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: 3J9ZL

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1884169.086419
FMO2-HF: Nuclear repulsion 1812656.158785
FMO2-HF: Total energy -71512.927634
FMO2-MP2: Total energy -71719.694562


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.
-54.231-52.627-0.01-0.818-0.7760.002
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 : 0.957 / q_NPA : 0.955
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].
3A4SER00.025-0.0093.8521.9963.600-0.010-0.818-0.7760.002
4A5HIS00.0250.0056.5081.1471.1470.0000.0000.0000.000
5A6PHE00.0680.0469.6231.7921.7920.0000.0000.0000.000
6A7PHE00.0680.01811.5371.2671.2670.0000.0000.0000.000
7A8ALA0-0.035-0.01112.5631.1851.1850.0000.0000.0000.000
8A9HIS0-0.032-0.03312.7401.8741.8740.0000.0000.0000.000
9A10LEU00.0720.04615.5931.0371.0370.0000.0000.0000.000
10A11SER0-0.021-0.00117.2401.3291.3290.0000.0000.0000.000
11A12ARG10.9560.97117.83115.93015.9300.0000.0000.0000.000
12A13LEU00.0630.04020.8420.5710.5710.0000.0000.0000.000
13A14LYS10.8510.92121.41314.63914.6390.0000.0000.0000.000
14A15LEU0-0.079-0.03622.5470.2890.2890.0000.0000.0000.000
15A16ILE0-0.0010.02122.9860.3400.3400.0000.0000.0000.000
16A17ASN0-0.060-0.04027.1580.3340.3340.0000.0000.0000.000
17A18ARG10.9130.95930.0639.4719.4710.0000.0000.0000.000
18A19TRP0-0.084-0.04532.7850.3090.3090.0000.0000.0000.000
19A20PRO00.0120.00333.5750.2140.2140.0000.0000.0000.000
20A21LEU0-0.050-0.02636.1800.1050.1050.0000.0000.0000.000
21A22MET00.0050.01439.5980.1590.1590.0000.0000.0000.000
22A23ARG10.8130.90240.5076.6436.6430.0000.0000.0000.000
23A24ASN0-0.019-0.00938.3190.0500.0500.0000.0000.0000.000
24A25VAL0-0.039-0.02341.2650.0300.0300.0000.0000.0000.000
25A26ARG10.7930.86134.1358.9318.9310.0000.0000.0000.000
26A27THR0-0.0170.00034.4350.0870.0870.0000.0000.0000.000
27A28GLU-1-0.733-0.84832.986-8.791-8.7910.0000.0000.0000.000
28A29ASN00.0040.00228.436-0.320-0.3200.0000.0000.0000.000
29A30VAL00.0850.02825.5230.1400.1400.0000.0000.0000.000
30A31SER0-0.041-0.00225.359-0.204-0.2040.0000.0000.0000.000
31A32GLU-1-0.847-0.89826.753-9.604-9.6040.0000.0000.0000.000
32A33HIS0-0.0050.00730.4830.2610.2610.0000.0000.0000.000
33A34SER00.024-0.00726.6370.1170.1170.0000.0000.0000.000
34A35LEU0-0.042-0.00728.2750.0280.0280.0000.0000.0000.000
35A36GLN00.0360.00929.7440.2450.2450.0000.0000.0000.000
36A37VAL00.0700.01230.9940.2440.2440.0000.0000.0000.000
37A38ALA0-0.018-0.01228.6240.1480.1480.0000.0000.0000.000
38A39MET0-0.053-0.02630.6740.2430.2430.0000.0000.0000.000
39A40VAL00.0220.00933.7190.2230.2230.0000.0000.0000.000
40A41ALA00.0210.01032.2040.2150.2150.0000.0000.0000.000
41A42HIS0-0.017-0.00832.4410.0120.0120.0000.0000.0000.000
