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: 8243Y

Calculation Name: 2HLY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLY

Chain ID: A

ChEMBL ID:

UniProt ID: A9CI22

Base Structure: X-ray

Registration Date: 2023-06-19

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2331961.391563
FMO2-HF: Nuclear repulsion 2251244.320973
FMO2-HF: Total energy -80717.07059
FMO2-MP2: Total energy -80949.507084


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.
-0.7951.336-0.02-0.999-1.111-0.002
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 : 0.011 / q_NPA : -0.005
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].
3A2PHE00.0140.0073.851-1.2910.755-0.019-0.995-1.031-0.002
4A3GLU-1-0.840-0.9104.9231.3501.435-0.001-0.004-0.0800.000
5A4GLY00.0110.0036.518-0.160-0.1600.0000.0000.0000.000
6A5MET0-0.080-0.0268.098-0.266-0.2660.0000.0000.0000.000
7A6LEU00.0070.02110.458-0.034-0.0340.0000.0000.0000.000
8A7ILE0-0.004-0.00813.026-0.072-0.0720.0000.0000.0000.000
9A8LYS10.8320.9079.586-0.165-0.1650.0000.0000.0000.000
10A9GLN00.0710.02910.364-0.100-0.1000.0000.0000.0000.000
11A10THR00.0010.00211.698-0.048-0.0480.0000.0000.0000.000
12A11ASP-1-0.740-0.87613.6350.1440.1440.0000.0000.0000.000
13A12TYR00.031-0.01214.924-0.019-0.0190.0000.0000.0000.000
14A13PHE00.0160.00515.336-0.016-0.0160.0000.0000.0000.000
15A14ARG10.7850.89917.152-0.064-0.0640.0000.0000.0000.000
16A15ILE0-0.0070.00118.823-0.012-0.0120.0000.0000.0000.000
17A16TYR0-0.001-0.02320.866-0.008-0.0080.0000.0000.0000.000
18A17ARG10.8410.91120.869-0.061-0.0610.0000.0000.0000.000
19A18VAL0-0.0390.00623.998-0.009-0.0090.0000.0000.0000.000
20A19ILE0-0.005-0.00624.645-0.006-0.0060.0000.0000.0000.000
21A20ASN00.0490.01826.749-0.008-0.0080.0000.0000.0000.000
22A21SER0-0.041-0.03427.692-0.008-0.0080.0000.0000.0000.000
23A22LEU0-0.061-0.02429.704-0.005-0.0050.0000.0000.0000.000
24A23LEU0-0.006-0.00531.340-0.002-0.0020.0000.0000.0000.000
25A24ILE00.0150.02332.218-0.003-0.0030.0000.0000.0000.000
26A25SER0-0.037-0.02434.034-0.002-0.0020.0000.0000.0000.000
27A26GLN0-0.066-0.04436.589-0.002-0.0020.0000.0000.0000.000
28A27ASN0-0.044-0.02237.129-0.001-0.0010.0000.0000.0000.000
29A28ALA00.0000.01134.8160.0000.0000.0000.0000.0000.000
30A29ASP-1-0.723-0.81735.9270.0600.0600.0000.0000.0000.000
31A30PRO00.0550.01333.4650.0040.0040.0000.0000.0000.000
32A31ALA0-0.0060.02032.7740.0060.0060.0000.0000.0000.000
33A32SER0-0.011-0.05033.5380.0070.0070.0000.0000.0000.000
34A33ALA0-0.0010.00231.2110.0040.0040.0000.0000.0000.000
35A34SER0-0.003-0.01729.0320.0070.0070.0000.0000.0000.000
36A35MET0-0.0360.00429.2340.0080.0080.0000.0000.0000.000
37A36TYR00.0600.04030.8540.0030.0030.0000.0000.0000.000
38A37PHE0-0.011-0.01225.4950.0050.0050.0000.0000.0000.000
39A38SER0-0.026-0.02525.7780.0140.0140.0000.0000.0000.000
40A39THR0-0.025-0.03926.7790.0060.0060.0000.0000.0000.000
41A40PHE00.010-0.00127.8010.0030.0030.0000.0000.0000.000
42A41GLY00.0450.02823.7640.0020.0020.0000.0000.0000.000
43A42ALA00.002-0.00523.3060.0130.0130.0000.0000.0000.000
44A43PHE00.0060.00925.0550.0040.0040.0000.0000.0000.000
45A44ILE00.0280.00521.545-0.001-0.0010.0000.0000.0000.000
46A45LEU00.0000.00218.4580.0030.0030.0000.0000.0000.000
