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: 856LY

Calculation Name: 5HC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HC1

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2487953.275163
FMO2-HF: Nuclear repulsion 2402733.150168
FMO2-HF: Total energy -85220.124995
FMO2-MP2: Total energy -85465.36176


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.2261.534-0.02-0.698-0.59-0.001
Interaction energy analysis for fragmet #1(A:0:GLY)
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 : -0.006
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].
3A2ASN00.0030.0153.8221.1202.428-0.020-0.698-0.590-0.001
4A3LYS10.8430.8956.951-0.220-0.2200.0000.0000.0000.000
5A4ILE0-0.0100.01610.0760.0200.0200.0000.0000.0000.000
6A5SER00.0600.03012.815-0.054-0.0540.0000.0000.0000.000
7A6CYS00.0090.02716.0060.0050.0050.0000.0000.0000.000
8A7LEU00.0330.01119.7440.0210.0210.0000.0000.0000.000
9A8PRO00.0280.01320.419-0.016-0.0160.0000.0000.0000.000
10A9ARG10.8760.91522.388-0.046-0.0460.0000.0000.0000.000
11A10VAL0-0.034-0.00723.120-0.007-0.0070.0000.0000.0000.000
12A11ALA00.0560.01821.102-0.009-0.0090.0000.0000.0000.000
13A12GLN0-0.015-0.01023.210-0.005-0.0050.0000.0000.0000.000
14A13ASN0-0.114-0.06825.6500.0010.0010.0000.0000.0000.000
15A14LEU0-0.060-0.01825.055-0.003-0.0030.0000.0000.0000.000
16A15GLY0-0.0320.00027.018-0.005-0.0050.0000.0000.0000.000
17A16TYR0-0.066-0.04621.338-0.005-0.0050.0000.0000.0000.000
18A17HIS00.024-0.01223.0930.0130.0130.0000.0000.0000.000
19A18TYR00.000-0.00119.7190.0120.0120.0000.0000.0000.000
20A19SER00.017-0.01514.640-0.013-0.0130.0000.0000.0000.000
21A20PRO0-0.003-0.00412.1830.0370.0370.0000.0000.0000.000
22A21ASP-1-0.790-0.8589.201-0.055-0.0550.0000.0000.0000.000
23A22LEU0-0.027-0.00511.0920.1280.1280.0000.0000.0000.000
24A23PRO0-0.007-0.01412.695-0.013-0.0130.0000.0000.0000.000
25A24GLY0-0.022-0.00215.383-0.012-0.0120.0000.0000.0000.000
26A25PHE0-0.024-0.00516.880-0.029-0.0290.0000.0000.0000.000
27A26CYS0-0.040-0.01219.2290.0210.0210.0000.0000.0000.000
28A27PRO00.0620.03317.141-0.012-0.0120.0000.0000.0000.000
29A28ILE00.005-0.01316.551-0.016-0.0160.0000.0000.0000.000
30A29PRO0-0.008-0.00115.7110.0100.0100.0000.0000.0000.000
31A30LYS10.9220.92411.484-0.135-0.1350.0000.0000.0000.000
32A31GLU-1-0.836-0.89013.9270.0350.0350.0000.0000.0000.000
33A32LEU0-0.005-0.01916.766-0.014-0.0140.0000.0000.0000.000
34A33ALA0-0.0270.00215.287-0.002-0.0020.0000.0000.0000.000
35A34GLU-1-0.921-0.95817.188-0.114-0.1140.0000.0000.0000.000
36A35HIS0-0.082-0.04119.0920.0020.0020.0000.0000.0000.000
37A36TRP0-0.036-0.01521.1310.0110.0110.0000.0000.0000.000
38A37PRO00.0190.01620.773-0.012-0.0120.0000.0000.0000.000
