Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Q89LY

Calculation Name: 4HYN-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYN

Chain ID: A

ChEMBL ID:

UniProt ID: G4FDE4

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2205861.848337
FMO2-HF: Nuclear repulsion 2126761.686656
FMO2-HF: Total energy -79100.161681
FMO2-MP2: Total energy -79324.360932


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:1:ALA )


Summations of interaction energy for fragment #1(A:1:ALA )
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.
-5.366-4.018-0.002-0.592-0.7530
Interaction energy analysis for fragmet #1(A:1:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.062
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].
3A24VAL 0-0.045-0.0443.8420.4401.736-0.002-0.583-0.7100.000
4A25LEU 0-0.0220.0065.6890.7030.7030.0000.0000.0000.000
5A26THR 0-0.043-0.0259.0350.2400.2400.0000.0000.0000.000
6A27PRO 0-0.032-0.04410.751-0.037-0.0370.0000.0000.0000.000
7A28GLU -1-0.857-0.91513.815-0.085-0.0850.0000.0000.0000.000
8A29GLU -1-0.853-0.92911.287-0.649-0.6490.0000.0000.0000.000
9A30LYS 10.8640.9349.3010.4440.4440.0000.0000.0000.000
10A31ASP -1-0.877-0.94015.411-0.050-0.0500.0000.0000.0000.000
11A32MET 0-0.0120.02417.1480.0090.0090.0000.0000.0000.000
12A33ILE 0-0.061-0.02716.0950.0050.0050.0000.0000.0000.000
13A34GLY 00.0450.01619.2970.0140.0140.0000.0000.0000.000
14A35GLU -1-0.962-0.97621.424-0.084-0.0840.0000.0000.0000.000
15A36ILE 0-0.025-0.02221.8500.0100.0100.0000.0000.0000.000
16A37GLY 00.0040.00923.2530.0040.0040.0000.0000.0000.000
17A38ASN 0-0.012-0.03124.3780.0170.0170.0000.0000.0000.000
18A39ILE 0-0.0300.00227.2760.0090.0090.0000.0000.0000.000
19A40ALA 0-0.006-0.00626.6090.0060.0060.0000.0000.0000.000
20A41MET 00.004-0.00226.5750.0030.0030.0000.0000.0000.000
21A42GLY 00.0670.03728.6600.0090.0090.0000.0000.0000.000
22A43SER 0-0.028-0.02131.3170.0110.0110.0000.0000.0000.000
23A44ALA 0-0.031-0.02131.0060.0050.0050.0000.0000.0000.000
24A45ALA 00.0300.01732.4980.0040.0040.0000.0000.0000.000
25A46THR 00.0150.00934.1710.0080.0080.0000.0000.0000.000
26A47THR 0-0.039-0.01936.1750.0050.0050.0000.0000.0000.000
27A48LEU 0-0.003-0.00335.1560.0040.0040.0000.0000.0000.000
28A49SER 0-0.030-0.06337.8220.0050.0050.0000.0000.0000.000
29A50MET 0-0.056-0.01939.8210.0040.0040.0000.0000.0000.000
30A51ILE 0-0.054-0.01439.5990.0020.0020.0000.0000.0000.000
31A52LEU 0-0.040-0.01439.1680.0030.0030.0000.0000.0000.000
32A53GLY 0-0.025-0.01243.1290.0010.0010.0000.0000.0000.000
33A54ARG 10.8630.92741.3750.0460.0460.0000.0000.0000.000
