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: 85ZKY

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2442524.492734
FMO2-HF: Nuclear repulsion 2361327.112323
FMO2-HF: Total energy -81197.38041
FMO2-MP2: Total energy -81433.706886


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.
-5.551-2.3327.799-4.93-6.09-0.046
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 : 0.006 / q_NPA : -0.010
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].
3A4PHE0-0.003-0.0073.153-0.5471.5560.004-0.958-1.1490.000
4A5THR0-0.006-0.0142.317-0.2580.8871.472-0.988-1.629-0.006
5A6ASN0-0.079-0.0334.4920.6940.752-0.001-0.018-0.0400.000
6A7ARG10.8090.8857.6090.3120.3120.0000.0000.0000.000
7A8THR0-0.004-0.0049.489-0.238-0.2380.0000.0000.0000.000
8A9ILE0-0.044-0.0169.6000.1090.1090.0000.0000.0000.000
9A10VAL00.0210.01212.822-0.035-0.0350.0000.0000.0000.000
10A11VAL0-0.010-0.00914.0250.0620.0620.0000.0000.0000.000
11A12ALA00.0430.02416.7160.0020.0020.0000.0000.0000.000
12A13GLY00.038-0.00220.4690.0340.0340.0000.0000.0000.000
13A14ALA0-0.0130.00418.4160.0090.0090.0000.0000.0000.000
14A15GLY0-0.0010.00320.286-0.006-0.0060.0000.0000.0000.000
15A16ARG10.8220.92822.3430.1630.1630.0000.0000.0000.000
16A17ASP-1-0.757-0.84821.061-0.305-0.3050.0000.0000.0000.000
17A18ILE00.0330.01317.501-0.028-0.0280.0000.0000.0000.000
18A19GLY00.0380.01717.170-0.021-0.0210.0000.0000.0000.000
19A20ARG10.7760.84716.4220.3220.3220.0000.0000.0000.000
20A21ALA00.0100.01315.105-0.075-0.0750.0000.0000.0000.000
21A22CYS0-0.057-0.03112.806-0.050-0.0500.0000.0000.0000.000
22A23ALA0-0.0060.00011.515-0.113-0.1130.0000.0000.0000.000
23A24ILE00.0340.01711.265-0.152-0.1520.0000.0000.0000.000
24A25ARG10.8640.9287.481-0.097-0.0970.0000.0000.0000.000
25A26PHE00.002-0.0167.062-0.167-0.1670.0000.0000.0000.000
26A27ALA00.0110.0126.260-0.600-0.6000.0000.0000.0000.000
27A28GLN0-0.015-0.0096.246-0.424-0.4240.0000.0000.0000.000
28A29GLU-1-0.784-0.8512.373-0.1270.4180.723-0.309-0.9590.000
29A30GLY00.0180.0042.062-6.985-7.7075.602-2.624-2.257-0.040
30A31ALA00.0030.0084.3610.7650.855-0.001-0.033-0.0560.000
31A32ASN0-0.0150.0057.457-0.103-0.1030.0000.0000.0000.000
32A33VAL0-0.009-0.0019.9620.1720.1720.0000.0000.0000.000
33A34VAL00.0130.00912.4030.0570.0570.0000.0000.0000.000
34A35LEU0-0.034-0.01215.7600.0030.0030.0000.0000.0000.000
35A36THR00.0240.00717.9150.0140.0140.0000.0000.0000.000
36A37TYR0-0.001-0.01121.6410.0110.0110.0000.0000.0000.000
37A38ASN00.027-0.01724.2360.0090.0090.0000.0000.0000.000
38A39GLY00.0150.00927.699-0.005-0.0050.0000.0000.0000.000
39A40ALA00.0360.00929.586-0.007-0.0070.0000.0000.0000.000
