FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: L7Z99

Calculation Name: 5GJ7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GJ7

Chain ID: A

ChEMBL ID:

UniProt ID: C8WV06

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 388
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6463563.408995
FMO2-HF: Nuclear repulsion 6313345.474115
FMO2-HF: Total energy -150217.93488
FMO2-MP2: Total energy -150657.902074


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:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-13.263-6.2413.268-4.795-5.496-0.022
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : 0.001
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].
3A0ALA00.0250.0002.9360.8713.1980.033-1.196-1.1640.002
4A1MET0-0.048-0.0183.859-0.955-0.7490.001-0.089-0.1180.000
5A2TYR00.0750.0446.5690.5570.5570.0000.0000.0000.000
6A3ASP-1-0.829-0.8867.759-1.088-1.0880.0000.0000.0000.000
7A4ILE0-0.048-0.0128.5280.2610.2610.0000.0000.0000.000
8A5TYR0-0.023-0.0275.1530.4740.4740.0000.0000.0000.000
9A6GLY00.0170.0278.2600.1630.1630.0000.0000.0000.000
10A7GLU-1-0.807-0.9098.428-1.872-1.8720.0000.0000.0000.000
11A8ALA0-0.095-0.04710.627-0.106-0.1060.0000.0000.0000.000
12A9ALA00.0120.0086.5700.1980.1980.0000.0000.0000.000
13A10LEU0-0.0170.0156.182-0.358-0.3580.0000.0000.0000.000
14A11PRO00.0420.0245.9150.6610.6610.0000.0000.0000.000
15A12ALA00.009-0.0158.962-0.062-0.0620.0000.0000.0000.000
16A13ASP-1-0.797-0.89710.492-1.247-1.2470.0000.0000.0000.000
17A14VAL00.0270.0287.3900.0410.0410.0000.0000.0000.000
18A15ARG10.8980.95010.6061.3741.3740.0000.0000.0000.000
19A16GLU-1-0.807-0.86612.553-0.557-0.5570.0000.0000.0000.000
20A17ARG10.7360.82110.6071.3101.3100.0000.0000.0000.000
21A18LEU0-0.014-0.0219.9020.0420.0420.0000.0000.0000.000
22A19ARG10.7640.86714.5000.6860.6860.0000.0000.0000.000
23A20ILE00.0070.01417.8650.0770.0770.0000.0000.0000.000
24A21THR00.000-0.02414.9710.0550.0550.0000.0000.0000.000
25A22ARG10.8120.88312.5511.3421.3420.0000.0000.0000.000
26A23ASP-1-0.871-0.92818.518-0.499-0.4990.0000.0000.0000.000
27A24LEU0-0.036-0.01720.4190.0430.0430.0000.0000.0000.000
28A25ALA0-0.023-0.01019.3340.0440.0440.0000.0000.0000.000
29A26GLN0-0.038-0.03221.4660.0110.0110.0000.0000.0000.000
30A27ALA00.0510.02823.8900.0370.0370.0000.0000.0000.000
31A28PHE0-0.036-0.04322.0340.0240.0240.0000.0000.0000.000
32A29HIS0-0.008-0.00824.2340.0250.0250.0000.0000.0000.000
33A30GLU-1-0.940-0.95326.151-0.293-0.2930.0000.0000.0000.000
34A31ARG10.8230.89128.7840.3060.3060.0000.0000.0000.000
35A32ALA0-0.0310.00227.5000.0180.0180.0000.0000.0000.000
36A33PRO0-0.053-0.02629.6590.0160.0160.0000.0000.0000.000
