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: 6YL3Z

Calculation Name: 1UDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UDD

Chain ID: A

ChEMBL ID:

UniProt ID: O58873

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2802765.28609
FMO2-HF: Nuclear repulsion 2715240.577768
FMO2-HF: Total energy -87524.708321
FMO2-MP2: Total energy -87782.366756


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-4.18-1.973-0.019-1.08-1.108-0.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.010
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].
3A3VAL00.0250.0473.806-3.410-1.203-0.019-1.080-1.108-0.001
4A4MET0-0.010-0.0165.6100.1930.1930.0000.0000.0000.000
5A5ILE0-0.031-0.0149.0980.1360.1360.0000.0000.0000.000
6A6THR0-0.029-0.07012.1940.0280.0280.0000.0000.0000.000
7A7ASP-1-0.782-0.8788.7590.2210.2210.0000.0000.0000.000
8A8LYS10.8160.9198.901-0.817-0.8170.0000.0000.0000.000
9A9LEU0-0.0050.01911.813-0.010-0.0100.0000.0000.0000.000
10A10ARG10.9090.97014.365-0.187-0.1870.0000.0000.0000.000
11A11ARG10.9080.9308.330-0.862-0.8620.0000.0000.0000.000
12A12ASP-1-0.839-0.89713.8790.5570.5570.0000.0000.0000.000
13A13SER0-0.070-0.04915.889-0.033-0.0330.0000.0000.0000.000
14A14GLU-1-0.884-0.94314.9850.2190.2190.0000.0000.0000.000
15A15GLN0-0.021-0.00619.178-0.036-0.0360.0000.0000.0000.000
16A16ILE0-0.042-0.03022.204-0.014-0.0140.0000.0000.0000.000
17A17TRP00.0720.02721.111-0.013-0.0130.0000.0000.0000.000
18A18LYS10.8930.97823.188-0.101-0.1010.0000.0000.0000.000
19A19LYS10.8910.93324.722-0.127-0.1270.0000.0000.0000.000
20A20ILE00.0080.00825.737-0.008-0.0080.0000.0000.0000.000
21A21PHE0-0.032-0.01621.922-0.006-0.0060.0000.0000.0000.000
22A22GLU-1-0.884-0.95627.7940.0720.0720.0000.0000.0000.000
23A23HIS00.0030.00630.455-0.006-0.0060.0000.0000.0000.000
24A24PRO00.0150.00432.867-0.003-0.0030.0000.0000.0000.000
25A25PHE00.0460.02435.991-0.003-0.0030.0000.0000.0000.000
26A26VAL00.0380.02530.452-0.003-0.0030.0000.0000.0000.000
27A27VAL0-0.007-0.01232.397-0.004-0.0040.0000.0000.0000.000
28A28GLN00.004-0.01734.456-0.004-0.0040.0000.0000.0000.000
29A29LEU0-0.0460.00735.565-0.004-0.0040.0000.0000.0000.000
30A30TYR00.046-0.00631.552-0.004-0.0040.0000.0000.0000.000
31A31SER0-0.0040.00335.632-0.002-0.0020.0000.0000.0000.000
32A32GLY00.007-0.00437.744-0.003-0.0030.0000.0000.0000.000
33A33THR0-0.070-0.03340.462-0.001-0.0010.0000.0000.0000.000
34A34LEU0-0.0160.01239.4150.0000.0000.0000.0000.0000.000
35A35PRO00.0160.01442.116-0.002-0.0020.0000.0000.0000.000
36A36LEU00.0630.02745.0630.0020.0020.0000.0000.0000.000
37A37GLU-1-0.807-0.89446.3390.0320.0320.0000.0000.0000.000
