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: 2NL3R

Calculation Name: 1BDF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BDF

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7Z4

Base Structure: X-ray

Registration Date: 2023-09-22

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499285.911538
FMO2-HF: Nuclear repulsion 2410420.013876
FMO2-HF: Total energy -88865.897662
FMO2-MP2: Total energy -89125.792235


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:GLN)


Summations of interaction energy for fragment #1(A:2:GLN)
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.
-17.612-16.4519.554-5.012-5.7040.037
Interaction energy analysis for fragmet #1(A:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.032
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].
3A4SER0-0.005-0.0161.831-12.310-11.5119.455-4.959-5.2950.034
4A5VAL0-0.022-0.0073.598-3.878-3.5160.099-0.053-0.4090.003
5A6THR0-0.036-0.0146.555-0.955-0.9550.0000.0000.0000.000
6A7GLU-1-0.908-0.9437.8492.8722.8720.0000.0000.0000.000
7A8PHE00.0120.0107.185-0.420-0.4200.0000.0000.0000.000
8A9LEU0-0.015-0.01210.9110.0630.0630.0000.0000.0000.000
9A10LYS10.8440.90810.317-1.949-1.9490.0000.0000.0000.000
10A11PRO00.0340.03214.787-0.064-0.0640.0000.0000.0000.000
11A12ARG10.9350.95017.978-0.469-0.4690.0000.0000.0000.000
12A13LEU00.0180.00920.780-0.006-0.0060.0000.0000.0000.000
13A14VAL0-0.081-0.04624.1690.0130.0130.0000.0000.0000.000
14A15ASP-1-0.864-0.92326.6590.1770.1770.0000.0000.0000.000
15A16ILE0-0.035-0.02828.9430.0040.0040.0000.0000.0000.000
16A17GLU-1-0.771-0.86431.6190.1210.1210.0000.0000.0000.000
17A18GLN00.019-0.00834.466-0.003-0.0030.0000.0000.0000.000
18A19VAL0-0.040-0.00936.088-0.004-0.0040.0000.0000.0000.000
19A20SER0-0.014-0.01338.502-0.006-0.0060.0000.0000.0000.000
20A21SER0-0.016-0.01438.7960.0050.0050.0000.0000.0000.000
21A22THR00.0030.00837.915-0.002-0.0020.0000.0000.0000.000
22A23HIS0-0.055-0.01635.6830.0000.0000.0000.0000.0000.000
23A24ALA00.0010.01232.9840.0030.0030.0000.0000.0000.000
24A25LYS10.8180.90030.864-0.125-0.1250.0000.0000.0000.000
25A26VAL00.0150.02725.5960.0070.0070.0000.0000.0000.000
26A27THR0-0.032-0.01826.0120.0120.0120.0000.0000.0000.000
27A28LEU00.018-0.00120.3600.0140.0140.0000.0000.0000.000
28A29GLU-1-0.862-0.95021.9240.3700.3700.0000.0000.0000.000
29A30PRO0-0.016-0.02718.4340.0130.0130.0000.0000.0000.000
30A31LEU0-0.0150.01016.1120.0830.0830.0000.0000.0000.000
31A32GLU-1-0.728-0.83212.7331.0531.0530.0000.0000.0000.000
32A33ARG10.8220.88115.983-0.499-0.4990.0000.0000.0000.000
33A34GLY00.0260.02215.7700.0350.0350.0000.0000.0000.000
34A35PHE0-0.005-0.0019.677-0.082-0.0820.0000.0000.0000.000
35A36GLY00.0380.02815.390-0.046-0.0460.0000.0000.0000.000
