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

tag_button

FMODB ID: 17GVZ

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 OptH
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 -2429232.361545
FMO2-HF: Nuclear repulsion 2348036.456481
FMO2-HF: Total energy -81195.905065
FMO2-MP2: Total energy -81432.332424


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.
-3.522.0453.212-4.36-4.418-0.031
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 : -0.012 / q_NPA : -0.020
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].
3A4PHE0-0.016-0.0163.278-0.5211.403-0.002-0.880-1.0420.002
4A5THR00.0370.0232.348-1.856-0.6272.595-1.878-1.945-0.014
5A6ASN0-0.051-0.0194.3050.6730.7280.000-0.027-0.0280.000
6A7ARG10.8540.9257.5730.4780.4780.0000.0000.0000.000
7A8THR00.0330.0109.428-0.208-0.2080.0000.0000.0000.000
8A9ILE0-0.045-0.0209.7970.1180.1180.0000.0000.0000.000
9A10VAL00.0340.01312.896-0.023-0.0230.0000.0000.0000.000
10A11VAL0-0.021-0.01214.4540.0550.0550.0000.0000.0000.000
11A12ALA00.0450.02217.186-0.009-0.0090.0000.0000.0000.000
12A13GLY00.0360.00221.0030.0280.0280.0000.0000.0000.000
13A14ALA0-0.026-0.00719.2130.0140.0140.0000.0000.0000.000
14A15GLY00.0110.00921.142-0.007-0.0070.0000.0000.0000.000
15A16ARG10.8160.92523.2400.0630.0630.0000.0000.0000.000
16A17ASP-1-0.777-0.89421.891-0.143-0.1430.0000.0000.0000.000
17A18ILE00.0180.01218.346-0.015-0.0150.0000.0000.0000.000
18A19GLY00.0400.01617.937-0.007-0.0070.0000.0000.0000.000
19A20ARG10.7880.88316.8910.1420.1420.0000.0000.0000.000
20A21ALA00.0070.00815.891-0.047-0.0470.0000.0000.0000.000
21A22CYS0-0.046-0.03213.535-0.007-0.0070.0000.0000.0000.000
22A23ALA0-0.008-0.00112.217-0.070-0.0700.0000.0000.0000.000
23A24ILE00.0500.02011.695-0.118-0.1180.0000.0000.0000.000
24A25ARG10.8990.9758.054-0.433-0.4330.0000.0000.0000.000
25A26PHE00.017-0.0097.685-0.056-0.0560.0000.0000.0000.000
26A27ALA00.0060.0106.602-0.455-0.4550.0000.0000.0000.000
27A28GLN0-0.012-0.0146.622-0.347-0.3470.0000.0000.0000.000
28A29GLU-1-0.796-0.8573.1111.3501.8240.030-0.113-0.3910.000
29A30GLY0-0.010-0.0072.608-5.437-3.5930.590-1.453-0.982-0.019
30A31ALA0-0.019-0.0044.3960.4980.537-0.001-0.009-0.0300.000
31A32ASN0-0.033-0.0017.365-0.064-0.0640.0000.0000.0000.000
32A33VAL00.003-0.00510.3650.1130.1130.0000.0000.0000.000
33A34VAL00.0300.02412.7810.0320.0320.0000.0000.0000.000
34A35LEU0-0.018-0.00716.0350.0250.0250.0000.0000.0000.000
35A36THR00.0400.01718.3460.0050.0050.0000.0000.0000.000
36A37TYR0-0.011-0.01822.0060.0010.0010.0000.0000.0000.000
37A38ASN00.0570.00824.4180.0010.0010.0000.0000.0000.000
38A39GLY00.000-0.00627.738-0.001-0.0010.0000.0000.0000.000
39A40ALA00.0460.02229.846-0.007-0.0070.0000.0000.0000.000
40A41ALA0-0.012-0.00225.181-0.011-0.0110.0000.0000.0000.000
