FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

tag_button

FMODB ID: R91M8

Calculation Name: 5UDF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5UDF

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0D5

Base Structure: X-ray

Registration Date: 2023-06-21

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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2307674.964279
FMO2-HF: Nuclear repulsion 2228143.637152
FMO2-HF: Total energy -79531.327127
FMO2-MP2: Total energy -79765.459943


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:67:ASP)


Summations of interaction energy for fragment #1(A:67:ASP)
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.
-123.435-126.4534.4-14.954-16.4320.185
Interaction energy analysis for fragmet #1(A:67:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.762 / q_NPA : -0.882
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].
3A69GLU-1-0.797-0.9091.94328.29728.1199.240-4.186-4.8760.046
4A70LEU0-0.0150.0052.054-20.261-20.54010.620-3.963-6.3780.059
5A71LYS10.9550.9863.799-43.185-42.6340.060-0.175-0.4370.003
6A72ASN0-0.035-0.0205.850-8.911-8.9110.0000.0000.0000.000
7A73ARG10.8940.9381.700-109.512-112.62114.480-6.630-4.7410.077
8A74VAL00.0380.0237.390-4.353-4.3530.0000.0000.0000.000
9A75LEU0-0.018-0.0209.621-3.244-3.2440.0000.0000.0000.000
10A76GLY00.0390.02211.119-2.305-2.3050.0000.0000.0000.000
11A77MET0-0.034-0.00412.225-2.069-2.0690.0000.0000.0000.000
12A78VAL00.0090.01413.475-1.624-1.6240.0000.0000.0000.000
13A79PRO0-0.0040.00415.973-0.117-0.1170.0000.0000.0000.000
14A80GLN00.000-0.00515.134-1.419-1.4190.0000.0000.0000.000
15A81ALA00.0660.01719.268-0.459-0.4590.0000.0000.0000.000
16A82THR0-0.094-0.04123.1050.0970.0970.0000.0000.0000.000
17A83VAL00.0410.02626.139-0.265-0.2650.0000.0000.0000.000
18A84SER00.004-0.00828.8810.0640.0640.0000.0000.0000.000
19A85SER00.005-0.00431.522-0.341-0.3410.0000.0000.0000.000
20A86THR0-0.046-0.03335.1030.0380.0380.0000.0000.0000.000
21A87GLN0-0.053-0.02337.549-0.183-0.1830.0000.0000.0000.000
22A88ILE0-0.0230.00535.5310.1760.1760.0000.0000.0000.000
23A89LEU00.0730.04433.534-0.201-0.2010.0000.0000.0000.000
24A90THR0-0.019-0.02636.2880.1970.1970.0000.0000.0000.000
25A91ASP-1-0.907-0.95038.1998.5198.5190.0000.0000.0000.000
26A92TRP00.004-0.00930.7530.2280.2280.0000.0000.0000.000
27A93PRO00.016-0.00133.2590.2320.2320.0000.0000.0000.000
28A94GLU-1-0.818-0.88234.2478.6738.6730.0000.0000.0000.000
29A95LEU00.0090.00932.0160.0510.0510.0000.0000.0000.000
30A96VAL00.005-0.00628.8370.1970.1970.0000.0000.0000.000
31A97LYS10.8010.88430.823-8.611-8.6110.0000.0000.0000.000
32A98ARG10.8390.92033.168-8.666-8.6660.0000.0000.0000.000
