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: Z6MKN

Calculation Name: 5HK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HK8

Chain ID: A

ChEMBL ID:

UniProt ID: O23512

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3036147.037763
FMO2-HF: Nuclear repulsion 2944589.671687
FMO2-HF: Total energy -91557.366076
FMO2-MP2: Total energy -91827.5593


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
-7.103-1.2111.757-2.783-4.867-0.02
Interaction energy analysis for fragmet #1(A:10:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023
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].
3A12HIS00.0300.0203.003-2.777-0.4620.221-1.144-1.393-0.003
4A13PHE00.0380.0154.6490.3910.491-0.001-0.013-0.0860.000
5A14VAL0-0.015-0.0198.015-0.054-0.0540.0000.0000.0000.000
6A15PHE00.012-0.0019.8730.0720.0720.0000.0000.0000.000
7A16VAL00.002-0.00913.8320.0000.0000.0000.0000.0000.000
8A17HIS0-0.0080.00117.4820.0100.0100.0000.0000.0000.000
9A18GLY00.1160.05620.3170.0090.0090.0000.0000.0000.000
10A19ALA00.0170.00223.870-0.005-0.0050.0000.0000.0000.000
11A20SER0-0.017-0.00927.2500.0010.0010.0000.0000.0000.000
12A21HIS0-0.0140.01223.166-0.001-0.0010.0000.0000.0000.000
13A22GLY00.0700.01121.8860.0060.0060.0000.0000.0000.000
14A23ALA0-0.011-0.00916.883-0.004-0.0040.0000.0000.0000.000
15A24TRP00.0300.00017.459-0.022-0.0220.0000.0000.0000.000
16A25CYS0-0.069-0.02319.640-0.003-0.0030.0000.0000.0000.000
17A26TRP00.0650.01514.9310.0010.0010.0000.0000.0000.000
18A27TYR0-0.039-0.02315.555-0.025-0.0250.0000.0000.0000.000
19A28LYS10.7790.87615.8660.1230.1230.0000.0000.0000.000
20A29LEU0-0.0170.00413.3270.0130.0130.0000.0000.0000.000
21A30THR00.004-0.00810.7850.0070.0070.0000.0000.0000.000
22A31THR00.003-0.00210.318-0.079-0.0790.0000.0000.0000.000
23A32LEU0-0.026-0.00411.633-0.003-0.0030.0000.0000.0000.000
24A33LEU0-0.0010.0018.0470.0240.0240.0000.0000.0000.000
25A34ASP-1-0.830-0.9076.369-1.051-1.0510.0000.0000.0000.000
26A35ALA0-0.045-0.0187.104-0.060-0.0600.0000.0000.0000.000
27A36ALA0-0.055-0.0208.3990.0930.0930.0000.0000.0000.000
28A37GLY0-0.023-0.0044.9520.1850.258-0.001-0.013-0.0590.000
29A38PHE0-0.036-0.0212.669-4.210-1.8670.720-1.263-1.801-0.016
30A39LYS10.8490.9262.6660.2931.3360.814-0.365-1.491-0.001
31A40SER00.023-0.0123.9320.0470.0650.0040.015-0.0370.000
32A41THR0-0.024-0.0197.488-0.022-0.0220.0000.0000.0000.000
33A42SER0-0.0020.01210.1310.0110.0110.0000.0000.0000.000
34A43VAL0-0.0040.00713.7920.0080.0080.0000.0000.0000.000
35A44ASP-1-0.791-0.88016.528-0.194-0.1940.0000.0000.0000.000
36A45LEU0-0.036-0.01220.000-0.003-0.0030.0000.0000.0000.000
37A46THR0-0.052-0.05022.3080.0000.0000.0000.0000.0000.000
38A47GLY00.0470.01025.6500.0090.0090.0000.0000.0000.000
