Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: NN31Q

Calculation Name: 3DTO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DTO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K916

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2154469.574207
FMO2-HF: Nuclear repulsion 2075072.907289
FMO2-HF: Total energy -79396.666917
FMO2-MP2: Total energy -79627.504182


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-20.728-20.11414.791-6.471-8.9330.036
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.004
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].
3A4GLN0-0.026-0.0203.525-2.5321.3240.116-1.768-2.2050.006
4A5ALA00.0340.0191.877-4.807-9.67612.789-4.026-3.8930.014
5A6ILE00.0250.0212.433-8.293-6.7701.887-0.640-2.7700.016
6A7LEU00.0450.0204.423-2.697-2.6000.000-0.036-0.0610.000
7A8GLN00.0060.0106.061-0.211-0.2110.0000.0000.0000.000
8A9SER0-0.038-0.0076.380-1.011-1.0110.0000.0000.0000.000
9A10ALA00.0470.0298.740-0.446-0.4460.0000.0000.0000.000
10A11GLU-1-1.014-1.01510.3840.8400.8400.0000.0000.0000.000
11A12ALA0-0.023-0.00611.997-0.202-0.2020.0000.0000.0000.000
12A13TRP0-0.045-0.02813.230-0.137-0.1370.0000.0000.0000.000
13A14VAL00.0710.02714.364-0.092-0.0920.0000.0000.0000.000
14A15LYS10.9340.97616.367-0.478-0.4780.0000.0000.0000.000
15A16LYS10.8620.92317.195-0.312-0.3120.0000.0000.0000.000
16A17GLN0-0.080-0.06219.267-0.046-0.0460.0000.0000.0000.000
17A18LEU00.1200.10320.443-0.012-0.0120.0000.0000.0000.000
18A19MET0-0.169-0.07922.396-0.006-0.0060.0000.0000.0000.000
19A20ASP-1-0.954-0.97624.2470.1600.1600.0000.0000.0000.000
20A21GLU-1-0.833-0.88526.4840.1520.1520.0000.0000.0000.000
21A22TYR0-0.082-0.06129.006-0.013-0.0130.0000.0000.0000.000
22A23SER0-0.024-0.00628.6180.0030.0030.0000.0000.0000.000
23A24GLY00.0500.01828.591-0.011-0.0110.0000.0000.0000.000
24A25HIS0-0.062-0.04727.3590.0250.0250.0000.0000.0000.000
25A26ASP-1-0.837-0.91325.8070.2430.2430.0000.0000.0000.000
26A27TRP00.1130.04915.8260.0030.0030.0000.0000.0000.000
27A28TYR0-0.065-0.03821.2850.0440.0440.0000.0000.0000.000
28A29HIS10.8110.92522.412-0.249-0.2490.0000.0000.0000.000
29A30ILE00.1310.06917.8200.0160.0160.0000.0000.0000.000
30A31ARG10.9240.99917.795-0.421-0.4210.0000.0000.0000.000
31A32ARG10.7800.87518.657-0.235-0.2350.0000.0000.0000.000
32A33VAL00.0060.04319.7310.0090.0090.0000.0000.0000.000
33A34THR00.025-0.01414.2850.0210.0210.0000.0000.0000.000
34A35LEU0-0.064-0.05115.8390.0300.0300.0000.0000.0000.000
35A36MET0-0.049-0.00817.770-0.018-0.0180.0000.0000.0000.000
36A37ALA00.0830.03217.284-0.016-0.0160.0000.0000.0000.000
37A38LYS10.9470.98712.267-1.073-1.0730.0000.0000.0000.000
38A39ALA0-0.0280.00916.284-0.047-0.0470.0000.0000.0000.000
39A40ILE0-0.035-0.04319.075-0.038-0.0380.0000.0000.0000.000
40A41GLY00.0530.02217.202-0.042-0.0420.0000.0000.0000.000
41A42GLU-1-0.892-0.97014.7140.5950.5950.0000.0000.0000.000
42A43GLN0-0.071-0.03017.532-0.042-0.0420.0000.0000.0000.000
43A44GLU-1-0.857-0.93320.6160.1320.1320.0000.0000.0000.000
44A45LYS10.8250.90517.513-0.254-0.2540.0000.0000.0000.000
