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: 76MVK

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2502541.243194
FMO2-HF: Nuclear repulsion 2413676.598287
FMO2-HF: Total energy -88864.644908
FMO2-MP2: Total energy -89124.744936


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.
-16.963-14.7788.11-4.861-5.4350.038
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 : 0.045 / q_NPA : 0.030
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].
3A4SER0-0.004-0.0211.886-12.032-10.2798.065-4.664-5.1540.036
4A5VAL00.0010.0043.800-3.778-3.3460.045-0.197-0.2810.002
5A6THR0-0.089-0.0546.887-0.364-0.3640.0000.0000.0000.000
6A7GLU-1-0.881-0.9238.0423.2853.2850.0000.0000.0000.000
7A8PHE00.0390.0237.479-0.309-0.3090.0000.0000.0000.000
8A9LEU0-0.025-0.02710.996-0.111-0.1110.0000.0000.0000.000
9A10LYS10.8590.93410.267-1.704-1.7040.0000.0000.0000.000
10A11PRO00.0290.03214.849-0.052-0.0520.0000.0000.0000.000
11A12ARG10.9220.93418.189-0.368-0.3680.0000.0000.0000.000
12A13LEU0-0.006-0.00520.9650.0050.0050.0000.0000.0000.000
13A14VAL0-0.056-0.04024.265-0.001-0.0010.0000.0000.0000.000
14A15ASP-1-0.885-0.92926.5420.1440.1440.0000.0000.0000.000
15A16ILE0-0.049-0.02829.127-0.002-0.0020.0000.0000.0000.000
16A17GLU-1-0.798-0.88331.6730.1030.1030.0000.0000.0000.000
17A18GLN00.004-0.01534.680-0.003-0.0030.0000.0000.0000.000
18A19VAL0-0.0150.00136.295-0.001-0.0010.0000.0000.0000.000
19A20SER0-0.029-0.02838.703-0.005-0.0050.0000.0000.0000.000
20A21SER00.0110.00239.0360.0030.0030.0000.0000.0000.000
21A22THR0-0.025-0.01137.716-0.001-0.0010.0000.0000.0000.000
22A23HIS0-0.0210.00735.620-0.001-0.0010.0000.0000.0000.000
23A24ALA0-0.0040.00832.5950.0030.0030.0000.0000.0000.000
24A25LYS10.8410.92331.131-0.106-0.1060.0000.0000.0000.000
25A26VAL00.0100.02025.6560.0070.0070.0000.0000.0000.000
26A27THR00.0100.00225.9290.0140.0140.0000.0000.0000.000
27A28LEU00.0050.01020.1720.0090.0090.0000.0000.0000.000
28A29GLU-1-0.887-0.97022.5650.3270.3270.0000.0000.0000.000
29A30PRO0-0.005-0.01018.4440.0180.0180.0000.0000.0000.000
30A31LEU00.0140.02916.8770.0430.0430.0000.0000.0000.000
31A32GLU-1-0.765-0.83513.1591.0991.0990.0000.0000.0000.000
32A33ARG10.8550.90616.405-0.523-0.5230.0000.0000.0000.000
33A34GLY00.0090.00916.1300.0710.0710.0000.0000.0000.000
34A35PHE0-0.006-0.00910.158-0.079-0.0790.0000.0000.0000.000
35A36GLY00.0220.02416.039-0.055-0.0550.0000.0000.0000.000
36A37HIS00.0890.02319.603-0.015-0.0150.0000.0000.0000.000
37A38THR0-0.066-0.02113.252-0.060-0.0600.0000.0000.0000.000
38A39LEU00.0250.00813.956-0.064-0.0640.0000.0000.0000.000
39A40GLY00.0440.02117.318-0.046-0.0460.0000.0000.0000.000
