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: 7MJLK

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1861859.316308
FMO2-HF: Nuclear repulsion 1789293.676794
FMO2-HF: Total energy -72565.639514
FMO2-MP2: Total energy -72777.549942


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.
-2.5360.5072.613-2.009-3.6460.001
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 : 0.047 / q_NPA : 0.022
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].
3A5LYS10.8710.9343.6640.0702.2600.000-1.103-1.0870.005
4A6ALA00.0050.0075.7700.2670.2670.0000.0000.0000.000
5A7THR0-0.045-0.0279.334-0.075-0.0750.0000.0000.0000.000
6A8LEU0-0.004-0.01312.4000.0780.0780.0000.0000.0000.000
7A9TRP0-0.045-0.03515.485-0.009-0.0090.0000.0000.0000.000
8A10ALA00.0280.00219.1360.0130.0130.0000.0000.0000.000
9A11GLU-1-0.819-0.85722.761-0.258-0.2580.0000.0000.0000.000
10A12PRO00.029-0.00625.9690.0060.0060.0000.0000.0000.000
11A13GLY00.0300.00625.927-0.002-0.0020.0000.0000.0000.000
12A14SER0-0.008-0.00323.4530.0030.0030.0000.0000.0000.000
13A15VAL00.0260.01025.5400.0020.0020.0000.0000.0000.000
14A16ILE0-0.027-0.00128.8290.0050.0050.0000.0000.0000.000
15A17SER00.0430.03331.5190.0000.0000.0000.0000.0000.000
16A18ARG10.8520.90034.6040.0940.0940.0000.0000.0000.000
17A19GLY0-0.0070.00535.3360.0060.0060.0000.0000.0000.000
18A20ASN0-0.0160.00434.5150.0040.0040.0000.0000.0000.000
19A21SER0-0.016-0.02431.988-0.003-0.0030.0000.0000.0000.000
20A22VAL0-0.0180.00226.252-0.003-0.0030.0000.0000.0000.000
21A23THR0-0.044-0.02324.1320.0090.0090.0000.0000.0000.000
22A24ILE00.0570.04619.644-0.014-0.0140.0000.0000.0000.000
23A25ARG10.8120.89019.8740.2790.2790.0000.0000.0000.000
24A26CYS0-0.037-0.00413.0380.0120.0120.0000.0000.0000.000
25A27GLN00.0000.00013.4980.1320.1320.0000.0000.0000.000
26A28GLY00.0580.02010.678-0.129-0.1290.0000.0000.0000.000
27A29THR0-0.069-0.0508.946-0.057-0.0570.0000.0000.0000.000
28A30LEU0-0.001-0.00511.8320.0380.0380.0000.0000.0000.000
29A31GLU-1-0.805-0.89110.454-0.269-0.2690.0000.0000.0000.000
30A32ALA0-0.0350.00512.6880.0380.0380.0000.0000.0000.000
31A33GLN0-0.062-0.04713.6950.0480.0480.0000.0000.0000.000
32A34GLU-1-0.794-0.88014.716-0.151-0.1510.0000.0000.0000.000
33A35TYR0-0.021-0.02413.063-0.085-0.0850.0000.0000.0000.000
34A36ARG10.8530.91114.2610.2420.2420.0000.0000.0000.000
35A37LEU0-0.0130.00314.669-0.062-0.0620.0000.0000.0000.000
36A38VAL00.0270.00714.6700.0340.0340.0000.0000.0000.000
37A39LYS10.8630.95217.2450.1460.1460.0000.0000.0000.000
38A40GLU-1-0.791-0.85217.557-0.271-0.2710.0000.0000.0000.000
39A41GLY00.010-0.00320.1940.0100.0100.0000.0000.0000.000
40A42SER0-0.052-0.03021.4660.0160.0160.0000.0000.0000.000
41A43PRO0-0.025-0.01520.320-0.015-0.0150.0000.0000.0000.000