36A37HIS00.0840.02119.037-0.015-0.0150.0000.0000.0000.000
37A38THR0-0.077-0.03213.139-0.058-0.0580.0000.0000.0000.000
38A39LEU00.0220.00013.856-0.050-0.0500.0000.0000.0000.000
39A40GLY00.0560.03217.226-0.031-0.0310.0000.0000.0000.000
40A41ASN0-0.030-0.01719.643-0.028-0.0280.0000.0000.0000.000
41A42ALA00.0090.01716.843-0.023-0.0230.0000.0000.0000.000
42A43LEU00.0360.01218.914-0.019-0.0190.0000.0000.0000.000
43A44ARG10.9350.97221.075-0.083-0.0830.0000.0000.0000.000
44A45ALA0-0.011-0.00121.639-0.010-0.0100.0000.0000.0000.000
45A46ILE0-0.0020.02520.197-0.013-0.0130.0000.0000.0000.000
46A47LEU00.025-0.02223.426-0.005-0.0050.0000.0000.0000.000
47A48LEU0-0.036-0.00726.221-0.001-0.0010.0000.0000.0000.000
48A49SER0-0.062-0.03825.619-0.012-0.0120.0000.0000.0000.000
49A50SER0-0.029-0.01824.856-0.014-0.0140.0000.0000.0000.000
50A51MET0-0.0360.02226.266-0.004-0.0040.0000.0000.0000.000
51A52PRO0-0.039-0.03427.724-0.002-0.0020.0000.0000.0000.000
52A53GLY00.0760.03530.860-0.001-0.0010.0000.0000.0000.000
53A54CYS0-0.031-0.01934.020-0.006-0.0060.0000.0000.0000.000
54A55ALA00.0380.02937.5950.0040.0040.0000.0000.0000.000
55A56VAL00.0110.00940.589-0.003-0.0030.0000.0000.0000.000
56A57THR0-0.058-0.04441.426-0.001-0.0010.0000.0000.0000.000
57A58GLU-1-0.836-0.91944.629-0.029-0.0290.0000.0000.0000.000
58A59VAL0-0.017-0.01848.1730.0030.0030.0000.0000.0000.000
59A60GLU-1-0.862-0.92451.335-0.014-0.0140.0000.0000.0000.000
60A61ILE00.0520.01454.6250.0020.0020.0000.0000.0000.000
61A62ASP-1-0.813-0.87657.351-0.009-0.0090.0000.0000.0000.000
62A63GLY0-0.040-0.02960.8610.0010.0010.0000.0000.0000.000
63A64VAL0-0.0230.00558.5270.0000.0000.0000.0000.0000.000
64A65LEU00.005-0.00159.996-0.001-0.0010.0000.0000.0000.000
65A66HIS0-0.002-0.01656.3020.0000.0000.0000.0000.0000.000
66A67GLU-1-0.858-0.94254.453-0.015-0.0150.0000.0000.0000.000
67A68TYR0-0.039-0.01657.0070.0010.0010.0000.0000.0000.000
68A69SER0-0.055-0.01660.3190.0000.0000.0000.0000.0000.000
69A70THR00.0720.03560.9520.0000.0000.0000.0000.0000.000
70A71LYS10.8550.91261.958-0.001-0.0010.0000.0000.0000.000
71A72GLU-1-0.892-0.94664.2650.0000.0000.0000.0000.0000.000
72A73GLY00.0180.00766.1860.0000.0000.0000.0000.0000.000
73A74VAL0-0.042-0.02360.4360.0010.0010.0000.0000.0000.000
74A75GLN0-0.068-0.03360.0370.0000.0000.0000.0000.0000.000
75A76GLU-1-0.755-0.84557.1860.0090.0090.0000.0000.0000.000
76A77ASP-1-0.856-0.93257.989-0.003-0.0030.0000.0000.0000.000
77A78ILE00.009-0.01056.1320.0010.0010.0000.0000.0000.000
78A79LEU0-0.010-0.00353.5960.0000.0000.0000.0000.0000.000
79A80GLU-1-0.898-0.94253.2800.0050.0050.0000.0000.0000.000
80A81ILE0-0.001-0.00453.4360.0010.0010.0000.0000.0000.000
81A82LEU0-0.024-0.01750.7340.0010.0010.0000.0000.0000.000
82A83LEU0-0.045-0.03048.5060.0000.0000.0000.0000.0000.000
