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: G5JM1

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010757.815959
FMO2-HF: Nuclear repulsion 1938513.135824
FMO2-HF: Total energy -72244.680135
FMO2-MP2: Total energy -72454.347933


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.
-38.879-32.68214.463-10.187-10.474-0.066
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 : -0.046 / q_NPA : -0.032
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].
3A83SER00.0320.0032.648-9.281-4.8470.870-2.426-2.8790.007
4A84ASP-1-0.897-0.9432.038-26.166-26.41113.430-6.782-6.403-0.084
5A85PHE0-0.043-0.0294.1751.1561.6390.002-0.113-0.3720.000
6A86SER0-0.0130.0026.8010.8190.8190.0000.0000.0000.000
7A87VAL0-0.111-0.0548.885-0.247-0.2470.0000.0000.0000.000
8A88ALA00.0600.04012.2700.0170.0170.0000.0000.0000.000
9A89SER0-0.067-0.01610.8030.1810.1810.0000.0000.0000.000
10A90ARG10.8160.86112.7070.2310.2310.0000.0000.0000.000
11A91ASP-1-0.879-0.90715.6460.2010.2010.0000.0000.0000.000
12A92VAL00.000-0.00416.839-0.023-0.0230.0000.0000.0000.000
13A93ASN00.005-0.02719.551-0.019-0.0190.0000.0000.0000.000
14A94HIS00.0450.03221.1850.0290.0290.0000.0000.0000.000
15A95ASN0-0.065-0.04622.8950.0070.0070.0000.0000.0000.000
16A96ASN0-0.086-0.03323.8080.0240.0240.0000.0000.0000.000
17A97ILE00.0260.01124.4260.0010.0010.0000.0000.0000.000
18A98CYS0-0.0030.02021.465-0.013-0.0130.0000.0000.0000.000
19A99ALA00.0250.00323.044-0.001-0.0010.0000.0000.0000.000
20A100GLY00.0340.01725.118-0.008-0.0080.0000.0000.0000.000
21A101LEU00.0320.01122.077-0.014-0.0140.0000.0000.0000.000
22A102SER0-0.009-0.01621.055-0.008-0.0080.0000.0000.0000.000
23A103THR0-0.046-0.03022.606-0.007-0.0070.0000.0000.0000.000
24A104GLU-1-0.781-0.87625.8490.0070.0070.0000.0000.0000.000
25A105TRP0-0.011-0.01818.2270.0160.0160.0000.0000.0000.000
26A106LEU0-0.065-0.04622.361-0.015-0.0150.0000.0000.0000.000
27A107VAL0-0.072-0.03124.340-0.011-0.0110.0000.0000.0000.000
28A108MET0-0.0030.03723.863-0.003-0.0030.0000.0000.0000.000
29A109SER0-0.029-0.00421.525-0.023-0.0230.0000.0000.0000.000
30A110SER0-0.060-0.04922.011-0.020-0.0200.0000.0000.0000.000
31A111ASP-1-0.934-0.95324.384-0.073-0.0730.0000.0000.0000.000
32A112GLY0-0.0040.00824.255-0.009-0.0090.0000.0000.0000.000
33A113ASP-1-0.909-0.96020.010-0.314-0.3140.0000.0000.0000.000
34A114ALA00.022-0.00616.3350.0280.0280.0000.0000.0000.000
35A115GLU-1-0.852-0.93815.999-0.497-0.4970.0000.0000.0000.000
36A116SER0-0.0090.00119.2600.0470.0470.0000.0000.0000.000
37A117ARG10.7660.86018.3960.1970.1970.0000.0000.0000.000
38A118MET0-0.049-0.01916.6890.0620.0620.0000.0000.0000.000
39A119ASP-1-0.848-0.92320.141-0.212-0.2120.0000.0000.0000.000
40A120HIS0-0.088-0.04922.9450.0110.0110.0000.0000.0000.000
41A121LEU0-0.044-0.03121.0410.0220.0220.0000.0000.0000.000
42A122ASP-1-0.761-0.86721.564-0.088-0.0880.0000.0000.0000.000
43A123TYR0-0.077-0.04220.6040.0210.0210.0000.0000.0000.000
