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: JQLY9

Calculation Name: 2PAQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PAQ

Chain ID: A

ChEMBL ID:

UniProt ID: P76491

Base Structure: X-ray

Registration Date: 2023-09-21

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1879849.494094
FMO2-HF: Nuclear repulsion 1808337.303937
FMO2-HF: Total energy -71512.190157
FMO2-MP2: Total energy -71718.957274


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-54.295-52.689-0.008-0.76-0.8380.003
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.959 / q_NPA : 0.962
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].
3A4SER00.0290.0003.8242.5054.111-0.008-0.760-0.8380.003
4A5HIS00.021-0.0036.1660.5860.5860.0000.0000.0000.000
5A6PHE00.0590.0409.3621.9921.9920.0000.0000.0000.000
6A7PHE00.0850.02811.3911.3111.3110.0000.0000.0000.000
7A8ALA0-0.045-0.01512.3731.3461.3460.0000.0000.0000.000
8A9HIS0-0.018-0.03912.4371.9901.9900.0000.0000.0000.000
9A10LEU00.0890.05415.1941.0441.0440.0000.0000.0000.000
10A11SER0-0.039-0.01317.2191.4201.4200.0000.0000.0000.000
11A12ARG10.9480.96917.56916.13016.1300.0000.0000.0000.000
12A13LEU00.0740.04320.7760.5210.5210.0000.0000.0000.000
13A14LYS10.8550.92621.59614.59314.5930.0000.0000.0000.000
14A15LEU0-0.110-0.05622.3710.3290.3290.0000.0000.0000.000
15A16ILE00.0010.03322.9140.2350.2350.0000.0000.0000.000
16A17ASN0-0.040-0.02827.0220.2210.2210.0000.0000.0000.000
17A18ARG10.9570.97730.3529.3889.3880.0000.0000.0000.000
18A19TRP0-0.111-0.05732.9760.2940.2940.0000.0000.0000.000
19A20PRO00.0510.02433.6970.1940.1940.0000.0000.0000.000
20A21LEU0-0.067-0.03736.1310.1010.1010.0000.0000.0000.000
21A22MET0-0.0040.01639.4650.1480.1480.0000.0000.0000.000
22A23ARG10.8550.92440.4416.6486.6480.0000.0000.0000.000
23A24ASN0-0.039-0.00938.4900.0160.0160.0000.0000.0000.000
24A25VAL0-0.024-0.02641.3040.0070.0070.0000.0000.0000.000
25A26ARG10.8150.87234.1068.9558.9550.0000.0000.0000.000
26A27THR0-0.0060.00134.7680.0910.0910.0000.0000.0000.000
27A28GLU-1-0.778-0.86433.044-8.885-8.8850.0000.0000.0000.000
28A29ASN00.0390.01628.556-0.309-0.3090.0000.0000.0000.000
29A30VAL00.0890.02425.7720.1810.1810.0000.0000.0000.000
30A31SER0-0.052-0.00225.484-0.244-0.2440.0000.0000.0000.000
31A32GLU-1-0.863-0.91826.800-9.629-9.6290.0000.0000.0000.000
32A33HIS00.0140.01130.1710.2630.2630.0000.0000.0000.000
33A34SER00.0270.00826.4080.1350.1350.0000.0000.0000.000
34A35LEU0-0.041-0.01027.8570.0330.0330.0000.0000.0000.000
35A36GLN00.0250.01329.3540.1960.1960.0000.0000.0000.000
36A37VAL00.0660.01430.5130.2330.2330.0000.0000.0000.000
37A38ALA0-0.006-0.01128.2030.1800.1800.0000.0000.0000.000
38A39MET0-0.052-0.02230.2550.2240.2240.0000.0000.0000.000
39A40VAL00.0120.00133.2060.2320.2320.0000.0000.0000.000