83A84ASN0-0.026-0.01948.5920.0020.0020.0000.0000.0000.000
84A85LEU0-0.002-0.00448.3730.0020.0020.0000.0000.0000.000
85A86LYS10.8360.92544.5870.0060.0060.0000.0000.0000.000
86A87GLY0-0.023-0.00343.5070.0010.0010.0000.0000.0000.000
87A88LEU0-0.060-0.02044.9130.0040.0040.0000.0000.0000.000
88A89ALA00.0080.00541.090-0.002-0.0020.0000.0000.0000.000
89A90VAL0-0.031-0.02440.8960.0020.0020.0000.0000.0000.000
90A91ARG10.7720.86534.091-0.064-0.0640.0000.0000.0000.000
91A92VAL00.012-0.00537.3790.0000.0000.0000.0000.0000.000
92A93GLN0-0.030-0.03236.5180.0010.0010.0000.0000.0000.000
93A94GLY0-0.0120.00635.502-0.001-0.0010.0000.0000.0000.000
94A95LYN0-0.027-0.01636.575-0.006-0.0060.0000.0000.0000.000
95A96ASP-1-0.872-0.93034.721-0.024-0.0240.0000.0000.0000.000
96A97GLU-1-0.849-0.92737.524-0.031-0.0310.0000.0000.0000.000
97A98VAL00.0240.02241.2710.0000.0000.0000.0000.0000.000
98A99ILE0-0.011-0.00444.0270.0000.0000.0000.0000.0000.000
99A100LEU00.0520.03945.2490.0020.0020.0000.0000.0000.000
100A101THR0-0.021-0.01848.985-0.002-0.0020.0000.0000.0000.000
101A102LEU00.0310.02552.7090.0020.0020.0000.0000.0000.000
102A103ASN0-0.0060.01354.791-0.003-0.0030.0000.0000.0000.000
103A104LYS10.8400.91858.533-0.013-0.0130.0000.0000.0000.000
104A105SER00.015-0.00860.578-0.002-0.0020.0000.0000.0000.000
105A106GLY0-0.0050.01864.3090.0010.0010.0000.0000.0000.000
106A107ILE0-0.040-0.02064.9030.0000.0000.0000.0000.0000.000
107A108GLY00.0000.00363.1100.0010.0010.0000.0000.0000.000
108A109PRO0-0.019-0.00557.517-0.001-0.0010.0000.0000.0000.000
109A110VAL0-0.030-0.00655.9480.0000.0000.0000.0000.0000.000
110A111THR0-0.023-0.03753.0450.0010.0010.0000.0000.0000.000
111A112ALA00.0650.01548.431-0.002-0.0020.0000.0000.0000.000
112A113ALA0-0.024-0.01350.5280.0000.0000.0000.0000.0000.000
113A114ASP-1-0.806-0.87352.3290.0160.0160.0000.0000.0000.000
114A115ILE0-0.041-0.01548.951-0.003-0.0030.0000.0000.0000.000
115A116THR0-0.080-0.04852.0580.0010.0010.0000.0000.0000.000
116A117HIS0-0.015-0.01149.6710.0000.0000.0000.0000.0000.000
117A118ASP-1-0.831-0.92945.4700.0070.0070.0000.0000.0000.000
118A119GLY0-0.066-0.02546.0910.0030.0030.0000.0000.0000.000
119A120ASP-1-0.862-0.91441.3320.0130.0130.0000.0000.0000.000
120A121VAL0-0.041-0.02641.0810.0010.0010.0000.0000.0000.000
121A122GLU-1-0.846-0.90239.0610.0520.0520.0000.0000.0000.000
122A123ILE00.009-0.01342.125-0.001-0.0010.0000.0000.0000.000
123A124VAL0-0.0010.00739.6680.0020.0020.0000.0000.0000.000
124A125LYS10.8550.93042.752-0.025-0.0250.0000.0000.0000.000
125A126PRO00.0530.03045.757-0.004-0.0040.0000.0000.0000.000
126A127GLN00.006-0.01448.216-0.003-0.0030.0000.0000.0000.000
127A128HIS00.003-0.00147.6360.0030.0030.0000.0000.0000.000