37A34GLU-1-0.885-0.95232.613-0.180-0.1800.0000.0000.0000.000
38A35HIS00.0220.00130.996-0.002-0.0020.0000.0000.0000.000
39A36ASP-1-0.800-0.86631.330-0.164-0.1640.0000.0000.0000.000
40A37ARG10.8850.93933.2040.1470.1470.0000.0000.0000.000
41A38ALA0-0.033-0.02436.7980.0110.0110.0000.0000.0000.000
42A39GLY0-0.049-0.01635.0730.0080.0080.0000.0000.0000.000
43A40ASP-1-0.868-0.91635.844-0.166-0.1660.0000.0000.0000.000
44A41PHE00.015-0.00130.146-0.014-0.0140.0000.0000.0000.000
45A42PRO00.0080.02228.9810.0020.0020.0000.0000.0000.000
46A43PHE0-0.008-0.03730.432-0.016-0.0160.0000.0000.0000.000
47A44GLU-1-0.884-0.93231.633-0.228-0.2280.0000.0000.0000.000
48A45ASN00.0120.00626.674-0.014-0.0140.0000.0000.0000.000
49A46ILE0-0.037-0.01626.652-0.025-0.0250.0000.0000.0000.000
50A47GLU-1-0.806-0.89027.994-0.226-0.2260.0000.0000.0000.000
51A48ASP-1-0.759-0.86126.410-0.318-0.3180.0000.0000.0000.000
52A49LEU0-0.053-0.02921.802-0.031-0.0310.0000.0000.0000.000
53A50LYS10.7920.87724.2530.1920.1920.0000.0000.0000.000
54A51ALA0-0.0150.00726.464-0.004-0.0040.0000.0000.0000.000
55A52SER0-0.038-0.02522.547-0.023-0.0230.0000.0000.0000.000
56A53GLY0-0.007-0.00222.581-0.030-0.0300.0000.0000.0000.000
57A54TYR0-0.019-0.03116.192-0.025-0.0250.0000.0000.0000.000
58A55VAL00.0040.00519.746-0.013-0.0130.0000.0000.0000.000
59A56ARG10.9670.99721.7130.3480.3480.0000.0000.0000.000
60A57TRP00.0040.00315.249-0.015-0.0150.0000.0000.0000.000
61A58THR0-0.042-0.03515.275-0.021-0.0210.0000.0000.0000.000
62A59VAL00.0380.03317.4470.0520.0520.0000.0000.0000.000
63A60PRO00.021-0.00119.068-0.033-0.0330.0000.0000.0000.000
64A61VAL00.0440.01617.2620.0040.0040.0000.0000.0000.000
65A62GLU-1-0.888-0.92420.249-0.061-0.0610.0000.0000.0000.000
66A63TYR0-0.087-0.06723.4930.0110.0110.0000.0000.0000.000
67A64GLY00.0090.00723.534-0.002-0.0020.0000.0000.0000.000
68A65GLY0-0.003-0.00420.672-0.022-0.0220.0000.0000.0000.000
69A66LEU0-0.066-0.03415.7470.0050.0050.0000.0000.0000.000
70A67GLY0-0.027-0.00515.317-0.025-0.0250.0000.0000.0000.000
71A68LEU0-0.041-0.01011.6100.0220.0220.0000.0000.0000.000
72A69SER0-0.003-0.0127.703-0.048-0.0480.0000.0000.0000.000
73A70LEU00.025-0.00610.352-0.129-0.1290.0000.0000.0000.000
74A71GLU-1-0.818-0.9132.856-11.653-7.7530.340-2.368-1.873-0.024
75A72GLU-1-0.689-0.8327.554-1.905-1.9050.0000.0000.0000.000
76A73MET00.0010.0228.7750.1200.1200.0000.0000.0000.000
77A74LEU0-0.058-0.0329.5020.0750.0750.0000.0000.0000.000
78A75MET0-0.0090.0146.585-0.379-0.3790.0000.0000.0000.000
79A76HIS0-0.001-0.0029.8800.1980.1980.0000.0000.0000.000
80A77GLN00.0070.00913.3860.1110.1110.0000.0000.0000.000
81A78GLU-1-0.773-0.83110.618-1.152-1.1520.0000.0000.0000.000
