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: G6K71

Calculation Name: 3EDM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EDM

Chain ID: A

ChEMBL ID:

UniProt ID: A9CEK0

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2430986.680051
FMO2-HF: Nuclear repulsion 2349789.819005
FMO2-HF: Total energy -81196.861045
FMO2-MP2: Total energy -81433.224485


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:2:GLN)


Summations of interaction energy for fragment #1(A:2: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.
-4.6341.3823.38-4.809-4.586-0.032
Interaction energy analysis for fragmet #1(A:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.021
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].
3A4PHE0-0.005-0.0113.294-0.6911.263-0.002-0.888-1.0640.002
4A5THR00.0250.0192.103-1.1990.3122.761-2.202-2.070-0.014
5A6ASN0-0.063-0.0294.2980.4310.5540.000-0.071-0.0520.000
6A7ARG10.8330.9067.6050.4480.4480.0000.0000.0000.000
7A8THR00.0270.0119.420-0.198-0.1980.0000.0000.0000.000
8A9ILE0-0.040-0.0199.8540.1090.1090.0000.0000.0000.000
9A10VAL00.0260.00912.902-0.019-0.0190.0000.0000.0000.000
10A11VAL0-0.018-0.01314.3880.0500.0500.0000.0000.0000.000
11A12ALA00.0440.02317.188-0.006-0.0060.0000.0000.0000.000
12A13GLY00.0400.00521.0050.0260.0260.0000.0000.0000.000
13A14ALA0-0.030-0.00919.2080.0120.0120.0000.0000.0000.000
14A15GLY00.0140.01121.140-0.007-0.0070.0000.0000.0000.000
15A16ARG10.8140.91923.2090.0980.0980.0000.0000.0000.000
16A17ASP-1-0.756-0.86321.887-0.185-0.1850.0000.0000.0000.000
17A18ILE00.0370.01618.338-0.017-0.0170.0000.0000.0000.000
18A19GLY00.0400.02017.932-0.011-0.0110.0000.0000.0000.000
19A20ARG10.7690.86016.8870.1860.1860.0000.0000.0000.000
20A21ALA00.0060.01015.888-0.049-0.0490.0000.0000.0000.000
21A22CYS0-0.048-0.03413.534-0.017-0.0170.0000.0000.0000.000
22A23ALA0-0.010-0.00312.213-0.071-0.0710.0000.0000.0000.000
23A24ILE00.0510.02111.691-0.114-0.1140.0000.0000.0000.000
24A25ARG10.8450.9248.267-0.268-0.2680.0000.0000.0000.000
25A26PHE00.021-0.0047.678-0.065-0.0650.0000.0000.0000.000
26A27ALA00.0000.0116.601-0.429-0.4290.0000.0000.0000.000
27A28GLN0-0.010-0.0166.618-0.354-0.3540.0000.0000.0000.000
28A29GLU-1-0.780-0.8413.1020.4660.9180.031-0.115-0.3680.000
29A30GLY0-0.013-0.0092.613-5.321-3.3870.591-1.524-1.001-0.020
30A31ALA0-0.0110.0064.4000.4760.518-0.001-0.009-0.0310.000
31A32ASN0-0.0170.0007.371-0.076-0.0760.0000.0000.0000.000
32A33VAL00.0100.00110.2920.1090.1090.0000.0000.0000.000
33A34VAL00.0300.02012.7840.0350.0350.0000.0000.0000.000
34A35LEU0-0.019-0.00316.1200.0200.0200.0000.0000.0000.000
35A36THR00.0450.01618.3470.0060.0060.0000.0000.0000.000
36A37TYR0-0.026-0.02122.0060.0070.0070.0000.0000.0000.000
