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: GNZ91

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2328632.026685
FMO2-HF: Nuclear repulsion 2247915.345395
FMO2-HF: Total energy -80716.68129
FMO2-MP2: Total energy -80949.207936


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.
-1.0311.473-0.028-1.207-1.267-0.002
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 : 0.014 / q_NPA : -0.003
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].
3A2PHE00.0030.0043.806-1.9310.507-0.027-1.200-1.210-0.002
4A3GLU-1-0.896-0.9544.8241.8271.893-0.001-0.007-0.0570.000
5A4GLY00.007-0.0037.077-0.202-0.2020.0000.0000.0000.000
6A5MET0-0.083-0.0328.666-0.289-0.2890.0000.0000.0000.000
7A6LEU00.0100.02911.080-0.035-0.0350.0000.0000.0000.000
8A7ILE00.000-0.00513.623-0.062-0.0620.0000.0000.0000.000
9A8LYS10.9751.0079.656-0.124-0.1240.0000.0000.0000.000
10A9GLN00.0630.01710.361-0.124-0.1240.0000.0000.0000.000
11A10THR0-0.022-0.01011.838-0.059-0.0590.0000.0000.0000.000
12A11ASP-1-0.762-0.90013.6980.1480.1480.0000.0000.0000.000
13A12TYR00.014-0.01214.974-0.021-0.0210.0000.0000.0000.000
14A13PHE00.0190.00315.275-0.020-0.0200.0000.0000.0000.000
15A14ARG10.8010.90617.341-0.091-0.0910.0000.0000.0000.000
16A15ILE0-0.0090.00319.078-0.015-0.0150.0000.0000.0000.000
17A16TYR00.0290.01720.967-0.009-0.0090.0000.0000.0000.000
18A17ARG10.8310.90021.056-0.080-0.0800.0000.0000.0000.000
19A18VAL0-0.0360.00624.007-0.010-0.0100.0000.0000.0000.000
20A19ILE00.000-0.00224.926-0.007-0.0070.0000.0000.0000.000
21A20ASN00.0580.02126.798-0.007-0.0070.0000.0000.0000.000
22A21SER0-0.051-0.04227.675-0.008-0.0080.0000.0000.0000.000
23A22LEU0-0.068-0.03129.789-0.006-0.0060.0000.0000.0000.000
24A23LEU0-0.022-0.01931.186-0.003-0.0030.0000.0000.0000.000
25A24ILE00.0270.04432.402-0.003-0.0030.0000.0000.0000.000
26A25SER0-0.030-0.02434.154-0.002-0.0020.0000.0000.0000.000
27A26GLN0-0.079-0.04736.829-0.001-0.0010.0000.0000.0000.000
28A27ASN0-0.037-0.01137.405-0.002-0.0020.0000.0000.0000.000
29A28ALA0-0.0170.00135.215-0.001-0.0010.0000.0000.0000.000
30A29ASP-1-0.714-0.81036.3380.0620.0620.0000.0000.0000.000
31A30PRO00.0760.01833.5330.0040.0040.0000.0000.0000.000
32A31ALA0-0.0010.01833.1760.0060.0060.0000.0000.0000.000
33A32SER0-0.017-0.05334.2470.0060.0060.0000.0000.0000.000
34A33ALA00.0080.00331.5710.0040.0040.0000.0000.0000.000
35A34SER0-0.014-0.02229.6360.0070.0070.0000.0000.0000.000
36A35MET0-0.0300.00129.8900.0070.0070.0000.0000.0000.000
37A36TYR00.0600.04231.3600.0020.0020.0000.0000.0000.000
38A37PHE0-0.015-0.01025.6700.0060.0060.0000.0000.0000.000
39A38SER0-0.026-0.01826.3160.0140.0140.0000.0000.0000.000
40A39THR0-0.017-0.03727.2670.0060.0060.0000.0000.0000.000
41A40PHE00.005-0.00428.1200.0010.0010.0000.0000.0000.000
42A41GLY00.0400.02424.1400.0020.0020.0000.0000.0000.000
43A42ALA0-0.005-0.00323.8110.0110.0110.0000.0000.0000.000
44A43PHE00.0030.00825.4980.0030.0030.0000.0000.0000.000
45A44ILE00.0370.00921.894-0.001-0.0010.0000.0000.0000.000
46A45LEU0-0.001-0.00418.9360.0030.0030.0000.0000.0000.000
47A46GLN0-0.031-0.01622.237-0.004-0.0040.0000.0000.0000.000
48A47GLN0-0.030-0.02225.043-0.003-0.0030.0000.0000.0000.000
