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: N1LRQ

Calculation Name: 4UQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UQF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y5X1

Base Structure: X-ray

Registration Date: 2023-03-14

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1898030.192361
FMO2-HF: Nuclear repulsion 1823413.727562
FMO2-HF: Total energy -74616.464798
FMO2-MP2: Total energy -74829.547271


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:3:GLN)


Summations of interaction energy for fragment #1(A:3: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.
-18.632-15.9195.606-3.555-4.7620.03
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.011
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].
3A5ASP-1-0.826-0.9113.1492.1074.7040.084-1.115-1.5650.000
4A6LYS10.8420.8851.951-28.267-29.5305.474-1.896-2.3150.029
5A7GLN00.0440.0257.010-0.473-0.4730.0000.0000.0000.000
6A8LYS10.9210.9668.633-0.483-0.4830.0000.0000.0000.000
7A9ILE0-0.028-0.0118.679-0.133-0.1330.0000.0000.0000.000
8A10ALA0-0.001-0.00711.096-0.187-0.1870.0000.0000.0000.000
9A11ASP-1-0.871-0.93812.9820.6890.6890.0000.0000.0000.000
10A12ALA0-0.015-0.01314.352-0.117-0.1170.0000.0000.0000.000
11A13VAL0-0.043-0.02014.871-0.075-0.0750.0000.0000.0000.000
12A14LYS10.8810.94917.198-0.589-0.5890.0000.0000.0000.000
13A15VAL00.0340.01718.963-0.069-0.0690.0000.0000.0000.000
14A16ILE0-0.035-0.01318.692-0.050-0.0500.0000.0000.0000.000
15A17LEU0-0.019-0.02020.127-0.039-0.0390.0000.0000.0000.000
16A18GLU-1-0.874-0.95023.2240.3940.3940.0000.0000.0000.000
17A19ALA0-0.047-0.01724.742-0.036-0.0360.0000.0000.0000.000
18A20VAL0-0.093-0.04325.464-0.026-0.0260.0000.0000.0000.000
19A21GLY0-0.0140.00427.916-0.019-0.0190.0000.0000.0000.000
20A22GLU-1-0.812-0.85725.4940.4040.4040.0000.0000.0000.000
21A23ASN00.005-0.01727.4690.0070.0070.0000.0000.0000.000
22A24PRO0-0.016-0.02322.0880.0180.0180.0000.0000.0000.000
23A25ASP-1-0.853-0.92522.6350.5060.5060.0000.0000.0000.000
24A26ARG10.7890.87524.848-0.442-0.4420.0000.0000.0000.000
25A27GLU-1-0.858-0.94124.5010.4450.4450.0000.0000.0000.000
26A28GLY0-0.059-0.03323.5520.0400.0400.0000.0000.0000.000
27A29LEU0-0.074-0.05421.5080.0550.0550.0000.0000.0000.000
28A30ILE00.0740.06719.5170.0880.0880.0000.0000.0000.000
29A31ASP-1-0.788-0.89715.3121.2501.2500.0000.0000.0000.000
30A32THR0-0.038-0.01215.8210.1580.1580.0000.0000.0000.000
31A33PRO00.0310.03115.0720.1510.1510.0000.0000.0000.000
32A34MET00.0700.0319.4640.5190.5190.0000.0000.0000.000
33A35ARG10.7890.90111.136-0.511-0.5110.0000.0000.0000.000
34A36VAL00.0350.01812.9420.1230.1230.0000.0000.0000.000
35A37ALA0-0.0080.0048.8460.1370.1370.0000.0000.0000.000
36A38ARG10.8450.8938.130-1.522-1.5220.0000.0000.0000.000
37A39MET00.0340.0329.324-0.034-0.0340.0000.0000.0000.000
38A40TYR0-0.008-0.01810.872-0.092-0.0920.0000.0000.0000.000
39A41GLU-1-0.871-0.9243.71113.56214.2710.032-0.246-0.494-0.001
