0.022-0.01316.2740.0390.0390.0000.0000.0000.000
43A43ALA00.0130.01917.4280.0270.0270.0000.0000.0000.000
44A44LEU0-0.036-0.01813.5500.0460.0460.0000.0000.0000.000
45A45ALA0-0.010-0.00612.5140.0980.0980.0000.0000.0000.000
46A46GLU-1-0.947-0.95812.8720.2510.2510.0000.0000.0000.000
47A47ARG10.8100.88811.805-0.400-0.4000.0000.0000.0000.000
48A48ALA0-0.066-0.0448.9230.1200.1200.0000.0000.0000.000
49A49GLY00.0450.0258.5220.2130.2130.0000.0000.0000.000
50A50GLU-1-0.878-0.9466.594-0.138-0.1380.0000.0000.0000.000
51A51ARG10.8270.9293.600-4.434-3.6390.159-0.195-0.7600.001
52A52LEU0-0.043-0.0135.580-0.059-0.0590.0000.0000.0000.000
53A53GLN0-0.055-0.0267.560-0.095-0.0950.0000.0000.0000.000
54A54ALA0-0.018-0.01110.283-0.055-0.0550.0000.0000.0000.000
55A55VAL00.0350.01613.206-0.014-0.0140.0000.0000.0000.000
56A56THR0-0.031-0.02815.7330.0410.0410.0000.0000.0000.000
57A57GLY00.0570.01619.539-0.021-0.0210.0000.0000.0000.000
58A58ASP-1-0.869-0.94420.942-0.192-0.1920.0000.0000.0000.000
59A59LEU00.0420.01721.459-0.005-0.0050.0000.0000.0000.000
60A60ASN0-0.002-0.02923.504-0.012-0.0120.0000.0000.0000.000
61A61GLN0-0.065-0.02526.1230.0180.0180.0000.0000.0000.000
62A62HIS00.008-0.02225.559-0.034-0.0340.0000.0000.0000.000
63A63ASP-1-0.833-0.89624.270-0.281-0.2810.0000.0000.0000.000
64A64CYS0-0.043-0.00819.753-0.021-0.0210.0000.0000.0000.000
65A65ALA00.0440.00919.266-0.037-0.0370.0000.0000.0000.000
66A66GLU-1-0.869-0.91018.440-0.364-0.3640.0000.0000.0000.000
67A67ARG10.7350.82518.6250.2800.2800.0000.0000.0000.000
68A68ILE0-0.030-0.02314.099-0.028-0.0280.0000.0000.0000.000
69A69GLY0-0.026-0.01513.994-0.103-0.1030.0000.0000.0000.000
70A70GLU-1-0.827-0.88714.754-0.401-0.4010.0000.0000.0000.000
71A71MET0-0.036-0.01011.5710.0060.0060.0000.0000.0000.000
72A72LEU0-0.029-0.0188.804-0.114-0.1140.0000.0000.0000.000
73A73GLY00.0250.03410.029-0.187-0.1870.0000.0000.0000.000
74A74GLU-1-0.920-0.97310.009-1.332-1.3320.0000.0000.0000.000
75A75ARG10.8620.9515.4051.6751.6750.0000.0000.0000.000
76A76ARG10.8440.8998.0641.5421.5420.0000.0000.0000.000
77A77ILE0-0.014-0.0148.018-0.573-0.5730.0000.0000.0000.000
78A78ASP-1-0.782-0.8675.939-4.482-4.4820.0000.0000.0000.000
79A79ARG10.7880.8629.1331.8671.8670.0000.0000.0000.000
80A80LEU00.0110.01410.625-0.056-0.0560.0000.0000.0000.000
81A81ILE00.0050.01113.1000.1010.1010.0000.0000.0000.000
82A82VAL00.0000.00015.5480.0150.0150.0000.0000.0000.000
83A83ASN0-0.061-0.03918.7200.0430.0430.0000.0000.0000.000
84A84ALA00.0260.01620.4340.0150.0150.0000.0000.0000.000
85A85GLY0-0.004-0.02223.8570.0010.0010.0000.0000.0000.000
