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: LNV49

Calculation Name: 3E7D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E7D

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YRF5

Base Structure: X-ray

Registration Date: 2023-09-23

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2073029.448321
FMO2-HF: Nuclear repulsion 1999151.927511
FMO2-HF: Total energy -73877.520809
FMO2-MP2: Total energy -74093.684509


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
-24.914-21.58814.147-6.04-11.4340.032
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.037
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].
3A6ARG10.9140.9422.013-25.686-22.63114.149-6.014-11.1900.032
4A7ASP-1-0.768-0.8764.579-0.859-0.664-0.001-0.020-0.1750.000
5A8GLY00.0230.0147.735-0.284-0.2840.0000.0000.0000.000
6A9GLN0-0.047-0.0349.3050.0790.0790.0000.0000.0000.000
7A10ALA00.0260.0018.8410.0420.0420.0000.0000.0000.000
8A11ILE0-0.054-0.0314.477-0.0180.058-0.001-0.006-0.0690.000
9A12TYR00.0220.0298.7030.2850.2850.0000.0000.0000.000
10A13ASP-1-0.798-0.88612.259-0.645-0.6450.0000.0000.0000.000
11A14ARG10.9080.9597.6270.9330.9330.0000.0000.0000.000
12A15SER0-0.032-0.02711.1230.1490.1490.0000.0000.0000.000
13A16PHE00.010-0.01312.5080.1250.1250.0000.0000.0000.000
14A17ALA0-0.033-0.01014.2840.0770.0770.0000.0000.0000.000
15A18ILE0-0.016-0.00410.4640.0340.0340.0000.0000.0000.000
16A19ILE00.0040.00715.0620.0560.0560.0000.0000.0000.000
17A20ARG10.8060.85817.7570.3940.3940.0000.0000.0000.000
18A21ALA0-0.046-0.00217.4780.0280.0280.0000.0000.0000.000
19A22GLU-1-0.944-0.97015.804-0.207-0.2070.0000.0000.0000.000
20A23ALA0-0.027-0.01820.0940.0230.0230.0000.0000.0000.000
21A24ASP-1-0.825-0.88722.712-0.127-0.1270.0000.0000.0000.000
22A25LEU00.006-0.01523.648-0.004-0.0040.0000.0000.0000.000
23A26ARG10.8250.89927.7940.1160.1160.0000.0000.0000.000
24A27HIS0-0.040-0.01729.3220.0100.0100.0000.0000.0000.000
25A28ILE0-0.018-0.00528.3550.0000.0000.0000.0000.0000.000
26A29PRO00.0470.03931.476-0.005-0.0050.0000.0000.0000.000
27A30ALA00.0500.01531.175-0.012-0.0120.0000.0000.0000.000
28A31ASP-1-0.880-0.93730.822-0.173-0.1730.0000.0000.0000.000
29A32LEU00.0170.00530.391-0.012-0.0120.0000.0000.0000.000
30A33GLU-1-0.773-0.84524.706-0.299-0.2990.0000.0000.0000.000
31A34LYS10.9890.98124.6510.2610.2610.0000.0000.0000.000
32A35LEU0-0.024-0.00324.284-0.027-0.0270.0000.0000.0000.000
33A36ALA00.0430.01724.927-0.014-0.0140.0000.0000.0000.000
34A37VAL00.0080.00720.005-0.015-0.0150.0000.0000.0000.000
35A38ARG10.8960.93918.6830.4550.4550.0000.0000.0000.000
36A39VAL0-0.001-0.00420.910-0.023-0.0230.0000.0000.0000.000
37A40ILE00.0380.03218.386-0.004-0.0040.0000.0000.0000.000
38A41HIS0-0.037-0.02913.7910.0460.0460.0000.0000.0000.000
39A42ALA0-0.053-0.02316.575-0.044-0.0440.0000.0000.0000.000
40A43CYS0-0.111-0.04018.7540.0220.0220.0000.0000.0000.000
41A44GLY00.0150.02016.2940.0220.0220.0000.0000.0000.000
42A45MET0-0.0050.00516.9310.0390.0390.0000.0000.0000.000
43A46VAL00.0760.02818.225-0.001-0.0010.0000.0000.0000.000
44A47ASP-1-0.828-0.89320.895-0.140-0.1400.0000.0000.0000.000
45A48VAL00.0120.00223.4020.0130.0130.0000.0000.0000.000
