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: JL889

Calculation Name: 1Q0U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q0U

Chain ID: A

ChEMBL ID:

UniProt ID: P83699

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2580628.407617
FMO2-HF: Nuclear repulsion 2497063.580087
FMO2-HF: Total energy -83564.82753
FMO2-MP2: Total energy -83807.103313


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-9.664-2.53513.653-7.472-13.304-0.021
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.026
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].
3A6PHE00.0280.0001.812-1.204-1.0617.010-2.841-4.3120.004
4A7THR00.0220.0193.3000.1040.0430.0010.467-0.4060.000
5A8ARG10.7870.8815.1000.6610.747-0.001-0.003-0.0810.000
6A9PHE0-0.030-0.0116.3350.2650.2650.0000.0000.0000.000
7A10PRO00.0130.0157.865-0.208-0.2080.0000.0000.0000.000
8A11PHE00.000-0.0186.2030.1440.1440.0000.0000.0000.000
9A12GLN0-0.005-0.0329.524-0.119-0.1190.0000.0000.0000.000
10A13PRO00.0560.0098.961-0.052-0.0520.0000.0000.0000.000
11A14PHE00.0260.0068.435-0.069-0.0690.0000.0000.0000.000
12A15ILE00.0120.0227.2980.1040.1040.0000.0000.0000.000
13A16ILE0-0.0030.0033.544-0.2490.0720.008-0.048-0.2800.000
14A17GLU-1-0.801-0.8914.084-1.028-0.8500.000-0.055-0.1230.000
15A18ALA00.0200.0246.6830.4090.4090.0000.0000.0000.000
16A19ILE0-0.016-0.0172.443-0.074-0.0161.214-0.273-0.998-0.001
17A20LYS10.8340.9092.2531.7133.0481.579-0.858-2.0560.005
18A21THR0-0.032-0.0184.148-0.639-0.4680.005-0.064-0.1110.000
19A22LEU0-0.124-0.0516.912-0.131-0.1310.0000.0000.0000.000
20A23ARG10.8880.9436.371-0.921-0.9210.0000.0000.0000.000
21A24PHE0-0.0260.0014.357-0.392-0.239-0.001-0.031-0.1200.000
22A25TYR00.0940.0492.367-4.142-1.0893.080-2.589-3.544-0.015
23A26LYS10.8790.9192.789-3.252-1.6330.759-1.174-1.204-0.014
24A27PRO0-0.0300.0044.788-0.0060.067-0.001-0.003-0.0690.000
25A28THR00.0260.0037.1920.0030.0030.0000.0000.0000.000
26A29GLU-1-0.782-0.86910.5690.0800.0800.0000.0000.0000.000
27A30ILE00.0350.01413.667-0.045-0.0450.0000.0000.0000.000
28A31GLN0-0.008-0.0098.4650.0070.0070.0000.0000.0000.000
29A32GLU-1-0.804-0.89110.0330.0560.0560.0000.0000.0000.000
30A33ARG10.8030.89511.976-0.142-0.1420.0000.0000.0000.000
31A34ILE00.0090.01214.250-0.008-0.0080.0000.0000.0000.000
32A35ILE00.0030.0049.098-0.014-0.0140.0000.0000.0000.000
33A36PRO00.0140.00012.323-0.024-0.0240.0000.0000.0000.000
34A37GLY00.0310.02314.374-0.004-0.0040.0000.0000.0000.000
35A38ALA00.0600.01515.426-0.002-0.0020.0000.0000.0000.000
36A39LEU0-0.049-0.02011.597-0.003-0.0030.0000.0000.0000.000
