Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: NNKRQ

Calculation Name: 1UKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q52430

Base Structure: X-ray

Registration Date: 2023-09-23

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014291.748875
FMO2-HF: Nuclear repulsion 1942046.294527
FMO2-HF: Total energy -72245.454347
FMO2-MP2: Total energy -72455.07854


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:81:SER)


Summations of interaction energy for fragment #1(A:81:SER)
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.
-50.24-48.12525.662-14.132-13.647-0.063
Interaction energy analysis for fragmet #1(A:81:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.035
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].
3A83SER00.008-0.0111.916-12.901-11.2877.844-4.779-4.680-0.009
4A84ASP-1-0.861-0.9131.892-29.173-28.81412.971-6.996-6.334-0.085
5A85PHE0-0.028-0.0153.9411.0131.5840.006-0.173-0.4050.001
6A86SER0-0.0010.0087.2060.8770.8770.0000.0000.0000.000
7A87VAL0-0.095-0.0479.018-0.170-0.1700.0000.0000.0000.000
8A88ALA00.0280.02112.6740.0570.0570.0000.0000.0000.000
9A89SER0-0.087-0.01810.5340.1080.1080.0000.0000.0000.000
10A90ARG10.8150.81912.5530.3680.3680.0000.0000.0000.000
11A91ASP-1-0.842-0.89615.6680.0630.0630.0000.0000.0000.000
12A92VAL0-0.021-0.00816.747-0.026-0.0260.0000.0000.0000.000
13A93ASN00.017-0.02419.4960.0030.0030.0000.0000.0000.000
14A94HIS00.0430.03721.2420.0340.0340.0000.0000.0000.000
15A95ASN0-0.049-0.04922.7290.0160.0160.0000.0000.0000.000
16A96ASN0-0.131-0.06123.5540.0290.0290.0000.0000.0000.000
17A97ILE00.0240.01724.4130.0070.0070.0000.0000.0000.000
18A98CYS0-0.0220.00321.035-0.010-0.0100.0000.0000.0000.000
19A99ALA00.0430.01522.7620.0020.0020.0000.0000.0000.000
20A100GLY00.0160.02024.785-0.006-0.0060.0000.0000.0000.000
21A101LEU00.0410.01622.000-0.011-0.0110.0000.0000.0000.000
22A102SER0-0.015-0.02120.771-0.016-0.0160.0000.0000.0000.000
23A103THR0-0.051-0.04222.354-0.002-0.0020.0000.0000.0000.000
24A104GLU-1-0.779-0.87225.692-0.021-0.0210.0000.0000.0000.000
25A105TRP0-0.004-0.01718.0780.0260.0260.0000.0000.0000.000
26A106LEU0-0.060-0.04022.131-0.012-0.0120.0000.0000.0000.000
27A107VAL0-0.053-0.02524.201-0.006-0.0060.0000.0000.0000.000
28A108MET00.0000.02724.594-0.007-0.0070.0000.0000.0000.000
29A109SER00.0200.01421.375-0.022-0.0220.0000.0000.0000.000
30A110SER0-0.088-0.05821.880-0.019-0.0190.0000.0000.0000.000
31A111ASP-1-0.901-0.92724.501-0.104-0.1040.0000.0000.0000.000
32A112GLY00.0180.02124.331-0.011-0.0110.0000.0000.0000.000
33A113ASP-1-0.888-0.91120.171-0.381-0.3810.0000.0000.0000.000
34A114ALA00.0310.00116.2160.0310.0310.0000.0000.0000.000
35A115GLU-1-0.804-0.90515.657-0.606-0.6060.0000.0000.0000.000
36A116SER0-0.011-0.02818.9350.0560.0560.0000.0000.0000.000
37A117ARG10.7350.82718.6400.2690.2690.0000.0000.0000.000
38A118MET0-0.058-0.01416.5210.0610.0610.0000.0000.0000.000
39A119ASP-1-0.836-0.91019.974-0.278-0.2780.0000.0000.0000.000