49A48HIS0-0.074-0.04220.765-0.002-0.0020.0000.0000.0000.000
50A49TYR00.001-0.01615.081-0.015-0.0150.0000.0000.0000.000
51A50LYS10.8120.93720.091-0.104-0.1040.0000.0000.0000.000
52A51VAL00.0650.05719.3120.0000.0000.0000.0000.0000.000
53A52LYS10.9260.95422.586-0.149-0.1490.0000.0000.0000.000
54A53ALA00.0150.00823.3280.0180.0180.0000.0000.0000.000
55A54VAL0-0.009-0.01325.017-0.016-0.0160.0000.0000.0000.000
56A55PRO0-0.0030.01227.1730.0090.0090.0000.0000.0000.000
57A56LYS10.8270.89627.957-0.151-0.1510.0000.0000.0000.000
58A57GLY00.0910.03930.0630.0030.0030.0000.0000.0000.000
59A58GLY0-0.014-0.00732.240-0.002-0.0020.0000.0000.0000.000
60A59LEU0-0.0220.01531.583-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.026-0.01627.9270.0080.0080.0000.0000.0000.000
62A61ALA00.0130.01328.016-0.009-0.0090.0000.0000.0000.000
63A62TYR0-0.001-0.02722.7990.0170.0170.0000.0000.0000.000
64A63ASN00.0080.00923.601-0.012-0.0120.0000.0000.0000.000
65A64LEU0-0.006-0.01622.1360.0180.0180.0000.0000.0000.000
66A65GLY00.008-0.01321.952-0.011-0.0110.0000.0000.0000.000
67A66GLY0-0.016-0.00322.926-0.010-0.0100.0000.0000.0000.000
68A67THR0-0.0300.00825.874-0.006-0.0060.0000.0000.0000.000
69A68VAL00.013-0.00526.9020.0090.0090.0000.0000.0000.000
70A69LEU0-0.0030.02027.304-0.006-0.0060.0000.0000.0000.000
71A70LEU0-0.007-0.02329.2140.0080.0080.0000.0000.0000.000
72A71PHE0-0.019-0.00428.200-0.005-0.0050.0000.0000.0000.000
73A72ALA00.000-0.02232.9960.0030.0030.0000.0000.0000.000
74A73ASP-1-0.788-0.87536.1570.0560.0560.0000.0000.0000.000
75A74HIS0-0.050-0.01639.8720.0000.0000.0000.0000.0000.000
76A75ARG10.8630.89641.549-0.052-0.0520.0000.0000.0000.000
77A76GLU-1-0.891-0.92844.1990.0470.0470.0000.0000.0000.000
78A77ASP-1-0.878-0.93444.7570.0420.0420.0000.0000.0000.000
79A78GLY0-0.0080.01641.0300.0020.0020.0000.0000.0000.000
80A79TYR0-0.004-0.02437.1920.0000.0000.0000.0000.0000.000
81A80VAL0-0.046-0.02538.9500.0020.0020.0000.0000.0000.000
82A81THR0-0.019-0.04836.5940.0030.0030.0000.0000.0000.000
83A82GLY00.0100.02537.121-0.003-0.0030.0000.0000.0000.000
84A83ALA0-0.013-0.02638.8740.0010.0010.0000.0000.0000.000
85A84GLY00.004-0.00741.031-0.002-0.0020.0000.0000.0000.000
86A85GLU-1-0.890-0.96038.4900.0570.0570.0000.0000.0000.000
87A86ASN0-0.018-0.00836.0530.0040.0040.0000.0000.0000.000
88A87PHE0-0.073-0.02734.9790.0050.0050.0000.0000.0000.000
89A88HIS10.8470.90827.114-0.115-0.1150.0000.0000.0000.000
90A89CYS0-0.028-0.01230.208-0.002-0.0020.0000.0000.0000.000
91A90TRP0-0.002-0.00424.8640.0000.0000.0000.0000.0000.000
92A91VAL0-0.023-0.02123.068-0.009-0.0090.0000.0000.0000.000
93A92GLU-1-0.786-0.86022.9750.1810.1810.0000.0000.0000.000
94A93ALA0-0.004-0.02420.668-0.019-0.0190.0000.0000.0000.000
95A94ASP-1-0.877-0.93618.6060.3030.3030.0000.0000.0000.000
96A95GLY0-0.0110.00218.8030.0360.0360.0000.0000.0000.000
97A96TRP0-0.012-0.01111.5500.0240.0240.0000.0000.0000.000
98A97ALA00.0310.03218.575-0.035-0.0350.0000.0000.0000.000
99A98ILE0-0.024-0.03017.4230.0320.0320.0000.0000.0000.000
100A99ASP-1-0.697-0.79520.3790.1220.1220.0000.0000.0000.000
101A100PHE0-0.016-0.01219.2940.0060.0060.0000.0000.0000.000
102A101MET00.0170.03222.660-0.007-0.0070.0000.0000.0000.000
