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: V54J1

Calculation Name: 5HA8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HA8

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0K0

Base Structure: X-ray

Registration Date: 2023-09-20

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1786414.291288
FMO2-HF: Nuclear repulsion 1719741.728478
FMO2-HF: Total energy -66672.56281
FMO2-MP2: Total energy -66868.565406


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-2.754-1.137-0.018-0.625-0.9730.002
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.027
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].
3A6ARG10.9370.9823.8151.1892.686-0.017-0.598-0.8820.002
4A7THR00.0070.0016.2500.1440.1440.0000.0000.0000.000
5A8VAL00.0260.0159.7380.0480.0480.0000.0000.0000.000
6A9VAL00.0000.00612.6680.0390.0390.0000.0000.0000.000
7A10LEU0-0.029-0.01216.352-0.010-0.0100.0000.0000.0000.000
8A11ALA00.018-0.00118.3650.0340.0340.0000.0000.0000.000
9A12ILE0-0.028-0.03621.573-0.001-0.0010.0000.0000.0000.000
10A13ASP-1-0.720-0.88224.396-0.177-0.1770.0000.0000.0000.000
11A14LEU0-0.0390.00725.7270.0150.0150.0000.0000.0000.000
12A15GLN0-0.008-0.00628.973-0.003-0.0030.0000.0000.0000.000
13A16ALA00.0330.00831.8660.0060.0060.0000.0000.0000.000
14A17GLY0-0.009-0.01035.3810.0070.0070.0000.0000.0000.000
15A18VAL0-0.118-0.04631.7520.0020.0020.0000.0000.0000.000
16A19THR00.024-0.01131.9330.0010.0010.0000.0000.0000.000
17A20PRO00.0180.02234.7260.0060.0060.0000.0000.0000.000
18A21GLY0-0.025-0.00438.5010.0000.0000.0000.0000.0000.000
19A22CYS0-0.091-0.02534.7510.0000.0000.0000.0000.0000.000
20A23PHE00.0420.00934.2290.0030.0030.0000.0000.0000.000
21A24ASP-1-0.838-0.89233.772-0.065-0.0650.0000.0000.0000.000
22A25GLU-1-0.858-0.92434.282-0.082-0.0820.0000.0000.0000.000
23A26GLU-1-0.915-0.95333.728-0.061-0.0610.0000.0000.0000.000
24A27GLY00.0150.00133.453-0.002-0.0020.0000.0000.0000.000
25A28VAL0-0.031-0.02128.771-0.004-0.0040.0000.0000.0000.000
26A29LEU00.0190.00928.954-0.011-0.0110.0000.0000.0000.000
27A30SER0-0.036-0.00829.391-0.007-0.0070.0000.0000.0000.000
28A31ARG10.7920.86326.8750.0660.0660.0000.0000.0000.000
29A32ALA00.0150.00824.872-0.008-0.0080.0000.0000.0000.000
30A33ALA00.0160.00724.503-0.016-0.0160.0000.0000.0000.000
31A34ALA0-0.0050.00225.252-0.005-0.0050.0000.0000.0000.000
32A35LEU0-0.034-0.02118.8040.0010.0010.0000.0000.0000.000
33A36VAL00.0060.00420.505-0.018-0.0180.0000.0000.0000.000
34A37GLU-1-0.895-0.94821.074-0.135-0.1350.0000.0000.0000.000
35A38ARG10.8150.88217.7710.0720.0720.0000.0000.0000.000
36A39ALA0-0.034-0.01016.8300.0040.0040.0000.0000.0000.000
37A40ARG10.7780.84216.7670.1670.1670.0000.0000.0000.000
38A41ALA0-0.042-0.01618.4320.0020.0020.0000.0000.0000.000