40A120HIS0-0.088-0.04923.0230.0150.0150.0000.0000.0000.000
41A121LEU0-0.029-0.02320.9420.0270.0270.0000.0000.0000.000
42A122ASP-1-0.777-0.86321.047-0.182-0.1820.0000.0000.0000.000
43A123TYR0-0.088-0.05520.3450.0340.0340.0000.0000.0000.000
44A124ASN0-0.087-0.04225.4460.0040.0040.0000.0000.0000.000
45A125GLY00.0270.03026.839-0.007-0.0070.0000.0000.0000.000
46A126GLU-1-0.865-0.93427.786-0.034-0.0340.0000.0000.0000.000
47A127GLY00.0110.00526.5160.0170.0170.0000.0000.0000.000
48A128GLN0-0.038-0.01823.6420.0390.0390.0000.0000.0000.000
49A129SER0-0.016-0.02627.0840.0180.0180.0000.0000.0000.000
50A130ARG10.8130.90529.934-0.006-0.0060.0000.0000.0000.000
51A131GLY00.0260.00627.0000.0140.0140.0000.0000.0000.000
52A132SER0-0.008-0.00727.9660.0250.0250.0000.0000.0000.000
53A133GLU-1-0.856-0.92030.0780.0210.0210.0000.0000.0000.000
54A134ARG10.7710.88428.869-0.017-0.0170.0000.0000.0000.000
55A135HIS00.0260.01526.3290.0120.0120.0000.0000.0000.000
56A136GLN0-0.030-0.00729.9010.0080.0080.0000.0000.0000.000
57A137VAL00.0260.01833.3310.0060.0060.0000.0000.0000.000
58A138TYR0-0.037-0.01826.8230.0100.0100.0000.0000.0000.000
59A139ASN00.016-0.01230.9670.0200.0200.0000.0000.0000.000
60A140ASP-1-0.830-0.89233.1970.0750.0750.0000.0000.0000.000
61A141ALA00.0040.01433.9140.0010.0010.0000.0000.0000.000
62A142LEU0-0.023-0.00830.5170.0040.0040.0000.0000.0000.000
63A143ARG10.8040.87934.221-0.081-0.0810.0000.0000.0000.000
64A144ALA0-0.009-0.00737.352-0.002-0.0020.0000.0000.0000.000
65A145ALA00.0070.01435.806-0.001-0.0010.0000.0000.0000.000
66A146LEU0-0.021-0.02633.8550.0020.0020.0000.0000.0000.000
67A147SER0-0.086-0.03238.026-0.003-0.0030.0000.0000.0000.000
68A148ASN0-0.116-0.07240.891-0.011-0.0110.0000.0000.0000.000
69A149ASP-1-0.938-0.95540.4900.1180.1180.0000.0000.0000.000
70A150ASP-1-0.808-0.88636.4030.1540.1540.0000.0000.0000.000
71A151GLU-1-0.897-0.94336.7540.1660.1660.0000.0000.0000.000
72A152ALA0-0.069-0.03532.4290.0170.0170.0000.0000.0000.000
73A153PRO00.0390.02932.7710.0030.0030.0000.0000.0000.000
74A154PHE00.038-0.01327.8670.0010.0010.0000.0000.0000.000
75A155PHE0-0.021-0.00126.8040.0080.0080.0000.0000.0000.000
76A156THR00.0150.00030.123-0.006-0.0060.0000.0000.0000.000
77A157ALA0-0.0060.00130.479-0.010-0.0100.0000.0000.0000.000
78A158SER0-0.042-0.04926.782-0.005-0.0050.0000.0000.0000.000
79A159THR0-0.050-0.03328.649-0.001-0.0010.0000.0000.0000.000
80A160ALA00.0350.01131.183-0.011-0.0110.0000.0000.0000.000
81A161VAL0-0.025-0.00427.975-0.011-0.0110.0000.0000.0000.000
82A162ILE0-0.025-0.01726.874-0.011-0.0110.0000.0000.0000.000
83A163GLU-1-0.938-0.97629.9760.0950.0950.0000.0000.0000.000
84A164ASP-1-0.825-0.90133.1950.0380.0380.0000.0000.0000.000
85A165ALA0-0.051-0.02830.094-0.011-0.0110.0000.0000.0000.000
86A166GLY00.0020.02132.109-0.008-0.0080.0000.0000.0000.000
87A167PHE0-0.067-0.02927.5390.0000.0000.0000.0000.0000.000
88A168SER00.0690.03831.6740.0010.0010.0000.0000.0000.000
89A169LEU00.0680.03528.5280.0060.0060.0000.0000.0000.000