38A38LYS10.8110.90642.543-0.045-0.0450.0000.0000.0000.000
39A39PHE00.0290.01338.7420.0020.0020.0000.0000.0000.000
40A40LYS10.8820.94042.570-0.029-0.0290.0000.0000.0000.000
41A41PHE00.0010.01442.1310.0010.0010.0000.0000.0000.000
42A42TYR0-0.049-0.05135.8100.0020.0020.0000.0000.0000.000
43A43VAL00.0750.02540.5750.0010.0010.0000.0000.0000.000
44A44LEU0-0.0020.01941.7040.0010.0010.0000.0000.0000.000
45A45GLN0-0.0320.00040.3480.0040.0040.0000.0000.0000.000
46A46ASP-1-0.777-0.87637.4160.0620.0620.0000.0000.0000.000
47A47PHE00.0090.02639.1850.0010.0010.0000.0000.0000.000
48A48ASN0-0.014-0.03039.559-0.001-0.0010.0000.0000.0000.000
49A49TYR00.031-0.02130.7170.0030.0030.0000.0000.0000.000
50A50LEU00.0440.02736.1070.0030.0030.0000.0000.0000.000
51A51VAL0-0.002-0.00137.4790.0010.0010.0000.0000.0000.000
52A52GLY0-0.014-0.02236.8720.0010.0010.0000.0000.0000.000
53A53LEU00.030-0.00830.2280.0050.0050.0000.0000.0000.000
54A54THR00.0160.00333.6620.0010.0010.0000.0000.0000.000
55A55ARG10.8940.94836.049-0.057-0.0570.0000.0000.0000.000
56A56ALA00.0020.00031.7870.0010.0010.0000.0000.0000.000
57A57LEU00.0250.01329.4910.0040.0040.0000.0000.0000.000
58A58ALA00.0300.03232.579-0.001-0.0010.0000.0000.0000.000
59A59VAL0-0.0010.01533.372-0.001-0.0010.0000.0000.0000.000
60A60ILE0-0.020-0.00127.8640.0020.0020.0000.0000.0000.000
61A61SER0-0.049-0.03631.219-0.002-0.0020.0000.0000.0000.000
62A62SER0-0.073-0.05932.758-0.002-0.0020.0000.0000.0000.000
63A63LYS10.7940.88430.683-0.102-0.1020.0000.0000.0000.000
64A64ALA0-0.054-0.01129.3630.0030.0030.0000.0000.0000.000
65A65GLU-1-0.833-0.91428.9190.0510.0510.0000.0000.0000.000
66A66TYR0-0.0150.01630.4610.0010.0010.0000.0000.0000.000
67A67PRO00.002-0.01929.0060.0000.0000.0000.0000.0000.000
68A68LEU00.0110.00225.2730.0010.0010.0000.0000.0000.000
69A69MET0-0.002-0.00728.8560.0000.0000.0000.0000.0000.000
70A70ALA0-0.013-0.01131.9820.0000.0000.0000.0000.0000.000
71A71GLU-1-0.849-0.91226.8490.0560.0560.0000.0000.0000.000
72A72LEU0-0.025-0.03227.0970.0020.0020.0000.0000.0000.000
73A73ILE0-0.011-0.00131.0920.0010.0010.0000.0000.0000.000
74A74GLU-1-0.854-0.91133.4300.0360.0360.0000.0000.0000.000
75A75LEU00.0010.00428.8010.0000.0000.0000.0000.0000.000
76A76ALA0-0.016-0.01332.9420.0000.0000.0000.0000.0000.000
77A77ARG10.8240.89735.218-0.038-0.0380.0000.0000.0000.000
78A78ASP-1-0.834-0.90935.1780.0380.0380.0000.0000.0000.000
79A79GLU-1-0.943-0.96733.6220.0590.0590.0000.0000.0000.000
80A80VAL0-0.053-0.03236.862-0.001-0.0010.0000.0000.0000.000
81A81THR0-0.058-0.05440.054-0.003-0.0030.0000.0000.0000.000
82A82VAL00.0080.01338.544-0.001-0.0010.0000.0000.0000.000
83A83GLU-1-0.798-0.90335.7010.0410.0410.0000.0000.0000.000
