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

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FMODB ID: YV4N2

Calculation Name: 5DBU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DBU

Chain ID: A

ChEMBL ID:

UniProt ID: D5AHU8

Base Structure: X-ray

Registration Date: 2023-09-23

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287029.394222
FMO2-HF: Nuclear repulsion 2208589.652557
FMO2-HF: Total energy -78439.741665
FMO2-MP2: Total energy -78665.421024


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-0.5781.903-0.002-1.303-1.1750.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.012
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].
3A3LEU00.003-0.0013.690-0.7541.727-0.002-1.303-1.1750.004
4A4ASN00.0750.0316.2600.1010.1010.0000.0000.0000.000
5A5LYS10.7830.8898.1931.0211.0210.0000.0000.0000.000
6A6TYR0-0.013-0.0106.0050.0540.0540.0000.0000.0000.000
7A7ILE0-0.019-0.00510.8690.1080.1080.0000.0000.0000.000
8A8ASP-1-0.672-0.78614.219-0.257-0.2570.0000.0000.0000.000
9A9HIS0-0.024-0.02217.4540.0510.0510.0000.0000.0000.000
10A10THR0-0.056-0.04519.7330.0080.0080.0000.0000.0000.000
11A11ILE0-0.022-0.01722.8910.0120.0120.0000.0000.0000.000
12A12LEU00.0330.01425.430-0.001-0.0010.0000.0000.0000.000
13A13LYS10.8260.92229.1080.0420.0420.0000.0000.0000.000
14A14PRO00.0130.02332.179-0.005-0.0050.0000.0000.0000.000
15A15GLU-1-0.810-0.90435.461-0.039-0.0390.0000.0000.0000.000
16A16THR0-0.089-0.05530.610-0.002-0.0020.0000.0000.0000.000
17A17THR0-0.018-0.04133.872-0.001-0.0010.0000.0000.0000.000
18A18GLN0-0.001-0.01633.4420.0010.0010.0000.0000.0000.000
19A19GLU-1-0.794-0.87732.377-0.084-0.0840.0000.0000.0000.000
20A20GLN0-0.062-0.02730.903-0.005-0.0050.0000.0000.0000.000
21A21VAL00.0190.00828.123-0.009-0.0090.0000.0000.0000.000
22A22GLU-1-0.831-0.91327.559-0.124-0.1240.0000.0000.0000.000
23A23LYS10.8480.91526.4420.1070.1070.0000.0000.0000.000
24A24ILE0-0.026-0.00823.133-0.013-0.0130.0000.0000.0000.000
25A25LEU0-0.002-0.00123.049-0.025-0.0250.0000.0000.0000.000
26A26ALA0-0.034-0.00923.342-0.025-0.0250.0000.0000.0000.000
27A27GLU-1-0.779-0.87721.369-0.176-0.1760.0000.0000.0000.000
28A28ALA0-0.005-0.01818.926-0.031-0.0310.0000.0000.0000.000
29A29LYS10.8730.94018.0300.1900.1900.0000.0000.0000.000
30A30GLU-1-0.951-0.94418.600-0.265-0.2650.0000.0000.0000.000
31A31TYR0-0.071-0.05715.393-0.021-0.0210.0000.0000.0000.000
32A32ASP-1-0.836-0.91512.906-0.885-0.8850.0000.0000.0000.000
33A33PHE00.0060.00613.317-0.101-0.1010.0000.0000.0000.000
34A34ALA0-0.012-0.00612.485-0.055-0.0550.0000.0000.0000.000
35A35SER0-0.053-0.03513.9080.0300.0300.0000.0000.0000.000