40A42GLU-1-0.954-0.9667.7901.2581.2580.0000.0000.0000.000
41A43VAL0-0.023-0.03010.270-0.249-0.2490.0000.0000.0000.000
42A44PHE0-0.022-0.0249.943-0.284-0.2840.0000.0000.0000.000
43A45ALA00.0570.0317.9120.1210.1210.0000.0000.0000.000
44A46GLY00.0360.0118.6840.0190.0190.0000.0000.0000.000
45A47LEU0-0.094-0.0338.787-0.241-0.2410.0000.0000.0000.000
46A48LYS10.8840.9453.577-5.047-4.3770.016-0.298-0.3880.002
47A49LYS10.8540.9317.730-1.113-1.1130.0000.0000.0000.000
48A50ASP-1-0.770-0.86010.5500.1120.1120.0000.0000.0000.000
49A51PRO0-0.025-0.01914.014-0.036-0.0360.0000.0000.0000.000
50A52SER0-0.001-0.03216.283-0.034-0.0340.0000.0000.0000.000
51A53VAL00.0420.01714.609-0.028-0.0280.0000.0000.0000.000
52A54HIS0-0.081-0.04515.326-0.088-0.0880.0000.0000.0000.000
53A55PHE0-0.049-0.04519.3610.0010.0010.0000.0000.0000.000
54A56ASP-1-0.852-0.89920.167-0.090-0.0900.0000.0000.0000.000
55A57THR0-0.043-0.03121.841-0.026-0.0260.0000.0000.0000.000
56A58ILE0-0.043-0.00424.1460.0070.0070.0000.0000.0000.000
57A59PHE0-0.025-0.02126.5250.0090.0090.0000.0000.0000.000
58A60GLU-1-0.892-0.95528.571-0.003-0.0030.0000.0000.0000.000
59A61GLU-1-0.952-0.97132.149-0.009-0.0090.0000.0000.0000.000
60A62GLN0-0.052-0.02135.8360.0080.0080.0000.0000.0000.000
61A63HIS00.0600.02937.265-0.002-0.0020.0000.0000.0000.000
62A64GLU-1-0.974-0.99638.2260.0070.0070.0000.0000.0000.000
63A65GLU-1-0.936-0.95340.2710.0380.0380.0000.0000.0000.000
64A66LEU0-0.054-0.03837.4650.0030.0030.0000.0000.0000.000
65A67VAL00.0060.01333.4230.0010.0010.0000.0000.0000.000
66A68LEU0-0.019-0.01933.9660.0050.0050.0000.0000.0000.000
67A69VAL0-0.024-0.00528.962-0.001-0.0010.0000.0000.0000.000
68A70LYS10.8420.91231.305-0.133-0.1330.0000.0000.0000.000
69A71ASP-1-0.868-0.95230.9740.1890.1890.0000.0000.0000.000
70A72ILE00.0020.01424.9050.0060.0060.0000.0000.0000.000
71A73ARG10.9380.96225.017-0.263-0.2630.0000.0000.0000.000
72A74PHE00.0130.01521.8340.0100.0100.0000.0000.0000.000
73A75SER0-0.023-0.02319.9120.0110.0110.0000.0000.0000.000
74A76SER00.014-0.00918.3910.0250.0250.0000.0000.0000.000
75A77MET00.0040.01616.333-0.017-0.0170.0000.0000.0000.000
76A78CYS0-0.082-0.02419.340-0.029-0.0290.0000.0000.0000.000
77A79GLU-1-0.724-0.86219.6810.4550.4550.0000.0000.0000.000
78A80HIS0-0.050-0.01620.6420.0080.0080.0000.0000.0000.000
79A81HIS0-0.025-0.04222.992-0.034-0.0340.0000.0000.0000.000
80A82LEU0-0.0060.01716.7650.0300.0300.0000.0000.0000.000
81A83VAL00.0180.00619.8570.0430.0430.0000.0000.0000.000
82A84PRO00.0590.01120.240-0.023-0.0230.0000.0000.0000.000
83A85PHE0-0.048-0.01221.867-0.053-0.0530.0000.0000.0000.000
84A86PHE00.025-0.00322.8730.0410.0410.0000.0000.0000.000
85A87GLY00.0140.01024.999-0.029-0.0290.0000.0000.0000.000
86A88VAL0-0.051-0.00726.7420.0150.0150.0000.0000.0000.000
87A89ALA0-0.006-0.00526.400-0.002-0.0020.0000.0000.0000.000
88A90HIS00.0350.01728.395-0.010-0.0100.0000.0000.0000.000