40A41ASN0-0.024-0.01819.700-0.038-0.0380.0000.0000.0000.000
41A42ALA0-0.0110.01116.794-0.029-0.0290.0000.0000.0000.000
42A43LEU00.0480.00818.865-0.027-0.0270.0000.0000.0000.000
43A44ARG10.9330.97621.118-0.078-0.0780.0000.0000.0000.000
44A45ALA0-0.0090.00321.860-0.007-0.0070.0000.0000.0000.000
45A46ILE00.0020.02219.974-0.014-0.0140.0000.0000.0000.000
46A47LEU00.025-0.02023.402-0.005-0.0050.0000.0000.0000.000
47A48LEU0-0.048-0.02026.288-0.002-0.0020.0000.0000.0000.000
48A49SER0-0.049-0.02625.963-0.011-0.0110.0000.0000.0000.000
49A50SER0-0.057-0.02124.652-0.018-0.0180.0000.0000.0000.000
50A51MET0-0.0420.02126.457-0.013-0.0130.0000.0000.0000.000
51A52PRO0-0.039-0.04027.811-0.001-0.0010.0000.0000.0000.000
52A53GLY00.0650.05530.9260.0030.0030.0000.0000.0000.000
53A54CYS0-0.021-0.02234.260-0.007-0.0070.0000.0000.0000.000
54A55ALA00.0350.01237.6800.0050.0050.0000.0000.0000.000
55A56VAL00.0080.01740.426-0.004-0.0040.0000.0000.0000.000
56A57THR0-0.046-0.02941.5160.0010.0010.0000.0000.0000.000
57A58GLU-1-0.837-0.91844.480-0.055-0.0550.0000.0000.0000.000
58A59VAL0-0.016-0.01348.0820.0020.0020.0000.0000.0000.000
59A60GLU-1-0.869-0.93151.216-0.036-0.0360.0000.0000.0000.000
60A61ILE00.012-0.01354.4750.0010.0010.0000.0000.0000.000
61A62ASP-1-0.792-0.87157.350-0.027-0.0270.0000.0000.0000.000
62A63GLY0-0.067-0.03560.7530.0020.0020.0000.0000.0000.000
63A64VAL0-0.017-0.00158.4100.0010.0010.0000.0000.0000.000
64A65LEU0-0.001-0.00159.644-0.002-0.0020.0000.0000.0000.000
65A66HIS00.0260.00256.7990.0000.0000.0000.0000.0000.000
66A67GLU-1-0.877-0.95254.101-0.029-0.0290.0000.0000.0000.000
67A68TYR0-0.067-0.03257.2320.0020.0020.0000.0000.0000.000
68A69SER0-0.059-0.01860.3210.0010.0010.0000.0000.0000.000
69A70THR00.0840.03560.8660.0000.0000.0000.0000.0000.000
70A71LYS10.8680.92561.8790.0140.0140.0000.0000.0000.000
71A72GLU-1-0.901-0.93864.077-0.012-0.0120.0000.0000.0000.000
72A73GLY00.020-0.00766.472-0.001-0.0010.0000.0000.0000.000
73A74VAL0-0.069-0.03760.0860.0010.0010.0000.0000.0000.000
74A75GLN0-0.070-0.03260.0730.0010.0010.0000.0000.0000.000
75A76GLU-1-0.764-0.86756.979-0.007-0.0070.0000.0000.0000.000
76A77ASP-1-0.845-0.92758.199-0.015-0.0150.0000.0000.0000.000
77A78ILE00.032-0.01556.2100.0000.0000.0000.0000.0000.000
78A79LEU0-0.0100.01253.894-0.001-0.0010.0000.0000.0000.000
79A80GLU-1-0.893-0.94953.439-0.008-0.0080.0000.0000.0000.000
80A81ILE0-0.013-0.00153.4800.0010.0010.0000.0000.0000.000
81A82LEU0-0.005-0.00550.6700.0000.0000.0000.0000.0000.000
82A83LEU0-0.042-0.03148.420-0.002-0.0020.0000.0000.0000.000
83A84ASN0-0.021-0.00948.7490.0020.0020.0000.0000.0000.000
84A85LEU0-0.023-0.02148.6140.0010.0010.0000.0000.0000.000
