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: N9RRQ

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 OptH
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 -2579544.054027
FMO2-HF: Nuclear repulsion 2495981.263466
FMO2-HF: Total energy -83562.790561
FMO2-MP2: Total energy -83805.332673


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.
-13.848-9.71719.689-8.895-14.921-0.026
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 : -0.011 / q_NPA : -0.019
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].
3A6PHE00.0050.0001.681-0.069-1.4219.242-3.388-4.5010.006
4A7THR00.0370.0293.2400.6500.335-0.0010.689-0.3730.000
5A8ARG10.8390.9315.2721.5231.612-0.001-0.003-0.0850.000
6A9PHE0-0.023-0.0086.0780.3100.3100.0000.0000.0000.000
7A10PRO00.0120.0167.968-0.168-0.1680.0000.0000.0000.000
8A11PHE0-0.004-0.0136.2890.0620.0620.0000.0000.0000.000
9A12GLN0-0.004-0.0139.6230.0590.0590.0000.0000.0000.000
10A13PRO00.0450.0019.086-0.111-0.1110.0000.0000.0000.000
11A14PHE00.0170.0049.0300.0210.0210.0000.0000.0000.000
12A15ILE00.0100.0257.593-0.012-0.0120.0000.0000.0000.000
13A16ILE0-0.011-0.0033.791-0.525-0.2840.001-0.028-0.2140.000
14A17GLU-1-0.902-0.9604.6440.6170.703-0.001-0.005-0.0800.000
15A18ALA00.0020.0197.1140.0040.0040.0000.0000.0000.000
16A19ILE0-0.028-0.0212.253-0.480-0.4881.566-0.420-1.138-0.003
17A20LYS10.9430.9722.285-4.458-4.5214.055-1.219-2.7720.010
18A21THR0-0.0080.0033.746-0.0030.1740.006-0.059-0.1230.000
19A22LEU0-0.124-0.0486.7300.2390.2390.0000.0000.0000.000
20A23ARG10.8880.9415.7230.4420.4420.0000.0000.0000.000
21A24PHE0-0.0220.0064.1980.4960.698-0.001-0.037-0.1640.000
22A25TYR00.0720.0302.389-10.027-6.9513.640-2.967-3.748-0.018
23A26LYS10.9460.9642.779-2.306-0.3911.184-1.455-1.645-0.021
24A27PRO0-0.009-0.0034.687-0.0400.043-0.001-0.003-0.0780.000
25A28THR00.019-0.0026.8520.2550.2550.0000.0000.0000.000
26A29GLU-1-0.822-0.90910.234-0.281-0.2810.0000.0000.0000.000
27A30ILE00.0110.00313.494-0.024-0.0240.0000.0000.0000.000
28A31GLN0-0.016-0.0038.108-0.168-0.1680.0000.0000.0000.000
29A32GLU-1-0.897-0.9719.981-0.534-0.5340.0000.0000.0000.000
30A33ARG10.8480.93911.7500.3100.3100.0000.0000.0000.000
31A34ILE0-0.0010.00714.0230.0400.0400.0000.0000.0000.000
32A35ILE00.0010.0008.9420.0220.0220.0000.0000.0000.000
33A36PRO00.007-0.00511.8600.0290.0290.0000.0000.0000.000
34A37GLY00.0320.02614.2750.0380.0380.0000.0000.0000.000
35A38ALA00.0620.01215.2640.0260.0260.0000.0000.0000.000
36A39LEU0-0.070-0.03111.5910.0230.0230.0000.0000.0000.000
37A40ARG10.7970.89216.1630.3890.3890.0000.0000.0000.000
