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: JQM39

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2153620.941101
FMO2-HF: Nuclear repulsion 2074222.028385
FMO2-HF: Total energy -79398.912716
FMO2-MP2: Total energy -79629.441408


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.
-22.471-18.5198.138-5.066-7.0240.037
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 : -0.008
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].
3A4GLN0-0.012-0.0053.289-2.7591.3320.149-2.129-2.1110.006
4A5ALA00.0240.0072.093-7.794-9.5457.779-2.598-3.4300.024
5A6ILE00.0200.0182.948-6.614-5.0780.212-0.332-1.4160.007
6A7LEU00.0530.0244.990-1.824-1.760-0.001-0.006-0.0570.000
7A8GLN0-0.019-0.0016.260-0.103-0.1030.0000.0000.0000.000
8A9SER0-0.038-0.0116.762-0.935-0.9350.0000.0000.0000.000
9A10ALA00.0510.0329.198-0.375-0.3750.0000.0000.0000.000
10A11GLU-1-1.006-1.01210.7540.9920.9920.0000.0000.0000.000
11A12ALA0-0.032-0.01412.343-0.160-0.1600.0000.0000.0000.000
12A13TRP0-0.042-0.01513.635-0.119-0.1190.0000.0000.0000.000
13A14VAL00.0550.02015.191-0.073-0.0730.0000.0000.0000.000
14A15LYS10.9310.98016.755-0.467-0.4670.0000.0000.0000.000
15A16LYS10.8810.92217.745-0.195-0.1950.0000.0000.0000.000
16A17GLN0-0.064-0.03219.697-0.042-0.0420.0000.0000.0000.000
17A18LEU00.0880.06321.011-0.012-0.0120.0000.0000.0000.000
18A19MET0-0.166-0.07722.5680.0060.0060.0000.0000.0000.000
19A20ASP-1-0.957-0.97924.5740.1100.1100.0000.0000.0000.000
20A21GLU-1-0.833-0.90827.1430.0960.0960.0000.0000.0000.000
21A22TYR0-0.056-0.03129.422-0.008-0.0080.0000.0000.0000.000
22A23SER0-0.037-0.00829.0080.0070.0070.0000.0000.0000.000
23A24GLY00.0450.01328.863-0.011-0.0110.0000.0000.0000.000
24A25HIS0-0.063-0.04427.6570.0240.0240.0000.0000.0000.000
25A26ASP-1-0.876-0.92325.4850.2120.2120.0000.0000.0000.000
26A27TRP00.1460.05216.2040.0100.0100.0000.0000.0000.000
27A28TYR0-0.050-0.03321.6050.0500.0500.0000.0000.0000.000
28A29HIS10.7790.91122.671-0.214-0.2140.0000.0000.0000.000
29A30ILE00.1080.06118.1700.0220.0220.0000.0000.0000.000
30A31ARG10.9210.98717.359-0.532-0.5320.0000.0000.0000.000
31A32ARG10.7580.84218.881-0.225-0.2250.0000.0000.0000.000
32A33VAL00.0160.04320.1510.0160.0160.0000.0000.0000.000
33A34THR00.032-0.00414.5660.0160.0160.0000.0000.0000.000
34A35LEU0-0.061-0.04716.0840.0410.0410.0000.0000.0000.000
35A36MET0-0.057-0.00717.913-0.006-0.0060.0000.0000.0000.000
36A37ALA00.0780.03217.586-0.020-0.0200.0000.0000.0000.000
37A38LYS10.8730.92712.779-1.086-1.0860.0000.0000.0000.000
38A39ALA0-0.0370.00616.425-0.043-0.0430.0000.0000.0000.000
39A40ILE0-0.025-0.03819.116-0.036-0.0360.0000.0000.0000.000
40A41GLY00.0600.03017.369-0.046-0.0460.0000.0000.0000.000
41A42GLU-1-0.832-0.91314.8100.7710.7710.0000.0000.0000.000
42A43GLN0-0.021-0.00917.525-0.043-0.0430.0000.0000.0000.000
43A44GLU-1-0.777-0.88820.6210.1390.1390.0000.0000.0000.000
44A45LYS10.7310.86617.515-0.319-0.3190.0000.0000.0000.000
45A46VAL00.0120.03016.824-0.050-0.0500.0000.0000.0000.000