34A55ASP -1-0.871-0.88540.087-0.046-0.0460.0000.0000.0000.000
35A56ILE 0-0.058-0.04634.351-0.001-0.0010.0000.0000.0000.000
36A57HIS 00.0020.01332.338-0.005-0.0050.0000.0000.0000.000
37A58ILE 0-0.015-0.02327.944-0.003-0.0030.0000.0000.0000.000
38A59THR 00.0130.02126.1530.0040.0040.0000.0000.0000.000
39A60VAL 0-0.015-0.00821.100-0.009-0.0090.0000.0000.0000.000
40A61PRO 0-0.050-0.01022.4130.0030.0030.0000.0000.0000.000
41A62THR 0-0.0010.00116.6120.0170.0170.0000.0000.0000.000
42A63VAL 00.0220.01514.474-0.031-0.0310.0000.0000.0000.000
43A64ARG 10.8310.89911.5340.2480.2480.0000.0000.0000.000
44A65GLU -1-0.784-0.8856.567-2.369-2.3690.0000.0000.0000.000
45A66GLU -1-0.874-0.9268.257-0.344-0.3440.0000.0000.0000.000
46A67LYS 10.9480.9774.3420.4650.5170.000-0.009-0.0430.000
47A68MET 00.0290.0208.0350.2360.2360.0000.0000.0000.000
48A69LYS 10.7640.8758.5780.4450.4450.0000.0000.0000.000
49A70ASN 0-0.032-0.0278.8830.1310.1310.0000.0000.0000.000
50A71VAL 00.0650.05712.2810.0500.0500.0000.0000.0000.000
51A72LYS 10.8000.89214.4390.1990.1990.0000.0000.0000.000
52A73SER 0-0.044-0.02414.9670.0280.0280.0000.0000.0000.000
53A74ASP -1-0.900-0.93514.319-0.242-0.2420.0000.0000.0000.000
54A75PHE 0-0.077-0.03917.1960.0210.0210.0000.0000.0000.000
55A76SER 0-0.016-0.00920.8100.0030.0030.0000.0000.0000.000
56A77GLY 00.0470.02823.861-0.001-0.0010.0000.0000.0000.000
57A78GLU -1-0.923-0.97626.582-0.092-0.0920.0000.0000.0000.000
58A79GLN 0-0.043-0.03424.418-0.002-0.0020.0000.0000.0000.000
59A80VAL 0-0.0060.00128.047-0.001-0.0010.0000.0000.0000.000
60A81VAL 0-0.015-0.00423.800-0.009-0.0090.0000.0000.0000.000
61A82VAL 00.0150.00026.3410.0080.0080.0000.0000.0000.000
62A83SER 0-0.025-0.01424.754-0.016-0.0160.0000.0000.0000.000
63A84VAL 0-0.001-0.00225.4160.0170.0170.0000.0000.0000.000
64A85GLU -1-0.931-0.98023.868-0.283-0.2830.0000.0000.0000.000
65A86TYR 0-0.041-0.02522.4360.0260.0260.0000.0000.0000.000
66A87THR 0-0.020-0.02325.529-0.011-0.0110.0000.0000.0000.000
67A88GLU -1-0.899-0.95727.792-0.140-0.1400.0000.0000.0000.000
68A89GLY 00.0570.04026.5590.0080.0080.0000.0000.0000.000
69A90LEU 0-0.063-0.05321.107-0.022-0.0220.0000.0000.0000.000
70A91GLU -1-0.943-0.96721.932-0.243-0.2430.0000.0000.0000.000
71A92GLY 00.003-0.00220.155-0.046-0.0460.0000.0000.0000.000
72A93LEU 0-0.0070.01620.0770.0310.0310.0000.0000.0000.000
73A94ASN 0-0.012-0.00420.012-0.052-0.0520.0000.0000.0000.000
74A95VAL 0-0.007-0.00620.5510.0310.0310.0000.0000.0000.000
75A96LEU 00.0260.01421.752-0.011-0.0110.0000.0000.0000.000
76A97VAL 0-0.038-0.01821.1190.0060.0060.0000.0000.0000.000