89A91VAL0-0.011-0.00627.1880.0000.0000.0000.0000.0000.000
90A92ALA00.0350.01830.678-0.008-0.0080.0000.0000.0000.000
91A93TYR0-0.007-0.01531.140-0.002-0.0020.0000.0000.0000.000
92A94LEU00.0730.04434.412-0.002-0.0020.0000.0000.0000.000
93A95PRO00.0290.03134.896-0.003-0.0030.0000.0000.0000.000
94A96GLN00.0230.01535.445-0.008-0.0080.0000.0000.0000.000
95A97ASN0-0.006-0.02136.002-0.004-0.0040.0000.0000.0000.000
96A98GLY00.0500.03437.068-0.006-0.0060.0000.0000.0000.000
97A99ARG10.8200.90931.4300.0050.0050.0000.0000.0000.000
98A100VAL00.0380.02131.8990.0110.0110.0000.0000.0000.000
99A101ALA00.0250.00827.031-0.010-0.0100.0000.0000.0000.000
100A102GLY00.0750.02226.9100.0050.0050.0000.0000.0000.000
101A103LEU00.010-0.00226.2720.0150.0150.0000.0000.0000.000
102A104SER0-0.001-0.01423.1380.0180.0180.0000.0000.0000.000
103A105LYS10.8700.95021.6830.0320.0320.0000.0000.0000.000
104A106LEU00.0570.02921.8290.0230.0230.0000.0000.0000.000
105A107ALA00.000-0.00122.8780.0270.0270.0000.0000.0000.000
106A108ARG10.9550.98317.424-0.113-0.1130.0000.0000.0000.000
107A109VAL00.0270.02917.9610.0590.0590.0000.0000.0000.000
108A110VAL00.0010.00419.2610.0420.0420.0000.0000.0000.000
109A111ASP-1-0.805-0.88516.9880.5910.5910.0000.0000.0000.000
110A112ASP-1-0.824-0.89713.8170.6410.6410.0000.0000.0000.000
111A113VAL0-0.055-0.02515.0880.0890.0890.0000.0000.0000.000
112A114SER00.001-0.01317.4200.0170.0170.0000.0000.0000.000
113A115ARG10.8020.93812.792-0.762-0.7620.0000.0000.0000.000
114A116ARG10.9030.92512.750-0.479-0.4790.0000.0000.0000.000
115A117PRO0-0.0040.01413.717-0.082-0.0820.0000.0000.0000.000
116A118GLN0-0.002-0.01116.965-0.094-0.0940.0000.0000.0000.000
117A119LEU0-0.0030.01820.058-0.008-0.0080.0000.0000.0000.000
118A120GLN00.0560.00423.5350.0180.0180.0000.0000.0000.000
119A121GLU-1-0.848-0.92725.5520.2570.2570.0000.0000.0000.000
120A122ARG10.8060.87120.521-0.388-0.3880.0000.0000.0000.000
121A123ILE00.0190.02520.700-0.014-0.0140.0000.0000.0000.000
122A124THR00.0030.00623.005-0.023-0.0230.0000.0000.0000.000
123A125THR0-0.027-0.03026.546-0.017-0.0170.0000.0000.0000.000
124A126THR0-0.020-0.01120.192-0.019-0.0190.0000.0000.0000.000
125A127VAL00.0230.01622.481-0.018-0.0180.0000.0000.0000.000
126A128ALA00.001-0.00324.249-0.023-0.0230.0000.0000.0000.000
127A129GLU-1-0.770-0.85625.0310.0890.0890.0000.0000.0000.000
128A130ILE00.0210.01219.976-0.018-0.0180.0000.0000.0000.000
129A131MET0-0.0150.00024.136-0.016-0.0160.0000.0000.0000.000
130A132MET0-0.043-0.02026.958-0.016-0.0160.0000.0000.0000.000
131A133GLU-1-0.973-0.98423.7190.0460.0460.0000.0000.0000.000
132A134LYS10.7790.86720.6110.0170.0170.0000.0000.0000.000
133A135LEU00.0030.00826.244-0.011-0.0110.0000.0000.0000.000
134A136LYS10.8980.97729.245-0.006-0.0060.0000.0000.0000.000
135A137PRO00.0260.02530.983-0.007-0.0070.0000.0000.0000.000
136A138LEU0-0.014-0.02134.076-0.001-0.0010.0000.0000.0000.000
137A139GLY00.010-0.00735.3390.0010.0010.0000.0000.0000.000