86A86ILE0-0.075-0.02127.2560.0090.0090.0000.0000.0000.000
87A87TYR00.0630.02130.607-0.005-0.0050.0000.0000.0000.000
88A88GLY00.0550.03633.706-0.002-0.0020.0000.0000.0000.000
89A89PRO00.0510.02036.1980.0040.0040.0000.0000.0000.000
90A90GLN0-0.017-0.01938.932-0.002-0.0020.0000.0000.0000.000
91A91GLN00.0530.03440.6130.0020.0020.0000.0000.0000.000
92A92GLN0-0.117-0.06337.116-0.002-0.0020.0000.0000.0000.000
93A93ASP-1-0.795-0.89641.830-0.068-0.0680.0000.0000.0000.000
94A94VAL0-0.018-0.02843.725-0.002-0.0020.0000.0000.0000.000
95A95ALA0-0.060-0.02245.566-0.001-0.0010.0000.0000.0000.000
96A96GLU-1-0.959-0.98345.906-0.065-0.0650.0000.0000.0000.000
97A97ILE0-0.070-0.01339.514-0.002-0.0020.0000.0000.0000.000
98A98ASP-1-0.760-0.85543.036-0.090-0.0900.0000.0000.0000.000
99A99ALA00.016-0.01142.493-0.005-0.0050.0000.0000.0000.000
100A100GLU-1-0.930-0.96140.312-0.101-0.1010.0000.0000.0000.000
101A101GLN00.007-0.02438.559-0.009-0.0090.0000.0000.0000.000
102A102THR0-0.019-0.02137.628-0.007-0.0070.0000.0000.0000.000
103A103ALA0-0.009-0.00336.907-0.009-0.0090.0000.0000.0000.000
104A104GLN00.000-0.00133.614-0.010-0.0100.0000.0000.0000.000
105A105LEU00.0030.00932.853-0.012-0.0120.0000.0000.0000.000
106A106PHE00.022-0.00432.379-0.012-0.0120.0000.0000.0000.000
107A107LEU0-0.030-0.00931.252-0.017-0.0170.0000.0000.0000.000
108A108THR0-0.025-0.01327.927-0.020-0.0200.0000.0000.0000.000
109A109ASN0-0.036-0.03327.335-0.023-0.0230.0000.0000.0000.000
110A110ALA00.0130.01227.856-0.011-0.0110.0000.0000.0000.000
111A111ILE00.006-0.00327.719-0.021-0.0210.0000.0000.0000.000
112A112ALA0-0.019-0.00326.298-0.019-0.0190.0000.0000.0000.000
113A113PRO00.014-0.00423.076-0.032-0.0320.0000.0000.0000.000
114A114LEU00.0330.03122.517-0.043-0.0430.0000.0000.0000.000
115A115ARG10.8840.95423.8570.2410.2410.0000.0000.0000.000
116A116LEU0-0.013-0.00218.831-0.014-0.0140.0000.0000.0000.000
117A117ALA00.0250.00319.045-0.048-0.0480.0000.0000.0000.000
118A118ARG10.8490.89919.7320.2780.2780.0000.0000.0000.000
119A119ALA0-0.0120.01721.620-0.017-0.0170.0000.0000.0000.000
120A120LEU0-0.009-0.01115.772-0.023-0.0230.0000.0000.0000.000
121A121SER0-0.021-0.01016.773-0.100-0.1000.0000.0000.0000.000
122A122GLY00.0320.02117.176-0.048-0.0480.0000.0000.0000.000
123A123ARG10.8720.92313.4840.8500.8500.0000.0000.0000.000
124A124VAL0-0.0100.01312.283-0.243-0.2430.0000.0000.0000.000
125A125SER0-0.073-0.0388.2630.2670.2670.0000.0000.0000.000
126A126ARG10.9730.97711.4170.8030.8030.0000.0000.0000.000
127A127GLY00.0180.02312.204-0.089-0.0890.0000.0000.0000.000
128A128GLY0-0.0020.00811.738-0.057-0.0570.0000.0000.0000.000
