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: 89R1Y

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010949.654908
FMO2-HF: Nuclear repulsion 1938704.447162
FMO2-HF: Total energy -72245.207746
FMO2-MP2: Total energy -72454.848982


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.
-43.152-37.19817.282-11.558-11.678-0.073
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 : -0.053 / q_NPA : -0.039
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].
3A83SER00.0290.0102.221-10.340-6.3452.720-3.107-3.6080.000
4A84ASP-1-0.877-0.9381.888-28.578-28.70714.153-7.364-6.661-0.087
5A85PHE0-0.042-0.0264.3191.2051.6770.002-0.112-0.3610.000
6A86SER0-0.0150.0056.8690.8560.8560.0000.0000.0000.000
7A87VAL0-0.099-0.0508.942-0.237-0.2370.0000.0000.0000.000
8A88ALA00.0360.02612.3560.0240.0240.0000.0000.0000.000
9A89SER0-0.070-0.01110.6220.1200.1200.0000.0000.0000.000
10A90ARG10.7920.82012.5230.2940.2940.0000.0000.0000.000
11A91ASP-1-0.870-0.90415.4620.1620.1620.0000.0000.0000.000
12A92VAL0-0.0030.00216.648-0.018-0.0180.0000.0000.0000.000
13A93ASN00.011-0.02719.363-0.015-0.0150.0000.0000.0000.000
14A94HIS00.0450.03421.0650.0300.0300.0000.0000.0000.000
15A95ASN0-0.066-0.05622.7110.0090.0090.0000.0000.0000.000
16A96ASN0-0.105-0.04323.7350.0270.0270.0000.0000.0000.000
17A97ILE00.0250.02224.3560.0030.0030.0000.0000.0000.000
18A98CYS0-0.0020.02521.282-0.013-0.0130.0000.0000.0000.000
19A99ALA00.0370.01722.974-0.002-0.0020.0000.0000.0000.000
20A100GLY00.0340.02425.118-0.008-0.0080.0000.0000.0000.000
21A101LEU00.0300.01222.051-0.014-0.0140.0000.0000.0000.000
22A102SER0-0.016-0.02721.177-0.009-0.0090.0000.0000.0000.000
23A103THR0-0.054-0.04222.606-0.006-0.0060.0000.0000.0000.000
24A104GLU-1-0.774-0.88225.878-0.003-0.0030.0000.0000.0000.000
25A105TRP0-0.010-0.01618.3320.0180.0180.0000.0000.0000.000
26A106LEU0-0.063-0.04222.348-0.014-0.0140.0000.0000.0000.000
27A107VAL0-0.068-0.02824.340-0.010-0.0100.0000.0000.0000.000
28A108MET00.0030.03224.211-0.005-0.0050.0000.0000.0000.000
29A109SER0-0.0020.00521.689-0.022-0.0220.0000.0000.0000.000
30A110SER0-0.073-0.04622.085-0.021-0.0210.0000.0000.0000.000
31A111ASP-1-0.925-0.95124.457-0.088-0.0880.0000.0000.0000.000
32A112GLY0-0.0030.01224.323-0.011-0.0110.0000.0000.0000.000
33A113ASP-1-0.893-0.92820.190-0.343-0.3430.0000.0000.0000.000
34A114ALA00.026-0.00216.3700.0240.0240.0000.0000.0000.000
35A115GLU-1-0.815-0.91815.695-0.533-0.5330.0000.0000.0000.000
36A116SER0-0.003-0.02219.0910.0490.0490.0000.0000.0000.000
37A117ARG10.7420.85118.6220.2250.2250.0000.0000.0000.000
38A118MET0-0.050-0.01716.4800.0640.0640.0000.0000.0000.000
39A119ASP-1-0.830-0.89819.946-0.244-0.2440.0000.0000.0000.000
40A120HIS0-0.080-0.03822.7610.0140.0140.0000.0000.0000.000
41A121LEU0-0.042-0.02820.9900.0250.0250.0000.0000.0000.000
42A122ASP-1-0.774-0.86920.949-0.124-0.1240.0000.0000.0000.000
43A123TYR0-0.071-0.05120.3370.0260.0260.0000.0000.0000.000