41A42GLU-1-0.848-0.92825.102-0.159-0.1590.0000.0000.0000.000
42A43GLY0-0.016-0.00822.681-0.017-0.0170.0000.0000.0000.000
43A44ALA00.0200.00020.450-0.026-0.0260.0000.0000.0000.000
44A45ALA00.0110.00820.234-0.037-0.0370.0000.0000.0000.000
45A46THR00.0030.00119.304-0.022-0.0220.0000.0000.0000.000
46A47ALA00.0240.00716.258-0.033-0.0330.0000.0000.0000.000
47A48VAL0-0.033-0.00716.106-0.065-0.0650.0000.0000.0000.000
48A49ALA00.0200.00717.328-0.045-0.0450.0000.0000.0000.000
49A50GLU-1-0.899-0.96515.065-0.456-0.4560.0000.0000.0000.000
50A51ILE0-0.043-0.03111.910-0.088-0.0880.0000.0000.0000.000
51A52GLU-1-0.852-0.91713.200-0.662-0.6620.0000.0000.0000.000
52A53LYS10.8270.93015.4440.3960.3960.0000.0000.0000.000
53A54LEU0-0.078-0.0339.145-0.049-0.0490.0000.0000.0000.000
54A55GLY0-0.044-0.02011.153-0.178-0.1780.0000.0000.0000.000
55A56ARG10.8620.9347.4581.8901.8900.0000.0000.0000.000
56A57SER00.0110.00012.6100.0890.0890.0000.0000.0000.000
57A58ALA0-0.026-0.01114.359-0.046-0.0460.0000.0000.0000.000
58A59LEU0-0.0250.00015.4890.0440.0440.0000.0000.0000.000
59A60ALA00.000-0.00718.3430.0120.0120.0000.0000.0000.000
60A61ILE0-0.019-0.01020.5070.0140.0140.0000.0000.0000.000
61A62LYS10.9280.97423.5910.1350.1350.0000.0000.0000.000
62A63ALA0-0.010-0.02025.9020.0040.0040.0000.0000.0000.000
63A64ASP-1-0.876-0.89527.410-0.080-0.0800.0000.0000.0000.000
64A65LEU0-0.043-0.04324.0500.0020.0020.0000.0000.0000.000
65A66THR0-0.050-0.04228.5770.0100.0100.0000.0000.0000.000
66A67ASN00.0350.03131.4330.0050.0050.0000.0000.0000.000
67A68ALA00.0410.00431.380-0.008-0.0080.0000.0000.0000.000
68A69ALA00.0690.04231.427-0.005-0.0050.0000.0000.0000.000
69A70GLU-1-0.897-0.96329.767-0.121-0.1210.0000.0000.0000.000
70A71VAL0-0.042-0.01926.379-0.016-0.0160.0000.0000.0000.000
71A72GLU-1-0.925-0.97226.597-0.086-0.0860.0000.0000.0000.000
72A73ALA00.0030.01427.397-0.012-0.0120.0000.0000.0000.000
73A74ALA0-0.017-0.00723.409-0.017-0.0170.0000.0000.0000.000
74A75ILE0-0.019-0.01622.187-0.025-0.0250.0000.0000.0000.000
75A76SER0-0.069-0.04222.837-0.012-0.0120.0000.0000.0000.000
76A77ALA00.0680.04223.611-0.012-0.0120.0000.0000.0000.000
77A78ALA0-0.039-0.01618.764-0.033-0.0330.0000.0000.0000.000
78A79ALA0-0.037-0.02119.290-0.033-0.0330.0000.0000.0000.000
79A80ASP-1-0.929-0.96220.689-0.214-0.2140.0000.0000.0000.000
80A81LYS10.8670.94917.5760.4540.4540.0000.0000.0000.000
81A82PHE0-0.028-0.03914.759-0.047-0.0470.0000.0000.0000.000
82A83GLY00.0120.02115.919-0.028-0.0280.0000.0000.0000.000
83A84GLU-1-0.947-0.98616.437-0.068-0.0680.0000.0000.0000.000
84A85ILE0-0.008-0.00415.543-0.072-0.0720.0000.0000.0000.000
85A86HIS00.0610.03912.299-0.014-0.0140.0000.0000.0000.000
86A87GLY00.0200.01413.7690.0880.0880.0000.0000.0000.000
87A88LEU0-0.0230.01014.708-0.059-0.0590.0000.0000.0000.000