77A98LEU 00.0330.00024.1600.0070.0070.0000.0000.0000.000
78A99ASP -1-0.816-0.91427.349-0.082-0.0820.0000.0000.0000.000
79A100LYS 10.9210.95128.7850.0840.0840.0000.0000.0000.000
80A101LYS 10.9280.97432.1500.0540.0540.0000.0000.0000.000
81A102LEU 00.0320.03729.2160.0030.0030.0000.0000.0000.000
82A103VAL 0-0.018-0.01431.2770.0020.0020.0000.0000.0000.000
83A104ALA 0-0.023-0.01633.7850.0030.0030.0000.0000.0000.000
84A105VAL 0-0.0010.01435.7630.0030.0030.0000.0000.0000.000
85A106ILE 00.0370.00632.9740.0020.0020.0000.0000.0000.000
86A107ALA 0-0.022-0.00937.1030.0020.0020.0000.0000.0000.000
87A108ASP -1-0.879-0.95739.257-0.045-0.0450.0000.0000.0000.000
88A109LEU 0-0.0310.00038.5920.0020.0020.0000.0000.0000.000
89A110MET 0-0.057-0.01939.1110.0010.0010.0000.0000.0000.000
90A111MET 0-0.093-0.04042.1430.0010.0010.0000.0000.0000.000
91A112GLY 0-0.046-0.01645.0120.0030.0030.0000.0000.0000.000
92A113GLY 0-0.0140.00845.5450.0030.0030.0000.0000.0000.000
93A114SER 0-0.043-0.03745.100-0.001-0.0010.0000.0000.0000.000
94A115GLY 00.0630.02641.041-0.001-0.0010.0000.0000.0000.000
95A116GLU -1-0.985-0.99640.159-0.035-0.0350.0000.0000.0000.000
96A117VAL 0-0.0170.01139.8810.0020.0020.0000.0000.0000.000
97A118GLU -1-0.965-0.99640.181-0.032-0.0320.0000.0000.0000.000
98A119THR 0-0.046-0.03439.4330.0010.0010.0000.0000.0000.000
99A120GLU -1-0.934-0.97633.027-0.063-0.0630.0000.0000.0000.000
100A121GLU -1-0.930-0.96536.508-0.054-0.0540.0000.0000.0000.000
101A122LEU 0-0.028-0.01333.835-0.001-0.0010.0000.0000.0000.000
102A123ASP -1-0.825-0.92038.608-0.059-0.0590.0000.0000.0000.000
103A124GLU -1-0.891-0.96738.744-0.084-0.0840.0000.0000.0000.000
104A125ILE 0-0.048-0.01640.756-0.002-0.0020.0000.0000.0000.000
105A126LYS 10.8950.94639.1230.0550.0550.0000.0000.0000.000
106A127LEU 00.012-0.00934.948-0.003-0.0030.0000.0000.0000.000
107A128SER 0-0.047-0.00936.926-0.006-0.0060.0000.0000.0000.000
108A129ALA 00.0150.00839.486-0.002-0.0020.0000.0000.0000.000
109A130VAL 0-0.003-0.00433.428-0.001-0.0010.0000.0000.0000.000
110A131GLY 00.0150.01034.671-0.006-0.0060.0000.0000.0000.000
111A132GLU -1-0.933-0.96135.755-0.086-0.0860.0000.0000.0000.000
112A133ALA 00.0220.01135.779-0.002-0.0020.0000.0000.0000.000
113A134MET 0-0.042-0.03230.862-0.007-0.0070.0000.0000.0000.000
114A135ASN 0-0.041-0.01432.792-0.010-0.0100.0000.0000.0000.000
115A136GLN 00.0320.01534.915-0.005-0.0050.0000.0000.0000.000
116A137MET 0-0.038-0.00431.688-0.003-0.0030.0000.0000.0000.000
117A138MET 00.013-0.00826.471-0.002-0.0020.0000.0000.0000.000
118A139GLY 00.0440.03430.655-0.007-0.0070.0000.0000.0000.000