46A49ALA00.008-0.00525.0260.0050.0050.0000.0000.0000.000
47A50ASN0-0.035-0.01526.8080.0090.0090.0000.0000.0000.000
48A51ASP-1-0.844-0.91128.785-0.116-0.1160.0000.0000.0000.000
49A52LEU0-0.078-0.01926.544-0.001-0.0010.0000.0000.0000.000
50A53ALA00.0240.01930.6860.0080.0080.0000.0000.0000.000
51A54PHE0-0.025-0.03432.650-0.010-0.0100.0000.0000.0000.000
52A55SER00.0330.04936.1690.0060.0060.0000.0000.0000.000
53A56GLU-1-0.858-0.96238.007-0.127-0.1270.0000.0000.0000.000
54A57GLY0-0.0060.01137.6290.0030.0030.0000.0000.0000.000
55A58ALA00.0070.00435.616-0.003-0.0030.0000.0000.0000.000
56A59GLY00.0400.01233.212-0.006-0.0060.0000.0000.0000.000
57A60LYS10.8730.91433.9060.1260.1260.0000.0000.0000.000
58A61ALA0-0.0110.00836.481-0.001-0.0010.0000.0000.0000.000
59A62GLY00.0540.01934.7640.0000.0000.0000.0000.0000.000
60A63ARG10.8160.89728.8540.2180.2180.0000.0000.0000.000
61A64ASN0-0.030-0.02234.1850.0030.0030.0000.0000.0000.000
62A65ALA00.0660.04137.7010.0030.0030.0000.0000.0000.000
63A66LEU0-0.029-0.01531.315-0.001-0.0010.0000.0000.0000.000
64A67LEU0-0.013-0.01533.639-0.001-0.0010.0000.0000.0000.000
65A68ALA0-0.0220.00536.3150.0040.0040.0000.0000.0000.000
66A69GLY00.0420.02537.3780.0060.0060.0000.0000.0000.000
67A70ALA0-0.061-0.01537.5390.0020.0020.0000.0000.0000.000
68A71PRO00.0110.01036.518-0.012-0.0120.0000.0000.0000.000
69A72ILE0-0.002-0.01531.250-0.002-0.0020.0000.0000.0000.000
70A73LEU0-0.0060.00734.874-0.003-0.0030.0000.0000.0000.000
71A74CYS0-0.0230.00332.122-0.007-0.0070.0000.0000.0000.000
72A75ASP-1-0.729-0.87032.979-0.152-0.1520.0000.0000.0000.000
73A76ALA0-0.016-0.01331.0110.0070.0070.0000.0000.0000.000
74A77ARG10.8920.93026.5610.1980.1980.0000.0000.0000.000
75A78MET00.004-0.00525.105-0.013-0.0130.0000.0000.0000.000
76A79VAL0-0.0230.00025.909-0.024-0.0240.0000.0000.0000.000
77A80ALA00.011-0.01127.655-0.013-0.0130.0000.0000.0000.000
78A81GLU-1-0.871-0.92424.991-0.244-0.2440.0000.0000.0000.000
79A82GLY00.0180.02423.034-0.025-0.0250.0000.0000.0000.000
80A83ILE0-0.015-0.00623.371-0.025-0.0250.0000.0000.0000.000
81A84THR0-0.026-0.02021.465-0.015-0.0150.0000.0000.0000.000
82A85ARG10.9940.97823.9430.2300.2300.0000.0000.0000.000
83A86SER00.0110.01323.0870.0140.0140.0000.0000.0000.000
84A87ARG10.7930.88321.9490.3610.3610.0000.0000.0000.000
85A88LEU0-0.059-0.01826.2770.0080.0080.0000.0000.0000.000
86A89PRO0-0.030-0.00629.9120.0010.0010.0000.0000.0000.000
87A90ALA00.0130.00832.2150.0080.0080.0000.0000.0000.000
88A91ASP-1-0.907-0.94334.083-0.169-0.1690.0000.0000.0000.000
89A92ASN0-0.074-0.03933.033-0.002-0.0020.0000.0000.0000.000
90A93ARG10.9830.97733.7410.1270.1270.0000.0000.0000.000
91A94VAL0-0.0220.00530.2960.0050.0050.0000.0000.0000.000
92A95ILE0-0.040-0.01733.6970.0040.0040.0000.0000.0000.000
93A96TYR0-0.009-0.02033.821-0.006-0.0060.0000.0000.0000.000
94A97THR00.026-0.01435.9040.0000.0000.0000.0000.0000.000
95A98LEU00.0010.01035.3830.0070.0070.0000.0000.0000.000
96A99SER0-0.034-0.01335.9550.0010.0010.0000.0000.0000.000
97A100ASP-1-0.790-0.85838.308-0.090-0.0900.0000.0000.0000.000
98A101PRO0-0.006-0.01141.7430.0020.0020.0000.0000.0000.000