129A129VAL0-0.034-0.01912.5500.1750.1750.0000.0000.0000.000
130A130VAL00.0080.01614.066-0.113-0.1130.0000.0000.0000.000
131A131ALA0-0.021-0.01116.7370.0760.0760.0000.0000.0000.000
132A132PHE0-0.015-0.00818.333-0.016-0.0160.0000.0000.0000.000
133A133MET00.0110.02119.3700.0280.0280.0000.0000.0000.000
134A134SER0-0.004-0.02222.5160.0170.0170.0000.0000.0000.000
135A135SER00.019-0.00526.0780.0170.0170.0000.0000.0000.000
136A136GLN00.0540.01728.822-0.004-0.0040.0000.0000.0000.000
137A137MET0-0.055-0.03431.2500.0040.0040.0000.0000.0000.000
138A138ALA0-0.0100.01430.8510.0040.0040.0000.0000.0000.000
139A139SER0-0.060-0.04332.8280.0010.0010.0000.0000.0000.000
140A140LEU00.012-0.01034.3120.0090.0090.0000.0000.0000.000
141A141ALA0-0.046-0.03136.9460.0070.0070.0000.0000.0000.000
142A142LEU0-0.018-0.01033.4560.0060.0060.0000.0000.0000.000
143A143GLY00.0230.02737.7630.0060.0060.0000.0000.0000.000
144A144LEU0-0.004-0.01635.1450.0050.0050.0000.0000.0000.000
145A145SER00.011-0.01236.9880.0010.0010.0000.0000.0000.000
146A146ALA0-0.0090.00038.5780.0000.0000.0000.0000.0000.000
147A147THR00.0060.00240.3180.0000.0000.0000.0000.0000.000
148A148MET0-0.051-0.00735.641-0.002-0.0020.0000.0000.0000.000
149A149PRO00.0500.03837.831-0.008-0.0080.0000.0000.0000.000
150A150LEU00.0270.01638.501-0.008-0.0080.0000.0000.0000.000
151A151TYR00.0150.01029.272-0.015-0.0150.0000.0000.0000.000
152A152GLY00.0580.03333.682-0.011-0.0110.0000.0000.0000.000
153A153ALA00.0040.00834.391-0.010-0.0100.0000.0000.0000.000
154A154SER0-0.056-0.03832.718-0.011-0.0110.0000.0000.0000.000
155A155LYS10.8390.90826.0420.1960.1960.0000.0000.0000.000
156A156ALA00.0330.02130.495-0.013-0.0130.0000.0000.0000.000
157A157ALA0-0.025-0.01032.594-0.008-0.0080.0000.0000.0000.000
158A158LEU0-0.023-0.00325.090-0.011-0.0110.0000.0000.0000.000
159A159ASN00.0290.01828.143-0.028-0.0280.0000.0000.0000.000
160A160SER0-0.0110.00329.194-0.011-0.0110.0000.0000.0000.000
161A161LEU00.0000.00029.012-0.006-0.0060.0000.0000.0000.000
162A162VAL00.0010.00224.260-0.013-0.0130.0000.0000.0000.000
163A163ARG10.8640.91426.8520.2150.2150.0000.0000.0000.000
164A164SER0-0.042-0.02829.1610.0060.0060.0000.0000.0000.000
165A165TRP0-0.020-0.01720.312-0.017-0.0170.0000.0000.0000.000
166A166GLU-1-0.801-0.90825.595-0.287-0.2870.0000.0000.0000.000
167A167GLY0-0.0090.00426.596-0.001-0.0010.0000.0000.0000.000
168A168GLU-1-0.890-0.92627.528-0.294-0.2940.0000.0000.0000.000
169A169PHE0-0.103-0.04922.160-0.016-0.0160.0000.0000.0000.000
170A170GLU-1-0.983-0.98226.521-0.243-0.2430.0000.0000.0000.000
171A171GLU-1-0.865-0.94321.911-0.337-0.3370.0000.0000.0000.000