44A124ASN0-0.079-0.03425.8610.0070.0070.0000.0000.0000.000
45A125GLY00.0230.02327.129-0.008-0.0080.0000.0000.0000.000
46A126GLU-1-0.914-0.97028.110-0.004-0.0040.0000.0000.0000.000
47A127GLY00.0280.00626.8550.0140.0140.0000.0000.0000.000
48A128GLN0-0.035-0.00324.0600.0360.0360.0000.0000.0000.000
49A129SER00.014-0.00727.3520.0180.0180.0000.0000.0000.000
50A130ARG10.9841.01029.824-0.022-0.0220.0000.0000.0000.000
51A131GLY00.031-0.00227.2290.0120.0120.0000.0000.0000.000
52A132SER0-0.019-0.01228.2220.0220.0220.0000.0000.0000.000
53A133GLU-1-0.928-0.96630.1580.0380.0380.0000.0000.0000.000
54A134ARG10.8470.91828.850-0.045-0.0450.0000.0000.0000.000
55A135HIS00.0260.01626.6790.0100.0100.0000.0000.0000.000
56A136GLN0-0.043-0.01630.2020.0060.0060.0000.0000.0000.000
57A137VAL00.0530.05333.3690.0030.0030.0000.0000.0000.000
58A138TYR0-0.046-0.02428.2200.0130.0130.0000.0000.0000.000
59A139ASN0-0.001-0.02331.4990.0170.0170.0000.0000.0000.000
60A140ASP-1-0.847-0.91133.6790.0880.0880.0000.0000.0000.000
61A141ALA0-0.0050.00334.479-0.001-0.0010.0000.0000.0000.000
62A142LEU0-0.022-0.00631.1470.0040.0040.0000.0000.0000.000
63A143ARG10.8170.89534.787-0.095-0.0950.0000.0000.0000.000
64A144ALA0-0.010-0.00537.792-0.002-0.0020.0000.0000.0000.000
65A145ALA00.0110.01036.256-0.001-0.0010.0000.0000.0000.000
66A146LEU0-0.037-0.03134.5770.0020.0020.0000.0000.0000.000
67A147SER0-0.053-0.01638.489-0.004-0.0040.0000.0000.0000.000
68A148ASN0-0.076-0.03741.503-0.008-0.0080.0000.0000.0000.000
69A149ASP-1-0.955-0.96240.7760.1190.1190.0000.0000.0000.000
70A150ASP-1-0.863-0.91237.1600.1540.1540.0000.0000.0000.000
71A151GLU-1-0.892-0.94837.5820.1610.1610.0000.0000.0000.000
72A152ALA0-0.098-0.05132.7240.0160.0160.0000.0000.0000.000
73A153PRO00.0530.02333.1730.0010.0010.0000.0000.0000.000
74A154PHE00.013-0.01628.5130.0010.0010.0000.0000.0000.000
75A155PHE0-0.009-0.00827.1690.0070.0070.0000.0000.0000.000
76A156THR00.008-0.00430.674-0.003-0.0030.0000.0000.0000.000
77A157ALA00.0050.00631.026-0.009-0.0090.0000.0000.0000.000
78A158SER0-0.031-0.02927.424-0.002-0.0020.0000.0000.0000.000
79A159THR0-0.036-0.03129.264-0.003-0.0030.0000.0000.0000.000
80A160ALA00.0410.02331.680-0.010-0.0100.0000.0000.0000.000
81A161VAL00.0020.00128.327-0.010-0.0100.0000.0000.0000.000
82A162ILE0-0.056-0.02327.504-0.008-0.0080.0000.0000.0000.000
83A163GLU-1-0.944-0.99030.4020.1000.1000.0000.0000.0000.000
84A164ASP-1-0.960-0.96433.7480.0600.0600.0000.0000.0000.000
85A165ALA0-0.082-0.03930.647-0.010-0.0100.0000.0000.0000.000
86A166GLY0-0.0140.00232.613-0.009-0.0090.0000.0000.0000.000
87A167PHE0-0.093-0.03927.767-0.001-0.0010.0000.0000.0000.000
88A168SER00.0220.01432.1380.0010.0010.0000.0000.0000.000
89A169LEU00.0780.03229.3310.0070.0070.0000.0000.0000.000
90A170ARG10.8280.91029.618-0.120-0.1200.0000.0000.0000.000
91A171ARG10.8290.89028.957-0.172-0.1720.0000.0000.0000.000
92A172GLU-1-0.840-0.90030.6530.1910.1910.0000.0000.0000.000