37A40ARG10.8300.91216.2220.1460.1460.0000.0000.0000.000
38A41GLY0-0.0160.00019.4150.0070.0070.0000.0000.0000.000
39A42GLU-1-0.793-0.86120.782-0.082-0.0820.0000.0000.0000.000
40A43SER00.0760.04121.7050.0000.0000.0000.0000.0000.000
41A44MET0-0.065-0.03118.367-0.003-0.0030.0000.0000.0000.000
42A45VAL00.0080.00522.9010.0060.0060.0000.0000.0000.000
43A46GLY00.004-0.00320.6410.0000.0000.0000.0000.0000.000
44A47GLN0-0.037-0.03121.6510.0100.0100.0000.0000.0000.000
45A48SER0-0.009-0.03418.6270.0140.0140.0000.0000.0000.000
46A49GLN00.0020.01820.283-0.016-0.0160.0000.0000.0000.000
47A50THR00.021-0.02119.4360.0140.0140.0000.0000.0000.000
48A51GLY00.0530.01816.9570.0210.0210.0000.0000.0000.000
49A52THR00.0210.01213.360-0.005-0.0050.0000.0000.0000.000
50A53GLY00.0260.01611.2870.0020.0020.0000.0000.0000.000
51A54LYS10.8600.91012.318-0.151-0.1510.0000.0000.0000.000
52A55THR0-0.019-0.00814.869-0.020-0.0200.0000.0000.0000.000
53A56HIS10.8030.8769.930-0.275-0.2750.0000.0000.0000.000
54A57ALA00.0070.01511.704-0.049-0.0490.0000.0000.0000.000
55A58TYR00.014-0.02713.083-0.043-0.0430.0000.0000.0000.000
56A59LEU0-0.013-0.01713.254-0.025-0.0250.0000.0000.0000.000
57A60LEU0-0.065-0.0207.407-0.010-0.0100.0000.0000.0000.000
58A61PRO00.0260.01711.219-0.060-0.0600.0000.0000.0000.000
59A62ILE00.0100.01313.391-0.014-0.0140.0000.0000.0000.000
60A63MET0-0.042-0.03512.6150.0000.0000.0000.0000.0000.000
61A64GLU-1-0.826-0.88611.841-0.482-0.4820.0000.0000.0000.000
62A65LYS10.9030.95013.9830.1670.1670.0000.0000.0000.000
63A66ILE0-0.049-0.00617.3500.0180.0180.0000.0000.0000.000
64A67LYS10.8740.93819.1460.1190.1190.0000.0000.0000.000
65A68PRO00.021-0.00319.1460.0150.0150.0000.0000.0000.000
66A69GLU-1-0.887-0.94121.929-0.155-0.1550.0000.0000.0000.000
67A70ARG10.8290.91425.2470.1000.1000.0000.0000.0000.000
68A71ALA00.000-0.00225.8120.0000.0000.0000.0000.0000.000
69A72GLU-1-0.817-0.90626.888-0.066-0.0660.0000.0000.0000.000
70A73VAL00.0020.01226.096-0.005-0.0050.0000.0000.0000.000
71A74GLN0-0.001-0.00822.903-0.015-0.0150.0000.0000.0000.000
72A75ALA0-0.007-0.00321.169-0.004-0.0040.0000.0000.0000.000
73A76VAL00.0200.02223.0880.0070.0070.0000.0000.0000.000
74A77ILE0-0.004-0.00819.3010.0010.0010.0000.0000.0000.000
75A78THR00.000-0.00923.6190.0040.0040.0000.0000.0000.000
76A79ALA00.0250.00324.3020.0050.0050.0000.0000.0000.000
77A80PRO00.0380.01926.325-0.005-0.0050.0000.0000.0000.000
78A81THR00.0530.02428.096-0.002-0.0020.0000.0000.0000.000
79A82ARG10.9340.93827.763-0.048-0.0480.0000.0000.0000.000
80A83GLU-1-0.919-0.93825.6410.1100.1100.0000.0000.0000.000
81A84LEU00.0220.00523.3130.0100.0100.0000.0000.0000.000