33A99VAL00.0030.00327.967-0.017-0.0170.0000.0000.0000.000
34A100GLU-1-0.885-0.96425.71612.64012.6400.0000.0000.0000.000
35A101ASN0-0.046-0.02127.9560.2350.2350.0000.0000.0000.000
36A102HIS0-0.0140.00028.456-0.540-0.5400.0000.0000.0000.000
37A103PRO00.0280.00527.7950.4600.4600.0000.0000.0000.000
38A104HIS10.8580.88122.780-13.245-13.2450.0000.0000.0000.000
39A105VAL0-0.0050.02622.7950.7870.7870.0000.0000.0000.000
40A106THR0-0.034-0.03119.242-0.067-0.0670.0000.0000.0000.000
41A107GLY0-0.0030.00821.1860.5480.5480.0000.0000.0000.000
42A108VAL0-0.0020.00622.5540.1900.1900.0000.0000.0000.000
43A109ALA00.0190.01323.701-0.072-0.0720.0000.0000.0000.000
44A110PRO0-0.0060.01325.561-0.011-0.0110.0000.0000.0000.000
45A111PHE0-0.060-0.03325.8320.4570.4570.0000.0000.0000.000
46A112THR00.0480.00827.849-0.461-0.4610.0000.0000.0000.000
47A113GLN00.0040.02823.3460.1380.1380.0000.0000.0000.000
48A114LEU0-0.0140.00227.691-0.548-0.5480.0000.0000.0000.000
49A115GLN00.0590.01727.5080.7410.7410.0000.0000.0000.000
50A116GLY0-0.029-0.01828.724-0.490-0.4900.0000.0000.0000.000
51A117MET0-0.042-0.01529.1680.2190.2190.0000.0000.0000.000
52A118LEU00.0150.01426.175-0.256-0.2560.0000.0000.0000.000
53A119THR0-0.029-0.03229.979-0.119-0.1190.0000.0000.0000.000
54A120ALA00.035-0.00231.419-0.104-0.1040.0000.0000.0000.000
55A121GLN0-0.020-0.01532.628-0.145-0.1450.0000.0000.0000.000
56A122GLY00.0170.02235.532-0.053-0.0530.0000.0000.0000.000
57A123GLN00.0060.02529.156-0.303-0.3030.0000.0000.0000.000
58A124VAL0-0.016-0.01831.273-0.127-0.1270.0000.0000.0000.000
59A125ALA00.0390.03125.8180.1820.1820.0000.0000.0000.000
60A126GLY0-0.016-0.00127.216-0.241-0.2410.0000.0000.0000.000
61A127ILE0-0.030-0.01523.5510.4530.4530.0000.0000.0000.000
62A128MET00.0000.01222.711-0.676-0.6760.0000.0000.0000.000
63A129VAL0-0.009-0.02123.6420.4600.4600.0000.0000.0000.000
64A130THR0-0.006-0.01623.439-0.166-0.1660.0000.0000.0000.000
65A131GLY00.012-0.00225.4950.1130.1130.0000.0000.0000.000
66A132ILE00.0200.00522.8410.0650.0650.0000.0000.0000.000
67A133ASP-1-0.748-0.87126.76310.68610.6860.0000.0000.0000.000
68A134PRO00.0050.00324.3880.4310.4310.0000.0000.0000.000
69A135LYS10.8180.90224.122-10.314-10.3140.0000.0000.0000.000
70A136TYR00.0350.01425.2850.0020.0020.0000.0000.0000.000
71A137GLU-1-0.791-0.88820.12316.35516.3550.0000.0000.0000.000
72A138LYS10.7910.87019.459-13.265-13.2650.0000.0000.0000.000
73A139ASN0-0.0150.00419.0920.9540.9540.0000.0000.0000.000
74A140VAL0-0.072-0.03118.6930.3630.3630.0000.0000.0000.000
75A141SER0-0.016-0.00516.2141.2461.2460.0000.0000.0000.000
76A142ILE00.0010.01211.0320.3550.3550.0000.0000.0000.000
77A143ILE00.0440.03613.7771.0121.0120.0000.0000.0000.000
78A144GLN0-0.014-0.03415.909-0.489-0.4890.0000.0000.0000.000