39A38VAL0-0.041-0.00416.3520.0180.0180.0000.0000.0000.000
40A39VAL00.0190.01217.098-0.020-0.0200.0000.0000.0000.000
41A40SER0-0.007-0.01511.961-0.001-0.0010.0000.0000.0000.000
42A41ASN0-0.043-0.0339.4750.0630.0630.0000.0000.0000.000
43A42ASP-1-0.860-0.8958.636-0.811-0.8110.0000.0000.0000.000
44A43ARG10.8200.91311.5400.3300.3300.0000.0000.0000.000
45A44TYR0-0.001-0.03111.1130.0200.0200.0000.0000.0000.000
46A45PRO0-0.006-0.00517.113-0.002-0.0020.0000.0000.0000.000
47A46ASN00.002-0.00420.6810.0040.0040.0000.0000.0000.000
48A47CYS0-0.055-0.01216.0330.0070.0070.0000.0000.0000.000
49A48LEU00.0240.03819.206-0.004-0.0040.0000.0000.0000.000
50A49GLN00.006-0.01312.5650.0560.0560.0000.0000.0000.000
51A50ILE0-0.024-0.01614.8460.0220.0220.0000.0000.0000.000
52A51THR00.0120.00612.960-0.091-0.0910.0000.0000.0000.000
53A52LEU00.0450.01110.7200.0610.0610.0000.0000.0000.000
54A53GLN0-0.0020.00314.3660.0400.0400.0000.0000.0000.000
55A54GLN0-0.024-0.00416.417-0.011-0.0110.0000.0000.0000.000
56A55VAL0-0.0050.00615.405-0.030-0.0300.0000.0000.0000.000
57A56CYS0-0.059-0.02918.0670.0050.0050.0000.0000.0000.000
58A57GLU-1-0.893-0.95821.741-0.124-0.1240.0000.0000.0000.000
59A58LEU0-0.020-0.01724.7170.0100.0100.0000.0000.0000.000
60A59SER0-0.041-0.02720.0980.0010.0010.0000.0000.0000.000
61A60LYS10.8820.92122.5520.0700.0700.0000.0000.0000.000
62A61PRO00.0060.01522.392-0.002-0.0020.0000.0000.0000.000
63A62CYS0-0.024-0.01322.4060.0140.0140.0000.0000.0000.000
64A63SER0-0.0010.00022.6150.0020.0020.0000.0000.0000.000
65A64ALA0-0.020-0.01723.5570.0040.0040.0000.0000.0000.000
66A65GLY00.0770.05022.8250.0000.0000.0000.0000.0000.000
67A66TYR0-0.051-0.02916.502-0.009-0.0090.0000.0000.0000.000
68A67MET0-0.0020.00317.0990.0010.0010.0000.0000.0000.000
69A68VAL00.0010.01311.414-0.015-0.0150.0000.0000.0000.000
70A69GLY00.003-0.01313.0740.0660.0660.0000.0000.0000.000
71A70GLN00.023-0.01713.531-0.083-0.0830.0000.0000.0000.000
72A71SER0-0.0460.00716.452-0.025-0.0250.0000.0000.0000.000
73A72VAL00.012-0.01117.7700.0010.0010.0000.0000.0000.000
74A73PHE0-0.042-0.02016.3140.0050.0050.0000.0000.0000.000
75A74VAL0-0.007-0.00221.085-0.012-0.0120.0000.0000.0000.000
76A75GLN0-0.026-0.01223.1310.0030.0030.0000.0000.0000.000
77A76THR00.000-0.00123.0940.0040.0040.0000.0000.0000.000
78A77PRO00.0090.01324.816-0.009-0.0090.0000.0000.0000.000
79A78GLY00.0120.00927.6210.0000.0000.0000.0000.0000.000
80A79VAL0-0.029-0.01321.452-0.010-0.0100.0000.0000.0000.000
81A80THR0-0.047-0.01220.7050.0130.0130.0000.0000.0000.000
82A81SER0-0.041-0.04519.657-0.005-0.0050.0000.0000.0000.000
83A82TYR00.005-0.01117.180-0.004-0.0040.0000.0000.0000.000
84A83TRP00.0220.00717.5770.0110.0110.0000.0000.0000.000