39A42GLY0-0.039-0.01215.7000.0270.0270.0000.0000.0000.000
40A43GLY0-0.036-0.00913.890-0.009-0.0090.0000.0000.0000.000
41A44VAL0-0.085-0.04111.949-0.091-0.0910.0000.0000.0000.000
42A45PRO0-0.011-0.00711.4350.0460.0460.0000.0000.0000.000
43A46VAL00.0400.02114.552-0.023-0.0230.0000.0000.0000.000
44A47VAL0-0.014-0.00915.7590.0020.0020.0000.0000.0000.000
45A48TRP0-0.011-0.01818.5000.0160.0160.0000.0000.0000.000
46A49VAL0-0.026-0.00621.382-0.015-0.0150.0000.0000.0000.000
47A50HIS00.0040.00723.8800.0090.0090.0000.0000.0000.000
48A51HIS00.0340.01527.619-0.016-0.0160.0000.0000.0000.000
49A52ASP-1-0.744-0.88430.115-0.162-0.1620.0000.0000.0000.000
50A53PRO0-0.094-0.05432.4230.0100.0100.0000.0000.0000.000
51A54VAL0-0.0350.00433.1120.0070.0070.0000.0000.0000.000
52A55GLY00.0220.01735.8070.0080.0080.0000.0000.0000.000
53A56VAL0-0.026-0.00433.7940.0000.0000.0000.0000.0000.000
54A57GLY0-0.017-0.00535.8570.0060.0060.0000.0000.0000.000
55A58THR0-0.065-0.03437.7200.0070.0070.0000.0000.0000.000
56A59PRO00.0520.00037.172-0.006-0.0060.0000.0000.0000.000
57A60GLU-1-0.868-0.92836.721-0.093-0.0930.0000.0000.0000.000
58A61TRP0-0.059-0.02429.292-0.009-0.0090.0000.0000.0000.000
59A62GLU-1-0.892-0.95932.142-0.147-0.1470.0000.0000.0000.000
60A63LEU0-0.012-0.00326.9470.0020.0020.0000.0000.0000.000
61A64ALA00.0090.01831.0700.0090.0090.0000.0000.0000.000
62A65ALA00.0020.02231.936-0.004-0.0040.0000.0000.0000.000
63A66PRO0-0.030-0.02931.5440.0010.0010.0000.0000.0000.000
64A67LEU0-0.014-0.01826.739-0.003-0.0030.0000.0000.0000.000
65A68HIS00.0160.00728.0100.0060.0060.0000.0000.0000.000
66A69ARG10.8830.95323.2050.2260.2260.0000.0000.0000.000
67A70ALA0-0.0130.00222.7250.0160.0160.0000.0000.0000.000
68A71GLU-1-0.900-0.97123.512-0.182-0.1820.0000.0000.0000.000
69A72GLY0-0.040-0.01720.262-0.006-0.0060.0000.0000.0000.000
70A73GLU-1-0.740-0.82018.788-0.285-0.2850.0000.0000.0000.000
71A74PRO00.0000.01016.9540.0350.0350.0000.0000.0000.000
72A75LEU0-0.0030.00120.2820.0050.0050.0000.0000.0000.000
73A76VAL0-0.021-0.00919.9550.0010.0010.0000.0000.0000.000
74A77ARG10.8590.92923.1800.1900.1900.0000.0000.0000.000
75A78LYS10.8060.90925.2560.1940.1940.0000.0000.0000.000
76A79ASN00.0590.01127.6980.0200.0200.0000.0000.0000.000
77A80TYR00.0130.00928.8200.0180.0180.0000.0000.0000.000
78A81ARG10.9440.96628.3360.1200.1200.0000.0000.0000.000
79A82ASP-1-0.761-0.88423.216-0.288-0.2880.0000.0000.0000.000
80A83SER00.027-0.00921.8910.0070.0070.0000.0000.0000.000
81A84PHE0-0.0040.01816.481-0.018-0.0180.0000.0000.0000.000
82A85ALA0-0.096-0.03821.875-0.002-0.0020.0000.0000.0000.000
83A86ASP-1-0.952-0.97325.340-0.195-0.1950.0000.0000.0000.000
84A87THR0-0.018-0.02722.427-0.002-0.0020.0000.0000.0000.000
85A88THR00.0610.02120.989-0.009-0.0090.0000.0000.0000.000