37A38ASN00.032-0.00724.4180.0030.0030.0000.0000.0000.000
38A39GLY00.013-0.00227.736-0.002-0.0020.0000.0000.0000.000
39A40ALA00.0460.02329.843-0.006-0.0060.0000.0000.0000.000
40A41ALA0-0.016-0.00725.216-0.011-0.0110.0000.0000.0000.000
41A42GLU-1-0.833-0.91825.097-0.179-0.1790.0000.0000.0000.000
42A43GLY0-0.022-0.01022.674-0.019-0.0190.0000.0000.0000.000
43A44ALA00.020-0.00120.452-0.028-0.0280.0000.0000.0000.000
44A45ALA00.0110.00920.230-0.037-0.0370.0000.0000.0000.000
45A46THR0-0.002-0.00719.415-0.021-0.0210.0000.0000.0000.000
46A47ALA00.0250.00816.248-0.035-0.0350.0000.0000.0000.000
47A48VAL0-0.040-0.00916.100-0.065-0.0650.0000.0000.0000.000
48A49ALA00.0220.01117.324-0.044-0.0440.0000.0000.0000.000
49A50GLU-1-0.831-0.91015.070-0.505-0.5050.0000.0000.0000.000
50A51ILE0-0.038-0.02911.927-0.090-0.0900.0000.0000.0000.000
51A52GLU-1-0.824-0.88413.195-0.666-0.6660.0000.0000.0000.000
52A53LYS10.7710.87915.4380.4520.4520.0000.0000.0000.000
53A54LEU0-0.085-0.0348.964-0.054-0.0540.0000.0000.0000.000
54A55GLY0-0.043-0.02011.148-0.174-0.1740.0000.0000.0000.000
55A56ARG10.8420.9227.8601.7751.7750.0000.0000.0000.000
56A57SER0-0.006-0.02412.6090.0830.0830.0000.0000.0000.000
57A58ALA0-0.034-0.01614.361-0.043-0.0430.0000.0000.0000.000
58A59LEU0-0.047-0.01315.4900.0450.0450.0000.0000.0000.000
59A60ALA00.006-0.00118.3450.0090.0090.0000.0000.0000.000
60A61ILE0-0.033-0.02320.5080.0160.0160.0000.0000.0000.000
61A62LYS10.8870.95623.5940.1450.1450.0000.0000.0000.000
62A63ALA0-0.005-0.02225.8840.0050.0050.0000.0000.0000.000
63A64ASP-1-0.851-0.89227.411-0.101-0.1010.0000.0000.0000.000
64A65LEU0-0.046-0.03524.0760.0030.0030.0000.0000.0000.000
65A66THR0-0.044-0.03628.5800.0090.0090.0000.0000.0000.000
66A67ASN0-0.017-0.01131.4240.0120.0120.0000.0000.0000.000
67A68ALA00.0490.01031.384-0.008-0.0080.0000.0000.0000.000
68A69ALA00.0640.03731.433-0.005-0.0050.0000.0000.0000.000
69A70GLU-1-0.815-0.89429.535-0.134-0.1340.0000.0000.0000.000
70A71VAL0-0.031-0.01626.475-0.017-0.0170.0000.0000.0000.000
71A72GLU-1-0.886-0.95726.603-0.091-0.0910.0000.0000.0000.000
72A73ALA00.0010.01227.404-0.011-0.0110.0000.0000.0000.000
73A74ALA0-0.011-0.00323.498-0.016-0.0160.0000.0000.0000.000
74A75ILE0-0.001-0.00521.960-0.026-0.0260.0000.0000.0000.000
75A76SER0-0.077-0.04922.845-0.011-0.0110.0000.0000.0000.000
76A77ALA00.0750.04823.610-0.010-0.0100.0000.0000.0000.000
77A78ALA0-0.033-0.01518.839-0.031-0.0310.0000.0000.0000.000
78A79ALA0-0.043-0.02619.276-0.029-0.0290.0000.0000.0000.000
79A80ASP-1-0.930-0.96620.677-0.207-0.2070.0000.0000.0000.000
80A81LYS10.8780.95817.3720.4760.4760.0000.0000.0000.000
81A82PHE0-0.030-0.04514.825-0.049-0.0490.0000.0000.0000.000