40A41ALA0-0.0030.00425.024-0.011-0.0110.0000.0000.0000.000
41A42GLU-1-0.851-0.92424.290-0.249-0.2490.0000.0000.0000.000
42A43GLY00.0000.01222.065-0.025-0.0250.0000.0000.0000.000
43A44ALA00.0250.00519.870-0.043-0.0430.0000.0000.0000.000
44A45ALA00.0060.00619.950-0.044-0.0440.0000.0000.0000.000
45A46THR0-0.007-0.01619.171-0.028-0.0280.0000.0000.0000.000
46A47ALA0-0.007-0.01116.031-0.049-0.0490.0000.0000.0000.000
47A48VAL0-0.017-0.00915.825-0.083-0.0830.0000.0000.0000.000
48A49ALA00.0120.01417.086-0.055-0.0550.0000.0000.0000.000
49A50GLU-1-0.821-0.90514.620-0.698-0.6980.0000.0000.0000.000
50A51ILE0-0.041-0.02111.906-0.123-0.1230.0000.0000.0000.000
51A52GLU-1-0.815-0.88613.140-0.797-0.7970.0000.0000.0000.000
52A53LYS10.7590.86315.5380.6330.6330.0000.0000.0000.000
53A54LEU0-0.068-0.0248.808-0.070-0.0700.0000.0000.0000.000
54A55GLY0-0.023-0.00510.952-0.192-0.1920.0000.0000.0000.000
55A56ARG10.8290.9037.9521.9221.9220.0000.0000.0000.000
56A57SER0-0.012-0.02212.8890.0560.0560.0000.0000.0000.000
57A58ALA00.008-0.00214.642-0.019-0.0190.0000.0000.0000.000
58A59LEU0-0.041-0.02315.5490.0520.0520.0000.0000.0000.000
59A60ALA00.0170.01318.3720.0080.0080.0000.0000.0000.000
60A61ILE0-0.033-0.01520.4580.0240.0240.0000.0000.0000.000
61A62LYS10.8590.92323.4750.1770.1770.0000.0000.0000.000
62A63ALA00.022-0.00825.2950.0070.0070.0000.0000.0000.000
63A64ASP-1-0.859-0.89626.893-0.135-0.1350.0000.0000.0000.000
64A65LEU0-0.042-0.02723.4480.0060.0060.0000.0000.0000.000
65A66THR0-0.042-0.03727.9900.0120.0120.0000.0000.0000.000
66A67ASN0-0.022-0.02131.3660.0170.0170.0000.0000.0000.000
67A68ALA00.0400.00930.882-0.010-0.0100.0000.0000.0000.000
68A69ALA00.0700.03930.770-0.006-0.0060.0000.0000.0000.000
69A70GLU-1-0.777-0.85628.960-0.167-0.1670.0000.0000.0000.000
70A71VAL0-0.023-0.00825.741-0.021-0.0210.0000.0000.0000.000
71A72GLU-1-0.865-0.93726.167-0.102-0.1020.0000.0000.0000.000
72A73ALA0-0.0070.01527.647-0.006-0.0060.0000.0000.0000.000
73A74ALA0-0.002-0.00823.263-0.016-0.0160.0000.0000.0000.000
74A75ILE0-0.015-0.01721.442-0.029-0.0290.0000.0000.0000.000
75A76SER0-0.065-0.03123.4230.0090.0090.0000.0000.0000.000
76A77ALA00.0760.03423.467-0.012-0.0120.0000.0000.0000.000
77A78ALA0-0.049-0.03018.920-0.033-0.0330.0000.0000.0000.000
78A79ALA0-0.018-0.00718.773-0.035-0.0350.0000.0000.0000.000
79A80ASP-1-0.909-0.95720.358-0.211-0.2110.0000.0000.0000.000
80A81LYS10.8500.95016.9680.5840.5840.0000.0000.0000.000
81A82PHE0-0.033-0.03614.526-0.063-0.0630.0000.0000.0000.000
82A83GLY00.0090.01815.836-0.012-0.0120.0000.0000.0000.000
83A84GLU-1-0.915-0.96816.542-0.019-0.0190.0000.0000.0000.000
84A85ILE0-0.016-0.01715.930-0.077-0.0770.0000.0000.0000.000