40A41ALA00.0250.00731.7230.2190.2190.0000.0000.0000.000
41A42HIS0-0.022-0.00831.9010.0490.0490.0000.0000.0000.000
42A43ALA00.0140.00633.6420.1900.1900.0000.0000.0000.000
43A44LEU0-0.023-0.00936.9380.2520.2520.0000.0000.0000.000
44A45ALA00.0190.01234.6800.1750.1750.0000.0000.0000.000
45A46ALA0-0.022-0.01536.6950.1710.1710.0000.0000.0000.000
46A47ILE00.000-0.00338.3080.2200.2200.0000.0000.0000.000
47A48LYS10.8210.91838.7947.6537.6530.0000.0000.0000.000
48A49ASN0-0.019-0.01836.5040.2330.2330.0000.0000.0000.000
49A50ARG10.8700.95540.8717.3007.3000.0000.0000.0000.000
50A51LYS10.8630.91643.3836.4626.4620.0000.0000.0000.000
51A52PHE0-0.011-0.00244.4430.1520.1520.0000.0000.0000.000
52A53GLY0-0.0020.01244.9440.0010.0010.0000.0000.0000.000
53A54GLY0-0.0030.00740.604-0.035-0.0350.0000.0000.0000.000
54A55ASN0-0.038-0.03037.8490.0080.0080.0000.0000.0000.000
55A56VAL00.0190.01534.273-0.166-0.1660.0000.0000.0000.000
56A57ASN00.0450.03429.054-0.027-0.0270.0000.0000.0000.000
57A58ALA00.0300.00531.022-0.200-0.2000.0000.0000.0000.000
58A59GLU-1-0.834-0.92828.162-9.423-9.4230.0000.0000.0000.000
59A60ARG10.9110.95821.85411.36711.3670.0000.0000.0000.000
60A61ILE00.0210.01726.803-0.311-0.3110.0000.0000.0000.000
61A62ALA00.0010.00328.217-0.098-0.0980.0000.0000.0000.000
62A63LEU00.0080.00121.000-0.231-0.2310.0000.0000.0000.000
63A64LEU0-0.032-0.01723.770-0.404-0.4040.0000.0000.0000.000
64A65ALA00.0260.02025.367-0.123-0.1230.0000.0000.0000.000
65A66MET0-0.081-0.04423.338-0.025-0.0250.0000.0000.0000.000
66A67TYR0-0.074-0.04417.040-0.662-0.6620.0000.0000.0000.000
67A68HIS0-0.0490.00122.6860.1360.1360.0000.0000.0000.000
68A69ASP-1-0.782-0.89425.125-10.444-10.4440.0000.0000.0000.000
69A70ALA0-0.015-0.01619.488-0.259-0.2590.0000.0000.0000.000
70A71SER00.023-0.01219.721-0.520-0.5200.0000.0000.0000.000
71A72GLU-1-0.858-0.93520.788-10.807-10.8070.0000.0000.0000.000
72A73VAL0-0.101-0.04917.8330.0670.0670.0000.0000.0000.000
73A74LEU0-0.131-0.07116.086-0.449-0.4490.0000.0000.0000.000
74A75THR0-0.027-0.00820.1760.0130.0130.0000.0000.0000.000
75A76GLY0-0.055-0.01323.8140.3770.3770.0000.0000.0000.000
76A77ASP-1-0.827-0.91626.008-9.461-9.4610.0000.0000.0000.000
77A78LEU0-0.060-0.03129.0590.2180.2180.0000.0000.0000.000
78A79PRO00.0260.01331.4820.1310.1310.0000.0000.0000.000
79A80THR0-0.036-0.02334.8200.1050.1050.0000.0000.0000.000
80A81PRO00.0160.02235.4490.2700.2700.0000.0000.0000.000
81A91GLN00.020-0.01833.317-0.155-0.1550.0000.0000.0000.000
82A92GLU-1-0.880-0.94230.120-9.342-9.3420.0000.0000.0000.000
83A93TYR00.024-0.00727.547-0.259-0.2590.0000.0000.0000.000
84A94LYS10.8300.90328.4089.4509.4500.0000.0000.0000.000
85A95ALA00.0200.01427.138-0.344-0.3440.0000.0000.0000.000
86A96ILE0-0.001-0.01125.097-0.418-0.4180.0000.0000.0000.000