84A84VAL0-0.0090.01839.1760.0000.0000.0000.0000.0000.000
85A85GLU-1-0.867-0.92342.3550.0260.0260.0000.0000.0000.000
86A86ASN0-0.081-0.06038.489-0.004-0.0040.0000.0000.0000.000
87A87TYR0-0.017-0.02540.779-0.002-0.0020.0000.0000.0000.000
88A88VAL00.002-0.00642.302-0.001-0.0010.0000.0000.0000.000
89A89LYS10.7780.88243.506-0.029-0.0290.0000.0000.0000.000
90A90LEU0-0.011-0.00240.408-0.001-0.0010.0000.0000.0000.000
91A91LEU00.000-0.01044.368-0.001-0.0010.0000.0000.0000.000
92A92LYS10.9851.00346.723-0.023-0.0230.0000.0000.0000.000
93A93GLH0-0.124-0.07544.7880.0000.0000.0000.0000.0000.000
94A94LEU0-0.066-0.02844.1440.0000.0000.0000.0000.0000.000
95A95ASP-1-0.960-0.97448.7760.0250.0250.0000.0000.0000.000
96A96LEU0-0.041-0.01747.6200.0010.0010.0000.0000.0000.000
97A97THR00.000-0.02750.667-0.001-0.0010.0000.0000.0000.000
98A98LEU00.0450.00046.2750.0010.0010.0000.0000.0000.000
99A99GLU-1-0.933-0.95449.0780.0290.0290.0000.0000.0000.000
100A100ASP-1-0.853-0.91450.5040.0320.0320.0000.0000.0000.000
101A101ALA00.0130.02045.4310.0010.0010.0000.0000.0000.000
102A102ILE0-0.048-0.02847.1200.0020.0020.0000.0000.0000.000
103A103LYS10.8510.92348.374-0.031-0.0310.0000.0000.0000.000
104A104THR0-0.060-0.02945.8420.0000.0000.0000.0000.0000.000
105A105GLU-1-0.957-0.96447.0940.0480.0480.0000.0000.0000.000
106A106PRO0-0.009-0.00442.2000.0010.0010.0000.0000.0000.000
107A107THR00.020-0.02940.7160.0020.0020.0000.0000.0000.000
108A108LEU00.0300.00739.3320.0020.0020.0000.0000.0000.000
109A109VAL0-0.024-0.02535.5430.0030.0030.0000.0000.0000.000
110A110ASN0-0.008-0.00236.6530.0070.0070.0000.0000.0000.000
111A111SER00.0400.01837.4170.0020.0020.0000.0000.0000.000
112A112ALA00.0240.01236.1710.0030.0030.0000.0000.0000.000
113A113TYR0-0.078-0.06129.0530.0090.0090.0000.0000.0000.000
114A114MET00.0050.04233.2500.0040.0040.0000.0000.0000.000
115A115ASP-1-0.895-0.94634.9740.0780.0780.0000.0000.0000.000
116A116PHE0-0.082-0.03726.5460.0060.0060.0000.0000.0000.000
117A117MET0-0.0190.01430.0080.0080.0080.0000.0000.0000.000
118A118LEU00.0330.02231.4590.0030.0030.0000.0000.0000.000
119A119ALA00.001-0.00533.3350.0010.0010.0000.0000.0000.000
120A120THR0-0.112-0.07926.8990.0070.0070.0000.0000.0000.000
121A121ALA00.0110.01629.4650.0050.0050.0000.0000.0000.000
122A122TYR0-0.0230.00230.7650.0000.0000.0000.0000.0000.000
123A123LYS10.9420.96429.343-0.131-0.1310.0000.0000.0000.000
124A124GLY00.0040.02827.4120.0040.0040.0000.0000.0000.000
125A125ASN00.013-0.01223.115-0.006-0.0060.0000.0000.0000.000
126A126ILE00.1180.03724.5060.0050.0050.0000.0000.0000.000
127A127ILE00.0050.01919.3210.0010.0010.0000.0000.0000.000
128A128GLU-1-0.853-0.92122.4520.1920.1920.0000.0000.0000.000