85A86HIS00.0760.03212.193-0.033-0.0330.0000.0000.0000.000
86A87GLY00.0210.01113.8300.0830.0830.0000.0000.0000.000
87A88LEU0-0.049-0.01014.681-0.062-0.0620.0000.0000.0000.000
88A89VAL00.0150.00413.5040.0500.0500.0000.0000.0000.000
89A90HIS00.0260.03216.892-0.040-0.0400.0000.0000.0000.000
90A91VAL0-0.011-0.01718.2830.0310.0310.0000.0000.0000.000
91A92ALA0-0.0150.00421.3170.0030.0030.0000.0000.0000.000
92A93GLY00.0260.01924.6050.0170.0170.0000.0000.0000.000
93A94GLY0-0.064-0.04227.457-0.015-0.0150.0000.0000.0000.000
94A95LEU00.0030.00029.2140.0080.0080.0000.0000.0000.000
95A96ILE0-0.0050.01631.9060.0050.0050.0000.0000.0000.000
96A97ALA00.009-0.00434.308-0.003-0.0030.0000.0000.0000.000
97A98ARG10.8410.92133.7860.0630.0630.0000.0000.0000.000
98A99LYS10.9050.94539.2170.0510.0510.0000.0000.0000.000
99A100THR0-0.043-0.05342.1130.0040.0040.0000.0000.0000.000
100A101ILE00.026-0.01244.773-0.002-0.0020.0000.0000.0000.000
101A102ALA0-0.0030.00645.9330.0000.0000.0000.0000.0000.000
102A103GLU-1-0.827-0.88145.505-0.043-0.0430.0000.0000.0000.000
103A104MET0-0.092-0.02141.373-0.005-0.0050.0000.0000.0000.000
104A105ASP-1-0.801-0.88244.656-0.048-0.0480.0000.0000.0000.000
105A106GLU-1-0.852-0.93643.902-0.034-0.0340.0000.0000.0000.000
106A107ALA00.0020.01042.582-0.001-0.0010.0000.0000.0000.000
107A108PHE00.009-0.00538.215-0.004-0.0040.0000.0000.0000.000
108A109TRP00.008-0.00838.943-0.002-0.0020.0000.0000.0000.000
109A110HIS0-0.002-0.02338.152-0.002-0.0020.0000.0000.0000.000
110A111GLN0-0.0020.01435.9710.0000.0000.0000.0000.0000.000
111A112VAL0-0.025-0.01333.920-0.007-0.0070.0000.0000.0000.000
112A113LEU00.0210.00433.213-0.003-0.0030.0000.0000.0000.000
113A114ASP-1-0.824-0.89832.816-0.062-0.0620.0000.0000.0000.000
114A115VAL0-0.029-0.01929.124-0.007-0.0070.0000.0000.0000.000
115A116ASN0-0.066-0.04028.529-0.014-0.0140.0000.0000.0000.000
116A117LEU00.0090.01428.3720.0050.0050.0000.0000.0000.000
117A118THR00.010-0.01529.7750.0030.0030.0000.0000.0000.000
118A119SER00.008-0.01327.430-0.001-0.0010.0000.0000.0000.000
119A120LEU0-0.046-0.00823.736-0.008-0.0080.0000.0000.0000.000
120A121PHE00.0110.00426.3690.0030.0030.0000.0000.0000.000
121A122LEU00.0200.01228.6060.0020.0020.0000.0000.0000.000
122A123THR0-0.022-0.02523.1420.0010.0010.0000.0000.0000.000
123A124ALA00.0190.01023.928-0.005-0.0050.0000.0000.0000.000
124A125LYS10.8690.93524.9590.0740.0740.0000.0000.0000.000
125A126THR0-0.028-0.02925.9660.0070.0070.0000.0000.0000.000
126A127ALA00.0000.00221.072-0.007-0.0070.0000.0000.0000.000
127A128LEU00.0250.00922.6700.0000.0000.0000.0000.0000.000
128A129PRO0-0.048-0.03023.8730.0140.0140.0000.0000.0000.000