38A41GLY0-0.0130.00019.3240.0290.0290.0000.0000.0000.000
39A42GLU-1-0.795-0.86620.754-0.284-0.2840.0000.0000.0000.000
40A43SER00.0740.04121.562-0.026-0.0260.0000.0000.0000.000
41A44MET0-0.076-0.03118.015-0.014-0.0140.0000.0000.0000.000
42A45VAL00.0160.01122.6580.0040.0040.0000.0000.0000.000
43A46GLY0-0.012-0.01020.545-0.001-0.0010.0000.0000.0000.000
44A47GLN0-0.046-0.03421.5470.0140.0140.0000.0000.0000.000
45A48SER0-0.007-0.02818.472-0.017-0.0170.0000.0000.0000.000
46A49GLN00.0020.01719.9740.0100.0100.0000.0000.0000.000
47A50THR00.007-0.02319.334-0.041-0.0410.0000.0000.0000.000
48A51GLY00.0620.02216.9050.0060.0060.0000.0000.0000.000
49A52THR00.006-0.00113.246-0.059-0.0590.0000.0000.0000.000
50A53GLY00.0360.01711.278-0.097-0.0970.0000.0000.0000.000
51A54LYS10.9470.97512.2880.2250.2250.0000.0000.0000.000
52A55THR0-0.034-0.00814.655-0.006-0.0060.0000.0000.0000.000
53A56HIS10.8020.8719.7070.8350.8350.0000.0000.0000.000
54A57ALA00.0220.02211.478-0.085-0.0850.0000.0000.0000.000
55A58TYR00.029-0.00612.987-0.002-0.0020.0000.0000.0000.000
56A59LEU0-0.019-0.01713.001-0.009-0.0090.0000.0000.0000.000
57A60LEU0-0.055-0.0227.3750.0010.0010.0000.0000.0000.000
58A61PRO00.0370.01811.2370.0100.0100.0000.0000.0000.000
59A62ILE00.0110.01413.2930.0520.0520.0000.0000.0000.000
60A63MET0-0.051-0.03912.7910.0620.0620.0000.0000.0000.000
61A64GLU-1-0.848-0.91812.139-0.600-0.6000.0000.0000.0000.000
62A65LYS10.9520.97414.1480.3780.3780.0000.0000.0000.000
63A66ILE0-0.0460.00317.6690.0410.0410.0000.0000.0000.000
64A67LYS10.8870.94419.5410.2270.2270.0000.0000.0000.000
65A68PRO00.0200.00119.4100.0170.0170.0000.0000.0000.000
66A69GLU-1-0.886-0.94322.373-0.191-0.1910.0000.0000.0000.000
67A70ARG10.8760.95725.6650.1700.1700.0000.0000.0000.000
68A71ALA00.007-0.00226.176-0.013-0.0130.0000.0000.0000.000
69A72GLU-1-0.873-0.95127.199-0.134-0.1340.0000.0000.0000.000
70A73VAL00.0050.00926.224-0.014-0.0140.0000.0000.0000.000
71A74GLN00.011-0.00223.085-0.018-0.0180.0000.0000.0000.000
72A75ALA0-0.004-0.00521.194-0.011-0.0110.0000.0000.0000.000
73A76VAL00.0300.02823.1730.0090.0090.0000.0000.0000.000
74A77ILE0-0.016-0.01019.314-0.012-0.0120.0000.0000.0000.000
75A78THR00.011-0.00723.4970.0170.0170.0000.0000.0000.000
76A79ALA00.0290.00024.051-0.013-0.0130.0000.0000.0000.000
77A80PRO00.0240.01826.0660.0100.0100.0000.0000.0000.000
78A81THR00.0490.03127.8750.0080.0080.0000.0000.0000.000
79A82ARG10.9010.92127.4590.0970.0970.0000.0000.0000.000
80A83GLU-1-0.918-0.94925.525-0.145-0.1450.0000.0000.0000.000
81A84LEU00.0260.00823.223-0.015-0.0150.0000.0000.0000.000