129A129GLY00.0300.01923.9330.0000.0000.0000.0000.0000.000
130A130LEU00.0600.01423.341-0.001-0.0010.0000.0000.0000.000
131A131THR0-0.055-0.04520.2110.0080.0080.0000.0000.0000.000
132A132ALA0-0.051-0.03922.4040.0060.0060.0000.0000.0000.000
133A133LEU00.0270.00625.387-0.006-0.0060.0000.0000.0000.000
134A134LEU0-0.0400.00418.615-0.004-0.0040.0000.0000.0000.000
135A135PRO0-0.023-0.00622.707-0.005-0.0050.0000.0000.0000.000
136A136CYS00.0390.04823.990-0.006-0.0060.0000.0000.0000.000
137A137PHE00.0780.02925.036-0.003-0.0030.0000.0000.0000.000
138A138TRP0-0.064-0.06315.2450.0020.0020.0000.0000.0000.000
139A139SER0-0.013-0.02823.085-0.007-0.0070.0000.0000.0000.000
140A140TYR00.0300.01324.620-0.005-0.0050.0000.0000.0000.000
141A141ALA00.0080.01323.974-0.007-0.0070.0000.0000.0000.000
142A142GLU-1-0.841-0.90919.3290.1270.1270.0000.0000.0000.000
143A143ILE0-0.021-0.00323.765-0.005-0.0050.0000.0000.0000.000
144A144ALA00.0070.01327.064-0.006-0.0060.0000.0000.0000.000
145A145GLU-1-0.797-0.89422.8510.0420.0420.0000.0000.0000.000
146A146TYR0-0.051-0.02923.902-0.005-0.0050.0000.0000.0000.000
147A147HIS0-0.067-0.03826.304-0.009-0.0090.0000.0000.0000.000
148A148LYS10.8410.91025.833-0.045-0.0450.0000.0000.0000.000
149A149ASP-1-0.899-0.94230.3370.0320.0320.0000.0000.0000.000
150A150LYS10.8940.91730.738-0.045-0.0450.0000.0000.0000.000
151A151LEU00.0120.03232.571-0.002-0.0020.0000.0000.0000.000
152A152ARG10.8280.91730.447-0.024-0.0240.0000.0000.0000.000
153A153ASP-1-0.909-0.95736.4140.0150.0150.0000.0000.0000.000
154A154ASN0-0.0310.00937.881-0.002-0.0020.0000.0000.0000.000
155A155PRO00.0480.02140.065-0.001-0.0010.0000.0000.0000.000
156A156ILE0-0.0040.01242.954-0.002-0.0020.0000.0000.0000.000
157A157LYS10.9140.96042.350-0.019-0.0190.0000.0000.0000.000
158A158ILE00.0590.02842.3410.0010.0010.0000.0000.0000.000
159A159TYR00.001-0.01639.2080.0020.0020.0000.0000.0000.000
160A160ARG10.8730.93638.089-0.020-0.0200.0000.0000.0000.000
161A161GLU-1-0.935-0.97437.5610.0260.0260.0000.0000.0000.000
162A162TRP00.0290.00933.5970.0010.0010.0000.0000.0000.000
163A163GLY00.0560.02734.1040.0020.0020.0000.0000.0000.000
164A164LYS10.8900.93332.828-0.026-0.0260.0000.0000.0000.000
165A165VAL00.0240.03132.799-0.001-0.0010.0000.0000.0000.000
166A166TYR00.0280.01028.8650.0020.0020.0000.0000.0000.000
167A167LEU0-0.046-0.01927.6480.0030.0030.0000.0000.0000.000
168A168SER0-0.036-0.00628.662-0.003-0.0030.0000.0000.0000.000
169A169ASN00.0360.00127.1680.0060.0060.0000.0000.0000.000
170A170GLU-1-0.879-0.94627.0070.0330.0330.0000.0000.0000.000
171A171TYR0-0.0030.00527.0860.0030.0030.0000.0000.0000.000