129A130LYS10.8990.96021.5540.1650.1650.0000.0000.0000.000
130A131MET0-0.0410.00017.566-0.021-0.0210.0000.0000.0000.000
131A132ALA00.0360.03616.1580.0320.0320.0000.0000.0000.000
132A133LYS10.9330.95418.139-0.255-0.2550.0000.0000.0000.000
133A134GLY0-0.013-0.00416.3590.0270.0270.0000.0000.0000.000
134A135GLY00.0170.01815.3260.0220.0220.0000.0000.0000.000
135A136ALA0-0.011-0.00814.4290.0440.0440.0000.0000.0000.000
136A137ILE00.0090.00416.209-0.072-0.0720.0000.0000.0000.000
137A138VAL0-0.040-0.01614.9980.0450.0450.0000.0000.0000.000
138A139THR0-0.004-0.00918.227-0.040-0.0400.0000.0000.0000.000
139A140PHE00.0660.01420.0130.0100.0100.0000.0000.0000.000
140A141SER00.010-0.00922.929-0.001-0.0010.0000.0000.0000.000
141A142SER0-0.033-0.03725.386-0.015-0.0150.0000.0000.0000.000
142A143GLN00.0770.02826.2890.0130.0130.0000.0000.0000.000
143A144ALA00.0210.02529.8620.0040.0040.0000.0000.0000.000
144A145GLY0-0.015-0.01030.896-0.001-0.0010.0000.0000.0000.000
145A146ARG10.7360.84026.876-0.069-0.0690.0000.0000.0000.000
146A147ASP-1-0.875-0.94433.0120.0080.0080.0000.0000.0000.000
147A148GLY00.0160.02435.4590.0000.0000.0000.0000.0000.000
148A149GLY0-0.038-0.02835.048-0.007-0.0070.0000.0000.0000.000
149A150GLY00.0100.01335.7050.0020.0020.0000.0000.0000.000
150A151PRO00.008-0.02337.543-0.002-0.0020.0000.0000.0000.000
151A152GLY00.0110.01339.170-0.005-0.0050.0000.0000.0000.000
152A153ALA00.0180.00635.043-0.005-0.0050.0000.0000.0000.000
153A154LEU00.0550.03736.123-0.001-0.0010.0000.0000.0000.000
154A155ALA00.0740.05137.3670.0040.0040.0000.0000.0000.000
155A156TYR00.0160.01127.997-0.002-0.0020.0000.0000.0000.000
156A157ALA00.0230.02332.5050.0010.0010.0000.0000.0000.000
157A158THR00.012-0.00733.3100.0070.0070.0000.0000.0000.000
158A159SER0-0.042-0.03431.8000.0020.0020.0000.0000.0000.000
159A160LYS10.8040.91626.5470.0650.0650.0000.0000.0000.000
160A161GLY00.0950.05329.3570.0090.0090.0000.0000.0000.000
161A162ALA0-0.0210.00031.7030.0090.0090.0000.0000.0000.000
162A163VAL00.0030.00225.5890.0070.0070.0000.0000.0000.000
163A164MET0-0.0230.01027.2850.0160.0160.0000.0000.0000.000
164A165THR0-0.045-0.02828.3460.0170.0170.0000.0000.0000.000
165A166PHE00.0350.00725.9880.0090.0090.0000.0000.0000.000
166A167THR0-0.021-0.01023.5900.0020.0020.0000.0000.0000.000
167A168ARG10.9090.93926.300-0.063-0.0630.0000.0000.0000.000
168A169GLY0-0.0190.00028.4870.0110.0110.0000.0000.0000.000
169A170LEU00.0650.02724.7800.0080.0080.0000.0000.0000.000
170A171ALA00.0010.00125.0590.0060.0060.0000.0000.0000.000
171A172LYS10.8680.93426.006-0.081-0.0810.0000.0000.0000.000
172A173GLU-1-0.974-0.96428.8050.0350.0350.0000.0000.0000.000