85A84LEU0-0.019-0.00417.949-0.011-0.0110.0000.0000.0000.000
86A85THR00.0210.01718.4000.0050.0050.0000.0000.0000.000
87A86GLU-1-0.758-0.84019.855-0.080-0.0800.0000.0000.0000.000
88A87TRP0-0.032-0.02917.3850.0010.0010.0000.0000.0000.000
89A88VAL00.025-0.00722.2020.0110.0110.0000.0000.0000.000
90A89ASP-1-0.839-0.91025.131-0.076-0.0760.0000.0000.0000.000
91A90GLY0-0.036-0.01422.135-0.002-0.0020.0000.0000.0000.000
92A91LYS10.9140.96222.4910.0760.0760.0000.0000.0000.000
93A92ALA00.0240.02522.4690.0050.0050.0000.0000.0000.000
94A93ARG10.8170.87224.2360.0800.0800.0000.0000.0000.000
95A94ALA00.0060.00926.012-0.004-0.0040.0000.0000.0000.000
96A95LEU00.0140.01123.2780.0070.0070.0000.0000.0000.000
97A96PRO0-0.023-0.00527.8370.0010.0010.0000.0000.0000.000
98A97ASP-1-0.801-0.90629.376-0.054-0.0540.0000.0000.0000.000
99A98SER0-0.065-0.05929.0610.0060.0060.0000.0000.0000.000
100A99LEU0-0.0190.01230.292-0.003-0.0030.0000.0000.0000.000
101A100PHE00.0260.00926.118-0.001-0.0010.0000.0000.0000.000
102A101SER0-0.015-0.02728.0750.0020.0020.0000.0000.0000.000
103A102SER0-0.006-0.01526.736-0.002-0.0020.0000.0000.0000.000
104A103GLY00.0280.01625.4250.0030.0030.0000.0000.0000.000
105A104ARG10.7630.89026.438-0.013-0.0130.0000.0000.0000.000
106A105PHE0-0.015-0.02129.2560.0050.0050.0000.0000.0000.000
107A106GLU-1-0.816-0.89825.0310.0590.0590.0000.0000.0000.000
108A107THR0-0.025-0.01724.6560.0110.0110.0000.0000.0000.000
109A108ASN0-0.082-0.03327.444-0.006-0.0060.0000.0000.0000.000
110A109SER00.0390.02830.023-0.004-0.0040.0000.0000.0000.000
111A110ARG10.9050.93431.888-0.049-0.0490.0000.0000.0000.000
112A111ALA00.0220.02532.508-0.003-0.0030.0000.0000.0000.000
113A112PHE00.0160.00033.508-0.001-0.0010.0000.0000.0000.000
114A113LEU0-0.046-0.02428.6020.0020.0020.0000.0000.0000.000
115A114ASP-1-0.839-0.89131.158-0.005-0.0050.0000.0000.0000.000
116A115GLU-1-0.801-0.87933.4530.0040.0040.0000.0000.0000.000
117A116ALA00.032-0.00735.5760.0000.0000.0000.0000.0000.000
118A117GLU-1-0.752-0.86834.0910.0100.0100.0000.0000.0000.000
119A118GLU-1-0.901-0.94537.0030.0130.0130.0000.0000.0000.000
120A119LYS10.8450.89539.611-0.001-0.0010.0000.0000.0000.000
121A120PHE0-0.0080.01439.274-0.001-0.0010.0000.0000.0000.000
122A121ALA00.0460.01440.667-0.001-0.0010.0000.0000.0000.000
123A122ALA0-0.011-0.00642.4070.0000.0000.0000.0000.0000.000
124A123ALA0-0.043-0.02544.0820.0000.0000.0000.0000.0000.000
125A124HIS10.7900.89742.7410.0040.0040.0000.0000.0000.000
126A125PRO00.0700.03245.4510.0010.0010.0000.0000.0000.000
127A126HIS0-0.063-0.05547.6190.0020.0020.0000.0000.0000.000
128A127ALA00.0010.01743.0180.0000.0000.0000.0000.0000.000
129A128CYS0-0.0300.00242.8690.0010.0010.0000.0000.0000.000