82A85ALA00.0380.02022.7170.0050.0050.0000.0000.0000.000
83A86THR0-0.044-0.05222.855-0.004-0.0040.0000.0000.0000.000
84A87GLN00.0420.02819.8090.0170.0170.0000.0000.0000.000
85A88ILE00.0240.02418.2170.0160.0160.0000.0000.0000.000
86A89TYR00.0040.00217.996-0.002-0.0020.0000.0000.0000.000
87A90HIS0-0.029-0.03118.261-0.016-0.0160.0000.0000.0000.000
88A91GLU-1-0.817-0.88213.3630.3360.3360.0000.0000.0000.000
89A92THR00.020-0.01113.801-0.005-0.0050.0000.0000.0000.000
90A93LEU00.0060.02315.139-0.021-0.0210.0000.0000.0000.000
91A94LYS10.7670.87712.136-0.332-0.3320.0000.0000.0000.000
92A95ILE00.0150.00510.0970.0230.0230.0000.0000.0000.000
93A96THR00.049-0.00111.995-0.040-0.0400.0000.0000.0000.000
94A97LYS10.8990.96713.556-0.121-0.1210.0000.0000.0000.000
95A98PHE0-0.027-0.02511.0140.0120.0120.0000.0000.0000.000
96A99CYS0-0.067-0.00513.268-0.049-0.0490.0000.0000.0000.000
97A100PRO00.0240.00814.9360.0110.0110.0000.0000.0000.000
98A101LYS10.9640.96617.4360.1370.1370.0000.0000.0000.000
99A102ASP-1-0.904-0.93120.831-0.147-0.1470.0000.0000.0000.000
100A103ARG10.8970.93516.6590.2880.2880.0000.0000.0000.000
101A104MET0-0.0300.00618.188-0.004-0.0040.0000.0000.0000.000
102A105ILE00.0250.01316.0660.0040.0040.0000.0000.0000.000
103A106VAL0-0.028-0.02519.7620.0140.0140.0000.0000.0000.000
104A107ALA00.0340.01420.097-0.001-0.0010.0000.0000.0000.000
105A108ARG10.8210.90122.1580.0060.0060.0000.0000.0000.000
106A109CYS0-0.0080.00624.1130.0000.0000.0000.0000.0000.000
107A110LEU0-0.039-0.00725.8780.0000.0000.0000.0000.0000.000
108A111ILE00.028-0.00727.8500.0030.0030.0000.0000.0000.000
109A112GLY0-0.011-0.00230.7600.0010.0010.0000.0000.0000.000
110A113GLY0-0.034-0.01233.7230.0050.0050.0000.0000.0000.000
111A114THR00.010-0.00435.889-0.003-0.0030.0000.0000.0000.000
112A115ASP-1-0.756-0.87538.7930.0200.0200.0000.0000.0000.000
113A116LYS10.9570.96340.657-0.021-0.0210.0000.0000.0000.000
114A117GLN00.0210.01334.774-0.001-0.0010.0000.0000.0000.000
115A118LYS10.8660.92636.000-0.023-0.0230.0000.0000.0000.000
116A119ALA0-0.020-0.00237.248-0.003-0.0030.0000.0000.0000.000
117A120LEU0-0.024-0.00735.526-0.002-0.0020.0000.0000.0000.000
118A121GLU-1-0.761-0.84131.7880.0210.0210.0000.0000.0000.000
119A122LYS10.9690.97433.403-0.002-0.0020.0000.0000.0000.000
120A123LEU00.0280.01729.8830.0010.0010.0000.0000.0000.000
121A124ASN0-0.0210.01131.7650.0010.0010.0000.0000.0000.000
122A125VAL00.0440.00928.378-0.002-0.0020.0000.0000.0000.000
123A126GLN00.0310.00729.8180.0050.0050.0000.0000.0000.000
124A127PRO0-0.038-0.01925.225-0.006-0.0060.0000.0000.0000.000