88A89VAL00.0100.00314.4330.0540.0540.0000.0000.0000.000
89A90HIS00.0240.01817.635-0.039-0.0390.0000.0000.0000.000
90A91VAL00.003-0.01018.7980.0260.0260.0000.0000.0000.000
91A92ALA00.0100.01121.9990.0010.0010.0000.0000.0000.000
92A93GLY0-0.006-0.00125.2080.0150.0150.0000.0000.0000.000
93A94GLY0-0.069-0.05228.318-0.009-0.0090.0000.0000.0000.000
94A95LEU00.0110.00229.9920.0040.0040.0000.0000.0000.000
95A96ILE0-0.0050.01632.9520.0020.0020.0000.0000.0000.000
96A97ALA00.005-0.00735.103-0.004-0.0040.0000.0000.0000.000
97A98ARG10.8600.93834.5600.0020.0020.0000.0000.0000.000
98A99LYS10.9710.99939.9470.0150.0150.0000.0000.0000.000
99A100THR0-0.027-0.02442.8720.0040.0040.0000.0000.0000.000
100A101ILE00.038-0.00645.459-0.002-0.0020.0000.0000.0000.000
101A102ALA0-0.0160.00146.581-0.001-0.0010.0000.0000.0000.000
102A103GLU-1-0.877-0.93546.121-0.006-0.0060.0000.0000.0000.000
103A104MET0-0.124-0.04142.369-0.003-0.0030.0000.0000.0000.000
104A105ASP-1-0.796-0.88745.414-0.016-0.0160.0000.0000.0000.000
105A106GLU-1-0.875-0.95744.722-0.006-0.0060.0000.0000.0000.000
106A107ALA00.0150.00543.3730.0000.0000.0000.0000.0000.000
107A108PHE0-0.002-0.00938.883-0.003-0.0030.0000.0000.0000.000
108A109TRP00.002-0.00739.7990.0000.0000.0000.0000.0000.000
109A110HIS00.004-0.01238.8890.0010.0010.0000.0000.0000.000
110A111GLN00.0350.04936.1140.0000.0000.0000.0000.0000.000
111A112VAL0-0.033-0.02334.492-0.003-0.0030.0000.0000.0000.000
112A113LEU00.008-0.01533.8990.0010.0010.0000.0000.0000.000
113A114ASP-1-0.785-0.85933.702-0.022-0.0220.0000.0000.0000.000
114A115VAL0-0.040-0.02129.758-0.005-0.0050.0000.0000.0000.000
115A116ASN0-0.088-0.05229.260-0.004-0.0040.0000.0000.0000.000
116A117LEU0-0.024-0.00229.0130.0060.0060.0000.0000.0000.000
117A118THR00.002-0.03030.4260.0030.0030.0000.0000.0000.000
118A119SER0-0.005-0.01228.159-0.002-0.0020.0000.0000.0000.000
119A120LEU0-0.027-0.00324.607-0.007-0.0070.0000.0000.0000.000
120A121PHE00.002-0.00527.0150.0000.0000.0000.0000.0000.000
121A122LEU00.0210.01229.163-0.001-0.0010.0000.0000.0000.000
122A123THR0-0.027-0.01324.110-0.004-0.0040.0000.0000.0000.000
123A124ALA00.0330.02224.175-0.008-0.0080.0000.0000.0000.000
124A125LYS10.9560.98025.2320.0250.0250.0000.0000.0000.000
125A126THR0-0.033-0.03526.2680.0020.0020.0000.0000.0000.000
126A127ALA0-0.001-0.01021.493-0.008-0.0080.0000.0000.0000.000
127A128LEU00.0160.01422.956-0.005-0.0050.0000.0000.0000.000
128A129PRO0-0.055-0.02623.8230.0050.0050.0000.0000.0000.000
129A130LYS10.9300.97021.7440.1240.1240.0000.0000.0000.000
130A131MET0-0.0360.00117.999-0.023-0.0230.0000.0000.0000.000
131A132ALA00.0510.03416.0790.0280.0280.0000.0000.0000.000
132A133LYS10.9350.93718.151-0.188-0.1880.0000.0000.0000.000
133A134GLY0-0.046-0.02116.8070.0080.0080.0000.0000.0000.000
134A135GLY00.0070.01815.5200.0200.0200.0000.0000.0000.000