47A46GLN0-0.006-0.00921.904-0.004-0.0040.0000.0000.0000.000
48A47GLN0-0.016-0.00724.938-0.005-0.0050.0000.0000.0000.000
49A48HIS0-0.057-0.03720.4520.0000.0000.0000.0000.0000.000
50A49TYR00.008-0.01614.878-0.012-0.0120.0000.0000.0000.000
51A50LYS10.8060.93319.911-0.102-0.1020.0000.0000.0000.000
52A51VAL00.0350.02218.653-0.012-0.0120.0000.0000.0000.000
53A52LYS10.8380.91321.951-0.180-0.1800.0000.0000.0000.000
54A53ALA0-0.0130.00422.5910.0080.0080.0000.0000.0000.000
55A54VAL0-0.010-0.00824.239-0.018-0.0180.0000.0000.0000.000
56A55PRO0-0.0180.00326.5100.0100.0100.0000.0000.0000.000
57A56LYS10.8270.90227.786-0.158-0.1580.0000.0000.0000.000
58A57GLY00.0950.02929.8450.0020.0020.0000.0000.0000.000
59A58GLY0-0.025-0.01432.038-0.001-0.0010.0000.0000.0000.000
60A59LEU00.0120.02931.653-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.048-0.03128.1220.0080.0080.0000.0000.0000.000
62A61ALA00.0060.00627.966-0.009-0.0090.0000.0000.0000.000
63A62TYR0-0.008-0.03222.6090.0180.0180.0000.0000.0000.000
64A63ASN00.0150.01123.567-0.013-0.0130.0000.0000.0000.000
65A64LEU0-0.014-0.01522.3460.0180.0180.0000.0000.0000.000
66A65GLY00.0170.00022.243-0.011-0.0110.0000.0000.0000.000
67A66GLY0-0.0210.00023.307-0.010-0.0100.0000.0000.0000.000
68A67THR0-0.044-0.01026.078-0.003-0.0030.0000.0000.0000.000
69A68VAL00.014-0.00726.9460.0100.0100.0000.0000.0000.000
70A69LEU00.0030.02527.175-0.006-0.0060.0000.0000.0000.000
71A70LEU00.002-0.02029.2220.0090.0090.0000.0000.0000.000
72A71PHE0-0.0040.00628.153-0.005-0.0050.0000.0000.0000.000
73A72ALA00.014-0.01633.0530.0040.0040.0000.0000.0000.000
74A73ASP-1-0.784-0.87636.1900.0550.0550.0000.0000.0000.000
75A74HIS0-0.055-0.02939.950-0.001-0.0010.0000.0000.0000.000
76A75ARG10.8040.84041.519-0.052-0.0520.0000.0000.0000.000
77A76GLU-1-0.817-0.86843.7580.0490.0490.0000.0000.0000.000
78A77ASP-1-0.903-0.94144.7410.0420.0420.0000.0000.0000.000
79A78GLY0-0.0120.00840.7340.0010.0010.0000.0000.0000.000
80A79TYR00.006-0.01137.191-0.001-0.0010.0000.0000.0000.000
81A80VAL0-0.054-0.02038.8520.0020.0020.0000.0000.0000.000
82A81THR0-0.022-0.06236.5450.0030.0030.0000.0000.0000.000
83A82GLY0-0.0010.01637.132-0.003-0.0030.0000.0000.0000.000
84A83ALA00.011-0.00338.8520.0010.0010.0000.0000.0000.000
85A84GLY00.0000.00741.419-0.002-0.0020.0000.0000.0000.000
86A85GLU-1-0.895-0.96837.8740.0540.0540.0000.0000.0000.000
87A86ASN0-0.033-0.01435.8550.0050.0050.0000.0000.0000.000
88A87PHE0-0.054-0.01834.7440.0050.0050.0000.0000.0000.000
89A88HIS10.8340.90026.788-0.112-0.1120.0000.0000.0000.000
90A89CYS0-0.026-0.00429.875-0.002-0.0020.0000.0000.0000.000
91A90TRP0-0.013-0.00224.634-0.002-0.0020.0000.0000.0000.000
92A91VAL0-0.021-0.01622.534-0.009-0.0090.0000.0000.0000.000
93A92GLU-1-0.786-0.87422.5180.1880.1880.0000.0000.0000.000
94A93ALA00.012-0.00920.034-0.020-0.0200.0000.0000.0000.000
95A94ASP-1-0.831-0.91419.0040.2860.2860.0000.0000.0000.000
96A95GLY00.0260.02018.6660.0380.0380.0000.0000.0000.000
97A96TRP0-0.021-0.01411.2770.0160.0160.0000.0000.0000.000
98A97ALA00.0330.03518.374-0.035-0.0350.0000.0000.0000.000
99A98ILE0-0.029-0.03516.7290.0330.0330.0000.0000.0000.000
100A99ASP-1-0.705-0.80619.9000.1190.1190.0000.0000.0000.000
101A100PHE0-0.023-0.00518.8400.0050.0050.0000.0000.0000.000