103A102ALA00.0230.01521.292-0.008-0.0080.0000.0000.0000.000
104A103PRO0-0.080-0.05120.632-0.007-0.0070.0000.0000.0000.000
105A104ALA00.0620.02823.215-0.008-0.0080.0000.0000.0000.000
106A105PHE0-0.052-0.02824.465-0.004-0.0040.0000.0000.0000.000
107A106SER00.009-0.00826.863-0.002-0.0020.0000.0000.0000.000
108A107GLU-1-0.989-0.97828.8380.0580.0580.0000.0000.0000.000
109A108GLY0-0.020-0.01631.9900.0030.0030.0000.0000.0000.000
110A109THR0-0.016-0.01830.209-0.001-0.0010.0000.0000.0000.000
111A110ASP-1-0.870-0.92233.0720.0480.0480.0000.0000.0000.000
112A111ALA0-0.038-0.03233.5480.0010.0010.0000.0000.0000.000
113A112LEU0-0.052-0.02830.2850.0000.0000.0000.0000.0000.000
114A113ALA0-0.032-0.00229.5030.0030.0030.0000.0000.0000.000
115A114VAL00.0240.02225.3300.0040.0040.0000.0000.0000.000
116A115PRO0-0.036-0.01422.1870.0000.0000.0000.0000.0000.000
117A116ALA00.0740.05422.6880.0090.0090.0000.0000.0000.000
118A117LYS10.8240.92017.340-0.136-0.1360.0000.0000.0000.000
119A118MET0-0.0080.00711.9760.0060.0060.0000.0000.0000.000
120A119PHE0-0.0050.00017.1320.0160.0160.0000.0000.0000.000
121A120GLN00.025-0.03413.289-0.001-0.0010.0000.0000.0000.000
122A121ARG10.8580.93114.584-0.219-0.2190.0000.0000.0000.000
123A122PRO00.0180.01514.285-0.028-0.0280.0000.0000.0000.000
124A123LEU00.0650.02217.080-0.026-0.0260.0000.0000.0000.000
125A124SER0-0.055-0.03018.250-0.014-0.0140.0000.0000.0000.000
126A125ALA0-0.048-0.02817.453-0.008-0.0080.0000.0000.0000.000
127A126MET0-0.0900.00919.615-0.013-0.0130.0000.0000.0000.000
128A127ALA00.0300.02422.890-0.005-0.0050.0000.0000.0000.000
129A128ALA00.002-0.01925.186-0.002-0.0020.0000.0000.0000.000
130A129SER0-0.043-0.03328.723-0.009-0.0090.0000.0000.0000.000
131A130ILE00.020-0.00229.3150.0050.0050.0000.0000.0000.000
132A131ASN0-0.024-0.01631.183-0.003-0.0030.0000.0000.0000.000
133A132ASP-1-0.895-0.92327.0820.1140.1140.0000.0000.0000.000
134A133LEU0-0.0050.00325.4390.0110.0110.0000.0000.0000.000
135A134GLY00.0410.03325.778-0.005-0.0050.0000.0000.0000.000
136A135GLN0-0.060-0.02318.848-0.012-0.0120.0000.0000.0000.000
137A136SER00.0020.00419.0960.0030.0030.0000.0000.0000.000
138A137GLY0-0.013-0.01718.3050.0180.0180.0000.0000.0000.000
139A138ASP-1-0.848-0.91019.3410.1890.1890.0000.0000.0000.000
140A139PHE0-0.014-0.01819.683-0.005-0.0050.0000.0000.0000.000
141A140PHE00.0070.01323.7900.0000.0000.0000.0000.0000.000
142A141TYR0-0.004-0.04423.5290.0040.0040.0000.0000.0000.000
143A142ARG10.8790.93528.428-0.083-0.0830.0000.0000.0000.000
144A143SER00.011-0.00731.046-0.002-0.0020.0000.0000.0000.000
145A144GLU-1-0.800-0.86832.5920.0740.0740.0000.0000.0000.000
146A145PRO00.0100.01735.535-0.001-0.0010.0000.0000.0000.000
147A146GLU-1-0.859-0.93736.8550.0700.0700.0000.0000.0000.000
148A147ALA0-0.025-0.01738.365-0.003-0.0030.0000.0000.0000.000
149A148THR00.019-0.00833.9500.0000.0000.0000.0000.0000.000
150A149ALA0-0.014-0.00937.084-0.001-0.0010.0000.0000.0000.000
151A150ARG10.9360.95539.481-0.058-0.0580.0000.0000.0000.000
152A151ARG10.8540.94438.115-0.068-0.0680.0000.0000.0000.000
153A152PHE00.0120.00433.037-0.001-0.0010.0000.0000.0000.000
154A153ALA0-0.0100.01239.086-0.001-0.0010.0000.0000.0000.000
