FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: Q1LMY

Calculation Name: 3DR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NRD3

Base Structure: X-ray

Registration Date: 2023-03-14

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357614.428109
FMO2-HF: Nuclear repulsion 2276788.919259
FMO2-HF: Total energy -80825.50885
FMO2-MP2: Total energy -81063.540788


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:3:ASN)


Summations of interaction energy for fragment #1(A:3: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.
-18.354-11.6553.366-4.718-5.348-0.041
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.011
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].
3A5PHE00.0440.0303.349-3.546-0.4110.000-1.539-1.5970.003
4A6GLU-1-0.827-0.9312.213-14.883-11.6383.367-3.159-3.453-0.044
5A7TYR00.0060.0544.7270.2010.520-0.001-0.020-0.2980.000
6A8LEU00.0020.0106.680-0.267-0.2670.0000.0000.0000.000
7A9ARG10.9540.9756.7350.4330.4330.0000.0000.0000.000
8A10THR0-0.031-0.0418.169-0.025-0.0250.0000.0000.0000.000
9A11TYR0-0.040-0.00610.648-0.061-0.0610.0000.0000.0000.000
10A12VAL00.0320.00012.600-0.071-0.0710.0000.0000.0000.000
11A13GLU-1-0.910-0.96513.0190.0130.0130.0000.0000.0000.000
12A14SER0-0.140-0.07914.238-0.018-0.0180.0000.0000.0000.000
13A15THR0-0.046-0.02616.211-0.014-0.0140.0000.0000.0000.000
14A16THR0-0.052-0.01217.757-0.023-0.0230.0000.0000.0000.000
15A17GLU-1-0.992-0.99120.0790.1190.1190.0000.0000.0000.000
16A18THR0-0.030-0.01521.957-0.010-0.0100.0000.0000.0000.000
17A19ASP-1-0.779-0.88724.0540.0680.0680.0000.0000.0000.000
18A20ALA0-0.002-0.01126.021-0.003-0.0030.0000.0000.0000.000
19A21ALA00.0140.00428.192-0.006-0.0060.0000.0000.0000.000
20A22VAL0-0.004-0.00622.953-0.008-0.0080.0000.0000.0000.000
21A23ALA0-0.022-0.01623.483-0.007-0.0070.0000.0000.0000.000
22A24ARG10.9090.95424.551-0.035-0.0350.0000.0000.0000.000
23A25ALA00.011-0.00625.885-0.007-0.0070.0000.0000.0000.000
24A26ARG10.8130.89418.095-0.034-0.0340.0000.0000.0000.000
25A27GLU-1-0.928-0.96222.5870.0110.0110.0000.0000.0000.000
26A28ASP-1-0.826-0.91024.4850.0110.0110.0000.0000.0000.000
27A29ALA0-0.054-0.04123.046-0.006-0.0060.0000.0000.0000.000
28A30ALA0-0.0130.00421.275-0.011-0.0110.0000.0000.0000.000
29A31GLU-1-0.942-0.96622.7750.0030.0030.0000.0000.0000.000
30A32PHE0-0.100-0.05226.164-0.002-0.0020.0000.0000.0000.000
31A33GLY0-0.042-0.00923.170-0.004-0.0040.0000.0000.0000.000
32A34LEU0-0.091-0.04723.675-0.006-0.0060.0000.0000.0000.000
33A35PRO0-0.005-0.00720.291-0.004-0.0040.0000.0000.0000.000
34A36ALA00.0310.00719.4140.0140.0140.0000.0000.0000.000
35A37PRO0-0.0060.00817.271-0.012-0.0120.0000.0000.0000.000
36A38ASP-1-0.794-0.88212.4230.0000.0000.0000.0000.0000.000