42A44GLU-1-0.929-0.94619.873-0.094-0.0940.0000.0000.0000.000
43A45PRO0-0.050-0.04317.906-0.017-0.0170.0000.0000.0000.000
44A46TRP0-0.0060.00519.6600.0150.0150.0000.0000.0000.000
45A47ASP-1-0.837-0.92520.215-0.178-0.1780.0000.0000.0000.000
46A48THR0-0.086-0.05818.430-0.024-0.0240.0000.0000.0000.000
47A49GLN00.0280.01918.8180.0070.0070.0000.0000.0000.000
48A50ASN0-0.021-0.02318.509-0.025-0.0250.0000.0000.0000.000
49A51PRO0-0.0070.01518.2300.0200.0200.0000.0000.0000.000
50A52LEU0-0.003-0.02021.1310.0140.0140.0000.0000.0000.000
51A53GLU-1-0.914-0.96722.412-0.147-0.1470.0000.0000.0000.000
52A54PRO00.0280.03620.740-0.003-0.0030.0000.0000.0000.000
53A55LYS10.8720.93316.8340.1350.1350.0000.0000.0000.000
54A56ASN00.0160.01814.956-0.006-0.0060.0000.0000.0000.000
55A57LYS10.8780.93715.4320.3250.3250.0000.0000.0000.000
56A58ALA00.0400.03817.3450.0340.0340.0000.0000.0000.000
57A59ARG10.9040.94918.9730.1540.1540.0000.0000.0000.000
58A60PHE00.0310.01717.3880.0140.0140.0000.0000.0000.000
59A61SER0-0.021-0.02722.958-0.003-0.0030.0000.0000.0000.000
60A62ILE00.0100.00625.2680.0080.0080.0000.0000.0000.000
61A63PRO00.008-0.00728.7540.0010.0010.0000.0000.0000.000
62A64SER0-0.037-0.01132.2620.0060.0060.0000.0000.0000.000
63A65MET0-0.0020.01527.960-0.004-0.0040.0000.0000.0000.000
64A66THR00.009-0.02331.3250.0100.0100.0000.0000.0000.000
65A67GLU-1-0.779-0.89731.220-0.109-0.1090.0000.0000.0000.000
66A68HIS0-0.016-0.00330.050-0.010-0.0100.0000.0000.0000.000
67A69HIS00.0690.03827.255-0.007-0.0070.0000.0000.0000.000
68A70ALA00.0090.04826.270-0.017-0.0170.0000.0000.0000.000
69A71GLY00.011-0.00324.5900.0070.0070.0000.0000.0000.000
70A72ARG10.7930.86018.0270.2630.2630.0000.0000.0000.000
71A73TYR0-0.028-0.03718.4420.0130.0130.0000.0000.0000.000
72A74ARG10.8450.90311.9970.4150.4150.0000.0000.0000.000
73A76TYR00.0430.0318.672-0.100-0.1000.0000.0000.0000.000
74A77TYR00.031-0.0077.792-0.036-0.0360.0000.0000.0000.000
75A78TYR00.0250.0279.456-0.049-0.0490.0000.0000.0000.000
76A79SER00.014-0.0038.7990.0060.0060.0000.0000.0000.000
77A80PRO00.0280.00210.8840.0430.0430.0000.0000.0000.000
78A81ALA0-0.0200.0066.4500.0690.0690.0000.0000.0000.000
79A82GLY00.0110.0166.7520.1790.1790.0000.0000.0000.000
80A83TRP0-0.070-0.0478.063-0.092-0.0920.0000.0000.0000.000
81A84SER0-0.018-0.0015.0530.1130.1130.0000.0000.0000.000
82A85GLU-1-0.870-0.9462.435-2.616-1.8252.614-0.899-2.506-0.004
83A86PRO0-0.029-0.0134.7010.1110.173-0.001-0.007-0.0530.000
84A87SER0-0.027-0.0168.136-0.175-0.1750.0000.0000.0000.000
85A88ASP-1-0.852-0.91710.610-0.931-0.9310.0000.0000.0000.000
86A89PRO0-0.040-0.01912.5310.0380.0380.0000.0000.0000.000
87A90LEU00.0290.02315.7750.0270.0270.0000.0000.0000.000
88A91GLU-1-0.849-0.90518.529-0.203-0.2030.0000.0000.0000.000