42A43ALA0-0.0040.00134.1630.1990.1990.0000.0000.0000.000
43A44LEU0-0.0090.00137.3210.2140.2140.0000.0000.0000.000
44A45ALA00.0250.01135.1010.1870.1870.0000.0000.0000.000
45A46ALA0-0.011-0.00537.1190.1600.1600.0000.0000.0000.000
46A47ILE0-0.047-0.02038.8150.2190.2190.0000.0000.0000.000
47A48LYS10.8160.89438.7977.6517.6510.0000.0000.0000.000
48A49ASN0-0.030-0.01836.8220.2180.2180.0000.0000.0000.000
49A50ARG10.8710.94541.2987.2587.2580.0000.0000.0000.000
50A51LYS10.8710.93443.8516.4476.4470.0000.0000.0000.000
51A52PHE0-0.006-0.00144.7720.1560.1560.0000.0000.0000.000
52A53GLY00.0080.01945.0700.0170.0170.0000.0000.0000.000
53A54GLY0-0.0040.00840.803-0.041-0.0410.0000.0000.0000.000
54A55ASN0-0.026-0.02738.0500.0330.0330.0000.0000.0000.000
55A56VAL00.0180.02334.354-0.172-0.1720.0000.0000.0000.000
56A57ASN00.010-0.00129.414-0.208-0.2080.0000.0000.0000.000
57A58ALA00.0430.01931.280-0.190-0.1900.0000.0000.0000.000
58A59GLU-1-0.831-0.92128.147-9.419-9.4190.0000.0000.0000.000
59A60ARG10.9270.97722.22111.18711.1870.0000.0000.0000.000
60A61ILE0-0.0030.00627.324-0.206-0.2060.0000.0000.0000.000
61A62ALA00.0050.00428.836-0.110-0.1100.0000.0000.0000.000
62A63LEU0-0.008-0.01121.362-0.230-0.2300.0000.0000.0000.000
63A64LEU0-0.022-0.01124.168-0.412-0.4120.0000.0000.0000.000
64A65ALA00.0090.00925.814-0.135-0.1350.0000.0000.0000.000
65A66MET0-0.082-0.03923.5130.0220.0220.0000.0000.0000.000
66A67TYR0-0.049-0.03217.673-0.685-0.6850.0000.0000.0000.000
67A68HIS0-0.047-0.00523.0510.0960.0960.0000.0000.0000.000
68A69ASP-1-0.794-0.90525.142-10.425-10.4250.0000.0000.0000.000
69A70ALA0-0.031-0.02220.067-0.248-0.2480.0000.0000.0000.000
70A71SER00.012-0.00320.167-0.592-0.5920.0000.0000.0000.000
71A72GLU-1-0.815-0.91421.249-10.902-10.9020.0000.0000.0000.000
72A73VAL0-0.101-0.05217.943-0.011-0.0110.0000.0000.0000.000
73A74LEU0-0.097-0.05416.247-0.600-0.6000.0000.0000.0000.000
74A75THR0-0.046-0.02320.3420.0050.0050.0000.0000.0000.000
75A76GLY0-0.057-0.01624.1540.3440.3440.0000.0000.0000.000
76A77ASP-1-0.796-0.92326.435-9.278-9.2780.0000.0000.0000.000
77A78LEU0-0.042-0.01429.5250.1110.1110.0000.0000.0000.000
78A79PRO0-0.0030.00431.7240.1260.1260.0000.0000.0000.000
79A80THR0-0.016-0.01535.2240.1080.1080.0000.0000.0000.000
80A81PRO00.0120.02835.7790.2860.2860.0000.0000.0000.000
81A91GLN00.019-0.01833.096-0.099-0.0990.0000.0000.0000.000
82A92GLU-1-0.871-0.93530.323-9.383-9.3830.0000.0000.0000.000
83A93TYR00.0320.01127.465-0.282-0.2820.0000.0000.0000.000
84A94LYS10.8440.90228.3859.4149.4140.0000.0000.0000.000
85A95ALA00.0170.02027.296-0.304-0.3040.0000.0000.0000.000
86A96ILE0-0.010-0.01325.365-0.432-0.4320.0000.0000.0000.000
87A97GLU-1-0.798-0.87023.819-10.670-10.6700.0000.0000.0000.000