85A86LYS10.8550.93444.7070.0240.0240.0000.0000.0000.000
86A87GLY0-0.068-0.01943.718-0.001-0.0010.0000.0000.0000.000
87A88LEU0-0.049-0.02145.0720.0040.0040.0000.0000.0000.000
88A89ALA00.0110.01640.997-0.003-0.0030.0000.0000.0000.000
89A90VAL0-0.024-0.02640.9490.0030.0030.0000.0000.0000.000
90A91ARG10.7990.88534.337-0.012-0.0120.0000.0000.0000.000
91A92VAL00.025-0.00137.9190.0020.0020.0000.0000.0000.000
92A93GLN0-0.020-0.03036.657-0.008-0.0080.0000.0000.0000.000
93A94GLY00.0160.01335.080-0.002-0.0020.0000.0000.0000.000
94A95LYN0-0.0060.00735.987-0.004-0.0040.0000.0000.0000.000
95A96ASP-1-0.897-0.96934.735-0.091-0.0910.0000.0000.0000.000
96A97GLU-1-0.855-0.94837.597-0.066-0.0660.0000.0000.0000.000
97A98VAL0-0.0200.01141.3110.0000.0000.0000.0000.0000.000
98A99ILE0-0.010-0.00144.0150.0010.0010.0000.0000.0000.000
99A100LEU00.0230.01345.3800.0020.0020.0000.0000.0000.000
100A101THR0-0.035-0.02249.1830.0000.0000.0000.0000.0000.000
101A102LEU00.0320.01752.9750.0020.0020.0000.0000.0000.000
102A103ASN0-0.0020.01354.906-0.001-0.0010.0000.0000.0000.000
103A104LYS10.8620.91858.4560.0060.0060.0000.0000.0000.000
104A105SER00.0300.01360.509-0.001-0.0010.0000.0000.0000.000
105A106GLY00.0030.00664.2010.0010.0010.0000.0000.0000.000
106A107ILE00.0010.02565.3870.0000.0000.0000.0000.0000.000
107A108GLY0-0.011-0.00662.8410.0010.0010.0000.0000.0000.000
108A109PRO0-0.034-0.02457.269-0.001-0.0010.0000.0000.0000.000
109A110VAL0-0.037-0.00755.7650.0000.0000.0000.0000.0000.000
110A111THR0-0.011-0.01852.9640.0000.0000.0000.0000.0000.000
111A112ALA00.0420.00748.555-0.002-0.0020.0000.0000.0000.000
112A113ALA0-0.031-0.01950.468-0.001-0.0010.0000.0000.0000.000
113A114ASP-1-0.848-0.91352.097-0.005-0.0050.0000.0000.0000.000
114A115ILE0-0.045-0.00949.058-0.002-0.0020.0000.0000.0000.000
115A116THR0-0.056-0.02251.5850.0010.0010.0000.0000.0000.000
116A117HIS0-0.037-0.02349.7920.0000.0000.0000.0000.0000.000
117A118ASP-1-0.811-0.92045.268-0.033-0.0330.0000.0000.0000.000
118A119GLY0-0.046-0.01646.1120.0020.0020.0000.0000.0000.000
119A120ASP-1-0.912-0.93841.310-0.039-0.0390.0000.0000.0000.000
120A121VAL0-0.065-0.04041.7470.0020.0020.0000.0000.0000.000
121A122GLU-1-0.837-0.88439.4930.0040.0040.0000.0000.0000.000
122A123ILE0-0.033-0.03642.379-0.002-0.0020.0000.0000.0000.000
123A124VAL00.0260.02339.8860.0030.0030.0000.0000.0000.000
124A125LYS10.8560.93342.964-0.002-0.0020.0000.0000.0000.000
125A126PRO00.0600.02545.973-0.002-0.0020.0000.0000.0000.000
126A127GLN00.014-0.00248.348-0.003-0.0030.0000.0000.0000.000
127A128HIS0-0.018-0.01847.9140.0040.0040.0000.0000.0000.000
128A129VAL0-0.001-0.00350.064-0.002-0.0020.0000.0000.0000.000