119A140SER 00.0040.00833.3310.0020.0020.0000.0000.0000.000
120A141ALA 0-0.0020.00928.0140.0000.0000.0000.0000.0000.000
121A142ALA 00.0340.01528.567-0.006-0.0060.0000.0000.0000.000
122A143THR 0-0.019-0.01129.605-0.001-0.0010.0000.0000.0000.000
123A144SER 0-0.010-0.00230.4880.0010.0010.0000.0000.0000.000
124A145LEU 00.0230.00423.7630.0000.0000.0000.0000.0000.000
125A146SER 0-0.024-0.02227.869-0.005-0.0050.0000.0000.0000.000
126A147GLU -1-0.973-0.98429.786-0.093-0.0930.0000.0000.0000.000
127A148LEU 0-0.062-0.02325.8770.0040.0040.0000.0000.0000.000
128A149LEU 0-0.006-0.02923.0120.0010.0010.0000.0000.0000.000
129A150GLY 0-0.081-0.01626.9680.0000.0000.0000.0000.0000.000
130A151ILE 0-0.064-0.03526.1410.0020.0020.0000.0000.0000.000
131A152THR 0-0.012-0.00829.5750.0030.0030.0000.0000.0000.000
132A153ILE 00.0160.02225.711-0.010-0.0100.0000.0000.0000.000
133A154ASN 0-0.039-0.00829.2430.0120.0120.0000.0000.0000.000
134A155ILE 00.018-0.00428.015-0.016-0.0160.0000.0000.0000.000
135A156SER 0-0.0230.00829.1110.0120.0120.0000.0000.0000.000
136A157PRO 0-0.006-0.01731.3640.0000.0000.0000.0000.0000.000
137A158PRO 00.0340.01930.434-0.006-0.0060.0000.0000.0000.000
138A159LYS 10.9260.97927.6790.1840.1840.0000.0000.0000.000
139A160VAL 0-0.014-0.01029.628-0.010-0.0100.0000.0000.0000.000
140A161GLU -1-0.922-0.96327.401-0.157-0.1570.0000.0000.0000.000
141A162ILE 0-0.035-0.00729.406-0.004-0.0040.0000.0000.0000.000
142A163LEU 00.0000.00023.183-0.001-0.0010.0000.0000.0000.000
143A164ASN 00.0590.00627.2290.0020.0020.0000.0000.0000.000
144A165PHE 00.0010.00420.541-0.009-0.0090.0000.0000.0000.000
145A166ASP -1-0.840-0.91823.646-0.079-0.0790.0000.0000.0000.000
146A167ASP -1-0.939-0.95426.216-0.089-0.0890.0000.0000.0000.000
147A168PRO 0-0.037-0.02423.864-0.014-0.0140.0000.0000.0000.000
148A169ASN 0-0.057-0.03623.638-0.011-0.0110.0000.0000.0000.000
149A170THR 0-0.0310.00024.677-0.015-0.0150.0000.0000.0000.000
150A171GLN 0-0.019-0.01620.682-0.025-0.0250.0000.0000.0000.000
151A172PHE 00.0370.02118.0710.0110.0110.0000.0000.0000.000
152A173PRO 00.0400.01919.987-0.015-0.0150.0000.0000.0000.000
153A174PRO 00.007-0.00118.329-0.033-0.0330.0000.0000.0000.000
154A175VAL 0-0.0110.00715.761-0.010-0.0100.0000.0000.0000.000
155A176THR 00.0070.00311.838-0.018-0.0180.0000.0000.0000.000
156A177ASP -1-0.859-0.92814.873-0.499-0.4990.0000.0000.0000.000
157A178ASN 0-0.043-0.03411.110-0.042-0.0420.0000.0000.0000.000
158A179PRO 00.0350.00611.671-0.101-0.1010.0000.0000.0000.000
159A180GLU -1-0.848-0.9387.048-0.645-0.6450.0000.0000.0000.000
160A181LYS 10.8510.9396.5840.3360.3360.0000.0000.0000.000