82A83GLY00.0170.02815.911-0.023-0.0230.0000.0000.0000.000
83A84GLU-1-0.933-0.97916.326-0.075-0.0750.0000.0000.0000.000
84A85ILE0-0.014-0.00615.537-0.071-0.0710.0000.0000.0000.000
85A86HIS00.0510.02912.302-0.026-0.0260.0000.0000.0000.000
86A87GLY00.0320.01913.7780.0760.0760.0000.0000.0000.000
87A88LEU0-0.0380.00514.716-0.051-0.0510.0000.0000.0000.000
88A89VAL00.0180.00314.4340.0490.0490.0000.0000.0000.000
89A90HIS00.0270.02317.638-0.037-0.0370.0000.0000.0000.000
90A91VAL00.002-0.01218.9250.0240.0240.0000.0000.0000.000
91A92ALA0-0.0020.01121.9980.0030.0030.0000.0000.0000.000
92A93GLY00.0070.01025.2080.0140.0140.0000.0000.0000.000
93A94GLY0-0.064-0.04328.317-0.010-0.0100.0000.0000.0000.000
94A95LEU0-0.002-0.00429.9890.0050.0050.0000.0000.0000.000
95A96ILE0-0.0130.00832.8250.0030.0030.0000.0000.0000.000
96A97ALA00.0230.00435.100-0.003-0.0030.0000.0000.0000.000
97A98ARG10.8520.92434.6850.0280.0280.0000.0000.0000.000
98A99LYS10.9220.96339.9420.0280.0280.0000.0000.0000.000
99A100THR0-0.055-0.06642.8690.0030.0030.0000.0000.0000.000
100A101ILE00.026-0.01045.456-0.002-0.0020.0000.0000.0000.000
101A102ALA0-0.0040.00646.579-0.001-0.0010.0000.0000.0000.000
102A103GLU-1-0.828-0.88246.286-0.021-0.0210.0000.0000.0000.000
103A104MET0-0.101-0.02442.166-0.004-0.0040.0000.0000.0000.000
104A105ASP-1-0.790-0.87745.475-0.029-0.0290.0000.0000.0000.000
105A106GLU-1-0.863-0.94544.721-0.019-0.0190.0000.0000.0000.000
106A107ALA00.0060.00143.373-0.001-0.0010.0000.0000.0000.000
107A108PHE0-0.015-0.00938.901-0.003-0.0030.0000.0000.0000.000
108A109TRP00.007-0.00639.798-0.001-0.0010.0000.0000.0000.000
109A110HIS00.007-0.02438.889-0.001-0.0010.0000.0000.0000.000
110A111GLN00.0270.04136.4570.0000.0000.0000.0000.0000.000
111A112VAL0-0.028-0.01934.615-0.005-0.0050.0000.0000.0000.000
112A113LEU00.016-0.00533.899-0.001-0.0010.0000.0000.0000.000
113A114ASP-1-0.802-0.87133.703-0.040-0.0400.0000.0000.0000.000
114A115VAL0-0.039-0.02129.853-0.006-0.0060.0000.0000.0000.000
115A116ASN0-0.085-0.04629.269-0.007-0.0070.0000.0000.0000.000
116A117LEU0-0.019-0.00629.0140.0040.0040.0000.0000.0000.000
117A118THR00.009-0.02030.4290.0020.0020.0000.0000.0000.000
118A119SER0-0.003-0.02128.149-0.002-0.0020.0000.0000.0000.000
119A120LEU0-0.0280.00024.564-0.007-0.0070.0000.0000.0000.000
120A121PHE0-0.001-0.00127.0190.0000.0000.0000.0000.0000.000
121A122LEU00.0290.01629.169-0.001-0.0010.0000.0000.0000.000
122A123THR0-0.008-0.01123.900-0.002-0.0020.0000.0000.0000.000
123A124ALA00.0100.00924.181-0.008-0.0080.0000.0000.0000.000
124A125LYS10.8930.95625.2390.0590.0590.0000.0000.0000.000
125A126THR0-0.040-0.04526.4370.0030.0030.0000.0000.0000.000
126A127ALA00.004-0.00521.508-0.007-0.0070.0000.0000.0000.000