45A46VAL0-0.0090.02116.797-0.046-0.0460.0000.0000.0000.000
46A47ASP-1-0.824-0.94610.7240.0510.0510.0000.0000.0000.000
47A48VAL0-0.038-0.05111.9860.0620.0620.0000.0000.0000.000
48A49PHE0-0.0270.0046.5920.2350.2350.0000.0000.0000.000
49A50VAL00.0500.03810.2320.1730.1730.0000.0000.0000.000
50A51VAL00.0110.02412.6520.0450.0450.0000.0000.0000.000
51A52GLN0-0.010-0.01610.9720.0590.0590.0000.0000.0000.000
52A53ILE0-0.010-0.0088.2630.0700.0700.0000.0000.0000.000
53A54ALA00.010-0.00312.066-0.084-0.0840.0000.0000.0000.000
54A55ALA0-0.021-0.02415.711-0.042-0.0420.0000.0000.0000.000
55A56LEU0-0.060-0.03311.691-0.025-0.0250.0000.0000.0000.000
56A57PHE00.015-0.04812.376-0.006-0.0060.0000.0000.0000.000
57A58HIS0-0.080-0.02217.493-0.056-0.0560.0000.0000.0000.000
58A59ASP-1-0.815-0.89920.3140.2580.2580.0000.0000.0000.000
59A60LEU0-0.073-0.01517.882-0.020-0.0200.0000.0000.0000.000
60A61ILE0-0.026-0.00321.4050.0010.0010.0000.0000.0000.000
61A62ASP-1-0.963-0.97524.1600.1290.1290.0000.0000.0000.000
62A70GLU-1-0.878-0.95925.9720.0790.0790.0000.0000.0000.000
63A71THR0-0.030-0.02324.0990.0070.0070.0000.0000.0000.000
64A72ALA00.0720.04822.7110.0030.0030.0000.0000.0000.000
65A73LYS11.0401.02620.078-0.002-0.0020.0000.0000.0000.000
66A74GLN0-0.137-0.09819.2000.0160.0160.0000.0000.0000.000
67A75GLN00.0530.01918.2030.0320.0320.0000.0000.0000.000
68A76LEU0-0.015-0.01115.4100.0170.0170.0000.0000.0000.000
69A77ILE0-0.012-0.00514.5120.0220.0220.0000.0000.0000.000
70A78ASP-1-0.803-0.88014.714-0.108-0.1080.0000.0000.0000.000
71A79TRP0-0.059-0.0268.201-0.018-0.0180.0000.0000.0000.000
72A80MET0-0.034-0.02210.1750.0850.0850.0000.0000.0000.000
73A81GLU-1-0.857-0.9449.489-0.413-0.4130.0000.0000.0000.000
74A82ALA0-0.110-0.03910.097-0.220-0.2200.0000.0000.0000.000
75A83ALA0-0.046-0.0216.196-0.001-0.0010.0000.0000.0000.000
76A84GLY0-0.053-0.0284.919-0.828-0.821-0.001-0.001-0.0040.000
77A85VAL0-0.048-0.0166.395-0.497-0.4970.0000.0000.0000.000
78A86PRO0-0.008-0.0016.5030.2300.2300.0000.0000.0000.000
79A87SER00.0790.0079.3930.1420.1420.0000.0000.0000.000
80A88GLN00.0260.01413.0340.0810.0810.0000.0000.0000.000
81A89LYS10.8870.9476.9240.7290.7290.0000.0000.0000.000
82A90ILE0-0.0200.01611.6120.1520.1520.0000.0000.0000.000
83A91ASP-1-0.925-0.97712.945-0.097-0.0970.0000.0000.0000.000
84A92HIS0-0.020-0.01414.6750.0280.0280.0000.0000.0000.000
85A93THR0-0.031-0.04713.2800.0950.0950.0000.0000.0000.000
86A94MET0-0.072-0.02515.5510.0190.0190.0000.0000.0000.000
87A95ASP-1-0.936-0.97418.2400.0160.0160.0000.0000.0000.000
88A96ILE0-0.0320.00518.3180.0030.0030.0000.0000.0000.000
89A97ILE0-0.062-0.00817.4800.0080.0080.0000.0000.0000.000
90A98ASN00.0030.02620.847-0.006-0.0060.0000.0000.0000.000
91A99THR0-0.047-0.02824.2810.0020.0020.0000.0000.0000.000
92A100ILE0-0.055-0.01623.117-0.001-0.0010.0000.0000.0000.000
93A111ALA00.0300.02024.508-0.001-0.0010.0000.0000.0000.000
94A112THR00.014-0.01119.464-0.020-0.0200.0000.0000.0000.000
95A113ARG10.8960.94420.910-0.107-0.1070.0000.0000.0000.000