129A130ILE0-0.0020.00450.203-0.001-0.0010.0000.0000.0000.000
130A131CYS0-0.057-0.03653.384-0.002-0.0020.0000.0000.0000.000
131A132HIS0-0.022-0.01857.1820.0040.0040.0000.0000.0000.000
132A133LEU0-0.0290.02260.607-0.001-0.0010.0000.0000.0000.000
133A134THR00.010-0.01363.5550.0010.0010.0000.0000.0000.000
134A135ASP-1-0.873-0.94866.774-0.007-0.0070.0000.0000.0000.000
135A136GLU-1-0.924-0.98268.173-0.003-0.0030.0000.0000.0000.000
136A137ASN0-0.107-0.04269.9150.0000.0000.0000.0000.0000.000
137A138ALA0-0.0050.03565.965-0.001-0.0010.0000.0000.0000.000
138A139SER0-0.006-0.03663.6280.0000.0000.0000.0000.0000.000
139A140ILE0-0.044-0.01457.237-0.001-0.0010.0000.0000.0000.000
140A141SER00.027-0.00358.6490.0000.0000.0000.0000.0000.000
141A142MET0-0.024-0.00253.862-0.001-0.0010.0000.0000.0000.000
142A143ARG10.7770.85652.0980.0300.0300.0000.0000.0000.000
143A144ILE0-0.004-0.01247.306-0.001-0.0010.0000.0000.0000.000
144A145LYS10.8300.93344.4970.0570.0570.0000.0000.0000.000
145A146VAL00.0110.00841.1020.0010.0010.0000.0000.0000.000
146A147GLN00.012-0.00739.420-0.001-0.0010.0000.0000.0000.000
147A148ARG10.8120.92233.1470.0690.0690.0000.0000.0000.000
148A149GLY00.0150.00733.955-0.007-0.0070.0000.0000.0000.000
149A150ARG10.8960.93626.0570.1270.1270.0000.0000.0000.000
150A151GLY00.0420.02732.272-0.002-0.0020.0000.0000.0000.000
151A152TYR0-0.020-0.01233.5130.0030.0030.0000.0000.0000.000
152A153VAL00.0040.01736.280-0.003-0.0030.0000.0000.0000.000
153A154PRO00.0640.01438.8600.0020.0020.0000.0000.0000.000
154A155ALA00.0750.04942.514-0.005-0.0050.0000.0000.0000.000
155A156SER00.0190.00745.064-0.002-0.0020.0000.0000.0000.000
156A157THR0-0.156-0.09040.158-0.004-0.0040.0000.0000.0000.000
157A158ARG10.8630.93141.6570.0520.0520.0000.0000.0000.000
158A159ILE0-0.0160.02245.525-0.001-0.0010.0000.0000.0000.000
159A160HIS0-0.017-0.00446.8680.0040.0040.0000.0000.0000.000
160A161SER0-0.046-0.04949.4910.0020.0020.0000.0000.0000.000
161A162GLU-1-0.799-0.86952.271-0.041-0.0410.0000.0000.0000.000
162A163GLU-1-0.971-0.99552.492-0.059-0.0590.0000.0000.0000.000
163A164ASP-1-0.903-0.96155.764-0.048-0.0480.0000.0000.0000.000
164A165GLU-1-1.001-1.00659.078-0.034-0.0340.0000.0000.0000.000
165A166ARG10.7350.85859.4560.0370.0370.0000.0000.0000.000
166A167PRO00.0070.01157.408-0.002-0.0020.0000.0000.0000.000
167A168ILE00.0610.02753.0180.0010.0010.0000.0000.0000.000
168A169GLY00.0170.02455.1470.0020.0020.0000.0000.0000.000
169A170ARG10.7640.88254.4630.0340.0340.0000.0000.0000.000
170A171LEU00.0310.00852.831-0.002-0.0020.0000.0000.0000.000
171A172LEU00.0660.06547.363-0.002-0.0020.0000.0000.0000.000
172A173VAL0-0.027-0.00946.0170.0030.0030.0000.0000.0000.000