37A39GLU-1-0.738-0.85315.5990.1170.1170.0000.0000.0000.000
38A40MET00.0010.00711.7390.0110.0110.0000.0000.0000.000
39A41THR0-0.018-0.02815.0650.0100.0100.0000.0000.0000.000
40A42GLY00.0070.00117.212-0.001-0.0010.0000.0000.0000.000
41A43GLN0-0.005-0.01218.3760.0070.0070.0000.0000.0000.000
42A44LEU0-0.0110.00418.668-0.001-0.0010.0000.0000.0000.000
43A45LEU0-0.035-0.02520.743-0.007-0.0070.0000.0000.0000.000
44A46THR00.003-0.01323.373-0.003-0.0030.0000.0000.0000.000
45A47THR0-0.030-0.01022.9150.0000.0000.0000.0000.0000.000
46A48LEU0-0.012-0.00623.421-0.005-0.0050.0000.0000.0000.000
47A49ALA0-0.0150.01726.618-0.005-0.0050.0000.0000.0000.000
48A50ALA00.0050.00828.441-0.003-0.0030.0000.0000.0000.000
49A51THR0-0.110-0.04927.395-0.003-0.0030.0000.0000.0000.000
50A52THR0-0.040-0.03129.637-0.005-0.0050.0000.0000.0000.000
51A53ASN00.027-0.00532.0410.0010.0010.0000.0000.0000.000
52A54GLY00.0520.03435.834-0.002-0.0020.0000.0000.0000.000
53A55ASN0-0.056-0.03537.557-0.004-0.0040.0000.0000.0000.000
54A56GLY0-0.035-0.01740.735-0.001-0.0010.0000.0000.0000.000
55A57SER0-0.086-0.05336.550-0.003-0.0030.0000.0000.0000.000
56A58THR00.009-0.00739.1000.0000.0000.0000.0000.0000.000
57A59GLY00.0300.01736.0250.0010.0010.0000.0000.0000.000
58A60ALA0-0.0190.00130.9160.0000.0000.0000.0000.0000.000
59A61ILE0-0.016-0.00931.753-0.002-0.0020.0000.0000.0000.000
60A62ALA00.0030.01128.4520.0010.0010.0000.0000.0000.000
61A63ILE0-0.032-0.03128.710-0.002-0.0020.0000.0000.0000.000
62A64THR00.0400.00724.646-0.004-0.0040.0000.0000.0000.000
63A65PRO00.0550.02925.8020.0040.0040.0000.0000.0000.000
64A66ALA00.0360.03424.5130.0030.0030.0000.0000.0000.000
65A67ALA0-0.021-0.02626.1010.0040.0040.0000.0000.0000.000
66A68GLY00.0280.01128.6800.0040.0040.0000.0000.0000.000
67A69LEU00.0470.03020.8700.0040.0040.0000.0000.0000.000
68A70VAL00.001-0.00423.0990.0060.0060.0000.0000.0000.000
69A71GLY00.021-0.01925.0980.0060.0060.0000.0000.0000.000
70A72LEU00.0090.00926.9230.0030.0030.0000.0000.0000.000
71A73TYR0-0.046-0.02820.463-0.004-0.0040.0000.0000.0000.000
72A74ILE0-0.008-0.00125.7480.0040.0040.0000.0000.0000.000
73A75LEU0-0.064-0.04628.1040.0010.0010.0000.0000.0000.000
74A76ASN00.0150.02126.440-0.003-0.0030.0000.0000.0000.000
75A77GLY0-0.023-0.00129.3790.0030.0030.0000.0000.0000.000
76A78LEU0-0.058-0.02930.223-0.002-0.0020.0000.0000.0000.000
77A79ALA00.0310.03032.9380.0010.0010.0000.0000.0000.000
78A80ASP-1-0.882-0.95036.4540.0400.0400.0000.0000.0000.000
79A81ASN0-0.120-0.05238.843-0.001-0.0010.0000.0000.0000.000
80A82THR00.0050.00536.599-0.002-0.0020.0000.0000.0000.000
81A83THR0-0.047-0.02837.7170.0000.0000.0000.0000.0000.000
82A84LEU00.0300.03430.8020.0000.0000.0000.0000.0000.000
