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: 3798L

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 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 388
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6458508.415249
FMO2-HF: Nuclear repulsion 6308292.042267
FMO2-HF: Total energy -150216.372982
FMO2-MP2: Total energy -150656.318236


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.
-12.152-7.6216.891-5.304-6.119-0.016
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 : -0.056 / q_NPA : -0.018
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].
3A0ALA00.000-0.0072.879-0.2572.0820.050-1.210-1.1800.000
4A1MET0-0.055-0.0213.996-0.844-0.6720.001-0.073-0.1000.000
5A2TYR00.0600.0416.6910.3980.3980.0000.0000.0000.000
6A3ASP-1-0.807-0.8887.874-0.708-0.7080.0000.0000.0000.000
7A4ILE0-0.057-0.0148.5810.1940.1940.0000.0000.0000.000
8A5TYR0-0.024-0.0305.4560.3500.3500.0000.0000.0000.000
9A6GLY00.0120.0238.2880.1660.1660.0000.0000.0000.000
10A7GLU-1-0.852-0.9568.499-1.100-1.1000.0000.0000.0000.000
11A8ALA0-0.103-0.05810.694-0.003-0.0030.0000.0000.0000.000
12A9ALA00.0130.0086.5440.1000.1000.0000.0000.0000.000
13A10LEU0-0.0210.0126.3300.1240.1240.0000.0000.0000.000
14A11PRO00.0330.0256.7860.2700.2700.0000.0000.0000.000
15A12ALA00.007-0.0169.826-0.108-0.1080.0000.0000.0000.000
16A13ASP-1-0.837-0.93111.085-0.803-0.8030.0000.0000.0000.000
17A14VAL00.0130.0178.042-0.009-0.0090.0000.0000.0000.000
18A15ARG10.9130.96511.3160.6470.6470.0000.0000.0000.000
19A16GLU-1-0.844-0.90613.364-0.366-0.3660.0000.0000.0000.000
20A17ARG10.8040.87711.1490.9140.9140.0000.0000.0000.000
21A18LEU0-0.004-0.0149.7540.0210.0210.0000.0000.0000.000
22A19ARG10.8010.90714.3630.4280.4280.0000.0000.0000.000
23A20ILE00.0140.01617.8260.0440.0440.0000.0000.0000.000
24A21THR0-0.005-0.02314.8730.0380.0380.0000.0000.0000.000
25A22ARG10.8700.93613.2880.7550.7550.0000.0000.0000.000
26A23ASP-1-0.896-0.93818.372-0.304-0.3040.0000.0000.0000.000
27A24LEU0-0.046-0.02520.3880.0260.0260.0000.0000.0000.000
28A25ALA0-0.022-0.00619.2140.0280.0280.0000.0000.0000.000
29A26GLN0-0.029-0.01321.3440.0100.0100.0000.0000.0000.000
30A27ALA00.0630.03223.7470.0250.0250.0000.0000.0000.000
31A28PHE0-0.046-0.04221.9960.0150.0150.0000.0000.0000.000
32A29HIS0-0.009-0.00724.1670.0140.0140.0000.0000.0000.000
33A30GLU-1-0.971-0.98926.028-0.187-0.1870.0000.0000.0000.000
34A31ARG10.8530.91928.9340.2120.2120.0000.0000.0000.000
35A32ALA0-0.0100.01327.4140.0110.0110.0000.0000.0000.000
36A33PRO0-0.072-0.03629.5590.0110.0110.0000.0000.0000.000
37A34GLU-1-0.879-0.95032.509-0.125-0.1250.0000.0000.0000.000
38A35HIS00.0300.02531.5150.0000.0000.0000.0000.0000.000
39A36ASP-1-0.812-0.88531.261-0.114-0.1140.0000.0000.0000.000
40A37ARG10.8640.93033.1300.0990.0990.0000.0000.0000.000
41A38ALA0-0.020-0.02036.7180.0070.0070.0000.0000.0000.000
42A39GLY0-0.057-0.01735.0200.0050.0050.0000.0000.0000.000
43A40ASP-1-0.878-0.93935.814-0.119-0.1190.0000.0000.0000.000
44A41PHE00.010-0.00330.007-0.010-0.0100.0000.0000.0000.000
45A42PRO00.0060.01928.9150.0020.0020.0000.0000.0000.000
46A43PHE0-0.007-0.03830.372-0.012-0.0120.0000.0000.0000.000
47A44GLU-1-0.878-0.93031.589-0.166-0.1660.0000.0000.0000.000
48A45ASN00.0090.00726.641-0.008-0.0080.0000.0000.0000.000
49A46ILE0-0.045-0.02226.713-0.020-0.0200.0000.0000.0000.000