127A128LEU00.0230.01522.966-0.004-0.0040.0000.0000.0000.000
128A129PRO0-0.050-0.02423.8200.0060.0060.0000.0000.0000.000
129A130LYS10.9120.97021.6810.1460.1460.0000.0000.0000.000
130A131MET0-0.0240.01017.961-0.022-0.0220.0000.0000.0000.000
131A132ALA00.0510.04416.1300.0310.0310.0000.0000.0000.000
132A133LYS10.9380.93918.154-0.184-0.1840.0000.0000.0000.000
133A134GLY0-0.040-0.02116.8180.0080.0080.0000.0000.0000.000
134A135GLY00.0090.01715.5220.0090.0090.0000.0000.0000.000
135A136ALA0-0.033-0.01915.0970.0530.0530.0000.0000.0000.000
136A137ILE00.0210.00016.833-0.062-0.0620.0000.0000.0000.000
137A138VAL0-0.039-0.02115.7040.0410.0410.0000.0000.0000.000
138A139THR0-0.012-0.03118.911-0.032-0.0320.0000.0000.0000.000
139A140PHE00.0590.01920.3540.0150.0150.0000.0000.0000.000
140A141SER0-0.012-0.01223.511-0.003-0.0030.0000.0000.0000.000
141A142SER00.014-0.01526.199-0.008-0.0080.0000.0000.0000.000
142A143GLN00.0990.04926.9840.0100.0100.0000.0000.0000.000
143A144ALA00.0060.00930.3810.0010.0010.0000.0000.0000.000
144A145GLY0-0.050-0.02931.474-0.002-0.0020.0000.0000.0000.000
145A146ARG10.7520.84927.615-0.102-0.1020.0000.0000.0000.000
146A147ASP-1-0.868-0.94034.0490.0380.0380.0000.0000.0000.000
147A148GLY00.0080.02036.316-0.002-0.0020.0000.0000.0000.000
148A149GLY0-0.041-0.02635.761-0.007-0.0070.0000.0000.0000.000
149A150GLY00.0220.01736.6940.0020.0020.0000.0000.0000.000
150A151PRO00.030-0.00738.507-0.002-0.0020.0000.0000.0000.000
151A152GLY00.0140.01240.211-0.004-0.0040.0000.0000.0000.000
152A153ALA0-0.013-0.01136.016-0.004-0.0040.0000.0000.0000.000
153A154LEU00.0850.05137.2050.0010.0010.0000.0000.0000.000
154A155ALA00.0560.03738.3130.0030.0030.0000.0000.0000.000
155A156TYR00.0170.00529.1000.0000.0000.0000.0000.0000.000
156A157ALA00.0270.02233.4030.0010.0010.0000.0000.0000.000
157A158THR00.015-0.00734.2330.0070.0070.0000.0000.0000.000
158A159SER0-0.043-0.02132.5450.0010.0010.0000.0000.0000.000
159A160LYS10.8460.93327.1390.0240.0240.0000.0000.0000.000
160A161GLY00.0830.03630.4280.0090.0090.0000.0000.0000.000
161A162ALA0-0.017-0.00532.5000.0070.0070.0000.0000.0000.000
162A163VAL00.008-0.00126.4590.0050.0050.0000.0000.0000.000
163A164MET0-0.0410.00428.1870.0120.0120.0000.0000.0000.000
164A165THR0-0.005-0.01029.2570.0140.0140.0000.0000.0000.000
165A166PHE00.0200.00926.6220.0070.0070.0000.0000.0000.000
166A167THR00.0030.00224.286-0.001-0.0010.0000.0000.0000.000
167A168ARG10.9160.95826.759-0.083-0.0830.0000.0000.0000.000
168A169GLY0-0.012-0.00728.7820.0080.0080.0000.0000.0000.000
169A170LEU00.0580.02125.2720.0040.0040.0000.0000.0000.000
170A171ALA0-0.008-0.00125.2180.0030.0030.0000.0000.0000.000