83A85THR0-0.038-0.03734.461-0.002-0.0020.0000.0000.0000.000
84A86CYS0-0.021-0.00232.5740.0000.0000.0000.0000.0000.000
85A87ILE0-0.017-0.01232.3830.0000.0000.0000.0000.0000.000
86A88ASP-1-0.744-0.87131.134-0.016-0.0160.0000.0000.0000.000
87A89PRO0-0.036-0.01833.0190.0030.0030.0000.0000.0000.000
88A90GLU-1-0.843-0.90833.156-0.016-0.0160.0000.0000.0000.000
89A91SER0-0.036-0.03035.4730.0020.0020.0000.0000.0000.000
90A92GLU-1-0.918-0.96433.391-0.008-0.0080.0000.0000.0000.000
91A93HIS10.9150.94130.1130.0180.0180.0000.0000.0000.000
92A94GLN00.0230.02633.0280.0040.0040.0000.0000.0000.000
93A95ARG10.8760.92035.803-0.005-0.0050.0000.0000.0000.000
94A96GLN00.0540.02330.4600.0020.0020.0000.0000.0000.000
95A97ALA00.0110.01531.7640.0030.0030.0000.0000.0000.000
96A98LYS10.8920.93732.723-0.008-0.0080.0000.0000.0000.000
97A99ALA0-0.059-0.01734.5160.0020.0020.0000.0000.0000.000
98A100LEU00.0960.07028.7160.0030.0030.0000.0000.0000.000
99A101PHE0-0.036-0.02130.5740.0030.0030.0000.0000.0000.000
100A102ARG10.9080.95734.272-0.020-0.0200.0000.0000.0000.000
101A103GLU-1-0.969-0.98733.6270.0310.0310.0000.0000.0000.000
102A104ALA00.0310.03232.0100.0040.0040.0000.0000.0000.000
103A105GLY0-0.008-0.00433.924-0.002-0.0020.0000.0000.0000.000
104A106TYR0-0.036-0.01831.315-0.002-0.0020.0000.0000.0000.000
105A107SER0-0.012-0.03037.302-0.003-0.0030.0000.0000.0000.000
106A108PRO00.024-0.01839.4210.0000.0000.0000.0000.0000.000
107A109SER0-0.0240.01941.100-0.001-0.0010.0000.0000.0000.000
108A110ARG10.9200.97435.543-0.036-0.0360.0000.0000.0000.000
109A111VAL00.0240.02734.9110.0000.0000.0000.0000.0000.000
110A112ARG10.9130.97337.065-0.013-0.0130.0000.0000.0000.000
111A113PHE0-0.009-0.01333.1510.0010.0010.0000.0000.0000.000
112A114LEU0-0.021-0.00836.9650.0000.0000.0000.0000.0000.000
113A115LEU0-0.009-0.00837.138-0.001-0.0010.0000.0000.0000.000
114A116SER0-0.024-0.01937.1760.0000.0000.0000.0000.0000.000
115A117ARG10.9881.01335.3880.0170.0170.0000.0000.0000.000
116A118PRO00.0610.00431.5420.0020.0020.0000.0000.0000.000
117A119LEU00.011-0.01432.8880.0020.0020.0000.0000.0000.000
118A120ASP-1-0.897-0.92036.104-0.011-0.0110.0000.0000.0000.000
119A121VAL0-0.019-0.02737.3760.0010.0010.0000.0000.0000.000
120A122MET00.0200.02132.8690.0020.0020.0000.0000.0000.000
121A123SER0-0.040-0.00838.2820.0010.0010.0000.0000.0000.000
122A124ARG10.8750.91741.4520.0030.0030.0000.0000.0000.000
123A125LEU0-0.0460.00637.6250.0010.0010.0000.0000.0000.000
124A126ALA00.0060.00241.613-0.001-0.0010.0000.0000.0000.000
125A127ASN00.0470.00040.7260.0010.0010.0000.0000.0000.000
126A128ASP-1-0.926-0.97139.4830.0160.0160.0000.0000.0000.000
127A129SER0-0.0030.01139.4010.0010.0010.0000.0000.0000.000