173A174VAL00.0110.00023.935-0.001-0.0010.0000.0000.0000.000
174A175GLY00.0200.04223.9590.0100.0100.0000.0000.0000.000
175A176PRO0-0.032-0.03123.371-0.010-0.0100.0000.0000.0000.000
176A177LYS10.8260.91721.6110.0130.0130.0000.0000.0000.000
177A178ILE0-0.001-0.00619.8010.0060.0060.0000.0000.0000.000
178A179ARG10.8310.93613.024-0.306-0.3060.0000.0000.0000.000
179A180VAL00.008-0.00119.838-0.043-0.0430.0000.0000.0000.000
180A181ASN0-0.013-0.02417.9920.0310.0310.0000.0000.0000.000
181A182ALA00.0230.02020.771-0.034-0.0340.0000.0000.0000.000
182A183VAL00.0110.01317.7370.0310.0310.0000.0000.0000.000
183A184CYS0-0.054-0.03220.827-0.021-0.0210.0000.0000.0000.000
184A185PRO00.0200.01621.6980.0110.0110.0000.0000.0000.000
185A186GLY00.0280.03224.2700.0040.0040.0000.0000.0000.000
186A187MET0-0.082-0.05127.032-0.011-0.0110.0000.0000.0000.000
187A188ILE00.0070.01724.6190.0070.0070.0000.0000.0000.000
188A189SER0-0.026-0.04328.6240.0000.0000.0000.0000.0000.000
189A190THR0-0.062-0.02831.987-0.004-0.0040.0000.0000.0000.000
190A213ARG10.9910.99421.333-0.010-0.0100.0000.0000.0000.000
191A214GLU-1-0.852-0.90025.533-0.041-0.0410.0000.0000.0000.000
192A215GLY0-0.007-0.00221.188-0.007-0.0070.0000.0000.0000.000
193A216SER0-0.015-0.04619.198-0.013-0.0130.0000.0000.0000.000
194A217SER00.000-0.04118.8270.0280.0280.0000.0000.0000.000
195A218GLU-1-0.760-0.86414.846-0.411-0.4110.0000.0000.0000.000
196A219ASP-1-0.857-0.89514.291-0.120-0.1200.0000.0000.0000.000
197A220VAL0-0.021-0.01515.6680.0470.0470.0000.0000.0000.000
198A221ALA00.0320.01013.0700.0280.0280.0000.0000.0000.000
199A222GLY0-0.0030.00311.259-0.017-0.0170.0000.0000.0000.000
200A223LEU0-0.030-0.00712.0050.1070.1070.0000.0000.0000.000
201A224VAL0-0.005-0.01813.3780.0550.0550.0000.0000.0000.000
202A225ALA00.0250.0098.4740.0080.0080.0000.0000.0000.000
203A226PHE0-0.035-0.0159.9370.0800.0800.0000.0000.0000.000
204A227LEU0-0.0060.00511.8470.0690.0690.0000.0000.0000.000
205A228ALA00.0150.00611.0140.0200.0200.0000.0000.0000.000
206A229SER0-0.041-0.0248.2560.0490.0490.0000.0000.0000.000
207A230ASP-1-0.763-0.8568.5110.7350.7350.0000.0000.0000.000
208A231ASP-1-0.875-0.9278.1832.0662.0660.0000.0000.0000.000
209A232ALA0-0.027-0.00710.957-0.113-0.1130.0000.0000.0000.000
210A233ALA0-0.013-0.01313.301-0.125-0.1250.0000.0000.0000.000
211A234TYR0-0.039-0.02314.912-0.056-0.0560.0000.0000.0000.000
212A235VAL0-0.033-0.00117.104-0.039-0.0390.0000.0000.0000.000
213A236THR00.0430.01818.933-0.036-0.0360.0000.0000.0000.000
214A237GLY00.0070.00421.7770.0080.0080.0000.0000.0000.000
215A238ALA0-0.0270.00021.718-0.010-0.0100.0000.0000.0000.000
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