128A129VAL0-0.024-0.01249.773-0.002-0.0020.0000.0000.0000.000
129A130ILE0-0.026-0.01050.171-0.001-0.0010.0000.0000.0000.000
130A131CYS0-0.037-0.01553.341-0.003-0.0030.0000.0000.0000.000
131A132HIS0-0.060-0.05057.1570.0040.0040.0000.0000.0000.000
132A133LEU0-0.0060.02260.545-0.002-0.0020.0000.0000.0000.000
133A134THR00.007-0.01263.6400.0010.0010.0000.0000.0000.000
134A135ASP-1-0.875-0.95266.9160.0050.0050.0000.0000.0000.000
135A136GLU-1-0.887-0.94968.3890.0110.0110.0000.0000.0000.000
136A137ASN0-0.090-0.04969.6020.0000.0000.0000.0000.0000.000
137A138ALA0-0.0420.01765.978-0.001-0.0010.0000.0000.0000.000
138A139SER00.015-0.01263.8530.0010.0010.0000.0000.0000.000
139A140ILE0-0.039-0.02157.927-0.001-0.0010.0000.0000.0000.000
140A141SER00.0080.00358.8070.0010.0010.0000.0000.0000.000
141A142MET0-0.0020.00153.971-0.001-0.0010.0000.0000.0000.000
142A143ARG10.7600.84452.0170.0090.0090.0000.0000.0000.000
143A144ILE00.003-0.00547.478-0.001-0.0010.0000.0000.0000.000
144A145LYS10.7730.90244.3440.0280.0280.0000.0000.0000.000
145A146VAL00.0130.00141.0350.0010.0010.0000.0000.0000.000
146A147GLN00.003-0.00639.352-0.001-0.0010.0000.0000.0000.000
147A148ARG10.7820.88033.1680.0070.0070.0000.0000.0000.000
148A149GLY00.0160.00134.423-0.006-0.0060.0000.0000.0000.000
149A150ARG10.8670.92425.7400.0570.0570.0000.0000.0000.000
150A151GLY00.0350.03131.850-0.004-0.0040.0000.0000.0000.000
151A152TYR0-0.015-0.00733.2210.0050.0050.0000.0000.0000.000
152A153VAL0-0.003-0.00136.480-0.005-0.0050.0000.0000.0000.000
153A154PRO00.0620.02138.9980.0020.0020.0000.0000.0000.000
154A155ALA00.0590.04142.693-0.004-0.0040.0000.0000.0000.000
155A156SER00.0200.00845.077-0.002-0.0020.0000.0000.0000.000
156A157THR0-0.126-0.07940.224-0.003-0.0030.0000.0000.0000.000
157A158ARG10.8280.91141.4440.0270.0270.0000.0000.0000.000
158A159ILE00.0100.02445.645-0.001-0.0010.0000.0000.0000.000
159A160HIS0-0.039-0.00346.7010.0030.0030.0000.0000.0000.000
160A161SER0-0.038-0.04949.5790.0010.0010.0000.0000.0000.000
161A162GLU-1-0.802-0.87052.446-0.026-0.0260.0000.0000.0000.000
162A163GLU-1-0.959-0.98952.664-0.038-0.0380.0000.0000.0000.000
163A164ASP-1-0.944-0.95655.831-0.030-0.0300.0000.0000.0000.000
164A165GLU-1-0.969-0.98659.114-0.021-0.0210.0000.0000.0000.000
165A166ARG10.7540.82259.5740.0250.0250.0000.0000.0000.000
166A167PRO0-0.0370.00757.636-0.001-0.0010.0000.0000.0000.000
167A168ILE00.0950.04052.9080.0010.0010.0000.0000.0000.000
168A169GLY00.0040.00855.3890.0020.0020.0000.0000.0000.000
169A170ARG10.7810.88454.6140.0140.0140.0000.0000.0000.000
170A171LEU00.001-0.00253.061-0.001-0.0010.0000.0000.0000.000
171A172LEU00.0380.04747.328-0.001-0.0010.0000.0000.0000.000
172A173VAL0-0.0100.00245.7770.0020.0020.0000.0000.0000.000
173A174ASP-1-0.843-0.90443.368-0.018-0.0180.0000.0000.0000.000