130A129LEU0-0.0160.00744.1950.0020.0020.0000.0000.0000.000
131A130GLY0-0.015-0.00847.128-0.001-0.0010.0000.0000.0000.000
132A131GLU-1-0.819-0.92245.1930.0160.0160.0000.0000.0000.000
133A132ILE0-0.027-0.00848.3240.0000.0000.0000.0000.0000.000
134A133ASN0-0.042-0.01950.4440.0000.0000.0000.0000.0000.000
135A134LYS10.9440.98849.302-0.007-0.0070.0000.0000.0000.000
136A135SER00.0200.01346.682-0.001-0.0010.0000.0000.0000.000
137A136THR0-0.013-0.02248.5760.0010.0010.0000.0000.0000.000
138A137VAL0-0.0530.00843.2120.0000.0000.0000.0000.0000.000
139A138GLY0-0.001-0.01046.3140.0010.0010.0000.0000.0000.000
140A139GLY00.0400.00542.4690.0010.0010.0000.0000.0000.000
141A140SER0-0.079-0.03242.441-0.002-0.0020.0000.0000.0000.000
142A141ALA00.0450.01741.4510.0010.0010.0000.0000.0000.000
143A142PHE00.0050.01636.5570.0000.0000.0000.0000.0000.000
144A143ILE0-0.029-0.02332.7980.0010.0010.0000.0000.0000.000
145A144PHE0-0.010-0.00635.8990.0020.0020.0000.0000.0000.000
146A145SER0-0.051-0.01737.9500.0000.0000.0000.0000.0000.000
147A146GLN00.0310.00341.6450.0010.0010.0000.0000.0000.000
148A147TYR0-0.015-0.02444.0620.0010.0010.0000.0000.0000.000
149A148LEU0-0.0200.01939.2050.0000.0000.0000.0000.0000.000
150A149PRO0-0.0010.00342.1740.0000.0000.0000.0000.0000.000
151A150PRO00.0220.00240.1570.0010.0010.0000.0000.0000.000
152A151LEU0-0.036-0.01037.7260.0030.0030.0000.0000.0000.000
153A152LEU00.019-0.00636.240-0.004-0.0040.0000.0000.0000.000
154A153PRO00.0170.02735.5800.0030.0030.0000.0000.0000.000
155A154ALA00.0720.00933.114-0.004-0.0040.0000.0000.0000.000
156A155ASP-1-0.912-0.95935.2500.0450.0450.0000.0000.0000.000
157A156ALA00.0030.01137.892-0.003-0.0030.0000.0000.0000.000
158A157VAL0-0.029-0.01337.698-0.004-0.0040.0000.0000.0000.000
159A158ALA0-0.020-0.02137.2270.0020.0020.0000.0000.0000.000
160A159LEU0-0.0240.00630.512-0.003-0.0030.0000.0000.0000.000
161A160VAL00.0300.01034.368-0.001-0.0010.0000.0000.0000.000
162A161GLY00.0270.02831.3820.0000.0000.0000.0000.0000.000
163A162ALA0-0.011-0.01230.5950.0000.0000.0000.0000.0000.000
164A163SER0-0.037-0.02032.197-0.005-0.0050.0000.0000.0000.000
165A164LEU0-0.0220.00534.6150.0030.0030.0000.0000.0000.000
166A165ALA0-0.0060.00534.1350.0000.0000.0000.0000.0000.000
167A166GLY00.0500.02335.969-0.001-0.0010.0000.0000.0000.000
168A167LYS10.9070.92538.172-0.033-0.0330.0000.0000.0000.000
169A168ALA00.0370.03941.657-0.002-0.0020.0000.0000.0000.000
170A169ALA00.0060.00642.930-0.001-0.0010.0000.0000.0000.000
171A170LYS10.9230.94945.071-0.017-0.0170.0000.0000.0000.000
172A171ALA00.0260.02541.6920.0020.0020.0000.0000.0000.000
173A172ALA0-0.017-0.00243.306-0.002-0.0020.0000.0000.0000.000
174A173CYS00.0270.01242.081-0.001-0.0010.0000.0000.0000.000