87A97GLU-1-0.781-0.84523.659-10.631-10.6310.0000.0000.0000.000
88A98LYS11.0010.99522.65210.39810.3980.0000.0000.0000.000
89A99ILE0-0.060-0.03120.216-0.541-0.5410.0000.0000.0000.000
90A100ALA0-0.0110.00319.033-0.744-0.7440.0000.0000.0000.000
91A101GLN00.039-0.00517.876-0.801-0.8010.0000.0000.0000.000
92A102GLN0-0.0230.00014.888-0.169-0.1690.0000.0000.0000.000
93A103LYS10.8540.92513.74415.83815.8380.0000.0000.0000.000
94A104LEU00.0170.00713.101-1.373-1.3730.0000.0000.0000.000
95A105VAL00.022-0.00212.681-1.415-1.4150.0000.0000.0000.000
96A106ASP-1-0.859-0.92311.003-18.242-18.2420.0000.0000.0000.000
97A107MET0-0.076-0.0248.453-2.186-2.1860.0000.0000.0000.000
98A108VAL0-0.0240.0267.653-3.101-3.1010.0000.0000.0000.000
99A109PRO0-0.018-0.0084.879-0.728-0.7280.0000.0000.0000.000
100A110GLU-1-0.851-0.9316.316-20.850-20.8500.0000.0000.0000.000
101A111GLU-1-0.971-0.9867.466-23.164-23.1640.0000.0000.0000.000
102A112LEU00.0080.0079.2591.1131.1130.0000.0000.0000.000
103A113ARG10.8460.9208.13223.57023.5700.0000.0000.0000.000
104A114ASP-1-0.878-0.94512.220-15.438-15.4380.0000.0000.0000.000
105A115ILE0-0.023-0.00514.6260.9320.9320.0000.0000.0000.000
106A116PHE0-0.014-0.02912.8200.5840.5840.0000.0000.0000.000
107A117ALA00.0010.00415.7280.5190.5190.0000.0000.0000.000
108A118PRO0-0.042-0.03716.9940.5030.5030.0000.0000.0000.000
109A119LEU0-0.048-0.01418.2630.5760.5760.0000.0000.0000.000
110A120ILE0-0.056-0.01316.7690.1380.1380.0000.0000.0000.000
111A121ASP-1-0.851-0.92020.129-11.451-11.4510.0000.0000.0000.000
112A122GLU-1-0.802-0.89022.249-10.777-10.7770.0000.0000.0000.000
113A123HIS0-0.107-0.05521.5840.6620.6620.0000.0000.0000.000
114A124ALA00.0190.00223.7290.1980.1980.0000.0000.0000.000
115A125TYR0-0.071-0.03324.7330.4600.4600.0000.0000.0000.000
116A126SER00.028-0.01228.2440.2780.2780.0000.0000.0000.000
117A127ASP-1-0.905-0.96731.468-8.345-8.3450.0000.0000.0000.000
118A128GLU-1-0.849-0.93234.402-7.558-7.5580.0000.0000.0000.000
119A129GLU-1-0.850-0.90229.460-9.715-9.7150.0000.0000.0000.000
120A130LYS10.8770.93428.7989.5579.5570.0000.0000.0000.000
121A131SER0-0.074-0.04032.0620.0360.0360.0000.0000.0000.000
122A132LEU00.0280.01834.0960.0840.0840.0000.0000.0000.000
123A133VAL00.0310.02629.2900.0580.0580.0000.0000.0000.000
124A134LYS10.9710.98632.5448.3078.3070.0000.0000.0000.000
125A135GLN00.0040.03534.7160.2440.2440.0000.0000.0000.000
126A136ALA00.0560.03333.8640.1280.1280.0000.0000.0000.000
127A137ASP-1-0.854-0.92332.769-8.841-8.8410.0000.0000.0000.000
128A138ALA0-0.043-0.02334.6590.1030.1030.0000.0000.0000.000
129A139LEU00.011-0.00438.2450.1590.1590.0000.0000.0000.000
130A140CYS0-0.0310.00035.4500.1110.1110.0000.0000.0000.000
131A141ALA00.0050.00636.8900.0430.0430.0000.0000.0000.000
132A142TYR0-0.021-0.04338.2760.1360.1360.0000.0000.0000.000