89A92LEU0-0.034-0.01221.6760.0000.0000.0000.0000.0000.000
90A93VAL00.0080.00024.3730.0120.0120.0000.0000.0000.000
91A94VAL0-0.0230.00327.8240.0000.0000.0000.0000.0000.000
92A95THR0-0.017-0.01531.1120.0060.0060.0000.0000.0000.000
93A96GLY00.0800.02234.5020.0010.0010.0000.0000.0000.000
94A97PHE0-0.057-0.02734.4010.0050.0050.0000.0000.0000.000
95A98TYR0-0.054-0.03434.9220.0070.0070.0000.0000.0000.000
96A99ASN00.0220.00441.023-0.003-0.0030.0000.0000.0000.000
97A100LYS10.8720.94741.6320.0720.0720.0000.0000.0000.000
98A101PRO0-0.074-0.02039.6400.0050.0050.0000.0000.0000.000
99A102THR0-0.045-0.03242.9260.0010.0010.0000.0000.0000.000
100A103LEU00.044-0.00340.504-0.002-0.0020.0000.0000.0000.000
101A104SER0-0.0070.00144.0710.0030.0030.0000.0000.0000.000
102A105ALA00.0230.02345.7430.0000.0000.0000.0000.0000.000
103A117VAL00.0620.03443.3530.0010.0010.0000.0000.0000.000
104A118THR0-0.051-0.02942.240-0.004-0.0040.0000.0000.0000.000
105A119LEU00.0050.00540.3700.0030.0030.0000.0000.0000.000
106A120GLN00.0290.01541.789-0.001-0.0010.0000.0000.0000.000
107A121CYS0-0.048-0.01136.803-0.003-0.0030.0000.0000.0000.000
108A122GLY00.0410.00741.8690.0010.0010.0000.0000.0000.000
109A123SER0-0.018-0.00143.4510.0010.0010.0000.0000.0000.000
110A124ARG10.9500.96245.4420.0520.0520.0000.0000.0000.000
111A125LEU0-0.0430.00642.9340.0020.0020.0000.0000.0000.000
112A126ARG10.8430.89437.9800.0710.0710.0000.0000.0000.000
113A127PHE0-0.0100.00538.269-0.003-0.0030.0000.0000.0000.000
114A128ASP-1-0.743-0.81535.149-0.079-0.0790.0000.0000.0000.000
115A129ARG10.8880.92527.1520.1300.1300.0000.0000.0000.000
116A130PHE0-0.0210.00434.7130.0020.0020.0000.0000.0000.000
117A131ILE0-0.011-0.00730.779-0.003-0.0030.0000.0000.0000.000
118A132LEU00.0100.02333.7200.0040.0040.0000.0000.0000.000
119A133THR0-0.017-0.03531.707-0.010-0.0100.0000.0000.0000.000
120A134GLU-1-0.785-0.89033.069-0.105-0.1050.0000.0000.0000.000
121A135GLU-1-0.820-0.90133.455-0.117-0.1170.0000.0000.0000.000
122A136GLY00.000-0.01534.078-0.001-0.0010.0000.0000.0000.000
123A137ASP-1-0.893-0.91535.162-0.109-0.1090.0000.0000.0000.000
124A138HIS0-0.073-0.03932.799-0.012-0.0120.0000.0000.0000.000
125A139LYS10.9260.95625.8980.2120.2120.0000.0000.0000.000
126A140LEU0-0.001-0.00327.952-0.012-0.0120.0000.0000.0000.000
127A141SER0-0.034-0.01428.0470.0060.0060.0000.0000.0000.000
128A142TRP00.0400.03429.586-0.006-0.0060.0000.0000.0000.000
129A143THR0-0.024-0.01329.2160.0040.0040.0000.0000.0000.000
130A144LEU0-0.0040.00731.2150.0000.0000.0000.0000.0000.000
131A145ASP-1-0.762-0.85232.017-0.107-0.1070.0000.0000.0000.000
132A146SER0-0.082-0.04734.5270.0020.0020.0000.0000.0000.000
133A147GLN00.0090.00738.1240.0010.0010.0000.0000.0000.000
134A148LEU0-0.001-0.00241.352-0.001-0.0010.0000.0000.0000.000