82A79VAL0-0.028-0.02412.8300.0760.0760.0000.0000.0000.000
83A80LEU00.001-0.00315.3190.0980.0980.0000.0000.0000.000
84A81ALA0-0.027-0.02717.5160.0650.0650.0000.0000.0000.000
85A82LYS10.7840.90215.6440.7630.7630.0000.0000.0000.000
86A83GLY0-0.0110.00719.3860.0400.0400.0000.0000.0000.000
87A84ASP-1-0.804-0.89621.999-0.246-0.2460.0000.0000.0000.000
88A85GLY00.0070.01021.928-0.018-0.0180.0000.0000.0000.000
89A86SER00.041-0.01223.0150.0020.0020.0000.0000.0000.000
90A87THR0-0.007-0.02624.0200.0130.0130.0000.0000.0000.000
91A88ALA0-0.0020.02719.206-0.005-0.0050.0000.0000.0000.000
92A89LEU00.019-0.00220.822-0.005-0.0050.0000.0000.0000.000
93A90ALA0-0.020-0.00822.0070.0150.0150.0000.0000.0000.000
94A91ILE00.0310.01420.6580.0160.0160.0000.0000.0000.000
95A92GLY00.0220.00319.245-0.010-0.0100.0000.0000.0000.000
96A93TRP0-0.035-0.02620.0920.0170.0170.0000.0000.0000.000
97A94HIS00.0270.02622.4190.0420.0420.0000.0000.0000.000
98A95VAL00.0210.00917.7480.0180.0180.0000.0000.0000.000
99A96GLY00.0430.01617.9370.0030.0030.0000.0000.0000.000
100A97ILE0-0.038-0.01018.9750.0390.0390.0000.0000.0000.000
101A98LEU00.0110.00520.8220.0340.0340.0000.0000.0000.000
102A99LEU0-0.0050.00713.5460.0240.0240.0000.0000.0000.000
103A100HIS10.8350.90618.1860.0750.0750.0000.0000.0000.000
104A101LEU0-0.036-0.00220.3070.0360.0360.0000.0000.0000.000
105A102ARG10.7840.88913.8100.2680.2680.0000.0000.0000.000
106A103GLU-1-0.809-0.88516.0990.0310.0310.0000.0000.0000.000
107A104THR0-0.028-0.02919.3420.0360.0360.0000.0000.0000.000
108A105GLY0-0.015-0.00422.7930.0150.0150.0000.0000.0000.000
109A106ALA0-0.016-0.01225.3700.0050.0050.0000.0000.0000.000
110A107PHE00.0060.00027.310-0.001-0.0010.0000.0000.0000.000
111A108PRO00.0720.03729.2330.0060.0060.0000.0000.0000.000
112A109ASP-1-0.824-0.89229.162-0.016-0.0160.0000.0000.0000.000
113A110GLU-1-0.853-0.91930.520-0.059-0.0590.0000.0000.0000.000
114A111LEU0-0.0030.01231.952-0.010-0.0100.0000.0000.0000.000
115A112PHE00.001-0.01122.543-0.013-0.0130.0000.0000.0000.000
116A113ARG10.9360.98128.1180.0410.0410.0000.0000.0000.000
117A114MET0-0.0070.01329.590-0.016-0.0160.0000.0000.0000.000
118A115VAL00.0350.01127.489-0.011-0.0110.0000.0000.0000.000
119A116CYS0-0.046-0.01325.202-0.021-0.0210.0000.0000.0000.000
120A117GLU-1-0.856-0.92026.921-0.129-0.1290.0000.0000.0000.000
121A118SER00.0200.01729.568-0.009-0.0090.0000.0000.0000.000
122A119VAL0-0.050-0.01924.192-0.012-0.0120.0000.0000.0000.000
123A120VAL0-0.063-0.05224.281-0.024-0.0240.0000.0000.0000.000
124A121LYS10.8080.88326.7440.1170.1170.0000.0000.0000.000
125A122GLU-1-0.944-0.96930.363-0.138-0.1380.0000.0000.0000.000
126A123GLY0-0.0050.01627.624-0.004-0.0040.0000.0000.0000.000