44A124ASN0-0.080-0.03625.6720.0050.0050.0000.0000.0000.000
45A125GLY00.0120.01826.950-0.007-0.0070.0000.0000.0000.000
46A126GLU-1-0.910-0.96827.918-0.017-0.0170.0000.0000.0000.000
47A127GLY00.0250.00426.6500.0150.0150.0000.0000.0000.000
48A128GLN0-0.035-0.00423.6810.0380.0380.0000.0000.0000.000
49A129SER00.009-0.00627.1470.0190.0190.0000.0000.0000.000
50A130ARG10.8810.94429.830-0.015-0.0150.0000.0000.0000.000
51A131GLY00.0250.00027.1640.0130.0130.0000.0000.0000.000
52A132SER0-0.014-0.01628.1720.0240.0240.0000.0000.0000.000
53A133GLU-1-0.852-0.92030.0990.0310.0310.0000.0000.0000.000
54A134ARG10.8200.91329.003-0.035-0.0350.0000.0000.0000.000
55A135HIS00.0140.00626.7560.0120.0120.0000.0000.0000.000
56A136GLN0-0.029-0.00930.1360.0070.0070.0000.0000.0000.000
57A137VAL00.0390.03833.4930.0040.0040.0000.0000.0000.000
58A138TYR0-0.042-0.02027.4800.0100.0100.0000.0000.0000.000
59A139ASN00.002-0.02331.4380.0170.0170.0000.0000.0000.000
60A140ASP-1-0.842-0.89733.6820.0830.0830.0000.0000.0000.000
61A141ALA0-0.0040.00334.4740.0000.0000.0000.0000.0000.000
62A142LEU0-0.020-0.00731.0330.0040.0040.0000.0000.0000.000
63A143ARG10.8120.88734.785-0.090-0.0900.0000.0000.0000.000
64A144ALA0-0.011-0.00637.793-0.002-0.0020.0000.0000.0000.000
65A145ALA00.0100.00936.245-0.001-0.0010.0000.0000.0000.000
66A146LEU0-0.034-0.02934.4320.0030.0030.0000.0000.0000.000
67A147SER0-0.047-0.01338.486-0.004-0.0040.0000.0000.0000.000
68A148ASN0-0.096-0.04841.486-0.008-0.0080.0000.0000.0000.000
69A149ASP-1-0.949-0.95840.7220.1190.1190.0000.0000.0000.000
70A150ASP-1-0.833-0.90337.2670.1500.1500.0000.0000.0000.000
71A151GLU-1-0.904-0.94837.5520.1600.1600.0000.0000.0000.000
72A152ALA0-0.078-0.04432.7280.0160.0160.0000.0000.0000.000
73A153PRO00.0390.02633.3510.0000.0000.0000.0000.0000.000
74A154PHE00.039-0.00628.4900.0020.0020.0000.0000.0000.000
75A155PHE0-0.008-0.00227.3870.0060.0060.0000.0000.0000.000
76A156THR00.011-0.00130.660-0.005-0.0050.0000.0000.0000.000
77A157ALA0-0.0090.00231.041-0.009-0.0090.0000.0000.0000.000
78A158SER0-0.038-0.04727.335-0.002-0.0020.0000.0000.0000.000
79A159THR0-0.038-0.03729.254-0.004-0.0040.0000.0000.0000.000
80A160ALA00.0290.01931.667-0.011-0.0110.0000.0000.0000.000
81A161VAL0-0.0060.00028.435-0.009-0.0090.0000.0000.0000.000
82A162ILE0-0.039-0.01927.359-0.009-0.0090.0000.0000.0000.000
83A163GLU-1-0.938-0.98230.3910.0970.0970.0000.0000.0000.000
84A164ASP-1-0.921-0.94633.6390.0520.0520.0000.0000.0000.000
85A165ALA0-0.069-0.03730.623-0.010-0.0100.0000.0000.0000.000
86A166GLY0-0.0090.01132.613-0.009-0.0090.0000.0000.0000.000
87A167PHE0-0.087-0.04727.791-0.002-0.0020.0000.0000.0000.000
88A168SER00.0530.03632.1450.0020.0020.0000.0000.0000.000
89A169LEU00.0790.03229.0240.0060.0060.0000.0000.0000.000
90A170ARG10.8170.90729.588-0.113-0.1130.0000.0000.0000.000
91A171ARG10.8190.88528.905-0.165-0.1650.0000.0000.0000.000
92A172GLU-1-0.835-0.90030.6270.1840.1840.0000.0000.0000.000