82A85ALA00.0200.01322.410-0.025-0.0250.0000.0000.0000.000
83A86THR0-0.033-0.02722.622-0.013-0.0130.0000.0000.0000.000
84A87GLN00.0470.02219.581-0.033-0.0330.0000.0000.0000.000
85A88ILE00.0370.03418.035-0.038-0.0380.0000.0000.0000.000
86A89TYR0-0.008-0.00317.815-0.030-0.0300.0000.0000.0000.000
87A90HIS0-0.034-0.03417.9940.0020.0020.0000.0000.0000.000
88A91GLU-1-0.818-0.89212.994-0.579-0.5790.0000.0000.0000.000
89A92THR00.0300.00413.696-0.065-0.0650.0000.0000.0000.000
90A93LEU0-0.0110.00515.201-0.014-0.0140.0000.0000.0000.000
91A94LYS10.7950.90012.0200.4680.4680.0000.0000.0000.000
92A95ILE00.0250.01210.053-0.057-0.0570.0000.0000.0000.000
93A96THR00.028-0.00512.1350.0500.0500.0000.0000.0000.000
94A97LYS10.9040.97413.5090.2270.2270.0000.0000.0000.000
95A98PHE0-0.021-0.02211.1750.0320.0320.0000.0000.0000.000
96A99CYS0-0.0540.00113.6730.0030.0030.0000.0000.0000.000
97A100PRO00.005-0.00615.4110.0390.0390.0000.0000.0000.000
98A101LYS10.9770.97218.0110.0620.0620.0000.0000.0000.000
99A102ASP-1-0.916-0.92921.367-0.098-0.0980.0000.0000.0000.000
100A103ARG10.9150.93717.5740.2020.2020.0000.0000.0000.000
101A104MET0-0.0160.00818.519-0.033-0.0330.0000.0000.0000.000
102A105ILE00.0270.01316.3090.0030.0030.0000.0000.0000.000
103A106VAL0-0.020-0.02320.0910.0030.0030.0000.0000.0000.000
104A107ALA00.0280.00920.210-0.007-0.0070.0000.0000.0000.000
105A108ARG10.8300.90122.2710.1530.1530.0000.0000.0000.000
106A109CYS0-0.0040.00724.037-0.011-0.0110.0000.0000.0000.000
107A110LEU0-0.040-0.00825.8040.0130.0130.0000.0000.0000.000
108A111ILE00.019-0.01727.586-0.003-0.0030.0000.0000.0000.000
109A112GLY0-0.014-0.00630.5780.0070.0070.0000.0000.0000.000
110A113GLY0-0.026-0.01733.531-0.002-0.0020.0000.0000.0000.000
111A114THR0-0.002-0.02035.6660.0020.0020.0000.0000.0000.000
112A115ASP-1-0.821-0.91738.621-0.067-0.0670.0000.0000.0000.000
113A116LYS10.9420.95440.5370.0490.0490.0000.0000.0000.000
114A117GLN00.0220.03234.445-0.002-0.0020.0000.0000.0000.000
115A118LYS10.9610.98135.9040.0770.0770.0000.0000.0000.000
116A119ALA0-0.0040.00937.188-0.003-0.0030.0000.0000.0000.000
117A120LEU0-0.021-0.00635.4080.0020.0020.0000.0000.0000.000
118A121GLU-1-0.762-0.84031.454-0.121-0.1210.0000.0000.0000.000
119A122LYS10.9910.98233.4650.0830.0830.0000.0000.0000.000
120A123LEU00.0030.00329.801-0.007-0.0070.0000.0000.0000.000
121A124ASN0-0.0210.01931.8780.0050.0050.0000.0000.0000.000
122A125VAL00.0760.01829.0820.0030.0030.0000.0000.0000.000
123A126GLN00.0280.01329.965-0.007-0.0070.0000.0000.0000.000
124A127PRO0-0.043-0.02325.243-0.004-0.0040.0000.0000.0000.000