172A172LEU00.0230.00423.2820.0080.0080.0000.0000.0000.000
173A173ASN0-0.020-0.01923.1190.0090.0090.0000.0000.0000.000
174A174LEU0-0.0310.00723.7700.0030.0030.0000.0000.0000.000
175A175VAL00.0310.01420.9440.0080.0080.0000.0000.0000.000
176A176GLY0-0.015-0.00519.5900.0110.0110.0000.0000.0000.000
177A177ARG10.8430.89819.497-0.047-0.0470.0000.0000.0000.000
178A178LEU00.0190.02121.3250.0050.0050.0000.0000.0000.000
179A179ARG10.9180.95514.592-0.138-0.1380.0000.0000.0000.000
180A180LYS10.9630.99816.695-0.037-0.0370.0000.0000.0000.000
181A181ILE00.0020.00617.5730.0030.0030.0000.0000.0000.000
182A182ILE00.000-0.00516.6290.0080.0080.0000.0000.0000.000
183A183ASP-1-0.749-0.85513.0970.2390.2390.0000.0000.0000.000
184A184SER0-0.126-0.03313.833-0.008-0.0080.0000.0000.0000.000
185A185SER0-0.025-0.02116.195-0.003-0.0030.0000.0000.0000.000
186A186GLY00.0210.00415.0360.0040.0040.0000.0000.0000.000
187A187HIS00.0360.0128.9370.2170.2170.0000.0000.0000.000
188A188SER0-0.027-0.01112.6920.0880.0880.0000.0000.0000.000
189A189GLY00.0510.01415.168-0.029-0.0290.0000.0000.0000.000
190A190TYR00.035-0.02713.795-0.004-0.0040.0000.0000.0000.000
191A191ASP-1-0.794-0.89015.8720.4840.4840.0000.0000.0000.000
192A192ARG10.7720.90317.949-0.263-0.2630.0000.0000.0000.000
193A193LEU00.0580.02717.291-0.018-0.0180.0000.0000.0000.000
194A194ARG10.8720.93615.656-0.444-0.4440.0000.0000.0000.000
195A195ARG10.9420.96918.554-0.274-0.2740.0000.0000.0000.000
196A196ILE00.0030.03222.138-0.018-0.0180.0000.0000.0000.000
197A197PHE00.0900.03919.501-0.014-0.0140.0000.0000.0000.000
198A198ILE0-0.023-0.01118.941-0.016-0.0160.0000.0000.0000.000
199A199THR0-0.091-0.05422.628-0.017-0.0170.0000.0000.0000.000
200A200GLY00.0650.03125.370-0.012-0.0120.0000.0000.0000.000
201A201SER00.017-0.00322.926-0.010-0.0100.0000.0000.0000.000
202A202LYS10.9100.94825.416-0.175-0.1750.0000.0000.0000.000
203A203PHE00.0110.01227.959-0.009-0.0090.0000.0000.0000.000
204A204GLU-1-0.703-0.81527.2250.0900.0900.0000.0000.0000.000
205A205LEU0-0.040-0.01728.400-0.007-0.0070.0000.0000.0000.000
206A206ALA0-0.047-0.02830.533-0.007-0.0070.0000.0000.0000.000
207A207PHE00.0310.01733.019-0.006-0.0060.0000.0000.0000.000
208A208TRP00.0450.02430.487-0.009-0.0090.0000.0000.0000.000
209A209GLU-1-0.817-0.88234.7320.0640.0640.0000.0000.0000.000
210A210MET0-0.0550.00836.526-0.006-0.0060.0000.0000.0000.000
211A211ALA00.0550.03637.932-0.004-0.0040.0000.0000.0000.000
212A212TRP0-0.056-0.03038.424-0.005-0.0050.0000.0000.0000.000
213A213ARG10.8090.87939.186-0.066-0.0660.0000.0000.0000.000
214A214GLY00.0010.02642.500-0.002-0.0020.0000.0000.0000.000
215A215GLY0-0.023-0.01242.231-0.001-0.0010.0000.0000.0000.000