102A101MET00.0210.03222.351-0.008-0.0080.0000.0000.0000.000
103A102ALA00.0080.00020.919-0.008-0.0080.0000.0000.0000.000
104A103PRO0-0.074-0.03620.550-0.006-0.0060.0000.0000.0000.000
105A104ALA00.0720.03323.025-0.008-0.0080.0000.0000.0000.000
106A105PHE0-0.025-0.00924.226-0.003-0.0030.0000.0000.0000.000
107A106SER0-0.001-0.00226.630-0.003-0.0030.0000.0000.0000.000
108A107GLU-1-0.977-0.97828.5690.0520.0520.0000.0000.0000.000
109A108GLY0-0.032-0.02331.6950.0040.0040.0000.0000.0000.000
110A109THR0-0.021-0.02529.986-0.001-0.0010.0000.0000.0000.000
111A110ASP-1-0.857-0.92432.9470.0440.0440.0000.0000.0000.000
112A111ALA0-0.032-0.02133.5480.0000.0000.0000.0000.0000.000
113A112LEU0-0.060-0.02930.2810.0000.0000.0000.0000.0000.000
114A113ALA0-0.019-0.01329.5190.0030.0030.0000.0000.0000.000
115A114VAL00.0160.02225.2610.0020.0020.0000.0000.0000.000
116A115PRO0-0.034-0.01222.1520.0000.0000.0000.0000.0000.000
117A116ALA00.0830.05522.7940.0130.0130.0000.0000.0000.000
118A117LYS10.7930.91317.310-0.135-0.1350.0000.0000.0000.000
119A118MET0-0.0080.00511.6450.0070.0070.0000.0000.0000.000
120A119PHE00.0040.00817.1750.0120.0120.0000.0000.0000.000
121A120GLN00.017-0.03712.7760.0090.0090.0000.0000.0000.000
122A121ARG10.8150.90514.825-0.224-0.2240.0000.0000.0000.000
123A122PRO00.0280.01614.129-0.027-0.0270.0000.0000.0000.000
124A123LEU00.0500.01116.989-0.026-0.0260.0000.0000.0000.000
125A124SER0-0.058-0.03018.182-0.015-0.0150.0000.0000.0000.000
126A125ALA0-0.034-0.01917.276-0.002-0.0020.0000.0000.0000.000
127A126MET0-0.0660.01119.354-0.006-0.0060.0000.0000.0000.000
128A127ALA00.0170.01722.521-0.003-0.0030.0000.0000.0000.000
129A128ALA00.009-0.01524.919-0.002-0.0020.0000.0000.0000.000
130A129SER0-0.050-0.04028.352-0.010-0.0100.0000.0000.0000.000
131A130ILE00.0470.00528.9630.0050.0050.0000.0000.0000.000
132A131ASN0-0.031-0.01330.650-0.003-0.0030.0000.0000.0000.000
133A132ASP-1-0.882-0.92226.8420.1170.1170.0000.0000.0000.000
134A133LEU0-0.0310.00825.3340.0110.0110.0000.0000.0000.000
135A134GLY00.0150.01625.283-0.006-0.0060.0000.0000.0000.000
136A135GLN0-0.069-0.04518.858-0.012-0.0120.0000.0000.0000.000
137A136SER0-0.017-0.01319.1770.0040.0040.0000.0000.0000.000
138A137GLY00.0290.00818.2900.0160.0160.0000.0000.0000.000
139A138ASP-1-0.841-0.88019.3210.2040.2040.0000.0000.0000.000
140A139PHE00.004-0.00819.488-0.010-0.0100.0000.0000.0000.000
141A140PHE00.0170.01123.6640.0010.0010.0000.0000.0000.000
142A141TYR0-0.003-0.03223.5460.0040.0040.0000.0000.0000.000
143A142ARG10.8620.90128.516-0.084-0.0840.0000.0000.0000.000
144A143SER00.0190.00230.670-0.002-0.0020.0000.0000.0000.000
145A144GLU-1-0.781-0.81832.3640.0760.0760.0000.0000.0000.000
146A145PRO00.0190.01935.428-0.002-0.0020.0000.0000.0000.000
147A146GLU-1-0.858-0.93536.8930.0730.0730.0000.0000.0000.000
148A147ALA0-0.0080.00438.308-0.004-0.0040.0000.0000.0000.000
149A148THR00.006-0.01133.6890.0000.0000.0000.0000.0000.000
150A149ALA0-0.008-0.01336.822-0.001-0.0010.0000.0000.0000.000
151A150ARG10.8930.93239.139-0.060-0.0600.0000.0000.0000.000
152A151ARG10.8570.93537.589-0.067-0.0670.0000.0000.0000.000
153A152PHE00.0270.00532.434-0.001-0.0010.0000.0000.0000.000
154A153ALA0-0.0050.02538.470-0.002-0.0020.0000.0000.0000.000