93A173PRO0-0.014-0.00127.7070.0150.0150.0000.0000.0000.000
94A174LYS10.8380.92623.179-0.388-0.3880.0000.0000.0000.000
95A175THR00.0310.01023.9980.0100.0100.0000.0000.0000.000
96A176VAL0-0.074-0.03019.202-0.013-0.0130.0000.0000.0000.000
97A177HIS00.0480.00720.6890.0470.0470.0000.0000.0000.000
98A178ALA00.0140.01217.6760.0270.0270.0000.0000.0000.000
99A179SER0-0.059-0.02818.7580.0120.0120.0000.0000.0000.000
100A180GLY00.0290.01919.084-0.018-0.0180.0000.0000.0000.000
101A181GLY00.0140.00715.1060.0420.0420.0000.0000.0000.000
102A182SER00.032-0.01410.017-0.072-0.0720.0000.0000.0000.000
103A183ALA00.009-0.00911.5020.0760.0760.0000.0000.0000.000
104A184GLN0-0.0170.00712.319-0.083-0.0830.0000.0000.0000.000
105A185LEU00.0350.02614.481-0.065-0.0650.0000.0000.0000.000
106A186GLY00.0630.01612.134-0.082-0.0820.0000.0000.0000.000
107A187GLN0-0.025-0.02013.168-0.183-0.1830.0000.0000.0000.000
108A188THR0-0.027-0.01615.312-0.128-0.1280.0000.0000.0000.000
109A189VAL00.0550.02315.656-0.076-0.0760.0000.0000.0000.000
110A190ALA00.0230.01513.983-0.085-0.0850.0000.0000.0000.000
111A191HIS0-0.0180.00916.092-0.090-0.0900.0000.0000.0000.000
112A192ASP-1-0.808-0.86119.2790.3460.3460.0000.0000.0000.000
113A193VAL00.001-0.01616.842-0.061-0.0610.0000.0000.0000.000
114A194ALA0-0.0090.01215.896-0.052-0.0520.0000.0000.0000.000
115A195GLN0-0.090-0.05717.925-0.061-0.0610.0000.0000.0000.000
116A196SER00.015-0.02821.352-0.021-0.0210.0000.0000.0000.000
117A197GLY0-0.062-0.02522.8020.0050.0050.0000.0000.0000.000
118A198ARG10.7880.90322.443-0.240-0.2400.0000.0000.0000.000
119A199LYS11.0281.02322.252-0.065-0.0650.0000.0000.0000.000
120A200HIS0-0.003-0.00820.8010.0010.0010.0000.0000.0000.000
121A201LEU00.0900.07221.612-0.002-0.0020.0000.0000.0000.000
122A202LEU0-0.064-0.05017.0310.0120.0120.0000.0000.0000.000
123A203SER00.0160.02120.580-0.016-0.0160.0000.0000.0000.000
124A204LEU00.0050.00115.0690.0300.0300.0000.0000.0000.000
125A205ARG10.8760.93219.166-0.379-0.3790.0000.0000.0000.000
126A206PHE00.0310.00316.2730.0330.0330.0000.0000.0000.000
127A207ALA00.006-0.01120.601-0.055-0.0550.0000.0000.0000.000
128A208ASN0-0.054-0.01221.872-0.004-0.0040.0000.0000.0000.000
129A209VAL0-0.002-0.01724.531-0.024-0.0240.0000.0000.0000.000
130A210GLN00.0500.04022.112-0.014-0.0140.0000.0000.0000.000
131A211GLY0-0.030-0.01622.4970.0350.0350.0000.0000.0000.000
132A212HIS0-0.031-0.04516.761-0.047-0.0470.0000.0000.0000.000
133A213ALA0-0.0010.00119.8180.0370.0370.0000.0000.0000.000
134A214ILE00.0340.02814.9650.0010.0010.0000.0000.0000.000
135A215ALA00.0190.01018.082-0.015-0.0150.0000.0000.0000.000
136A216CYS0-0.042-0.00516.6990.0170.0170.0000.0000.0000.000
137A217SER00.0480.02018.307-0.004-0.0040.0000.0000.0000.000
138A218CYS0-0.0410.00418.544-0.009-0.0090.0000.0000.0000.000
139A219GLU-1-0.823-0.89519.555-0.060-0.0600.0000.0000.0000.000
140A220GLY00.0550.02320.565-0.030-0.0300.0000.0000.0000.000