99A102SER0-0.017-0.02644.2430.0050.0050.0000.0000.0000.000
100A103VAL00.0330.01941.6790.0040.0040.0000.0000.0000.000
101A104PRO0-0.081-0.05043.3720.0020.0020.0000.0000.0000.000
102A105GLU-1-0.798-0.88045.614-0.059-0.0590.0000.0000.0000.000
103A106LEU0-0.020-0.01646.5080.0030.0030.0000.0000.0000.000
104A107ALA00.0370.00945.3860.0000.0000.0000.0000.0000.000
105A108LYS10.8060.87347.4350.0630.0630.0000.0000.0000.000
106A109LYS10.8000.91150.1350.0720.0720.0000.0000.0000.000
107A110ILE0-0.040-0.01646.8370.0010.0010.0000.0000.0000.000
108A111GLY00.0050.02450.7740.0000.0000.0000.0000.0000.000
109A112ASN00.0440.03044.941-0.002-0.0020.0000.0000.0000.000
110A113THR0-0.008-0.02641.367-0.001-0.0010.0000.0000.0000.000
111A114ARG10.9840.98240.8570.0810.0810.0000.0000.0000.000
112A115SER00.021-0.00837.532-0.001-0.0010.0000.0000.0000.000
113A116ALA00.0120.02639.750-0.004-0.0040.0000.0000.0000.000
114A117ALA00.0660.02642.708-0.001-0.0010.0000.0000.0000.000
115A118ALA0-0.023-0.00940.0040.0010.0010.0000.0000.0000.000
116A119LEU00.0130.01939.796-0.003-0.0030.0000.0000.0000.000
117A120ASP-1-0.783-0.86843.144-0.078-0.0780.0000.0000.0000.000
118A121LEU0-0.024-0.01743.0020.0010.0010.0000.0000.0000.000
119A122TRP0-0.025-0.02837.219-0.004-0.0040.0000.0000.0000.000
120A123LEU00.0190.01743.276-0.002-0.0020.0000.0000.0000.000
121A124PRO0-0.029-0.01745.7610.0010.0010.0000.0000.0000.000
122A125HIS0-0.038-0.01841.759-0.003-0.0030.0000.0000.0000.000
123A126ILE00.0100.00142.123-0.007-0.0070.0000.0000.0000.000
124A127GLU-1-0.887-0.92342.974-0.094-0.0940.0000.0000.0000.000
125A128GLY0-0.006-0.00542.826-0.003-0.0030.0000.0000.0000.000
126A129SER0-0.077-0.05538.984-0.008-0.0080.0000.0000.0000.000
127A130ILE0-0.022-0.00833.1400.0000.0000.0000.0000.0000.000
128A131VAL00.0190.01335.669-0.005-0.0050.0000.0000.0000.000
129A132ALA00.008-0.00531.449-0.006-0.0060.0000.0000.0000.000
130A133ILE0-0.008-0.00433.018-0.003-0.0030.0000.0000.0000.000
131A134GLY00.0540.00830.190-0.002-0.0020.0000.0000.0000.000
132A135ASN0-0.123-0.07829.837-0.010-0.0100.0000.0000.0000.000
133A136ALA00.000-0.00232.0960.0080.0080.0000.0000.0000.000
134A137PRO00.0340.01935.4190.0010.0010.0000.0000.0000.000
135A138THR00.0330.01838.0930.0020.0020.0000.0000.0000.000
136A139ALA0-0.0180.00538.0130.0040.0040.0000.0000.0000.000
137A140LEU0-0.021-0.00237.2460.0000.0000.0000.0000.0000.000
138A141PHE00.0310.00340.1490.0020.0020.0000.0000.0000.000
139A142ARG10.8310.89943.3160.0810.0810.0000.0000.0000.000
140A143LEU0-0.004-0.01240.0140.0010.0010.0000.0000.0000.000
141A144PHE00.0090.00641.4310.0010.0010.0000.0000.0000.000
142A145GLU-1-0.847-0.91246.108-0.073-0.0730.0000.0000.0000.000
143A146LEU0-0.032-0.01545.3370.0030.0030.0000.0000.0000.000
144A147LEU0-0.036-0.02043.7990.0010.0010.0000.0000.0000.000
145A148ASP-1-0.843-0.90648.288-0.072-0.0720.0000.0000.0000.000
146A149ALA0-0.074-0.02951.3030.0030.0030.0000.0000.0000.000
147A150GLY0-0.0110.00051.8780.0020.0020.0000.0000.0000.000
148A151ALA0-0.048-0.02048.052-0.001-0.0010.0000.0000.0000.000
149A152PRO00.005-0.00247.431-0.001-0.0010.0000.0000.0000.000
150A153LYS10.9150.95845.6780.0820.0820.0000.0000.0000.000