155A154ASP-1-0.815-0.91442.0440.0460.0460.0000.0000.0000.000
156A155TRP00.0180.00933.861-0.001-0.0010.0000.0000.0000.000
157A156HIS0-0.047-0.02940.114-0.003-0.0030.0000.0000.0000.000
158A157LYS10.8330.91341.493-0.046-0.0460.0000.0000.0000.000
159A158GLN0-0.025-0.01741.049-0.003-0.0030.0000.0000.0000.000
160A159ALA00.0220.01040.3760.0020.0020.0000.0000.0000.000
161A160MET00.0420.02737.4920.0020.0020.0000.0000.0000.000
162A161ILE00.0280.01735.3340.0020.0020.0000.0000.0000.000
163A162GLY00.0090.00735.0040.0040.0040.0000.0000.0000.000
164A163ASP-1-0.805-0.86735.0790.0440.0440.0000.0000.0000.000
165A164MET0-0.014-0.01133.609-0.001-0.0010.0000.0000.0000.000
166A165ALA00.0400.03330.9170.0030.0030.0000.0000.0000.000
167A166SER0-0.028-0.01530.2590.0050.0050.0000.0000.0000.000
168A167VAL00.0060.00830.9740.0000.0000.0000.0000.0000.000
169A168ALA00.0380.01227.5570.0000.0000.0000.0000.0000.000
170A169ALA0-0.022-0.01426.2790.0040.0040.0000.0000.0000.000
171A170ASN0-0.065-0.03226.627-0.002-0.0020.0000.0000.0000.000
172A171TRP0-0.060-0.03427.140-0.003-0.0030.0000.0000.0000.000
173A172PHE00.003-0.00218.094-0.004-0.0040.0000.0000.0000.000
174A173ARG10.8740.92421.517-0.034-0.0340.0000.0000.0000.000
175A174LYS10.8530.94516.088-0.184-0.1840.0000.0000.0000.000
176A175SER0-0.011-0.00214.008-0.036-0.0360.0000.0000.0000.000
177A176PRO00.001-0.00314.7570.0090.0090.0000.0000.0000.000
178A177LYS10.9390.96416.897-0.034-0.0340.0000.0000.0000.000
179A178GLN00.0730.03920.3320.0170.0170.0000.0000.0000.000
180A179MET0-0.036-0.00422.0950.0070.0070.0000.0000.0000.000
181A180ALA00.0230.02124.935-0.006-0.0060.0000.0000.0000.000
182A181ALA00.0550.02728.1180.0050.0050.0000.0000.0000.000
183A182SER00.0080.00429.0570.0010.0010.0000.0000.0000.000
184A183LEU0-0.036-0.00330.423-0.002-0.0020.0000.0000.0000.000
185A184SER00.0180.01233.787-0.001-0.0010.0000.0000.0000.000
186A185VAL0-0.033-0.02234.7360.0010.0010.0000.0000.0000.000
187A186THR00.0070.00237.771-0.001-0.0010.0000.0000.0000.000
188A187ASP-1-0.793-0.90640.1050.0310.0310.0000.0000.0000.000
189A188ARG10.8160.84840.933-0.040-0.0400.0000.0000.0000.000
190A189ASP-1-0.828-0.86945.1820.0250.0250.0000.0000.0000.000
191A190GLY0-0.030-0.01445.959-0.002-0.0020.0000.0000.0000.000
192A191LYS10.7700.86545.558-0.027-0.0270.0000.0000.0000.000
193A192ALA0-0.015-0.00842.0030.0020.0020.0000.0000.0000.000
194A193ARG10.9250.97137.380-0.036-0.0360.0000.0000.0000.000
195A194THR00.0090.00236.4500.0010.0010.0000.0000.0000.000
196A195VAL0-0.0010.00532.8500.0010.0010.0000.0000.0000.000
197A196PRO00.014-0.00132.2110.0000.0000.0000.0000.0000.000
198A197LEU0-0.011-0.01125.0690.0040.0040.0000.0000.0000.000
199A198THR00.0120.00027.570-0.003-0.0030.0000.0000.0000.000
200A199GLY00.0200.00526.5370.0020.0020.0000.0000.0000.000
201A200GLU-1-0.829-0.88223.9100.0610.0610.0000.0000.0000.000
202A201MET00.0000.00421.0460.0010.0010.0000.0000.0000.000
203A202LEU0-0.0110.00318.9950.0050.0050.0000.0000.0000.000
204A203THR0-0.027-0.02415.730-0.006-0.0060.0000.0000.0000.000
205A204GLY00.0590.02913.873-0.001-0.0010.0000.0000.0000.000
206A205ALA0-0.024-0.02713.1380.0170.0170.0000.0000.0000.000
207A206TRP00.0920.04515.008-0.016-0.0160.0000.0000.0000.000