36A36VAL00.0310.02717.7230.0030.0030.0000.0000.0000.000
37A37CYS0-0.098-0.04921.0040.0140.0140.0000.0000.0000.000
38A38VAL00.0710.03122.8770.0110.0110.0000.0000.0000.000
39A39ASN00.0160.00526.6620.0060.0060.0000.0000.0000.000
40A40PRO00.0680.02729.908-0.007-0.0070.0000.0000.0000.000
41A41THR0-0.027-0.01231.164-0.003-0.0030.0000.0000.0000.000
42A42TRP0-0.012-0.00230.067-0.001-0.0010.0000.0000.0000.000
43A43VAL0-0.0150.00226.861-0.010-0.0100.0000.0000.0000.000
44A44ALA00.0950.05028.084-0.012-0.0120.0000.0000.0000.000
45A45LEU0-0.034-0.00829.959-0.007-0.0070.0000.0000.0000.000
46A46ALA00.006-0.00325.260-0.010-0.0100.0000.0000.0000.000
47A47ALA00.0450.01625.230-0.018-0.0180.0000.0000.0000.000
48A48GLU-1-0.837-0.90425.978-0.161-0.1610.0000.0000.0000.000
49A49SER0-0.041-0.02826.636-0.003-0.0030.0000.0000.0000.000
50A50LEU0-0.065-0.02721.250-0.012-0.0120.0000.0000.0000.000
51A51LYS10.8370.93721.5680.1320.1320.0000.0000.0000.000
52A52ASP-1-0.959-0.98422.345-0.229-0.2290.0000.0000.0000.000
53A53SER0-0.078-0.04918.702-0.029-0.0290.0000.0000.0000.000
54A54ASP-1-0.797-0.89012.901-0.751-0.7510.0000.0000.0000.000
55A55VAL0-0.0410.00415.783-0.013-0.0130.0000.0000.0000.000
56A56LYS10.8920.92813.9320.5790.5790.0000.0000.0000.000
57A57VAL00.0450.01918.6090.0140.0140.0000.0000.0000.000
58A58CYS0-0.0250.01220.0490.0250.0250.0000.0000.0000.000
59A59THR0-0.011-0.02522.1220.0090.0090.0000.0000.0000.000
60A60VAL0-0.052-0.02624.8480.0050.0050.0000.0000.0000.000
61A61ILE00.0300.01227.330-0.001-0.0010.0000.0000.0000.000
62A62GLY0-0.012-0.02029.9770.0070.0070.0000.0000.0000.000
63A63PHE0-0.0040.02227.5820.0070.0070.0000.0000.0000.000
64A64PRO0-0.014-0.01931.102-0.002-0.0020.0000.0000.0000.000
65A65LEU00.033-0.01032.1240.0060.0060.0000.0000.0000.000
66A66GLY00.0520.04233.0940.0050.0050.0000.0000.0000.000
67A67ALA0-0.044-0.02933.7810.0010.0010.0000.0000.0000.000
68A68ASN0-0.0030.00635.8150.0020.0020.0000.0000.0000.000
69A69THR00.0330.00937.0480.0020.0020.0000.0000.0000.000
70A70PRO00.0810.03735.443-0.004-0.0040.0000.0000.0000.000
71A71ALA00.0090.00335.757-0.004-0.0040.0000.0000.0000.000
72A72VAL0-0.0110.00436.926-0.004-0.0040.0000.0000.0000.000
73A73LYS10.8120.88731.984-0.006-0.0060.0000.0000.0000.000
74A74ALA00.0200.02732.752-0.006-0.0060.0000.0000.0000.000
75A75PHE0-0.048-0.02134.193-0.003-0.0030.0000.0000.0000.000
76A76GLU-1-0.825-0.92232.694-0.039-0.0390.0000.0000.0000.000
77A77THR00.018-0.02328.702-0.006-0.0060.0000.0000.0000.000
78A78LYS10.9080.96630.1120.0280.0280.0000.0000.0000.000
79A79ASP-1-0.911-0.93232.226-0.069-0.0690.0000.0000.0000.000
80A80ALA00.0530.02228.747-0.007-0.0070.0000.0000.0000.000