125A128HIS00.0830.06621.948-0.011-0.0110.0000.0000.0000.000
126A129ILE0-0.029-0.01318.644-0.012-0.0120.0000.0000.0000.000
127A130VAL00.0350.00822.6570.0110.0110.0000.0000.0000.000
128A131ILE00.0090.00919.937-0.010-0.0100.0000.0000.0000.000
129A132GLY00.0340.01224.2850.0150.0150.0000.0000.0000.000
130A133THR0-0.0050.01327.171-0.006-0.0060.0000.0000.0000.000
131A134PRO00.0700.01529.5140.0020.0020.0000.0000.0000.000
132A135GLY00.0780.03531.6370.0040.0040.0000.0000.0000.000
133A136ARG10.7420.87131.7790.1070.1070.0000.0000.0000.000
134A137ILE00.0400.01727.5810.0040.0040.0000.0000.0000.000
135A138ASN0-0.028-0.02332.1270.0020.0020.0000.0000.0000.000
136A139ASP-1-0.859-0.90835.552-0.091-0.0910.0000.0000.0000.000
137A140PHE0-0.002-0.01133.5290.0040.0040.0000.0000.0000.000
138A141ILE0-0.036-0.00232.8020.0030.0030.0000.0000.0000.000
139A142ARG10.8990.95336.4640.0950.0950.0000.0000.0000.000
140A143GLU-1-1.004-1.00939.012-0.083-0.0830.0000.0000.0000.000
141A144GLN0-0.059-0.03039.3620.0050.0050.0000.0000.0000.000
142A145ALA0-0.0210.00436.0720.0000.0000.0000.0000.0000.000
143A146LEU0-0.079-0.04129.925-0.006-0.0060.0000.0000.0000.000
144A147ASP-1-0.838-0.91932.957-0.119-0.1190.0000.0000.0000.000
145A148VAL0-0.026-0.02530.149-0.007-0.0070.0000.0000.0000.000
146A149HIS0-0.045-0.01330.663-0.007-0.0070.0000.0000.0000.000
147A150THR00.0040.00229.1060.0010.0010.0000.0000.0000.000
148A151ALA0-0.082-0.03726.174-0.012-0.0120.0000.0000.0000.000
149A152HIS00.0150.00725.5240.0050.0050.0000.0000.0000.000
150A153ILE0-0.0190.00120.278-0.013-0.0130.0000.0000.0000.000
151A154LEU00.0100.00423.9070.0080.0080.0000.0000.0000.000
152A155VAL0-0.040-0.00919.937-0.012-0.0120.0000.0000.0000.000
153A156VAL00.0180.00023.2040.0140.0140.0000.0000.0000.000
154A157ASP-1-0.777-0.90220.588-0.307-0.3070.0000.0000.0000.000
155A158GLU-1-0.847-0.91622.786-0.211-0.2110.0000.0000.0000.000
156A159ALA00.030-0.02725.3860.0170.0170.0000.0000.0000.000
157A160ASP-1-0.806-0.86227.979-0.143-0.1430.0000.0000.0000.000
158A161LEU00.0810.03828.5070.0090.0090.0000.0000.0000.000
159A162MET0-0.083-0.03227.2050.0100.0100.0000.0000.0000.000
160A163LEU0-0.044-0.02731.2320.0070.0070.0000.0000.0000.000
161A164ASP-1-0.913-0.95733.768-0.099-0.0990.0000.0000.0000.000
162A165MET0-0.119-0.05032.7230.0040.0040.0000.0000.0000.000
163A166GLY0-0.0090.00335.6560.0040.0040.0000.0000.0000.000
164A167PHE0-0.040-0.02132.5020.0000.0000.0000.0000.0000.000
165A168ILE00.0180.00831.284-0.004-0.0040.0000.0000.0000.000
166A169THR00.0330.01834.698-0.001-0.0010.0000.0000.0000.000
167A170ASP-1-0.888-0.95534.493-0.108-0.1080.0000.0000.0000.000