141A221SER0-0.053-0.03816.9250.0410.0410.0000.0000.0000.000
142A222GLN0-0.015-0.01015.9390.0490.0490.0000.0000.0000.000
143A223PHE0-0.004-0.00512.6360.0350.0350.0000.0000.0000.000
144A224LYS10.8720.94013.8790.0550.0550.0000.0000.0000.000
145A225LEU0-0.016-0.01112.1040.0890.0890.0000.0000.0000.000
146A226PHE00.0770.03614.131-0.058-0.0580.0000.0000.0000.000
147A227ASP-1-0.705-0.81913.5790.6530.6530.0000.0000.0000.000
148A228PRO0-0.0030.00215.502-0.039-0.0390.0000.0000.0000.000
149A229ASN00.0280.00615.096-0.109-0.1090.0000.0000.0000.000
150A230LEU0-0.086-0.0399.8790.0260.0260.0000.0000.0000.000
151A231GLY00.0880.06612.793-0.135-0.1350.0000.0000.0000.000
152A232GLU-1-0.761-0.86014.167-0.056-0.0560.0000.0000.0000.000
153A233PHE00.015-0.0097.527-0.111-0.1110.0000.0000.0000.000
154A234GLN0-0.031-0.02510.3290.1160.1160.0000.0000.0000.000
155A235SER00.0240.0079.326-0.146-0.1460.0000.0000.0000.000
156A236SER00.0170.02510.8070.0700.0700.0000.0000.0000.000
157A237ARG10.9230.92312.698-0.018-0.0180.0000.0000.0000.000
158A238SER0-0.052-0.02913.3290.0810.0810.0000.0000.0000.000
159A239ALA00.0290.0198.2420.1020.1020.0000.0000.0000.000
160A240ALA00.0450.0409.1820.3260.3260.0000.0000.0000.000
161A241PRO0-0.021-0.02010.8960.1780.1780.0000.0000.0000.000
162A242GLN0-0.038-0.0103.077-4.939-3.4140.161-0.866-0.8200.011
163A243LEU00.0210.0286.5520.9880.9880.0000.0000.0000.000
164A244ILE00.001-0.0027.8240.1400.1400.0000.0000.0000.000
165A245LYS10.8210.9107.665-3.003-3.0030.0000.0000.0000.000
166A246GLY00.0110.0105.1830.1680.1680.0000.0000.0000.000
167A247LEU00.0090.0125.844-0.046-0.0460.0000.0000.0000.000
168A248ILE0-0.019-0.0148.900-0.168-0.1680.0000.0000.0000.000
169A249ASP-1-0.754-0.8736.9422.7412.7410.0000.0000.0000.000
170A250HIS00.0050.0187.763-0.207-0.2070.0000.0000.0000.000
171A251TYR0-0.005-0.0209.010-0.275-0.2750.0000.0000.0000.000
172A252ASN00.0530.01912.128-0.275-0.2750.0000.0000.0000.000
173A253SER0-0.125-0.06610.191-0.137-0.1370.0000.0000.0000.000
174A254LEU0-0.019-0.00512.254-0.159-0.1590.0000.0000.0000.000
175A255ASN0-0.073-0.04014.682-0.096-0.0960.0000.0000.0000.000
176A256TYR0-0.034-0.00216.076-0.098-0.0980.0000.0000.0000.000
177A257ASP-1-0.888-0.96016.4010.7820.7820.0000.0000.0000.000
178A258VAL0-0.0190.01614.505-0.094-0.0940.0000.0000.0000.000
179A259ALA00.0590.03717.4110.0230.0230.0000.0000.0000.000
180A260CYS0-0.066-0.04420.142-0.019-0.0190.0000.0000.0000.000
181A261VAL00.0140.01716.5220.0170.0170.0000.0000.0000.000
182A262ASN0-0.024-0.01919.889-0.026-0.0260.0000.0000.0000.000
183A263GLH0-0.078-0.07820.688-0.009-0.0090.0000.0000.0000.000
184A264PHE00.0790.04023.109-0.021-0.0210.0000.0000.0000.000
185A265ARG10.9210.96425.096-0.197-0.1970.0000.0000.0000.000
186A266VAL00.0440.02126.002-0.012-0.0120.0000.0000.0000.000
187A267SER0-0.033-0.02827.5960.0010.0010.0000.0000.0000.000
188A268VAL00.0450.03730.0760.0030.0030.0000.0000.0000.000