79A145ASN0-0.069-0.02811.786-2.172-2.1720.0000.0000.0000.000
80A146HIS0-0.021-0.0169.4634.5494.5490.0000.0000.0000.000
81A147ILE0-0.028-0.01013.862-0.577-0.5770.0000.0000.0000.000
82A148VAL0-0.0100.00315.6570.0970.0970.0000.0000.0000.000
83A149ALA0-0.005-0.00918.114-0.794-0.7940.0000.0000.0000.000
84A150GLY00.0190.01121.8960.0800.0800.0000.0000.0000.000
85A151SER00.008-0.00222.8090.2390.2390.0000.0000.0000.000
86A152LEU00.0530.02519.706-0.462-0.4620.0000.0000.0000.000
87A153ASP-1-0.821-0.90223.78812.96012.9600.0000.0000.0000.000
88A154SER0-0.014-0.01126.789-0.698-0.6980.0000.0000.0000.000
89A155LEU0-0.085-0.01825.037-0.510-0.5100.0000.0000.0000.000
90A156LYS10.8320.89629.033-10.174-10.1740.0000.0000.0000.000
91A157LYS10.8520.90632.515-8.543-8.5430.0000.0000.0000.000
92A158GLY0-0.031-0.01935.396-0.175-0.1750.0000.0000.0000.000
93A159GLU-1-0.860-0.91233.3219.2819.2810.0000.0000.0000.000
94A160PHE0-0.016-0.01233.375-0.080-0.0800.0000.0000.0000.000
95A161GLY00.0320.02530.3140.0230.0230.0000.0000.0000.000
96A162ILE0-0.043-0.03626.010-0.001-0.0010.0000.0000.0000.000
97A163VAL0-0.029-0.00221.0690.0070.0070.0000.0000.0000.000
98A164LEU00.0150.00321.807-0.041-0.0410.0000.0000.0000.000
99A165GLY00.0910.06017.8380.5230.5230.0000.0000.0000.000
100A166LYS10.8810.91216.363-16.866-16.8660.0000.0000.0000.000
101A167ASP-1-0.868-0.93416.37318.00818.0080.0000.0000.0000.000
102A168MET0-0.012-0.00219.166-1.182-1.1820.0000.0000.0000.000
103A169ALA0-0.0080.00321.555-0.813-0.8130.0000.0000.0000.000
104A170ASP-1-0.801-0.87721.36713.86613.8660.0000.0000.0000.000
105A171SER0-0.072-0.03323.329-0.720-0.7200.0000.0000.0000.000
106A172LEU0-0.018-0.01625.116-0.604-0.6040.0000.0000.0000.000
107A173GLY0-0.021-0.00626.992-0.431-0.4310.0000.0000.0000.000
108A174LEU0-0.054-0.00826.481-0.302-0.3020.0000.0000.0000.000
109A175ARG10.8180.86723.701-12.059-12.0590.0000.0000.0000.000
110A176LEU00.0100.00625.667-0.160-0.1600.0000.0000.0000.000
111A177ASN00.0310.01727.430-0.451-0.4510.0000.0000.0000.000
112A178ASP-1-0.785-0.86529.7669.9679.9670.0000.0000.0000.000
113A179SER0-0.124-0.06431.475-0.077-0.0770.0000.0000.0000.000
114A180VAL00.0380.02629.048-0.038-0.0380.0000.0000.0000.000
115A181THR0-0.045-0.02432.266-0.265-0.2650.0000.0000.0000.000
116A182LEU00.0170.02329.4110.1710.1710.0000.0000.0000.000
117A183VAL0-0.011-0.02532.442-0.414-0.4140.0000.0000.0000.000
118A184LEU00.0380.01631.8010.3270.3270.0000.0000.0000.000
119A185PRO0-0.006-0.01533.938-0.324-0.3240.0000.0000.0000.000
120A186GLU-1-0.800-0.86136.8568.4508.4500.0000.0000.0000.000
121A187ALA00.0180.00139.483-0.109-0.1090.0000.0000.0000.000
122A188THR0-0.039-0.02341.511-0.174-0.1740.0000.0000.0000.000