46A47ASP-1-0.784-0.91510.993-0.065-0.0650.0000.0000.0000.000
47A48VAL0-0.040-0.04512.0790.0270.0270.0000.0000.0000.000
48A49PHE00.0010.0136.4060.0550.0550.0000.0000.0000.000
49A50VAL00.0380.03410.5460.1320.1320.0000.0000.0000.000
50A51VAL0-0.0040.01513.0660.0480.0480.0000.0000.0000.000
51A52GLN0-0.001-0.01211.3980.0920.0920.0000.0000.0000.000
52A53ILE0-0.012-0.0118.4890.0470.0470.0000.0000.0000.000
53A54ALA0-0.002-0.00212.577-0.067-0.0670.0000.0000.0000.000
54A55ALA0-0.014-0.01916.239-0.028-0.0280.0000.0000.0000.000
55A56LEU0-0.056-0.03112.093-0.016-0.0160.0000.0000.0000.000
56A57PHE00.014-0.02613.174-0.014-0.0140.0000.0000.0000.000
57A58HIS0-0.084-0.03518.050-0.058-0.0580.0000.0000.0000.000
58A59ASP-1-0.829-0.90320.8490.2120.2120.0000.0000.0000.000
59A60LEU0-0.054-0.03618.552-0.021-0.0210.0000.0000.0000.000
60A61ILE0-0.0190.00321.634-0.015-0.0150.0000.0000.0000.000
61A62ASP-1-0.970-0.97624.7660.0540.0540.0000.0000.0000.000
62A70GLU-1-0.838-0.93126.200-0.015-0.0150.0000.0000.0000.000
63A71THR00.003-0.01724.101-0.011-0.0110.0000.0000.0000.000
64A72ALA00.0070.01922.717-0.010-0.0100.0000.0000.0000.000
65A73LYS10.9820.99920.1660.1390.1390.0000.0000.0000.000
66A74GLN0-0.083-0.06119.1990.0100.0100.0000.0000.0000.000
67A75GLN00.0420.01818.389-0.006-0.0060.0000.0000.0000.000
68A76LEU0-0.019-0.01015.776-0.011-0.0110.0000.0000.0000.000
69A77ILE0-0.020-0.01614.512-0.031-0.0310.0000.0000.0000.000
70A78ASP-1-0.822-0.89314.746-0.314-0.3140.0000.0000.0000.000
71A79TRP0-0.030-0.0228.923-0.093-0.0930.0000.0000.0000.000
72A80MET0-0.020-0.0139.958-0.008-0.0080.0000.0000.0000.000
73A81GLU-1-0.873-0.9469.513-0.816-0.8160.0000.0000.0000.000
74A82ALA0-0.115-0.04210.161-0.241-0.2410.0000.0000.0000.000
75A83ALA0-0.022-0.0166.248-0.051-0.0510.0000.0000.0000.000
76A84GLY0-0.071-0.0314.967-1.173-1.161-0.001-0.001-0.0100.000
77A85VAL0-0.036-0.0146.389-0.451-0.4510.0000.0000.0000.000
78A86PRO00.0060.0056.4260.3360.3360.0000.0000.0000.000
79A87SER00.0630.0109.3740.1450.1450.0000.0000.0000.000
80A88GLN00.0160.01013.0140.0730.0730.0000.0000.0000.000
81A89LYS10.8430.9087.5400.8370.8370.0000.0000.0000.000
82A90ILE0-0.0140.01511.5170.1700.1700.0000.0000.0000.000
83A91ASP-1-0.906-0.96412.918-0.257-0.2570.0000.0000.0000.000
84A92HIS0-0.048-0.03714.7920.0400.0400.0000.0000.0000.000
85A93THR0-0.063-0.05913.1840.0890.0890.0000.0000.0000.000
86A94MET0-0.026-0.00715.5490.0420.0420.0000.0000.0000.000
87A95ASP-1-0.890-0.94218.353-0.074-0.0740.0000.0000.0000.000
88A96ILE0-0.039-0.01318.5540.0170.0170.0000.0000.0000.000
89A97ILE0-0.084-0.01417.9260.0150.0150.0000.0000.0000.000
90A98ASN0-0.027-0.01021.4270.0070.0070.0000.0000.0000.000
91A99THR0-0.034-0.00524.5150.0120.0120.0000.0000.0000.000
92A100ILE0-0.037-0.01223.7530.0080.0080.0000.0000.0000.000
93A111ALA00.0290.01224.5070.0050.0050.0000.0000.0000.000
94A112THR00.0340.00219.765-0.017-0.0170.0000.0000.0000.000
95A113ARG10.8470.91221.150-0.104-0.1040.0000.0000.0000.000
96A114GLU-1-0.792-0.91115.9000.0720.0720.0000.0000.0000.000