127A124ALA0-0.024-0.01128.672-0.002-0.0020.0000.0000.0000.000
128A125LEU00.003-0.00525.943-0.016-0.0160.0000.0000.0000.000
129A126ILE0-0.010-0.02125.7460.0230.0230.0000.0000.0000.000
130A127ASN00.0650.02226.496-0.018-0.0180.0000.0000.0000.000
131A128SER0-0.0280.00027.5710.0160.0160.0000.0000.0000.000
132A129CYS0-0.042-0.03129.170-0.009-0.0090.0000.0000.0000.000
133A130ALA00.0530.02131.5710.0070.0070.0000.0000.0000.000
134A131THR00.0020.00731.7570.0060.0060.0000.0000.0000.000
135A132GLU-1-0.709-0.82234.262-0.042-0.0420.0000.0000.0000.000
136A133PRO00.0020.01437.8800.0020.0020.0000.0000.0000.000
137A144PRO0-0.041-0.03837.9010.0000.0000.0000.0000.0000.000
138A145GLU-1-0.930-0.95940.399-0.024-0.0240.0000.0000.0000.000
139A146THR0-0.055-0.04940.019-0.003-0.0030.0000.0000.0000.000
140A147THR0-0.041-0.01642.3880.0050.0050.0000.0000.0000.000
141A148ALA0-0.025-0.01442.388-0.004-0.0040.0000.0000.0000.000
142A149VAL00.0240.01144.5060.0040.0040.0000.0000.0000.000
143A150LYS10.8340.92645.7630.0180.0180.0000.0000.0000.000
144A151VAL0-0.015-0.01548.0640.0010.0010.0000.0000.0000.000
145A152PRO00.001-0.02549.1940.0000.0000.0000.0000.0000.000
146A153GLY00.0210.01748.020-0.002-0.0020.0000.0000.0000.000
147A154GLY00.002-0.00244.859-0.002-0.0020.0000.0000.0000.000
148A155TYR0-0.012-0.00142.9270.0050.0050.0000.0000.0000.000
149A156ARG10.8260.92144.9450.0380.0380.0000.0000.0000.000
150A157ILE00.003-0.00540.1460.0030.0030.0000.0000.0000.000
151A158THR00.0040.00044.053-0.004-0.0040.0000.0000.0000.000
152A159GLY00.0240.01042.8020.0040.0040.0000.0000.0000.000
153A160ARG10.8040.89240.7230.0620.0620.0000.0000.0000.000
154A161LYS10.7540.89035.4780.0510.0510.0000.0000.0000.000
155A162THR0-0.023-0.03834.875-0.004-0.0040.0000.0000.0000.000
156A163PHE0-0.034-0.01831.040-0.001-0.0010.0000.0000.0000.000
157A164SER00.0640.03830.625-0.005-0.0050.0000.0000.0000.000
158A165THR0-0.004-0.00726.845-0.003-0.0030.0000.0000.0000.000
159A166LEU00.0450.02125.947-0.005-0.0050.0000.0000.0000.000
160A167SER0-0.014-0.02129.4050.0010.0010.0000.0000.0000.000
161A168PRO00.0470.02632.6120.0050.0050.0000.0000.0000.000
162A169ALA0-0.006-0.00330.6690.0040.0040.0000.0000.0000.000
163A170LEU0-0.087-0.01628.897-0.007-0.0070.0000.0000.0000.000
164A171THR00.0290.01031.5550.0030.0030.0000.0000.0000.000
165A172TRP0-0.004-0.02230.4450.0200.0200.0000.0000.0000.000
166A173ILE00.0370.00131.335-0.010-0.0100.0000.0000.0000.000
167A174MET0-0.0650.00227.4760.0050.0050.0000.0000.0000.000
168A175VAL00.0260.02032.273-0.003-0.0030.0000.0000.0000.000
169A176THR00.007-0.00733.4690.0030.0030.0000.0000.0000.000
170A177ALA00.0140.00236.154-0.004-0.0040.0000.0000.0000.000