86A89LEU0-0.0030.01417.625-0.038-0.0380.0000.0000.0000.000
87A90ARG10.8960.93712.7360.7050.7050.0000.0000.0000.000
88A91GLU-1-0.885-0.94014.844-0.468-0.4680.0000.0000.0000.000
89A92THR0-0.020-0.01615.154-0.036-0.0360.0000.0000.0000.000
90A93LEU0-0.043-0.03412.341-0.059-0.0590.0000.0000.0000.000
91A94ASP-1-0.853-0.92010.658-1.139-1.1390.0000.0000.0000.000
92A95GLU-1-0.990-0.97310.384-0.732-0.7320.0000.0000.0000.000
93A96LEU0-0.071-0.04110.614-0.026-0.0260.0000.0000.0000.000
94A97GLY00.0000.0006.811-0.180-0.1800.0000.0000.0000.000
95A98ALA0-0.079-0.0416.043-0.718-0.7180.0000.0000.0000.000
96A99THR00.0460.0164.364-0.511-0.391-0.001-0.027-0.0910.000
97A100HIS0-0.0430.0027.5870.4820.4820.0000.0000.0000.000
98A101LEU00.0050.0079.9030.0160.0160.0000.0000.0000.000
99A102VAL00.0050.00313.6070.0920.0920.0000.0000.0000.000
100A103ILE00.004-0.00116.0600.0060.0060.0000.0000.0000.000
101A104THR0-0.042-0.04119.4950.0390.0390.0000.0000.0000.000
102A105GLY00.0400.00322.836-0.022-0.0220.0000.0000.0000.000
103A106ALA0-0.0130.01225.9140.0170.0170.0000.0000.0000.000
104A107GLN00.0440.01228.787-0.010-0.0100.0000.0000.0000.000
105A108SER00.013-0.02628.044-0.011-0.0110.0000.0000.0000.000
106A109ASP-1-0.808-0.89228.145-0.113-0.1130.0000.0000.0000.000
107A110PHE0-0.008-0.01530.126-0.001-0.0010.0000.0000.0000.000
108A111CYS0-0.0150.01027.138-0.006-0.0060.0000.0000.0000.000
109A112VAL00.0350.05223.791-0.021-0.0210.0000.0000.0000.000
110A113ARG10.9800.99623.8150.1010.1010.0000.0000.0000.000
111A114THR0-0.081-0.06324.323-0.005-0.0050.0000.0000.0000.000
112A115THR00.0520.03420.476-0.018-0.0180.0000.0000.0000.000
113A116MET0-0.0130.00819.537-0.032-0.0320.0000.0000.0000.000
114A117GLN0-0.036-0.02519.166-0.010-0.0100.0000.0000.0000.000
115A118ARG10.7910.89719.8790.3200.3200.0000.0000.0000.000
116A119ALA00.0290.00515.792-0.028-0.0280.0000.0000.0000.000
117A120ALA0-0.009-0.01115.475-0.052-0.0520.0000.0000.0000.000
118A121ALA0-0.029-0.00816.099-0.013-0.0130.0000.0000.0000.000
119A122GLU-1-0.887-0.94115.418-0.440-0.4400.0000.0000.0000.000
120A123GLY0-0.0190.00712.741-0.062-0.0620.0000.0000.0000.000
121A124TYR0-0.065-0.02610.687-0.032-0.0320.0000.0000.0000.000
122A125ASP-1-0.778-0.8678.144-0.443-0.4430.0000.0000.0000.000
123A126VAL0-0.056-0.03311.251-0.080-0.0800.0000.0000.0000.000
124A127THR0-0.006-0.04014.0210.1060.1060.0000.0000.0000.000
125A128LEU0-0.050-0.00416.446-0.026-0.0260.0000.0000.0000.000
126A129VAL00.0460.00919.9260.0310.0310.0000.0000.0000.000
127A130SER0-0.063-0.03321.9920.0080.0080.0000.0000.0000.000
128A131ASP-1-0.750-0.86025.078-0.072-0.0720.0000.0000.0000.000
129A132ALA00.0360.03124.2640.0040.0040.0000.0000.0000.000
130A133HIS10.8480.91425.2380.1000.1000.0000.0000.0000.000