39A48ALA0-0.057-0.00723.3570.0070.0070.0000.0000.0000.000
40A49GLY00.036-0.00323.104-0.004-0.0040.0000.0000.0000.000
41A50ILE0-0.044-0.01521.1650.0150.0150.0000.0000.0000.000
42A51SER0-0.0090.01624.3740.0070.0070.0000.0000.0000.000
43A52LEU0-0.006-0.00925.4000.0100.0100.0000.0000.0000.000
44A53ILE0-0.0140.00127.9270.0090.0090.0000.0000.0000.000
45A54ASP-1-0.794-0.89129.818-0.087-0.0870.0000.0000.0000.000
46A55SER00.063-0.01330.1490.0000.0000.0000.0000.0000.000
47A56ASN0-0.079-0.03631.6080.0060.0060.0000.0000.0000.000
48A57ILE0-0.0050.00033.5230.0050.0050.0000.0000.0000.000
49A58VAL0-0.063-0.01928.710-0.001-0.0010.0000.0000.0000.000
50A59PHE0-0.009-0.02232.0570.0010.0010.0000.0000.0000.000
51A60ASP-1-0.765-0.88030.646-0.079-0.0790.0000.0000.0000.000
52A61SER00.023-0.00127.524-0.010-0.0100.0000.0000.0000.000
53A62ASP-1-0.782-0.87926.391-0.114-0.1140.0000.0000.0000.000
54A63GLN0-0.076-0.05426.024-0.009-0.0090.0000.0000.0000.000
55A64TYR00.0090.00224.283-0.010-0.0100.0000.0000.0000.000
56A65ASN00.0660.03222.439-0.021-0.0210.0000.0000.0000.000
57A66ARG10.8460.92221.3800.0990.0990.0000.0000.0000.000
58A67PRO00.0050.00019.720-0.010-0.0100.0000.0000.0000.000
59A68LEU00.0080.01315.492-0.029-0.0290.0000.0000.0000.000
60A69PHE00.014-0.00317.041-0.015-0.0150.0000.0000.0000.000
61A70SER0-0.0340.00618.7700.0120.0120.0000.0000.0000.000
62A71LEU00.0110.01411.343-0.010-0.0100.0000.0000.0000.000
63A72LEU00.004-0.00513.365-0.034-0.0340.0000.0000.0000.000
64A73SER0-0.007-0.02015.4580.0240.0240.0000.0000.0000.000
65A74ASP-1-0.902-0.95315.515-0.228-0.2280.0000.0000.0000.000
66A75LEU0-0.079-0.0149.571-0.045-0.0450.0000.0000.0000.000
67A76PRO00.0180.0039.5880.0690.0690.0000.0000.0000.000
68A77PRO0-0.008-0.00812.107-0.004-0.0040.0000.0000.0000.000
69A78HIS00.0180.01510.0810.0570.0570.0000.0000.0000.000
70A79HIS0-0.040-0.0156.1680.2140.2140.0000.0000.0000.000
71A80LYS10.8770.9408.750-0.101-0.1010.0000.0000.0000.000
72A81VAL0-0.025-0.0037.722-0.230-0.2300.0000.0000.0000.000
73A82ILE0-0.0100.0218.5190.1920.1920.0000.0000.0000.000
74A83LEU00.0150.01410.676-0.085-0.0850.0000.0000.0000.000
75A84VAL00.004-0.00612.1680.0430.0430.0000.0000.0000.000
76A85GLY00.0330.02114.972-0.020-0.0200.0000.0000.0000.000
77A86HIS0-0.014-0.01718.5610.0080.0080.0000.0000.0000.000
78A87SER00.0110.00921.2360.0020.0020.0000.0000.0000.000
79A88ILE00.009-0.00824.7860.0010.0010.0000.0000.0000.000
80A89GLY00.0240.02122.0180.0030.0030.0000.0000.0000.000
81A90GLY0-0.026-0.01321.230-0.012-0.0120.0000.0000.0000.000
82A91GLY00.0760.04422.3800.0020.0020.0000.0000.0000.000
83A92SER0-0.066-0.04821.2660.0050.0050.0000.0000.0000.000
84A93VAL0-0.027-0.00517.314-0.012-0.0120.0000.0000.0000.000