171A178THR00.0180.01139.8170.0040.0040.0000.0000.0000.000
172A179VAL00.0090.00342.192-0.004-0.0040.0000.0000.0000.000
173A180ALA00.005-0.00144.6030.0030.0030.0000.0000.0000.000
174A181ASP-1-0.931-0.97848.179-0.008-0.0080.0000.0000.0000.000
175A182GLU-1-0.866-0.90245.6590.0010.0010.0000.0000.0000.000
176A183ASP-1-0.955-0.96545.7730.0050.0050.0000.0000.0000.000
177A184VAL0-0.0310.00241.4610.0040.0040.0000.0000.0000.000
178A185VAL00.0060.00136.851-0.004-0.0040.0000.0000.0000.000
179A186GLY00.003-0.00137.6250.0040.0040.0000.0000.0000.000
180A187GLN0-0.030-0.02529.930-0.011-0.0110.0000.0000.0000.000
181A188PHE00.0210.00435.3020.0030.0030.0000.0000.0000.000
182A189LEU00.0010.00331.498-0.006-0.0060.0000.0000.0000.000
183A190VAL00.0310.01235.0040.0040.0040.0000.0000.0000.000
184A191ARG10.7840.86335.6060.0750.0750.0000.0000.0000.000
185A192LYS10.8930.94735.0720.1370.1370.0000.0000.0000.000
186A193GLU-1-0.908-0.96037.143-0.091-0.0910.0000.0000.0000.000
187A194ASP-1-0.828-0.88440.260-0.071-0.0710.0000.0000.0000.000
188A195VAL0-0.074-0.03438.1970.0060.0060.0000.0000.0000.000
189A196GLU-1-0.854-0.91741.505-0.070-0.0700.0000.0000.0000.000
190A197ILE00.0070.00036.6980.0010.0010.0000.0000.0000.000
191A198VAL0-0.039-0.02339.7670.0020.0020.0000.0000.0000.000
192A199GLU-1-0.878-0.93439.210-0.112-0.1120.0000.0000.0000.000
193A200THR0-0.064-0.03937.9670.0060.0060.0000.0000.0000.000
194A201TRP0-0.033-0.01239.642-0.002-0.0020.0000.0000.0000.000
195A202ASP-1-0.809-0.88137.051-0.111-0.1110.0000.0000.0000.000
196A203THR0-0.027-0.03232.4270.0080.0080.0000.0000.0000.000
197A204LEU0-0.045-0.02731.807-0.004-0.0040.0000.0000.0000.000
198A205GLY00.0650.01130.029-0.004-0.0040.0000.0000.0000.000
199A206MET0-0.110-0.05123.1120.0010.0010.0000.0000.0000.000
200A207ARG10.8250.90328.8190.1380.1380.0000.0000.0000.000
201A208ALA00.0210.03529.7390.0060.0060.0000.0000.0000.000
202A209THR0-0.002-0.00527.6550.0000.0000.0000.0000.0000.000
203A210GLY00.0280.03130.9070.0100.0100.0000.0000.0000.000
204A211SER0-0.048-0.02832.124-0.004-0.0040.0000.0000.0000.000
205A212HIS0-0.004-0.00133.8270.0110.0110.0000.0000.0000.000
206A213ASP-1-0.766-0.84735.396-0.075-0.0750.0000.0000.0000.000
207A214ILE0-0.017-0.00335.825-0.004-0.0040.0000.0000.0000.000
208A215VAL0-0.019-0.02938.5430.0070.0070.0000.0000.0000.000
209A216LEU0-0.0020.00939.038-0.003-0.0030.0000.0000.0000.000
210A217LYS10.8620.91043.1890.0650.0650.0000.0000.0000.000
211A218ASP-1-0.850-0.91646.868-0.044-0.0440.0000.0000.0000.000
212A219VAL00.0380.03841.193-0.001-0.0010.0000.0000.0000.000
213A220PHE00.0060.00244.3370.0040.0040.0000.0000.0000.000
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