172A172LEU0-0.065-0.01421.038-0.025-0.0250.0000.0000.0000.000
173A173PRO0-0.018-0.00217.599-0.016-0.0160.0000.0000.0000.000
174A174PHE00.006-0.00915.455-0.105-0.1050.0000.0000.0000.000
175A175SER00.005-0.00716.6990.0890.0890.0000.0000.0000.000
176A176LEU0-0.031-0.00518.481-0.052-0.0520.0000.0000.0000.000
177A177LEU00.000-0.00718.1850.0470.0470.0000.0000.0000.000
178A178LEU0-0.031-0.00321.302-0.008-0.0080.0000.0000.0000.000
179A179LEU00.0190.00718.3660.0180.0180.0000.0000.0000.000
180A180HIS00.0490.01123.1220.0010.0010.0000.0000.0000.000
181A181PRO00.0260.00222.9170.0030.0030.0000.0000.0000.000
182A182GLY00.0100.03224.2880.0140.0140.0000.0000.0000.000
183A195LEU00.0440.02526.678-0.003-0.0030.0000.0000.0000.000
184A196SER0-0.100-0.05724.9340.0000.0000.0000.0000.0000.000
185A197VAL0-0.004-0.02520.602-0.013-0.0130.0000.0000.0000.000
186A198GLU-1-0.906-0.94819.8360.0800.0800.0000.0000.0000.000
187A199GLU-1-0.804-0.89719.786-0.018-0.0180.0000.0000.0000.000
188A200SER0-0.033-0.03321.290-0.022-0.0220.0000.0000.0000.000
189A201ALA00.011-0.00816.848-0.029-0.0290.0000.0000.0000.000
190A202ALA00.0140.00816.506-0.037-0.0370.0000.0000.0000.000
191A203GLY00.0020.00117.224-0.021-0.0210.0000.0000.0000.000
192A204LEU0-0.018-0.02518.206-0.032-0.0320.0000.0000.0000.000
193A205VAL0-0.0100.00412.034-0.054-0.0540.0000.0000.0000.000
194A206ALA0-0.045-0.01714.460-0.069-0.0690.0000.0000.0000.000
195A207ALA00.0170.01116.389-0.027-0.0270.0000.0000.0000.000
196A208VAL0-0.020-0.01813.151-0.033-0.0330.0000.0000.0000.000
197A209GLU-1-0.836-0.9159.900-1.163-1.1630.0000.0000.0000.000
198A210ASP-1-0.798-0.86313.554-0.280-0.2800.0000.0000.0000.000
199A211ALA0-0.007-0.00316.5490.0210.0210.0000.0000.0000.000
200A212ALA0-0.0130.00111.918-0.037-0.0370.0000.0000.0000.000
201A213GLY0-0.021-0.01114.0570.0680.0680.0000.0000.0000.000
202A214VAL0-0.087-0.03315.2010.0680.0680.0000.0000.0000.000
203A215ASN00.0200.01517.141-0.036-0.0360.0000.0000.0000.000
204A216ALA00.0710.03919.5010.0430.0430.0000.0000.0000.000
205A217CYS0-0.029-0.00121.625-0.029-0.0290.0000.0000.0000.000
206A218ARG10.8240.89420.2830.3270.3270.0000.0000.0000.000
207A219PHE00.0020.00224.282-0.017-0.0170.0000.0000.0000.000
208A220VAL00.0200.01222.0170.0180.0180.0000.0000.0000.000
209A221ASP-1-0.771-0.89724.695-0.130-0.1300.0000.0000.0000.000
210A222TYR0-0.051-0.02122.212-0.018-0.0180.0000.0000.0000.000
211A223ARG10.8670.94022.1960.0890.0890.0000.0000.0000.000
212A224ASN0-0.046-0.03121.062-0.017-0.0170.0000.0000.0000.000
213A225GLN0-0.0070.00823.3380.0080.0080.0000.0000.0000.000
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