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: 9MYJ2

Calculation Name: 2D3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3V

Chain ID: A

ChEMBL ID:

UniProt ID: A6NI73

Base Structure: X-ray

Registration Date: 2023-09-26

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1862621.184002
FMO2-HF: Nuclear repulsion 1790056.986991
FMO2-HF: Total energy -72564.197011
FMO2-MP2: Total energy -72776.184943


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:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-7.744-4.1913.799-2.884-4.467-0.023
Interaction energy analysis for fragmet #1(A:3:LEU)
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 : -0.009
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].
3A5LYS10.9630.9923.8280.1151.633-0.015-0.701-0.8010.002
4A6ALA00.0060.0046.2250.4420.4420.0000.0000.0000.000
5A7THR0-0.038-0.0129.794-0.107-0.1070.0000.0000.0000.000
6A8LEU00.0140.00012.7780.0770.0770.0000.0000.0000.000
7A9TRP0-0.070-0.04015.768-0.008-0.0080.0000.0000.0000.000
8A10ALA00.018-0.00219.2020.0090.0090.0000.0000.0000.000
9A11GLU-1-0.856-0.89422.883-0.124-0.1240.0000.0000.0000.000
10A12PRO00.0320.00125.9420.0000.0000.0000.0000.0000.000
11A13GLY00.0480.00525.8230.0030.0030.0000.0000.0000.000
12A14SER0-0.014-0.00623.3490.0050.0050.0000.0000.0000.000
13A15VAL00.0260.02325.419-0.008-0.0080.0000.0000.0000.000
14A16ILE0-0.022-0.00628.5790.0120.0120.0000.0000.0000.000
15A17SER00.0370.02331.243-0.003-0.0030.0000.0000.0000.000
16A18ARG10.9350.95834.5920.1120.1120.0000.0000.0000.000
17A19GLY0-0.078-0.03935.2590.0080.0080.0000.0000.0000.000
18A20ASN00.0050.01434.3020.0100.0100.0000.0000.0000.000
19A21SER0-0.032-0.02231.860-0.004-0.0040.0000.0000.0000.000
20A22VAL0-0.017-0.00625.992-0.001-0.0010.0000.0000.0000.000
21A23THR0-0.047-0.02324.2580.0060.0060.0000.0000.0000.000
22A24ILE00.0410.03019.677-0.007-0.0070.0000.0000.0000.000
23A25ARG10.8550.92819.9450.1470.1470.0000.0000.0000.000
24A26CYS0-0.0020.00813.1560.0340.0340.0000.0000.0000.000
25A27GLN0-0.042-0.02314.0040.0370.0370.0000.0000.0000.000
26A28GLY00.0520.01811.160-0.133-0.1330.0000.0000.0000.000
27A29THR0-0.017-0.0159.0990.0070.0070.0000.0000.0000.000
28A30LEU00.028-0.00812.270-0.058-0.0580.0000.0000.0000.000
29A31GLU-1-0.918-0.95111.6860.4530.4530.0000.0000.0000.000
30A32ALA0-0.064-0.01312.631-0.029-0.0290.0000.0000.0000.000
31A33GLN0-0.044-0.04613.7550.0300.0300.0000.0000.0000.000
32A34GLU-1-0.892-0.94514.959-0.217-0.2170.0000.0000.0000.000
33A35TYR0-0.051-0.05313.710-0.060-0.0600.0000.0000.0000.000
34A36ARG11.0051.00014.5290.4530.4530.0000.0000.0000.000
35A37LEU0-0.037-0.00614.965-0.077-0.0770.0000.0000.0000.000
36A38VAL00.0180.00115.0630.0320.0320.0000.0000.0000.000
37A39LYS10.8980.95517.5610.2420.2420.0000.0000.0000.000
38A40GLU-1-0.808-0.89217.782-0.488-0.4880.0000.0000.0000.000