85A94THR00.0320.02019.7160.0010.0010.0000.0000.0000.000
86A95GLU-1-0.794-0.89122.547-0.085-0.0850.0000.0000.0000.000
87A96ALA0-0.027-0.01717.9990.0030.0030.0000.0000.0000.000
88A97LEU0-0.005-0.00618.1630.0000.0000.0000.0000.0000.000
89A98CYS0-0.068-0.02419.8060.0220.0220.0000.0000.0000.000
90A99LYS10.7870.90621.8280.1070.1070.0000.0000.0000.000
91A100PHE00.005-0.00217.208-0.004-0.0040.0000.0000.0000.000
92A101THR00.0280.01117.233-0.012-0.0120.0000.0000.0000.000
93A102ASP-1-0.914-0.95516.8350.0160.0160.0000.0000.0000.000
94A103LYS10.7710.86813.2790.2350.2350.0000.0000.0000.000
95A104ILE0-0.0100.00212.728-0.074-0.0740.0000.0000.0000.000
96A105SER0-0.067-0.04210.5350.0720.0720.0000.0000.0000.000
97A106MET00.0140.02112.1040.0730.0730.0000.0000.0000.000
98A107ALA00.0010.00713.949-0.069-0.0690.0000.0000.0000.000
99A108ILE0-0.029-0.01713.3150.0320.0320.0000.0000.0000.000
100A109TYR0-0.003-0.00516.935-0.026-0.0260.0000.0000.0000.000
101A110LEU0-0.015-0.01218.3420.0130.0130.0000.0000.0000.000
102A111ALA00.0250.00521.082-0.008-0.0080.0000.0000.0000.000
103A112ALA0-0.047-0.02422.577-0.003-0.0030.0000.0000.0000.000
104A113SER0-0.037-0.03024.6190.0130.0130.0000.0000.0000.000
105A114MET0-0.005-0.00523.982-0.010-0.0100.0000.0000.0000.000
106A115VAL0-0.0040.00425.6270.0080.0080.0000.0000.0000.000
107A116GLN00.0060.00827.408-0.004-0.0040.0000.0000.0000.000
108A117PRO00.0100.00326.281-0.001-0.0010.0000.0000.0000.000
109A118GLY0-0.013-0.00629.2750.0070.0070.0000.0000.0000.000
110A119SER0-0.080-0.03531.9110.0020.0020.0000.0000.0000.000
111A135ILE00.0030.02837.3450.0000.0000.0000.0000.0000.000
112A136TRP00.0230.00633.273-0.004-0.0040.0000.0000.0000.000
113A137GLU-1-0.930-0.96938.399-0.058-0.0580.0000.0000.0000.000
114A138TYR00.004-0.01338.440-0.002-0.0020.0000.0000.0000.000
115A139THR0-0.0140.00338.1540.0010.0010.0000.0000.0000.000
116A140TYR00.0370.00640.190-0.001-0.0010.0000.0000.0000.000
117A141GLY00.0100.00140.2990.0020.0020.0000.0000.0000.000
118A142GLU-1-0.815-0.88441.319-0.053-0.0530.0000.0000.0000.000
119A143GLY00.0060.01044.0240.0030.0030.0000.0000.0000.000
120A144THR0-0.001-0.02446.028-0.001-0.0010.0000.0000.0000.000
121A145ASP-1-0.882-0.91047.769-0.038-0.0380.0000.0000.0000.000
122A146LYS10.8120.89944.6880.0420.0420.0000.0000.0000.000
123A147PRO00.0320.01141.9480.0000.0000.0000.0000.0000.000
124A148PRO00.0020.00739.741-0.001-0.0010.0000.0000.0000.000
125A149THR0-0.025-0.01937.3840.0010.0010.0000.0000.0000.000
126A150GLY00.0080.00135.096-0.004-0.0040.0000.0000.0000.000
127A151VAL0-0.036-0.02033.6950.0050.0050.0000.0000.0000.000
128A152LEU00.0200.02232.613-0.007-0.0070.0000.0000.0000.000
129A153MET0-0.0100.00833.2490.0050.0050.0000.0000.0000.000