135A149THR00.0290.02044.7030.0020.0020.0000.0000.0000.000
136A150PRO00.008-0.00348.1280.0000.0000.0000.0000.0000.000
137A151SER0-0.007-0.00450.9310.0010.0010.0000.0000.0000.000
138A152GLY00.0040.00648.9880.0000.0000.0000.0000.0000.000
139A153GLN00.0110.01747.5460.0000.0000.0000.0000.0000.000
140A154PHE00.0430.01542.0150.0000.0000.0000.0000.0000.000
141A155GLN0-0.008-0.03442.1890.0000.0000.0000.0000.0000.000
142A156ALA00.0230.01338.056-0.001-0.0010.0000.0000.0000.000
143A157LEU0-0.010-0.00639.6240.0020.0020.0000.0000.0000.000
144A158PHE00.0400.00234.223-0.002-0.0020.0000.0000.0000.000
145A159PRO0-0.016-0.00937.8360.0020.0020.0000.0000.0000.000
146A160VAL00.0140.01637.598-0.005-0.0050.0000.0000.0000.000
147A161GLY00.0130.01137.593-0.005-0.0050.0000.0000.0000.000
148A162PRO0-0.038-0.00737.2170.0060.0060.0000.0000.0000.000
149A163VAL00.0550.02140.242-0.003-0.0030.0000.0000.0000.000
150A164THR00.0120.00742.1050.0050.0050.0000.0000.0000.000
151A165PRO00.010-0.00344.026-0.003-0.0030.0000.0000.0000.000
152A166SER0-0.022-0.01142.2060.0000.0000.0000.0000.0000.000
153A167HIS0-0.008-0.00537.829-0.001-0.0010.0000.0000.0000.000
154A168ARG10.8930.95240.4820.0760.0760.0000.0000.0000.000
155A169TRP0-0.033-0.01334.575-0.007-0.0070.0000.0000.0000.000
156A170MET0-0.009-0.02038.6590.0050.0050.0000.0000.0000.000
157A171LEU00.0240.01936.734-0.006-0.0060.0000.0000.0000.000
158A172ARG10.8160.88137.5270.1040.1040.0000.0000.0000.000
159A174TYR00.0680.03634.3760.0020.0020.0000.0000.0000.000
160A175GLY00.0450.02036.6270.0010.0010.0000.0000.0000.000
161A176SER0-0.021-0.01332.975-0.004-0.0040.0000.0000.0000.000
162A177ARG10.8850.91334.1270.0890.0890.0000.0000.0000.000
163A178ARG10.8030.85931.3770.0940.0940.0000.0000.0000.000
164A179HIS00.0150.01430.691-0.006-0.0060.0000.0000.0000.000
165A180ILE0-0.005-0.00329.839-0.004-0.0040.0000.0000.0000.000
166A181LEU00.0120.01126.8890.0000.0000.0000.0000.0000.000
167A182GLN0-0.037-0.01725.1160.0070.0070.0000.0000.0000.000
168A183VAL00.0250.02328.546-0.002-0.0020.0000.0000.0000.000
169A184TRP0-0.021-0.02928.9750.0070.0070.0000.0000.0000.000
170A185SER0-0.018-0.03534.4540.0010.0010.0000.0000.0000.000
171A186GLU-1-0.858-0.92637.200-0.098-0.0980.0000.0000.0000.000
172A187PRO0-0.0050.01637.7450.0000.0000.0000.0000.0000.000
173A188SER0-0.011-0.01639.2240.0030.0030.0000.0000.0000.000
174A189ASP-1-0.845-0.92141.789-0.076-0.0760.0000.0000.0000.000
175A190LEU0-0.0230.01140.969-0.002-0.0020.0000.0000.0000.000
176A191LEU0-0.030-0.01442.5250.0050.0050.0000.0000.0000.000
177A192GLU-1-0.885-0.94142.655-0.083-0.0830.0000.0000.0000.000
178A193ILE0-0.044-0.00442.6590.0040.0040.0000.0000.0000.000
179A194PRO0-0.012-0.02943.632-0.003-0.0030.0000.0000.0000.000
180A195VAL0-0.0020.00546.8360.0030.0030.0000.0000.0000.000