155A154ASP-1-0.827-0.91642.5940.0450.0450.0000.0000.0000.000
156A155TRP00.004-0.00534.141-0.001-0.0010.0000.0000.0000.000
157A156HIS0-0.025-0.01340.498-0.003-0.0030.0000.0000.0000.000
158A157LYS10.8520.92741.600-0.046-0.0460.0000.0000.0000.000
159A158GLN0-0.031-0.01841.425-0.003-0.0030.0000.0000.0000.000
160A159ALA00.0190.00440.8570.0020.0020.0000.0000.0000.000
161A160MET00.0250.01737.4150.0010.0010.0000.0000.0000.000
162A161ILE00.0450.03135.7730.0020.0020.0000.0000.0000.000
163A162GLY00.0150.00535.5050.0040.0040.0000.0000.0000.000
164A163ASP-1-0.796-0.86135.4570.0460.0460.0000.0000.0000.000
165A164MET0-0.033-0.02033.878-0.001-0.0010.0000.0000.0000.000
166A165ALA00.0420.03131.2660.0030.0030.0000.0000.0000.000
167A166SER0-0.018-0.00630.5780.0050.0050.0000.0000.0000.000
168A167VAL00.0070.01131.2070.0010.0010.0000.0000.0000.000
169A168ALA00.0320.00927.8300.0000.0000.0000.0000.0000.000
170A169ALA0-0.028-0.01726.4970.0050.0050.0000.0000.0000.000
171A170ASN0-0.054-0.03226.634-0.001-0.0010.0000.0000.0000.000
172A171TRP0-0.067-0.02926.912-0.003-0.0030.0000.0000.0000.000
173A172PHE0-0.001-0.01118.157-0.003-0.0030.0000.0000.0000.000
174A173ARG10.9080.95121.617-0.044-0.0440.0000.0000.0000.000
175A174LYS10.8720.95616.205-0.181-0.1810.0000.0000.0000.000
176A175SER0-0.026-0.00714.085-0.039-0.0390.0000.0000.0000.000
177A176PRO0-0.016-0.01114.9270.0080.0080.0000.0000.0000.000
178A177LYS10.9510.96016.982-0.046-0.0460.0000.0000.0000.000
179A178GLN00.0440.06020.4620.0160.0160.0000.0000.0000.000
180A179MET0-0.050-0.04622.0890.0050.0050.0000.0000.0000.000
181A180ALA00.0240.02024.765-0.005-0.0050.0000.0000.0000.000
182A181ALA00.0630.03427.8380.0050.0050.0000.0000.0000.000
183A182SER00.0070.00129.1100.0020.0020.0000.0000.0000.000
184A183LEU0-0.035-0.00930.231-0.002-0.0020.0000.0000.0000.000
185A184SER00.0220.02033.707-0.001-0.0010.0000.0000.0000.000
186A185VAL0-0.026-0.02135.0990.0010.0010.0000.0000.0000.000
187A186THR0-0.003-0.00237.877-0.002-0.0020.0000.0000.0000.000
188A187ASP-1-0.829-0.92040.8480.0320.0320.0000.0000.0000.000
189A188ARG10.8340.85241.219-0.041-0.0410.0000.0000.0000.000
190A189ASP-1-0.851-0.88845.3040.0270.0270.0000.0000.0000.000
191A190GLY0-0.032-0.00946.201-0.002-0.0020.0000.0000.0000.000
192A191LYS10.7750.87445.862-0.029-0.0290.0000.0000.0000.000
193A192ALA0-0.012-0.00441.5890.0020.0020.0000.0000.0000.000
194A193ARG10.9580.98637.101-0.041-0.0410.0000.0000.0000.000
195A194THR00.0090.00136.1670.0010.0010.0000.0000.0000.000
196A195VAL0-0.012-0.00632.7100.0000.0000.0000.0000.0000.000
197A196PRO00.0150.00232.1610.0000.0000.0000.0000.0000.000
198A197LEU0-0.007-0.00825.0530.0040.0040.0000.0000.0000.000
199A198THR00.009-0.00227.860-0.003-0.0030.0000.0000.0000.000
200A199GLY00.021-0.00326.7960.0020.0020.0000.0000.0000.000
201A200GLU-1-0.853-0.90123.9030.0720.0720.0000.0000.0000.000
202A201MET00.0010.00020.7400.0030.0030.0000.0000.0000.000
203A202LEU0-0.0130.00219.2290.0040.0040.0000.0000.0000.000
204A203THR0-0.029-0.02216.0760.0010.0010.0000.0000.0000.000
205A204GLY00.0690.03914.768-0.007-0.0070.0000.0000.0000.000
206A205ALA0-0.026-0.02512.7090.0160.0160.0000.0000.0000.000
207A206TRP00.0740.03814.769-0.015-0.0150.0000.0000.0000.000