135A136ALA0-0.024-0.01815.1530.0550.0550.0000.0000.0000.000
136A137ILE00.0170.00216.826-0.066-0.0660.0000.0000.0000.000
137A138VAL0-0.035-0.01715.7270.0470.0470.0000.0000.0000.000
138A139THR0-0.008-0.02518.908-0.035-0.0350.0000.0000.0000.000
139A140PHE00.0320.00420.2430.0180.0180.0000.0000.0000.000
140A141SER0-0.022-0.01723.512-0.009-0.0090.0000.0000.0000.000
141A142SER00.013-0.02026.201-0.006-0.0060.0000.0000.0000.000
142A143GLN00.1200.06127.1720.0100.0100.0000.0000.0000.000
143A144ALA00.0110.01530.384-0.001-0.0010.0000.0000.0000.000
144A145GLY0-0.039-0.03131.475-0.004-0.0040.0000.0000.0000.000
145A146ARG10.7750.87627.383-0.148-0.1480.0000.0000.0000.000
146A147ASP-1-0.881-0.94334.0500.0680.0680.0000.0000.0000.000
147A148GLY00.0120.02036.319-0.004-0.0040.0000.0000.0000.000
148A149GLY0-0.042-0.02635.766-0.007-0.0070.0000.0000.0000.000
149A150GLY00.0240.01736.6970.0010.0010.0000.0000.0000.000
150A151PRO00.038-0.00438.512-0.003-0.0030.0000.0000.0000.000
151A152GLY00.0090.00940.216-0.003-0.0030.0000.0000.0000.000
152A153ALA0-0.017-0.01035.999-0.005-0.0050.0000.0000.0000.000
153A154LEU00.0970.05437.2080.0020.0020.0000.0000.0000.000
154A155ALA00.0500.03738.3140.0030.0030.0000.0000.0000.000
155A156TYR00.0190.00628.6410.0040.0040.0000.0000.0000.000
156A157ALA00.0280.02233.4040.0030.0030.0000.0000.0000.000
157A158THR00.010-0.01034.2330.0080.0080.0000.0000.0000.000
158A159SER0-0.046-0.02432.5660.0020.0020.0000.0000.0000.000
159A160LYS10.8950.95926.848-0.010-0.0100.0000.0000.0000.000
160A161GLY00.0650.03330.4280.0110.0110.0000.0000.0000.000
161A162ALA0-0.020-0.00332.4990.0080.0080.0000.0000.0000.000
162A163VAL00.0070.00026.4520.0060.0060.0000.0000.0000.000
163A164MET0-0.040-0.01328.1840.0140.0140.0000.0000.0000.000
164A165THR0-0.021-0.00729.2540.0150.0150.0000.0000.0000.000
165A166PHE00.0110.00126.6120.0070.0070.0000.0000.0000.000
166A167THR00.0110.01524.6260.0000.0000.0000.0000.0000.000
167A168ARG10.9290.96626.730-0.123-0.1230.0000.0000.0000.000
168A169GLY0-0.027-0.01228.7230.0080.0080.0000.0000.0000.000
169A170LEU00.0510.01825.2260.0040.0040.0000.0000.0000.000
170A171ALA00.0020.00025.0890.0030.0030.0000.0000.0000.000
171A172LYS10.8820.94626.246-0.111-0.1110.0000.0000.0000.000
172A173GLU-1-0.969-0.97029.1300.0570.0570.0000.0000.0000.000
173A174VAL0-0.010-0.00324.343-0.004-0.0040.0000.0000.0000.000
174A175GLY0-0.0030.02624.2190.0060.0060.0000.0000.0000.000
175A176PRO0-0.031-0.03523.622-0.011-0.0110.0000.0000.0000.000
176A177LYS10.8780.95221.2260.0010.0010.0000.0000.0000.000
177A178ILE00.0190.02120.0180.0070.0070.0000.0000.0000.000
178A179ARG10.8770.93813.090-0.386-0.3860.0000.0000.0000.000
179A180VAL00.0040.00720.290-0.038-0.0380.0000.0000.0000.000
180A181ASN0-0.006-0.01318.5910.0260.0260.0000.0000.0000.000