168A171VAL00.0590.00630.098-0.004-0.0040.0000.0000.0000.000
169A172ASP-1-0.826-0.87332.588-0.122-0.1220.0000.0000.0000.000
170A173GLN0-0.042-0.02234.874-0.002-0.0020.0000.0000.0000.000
171A174ILE0-0.036-0.00730.2810.0000.0000.0000.0000.0000.000
172A175ALA00.022-0.01531.171-0.003-0.0030.0000.0000.0000.000
173A176ALA0-0.068-0.01832.2320.0000.0000.0000.0000.0000.000
174A177ARG10.9010.94834.7450.1090.1090.0000.0000.0000.000
175A178MET0-0.0440.00527.0600.0000.0000.0000.0000.0000.000
176A179PRO0-0.011-0.00929.9750.0090.0090.0000.0000.0000.000
177A180LYS10.9710.96231.7600.1030.1030.0000.0000.0000.000
178A181ASP-1-0.972-0.97129.485-0.178-0.1780.0000.0000.0000.000
179A182LEU0-0.0160.02327.254-0.012-0.0120.0000.0000.0000.000
180A183GLN00.0020.01319.7210.0010.0010.0000.0000.0000.000
181A184MET0-0.038-0.03824.616-0.005-0.0050.0000.0000.0000.000
182A185LEU0-0.047-0.02918.521-0.015-0.0150.0000.0000.0000.000
183A186VAL00.0130.01222.5380.0070.0070.0000.0000.0000.000
184A187PHE0-0.025-0.01217.991-0.019-0.0190.0000.0000.0000.000
185A188SER0-0.009-0.01222.7720.0130.0130.0000.0000.0000.000
186A189ALA00.0020.02824.394-0.005-0.0050.0000.0000.0000.000
187A190THR0-0.030-0.04525.3470.0080.0080.0000.0000.0000.000
188A191ILE00.007-0.00927.476-0.008-0.0080.0000.0000.0000.000
189A192PRO00.0320.02130.7140.0080.0080.0000.0000.0000.000
190A193GLU-1-0.770-0.87834.137-0.095-0.0950.0000.0000.0000.000
191A194LYS10.9170.94637.1030.0780.0780.0000.0000.0000.000
192A195LEU00.0320.02730.1880.0000.0000.0000.0000.0000.000
193A196LYS10.8870.91533.6080.0980.0980.0000.0000.0000.000
194A197PRO00.0150.01834.660-0.003-0.0030.0000.0000.0000.000
195A198PHE00.0200.01929.557-0.001-0.0010.0000.0000.0000.000
196A199LEU00.032-0.00328.810-0.006-0.0060.0000.0000.0000.000
197A200LYS10.9260.97031.8100.1040.1040.0000.0000.0000.000
198A201LYS10.8110.90134.3550.1150.1150.0000.0000.0000.000
199A202TYR0-0.014-0.03231.0710.0030.0030.0000.0000.0000.000
200A203MET0-0.052-0.00826.995-0.016-0.0160.0000.0000.0000.000
201A204GLU-1-0.941-0.96230.488-0.118-0.1180.0000.0000.0000.000
202A205ASN0-0.064-0.03427.9030.0080.0080.0000.0000.0000.000
203A206PRO0-0.0160.01426.304-0.011-0.0110.0000.0000.0000.000
204A207THR00.002-0.01821.0740.0180.0180.0000.0000.0000.000
205A208PHE0-0.0010.00423.617-0.008-0.0080.0000.0000.0000.000
206A209VAL0-0.009-0.01418.264-0.005-0.0050.0000.0000.0000.000
207A210HIS00.0610.02521.663-0.003-0.0030.0000.0000.0000.000
208A211VAL0-0.040-0.02617.019-0.008-0.0080.0000.0000.0000.000
209A212LEU0-0.0130.01620.2520.0180.0180.0000.0000.0000.000