81A81ILE0-0.018-0.00326.302-0.010-0.0100.0000.0000.0000.000
82A82SER0-0.116-0.05528.462-0.007-0.0070.0000.0000.0000.000
83A83ASN0-0.069-0.04431.327-0.006-0.0060.0000.0000.0000.000
84A84GLY00.013-0.00127.436-0.005-0.0050.0000.0000.0000.000
85A85ALA0-0.059-0.03124.888-0.016-0.0160.0000.0000.0000.000
86A86ASP-1-0.848-0.92819.767-0.229-0.2290.0000.0000.0000.000
87A87GLU-1-0.805-0.88116.662-0.226-0.2260.0000.0000.0000.000
88A88ILE00.0210.00821.5830.0060.0060.0000.0000.0000.000
89A89ASP-1-0.695-0.84121.204-0.051-0.0510.0000.0000.0000.000
90A90MET0-0.0080.01823.9400.0020.0020.0000.0000.0000.000
91A91VAL0-0.034-0.00326.5290.0080.0080.0000.0000.0000.000
92A92ILE00.0270.03628.555-0.003-0.0030.0000.0000.0000.000
93A93ASN00.0310.01330.4000.0010.0010.0000.0000.0000.000
94A94ILE00.0360.00931.4300.0040.0040.0000.0000.0000.000
95A95GLY00.0190.01934.3740.0030.0030.0000.0000.0000.000
96A96ALA00.0080.01036.6930.0020.0020.0000.0000.0000.000
97A97LEU00.011-0.00531.5360.0020.0020.0000.0000.0000.000
98A98LYS10.7830.86835.101-0.046-0.0460.0000.0000.0000.000
99A99THR0-0.086-0.04438.015-0.001-0.0010.0000.0000.0000.000
100A100GLY00.0130.01538.3940.0000.0000.0000.0000.0000.000
101A101ASN0-0.038-0.01339.3310.0010.0010.0000.0000.0000.000
102A102TYR00.048-0.00834.754-0.001-0.0010.0000.0000.0000.000
103A103ASP-1-0.891-0.93235.3330.0350.0350.0000.0000.0000.000
104A104LEU00.0080.00936.723-0.002-0.0020.0000.0000.0000.000
105A105VAL0-0.029-0.01231.767-0.003-0.0030.0000.0000.0000.000
106A106LEU00.0150.00630.831-0.002-0.0020.0000.0000.0000.000
107A107GLU-1-0.963-0.98532.7110.0060.0060.0000.0000.0000.000
108A108ASP-1-0.842-0.92432.5210.0030.0030.0000.0000.0000.000
109A109ILE00.0030.00427.157-0.005-0.0050.0000.0000.0000.000
110A110LYS10.9410.98029.442-0.032-0.0320.0000.0000.0000.000
111A111ALA0-0.060-0.01731.182-0.005-0.0050.0000.0000.0000.000
112A112VAL00.002-0.00427.285-0.006-0.0060.0000.0000.0000.000
113A113VAL00.0210.01025.677-0.009-0.0090.0000.0000.0000.000
114A114ALA0-0.031-0.01727.979-0.007-0.0070.0000.0000.0000.000
115A115ALA0-0.118-0.06330.433-0.003-0.0030.0000.0000.0000.000
116A116SER00.012-0.01224.321-0.008-0.0080.0000.0000.0000.000
117A117GLY0-0.033-0.01026.091-0.012-0.0120.0000.0000.0000.000
118A118ASP-1-0.889-0.94622.556-0.125-0.1250.0000.0000.0000.000
119A119LYS10.7770.91021.4880.1480.1480.0000.0000.0000.000
120A120LEU00.0020.03915.8440.0200.0200.0000.0000.0000.000
121A121VAL00.004-0.01520.410-0.004-0.0040.0000.0000.0000.000
122A122LYS10.7550.84917.2930.1330.1330.0000.0000.0000.000
123A123VAL00.012-0.00221.409-0.007-0.0070.0000.0000.0000.000
124A124ILE0-0.042-0.02923.6710.0150.0150.0000.0000.0000.000