39A41GLY0-0.009-0.00920.1760.0310.0310.0000.0000.0000.000
40A42SER0-0.064-0.02921.6680.0360.0360.0000.0000.0000.000
41A43PRO0-0.004-0.00420.714-0.027-0.0270.0000.0000.0000.000
42A44GLU-1-0.947-0.96019.943-0.241-0.2410.0000.0000.0000.000
43A45PRO0-0.080-0.05818.253-0.015-0.0150.0000.0000.0000.000
44A46TRP00.0090.01220.0490.0200.0200.0000.0000.0000.000
45A47ASP-1-0.834-0.92620.414-0.175-0.1750.0000.0000.0000.000
46A48THR0-0.061-0.03518.626-0.052-0.0520.0000.0000.0000.000
47A49GLN0-0.012-0.01719.1100.0350.0350.0000.0000.0000.000
48A50ASN0-0.018-0.01218.816-0.024-0.0240.0000.0000.0000.000
49A51PRO0-0.0190.01418.6460.0150.0150.0000.0000.0000.000
50A52LEU00.009-0.01621.2240.0170.0170.0000.0000.0000.000
51A53GLU-1-0.908-0.97222.1620.0380.0380.0000.0000.0000.000
52A54PRO0-0.0090.01320.7300.0170.0170.0000.0000.0000.000
53A55LYS10.9340.98417.034-0.069-0.0690.0000.0000.0000.000
54A56ASN00.0220.02914.994-0.038-0.0380.0000.0000.0000.000
55A57LYS10.9200.94915.8790.0280.0280.0000.0000.0000.000
56A58ALA00.0530.05617.7580.0170.0170.0000.0000.0000.000
57A59ARG10.9140.95419.2660.0880.0880.0000.0000.0000.000
58A60PHE00.0000.00517.8260.0070.0070.0000.0000.0000.000
59A61SER0-0.002-0.00323.1900.0000.0000.0000.0000.0000.000
60A62ILE00.0220.01025.478-0.001-0.0010.0000.0000.0000.000
61A63PRO00.010-0.00428.8630.0040.0040.0000.0000.0000.000
62A64SER00.0170.01332.5080.0040.0040.0000.0000.0000.000
63A65MET0-0.0010.01728.370-0.009-0.0090.0000.0000.0000.000
64A66THR00.002-0.02531.5720.0100.0100.0000.0000.0000.000
65A67GLU-1-0.893-0.97031.322-0.145-0.1450.0000.0000.0000.000
66A68HIS0-0.029-0.01330.135-0.021-0.0210.0000.0000.0000.000
67A69HIS00.0910.07327.219-0.010-0.0100.0000.0000.0000.000
68A70ALA00.0200.05126.079-0.020-0.0200.0000.0000.0000.000
69A71GLY0-0.009-0.01624.2260.0000.0000.0000.0000.0000.000
70A72ARG10.8680.93617.2910.4570.4570.0000.0000.0000.000
71A73TYR0-0.039-0.04118.376-0.004-0.0040.0000.0000.0000.000
72A74ARG10.8720.92712.0260.7300.7300.0000.0000.0000.000
73A76TYR00.0200.0168.705-0.091-0.0910.0000.0000.0000.000
74A77TYR00.0460.0127.4700.0040.0040.0000.0000.0000.000
75A78TYR00.0300.0259.648-0.136-0.1360.0000.0000.0000.000
76A79SER00.000-0.0039.3530.1460.1460.0000.0000.0000.000
77A80PRO00.0540.02211.313-0.037-0.0370.0000.0000.0000.000
78A81ALA0-0.035-0.0046.6850.0280.0280.0000.0000.0000.000
79A82GLY00.0010.0107.061-0.054-0.0540.0000.0000.0000.000
80A83TRP0-0.050-0.0428.1020.0620.0620.0000.0000.0000.000
81A84SER0-0.046-0.0115.371-0.141-0.1410.0000.0000.0000.000
82A85GLU-1-0.875-0.9532.311-8.543-6.5513.815-2.180-3.627-0.025
83A86PRO0-0.026-0.0165.0370.5120.555-0.001-0.003-0.0390.000
84A87SER0-0.029-0.0168.202-0.169-0.1690.0000.0000.0000.000
85A88ASP-1-0.906-0.96010.517-0.994-0.9940.0000.0000.0000.000
86A89PRO0-0.071-0.03912.2470.0690.0690.0000.0000.0000.000