96A114GLU-1-0.755-0.88115.6980.1210.1210.0000.0000.0000.000
97A115ALA00.0620.02319.0920.0420.0420.0000.0000.0000.000
98A116MET0-0.016-0.01621.4470.0130.0130.0000.0000.0000.000
99A117VAL0-0.0450.00219.0660.0050.0050.0000.0000.0000.000
100A118VAL00.019-0.00117.8600.0210.0210.0000.0000.0000.000
101A119GLN00.0270.01520.7160.0010.0010.0000.0000.0000.000
102A120ASP-1-0.761-0.89124.4310.1750.1750.0000.0000.0000.000
103A121ALA00.0020.00921.361-0.005-0.0050.0000.0000.0000.000
104A122ASP-1-0.794-0.92123.2100.2520.2520.0000.0000.0000.000
105A123ARG10.9200.97224.570-0.161-0.1610.0000.0000.0000.000
106A124LEU0-0.043-0.03425.859-0.014-0.0140.0000.0000.0000.000
107A125ASP-1-0.810-0.91425.6280.2550.2550.0000.0000.0000.000
108A126ALA0-0.060-0.02527.697-0.007-0.0070.0000.0000.0000.000
109A127LEU00.0170.00530.860-0.014-0.0140.0000.0000.0000.000
110A128GLY00.010-0.01831.2450.0140.0140.0000.0000.0000.000
111A129ALA00.0320.00732.970-0.006-0.0060.0000.0000.0000.000
112A130ILE0-0.0090.00128.200-0.008-0.0080.0000.0000.0000.000
113A131GLY00.0550.04132.143-0.004-0.0040.0000.0000.0000.000
114A132ILE00.0110.01033.552-0.008-0.0080.0000.0000.0000.000
115A133ALA0-0.030-0.01434.618-0.007-0.0070.0000.0000.0000.000
116A134ARG10.8840.91828.122-0.201-0.2010.0000.0000.0000.000
117A135THR00.0210.01235.057-0.005-0.0050.0000.0000.0000.000
118A136PHE0-0.004-0.01337.991-0.006-0.0060.0000.0000.0000.000
119A137ALA0-0.048-0.00436.833-0.005-0.0050.0000.0000.0000.000
120A138TYR00.0300.00133.185-0.002-0.0020.0000.0000.0000.000
121A139SER0-0.008-0.00238.997-0.007-0.0070.0000.0000.0000.000
122A140GLY00.0100.00642.155-0.005-0.0050.0000.0000.0000.000
123A141ASN0-0.055-0.02539.769-0.005-0.0050.0000.0000.0000.000
124A142LYN00.0030.12641.170-0.003-0.0030.0000.0000.0000.000
125A143GLY0-0.0190.01643.807-0.004-0.0040.0000.0000.0000.000
126A144GLN0-0.056-0.02244.350-0.001-0.0010.0000.0000.0000.000
127A145PRO0-0.019-0.00547.4610.0020.0020.0000.0000.0000.000
128A146ILE00.019-0.00945.4070.0020.0020.0000.0000.0000.000
129A147TYR00.008-0.03646.9110.0030.0030.0000.0000.0000.000
130A148ASP-1-0.848-0.92749.6180.0530.0530.0000.0000.0000.000
131A149PRO0-0.031-0.00852.8930.0000.0000.0000.0000.0000.000
132A150GLU-1-0.952-0.96454.9520.0430.0430.0000.0000.0000.000
133A151LEU0-0.068-0.02251.209-0.001-0.0010.0000.0000.0000.000
134A152PRO0-0.046-0.01253.4230.0010.0010.0000.0000.0000.000
135A153ILE00.008-0.00948.3850.0020.0020.0000.0000.0000.000
136A154ARG10.8820.94746.777-0.065-0.0650.0000.0000.0000.000
137A155GLU-1-0.853-0.90548.4750.0540.0540.0000.0000.0000.000
138A156THR0-0.097-0.07349.310-0.002-0.0020.0000.0000.0000.000
139A157MET0-0.043-0.02042.8110.0010.0010.0000.0000.0000.000
140A158THR0-0.075-0.06144.1280.0000.0000.0000.0000.0000.000
141A159VAL00.0140.02744.8370.0020.0020.0000.0000.0000.000
142A160GLU-1-0.926-0.97947.0560.0570.0570.0000.0000.0000.000
143A161GLU-1-0.822-0.91641.6960.0820.0820.0000.0000.0000.000
144A162TYR00.038-0.10639.3610.0010.0010.0000.0000.0000.000
145A163ARG10.8550.96344.564-0.050-0.0500.0000.0000.0000.000