97A115ALA00.0560.02519.1290.0420.0420.0000.0000.0000.000
98A116MET0-0.016-0.01221.6830.0190.0190.0000.0000.0000.000
99A117VAL0-0.0240.01019.4070.0140.0140.0000.0000.0000.000
100A118VAL00.005-0.00518.3790.0290.0290.0000.0000.0000.000
101A119GLN00.0150.00121.0960.0040.0040.0000.0000.0000.000
102A120ASP-1-0.748-0.85324.7910.1640.1640.0000.0000.0000.000
103A121ALA00.0110.01221.5900.0000.0000.0000.0000.0000.000
104A122ASP-1-0.766-0.90523.4990.2180.2180.0000.0000.0000.000
105A123ARG10.8950.95924.932-0.133-0.1330.0000.0000.0000.000
106A124LEU0-0.024-0.01525.618-0.010-0.0100.0000.0000.0000.000
107A125ASP-1-0.787-0.87325.9430.2570.2570.0000.0000.0000.000
108A126ALA0-0.043-0.01227.970-0.006-0.0060.0000.0000.0000.000
109A127LEU00.0160.01031.126-0.012-0.0120.0000.0000.0000.000
110A128GLY00.030-0.02631.4570.0160.0160.0000.0000.0000.000
111A129ALA00.0110.00333.109-0.008-0.0080.0000.0000.0000.000
112A130ILE0-0.0010.00128.090-0.009-0.0090.0000.0000.0000.000
113A131GLY00.0520.04232.335-0.007-0.0070.0000.0000.0000.000
114A132ILE0-0.0010.00133.796-0.009-0.0090.0000.0000.0000.000
115A133ALA0-0.023-0.01234.832-0.008-0.0080.0000.0000.0000.000
116A134ARG10.8770.90929.121-0.191-0.1910.0000.0000.0000.000
117A135THR00.0180.01135.338-0.008-0.0080.0000.0000.0000.000
118A136PHE00.0110.00138.292-0.007-0.0070.0000.0000.0000.000
119A137ALA0-0.037-0.00137.103-0.005-0.0050.0000.0000.0000.000
120A138TYR00.0270.00133.515-0.002-0.0020.0000.0000.0000.000
121A139SER0-0.020-0.02039.347-0.007-0.0070.0000.0000.0000.000
122A140GLY00.0200.01242.473-0.005-0.0050.0000.0000.0000.000
123A141ASN0-0.065-0.02740.383-0.003-0.0030.0000.0000.0000.000
124A142LYN0-0.0420.00141.063-0.005-0.0050.0000.0000.0000.000
125A143GLY0-0.0200.01544.200-0.005-0.0050.0000.0000.0000.000
126A144GLN0-0.037-0.01144.951-0.001-0.0010.0000.0000.0000.000
127A145PRO0-0.0010.00147.7920.0030.0030.0000.0000.0000.000
128A146ILE00.002-0.01345.7770.0020.0020.0000.0000.0000.000
129A147TYR00.010-0.03047.1940.0030.0030.0000.0000.0000.000
130A148ASP-1-0.856-0.93149.9000.0500.0500.0000.0000.0000.000
131A149PRO0-0.042-0.00953.1910.0000.0000.0000.0000.0000.000
132A150GLU-1-0.950-0.96555.2320.0420.0420.0000.0000.0000.000
133A151LEU0-0.067-0.02451.451-0.002-0.0020.0000.0000.0000.000
134A152PRO0-0.019-0.00353.7480.0020.0020.0000.0000.0000.000
135A153ILE0-0.010-0.01648.6650.0020.0020.0000.0000.0000.000
136A154ARG10.8010.88946.632-0.057-0.0570.0000.0000.0000.000
137A155GLU-1-0.862-0.90348.8540.0460.0460.0000.0000.0000.000
138A156THR0-0.099-0.07449.498-0.002-0.0020.0000.0000.0000.000
139A157MET0-0.028-0.01443.3600.0010.0010.0000.0000.0000.000
140A158THR0-0.064-0.04144.973-0.001-0.0010.0000.0000.0000.000
141A159VAL00.0060.01645.3360.0010.0010.0000.0000.0000.000
142A160GLU-1-0.874-0.94947.5630.0450.0450.0000.0000.0000.000
143A161GLU-1-0.777-0.87941.4090.0670.0670.0000.0000.0000.000
144A162TYR00.056-0.01539.9610.0010.0010.0000.0000.0000.000
145A163ARG10.8860.96745.037-0.036-0.0360.0000.0000.0000.000
146A164HIS0-0.073-0.06447.510-0.003-0.0030.0000.0000.0000.000
