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: 1649Z

Calculation Name: 3EHR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EHR

Chain ID: A

ChEMBL ID:

UniProt ID: Q92882

Base Structure: X-ray

Registration Date: 2023-09-26

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1757403.31464
FMO2-HF: Nuclear repulsion 1687651.014513
FMO2-HF: Total energy -69752.300127
FMO2-MP2: Total energy -69955.62041


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:13:GLN)


Summations of interaction energy for fragment #1(A:13:GLN)
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.
-41.793-36.68810.211-7.353-7.961-0.001
Interaction energy analysis for fragmet #1(A:13:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.046
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].
3A15LYS10.9300.9692.308-6.912-3.3201.848-2.437-3.003-0.025
4A16VAL00.0140.0014.9981.7221.7220.0000.0000.0000.000
5A17PHE00.0240.0067.386-0.124-0.1240.0000.0000.0000.000
6A18ARG10.8070.87811.0621.5221.5220.0000.0000.0000.000
7A19ALA00.0130.02114.407-0.023-0.0230.0000.0000.0000.000
8A20LEU0-0.020-0.01017.4920.0680.0680.0000.0000.0000.000
9A21TYR00.004-0.00720.2210.1010.1010.0000.0000.0000.000
10A22THR00.0190.00621.632-0.069-0.0690.0000.0000.0000.000
11A23PHE0-0.085-0.02321.3710.0050.0050.0000.0000.0000.000
12A24GLU-1-0.864-0.92123.239-0.325-0.3250.0000.0000.0000.000
13A25PRO0-0.064-0.00223.838-0.006-0.0060.0000.0000.0000.000
14A26ARG10.7910.85723.1330.4470.4470.0000.0000.0000.000
15A27THR0-0.029-0.01624.3930.0290.0290.0000.0000.0000.000
16A28PRO00.005-0.00825.010-0.022-0.0220.0000.0000.0000.000
17A29ASP-1-0.909-0.95021.422-0.110-0.1100.0000.0000.0000.000
18A30GLU-1-0.768-0.86320.240-0.462-0.4620.0000.0000.0000.000
19A31LEU0-0.032-0.01216.4760.0390.0390.0000.0000.0000.000
20A32TYR0-0.071-0.06920.490-0.013-0.0130.0000.0000.0000.000
21A33ILE0-0.034-0.00816.8320.0050.0050.0000.0000.0000.000
22A34GLU-1-0.838-0.91420.411-0.390-0.3900.0000.0000.0000.000
23A35GLU-1-0.973-0.99320.247-0.727-0.7270.0000.0000.0000.000
24A36GLY00.0430.02118.9780.0450.0450.0000.0000.0000.000
25A37ASP-1-0.845-0.89717.264-0.663-0.6630.0000.0000.0000.000
26A38ILE0-0.056-0.03111.143-0.178-0.1780.0000.0000.0000.000
27A39ILE0-0.023-0.00312.1370.2100.2100.0000.0000.0000.000
28A40TYR0-0.055-0.0617.299-0.799-0.7990.0000.0000.0000.000
29A41ILE00.0400.0157.8830.7450.7450.0000.0000.0000.000
30A42THR0-0.021-0.0244.356-1.468-1.361-0.001-0.028-0.0770.000
31A43ASP-1-0.895-0.9254.185-1.998-1.854-0.001-0.041-0.1020.000
32A44MET0-0.039-0.0206.914-0.381-0.3810.0000.0000.0000.000
33A45SER0-0.072-0.0499.2260.1280.1280.0000.0000.0000.000
34A46ASP-1-0.869-0.92011.008-0.360-0.3600.0000.0000.0000.000
35A47THR0-0.034-0.01514.078-0.127-0.1270.0000.0000.0000.000
36A48ASN0-0.016-0.01416.964-0.082-0.0820.0000.0000.0000.000