90A170ARG10.8350.91729.132-0.120-0.1200.0000.0000.0000.000
91A171ARG10.7920.87628.602-0.174-0.1740.0000.0000.0000.000
92A172GLU-1-0.806-0.89430.2600.1860.1860.0000.0000.0000.000
93A173PRO0-0.025-0.00627.2610.0160.0160.0000.0000.0000.000
94A174LYS10.7920.90322.045-0.426-0.4260.0000.0000.0000.000
95A175THR00.014-0.01523.4360.0130.0130.0000.0000.0000.000
96A176VAL0-0.066-0.03618.988-0.010-0.0100.0000.0000.0000.000
97A177HIS00.0620.02119.9820.0520.0520.0000.0000.0000.000
98A178ALA00.0230.02017.2360.0430.0430.0000.0000.0000.000
99A179SER0-0.032-0.00818.3250.0020.0020.0000.0000.0000.000
100A180GLY00.001-0.01618.452-0.047-0.0470.0000.0000.0000.000
101A181GLY00.0140.02414.7090.0350.0350.0000.0000.0000.000
102A182SER00.029-0.0209.652-0.047-0.0470.0000.0000.0000.000
103A183ALA00.0200.00310.8070.0660.0660.0000.0000.0000.000
104A184GLN0-0.037-0.00611.733-0.081-0.0810.0000.0000.0000.000
105A185LEU00.0400.03614.196-0.074-0.0740.0000.0000.0000.000
106A186GLY00.0630.02311.583-0.087-0.0870.0000.0000.0000.000
107A187GLN0-0.004-0.01612.602-0.157-0.1570.0000.0000.0000.000
108A188THR0-0.066-0.04314.692-0.155-0.1550.0000.0000.0000.000
109A189VAL00.0460.02415.275-0.085-0.0850.0000.0000.0000.000
110A190ALA00.0300.01413.585-0.098-0.0980.0000.0000.0000.000
111A191HIS0-0.0140.00015.673-0.103-0.1030.0000.0000.0000.000
112A192ASP-1-0.749-0.83619.0040.3720.3720.0000.0000.0000.000
113A193VAL00.0060.00716.275-0.067-0.0670.0000.0000.0000.000
114A194ALA00.0010.01415.473-0.066-0.0660.0000.0000.0000.000
115A195GLN0-0.033-0.03017.537-0.054-0.0540.0000.0000.0000.000
116A196SER0-0.004-0.02020.983-0.022-0.0220.0000.0000.0000.000
117A197GLY0-0.022-0.00622.9040.0060.0060.0000.0000.0000.000
118A198ARG10.7390.88022.083-0.273-0.2730.0000.0000.0000.000
119A199LYS10.9330.96922.317-0.037-0.0370.0000.0000.0000.000
120A200HIS0-0.004-0.01120.660-0.007-0.0070.0000.0000.0000.000
121A201LEU00.0810.06721.153-0.003-0.0030.0000.0000.0000.000
122A202LEU0-0.051-0.03516.7030.0270.0270.0000.0000.0000.000
123A203SER00.010-0.00920.458-0.034-0.0340.0000.0000.0000.000
124A204LEU00.0050.02914.5580.0300.0300.0000.0000.0000.000
125A205ARG10.8300.90918.629-0.390-0.3900.0000.0000.0000.000
126A206PHE00.0240.00515.9170.0420.0420.0000.0000.0000.000
127A207ALA00.0110.00520.199-0.055-0.0550.0000.0000.0000.000
128A208ASN0-0.026-0.01021.574-0.002-0.0020.0000.0000.0000.000
129A209VAL00.0200.00824.204-0.031-0.0310.0000.0000.0000.000
130A210GLN00.0210.01922.031-0.003-0.0030.0000.0000.0000.000
131A211GLY00.006-0.00121.6950.0370.0370.0000.0000.0000.000
132A212HIS0-0.013-0.02416.533-0.042-0.0420.0000.0000.0000.000
133A213ALA0-0.024-0.00820.0900.0320.0320.0000.0000.0000.000
134A214ILE00.0240.02114.571-0.011-0.0110.0000.0000.0000.000
135A215ALA00.0150.00717.787-0.001-0.0010.0000.0000.0000.000
136A216CYS0-0.027-0.00816.2370.0390.0390.0000.0000.0000.000
137A217SER0-0.004-0.01718.059-0.002-0.0020.0000.0000.0000.000
138A218CYS0-0.0180.01518.2090.0000.0000.0000.0000.0000.000
139A219GLU-1-0.780-0.85119.578-0.043-0.0430.0000.0000.0000.000