147A165GLY00.0070.00749.3610.0000.0000.0000.0000.0000.000
148A166LYS10.9130.97248.388-0.041-0.0410.0000.0000.0000.000
149A167SER00.021-0.00346.245-0.001-0.0010.0000.0000.0000.000
150A168THR0-0.027-0.01947.3370.0010.0010.0000.0000.0000.000
151A169ALA00.0580.03443.0990.0020.0020.0000.0000.0000.000
152A170ILE00.0220.00743.3880.0040.0040.0000.0000.0000.000
153A171ASN00.0210.02344.8650.0030.0030.0000.0000.0000.000
154A172HIS00.0490.02637.597-0.001-0.0010.0000.0000.0000.000
155A173PHE0-0.022-0.01638.4240.0050.0050.0000.0000.0000.000
156A174TYR00.0400.01741.4880.0020.0020.0000.0000.0000.000
157A175GLU-1-0.829-0.88443.5120.0630.0630.0000.0000.0000.000
158A176LYS10.8630.91238.075-0.076-0.0760.0000.0000.0000.000
159A177LEU00.0160.00535.1240.0030.0030.0000.0000.0000.000
160A178PHE00.017-0.01837.0760.0060.0060.0000.0000.0000.000
161A179LYS10.8110.94238.777-0.075-0.0750.0000.0000.0000.000
162A180LEU00.0480.00133.030-0.001-0.0010.0000.0000.0000.000
163A181LYN0-0.0200.00833.7800.0030.0030.0000.0000.0000.000
164A182ASP-1-0.923-0.96634.2350.0950.0950.0000.0000.0000.000
165A183LEU0-0.024-0.01333.525-0.002-0.0020.0000.0000.0000.000
166A184MET0-0.0740.00829.0340.0080.0080.0000.0000.0000.000
167A185ASN0-0.073-0.05727.463-0.023-0.0230.0000.0000.0000.000
168A186THR0-0.061-0.03224.037-0.004-0.0040.0000.0000.0000.000
169A187GLU-1-0.870-0.93126.8350.1180.1180.0000.0000.0000.000
170A188THR0-0.054-0.04124.6050.0060.0060.0000.0000.0000.000
171A189GLY00.0240.01027.1630.0100.0100.0000.0000.0000.000
172A190LYS10.8900.93527.805-0.113-0.1130.0000.0000.0000.000
173A191GLN0-0.0020.01029.361-0.013-0.0130.0000.0000.0000.000
174A192LEU00.005-0.00925.052-0.002-0.0020.0000.0000.0000.000
175A193ALA00.0200.00029.711-0.005-0.0050.0000.0000.0000.000
176A194LYS10.9730.99331.898-0.128-0.1280.0000.0000.0000.000
177A195GLU-1-0.976-0.98830.8340.2050.2050.0000.0000.0000.000
178A196ARG10.8680.93026.425-0.245-0.2450.0000.0000.0000.000
179A197HIS0-0.019-0.01333.936-0.002-0.0020.0000.0000.0000.000
180A198VAL00.0250.01837.035-0.006-0.0060.0000.0000.0000.000
181A199PHE00.0220.02236.356-0.005-0.0050.0000.0000.0000.000
182A200MET0-0.0190.03035.973-0.002-0.0020.0000.0000.0000.000
183A201GLU-1-0.867-0.92939.4540.0900.0900.0000.0000.0000.000
184A202GLN0-0.067-0.04041.399-0.002-0.0020.0000.0000.0000.000
185A203PHE0-0.021-0.02640.898-0.004-0.0040.0000.0000.0000.000
186A204ILE0-0.009-0.00842.575-0.005-0.0050.0000.0000.0000.000
187A205GLU-1-0.825-0.88344.9650.0820.0820.0000.0000.0000.000
188A206ARG10.8080.89545.912-0.093-0.0930.0000.0000.0000.000
189A207PHE00.0160.01446.075-0.003-0.0030.0000.0000.0000.000
190A208LEU00.0180.01148.071-0.004-0.0040.0000.0000.0000.000
191A209SER0-0.075-0.05350.500-0.003-0.0030.0000.0000.0000.000
192A210GLU-1-0.971-0.98549.0600.0840.0840.0000.0000.0000.000
193A211TRP0-0.029-0.00651.440-0.001-0.0010.0000.0000.0000.000
194A212ASN0-0.079-0.03653.769-0.004-0.0040.0000.0000.0000.000
195A213GLY00.0040.00556.769-0.001-0.0010.0000.0000.0000.000