128A130TYR0-0.016-0.00434.7340.0010.0010.0000.0000.0000.000
129A131GLN00.0750.06132.591-0.004-0.0040.0000.0000.0000.000
130A132LEU00.008-0.00326.6390.0030.0030.0000.0000.0000.000
131A133VAL0-0.0110.00329.331-0.002-0.0020.0000.0000.0000.000
132A134PHE00.0450.03021.4400.0020.0020.0000.0000.0000.000
133A135GLY00.002-0.00725.350-0.002-0.0020.0000.0000.0000.000
134A136GLN0-0.032-0.01719.9560.0080.0080.0000.0000.0000.000
135A137VAL0-0.023-0.02124.3910.0000.0000.0000.0000.0000.000
136A138SER00.0450.02324.059-0.007-0.0070.0000.0000.0000.000
137A139PRO00.0620.01522.6850.0070.0070.0000.0000.0000.000
138A140MET0-0.036-0.02324.8030.0030.0030.0000.0000.0000.000
139A141ASP-1-0.922-0.95328.050-0.026-0.0260.0000.0000.0000.000
140A142LEU0-0.033-0.00823.0440.0050.0050.0000.0000.0000.000
141A143LYS10.9810.99727.6590.0200.0200.0000.0000.0000.000
142A144ALA00.0260.01730.3910.0030.0030.0000.0000.0000.000
143A145LEU00.009-0.00427.6030.0030.0030.0000.0000.0000.000
144A146VAL00.0070.01028.5000.0040.0040.0000.0000.0000.000
145A147ASP-1-0.864-0.93131.147-0.007-0.0070.0000.0000.0000.000
146A148ALA0-0.054-0.02534.2750.0020.0020.0000.0000.0000.000
147A149ALA00.015-0.01331.7340.0020.0020.0000.0000.0000.000
148A150TRP0-0.0020.01230.6840.0030.0030.0000.0000.0000.000
149A151PRO0-0.017-0.00734.6490.0020.0020.0000.0000.0000.000
150A152LEU00.0220.01835.6360.0010.0010.0000.0000.0000.000
151A153LEU0-0.0100.01430.8050.0020.0020.0000.0000.0000.000
152A154ARG10.9070.97935.432-0.021-0.0210.0000.0000.0000.000
153A155ARG10.9080.93935.109-0.015-0.0150.0000.0000.0000.000
154A156GLY0-0.045-0.01833.2150.0010.0010.0000.0000.0000.000
155A157GLY0-0.021-0.00732.1220.0040.0040.0000.0000.0000.000
156A158ALA00.002-0.00326.8440.0000.0000.0000.0000.0000.000
157A159LEU00.0020.01827.043-0.001-0.0010.0000.0000.0000.000
158A160VAL0-0.017-0.02121.8730.0030.0030.0000.0000.0000.000
159A161LEU0-0.021-0.01622.798-0.005-0.0050.0000.0000.0000.000
160A162ALA00.0520.00819.3080.0040.0040.0000.0000.0000.000
161A163ASP-1-0.856-0.93916.262-0.084-0.0840.0000.0000.0000.000
162A164ALA0-0.0080.00217.707-0.010-0.0100.0000.0000.0000.000
163A165LEU0-0.035-0.00116.0510.0020.0020.0000.0000.0000.000
164A166LEU0-0.0100.00316.305-0.004-0.0040.0000.0000.0000.000
165A167ASP-1-0.861-0.95111.158-0.262-0.2620.0000.0000.0000.000
166A168GLY0-0.077-0.02912.2160.0170.0170.0000.0000.0000.000
167A169THR0-0.098-0.04914.633-0.014-0.0140.0000.0000.0000.000
168A170ILE0-0.061-0.03916.422-0.003-0.0030.0000.0000.0000.000
169A171ALA0-0.003-0.01718.6080.0010.0010.0000.0000.0000.000
170A172ASP-1-0.832-0.91917.436-0.151-0.1510.0000.0000.0000.000
171A173GLN0-0.053-0.02420.588-0.006-0.0060.0000.0000.0000.000