88A98LYS10.9050.93522.93210.73510.7350.0000.0000.0000.000
89A99ILE0-0.066-0.03220.320-0.604-0.6040.0000.0000.0000.000
90A100ALA0-0.0020.00519.219-0.771-0.7710.0000.0000.0000.000
91A101GLN00.008-0.02618.395-0.618-0.6180.0000.0000.0000.000
92A102GLN0-0.052-0.03015.161-0.125-0.1250.0000.0000.0000.000
93A103LYS10.8520.91413.97915.72815.7280.0000.0000.0000.000
94A104LEU0-0.0020.00113.654-1.324-1.3240.0000.0000.0000.000
95A105VAL00.0300.00713.109-1.256-1.2560.0000.0000.0000.000
96A106ASP-1-0.843-0.91411.390-18.085-18.0850.0000.0000.0000.000
97A107MET0-0.085-0.0228.678-2.063-2.0630.0000.0000.0000.000
98A108VAL0-0.0130.0337.966-2.899-2.8990.0000.0000.0000.000
99A109PRO0-0.003-0.0155.586-0.678-0.6780.0000.0000.0000.000
100A110GLU-1-0.814-0.9086.390-20.877-20.8770.0000.0000.0000.000
101A111GLU-1-1.000-0.9967.888-22.429-22.4290.0000.0000.0000.000
102A112LEU00.0100.0089.4030.8540.8540.0000.0000.0000.000
103A113ARG10.8030.8948.41723.06523.0650.0000.0000.0000.000
104A114ASP-1-0.865-0.94012.607-15.495-15.4950.0000.0000.0000.000
105A115ILE0-0.032-0.00814.8030.8990.8990.0000.0000.0000.000
106A116PHE0-0.005-0.01813.2980.5160.5160.0000.0000.0000.000
107A117ALA00.0540.02716.1050.4920.4920.0000.0000.0000.000
108A118PRO0-0.068-0.03417.6630.5760.5760.0000.0000.0000.000
109A119LEU0-0.057-0.03318.6540.5060.5060.0000.0000.0000.000
110A120ILE0-0.0330.00017.1240.0730.0730.0000.0000.0000.000
111A121ASP-1-0.746-0.85220.415-11.301-11.3010.0000.0000.0000.000
112A122GLU-1-0.839-0.89622.593-10.798-10.7980.0000.0000.0000.000
113A123HIS0-0.068-0.04021.9320.6860.6860.0000.0000.0000.000
114A124ALA00.001-0.01024.0140.2890.2890.0000.0000.0000.000
115A125TYR0-0.038-0.01225.0550.2900.2900.0000.0000.0000.000
116A126SER00.042-0.02028.6150.2840.2840.0000.0000.0000.000
117A127ASP-1-0.890-0.96432.061-8.384-8.3840.0000.0000.0000.000
118A128GLU-1-0.832-0.91334.942-7.511-7.5110.0000.0000.0000.000
119A129GLU-1-0.816-0.88128.963-9.701-9.7010.0000.0000.0000.000
120A130LYS10.8610.92429.4329.4389.4380.0000.0000.0000.000
121A131SER0-0.0580.00432.7530.0800.0800.0000.0000.0000.000
122A132LEU00.021-0.00134.4530.0300.0300.0000.0000.0000.000
123A133VAL00.0400.02829.6010.0530.0530.0000.0000.0000.000
124A134LYS10.9130.94332.7958.3818.3810.0000.0000.0000.000
125A135GLN00.0010.02935.1010.2150.2150.0000.0000.0000.000
126A136ALA00.0450.02334.2290.1320.1320.0000.0000.0000.000
127A137ASP-1-0.825-0.89633.211-8.660-8.6600.0000.0000.0000.000
128A138ALA0-0.004-0.00335.0100.0810.0810.0000.0000.0000.000
129A139LEU0-0.0020.00038.6320.1580.1580.0000.0000.0000.000
130A140CYS0-0.0240.00835.5970.0830.0830.0000.0000.0000.000
131A141ALA00.0170.00836.9920.0620.0620.0000.0000.0000.000
132A142TYR0-0.028-0.04038.4140.1510.1510.0000.0000.0000.000