123A189PRO00.0170.01445.2980.0400.0400.0000.0000.0000.000
124A190SER0-0.0180.00848.141-0.080-0.0800.0000.0000.0000.000
125A191PRO00.044-0.00547.5360.1350.1350.0000.0000.0000.000
126A192ALA0-0.0010.01345.2760.0430.0430.0000.0000.0000.000
127A193GLY00.0100.02443.2810.1760.1760.0000.0000.0000.000
128A194VAL0-0.045-0.04738.5240.1340.1340.0000.0000.0000.000
129A195VAL0-0.008-0.01241.744-0.181-0.1810.0000.0000.0000.000
130A196PRO0-0.026-0.00338.4740.1230.1230.0000.0000.0000.000
131A197ARG10.8680.92738.052-8.328-8.3280.0000.0000.0000.000
132A198PHE0-0.016-0.00536.9280.2700.2700.0000.0000.0000.000
133A199LYS10.8220.92435.722-9.042-9.0420.0000.0000.0000.000
134A200ARG10.9360.96835.143-8.237-8.2370.0000.0000.0000.000
135A201PHE00.0290.00331.104-0.136-0.1360.0000.0000.0000.000
136A202LYS10.8620.92431.943-9.593-9.5930.0000.0000.0000.000
137A203VAL00.0340.02225.7100.2180.2180.0000.0000.0000.000
138A204VAL0-0.006-0.01326.736-0.198-0.1980.0000.0000.0000.000
139A205GLY00.024-0.00723.3420.1390.1390.0000.0000.0000.000
140A206ILE0-0.037-0.00519.000-0.315-0.3150.0000.0000.0000.000
141A207PHE0-0.0090.00814.8350.1470.1470.0000.0000.0000.000
142A208SER0-0.076-0.06413.178-0.442-0.4420.0000.0000.0000.000
143A209VAL0-0.031-0.0279.6721.4621.4620.0000.0000.0000.000
144A210GLY00.000-0.0288.7025.0445.0440.0000.0000.0000.000
145A211ALA00.0300.02310.491-1.833-1.8330.0000.0000.0000.000
146A212GLU-1-0.926-0.93513.07620.31520.3150.0000.0000.0000.000
147A213VAL00.0350.00512.623-1.276-1.2760.0000.0000.0000.000
148A214ASP-1-0.735-0.85713.55022.47422.4740.0000.0000.0000.000
149A215SER0-0.030-0.03115.993-1.371-1.3710.0000.0000.0000.000
150A216MET0-0.0080.00918.163-0.939-0.9390.0000.0000.0000.000
151A217VAL0-0.019-0.00318.206-0.709-0.7090.0000.0000.0000.000
152A218GLY00.003-0.00620.8660.1960.1960.0000.0000.0000.000
153A219TYR0-0.0130.00518.6380.0090.0090.0000.0000.0000.000
154A220ILE00.0300.00424.236-0.268-0.2680.0000.0000.0000.000
155A221ALA00.0630.03727.7350.2300.2300.0000.0000.0000.000
156A222LEU0-0.0060.00029.519-0.225-0.2250.0000.0000.0000.000
157A223TYR00.0410.02331.007-0.102-0.1020.0000.0000.0000.000
158A224ASP-1-0.813-0.88232.6509.1509.1500.0000.0000.0000.000
159A225ALA00.015-0.00330.745-0.170-0.1700.0000.0000.0000.000
160A226SER00.0110.01132.881-0.085-0.0850.0000.0000.0000.000
161A227THR00.003-0.01035.994-0.319-0.3190.0000.0000.0000.000
162A228LEU0-0.073-0.04332.746-0.280-0.2800.0000.0000.0000.000
163A229LEU0-0.007-0.00734.084-0.180-0.1800.0000.0000.0000.000
164A230ARG10.8290.93237.878-8.183-8.1830.0000.0000.0000.000
165A231LEU00.0080.01037.477-0.193-0.1930.0000.0000.0000.000
166A232PRO00.005-0.00539.7360.0940.0940.0000.0000.0000.000
167A233ASP-1-0.831-0.91937.6078.6548.6540.0000.0000.0000.000