146A164HIS0-0.068-0.06647.007-0.003-0.0030.0000.0000.0000.000
147A165GLY00.0200.01348.905-0.001-0.0010.0000.0000.0000.000
148A166LYS10.9320.97647.957-0.047-0.0470.0000.0000.0000.000
149A167SER00.0050.00945.675-0.002-0.0020.0000.0000.0000.000
150A168THR00.0110.01246.9270.0000.0000.0000.0000.0000.000
151A169ALA00.0720.04042.8580.0020.0020.0000.0000.0000.000
152A170ILE00.014-0.00143.0830.0040.0040.0000.0000.0000.000
153A171ASN00.0350.02244.5750.0030.0030.0000.0000.0000.000
154A172HIS00.0180.01537.4250.0020.0020.0000.0000.0000.000
155A173PHE0-0.042-0.02538.1360.0060.0060.0000.0000.0000.000
156A174TYR00.0390.01041.1930.0030.0030.0000.0000.0000.000
157A175GLU-1-0.888-0.94243.2220.0710.0710.0000.0000.0000.000
158A176LYS10.8840.92737.667-0.089-0.0890.0000.0000.0000.000
159A177LEU00.013-0.01034.7090.0030.0030.0000.0000.0000.000
160A178PHE00.006-0.03036.7790.0050.0050.0000.0000.0000.000
161A179LYS10.8980.98438.441-0.083-0.0830.0000.0000.0000.000
162A180LEU00.0190.00532.4550.0010.0010.0000.0000.0000.000
163A181LYN0-0.0270.00233.5370.0030.0030.0000.0000.0000.000
164A182ASP-1-0.932-0.97533.9830.0980.0980.0000.0000.0000.000
165A183LEU0-0.077-0.02733.110-0.001-0.0010.0000.0000.0000.000
166A184MET0-0.107-0.02228.8650.0130.0130.0000.0000.0000.000
167A185ASN0-0.052-0.03027.151-0.024-0.0240.0000.0000.0000.000
168A186THR0-0.035-0.00624.301-0.008-0.0080.0000.0000.0000.000
169A187GLU-1-0.883-0.93626.7790.1100.1100.0000.0000.0000.000
170A188THR0-0.054-0.04824.6710.0010.0010.0000.0000.0000.000
171A189GLY00.0300.01226.9780.0090.0090.0000.0000.0000.000
172A190LYS10.9940.99327.619-0.110-0.1100.0000.0000.0000.000
173A191GLN0-0.0100.00829.075-0.013-0.0130.0000.0000.0000.000
174A192LEU0-0.007-0.01524.933-0.004-0.0040.0000.0000.0000.000
175A193ALA00.0110.00129.597-0.004-0.0040.0000.0000.0000.000
176A194LYS10.9750.99431.717-0.116-0.1160.0000.0000.0000.000
177A195GLU-1-0.966-0.98631.1940.1690.1690.0000.0000.0000.000
178A196ARG10.8560.93326.618-0.223-0.2230.0000.0000.0000.000
179A197HIS00.0380.01533.799-0.002-0.0020.0000.0000.0000.000
180A198VAL00.0350.03036.762-0.006-0.0060.0000.0000.0000.000
181A199PHE00.0200.01735.778-0.004-0.0040.0000.0000.0000.000
182A200MET0-0.0370.02434.919-0.003-0.0030.0000.0000.0000.000
183A201GLU-1-0.894-0.94739.2710.0840.0840.0000.0000.0000.000
184A202GLN0-0.036-0.03041.102-0.003-0.0030.0000.0000.0000.000
185A203PHE0-0.042-0.03640.834-0.004-0.0040.0000.0000.0000.000
186A204ILE0-0.023-0.00742.336-0.004-0.0040.0000.0000.0000.000
187A205GLU-1-0.914-0.95444.7870.0700.0700.0000.0000.0000.000
188A206ARG10.9030.94445.811-0.082-0.0820.0000.0000.0000.000
189A207PHE00.0150.01345.921-0.002-0.0020.0000.0000.0000.000
190A208LEU00.0140.02047.915-0.003-0.0030.0000.0000.0000.000
191A209SER0-0.088-0.04650.326-0.003-0.0030.0000.0000.0000.000
192A210GLU-1-0.971-0.98948.6380.0750.0750.0000.0000.0000.000
193A211TRP0-0.033-0.00651.380-0.001-0.0010.0000.0000.0000.000
194A212ASN0-0.061-0.02253.595-0.003-0.0030.0000.0000.0000.000
195A213GLY0-0.014-0.00856.603-0.001-0.0010.0000.0000.0000.000