125A125ILE00.028-0.01024.555-0.003-0.0030.0000.0000.0000.000
126A126GLU-1-0.777-0.85926.7090.0230.0230.0000.0000.0000.000
127A127ALA00.0430.01425.7600.0000.0000.0000.0000.0000.000
128A128CYS0-0.050-0.00327.7890.0020.0020.0000.0000.0000.000
129A129LEU0-0.035-0.01030.173-0.004-0.0040.0000.0000.0000.000
130A130LEU0-0.067-0.02128.849-0.003-0.0030.0000.0000.0000.000
131A131THR00.008-0.02531.6720.0060.0060.0000.0000.0000.000
132A132ASP-1-0.826-0.92628.4160.1120.1120.0000.0000.0000.000
133A133ASP-1-0.868-0.93529.2470.0980.0980.0000.0000.0000.000
134A134GLU-1-0.776-0.84131.2520.0560.0560.0000.0000.0000.000
135A135LYS10.7680.87926.419-0.107-0.1070.0000.0000.0000.000
136A136VAL00.0130.01526.3410.0040.0040.0000.0000.0000.000
137A137LYS10.9240.96527.318-0.069-0.0690.0000.0000.0000.000
138A138ALA00.0290.01027.862-0.005-0.0050.0000.0000.0000.000
139A139CYS0-0.053-0.01523.264-0.002-0.0020.0000.0000.0000.000
140A140GLN00.010-0.00124.781-0.010-0.0100.0000.0000.0000.000
141A141LEU0-0.017-0.01326.794-0.004-0.0040.0000.0000.0000.000
142A142SER00.013-0.01624.197-0.012-0.0120.0000.0000.0000.000
143A143GLN0-0.018-0.01820.748-0.011-0.0110.0000.0000.0000.000
144A144GLU-1-0.939-0.97024.3560.0590.0590.0000.0000.0000.000
145A145ALA0-0.047-0.03927.717-0.006-0.0060.0000.0000.0000.000
146A146GLY0-0.0130.00324.758-0.009-0.0090.0000.0000.0000.000
147A147ALA0-0.010-0.00522.979-0.012-0.0120.0000.0000.0000.000
148A148ASP-1-0.790-0.88717.782-0.014-0.0140.0000.0000.0000.000
149A149TYR0-0.040-0.02512.4730.0000.0000.0000.0000.0000.000
150A150VAL0-0.0050.02318.799-0.011-0.0110.0000.0000.0000.000
151A151LYS10.8270.89619.0990.0390.0390.0000.0000.0000.000
152A152THR00.025-0.00920.309-0.002-0.0020.0000.0000.0000.000
153A153SER0-0.0250.00722.8590.0040.0040.0000.0000.0000.000
154A154THR0-0.025-0.05624.791-0.011-0.0110.0000.0000.0000.000
155A155GLY0-0.006-0.00627.222-0.010-0.0100.0000.0000.0000.000
156A156PHE0-0.087-0.04527.829-0.004-0.0040.0000.0000.0000.000
157A157SER00.0330.02030.9840.0010.0010.0000.0000.0000.000
158A158THR0-0.004-0.01331.7270.0000.0000.0000.0000.0000.000
159A159GLY00.0130.00429.2790.0030.0030.0000.0000.0000.000
160A160GLY0-0.037-0.01225.044-0.007-0.0070.0000.0000.0000.000
161A161ALA0-0.029-0.00420.6700.0050.0050.0000.0000.0000.000
162A162THR00.007-0.03722.6660.0020.0020.0000.0000.0000.000
163A163VAL00.0560.00918.4020.0070.0070.0000.0000.0000.000
164A164ALA00.0140.01820.0420.0240.0240.0000.0000.0000.000
165A165ASP-1-0.785-0.85622.5310.1280.1280.0000.0000.0000.000
166A166VAL0-0.016-0.01116.382-0.003-0.0030.0000.0000.0000.000
167A167ALA00.0590.03817.8860.0200.0200.0000.0000.0000.000