131A134THR00.013-0.02127.6810.0120.0120.0000.0000.0000.000
132A135THR0-0.048-0.03931.229-0.011-0.0110.0000.0000.0000.000
133A136VAL00.0470.03833.8120.0060.0060.0000.0000.0000.000
134A137ASP-1-0.841-0.92037.591-0.057-0.0570.0000.0000.0000.000
135A138THR0-0.031-0.01138.299-0.001-0.0010.0000.0000.0000.000
136A139GLU-1-0.946-0.98741.145-0.044-0.0440.0000.0000.0000.000
137A140TRP0-0.025-0.01241.724-0.004-0.0040.0000.0000.0000.000
138A141GLU-1-0.937-0.97042.961-0.050-0.0500.0000.0000.0000.000
139A142GLY0-0.0300.00146.0240.0030.0030.0000.0000.0000.000
140A143VAL0-0.043-0.01743.0320.0030.0030.0000.0000.0000.000
141A144ARG10.9640.96943.7800.0370.0370.0000.0000.0000.000
142A145ILE0-0.046-0.01436.2810.0020.0020.0000.0000.0000.000
143A146SER00.0320.01839.260-0.004-0.0040.0000.0000.0000.000
144A147GLY00.0850.01936.156-0.003-0.0030.0000.0000.0000.000
145A148GLU-1-0.941-0.96134.732-0.045-0.0450.0000.0000.0000.000
146A149GLN00.018-0.00734.533-0.003-0.0030.0000.0000.0000.000
147A150ILE0-0.0120.01331.982-0.001-0.0010.0000.0000.0000.000
148A151VAL0-0.0050.01529.635-0.008-0.0080.0000.0000.0000.000
149A152ALA00.0220.00229.650-0.003-0.0030.0000.0000.0000.000
150A153HIS00.002-0.00130.2190.0060.0060.0000.0000.0000.000
151A154THR0-0.034-0.03125.996-0.005-0.0050.0000.0000.0000.000
152A155ASN00.0400.02325.567-0.019-0.0190.0000.0000.0000.000
153A156MET0-0.0370.00525.5840.0040.0040.0000.0000.0000.000
154A157TYR00.0120.01123.5090.0010.0010.0000.0000.0000.000
155A158PHE00.014-0.01517.6640.0030.0030.0000.0000.0000.000
156A159SER0-0.081-0.04921.4780.0040.0040.0000.0000.0000.000
157A160GLY00.000-0.00422.4850.0180.0180.0000.0000.0000.000
158A161LEU0-0.0320.00719.3560.0070.0070.0000.0000.0000.000
159A162ARG10.8540.91418.4620.0310.0310.0000.0000.0000.000
160A163TYR00.0670.03315.968-0.008-0.0080.0000.0000.0000.000
161A164PRO0-0.041-0.01715.7760.0240.0240.0000.0000.0000.000
162A165GLY0-0.008-0.01012.290-0.036-0.0360.0000.0000.0000.000
163A166GLN0-0.043-0.00910.538-0.003-0.0030.0000.0000.0000.000
164A167GLU-1-0.955-0.97911.1330.2490.2490.0000.0000.0000.000
165A168PHE0-0.040-0.03312.911-0.086-0.0860.0000.0000.0000.000
166A169VAL00.0080.00814.8480.0550.0550.0000.0000.0000.000
167A170ILE0-0.030-0.00217.428-0.035-0.0350.0000.0000.0000.000
168A171ALA0-0.002-0.01619.2170.0280.0280.0000.0000.0000.000
169A172THR0-0.026-0.00621.230-0.016-0.0160.0000.0000.0000.000
170A173HIS00.031-0.02921.4960.0010.0010.0000.0000.0000.000
171A174ASP-1-0.873-0.91221.579-0.035-0.0350.0000.0000.0000.000
172A175HIS10.8300.90520.9160.0100.0100.0000.0000.0000.000
173A176VAL00.0100.03315.9660.0270.0270.0000.0000.0000.000
174A177ALA00.0150.01013.1450.0020.0020.0000.0000.0000.000
175A178LEU00.0030.00811.786-0.057-0.0570.0000.0000.0000.000