130A154LYS10.9060.94835.4280.0460.0460.0000.0000.0000.000
131A155PRO00.0300.01036.274-0.001-0.0010.0000.0000.0000.000
132A156GLU-1-0.867-0.95037.123-0.055-0.0550.0000.0000.0000.000
133A157PHE0-0.026-0.02137.5930.0020.0020.0000.0000.0000.000
134A158ILE00.0040.00232.106-0.001-0.0010.0000.0000.0000.000
135A159ARG10.9690.97632.6630.0570.0570.0000.0000.0000.000
136A160HIS0-0.027-0.00433.7370.0020.0020.0000.0000.0000.000
137A161TYR00.010-0.00533.5980.0020.0020.0000.0000.0000.000
138A162TYR00.0420.01328.507-0.001-0.0010.0000.0000.0000.000
139A163TYR0-0.039-0.01826.531-0.001-0.0010.0000.0000.0000.000
140A164SER00.0220.02330.107-0.001-0.0010.0000.0000.0000.000
141A165GLN0-0.062-0.03829.0890.0100.0100.0000.0000.0000.000
142A166SER0-0.002-0.01427.093-0.006-0.0060.0000.0000.0000.000
143A167PRO00.0000.00825.6430.0080.0080.0000.0000.0000.000
144A168LEU00.023-0.00328.824-0.003-0.0030.0000.0000.0000.000
145A169GLU-1-0.839-0.88825.860-0.115-0.1150.0000.0000.0000.000
146A170ASP-1-0.703-0.83724.313-0.143-0.1430.0000.0000.0000.000
147A171VAL0-0.0250.00527.014-0.002-0.0020.0000.0000.0000.000
148A172THR0-0.036-0.02730.2070.0020.0020.0000.0000.0000.000
149A173LEU00.0120.01923.4120.0020.0020.0000.0000.0000.000
150A174SER00.0430.00027.013-0.005-0.0050.0000.0000.0000.000
151A175SER0-0.078-0.04528.2280.0030.0030.0000.0000.0000.000
152A176LYS10.8000.88529.8330.0950.0950.0000.0000.0000.000
153A177LEU00.0130.01424.226-0.003-0.0030.0000.0000.0000.000
154A178LEU0-0.040-0.00727.249-0.005-0.0050.0000.0000.0000.000
155A179ARG10.7950.90227.2280.1320.1320.0000.0000.0000.000
156A180PRO00.0120.00230.4060.0010.0010.0000.0000.0000.000
157A181ALA00.0170.03029.865-0.006-0.0060.0000.0000.0000.000
158A182PRO00.0340.01628.7530.0070.0070.0000.0000.0000.000
159A183MET0-0.022-0.00331.8210.0010.0010.0000.0000.0000.000
160A184ARG10.7240.85334.3110.0590.0590.0000.0000.0000.000
161A185ALA00.0750.04629.5280.0020.0020.0000.0000.0000.000
162A186PHE00.008-0.02727.5330.0000.0000.0000.0000.0000.000
163A187GLN0-0.060-0.02331.1610.0060.0060.0000.0000.0000.000
164A188ASP-1-0.852-0.92132.170-0.050-0.0500.0000.0000.0000.000
165A189LEU0-0.0230.01025.826-0.001-0.0010.0000.0000.0000.000
166A190ASP-1-0.780-0.90526.714-0.062-0.0620.0000.0000.0000.000
167A191LYS10.7650.89828.9830.0550.0550.0000.0000.0000.000
168A192LEU0-0.024-0.01025.9330.0010.0010.0000.0000.0000.000
169A193PRO00.0230.00929.9060.0050.0050.0000.0000.0000.000
170A194PRO00.0100.00030.092-0.001-0.0010.0000.0000.0000.000
171A195ASN00.0470.02124.9130.0090.0090.0000.0000.0000.000
172A196PRO00.0110.00226.8950.0010.0010.0000.0000.0000.000
173A197GLU-1-0.819-0.89022.0230.0630.0630.0000.0000.0000.000
174A198ALA00.013-0.00721.9290.0070.0070.0000.0000.0000.000