168A168LEU0-0.074-0.02818.9100.0080.0080.0000.0000.0000.000
169A169MET00.0040.00220.007-0.006-0.0060.0000.0000.0000.000
170A170ARG10.8070.88812.816-0.430-0.4300.0000.0000.0000.000
171A171LYS10.9060.95017.868-0.191-0.1910.0000.0000.0000.000
172A172THR0-0.100-0.05719.648-0.015-0.0150.0000.0000.0000.000
173A173VAL0-0.0070.00818.035-0.014-0.0140.0000.0000.0000.000
174A174GLY00.0410.04917.624-0.009-0.0090.0000.0000.0000.000
175A175PRO0-0.043-0.02912.4760.0140.0140.0000.0000.0000.000
176A176ASP-1-0.919-0.96813.2970.3670.3670.0000.0000.0000.000
177A177MET0-0.0120.02915.039-0.054-0.0540.0000.0000.0000.000
178A178GLY0-0.027-0.01614.0930.0600.0600.0000.0000.0000.000
179A179VAL00.0090.00014.392-0.017-0.0170.0000.0000.0000.000
180A180LYS10.7600.85614.7210.0940.0940.0000.0000.0000.000
181A181ALA00.0360.02316.481-0.009-0.0090.0000.0000.0000.000
182A182SER0-0.016-0.01818.281-0.034-0.0340.0000.0000.0000.000
183A183GLY00.0570.02520.939-0.014-0.0140.0000.0000.0000.000
184A184GLY0-0.023-0.00622.2700.0170.0170.0000.0000.0000.000
185A185ALA0-0.0040.00518.467-0.003-0.0030.0000.0000.0000.000
186A186ARG10.8250.89820.577-0.006-0.0060.0000.0000.0000.000
187A187SER0-0.010-0.02019.199-0.030-0.0300.0000.0000.0000.000
188A188TYR00.007-0.0019.7970.0350.0350.0000.0000.0000.000
189A189GLU-1-0.813-0.89614.5410.1230.1230.0000.0000.0000.000
190A190ASP-1-0.777-0.88916.3640.1180.1180.0000.0000.0000.000
191A191ALA0-0.027-0.01212.8380.0310.0310.0000.0000.0000.000
192A192ILE00.0130.00310.4420.0700.0700.0000.0000.0000.000
193A193ALA00.0190.02312.3760.0960.0960.0000.0000.0000.000
194A194PHE0-0.018-0.03115.1620.0150.0150.0000.0000.0000.000
195A195ILE0-0.017-0.0058.2170.0060.0060.0000.0000.0000.000
196A196GLU-1-0.939-0.96010.1201.0131.0130.0000.0000.0000.000
197A197ALA0-0.078-0.02912.310-0.026-0.0260.0000.0000.0000.000
198A198GLY00.0240.01012.301-0.049-0.0490.0000.0000.0000.000
199A199ALA0-0.028-0.01512.929-0.021-0.0210.0000.0000.0000.000
200A200SER00.0080.0049.8420.1060.1060.0000.0000.0000.000
201A201ARG10.6850.79510.4770.0620.0620.0000.0000.0000.000
202A202ILE00.0340.01212.5590.0780.0780.0000.0000.0000.000
203A203GLY00.0130.00815.553-0.055-0.0550.0000.0000.0000.000
204A204ALA0-0.017-0.01218.9550.0290.0290.0000.0000.0000.000
205A205SER00.0100.03120.534-0.019-0.0190.0000.0000.0000.000
206A206SER0-0.045-0.05220.5110.0080.0080.0000.0000.0000.000
207A207GLY00.0470.03116.8460.0100.0100.0000.0000.0000.000
208A208VAL0-0.0020.00916.326-0.026-0.0260.0000.0000.0000.000
209A209ALA00.0120.00915.4020.0280.0280.0000.0000.0000.000
210A210ILE0-0.040-0.02014.249-0.015-0.0150.0000.0000.0000.000
211A211MET0-0.0220.00111.645-0.041-0.0410.0000.0000.0000.000