37A49TRP00.0030.01516.579-0.019-0.0190.0000.0000.0000.000
38A50TRP00.0240.00011.341-0.178-0.1780.0000.0000.0000.000
39A51LYS10.9710.99110.935-0.320-0.3200.0000.0000.0000.000
40A52GLY00.0240.00810.405-0.225-0.2250.0000.0000.0000.000
41A53THR0-0.026-0.01811.8820.2930.2930.0000.0000.0000.000
42A54SER00.030-0.00312.777-0.249-0.2490.0000.0000.0000.000
43A55LYS10.8440.91115.3710.6350.6350.0000.0000.0000.000
44A56GLY0-0.0060.00316.0510.0810.0810.0000.0000.0000.000
45A57ARG10.9160.96617.2730.2550.2550.0000.0000.0000.000
46A58THR0-0.022-0.03313.470-0.023-0.0230.0000.0000.0000.000
47A59GLY00.0260.01015.4470.0790.0790.0000.0000.0000.000
48A60LEU0-0.028-0.00615.277-0.097-0.0970.0000.0000.0000.000
49A61ILE00.0170.00214.2360.0070.0070.0000.0000.0000.000
50A62PRO00.0160.01616.242-0.057-0.0570.0000.0000.0000.000
51A63SER00.003-0.01515.410-0.045-0.0450.0000.0000.0000.000
52A64ASN0-0.031-0.03116.466-0.098-0.0980.0000.0000.0000.000
53A65TYR0-0.023-0.01317.539-0.052-0.0520.0000.0000.0000.000
54A66VAL0-0.016-0.00612.894-0.046-0.0460.0000.0000.0000.000
55A67ALA0-0.052-0.02215.891-0.114-0.1140.0000.0000.0000.000
56A68GLU-1-0.903-0.94617.151-0.686-0.6860.0000.0000.0000.000
57A69GLN0-0.044-0.03019.2290.0750.0750.0000.0000.0000.000
58A70ALA00.0090.01814.8570.0200.0200.0000.0000.0000.000
59A71GLU-1-0.836-0.88314.714-1.383-1.3830.0000.0000.0000.000
60A72SER0-0.001-0.0129.726-0.077-0.0770.0000.0000.0000.000
61A73ILE0-0.033-0.0209.1880.3090.3090.0000.0000.0000.000
62A74ASP-1-0.873-0.9287.518-3.808-3.8080.0000.0000.0000.000
63A75ASN0-0.067-0.0536.776-0.744-0.7440.0000.0000.0000.000
64A76PRO00.0640.0386.4650.7070.7070.0000.0000.0000.000
65A77LEU00.0560.0337.9180.4740.4740.0000.0000.0000.000
66A78HIS0-0.055-0.0418.9740.0960.0960.0000.0000.0000.000
67A79GLU-1-0.791-0.87011.977-1.171-1.1710.0000.0000.0000.000
68A80ALA00.0220.01312.8160.1910.1910.0000.0000.0000.000
69A81ALA00.008-0.00213.8320.1460.1460.0000.0000.0000.000
70A82LYS10.9120.96415.6830.6620.6620.0000.0000.0000.000
71A83ARG10.8350.92216.6490.8940.8940.0000.0000.0000.000
72A84GLY00.0360.03618.6990.0360.0360.0000.0000.0000.000
73A85ASN0-0.008-0.00416.8260.1000.1000.0000.0000.0000.000
74A86LEU00.0490.00916.405-0.048-0.0480.0000.0000.0000.000
75A87SER00.010-0.00216.5490.0550.0550.0000.0000.0000.000
76A88TRP0-0.010-0.00411.0760.1210.1210.0000.0000.0000.000
77A89LEU00.0170.00612.275-0.108-0.1080.0000.0000.0000.000
78A90ARG10.8930.90811.684-0.033-0.0330.0000.0000.0000.000
79A91GLU-1-0.771-0.84611.968-0.644-0.6440.0000.0000.0000.000
80A92CYS0-0.047-0.0197.971-0.157-0.1570.0000.0000.0000.000
81A93LEU0-0.061-0.0357.5020.0810.0810.0000.0000.0000.000
82A94ASP-1-0.909-0.9479.0200.9790.9790.0000.0000.0000.000
83A95ASN0-0.111-0.0577.5400.4350.4350.0000.0000.0000.000
84A96ARG10.9120.9611.964-31.841-31.4438.351-4.610-4.1390.025