93A173PRO0-0.012-0.00127.6260.0150.0150.0000.0000.0000.000
94A174LYS10.7910.89822.797-0.387-0.3870.0000.0000.0000.000
95A175THR00.030-0.00223.9610.0090.0090.0000.0000.0000.000
96A176VAL0-0.073-0.02919.318-0.011-0.0110.0000.0000.0000.000
97A177HIS00.0500.00920.6650.0510.0510.0000.0000.0000.000
98A178ALA00.0140.01017.6500.0280.0280.0000.0000.0000.000
99A179SER0-0.055-0.01818.7360.0130.0130.0000.0000.0000.000
100A180GLY00.0260.01319.057-0.017-0.0170.0000.0000.0000.000
101A181GLY00.0100.00515.0780.0430.0430.0000.0000.0000.000
102A182SER00.032-0.02910.110-0.087-0.0870.0000.0000.0000.000
103A183ALA0-0.004-0.00811.4390.0710.0710.0000.0000.0000.000
104A184GLN0-0.0040.00912.282-0.072-0.0720.0000.0000.0000.000
105A185LEU00.0420.03414.503-0.066-0.0660.0000.0000.0000.000
106A186GLY00.0620.01912.098-0.081-0.0810.0000.0000.0000.000
107A187GLN0-0.023-0.01913.132-0.151-0.1510.0000.0000.0000.000
108A188THR0-0.049-0.03215.312-0.130-0.1300.0000.0000.0000.000
109A189VAL00.0550.02415.703-0.075-0.0750.0000.0000.0000.000
110A190ALA00.0330.02513.980-0.087-0.0870.0000.0000.0000.000
111A191HIS0-0.0200.00216.092-0.092-0.0920.0000.0000.0000.000
112A192ASP-1-0.778-0.84019.2790.3400.3400.0000.0000.0000.000
113A193VAL00.011-0.00616.826-0.062-0.0620.0000.0000.0000.000
114A194ALA00.0010.01815.926-0.055-0.0550.0000.0000.0000.000
115A195GLN0-0.099-0.05717.999-0.055-0.0550.0000.0000.0000.000
116A196SER00.016-0.02221.423-0.021-0.0210.0000.0000.0000.000
117A197GLY0-0.055-0.02322.8720.0060.0060.0000.0000.0000.000
118A198ARG10.7870.90522.479-0.240-0.2400.0000.0000.0000.000
119A199LYS10.9740.99022.333-0.047-0.0470.0000.0000.0000.000
120A200HIS0-0.017-0.02220.866-0.001-0.0010.0000.0000.0000.000
121A201LEU00.0830.07121.606-0.003-0.0030.0000.0000.0000.000
122A202LEU0-0.060-0.04417.0380.0140.0140.0000.0000.0000.000
123A203SER00.0000.00520.570-0.022-0.0220.0000.0000.0000.000
124A204LEU00.0200.00914.9840.0310.0310.0000.0000.0000.000
125A205ARG10.8580.92119.159-0.373-0.3730.0000.0000.0000.000
126A206PHE00.0320.00416.1550.0330.0330.0000.0000.0000.000
127A207ALA00.006-0.01320.602-0.055-0.0550.0000.0000.0000.000
128A208ASN0-0.048-0.01121.877-0.003-0.0030.0000.0000.0000.000
129A209VAL0-0.010-0.02224.537-0.025-0.0250.0000.0000.0000.000
130A210GLN00.0550.05021.993-0.015-0.0150.0000.0000.0000.000
131A211GLY0-0.019-0.01122.4980.0350.0350.0000.0000.0000.000
132A212HIS0-0.011-0.03316.739-0.047-0.0470.0000.0000.0000.000
133A213ALA0-0.011-0.00419.8150.0390.0390.0000.0000.0000.000
134A214ILE00.0340.02514.840-0.001-0.0010.0000.0000.0000.000
135A215ALA00.0180.01218.072-0.011-0.0110.0000.0000.0000.000
136A216CYS0-0.0170.00116.6680.0320.0320.0000.0000.0000.000
137A217SER00.0000.00218.390-0.001-0.0010.0000.0000.0000.000
138A218CYS0-0.0270.00418.624-0.009-0.0090.0000.0000.0000.000
139A219GLU-1-0.781-0.86519.629-0.049-0.0490.0000.0000.0000.000
140A220GLY00.0600.02720.631-0.030-0.0300.0000.0000.0000.000