138A140VAL0-0.0130.00029.858-0.001-0.0010.0000.0000.0000.000
139A141MET0-0.019-0.00533.324-0.003-0.0030.0000.0000.0000.000
140A142VAL00.0070.01327.5160.0020.0020.0000.0000.0000.000
141A143ILE00.000-0.01030.941-0.002-0.0020.0000.0000.0000.000
142A144MET0-0.034-0.00224.1300.0060.0060.0000.0000.0000.000
143A145GLU-1-0.845-0.90429.7340.2010.2010.0000.0000.0000.000
144A146ALA0-0.029-0.02127.1240.0170.0170.0000.0000.0000.000
145A147GLU-1-0.801-0.88928.5870.2720.2720.0000.0000.0000.000
146A148HIS0-0.030-0.03126.2590.0510.0510.0000.0000.0000.000
147A149MET00.0640.02725.480-0.022-0.0220.0000.0000.0000.000
148A151MET0-0.015-0.01227.463-0.018-0.0180.0000.0000.0000.000
149A152THR0-0.0060.00530.330-0.020-0.0200.0000.0000.0000.000
150A153ILE00.0150.00926.524-0.011-0.0110.0000.0000.0000.000
151A154ARG10.8990.95828.190-0.326-0.3260.0000.0000.0000.000
152A155GLY00.0260.00431.952-0.012-0.0120.0000.0000.0000.000
153A156VAL0-0.016-0.00433.446-0.011-0.0110.0000.0000.0000.000
154A157ASN0-0.0110.01534.808-0.010-0.0100.0000.0000.0000.000
155A158LYS10.8650.91834.955-0.222-0.2220.0000.0000.0000.000
156A159PRO00.0580.04434.3160.0080.0080.0000.0000.0000.000
157A160GLY00.0030.00434.423-0.016-0.0160.0000.0000.0000.000
158A161THR0-0.079-0.04434.195-0.016-0.0160.0000.0000.0000.000
159A162LYS10.8820.93532.615-0.223-0.2230.0000.0000.0000.000
160A163THR00.0020.00030.530-0.017-0.0170.0000.0000.0000.000
161A164ILE00.0080.00531.6480.0110.0110.0000.0000.0000.000
162A165THR0-0.010-0.00628.885-0.006-0.0060.0000.0000.0000.000
163A166SER0-0.026-0.02831.844-0.005-0.0050.0000.0000.0000.000
164A167ALA00.0060.01230.240-0.001-0.0010.0000.0000.0000.000
165A168VAL0-0.0020.00832.204-0.002-0.0020.0000.0000.0000.000
166A169ARG10.7540.82929.748-0.114-0.1140.0000.0000.0000.000
167A170GLY00.0220.01034.573-0.001-0.0010.0000.0000.0000.000
168A171ALA00.0780.01537.0880.0020.0020.0000.0000.0000.000
169A172PHE00.0500.03236.6290.0010.0010.0000.0000.0000.000
170A173LYS10.9100.96035.606-0.068-0.0680.0000.0000.0000.000
171A174ASN0-0.047-0.03739.5190.0010.0010.0000.0000.0000.000
172A175ASP-1-0.801-0.87742.4940.0520.0520.0000.0000.0000.000
173A176ASP-1-0.853-0.93443.1940.0670.0670.0000.0000.0000.000
174A177LYS10.8620.91844.793-0.052-0.0520.0000.0000.0000.000
175A178LEU00.0950.06039.9510.0040.0040.0000.0000.0000.000
176A179ARG10.8290.89539.533-0.075-0.0750.0000.0000.0000.000
177A180SER0-0.041-0.01941.1110.0090.0090.0000.0000.0000.000
178A181GLU-1-0.905-0.94543.3360.0660.0660.0000.0000.0000.000
179A182VAL0-0.009-0.00636.7180.0050.0050.0000.0000.0000.000
180A183LEU0-0.019-0.01638.5380.0080.0080.0000.0000.0000.000
181A184ALA0-0.041-0.01140.5960.0050.0050.0000.0000.0000.000
182A185LEU0-0.025-0.02139.9890.0030.0030.0000.0000.0000.000
183A186ILE00.006-0.00735.3570.0050.0050.0000.0000.0000.000
184A187LYS10.9190.99138.334-0.095-0.0950.0000.0000.0000.000
185A188HIS00.0170.01539.6210.0090.0090.0000.0000.0000.000