85A97VAL0-0.0150.0003.1061.3602.0210.015-0.218-0.458-0.001
86A98GLY0-0.014-0.0053.6991.5331.736-0.001-0.019-0.1820.000
87A99VAL00.0400.0035.726-1.042-1.0420.0000.0000.0000.000
88A100ASN0-0.017-0.0139.007-0.526-0.5260.0000.0000.0000.000
89A101GLY0-0.0090.0117.2580.0420.0420.0000.0000.0000.000
90A102LEU0-0.029-0.0228.095-0.183-0.1830.0000.0000.0000.000
91A103ASP-1-0.743-0.86710.104-1.067-1.0670.0000.0000.0000.000
92A104LYS10.9060.92011.1242.1842.1840.0000.0000.0000.000
93A105ALA0-0.075-0.03114.1150.1220.1220.0000.0000.0000.000
94A106GLY00.0480.02914.9250.1060.1060.0000.0000.0000.000
95A107SER00.0180.01415.2350.1810.1810.0000.0000.0000.000
96A108THR00.0860.04312.443-0.153-0.1530.0000.0000.0000.000
97A109ALA00.0580.01611.228-0.076-0.0760.0000.0000.0000.000
98A110LEU00.0400.02013.195-0.013-0.0130.0000.0000.0000.000
99A111TYR00.0060.00116.220-0.019-0.0190.0000.0000.0000.000
100A112TRP0-0.011-0.02314.6400.0290.0290.0000.0000.0000.000
101A113ALA00.0170.02417.185-0.004-0.0040.0000.0000.0000.000
102A114CYS0-0.065-0.02518.8500.0300.0300.0000.0000.0000.000
103A115HIS0-0.014-0.00821.077-0.019-0.0190.0000.0000.0000.000
104A116GLY00.004-0.00221.698-0.001-0.0010.0000.0000.0000.000
105A117GLY0-0.071-0.03123.2210.0060.0060.0000.0000.0000.000
106A118HIS00.0050.00420.3030.0470.0470.0000.0000.0000.000
107A119LYS10.8820.91721.445-0.027-0.0270.0000.0000.0000.000
108A120ASP-1-0.816-0.91221.426-0.115-0.1150.0000.0000.0000.000
109A121ILE0-0.026-0.00416.1530.0380.0380.0000.0000.0000.000
110A122VAL0-0.024-0.01117.8160.0560.0560.0000.0000.0000.000
111A123GLU-1-0.866-0.94219.2880.1590.1590.0000.0000.0000.000
112A124MET00.0470.06415.1780.0470.0470.0000.0000.0000.000
113A125LEU00.0040.00612.9740.1050.1050.0000.0000.0000.000
114A126PHE0-0.001-0.01615.8200.1330.1330.0000.0000.0000.000
115A127THR0-0.052-0.02816.8740.0720.0720.0000.0000.0000.000
116A128GLN0-0.032-0.01712.2050.2590.2590.0000.0000.0000.000
117A129PRO0-0.003-0.00112.565-0.086-0.0860.0000.0000.0000.000
118A130ASN0-0.040-0.03413.7860.0670.0670.0000.0000.0000.000
119A131ILE00.0140.03114.1800.0620.0620.0000.0000.0000.000
120A132GLU-1-0.844-0.92414.5840.5060.5060.0000.0000.0000.000
121A133LEU0-0.052-0.02616.376-0.103-0.1030.0000.0000.0000.000
122A134ASN0-0.075-0.05319.336-0.125-0.1250.0000.0000.0000.000
123A135GLN0-0.0070.00015.4990.0700.0700.0000.0000.0000.000
124A136GLN0-0.064-0.03618.493-0.030-0.0300.0000.0000.0000.000
125A137ASN0-0.013-0.00118.6350.0270.0270.0000.0000.0000.000
126A138LYS10.9610.97318.8220.4820.4820.0000.0000.0000.000
127A139LEU0-0.014-0.00221.1370.0160.0160.0000.0000.0000.000
128A140GLY00.0320.01723.0490.0220.0220.0000.0000.0000.000
129A141ASP-1-0.855-0.90523.092-0.088-0.0880.0000.0000.0000.000
130A142THR00.046-0.00421.2170.0000.0000.0000.0000.0000.000
131A143ALA00.016-0.02019.354-0.040-0.0400.0000.0000.0000.000