140A220GLY00.0630.02720.696-0.033-0.0330.0000.0000.0000.000
141A221SER0-0.062-0.06216.9280.0550.0550.0000.0000.0000.000
142A222GLN0-0.0080.00416.0420.0520.0520.0000.0000.0000.000
143A223PHE00.002-0.01112.3760.0440.0440.0000.0000.0000.000
144A224LYS10.8510.91314.0570.0280.0280.0000.0000.0000.000
145A225LEU0-0.020-0.01411.4580.1150.1150.0000.0000.0000.000
146A226PHE00.0690.03114.268-0.100-0.1000.0000.0000.0000.000
147A227ASP-1-0.705-0.81713.3970.5440.5440.0000.0000.0000.000
148A228PRO00.0040.00715.364-0.062-0.0620.0000.0000.0000.000
149A229ASN00.0290.01815.005-0.095-0.0950.0000.0000.0000.000
150A230LEU0-0.064-0.0319.8480.0050.0050.0000.0000.0000.000
151A231GLY00.0640.04912.397-0.180-0.1800.0000.0000.0000.000
152A232GLU-1-0.759-0.83913.996-0.129-0.1290.0000.0000.0000.000
153A233PHE00.015-0.0087.271-0.140-0.1400.0000.0000.0000.000
154A234GLN0-0.046-0.03110.5480.1920.1920.0000.0000.0000.000
155A235SER00.015-0.0039.239-0.155-0.1550.0000.0000.0000.000
156A236SER00.0280.02010.8320.0600.0600.0000.0000.0000.000
157A237ARG10.8640.91612.306-0.049-0.0490.0000.0000.0000.000
158A238SER0-0.020-0.02113.0830.0950.0950.0000.0000.0000.000
159A239ALA00.0150.0198.0380.1210.1210.0000.0000.0000.000
160A240ALA00.0350.0358.7300.4020.4020.0000.0000.0000.000
161A241PRO0-0.024-0.01910.4870.1810.1810.0000.0000.0000.000
162A242GLN0-0.048-0.0162.227-9.318-9.7814.842-2.173-2.2060.030
163A243LEU00.0180.0236.0051.0951.0950.0000.0000.0000.000
164A244ILE00.0050.0007.4680.0540.0540.0000.0000.0000.000
165A245LYS10.7850.8796.808-3.463-3.4630.0000.0000.0000.000
166A246GLY00.0190.0124.7630.0610.095-0.001-0.011-0.0220.000
167A247LEU00.0070.0125.401-0.144-0.1440.0000.0000.0000.000
168A248ILE0-0.016-0.0128.706-0.206-0.2060.0000.0000.0000.000
169A249ASP-1-0.766-0.8626.2873.5033.5030.0000.0000.0000.000
170A250HIS00.0120.0177.639-0.329-0.3290.0000.0000.0000.000
171A251TYR0-0.014-0.0258.888-0.277-0.2770.0000.0000.0000.000
172A252ASN00.011-0.01511.704-0.151-0.1510.0000.0000.0000.000
173A253SER0-0.113-0.0579.995-0.136-0.1360.0000.0000.0000.000
174A254LEU0-0.0040.00711.970-0.172-0.1720.0000.0000.0000.000
175A255ASN0-0.066-0.04214.378-0.133-0.1330.0000.0000.0000.000
176A256TYR0-0.0340.00315.948-0.076-0.0760.0000.0000.0000.000
177A257ASP-1-0.867-0.94215.9660.8710.8710.0000.0000.0000.000
178A258VAL0-0.0080.00213.890-0.109-0.1090.0000.0000.0000.000
179A259ALA00.0250.01516.7480.0190.0190.0000.0000.0000.000
180A260CYS0-0.068-0.02919.589-0.024-0.0240.0000.0000.0000.000
181A261VAL00.0200.02015.9430.0170.0170.0000.0000.0000.000
182A262ASN00.0020.01119.381-0.015-0.0150.0000.0000.0000.000
183A263GLH0-0.063-0.07220.222-0.003-0.0030.0000.0000.0000.000
184A264PHE00.0730.02922.702-0.019-0.0190.0000.0000.0000.000
185A265ARG10.9380.97924.787-0.204-0.2040.0000.0000.0000.000
186A266VAL00.0270.00025.649-0.011-0.0110.0000.0000.0000.000
187A267SER0-0.044-0.02827.5070.0030.0030.0000.0000.0000.000
188A268VAL0-0.011-0.00229.9410.0060.0060.0000.0000.0000.000