141A221SER0-0.050-0.04117.0310.0440.0440.0000.0000.0000.000
142A222GLN0-0.015-0.01016.0590.0530.0530.0000.0000.0000.000
143A223PHE0-0.001-0.01012.7640.0330.0330.0000.0000.0000.000
144A224LYS10.8570.92313.9550.0510.0510.0000.0000.0000.000
145A225LEU0-0.016-0.01411.9260.0950.0950.0000.0000.0000.000
146A226PHE00.0760.03414.131-0.065-0.0650.0000.0000.0000.000
147A227ASP-1-0.710-0.82113.4830.6280.6280.0000.0000.0000.000
148A228PRO0-0.0080.00215.446-0.044-0.0440.0000.0000.0000.000
149A229ASN00.0300.01114.979-0.108-0.1080.0000.0000.0000.000
150A230LEU0-0.072-0.0349.5440.0120.0120.0000.0000.0000.000
151A231GLY00.0840.06212.591-0.154-0.1540.0000.0000.0000.000
152A232GLU-1-0.765-0.85714.048-0.090-0.0900.0000.0000.0000.000
153A233PHE00.020-0.0077.364-0.123-0.1230.0000.0000.0000.000
154A234GLN0-0.045-0.03410.4040.1350.1350.0000.0000.0000.000
155A235SER00.0240.0099.361-0.136-0.1360.0000.0000.0000.000
156A236SER00.0130.02010.8740.0620.0620.0000.0000.0000.000
157A237ARG10.9200.92812.761-0.024-0.0240.0000.0000.0000.000
158A238SER0-0.044-0.02813.2400.0810.0810.0000.0000.0000.000
159A239ALA00.0250.0188.3210.1000.1000.0000.0000.0000.000
160A240ALA00.0450.0409.2450.3340.3340.0000.0000.0000.000
161A241PRO0-0.015-0.01510.8960.1780.1780.0000.0000.0000.000
162A242GLN0-0.038-0.0102.886-5.757-4.1410.407-0.975-1.0480.014
163A243LEU00.0190.0246.5121.0081.0080.0000.0000.0000.000
164A244ILE00.007-0.0047.8240.1310.1310.0000.0000.0000.000
165A245LYS10.8270.9007.412-3.116-3.1160.0000.0000.0000.000
166A246GLY00.0110.0105.1620.1690.1690.0000.0000.0000.000
167A247LEU00.0050.0075.825-0.044-0.0440.0000.0000.0000.000
168A248ILE0-0.015-0.0138.893-0.169-0.1690.0000.0000.0000.000
169A249ASP-1-0.764-0.8486.9252.8882.8880.0000.0000.0000.000
170A250HIS00.0020.0157.683-0.256-0.2560.0000.0000.0000.000
171A251TYR00.002-0.0209.024-0.273-0.2730.0000.0000.0000.000
172A252ASN00.0570.02012.135-0.215-0.2150.0000.0000.0000.000
173A253SER0-0.114-0.05310.216-0.136-0.1360.0000.0000.0000.000
174A254LEU0-0.023-0.00612.063-0.162-0.1620.0000.0000.0000.000
175A255ASN0-0.086-0.04814.579-0.124-0.1240.0000.0000.0000.000
176A256TYR0-0.0270.00216.090-0.101-0.1010.0000.0000.0000.000
177A257ASP-1-0.910-0.96616.4060.8140.8140.0000.0000.0000.000
178A258VAL0-0.0120.01514.607-0.099-0.0990.0000.0000.0000.000
179A259ALA00.0470.03217.4050.0240.0240.0000.0000.0000.000
180A260CYS0-0.062-0.03920.108-0.019-0.0190.0000.0000.0000.000
181A261VAL00.0110.01516.4610.0160.0160.0000.0000.0000.000
182A262ASN0-0.025-0.00319.871-0.023-0.0230.0000.0000.0000.000
183A263GLH0-0.074-0.08520.655-0.004-0.0040.0000.0000.0000.000
184A264PHE00.0830.04223.086-0.020-0.0200.0000.0000.0000.000
185A265ARG10.9270.97125.074-0.188-0.1880.0000.0000.0000.000
186A266VAL00.0450.01725.962-0.012-0.0120.0000.0000.0000.000
187A267SER0-0.031-0.02527.6060.0020.0020.0000.0000.0000.000
188A268VAL00.0180.02530.1290.0040.0040.0000.0000.0000.000