175A199GLU-1-0.802-0.87222.3140.0130.0130.0000.0000.0000.000
176A200LYS10.7510.86221.524-0.046-0.0460.0000.0000.0000.000
177A201VAL0-0.0420.00216.4720.0250.0250.0000.0000.0000.000
178A202PRO0-0.0060.00815.880-0.014-0.0140.0000.0000.0000.000
179A203ARG10.8930.93017.752-0.034-0.0340.0000.0000.0000.000
180A204VAL0-0.031-0.02516.6850.0210.0210.0000.0000.0000.000
181A205TYR00.002-0.00819.525-0.023-0.0230.0000.0000.0000.000
182A206ILE0-0.031-0.02517.2930.0120.0120.0000.0000.0000.000
183A207LYS10.8740.90921.9290.0070.0070.0000.0000.0000.000
184A208THR0-0.046-0.02424.5780.0000.0000.0000.0000.0000.000
185A209ALA00.0060.01526.9540.0020.0020.0000.0000.0000.000
186A210LYS10.7640.87829.9650.0430.0430.0000.0000.0000.000
187A211ASP-1-0.738-0.85528.410-0.071-0.0710.0000.0000.0000.000
188A212ASN0-0.042-0.03130.9890.0060.0060.0000.0000.0000.000
189A213LEU0-0.077-0.03230.2360.0020.0020.0000.0000.0000.000
190A214PHE0-0.063-0.02527.6730.0020.0020.0000.0000.0000.000
191A215ASP-1-0.786-0.88030.981-0.030-0.0300.0000.0000.0000.000
192A216SER00.0450.00431.7530.0010.0010.0000.0000.0000.000
193A217VAL00.0180.01732.4420.0020.0020.0000.0000.0000.000
194A218ARG10.8790.93132.8390.0360.0360.0000.0000.0000.000
195A219GLN00.0130.00627.256-0.001-0.0010.0000.0000.0000.000
196A220ASP-1-0.787-0.87929.510-0.012-0.0120.0000.0000.0000.000
197A221LEU00.0290.02131.6070.0030.0030.0000.0000.0000.000
198A222LEU00.0050.00527.8690.0020.0020.0000.0000.0000.000
199A223VAL0-0.043-0.02426.5150.0030.0030.0000.0000.0000.000
200A224GLU-1-0.963-0.98628.8980.0060.0060.0000.0000.0000.000
201A225ASN0-0.092-0.05932.0410.0040.0040.0000.0000.0000.000
202A226TRP0-0.056-0.04723.707-0.003-0.0030.0000.0000.0000.000
203A227PRO00.0270.02426.947-0.002-0.0020.0000.0000.0000.000
204A228PRO0-0.0320.00122.5400.0030.0030.0000.0000.0000.000
205A229SER00.009-0.00220.1490.0060.0060.0000.0000.0000.000
206A230GLN0-0.0210.00016.0780.0020.0020.0000.0000.0000.000
207A231LEU00.0210.01121.671-0.016-0.0160.0000.0000.0000.000
208A232TYR0-0.061-0.03718.0970.0060.0060.0000.0000.0000.000
209A233VAL00.0370.02023.216-0.009-0.0090.0000.0000.0000.000
210A234LEU0-0.0290.00120.9880.0030.0030.0000.0000.0000.000
211A235GLU-1-0.842-0.95125.267-0.020-0.0200.0000.0000.0000.000
212A236ASP-1-0.863-0.92627.396-0.037-0.0370.0000.0000.0000.000
213A237SER0-0.045-0.03925.075-0.008-0.0080.0000.0000.0000.000
214A238ASP-1-0.710-0.80526.905-0.082-0.0820.0000.0000.0000.000
215A239HIS0-0.034-0.02026.775-0.009-0.0090.0000.0000.0000.000
216A240SER0-0.014-0.02324.045-0.011-0.0110.0000.0000.0000.000
217A241ALA00.0640.04021.245-0.006-0.0060.0000.0000.0000.000
218A242PHE0-0.014-0.01618.434-0.003-0.0030.0000.0000.0000.000
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