125A128HIS00.0850.06021.6950.0080.0080.0000.0000.0000.000
126A129ILE0-0.034-0.01918.1040.0000.0000.0000.0000.0000.000
127A130VAL00.0230.00722.5480.0080.0080.0000.0000.0000.000
128A131ILE00.0160.01520.0190.0020.0020.0000.0000.0000.000
129A132GLY00.0400.01424.3760.0000.0000.0000.0000.0000.000
130A133THR0-0.0060.01227.3310.0000.0000.0000.0000.0000.000
131A134PRO00.0660.01929.863-0.005-0.0050.0000.0000.0000.000
132A135GLY00.0900.04231.832-0.004-0.0040.0000.0000.0000.000
133A136ARG10.7270.85931.964-0.017-0.0170.0000.0000.0000.000
134A137ILE00.0470.01727.614-0.004-0.0040.0000.0000.0000.000
135A138ASN0-0.023-0.03132.214-0.007-0.0070.0000.0000.0000.000
136A139ASP-1-0.819-0.86935.6420.0100.0100.0000.0000.0000.000
137A140PHE0-0.021-0.01733.567-0.002-0.0020.0000.0000.0000.000
138A141ILE0-0.0140.00633.014-0.003-0.0030.0000.0000.0000.000
139A142ARG10.8660.91936.450-0.007-0.0070.0000.0000.0000.000
140A143GLU-1-0.990-1.00638.7420.0010.0010.0000.0000.0000.000
141A144GLN0-0.053-0.02739.2570.0000.0000.0000.0000.0000.000
142A145ALA0-0.0250.00036.064-0.002-0.0020.0000.0000.0000.000
143A146LEU0-0.054-0.02329.884-0.002-0.0020.0000.0000.0000.000
144A147ASP-1-0.810-0.90632.834-0.034-0.0340.0000.0000.0000.000
145A148VAL0-0.037-0.02929.956-0.003-0.0030.0000.0000.0000.000
146A149HIS0-0.056-0.03230.557-0.005-0.0050.0000.0000.0000.000
147A150THR0-0.002-0.00528.851-0.002-0.0020.0000.0000.0000.000
148A151ALA0-0.090-0.03226.235-0.009-0.0090.0000.0000.0000.000
149A152HIS00.0090.00125.5400.0040.0040.0000.0000.0000.000
150A153ILE0-0.018-0.00619.983-0.003-0.0030.0000.0000.0000.000
151A154LEU00.0130.01223.9750.0060.0060.0000.0000.0000.000
152A155VAL0-0.029-0.00920.094-0.001-0.0010.0000.0000.0000.000
153A156VAL00.0170.00223.3640.0030.0030.0000.0000.0000.000
154A157ASP-1-0.757-0.85520.6130.0940.0940.0000.0000.0000.000
155A158GLU-1-0.795-0.88222.1750.1150.1150.0000.0000.0000.000
156A159ALA00.041-0.01325.373-0.004-0.0040.0000.0000.0000.000
157A160ASP-1-0.798-0.87127.9680.0690.0690.0000.0000.0000.000
158A161LEU00.0560.03028.328-0.003-0.0030.0000.0000.0000.000
159A162MET0-0.077-0.02727.302-0.006-0.0060.0000.0000.0000.000
160A163LEU0-0.029-0.02831.290-0.006-0.0060.0000.0000.0000.000
161A164ASP-1-0.912-0.95333.7350.0470.0470.0000.0000.0000.000
162A165MET0-0.125-0.04932.8510.0010.0010.0000.0000.0000.000
163A166GLY0-0.0120.00235.726-0.002-0.0020.0000.0000.0000.000
164A167PHE0-0.031-0.02132.715-0.002-0.0020.0000.0000.0000.000
165A168ILE00.0310.01931.431-0.003-0.0030.0000.0000.0000.000
166A169THR00.0140.00434.850-0.004-0.0040.0000.0000.0000.000