173A174ASP-1-0.844-0.90943.675-0.038-0.0380.0000.0000.0000.000
174A175ALA00.0360.02740.0780.0030.0030.0000.0000.0000.000
175A176CYS0-0.023-0.02838.485-0.003-0.0030.0000.0000.0000.000
176A177TYR0-0.010-0.01234.9560.0020.0020.0000.0000.0000.000
177A178SER0-0.036-0.00432.564-0.001-0.0010.0000.0000.0000.000
178A179PRO0-0.0050.00531.1410.0060.0060.0000.0000.0000.000
179A180VAL0-0.025-0.02229.6970.0110.0110.0000.0000.0000.000
180A181GLU-1-0.826-0.90732.837-0.001-0.0010.0000.0000.0000.000
181A182ARG10.7510.83432.814-0.037-0.0370.0000.0000.0000.000
182A183ILE0-0.002-0.00426.6380.0050.0050.0000.0000.0000.000
183A184ALA0-0.031-0.00829.281-0.003-0.0030.0000.0000.0000.000
184A185TYR0-0.052-0.03523.0220.0150.0150.0000.0000.0000.000
185A186ASN00.0010.00826.860-0.002-0.0020.0000.0000.0000.000
186A187VAL0-0.040-0.03422.1990.0080.0080.0000.0000.0000.000
187A188GLU-1-0.837-0.92524.5420.2150.2150.0000.0000.0000.000
188A189ALA00.0350.03325.1930.0190.0190.0000.0000.0000.000
189A190ALA00.0000.01023.646-0.028-0.0280.0000.0000.0000.000
190A191ARG10.8760.91925.681-0.304-0.3040.0000.0000.0000.000
191A192VAL00.0420.02022.542-0.009-0.0090.0000.0000.0000.000
192A193GLU-1-0.930-0.95125.5680.2840.2840.0000.0000.0000.000
193A194GLN0-0.044-0.01818.7370.0070.0070.0000.0000.0000.000
194A195ARG10.7980.85115.571-0.894-0.8940.0000.0000.0000.000
195A196THR00.021-0.00822.566-0.050-0.0500.0000.0000.0000.000
196A197ASP-1-0.888-0.91620.1690.5010.5010.0000.0000.0000.000
197A198LEU0-0.028-0.02118.0050.0880.0880.0000.0000.0000.000
198A199ASP-1-0.860-0.93220.6430.3600.3600.0000.0000.0000.000
199A200LYS10.8760.95821.891-0.206-0.2060.0000.0000.0000.000
200A201LEU0-0.045-0.00320.330-0.021-0.0210.0000.0000.0000.000
201A202VAL00.005-0.00723.371-0.007-0.0070.0000.0000.0000.000
202A203ILE0-0.026-0.02922.574-0.011-0.0110.0000.0000.0000.000
203A204GLU-1-0.903-0.95427.0260.0870.0870.0000.0000.0000.000
204A205MET0-0.050-0.03628.029-0.012-0.0120.0000.0000.0000.000
205A206GLU-1-0.759-0.83431.7190.0380.0380.0000.0000.0000.000
206A207THR0-0.062-0.03033.398-0.006-0.0060.0000.0000.0000.000
207A208ASN00.1500.10435.1660.0040.0040.0000.0000.0000.000
208A209GLY0-0.034-0.03536.961-0.002-0.0020.0000.0000.0000.000
209A210THR0-0.096-0.06536.2790.0000.0000.0000.0000.0000.000
210A211ILE0-0.027-0.00829.465-0.006-0.0060.0000.0000.0000.000
211A212ASP-1-0.831-0.88931.9250.0350.0350.0000.0000.0000.000
212A213PRO00.060-0.00330.278-0.001-0.0010.0000.0000.0000.000
213A214GLU-1-0.797-0.89626.2060.1130.1130.0000.0000.0000.000
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215A216ALA00.0570.02826.711-0.015-0.0150.0000.0000.0000.000
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