172A174THR0-0.024-0.01720.0220.0030.0030.0000.0000.0000.000
173A175ARG10.9740.99415.0750.1960.1960.0000.0000.0000.000
174A176LYS10.8890.95621.8030.0980.0980.0000.0000.0000.000
175A177ASP-1-0.806-0.90823.206-0.110-0.1100.0000.0000.0000.000
176A178ARG10.7700.85823.6930.0920.0920.0000.0000.0000.000
177A179ASP-1-0.763-0.88823.310-0.070-0.0700.0000.0000.0000.000
178A180THR00.0110.01321.1560.0090.0090.0000.0000.0000.000
179A181GLN0-0.044-0.01922.9230.0100.0100.0000.0000.0000.000
180A182ALA00.0120.02426.3000.0050.0050.0000.0000.0000.000
181A183ALA00.0410.00821.7240.0050.0050.0000.0000.0000.000
182A184ARG00.0290.03121.9840.0090.0090.0000.0000.0000.000
183A185ASP-1-0.919-0.95024.403-0.021-0.0210.0000.0000.0000.000
184A186ALA00.0200.01625.2310.0050.0050.0000.0000.0000.000
185A187ASP-1-0.812-0.89222.1430.0060.0060.0000.0000.0000.000
186A188GLU-1-0.991-1.00324.678-0.021-0.0210.0000.0000.0000.000
187A189TYR0-0.032-0.02227.4100.0030.0030.0000.0000.0000.000
188A190ILE0-0.006-0.00825.2230.0040.0040.0000.0000.0000.000
189A191ARG10.7870.86723.8500.0110.0110.0000.0000.0000.000
190A192SER0-0.082-0.03528.0060.0010.0010.0000.0000.0000.000
191A193ILE00.0020.01130.7920.0000.0000.0000.0000.0000.000
192A194GLU-1-0.928-0.96632.5450.0060.0060.0000.0000.0000.000
193A195GLY0-0.045-0.02134.9690.0000.0000.0000.0000.0000.000
194A196ALA00.0080.00630.1940.0020.0020.0000.0000.0000.000
195A197HIS0-0.052-0.02027.7430.0000.0000.0000.0000.0000.000
196A198VAL00.0310.00923.4100.0000.0000.0000.0000.0000.000
197A199ALA0-0.0190.00121.1710.0040.0040.0000.0000.0000.000
198A200ARG10.8670.93018.278-0.030-0.0300.0000.0000.0000.000
199A201LEU0-0.009-0.01215.7080.0210.0210.0000.0000.0000.000
200A202PRO00.0100.01010.172-0.031-0.0310.0000.0000.0000.000
201A203LEU00.000-0.00110.9160.0170.0170.0000.0000.0000.000
202A204GLY00.0340.02812.281-0.006-0.0060.0000.0000.0000.000
203A205ALA00.0230.02911.518-0.014-0.0140.0000.0000.0000.000
204A206GLY0-0.009-0.02513.5020.0150.0150.0000.0000.0000.000
205A207LEU0-0.021-0.00514.827-0.014-0.0140.0000.0000.0000.000
206A208THR00.0400.01217.7220.0160.0160.0000.0000.0000.000
207A209VAL0-0.025-0.01120.966-0.006-0.0060.0000.0000.0000.000
208A210VAL00.0320.00823.4330.0030.0030.0000.0000.0000.000
209A211THR0-0.033-0.02526.783-0.003-0.0030.0000.0000.0000.000
210A212LYS10.8520.92729.358-0.014-0.0140.0000.0000.0000.000
211A213ALA00.0390.03033.0440.0020.0020.0000.0000.0000.000
212A214LEU00.006-0.01434.188-0.002-0.0020.0000.0000.0000.000
213A215GLU-1-1.027-1.01137.1950.0130.0130.0000.0000.0000.000
214A216HIS00.0180.00234.8320.0010.0010.0000.0000.0000.000
215A217HIS00.0360.03239.836-0.002-0.0020.0000.0000.0000.000
216A218HIS0-0.020-0.00938.188-0.002-0.0020.0000.0000.0000.000