133A143LEU0-0.006-0.00639.6530.1600.1600.0000.0000.0000.000
134A144LYS10.8510.93337.8008.2318.2310.0000.0000.0000.000
135A145CYS0-0.085-0.04540.5860.1170.1170.0000.0000.0000.000
136A146LEU0-0.0090.00343.5960.1560.1560.0000.0000.0000.000
137A147GLU-1-0.909-0.95740.563-7.634-7.6340.0000.0000.0000.000
138A148GLU-1-0.748-0.84841.346-7.406-7.4060.0000.0000.0000.000
139A149LEU0-0.038-0.03044.8390.1440.1440.0000.0000.0000.000
140A150ALA0-0.0180.00547.7630.1510.1510.0000.0000.0000.000
141A151ALA0-0.049-0.01246.3770.0940.0940.0000.0000.0000.000
142A152GLY00.0020.00048.3740.0340.0340.0000.0000.0000.000
143A153ASN0-0.073-0.05544.3240.2360.2360.0000.0000.0000.000
144A154ASN0-0.004-0.02847.8070.0020.0020.0000.0000.0000.000
145A155GLU-1-0.812-0.88345.255-6.833-6.8330.0000.0000.0000.000
146A156PHE00.0230.00340.270-0.046-0.0460.0000.0000.0000.000
147A157LEU00.0060.00745.688-0.018-0.0180.0000.0000.0000.000
148A158LEU0-0.007-0.00746.7870.0090.0090.0000.0000.0000.000
149A159ALA0-0.034-0.01142.460-0.039-0.0390.0000.0000.0000.000
150A160LYS10.8920.93444.2486.2196.2190.0000.0000.0000.000
151A161THR00.0350.01846.106-0.009-0.0090.0000.0000.0000.000
152A162ARG10.8920.93539.5747.4077.4070.0000.0000.0000.000
153A163LEU00.0080.01539.684-0.073-0.0730.0000.0000.0000.000
154A164GLU-1-0.739-0.84243.702-6.306-6.3060.0000.0000.0000.000
155A165ALA0-0.011-0.00146.7170.0370.0370.0000.0000.0000.000
156A166THR0-0.077-0.05340.096-0.065-0.0650.0000.0000.0000.000
157A167LEU0-0.003-0.00941.882-0.115-0.1150.0000.0000.0000.000
158A168GLU-1-0.827-0.91344.064-6.151-6.1510.0000.0000.0000.000
159A169ALA0-0.066-0.02843.7580.0110.0110.0000.0000.0000.000
160A170ARG10.7360.84736.2287.8507.8500.0000.0000.0000.000
161A171ARG10.7950.86142.1676.0246.0240.0000.0000.0000.000
162A172SER0-0.030-0.03041.8400.0280.0280.0000.0000.0000.000
163A173GLN00.0240.01144.7100.1660.1660.0000.0000.0000.000
164A174GLU-1-0.807-0.91840.351-7.163-7.1630.0000.0000.0000.000
165A175MET0-0.0110.01241.450-0.004-0.0040.0000.0000.0000.000
166A176ASP-1-0.788-0.85743.818-6.229-6.2290.0000.0000.0000.000
167A177TYR00.002-0.01645.2400.1190.1190.0000.0000.0000.000
168A178PHE00.018-0.00640.4900.0060.0060.0000.0000.0000.000
169A179MET0-0.005-0.01544.717-0.079-0.0790.0000.0000.0000.000
170A180GLU-1-0.920-0.95047.004-5.858-5.8580.0000.0000.0000.000
171A181ILE0-0.102-0.04647.1330.0710.0710.0000.0000.0000.000
172A182PHE0-0.055-0.03643.793-0.032-0.0320.0000.0000.0000.000
173A183VAL00.0000.00644.017-0.053-0.0530.0000.0000.0000.000
174A184PRO00.0340.02346.174-0.015-0.0150.0000.0000.0000.000
175A185SER0-0.015-0.00346.7320.1150.1150.0000.0000.0000.000
176A186PHE0-0.058-0.00241.112-0.042-0.0420.0000.0000.0000.000
177A187HIS0-0.077-0.04746.6600.1640.1640.0000.0000.0000.000