151A154PRO0-0.0140.00240.194-0.001-0.0010.0000.0000.0000.000
152A155ALA0-0.0030.00739.5240.0040.0040.0000.0000.0000.000
153A156LEU0-0.079-0.04133.789-0.003-0.0030.0000.0000.0000.000
154A157ILE00.0030.00637.288-0.001-0.0010.0000.0000.0000.000
155A158ILE0-0.017-0.01030.457-0.001-0.0010.0000.0000.0000.000
156A159GLY00.0370.01333.8390.0020.0020.0000.0000.0000.000
157A160MET0-0.032-0.01928.889-0.005-0.0050.0000.0000.0000.000
158A161PRO00.0020.01430.238-0.010-0.0100.0000.0000.0000.000
159A162VAL00.0120.01027.7480.0010.0010.0000.0000.0000.000
160A163GLY00.0120.00531.0430.0040.0040.0000.0000.0000.000
161A164PHE0-0.028-0.04630.6080.0020.0020.0000.0000.0000.000
162A165VAL00.0160.00935.3070.0060.0060.0000.0000.0000.000
163A166GLY00.0380.02237.916-0.005-0.0050.0000.0000.0000.000
164A167ALA0-0.0110.00034.009-0.003-0.0030.0000.0000.0000.000
165A168ALA0-0.0060.00335.665-0.004-0.0040.0000.0000.0000.000
166A169GLU-1-0.808-0.90836.611-0.082-0.0820.0000.0000.0000.000
167A170SER0-0.007-0.01838.502-0.002-0.0020.0000.0000.0000.000
168A171LYS10.7870.89331.9760.1330.1330.0000.0000.0000.000
169A172ASP-1-0.769-0.85337.668-0.095-0.0950.0000.0000.0000.000
170A173GLU-1-0.847-0.90539.856-0.074-0.0740.0000.0000.0000.000
171A174LEU0-0.061-0.03037.3330.0000.0000.0000.0000.0000.000
172A175ALA0-0.030-0.02138.692-0.001-0.0010.0000.0000.0000.000
173A176ALA0-0.0150.00740.6220.0020.0020.0000.0000.0000.000
174A177ASN00.0260.00744.2720.0010.0010.0000.0000.0000.000
175A178SER00.0050.01042.2870.0010.0010.0000.0000.0000.000
176A179ARG10.7310.82443.9560.0760.0760.0000.0000.0000.000
177A180GLY00.0060.00746.6740.0010.0010.0000.0000.0000.000
178A181VAL0-0.0380.00141.293-0.001-0.0010.0000.0000.0000.000
179A182PRO00.0290.01739.4130.0000.0000.0000.0000.0000.000
180A183TYR00.002-0.01237.042-0.005-0.0050.0000.0000.0000.000
181A184VAL00.005-0.01031.144-0.002-0.0020.0000.0000.0000.000
182A185ILE0-0.0190.00132.775-0.004-0.0040.0000.0000.0000.000
183A186VAL00.0170.00827.465-0.006-0.0060.0000.0000.0000.000
184A187ARG10.8310.88130.6530.1020.1020.0000.0000.0000.000
185A188GLY00.0580.03231.490-0.004-0.0040.0000.0000.0000.000
186A189ARG10.9310.95631.4410.0710.0710.0000.0000.0000.000
187A190ARG10.7770.85124.5780.1380.1380.0000.0000.0000.000
188A191GLY00.0580.00726.9870.0070.0070.0000.0000.0000.000
189A192GLY00.0330.01426.183-0.010-0.0100.0000.0000.0000.000
190A193SER00.002-0.00625.815-0.007-0.0070.0000.0000.0000.000
191A194ALA00.0240.02621.098-0.007-0.0070.0000.0000.0000.000
192A195MET00.0180.02323.090-0.010-0.0100.0000.0000.0000.000
193A196THR00.0330.00324.7270.0030.0030.0000.0000.0000.000
194A197ALA00.0230.01124.3570.0050.0050.0000.0000.0000.000
195A198ALA0-0.048-0.01321.973-0.010-0.0100.0000.0000.0000.000
196A199ALA00.0410.01623.650-0.005-0.0050.0000.0000.0000.000
197A200VAL00.0350.01527.0160.0020.0020.0000.0000.0000.000
198A201ASN0-0.009-0.00423.0210.0080.0080.0000.0000.0000.000
199A202ALA00.0040.01724.558-0.016-0.0160.0000.0000.0000.000
200A203LEU0-0.050-0.00325.7820.0090.0090.0000.0000.0000.000
201A204ALA00.0170.01027.7380.0090.0090.0000.0000.0000.000
202A205SER0-0.0080.00626.234-0.017-0.0170.0000.0000.0000.000