174A175ALA00.0610.04040.1040.0040.0040.0000.0000.0000.000
175A176CYS0-0.046-0.03338.772-0.004-0.0040.0000.0000.0000.000
176A177TYR00.004-0.00135.1190.0030.0030.0000.0000.0000.000
177A178SER0-0.012-0.00432.6440.0040.0040.0000.0000.0000.000
178A179PRO00.0040.01131.2270.0040.0040.0000.0000.0000.000
179A180VAL0-0.0360.00229.5550.0110.0110.0000.0000.0000.000
180A181GLU-1-0.792-0.88132.8910.0280.0280.0000.0000.0000.000
181A182ARG10.7490.82232.719-0.057-0.0570.0000.0000.0000.000
182A183ILE00.0180.01026.5490.0070.0070.0000.0000.0000.000
183A184ALA0-0.052-0.01929.006-0.009-0.0090.0000.0000.0000.000
184A185TYR0-0.053-0.04022.7630.0160.0160.0000.0000.0000.000
185A186ASN0-0.0190.00226.687-0.012-0.0120.0000.0000.0000.000
186A187VAL0-0.005-0.01621.5100.0120.0120.0000.0000.0000.000
187A188GLU-1-0.858-0.93023.9460.2320.2320.0000.0000.0000.000
188A189ALA00.0230.01724.7420.0190.0190.0000.0000.0000.000
189A190ALA00.0060.02023.248-0.021-0.0210.0000.0000.0000.000
190A191ARG10.8220.88725.351-0.321-0.3210.0000.0000.0000.000
191A192VAL00.0520.03522.210-0.010-0.0100.0000.0000.0000.000
192A193GLU-1-0.904-0.93625.0920.3090.3090.0000.0000.0000.000
193A194GLN0-0.082-0.04418.6700.0040.0040.0000.0000.0000.000
194A195ARG10.7800.83615.589-0.830-0.8300.0000.0000.0000.000
195A196THR00.0220.01422.995-0.048-0.0480.0000.0000.0000.000
196A197ASP-1-0.850-0.89820.7200.4380.4380.0000.0000.0000.000
197A198LEU0-0.0030.00418.2500.0830.0830.0000.0000.0000.000
198A199ASP-1-0.859-0.92620.2170.3280.3280.0000.0000.0000.000
199A200LYS10.8740.94121.486-0.215-0.2150.0000.0000.0000.000
200A201LEU0-0.047-0.00519.852-0.032-0.0320.0000.0000.0000.000
201A202VAL00.0050.01122.9210.0010.0010.0000.0000.0000.000
202A203ILE0-0.018-0.02722.343-0.012-0.0120.0000.0000.0000.000
203A204GLU-1-0.871-0.93526.8300.1040.1040.0000.0000.0000.000
204A205MET0-0.050-0.03627.805-0.009-0.0090.0000.0000.0000.000
205A206GLU-1-0.776-0.84631.4320.0570.0570.0000.0000.0000.000
206A207THR0-0.030-0.03133.446-0.005-0.0050.0000.0000.0000.000
207A208ASN00.0430.02435.4280.0050.0050.0000.0000.0000.000
208A209GLY00.0220.00336.786-0.002-0.0020.0000.0000.0000.000
209A210THR0-0.113-0.06136.1450.0010.0010.0000.0000.0000.000
210A211ILE0-0.030-0.01029.124-0.002-0.0020.0000.0000.0000.000
211A212ASP-1-0.815-0.87432.1620.0870.0870.0000.0000.0000.000
212A213PRO00.018-0.01330.0500.0040.0040.0000.0000.0000.000
213A214GLU-1-0.816-0.89426.3350.2120.2120.0000.0000.0000.000
214A215GLU-1-0.845-0.92826.1110.0850.0850.0000.0000.0000.000
215A216ALA00.0390.02526.393-0.007-0.0070.0000.0000.0000.000
216A217ILE00.0200.00022.154-0.004-0.0040.0000.0000.0000.000
217A218ARG10.8160.88921.993-0.205-0.2050.0000.0000.0000.000
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