161A182ASP -1-0.826-0.9305.567-3.402-3.4020.0000.0000.0000.000
162A183VAL 0-0.038-0.0148.4130.2500.2500.0000.0000.0000.000
163A184ALA 00.0050.00810.720-0.099-0.0990.0000.0000.0000.000
164A185VAL 00.003-0.00613.2940.0620.0620.0000.0000.0000.000
165A186VAL 0-0.019-0.02315.4370.0240.0240.0000.0000.0000.000
166A187GLU -1-0.927-0.97118.368-0.087-0.0870.0000.0000.0000.000
167A188PHE 0-0.005-0.00620.9580.0050.0050.0000.0000.0000.000
168A189GLU -1-0.941-0.98624.593-0.046-0.0460.0000.0000.0000.000
169A190MET 0-0.017-0.01627.395-0.002-0.0020.0000.0000.0000.000
170A191GLU -1-0.948-0.97930.814-0.038-0.0380.0000.0000.0000.000
171A192ILE 00.0390.01834.178-0.001-0.0010.0000.0000.0000.000
172A193GLU -1-0.860-0.93837.237-0.033-0.0330.0000.0000.0000.000
173A194GLY 0-0.040-0.02440.6420.0000.0000.0000.0000.0000.000
174A195LEU 0-0.0210.00538.2070.0010.0010.0000.0000.0000.000
175A196PRO 0-0.059-0.02735.5670.0010.0010.0000.0000.0000.000
176A197LYS 10.9440.97730.9920.0280.0280.0000.0000.0000.000
177A198SER 0-0.0360.00230.558-0.001-0.0010.0000.0000.0000.000
178A199LYS 10.9520.96923.7130.0890.0890.0000.0000.0000.000
179A200PHE 0-0.0090.00625.1600.0010.0010.0000.0000.0000.000
180A201TYR 00.0230.00919.4670.0050.0050.0000.0000.0000.000
181A202GLN 00.0320.03019.8310.0160.0160.0000.0000.0000.000
182A203VAL 0-0.041-0.00915.965-0.022-0.0220.0000.0000.0000.000
183A204ILE 00.0390.02116.4450.0240.0240.0000.0000.0000.000
184A205SER 00.0570.02113.688-0.079-0.0790.0000.0000.0000.000
185A206ALA 00.0380.00810.0440.0620.0620.0000.0000.0000.000
186A207ASP -1-0.963-0.98311.954-0.801-0.8010.0000.0000.0000.000
187A208LEU 00.0050.00013.7630.0810.0810.0000.0000.0000.000
188A209VAL 00.0050.01113.6850.0630.0630.0000.0000.0000.000
189A210LYS 11.0181.01611.6660.7580.7580.0000.0000.0000.000
190A211LYS 10.8710.95614.4180.3660.3660.0000.0000.0000.000
191A212MET 0-0.014-0.02117.8510.0460.0460.0000.0000.0000.000
192A213TYR 00.0790.02215.7770.0440.0440.0000.0000.0000.000
193A214GLU -1-0.947-0.96817.071-0.313-0.3130.0000.0000.0000.000
194A215TYR 0-0.091-0.05019.6170.0360.0360.0000.0000.0000.000
195A216PHE 00.0190.00520.6570.0200.0200.0000.0000.0000.000
196A217THR 0-0.003-0.01818.9250.0250.0250.0000.0000.0000.000
197A218LYS 10.8950.95921.9690.1490.1490.0000.0000.0000.000
198A219LYS 10.9310.95924.7420.1270.1270.0000.0000.0000.000
199A220GLN 00.0020.02022.4620.0050.0050.0000.0000.0000.000
200A221SER 0-0.076-0.03824.5560.0160.0160.0000.0000.0000.000
201A222GLU -1-1.063-1.02027.052-0.087-0.0870.0000.0000.0000.000
202A223ALA -1-0.945-0.96430.400-0.048-0.0480.0000.0000.0000.000