167A170ASP-1-0.905-0.95434.7490.0140.0140.0000.0000.0000.000
168A171VAL00.0360.00130.178-0.004-0.0040.0000.0000.0000.000
169A172ASP-1-0.813-0.85632.735-0.006-0.0060.0000.0000.0000.000
170A173GLN00.0420.01435.040-0.005-0.0050.0000.0000.0000.000
171A174ILE0-0.055-0.02030.311-0.003-0.0030.0000.0000.0000.000
172A175ALA00.028-0.01231.404-0.004-0.0040.0000.0000.0000.000
173A176ALA0-0.068-0.01732.302-0.004-0.0040.0000.0000.0000.000
174A177ARG10.8600.93534.9580.0060.0060.0000.0000.0000.000
175A178MET0-0.0380.01327.0720.0000.0000.0000.0000.0000.000
176A179PRO00.0020.00430.2810.0020.0020.0000.0000.0000.000
177A180LYS10.9790.96231.8690.0340.0340.0000.0000.0000.000
178A181ASP-1-0.964-0.96530.062-0.066-0.0660.0000.0000.0000.000
179A182LEU0-0.0390.00127.611-0.005-0.0050.0000.0000.0000.000
180A183GLN0-0.0130.00719.690-0.004-0.0040.0000.0000.0000.000
181A184MET0-0.037-0.03024.7570.0060.0060.0000.0000.0000.000
182A185LEU0-0.046-0.02918.728-0.001-0.0010.0000.0000.0000.000
183A186VAL00.0080.00922.7370.0090.0090.0000.0000.0000.000
184A187PHE0-0.017-0.00818.2890.0040.0040.0000.0000.0000.000
185A188SER0-0.008-0.02122.7610.0010.0010.0000.0000.0000.000
186A189ALA00.0030.02524.5240.0010.0010.0000.0000.0000.000
187A190THR0-0.025-0.03325.464-0.003-0.0030.0000.0000.0000.000
188A191ILE0-0.0020.00127.524-0.004-0.0040.0000.0000.0000.000
189A192PRO00.0290.02430.821-0.004-0.0040.0000.0000.0000.000
190A193GLU-1-0.752-0.87134.2240.0230.0230.0000.0000.0000.000
191A194LYS10.8970.93837.189-0.030-0.0300.0000.0000.0000.000
192A195LEU00.0350.01730.099-0.002-0.0020.0000.0000.0000.000
193A196LYS10.8910.92833.801-0.028-0.0280.0000.0000.0000.000
194A197PRO00.0180.01634.835-0.004-0.0040.0000.0000.0000.000
195A198PHE00.0160.01329.641-0.003-0.0030.0000.0000.0000.000
196A199LEU00.017-0.00828.903-0.003-0.0030.0000.0000.0000.000
197A200LYS10.8450.91932.0110.0080.0080.0000.0000.0000.000
198A201LYS10.7860.88034.5580.0020.0020.0000.0000.0000.000
199A202TYR0-0.020-0.03031.226-0.003-0.0030.0000.0000.0000.000
200A203MET0-0.046-0.00727.301-0.006-0.0060.0000.0000.0000.000
201A204GLU-1-0.854-0.91130.677-0.018-0.0180.0000.0000.0000.000
202A205ASN0-0.066-0.03128.114-0.002-0.0020.0000.0000.0000.000
203A206PRO0-0.0120.01226.403-0.007-0.0070.0000.0000.0000.000
204A207THR00.004-0.02121.3640.0080.0080.0000.0000.0000.000
205A208PHE00.0020.00223.8230.0060.0060.0000.0000.0000.000
206A209VAL0-0.018-0.01418.4300.0010.0010.0000.0000.0000.000
207A210HIS00.0620.02421.9090.0100.0100.0000.0000.0000.000
208A211VAL0-0.035-0.01917.496-0.001-0.0010.0000.0000.0000.000
209A212LEU0-0.0210.01220.5600.0130.0130.0000.0000.0000.000