133A143LEU00.006-0.00239.1960.1500.1500.0000.0000.0000.000
134A144LYS10.8430.93737.8578.2178.2170.0000.0000.0000.000
135A145CYS0-0.083-0.04640.4780.1200.1200.0000.0000.0000.000
136A146LEU00.000-0.00343.3790.1560.1560.0000.0000.0000.000
137A147GLU-1-0.919-0.95740.495-7.671-7.6710.0000.0000.0000.000
138A148GLU-1-0.774-0.85141.407-7.396-7.3960.0000.0000.0000.000
139A149LEU0-0.028-0.02844.7770.1450.1450.0000.0000.0000.000
140A150ALA0-0.0290.00247.7500.1530.1530.0000.0000.0000.000
141A151ALA0-0.0200.00346.3690.0860.0860.0000.0000.0000.000
142A152GLY0-0.025-0.01048.3310.0330.0330.0000.0000.0000.000
143A153ASN0-0.112-0.07844.2790.2200.2200.0000.0000.0000.000
144A154ASN00.036-0.00747.831-0.013-0.0130.0000.0000.0000.000
145A155GLU-1-0.833-0.90045.251-6.835-6.8350.0000.0000.0000.000
146A156PHE00.0280.00139.963-0.047-0.0470.0000.0000.0000.000
147A157LEU00.0070.01045.574-0.023-0.0230.0000.0000.0000.000
148A158LEU00.0320.01846.8280.0020.0020.0000.0000.0000.000
149A159ALA0-0.029-0.01042.317-0.020-0.0200.0000.0000.0000.000
150A160LYS10.8950.93844.1576.2366.2360.0000.0000.0000.000
151A161THR00.004-0.00145.9520.0050.0050.0000.0000.0000.000
152A162ARG10.8970.94139.3537.4387.4380.0000.0000.0000.000
153A163LEU0-0.010-0.00939.389-0.069-0.0690.0000.0000.0000.000
154A164GLU-1-0.727-0.84443.446-6.338-6.3380.0000.0000.0000.000
155A165ALA0-0.0210.00746.2280.0550.0550.0000.0000.0000.000
156A166THR0-0.074-0.04539.746-0.063-0.0630.0000.0000.0000.000
157A167LEU0-0.006-0.01441.384-0.100-0.1000.0000.0000.0000.000
158A168GLU-1-0.814-0.91343.861-6.148-6.1480.0000.0000.0000.000
159A169ALA0-0.062-0.02043.6120.0180.0180.0000.0000.0000.000
160A170ARG10.7750.87936.1937.8707.8700.0000.0000.0000.000
161A171ARG10.8270.90042.3596.0306.0300.0000.0000.0000.000
162A172SER0-0.028-0.03441.6910.0240.0240.0000.0000.0000.000
163A173GLN00.0360.00644.5950.1690.1690.0000.0000.0000.000
164A174GLU-1-0.832-0.91840.171-7.172-7.1720.0000.0000.0000.000
165A175MET0-0.0080.00741.219-0.019-0.0190.0000.0000.0000.000
166A176ASP-1-0.801-0.86643.377-6.265-6.2650.0000.0000.0000.000
167A177TYR0-0.008-0.02044.8180.1220.1220.0000.0000.0000.000
168A178PHE00.008-0.00539.9860.0130.0130.0000.0000.0000.000
169A179MET0-0.001-0.01344.215-0.067-0.0670.0000.0000.0000.000
170A180GLU-1-0.915-0.95646.453-5.909-5.9090.0000.0000.0000.000
171A181ILE0-0.128-0.05746.6690.0810.0810.0000.0000.0000.000
172A182PHE0-0.034-0.03243.428-0.002-0.0020.0000.0000.0000.000
173A183VAL0-0.0140.00143.637-0.095-0.0950.0000.0000.0000.000
174A184PRO00.0350.02846.048-0.001-0.0010.0000.0000.0000.000
175A185SER00.0040.01346.9000.1090.1090.0000.0000.0000.000
176A186PHE0-0.0540.01540.785-0.040-0.0400.0000.0000.0000.000
177A187HIS0-0.092-0.07146.4380.1500.1500.0000.0000.0000.000