132A144LEU00.0420.02321.337-0.024-0.0240.0000.0000.0000.000
133A145HIS00.0010.02624.877-0.005-0.0050.0000.0000.0000.000
134A146ALA00.0070.01022.838-0.015-0.0150.0000.0000.0000.000
135A147ALA00.0130.00824.625-0.013-0.0130.0000.0000.0000.000
136A148ALA0-0.010-0.01126.097-0.003-0.0030.0000.0000.0000.000
137A149TRP0-0.0050.00326.100-0.009-0.0090.0000.0000.0000.000
138A150LYS10.8830.96826.3530.1730.1730.0000.0000.0000.000
139A151GLY00.0210.01328.682-0.003-0.0030.0000.0000.0000.000
140A152TYR0-0.006-0.00927.6730.0040.0040.0000.0000.0000.000
141A153ALA00.0640.00929.3940.0100.0100.0000.0000.0000.000
142A154ASP-1-0.786-0.89629.7230.0200.0200.0000.0000.0000.000
143A155ILE00.0150.01424.0700.0200.0200.0000.0000.0000.000
144A156VAL0-0.015-0.00426.0540.0220.0220.0000.0000.0000.000
145A157GLN00.0060.00128.0080.0160.0160.0000.0000.0000.000
146A158LEU0-0.033-0.00824.4440.0240.0240.0000.0000.0000.000
147A159LEU00.012-0.00821.3450.0390.0390.0000.0000.0000.000
148A160LEU0-0.021-0.00924.6980.0320.0320.0000.0000.0000.000
149A161ALA0-0.029-0.00827.6220.0210.0210.0000.0000.0000.000
150A162LYS10.8320.93420.237-0.447-0.4470.0000.0000.0000.000
151A163GLY00.0310.01123.7770.0500.0500.0000.0000.0000.000
152A164ALA0-0.081-0.03223.8590.0080.0080.0000.0000.0000.000
153A165ARG10.8530.89024.850-0.246-0.2460.0000.0000.0000.000
154A166THR00.015-0.00626.941-0.018-0.0180.0000.0000.0000.000
155A167ASP-1-0.842-0.88129.1850.1560.1560.0000.0000.0000.000
156A168LEU0-0.0030.01224.270-0.001-0.0010.0000.0000.0000.000
157A169ARG10.8410.89928.304-0.042-0.0420.0000.0000.0000.000
158A170ASN0-0.0040.00127.0320.0150.0150.0000.0000.0000.000
159A171ILE00.0340.00125.6170.0080.0080.0000.0000.0000.000
160A172GLU-1-0.859-0.91529.262-0.107-0.1070.0000.0000.0000.000
161A173LYS10.8730.93631.5780.0340.0340.0000.0000.0000.000
162A174LYS10.8500.94131.3480.1030.1030.0000.0000.0000.000
163A175LEU0-0.014-0.01430.3990.0030.0030.0000.0000.0000.000
164A176ALA00.0430.01227.988-0.015-0.0150.0000.0000.0000.000
165A177PHE0-0.008-0.01429.785-0.012-0.0120.0000.0000.0000.000
166A178ASP-1-0.819-0.91433.388-0.005-0.0050.0000.0000.0000.000
167A179MET0-0.064-0.01828.180-0.013-0.0130.0000.0000.0000.000
168A180ALA0-0.040-0.01032.029-0.011-0.0110.0000.0000.0000.000
169A181THR0-0.0060.00432.5020.0040.0040.0000.0000.0000.000
170A182ASN0-0.032-0.02434.0620.0090.0090.0000.0000.0000.000
171A183ALA00.0550.00736.6520.0070.0070.0000.0000.0000.000
172A184ALA00.0030.01836.0960.0090.0090.0000.0000.0000.000
173A185CYS0-0.0150.00332.4270.0110.0110.0000.0000.0000.000
174A186ALA00.0300.01034.0720.0120.0120.0000.0000.0000.000
175A187SER0-0.023-0.02436.4650.0080.0080.0000.0000.0000.000
176A188LEU0-0.075-0.02532.2310.0090.0090.0000.0000.0000.000
177A189LEU0-0.0160.00030.0600.0130.0130.0000.0000.0000.000
178A190LYS10.9020.98034.136-0.023-0.0230.0000.0000.0000.000