168A234GLY00.0490.01636.155-0.137-0.1370.0000.0000.0000.000
169A235ALA0-0.050-0.01131.3460.1970.1970.0000.0000.0000.000
170A236GLN00.0580.02729.860-0.024-0.0240.0000.0000.0000.000
171A237GLY00.0450.00830.295-0.200-0.2000.0000.0000.0000.000
172A238VAL0-0.039-0.01327.7420.0700.0700.0000.0000.0000.000
173A239ARG10.8390.90716.656-17.839-17.8390.0000.0000.0000.000
174A240LEU00.012-0.00923.039-0.187-0.1870.0000.0000.0000.000
175A241LYS10.8080.90416.272-16.534-16.5340.0000.0000.0000.000
176A242LEU00.0300.02618.721-0.832-0.8320.0000.0000.0000.000
177A243ASP-1-0.839-0.88818.10315.43115.4310.0000.0000.0000.000
178A244ASP-1-0.872-0.95017.24517.19717.1970.0000.0000.0000.000
179A245ILE00.0130.00613.656-0.447-0.4470.0000.0000.0000.000
180A246PHE0-0.025-0.01914.214-0.423-0.4230.0000.0000.0000.000
181A247ALA00.0150.02419.428-0.791-0.7910.0000.0000.0000.000
182A248ALA00.001-0.00320.552-0.522-0.5220.0000.0000.0000.000
183A249PRO0-0.036-0.02322.126-0.389-0.3890.0000.0000.0000.000
184A250GLN00.0270.01623.763-0.256-0.2560.0000.0000.0000.000
185A251VAL00.0270.01224.702-0.392-0.3920.0000.0000.0000.000
186A252ALA00.0060.00826.229-0.340-0.3400.0000.0000.0000.000
187A253ASP-1-0.862-0.93928.14710.05610.0560.0000.0000.0000.000
188A254ASP-1-0.957-0.97430.4369.6609.6600.0000.0000.0000.000
189A255ILE0-0.021-0.00128.869-0.380-0.3800.0000.0000.0000.000
190A256VAL0-0.006-0.00932.104-0.324-0.3240.0000.0000.0000.000
191A257LYS10.8350.90732.662-9.892-9.8920.0000.0000.0000.000
192A258ASN0-0.088-0.02435.872-0.506-0.5060.0000.0000.0000.000
193A259LEU0-0.0050.00134.489-0.059-0.0590.0000.0000.0000.000
194A260PRO00.0190.02338.716-0.106-0.1060.0000.0000.0000.000
195A261SER00.0560.00839.5220.1570.1570.0000.0000.0000.000
196A262ASN0-0.0310.00038.622-0.113-0.1130.0000.0000.0000.000
197A263PHE00.0330.00534.5830.2010.2010.0000.0000.0000.000
198A264TYR0-0.024-0.01130.412-0.192-0.1920.0000.0000.0000.000
199A265ALA00.0560.03829.1500.2170.2170.0000.0000.0000.000
200A266THR0-0.034-0.01125.8330.0010.0010.0000.0000.0000.000
201A267ASN00.0770.05122.6760.5350.5350.0000.0000.0000.000
202A268TRP0-0.020-0.02116.7830.0620.0620.0000.0000.0000.000
203A269THR0-0.052-0.02919.6570.1030.1030.0000.0000.0000.000
204A270TYR0-0.047-0.02421.462-0.423-0.4230.0000.0000.0000.000
205A271THR00.010-0.00720.8330.0240.0240.0000.0000.0000.000
206A272HIS0-0.042-0.01823.0760.0130.0130.0000.0000.0000.000
207A273GLY00.0700.03526.616-0.265-0.2650.0000.0000.0000.000
208A274ASN0-0.062-0.03024.4570.2650.2650.0000.0000.0000.000
209A275LEU00.0170.02326.797-0.086-0.0860.0000.0000.0000.000
210A276PHE0-0.0030.00130.4470.0360.0360.0000.0000.0000.000
211A277ASN0-0.0030.00332.298-0.127-0.1270.0000.0000.0000.000