171A172LYS10.8810.94326.273-0.089-0.0890.0000.0000.0000.000
172A173GLU-1-0.981-0.97729.1380.0370.0370.0000.0000.0000.000
173A174VAL00.0010.00224.464-0.002-0.0020.0000.0000.0000.000
174A175GLY00.0020.02924.1930.0050.0050.0000.0000.0000.000
175A176PRO0-0.033-0.03823.520-0.008-0.0080.0000.0000.0000.000
176A177LYS10.8370.92221.2900.0210.0210.0000.0000.0000.000
177A178ILE00.0180.01919.8980.0040.0040.0000.0000.0000.000
178A179ARG10.8660.95013.110-0.285-0.2850.0000.0000.0000.000
179A180VAL00.0110.00920.297-0.037-0.0370.0000.0000.0000.000
180A181ASN00.000-0.01118.6740.0320.0320.0000.0000.0000.000
181A182ALA00.0070.01621.300-0.030-0.0300.0000.0000.0000.000
182A183VAL00.0120.01718.5130.0280.0280.0000.0000.0000.000
183A184CYS0-0.075-0.04921.747-0.025-0.0250.0000.0000.0000.000
184A185PRO00.0190.02022.5480.0110.0110.0000.0000.0000.000
185A186GLY00.0120.01825.0300.0000.0000.0000.0000.0000.000
186A187MET0-0.086-0.05727.653-0.009-0.0090.0000.0000.0000.000
187A188ILE00.0080.01925.4320.0060.0060.0000.0000.0000.000
188A189SER0-0.024-0.02729.494-0.006-0.0060.0000.0000.0000.000
189A190THR0-0.042-0.01432.884-0.004-0.0040.0000.0000.0000.000
190A213ARG10.9910.99421.612-0.101-0.1010.0000.0000.0000.000
191A214GLU-1-0.886-0.94226.2650.0170.0170.0000.0000.0000.000
192A215GLY00.0190.01721.945-0.008-0.0080.0000.0000.0000.000
193A216SER00.010-0.02020.268-0.017-0.0170.0000.0000.0000.000
194A217SER00.014-0.03519.5440.0260.0260.0000.0000.0000.000
195A218GLU-1-0.818-0.88116.051-0.235-0.2350.0000.0000.0000.000
196A219ASP-1-0.846-0.90715.3630.0190.0190.0000.0000.0000.000
197A220VAL0-0.035-0.02616.6780.0370.0370.0000.0000.0000.000
198A221ALA00.0250.00813.6060.0240.0240.0000.0000.0000.000
199A222GLY00.0060.00912.226-0.003-0.0030.0000.0000.0000.000
200A223LEU0-0.033-0.00612.9020.0900.0900.0000.0000.0000.000
201A224VAL00.005-0.01913.9700.0380.0380.0000.0000.0000.000
202A225ALA00.0240.0109.1610.0030.0030.0000.0000.0000.000
203A226PHE0-0.020-0.01110.8420.0210.0210.0000.0000.0000.000
204A227LEU00.0150.02012.0490.0630.0630.0000.0000.0000.000
205A228ALA0-0.0170.00611.497-0.001-0.0010.0000.0000.0000.000
206A229SER0-0.055-0.0428.2030.0130.0130.0000.0000.0000.000
207A230ASP-1-0.768-0.8648.4640.5630.5630.0000.0000.0000.000
208A231ASP-1-0.920-0.9498.7061.9431.9430.0000.0000.0000.000
209A232ALA0-0.040-0.01611.338-0.104-0.1040.0000.0000.0000.000
210A233ALA0-0.029-0.01513.611-0.119-0.1190.0000.0000.0000.000
211A234TYR0-0.039-0.03015.317-0.060-0.0600.0000.0000.0000.000
212A235VAL0-0.0150.00917.285-0.026-0.0260.0000.0000.0000.000
213A236THR00.0340.00319.285-0.034-0.0340.0000.0000.0000.000
214A237GLY00.0060.00321.9700.0050.0050.0000.0000.0000.000
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