181A182ALA00.0180.02121.297-0.032-0.0320.0000.0000.0000.000
182A183VAL0-0.0050.01218.4730.0310.0310.0000.0000.0000.000
183A184CYS0-0.097-0.05921.748-0.032-0.0320.0000.0000.0000.000
184A185PRO00.0230.01522.6440.0110.0110.0000.0000.0000.000
185A186GLY00.0100.01525.034-0.004-0.0040.0000.0000.0000.000
186A187MET0-0.114-0.06727.659-0.010-0.0100.0000.0000.0000.000
187A188ILE00.0130.02525.4360.0070.0070.0000.0000.0000.000
188A189SER00.0080.00429.503-0.008-0.0080.0000.0000.0000.000
189A190THR0-0.017-0.00432.894-0.003-0.0030.0000.0000.0000.000
190A213ARG10.9560.95421.758-0.176-0.1760.0000.0000.0000.000
191A214GLU-1-0.896-0.94126.2440.0660.0660.0000.0000.0000.000
192A215GLY00.0330.02721.952-0.007-0.0070.0000.0000.0000.000
193A216SER00.018-0.01020.437-0.023-0.0230.0000.0000.0000.000
194A217SER00.047-0.00819.4390.0280.0280.0000.0000.0000.000
195A218GLU-1-0.834-0.89116.237-0.155-0.1550.0000.0000.0000.000
196A219ASP-1-0.852-0.92015.3720.1290.1290.0000.0000.0000.000
197A220VAL0-0.043-0.02616.6850.0450.0450.0000.0000.0000.000
198A221ALA00.0220.00613.5830.0290.0290.0000.0000.0000.000
199A222GLY00.0010.00212.2330.0080.0080.0000.0000.0000.000
200A223LEU0-0.028-0.00312.9070.1090.1090.0000.0000.0000.000
201A224VAL00.002-0.01813.8380.0440.0440.0000.0000.0000.000
202A225ALA00.0130.0139.0790.0010.0010.0000.0000.0000.000
203A226PHE00.001-0.00510.8400.0320.0320.0000.0000.0000.000
204A227LEU00.0170.01911.9200.0720.0720.0000.0000.0000.000
205A228ALA00.0030.02511.474-0.010-0.0100.0000.0000.0000.000
206A229SER0-0.077-0.0608.1570.0270.0270.0000.0000.0000.000
207A230ASP-1-0.801-0.8968.4840.8800.8800.0000.0000.0000.000
208A231ASP-1-0.914-0.9489.5332.2662.2660.0000.0000.0000.000
209A232ALA0-0.060-0.02511.337-0.145-0.1450.0000.0000.0000.000
210A233ALA0-0.024-0.01213.632-0.146-0.1460.0000.0000.0000.000
211A234TYR0-0.046-0.03215.345-0.080-0.0800.0000.0000.0000.000
212A235VAL0-0.0050.01417.236-0.033-0.0330.0000.0000.0000.000
213A236THR00.0180.00519.259-0.034-0.0340.0000.0000.0000.000
214A237GLY00.0070.00121.9400.0020.0020.0000.0000.0000.000
215A238ALA0-0.0210.00221.928-0.010-0.0100.0000.0000.0000.000
216A239CYS0-0.078-0.04423.336-0.025-0.0250.0000.0000.0000.000
217A240TYR00.0180.00017.6230.0270.0270.0000.0000.0000.000
218A241ASP-1-0.767-0.86922.2060.1520.1520.0000.0000.0000.000
219A242ILE0-0.032-0.01919.2580.0320.0320.0000.0000.0000.000
220A243ASN00.0030.00323.126-0.028-0.0280.0000.0000.0000.000
221A244GLY00.0800.04324.1840.0030.0030.0000.0000.0000.000
222A245GLY0-0.041-0.02224.0220.0100.0100.0000.0000.0000.000
223A246VAL00.0090.00222.354-0.010-0.0100.0000.0000.0000.000
224A247LEU0-0.043-0.02224.834-0.016-0.0160.0000.0000.0000.000
225A248PHE00.0510.04228.5730.0090.0090.0000.0000.0000.000
226A249SER00.009-0.00431.839-0.002-0.0020.0000.0000.0000.000