87A90LEU00.0170.02015.4530.0370.0370.0000.0000.0000.000
88A91GLU-1-0.903-0.96418.409-0.311-0.3110.0000.0000.0000.000
89A92LEU0-0.048-0.02321.6420.0190.0190.0000.0000.0000.000
90A93VAL00.0270.00624.4120.0000.0000.0000.0000.0000.000
91A94VAL0-0.0220.01027.8880.0080.0080.0000.0000.0000.000
92A95THR0-0.017-0.00331.2880.0000.0000.0000.0000.0000.000
93A96GLY00.0750.01134.4800.0030.0030.0000.0000.0000.000
94A97PHE0-0.003-0.00534.9350.0060.0060.0000.0000.0000.000
95A98TYR0-0.035-0.02135.2530.0030.0030.0000.0000.0000.000
96A99ASN00.0380.01240.640-0.003-0.0030.0000.0000.0000.000
97A100LYS10.9480.99841.5430.0730.0730.0000.0000.0000.000
98A101PRO0-0.046-0.01139.7580.0040.0040.0000.0000.0000.000
99A102THR0-0.049-0.02743.0010.0040.0040.0000.0000.0000.000
100A103LEU00.0520.00440.287-0.003-0.0030.0000.0000.0000.000
101A104SER0-0.041-0.01243.8650.0050.0050.0000.0000.0000.000
102A105ALA00.0580.03645.147-0.003-0.0030.0000.0000.0000.000
103A117VAL0-0.002-0.01042.6400.0000.0000.0000.0000.0000.000
104A118THR00.001-0.00842.196-0.004-0.0040.0000.0000.0000.000
105A119LEU00.0030.01239.6190.0030.0030.0000.0000.0000.000
106A120GLN00.018-0.00441.780-0.005-0.0050.0000.0000.0000.000
107A121CYS0-0.0600.00136.656-0.004-0.0040.0000.0000.0000.000
108A122GLY00.0470.01141.664-0.002-0.0020.0000.0000.0000.000
109A123SER0-0.027-0.02543.3960.0030.0030.0000.0000.0000.000
110A124ARG11.0171.01645.0890.0690.0690.0000.0000.0000.000
111A125LEU0-0.029-0.00242.428-0.001-0.0010.0000.0000.0000.000
112A126ARG10.9820.99239.8740.1140.1140.0000.0000.0000.000
113A127PHE0-0.0180.00937.778-0.002-0.0020.0000.0000.0000.000
114A128ASP-1-0.784-0.85734.582-0.141-0.1410.0000.0000.0000.000
115A129ARG10.9080.95626.7770.2130.2130.0000.0000.0000.000
116A130PHE0-0.016-0.00934.4660.0060.0060.0000.0000.0000.000
117A131ILE0-0.011-0.00430.523-0.006-0.0060.0000.0000.0000.000
118A132LEU00.0110.01733.4630.0080.0080.0000.0000.0000.000
119A133THR0-0.003-0.03231.406-0.011-0.0110.0000.0000.0000.000
120A134GLU-1-0.833-0.92332.690-0.085-0.0850.0000.0000.0000.000
121A135GLU-1-0.903-0.96733.086-0.102-0.1020.0000.0000.0000.000
122A136GLY0-0.004-0.00433.8350.0000.0000.0000.0000.0000.000
123A137ASP-1-0.931-0.94134.861-0.057-0.0570.0000.0000.0000.000
124A138HIS0-0.058-0.03032.316-0.006-0.0060.0000.0000.0000.000
125A139LYS10.9480.95426.0990.1330.1330.0000.0000.0000.000
126A140LEU0-0.005-0.00227.806-0.011-0.0110.0000.0000.0000.000
127A141SER0-0.060-0.03027.9030.0040.0040.0000.0000.0000.000
128A142TRP00.0540.04629.159-0.009-0.0090.0000.0000.0000.000
129A143THR0-0.010-0.00928.8300.0040.0040.0000.0000.0000.000
130A144LEU0-0.013-0.00430.970-0.002-0.0020.0000.0000.0000.000
131A145ASP-1-0.798-0.89432.198-0.174-0.1740.0000.0000.0000.000
132A146SER0-0.098-0.06134.5570.0060.0060.0000.0000.0000.000
133A147GLN00.0200.00038.080-0.006-0.0060.0000.0000.0000.000