175A174SER0-0.035-0.02339.4030.0000.0000.0000.0000.0000.000
176A175VAL00.0240.03635.273-0.001-0.0010.0000.0000.0000.000
177A176VAL00.0200.00336.0280.0000.0000.0000.0000.0000.000
178A177ASP-1-0.749-0.88530.1070.0330.0330.0000.0000.0000.000
179A178VAL00.0200.00231.3120.0000.0000.0000.0000.0000.000
180A179TYR0-0.029-0.03030.650-0.001-0.0010.0000.0000.0000.000
181A180ALA00.0320.01832.648-0.004-0.0040.0000.0000.0000.000
182A181PRO00.016-0.00434.692-0.002-0.0020.0000.0000.0000.000
183A182SER0-0.063-0.03432.613-0.004-0.0040.0000.0000.0000.000
184A183PHE00.015-0.01134.667-0.002-0.0020.0000.0000.0000.000
185A184GLU-1-0.801-0.90137.919-0.013-0.0130.0000.0000.0000.000
186A185PRO0-0.005-0.00236.1760.0000.0000.0000.0000.0000.000
187A186TYR0-0.036-0.01435.552-0.001-0.0010.0000.0000.0000.000
188A187LEU0-0.045-0.03541.6550.0020.0020.0000.0000.0000.000
189A188HIS0-0.057-0.02743.6930.0010.0010.0000.0000.0000.000
190A189PRO0-0.067-0.01246.488-0.001-0.0010.0000.0000.0000.000
191A190GLU-1-0.800-0.91048.249-0.018-0.0180.0000.0000.0000.000
192A191THR0-0.095-0.04551.2680.0010.0010.0000.0000.0000.000
193A192LEU00.0010.00552.2560.0000.0000.0000.0000.0000.000
194A193SER00.0230.01151.3490.0000.0000.0000.0000.0000.000
195A194ARG10.9520.97845.8180.0150.0150.0000.0000.0000.000
196A195VAL00.0330.00245.3830.0010.0010.0000.0000.0000.000
197A196TYR00.0060.01341.365-0.002-0.0020.0000.0000.0000.000
198A197LYS10.9150.94740.6950.0190.0190.0000.0000.0000.000
199A198ILE00.0390.02136.615-0.003-0.0030.0000.0000.0000.000
200A199MET0-0.0090.00132.2480.0020.0020.0000.0000.0000.000
201A200ILE00.0410.04031.501-0.002-0.0020.0000.0000.0000.000
202A201ASP-1-0.772-0.88027.7770.0110.0110.0000.0000.0000.000
203A202PHE00.016-0.00924.5650.0010.0010.0000.0000.0000.000
204A203LYS10.9110.97330.027-0.012-0.0120.0000.0000.0000.000
205A204PRO0-0.014-0.02032.8700.0000.0000.0000.0000.0000.000
206A205CYS0-0.072-0.02836.1710.0040.0040.0000.0000.0000.000
207A206ARG10.9480.98138.9660.0030.0030.0000.0000.0000.000
208A207LEU00.0430.02839.6590.0020.0020.0000.0000.0000.000
209A208MET0-0.042-0.00542.507-0.002-0.0020.0000.0000.0000.000
210A209VAL0-0.004-0.01444.2500.0010.0010.0000.0000.0000.000
211A210TRP0-0.0020.00347.155-0.001-0.0010.0000.0000.0000.000
212A211ARG10.9310.95949.4770.0120.0120.0000.0000.0000.000
213A212ASN0-0.032-0.02049.3610.0000.0000.0000.0000.0000.000
214A213ALA0-0.0010.01650.1650.0010.0010.0000.0000.0000.000
215A214THR0-0.023-0.02247.6660.0010.0010.0000.0000.0000.000
216A215PHE00.005-0.00440.254-0.002-0.0020.0000.0000.0000.000
217A216TYR00.0480.01542.8870.0010.0010.0000.0000.0000.000
218A217VAL00.0430.02837.927-0.002-0.0020.0000.0000.0000.000
219A218GLN0-0.021-0.01741.1380.0000.0000.0000.0000.0000.000