134A148LEU00.003-0.00141.1820.0020.0020.0000.0000.0000.000
135A149THR00.0050.00844.4230.0010.0010.0000.0000.0000.000
136A150PRO00.0520.01547.5490.0000.0000.0000.0000.0000.000
137A151SER0-0.048-0.01950.5940.0000.0000.0000.0000.0000.000
138A152GLY0-0.006-0.00348.6900.0010.0010.0000.0000.0000.000
139A153GLN0-0.055-0.02447.0700.0010.0010.0000.0000.0000.000
140A154PHE00.0460.02141.647-0.002-0.0020.0000.0000.0000.000
141A155GLN00.008-0.01342.0760.0040.0040.0000.0000.0000.000
142A156ALA00.0450.02337.719-0.004-0.0040.0000.0000.0000.000
143A157LEU0-0.030-0.01939.5810.0040.0040.0000.0000.0000.000
144A158PHE00.0330.00334.132-0.004-0.0040.0000.0000.0000.000
145A159PRO00.0010.00637.2540.0060.0060.0000.0000.0000.000
146A160VAL00.0080.01837.327-0.005-0.0050.0000.0000.0000.000
147A161GLY00.004-0.00337.093-0.004-0.0040.0000.0000.0000.000
148A162PRO0-0.0220.00737.0850.0050.0050.0000.0000.0000.000
149A163VAL00.0370.01540.005-0.002-0.0020.0000.0000.0000.000
150A164THR00.0040.00241.1020.0050.0050.0000.0000.0000.000
151A165PRO0-0.005-0.01043.309-0.002-0.0020.0000.0000.0000.000
152A166SER0-0.019-0.02241.1320.0010.0010.0000.0000.0000.000
153A167HIS0-0.002-0.00137.673-0.002-0.0020.0000.0000.0000.000
154A168ARG10.9070.96839.8310.0460.0460.0000.0000.0000.000
155A169TRP00.0100.00834.933-0.004-0.0040.0000.0000.0000.000
156A170MET0-0.005-0.00138.2810.0050.0050.0000.0000.0000.000
157A171LEU00.0360.01436.289-0.007-0.0070.0000.0000.0000.000
158A172ARG10.8980.96037.3040.0930.0930.0000.0000.0000.000
159A174TYR00.0510.02234.4220.0050.0050.0000.0000.0000.000
160A175GLY00.0480.02336.286-0.002-0.0020.0000.0000.0000.000
161A176SER0-0.009-0.00732.578-0.006-0.0060.0000.0000.0000.000
162A177ARG10.8590.89933.9760.1300.1300.0000.0000.0000.000
163A178ARG10.7960.88630.5940.1690.1690.0000.0000.0000.000
164A179HIS0-0.011-0.00230.587-0.014-0.0140.0000.0000.0000.000
165A180ILE00.000-0.00129.543-0.010-0.0100.0000.0000.0000.000
166A181LEU00.0200.00826.2730.0070.0070.0000.0000.0000.000
167A182GLN0-0.040-0.00624.5680.0100.0100.0000.0000.0000.000
168A183VAL00.0240.02228.2880.0060.0060.0000.0000.0000.000
169A184TRP0-0.012-0.02028.6970.0080.0080.0000.0000.0000.000
170A185SER0-0.033-0.02734.0550.0020.0020.0000.0000.0000.000
171A186GLU-1-0.893-0.96036.907-0.104-0.1040.0000.0000.0000.000
172A187PRO0-0.0060.02437.463-0.002-0.0020.0000.0000.0000.000
173A188SER0-0.013-0.01639.0430.0040.0040.0000.0000.0000.000
174A189ASP-1-0.920-0.96141.555-0.074-0.0740.0000.0000.0000.000
175A190LEU0-0.043-0.01240.073-0.003-0.0030.0000.0000.0000.000
176A191LEU0-0.010-0.00942.0560.0050.0050.0000.0000.0000.000
177A192GLU-1-0.918-0.95142.261-0.062-0.0620.0000.0000.0000.000
178A193ILE0-0.0450.00342.5660.0030.0030.0000.0000.0000.000
179A194PRO0-0.021-0.03443.379-0.001-0.0010.0000.0000.0000.000
180A195VAL00.0130.00846.7580.0010.0010.0000.0000.0000.000