50A47GLU-1-0.901-0.95627.941-0.179-0.1790.0000.0000.0000.000
51A48ASP-1-0.784-0.88426.442-0.224-0.2240.0000.0000.0000.000
52A49LEU0-0.056-0.03421.773-0.024-0.0240.0000.0000.0000.000
53A50LYS10.8790.93924.2660.1560.1560.0000.0000.0000.000
54A51ALA0-0.0020.01626.474-0.005-0.0050.0000.0000.0000.000
55A52SER0-0.044-0.03122.543-0.017-0.0170.0000.0000.0000.000
56A53GLY0-0.018-0.01022.633-0.021-0.0210.0000.0000.0000.000
57A54TYR0-0.021-0.04016.137-0.033-0.0330.0000.0000.0000.000
58A55VAL00.0060.00219.760-0.021-0.0210.0000.0000.0000.000
59A56ARG10.9821.00121.5510.2870.2870.0000.0000.0000.000
60A57TRP00.0090.00515.223-0.023-0.0230.0000.0000.0000.000
61A58THR0-0.052-0.04215.281-0.031-0.0310.0000.0000.0000.000
62A59VAL00.0420.03517.4620.0210.0210.0000.0000.0000.000
63A60PRO00.020-0.00318.973-0.034-0.0340.0000.0000.0000.000
64A61VAL00.0390.02017.1500.0170.0170.0000.0000.0000.000
65A62GLU-1-0.963-0.97520.055-0.135-0.1350.0000.0000.0000.000
66A63TYR0-0.028-0.02223.2440.0200.0200.0000.0000.0000.000
67A64GLY00.0060.00723.4210.0060.0060.0000.0000.0000.000
68A65GLY0-0.008-0.00720.678-0.006-0.0060.0000.0000.0000.000
69A66LEU0-0.065-0.03615.8390.0050.0050.0000.0000.0000.000
70A67GLY0-0.024-0.00215.265-0.040-0.0400.0000.0000.0000.000
71A68LEU0-0.022-0.00411.546-0.038-0.0380.0000.0000.0000.000
72A69SER00.0360.0277.2180.1700.1700.0000.0000.0000.000
73A70LEU00.034-0.00310.367-0.002-0.0020.0000.0000.0000.000
74A71GLU-1-0.827-0.9323.035-9.801-6.3920.256-2.095-1.570-0.019
75A72GLU-1-0.719-0.8557.586-1.350-1.3500.0000.0000.0000.000
76A73MET00.0060.0198.7950.1480.1480.0000.0000.0000.000
77A74LEU0-0.059-0.0349.5330.0940.0940.0000.0000.0000.000
78A75MET0-0.0150.0116.671-0.264-0.2640.0000.0000.0000.000
79A76HIS00.000-0.0029.8180.1630.1630.0000.0000.0000.000
80A77GLN00.0190.02713.3160.0830.0830.0000.0000.0000.000
81A78GLU-1-0.791-0.86110.730-0.757-0.7570.0000.0000.0000.000
82A79VAL0-0.022-0.01912.7180.0650.0650.0000.0000.0000.000
83A80LEU0-0.002-0.00815.2090.0740.0740.0000.0000.0000.000
84A81ALA0-0.029-0.02417.4910.0470.0470.0000.0000.0000.000
85A82LYS10.7900.90515.7290.4950.4950.0000.0000.0000.000
86A83GLY0-0.0190.00419.2790.0290.0290.0000.0000.0000.000
87A84ASP-1-0.809-0.91921.908-0.173-0.1730.0000.0000.0000.000
88A85GLY00.0240.01421.872-0.015-0.0150.0000.0000.0000.000
89A86SER00.0390.01022.957-0.001-0.0010.0000.0000.0000.000
90A87THR0-0.003-0.01023.7290.0060.0060.0000.0000.0000.000
91A88ALA0-0.0110.02519.181-0.008-0.0080.0000.0000.0000.000
92A89LEU00.013-0.00820.802-0.011-0.0110.0000.0000.0000.000
93A90ALA0-0.015-0.00721.9960.0050.0050.0000.0000.0000.000
94A91ILE00.0340.01520.5820.0070.0070.0000.0000.0000.000
95A92GLY00.0100.00219.256-0.015-0.0150.0000.0000.0000.000
96A93TRP0-0.019-0.02020.1030.0010.0010.0000.0000.0000.000
97A94HIS00.0300.03422.5070.0250.0250.0000.0000.0000.000
98A95VAL00.0160.00717.7910.0060.0060.0000.0000.0000.000
99A96GLY00.0450.01817.966-0.016-0.0160.0000.0000.0000.000
100A97ILE0-0.041-0.01419.0050.0160.0160.0000.0000.0000.000
101A98LEU00.0170.00620.9640.0190.0190.0000.0000.0000.000
102A99LEU0-0.0050.00913.6050.0090.0090.0000.0000.0000.000
103A100HIS10.8570.89918.2090.1440.1440.0000.0000.0000.000
104A101LEU0-0.037-0.00620.3330.0210.0210.0000.0000.0000.000
105A102ARG10.7760.88613.7070.4420.4420.0000.0000.0000.000
106A103GLU-1-0.846-0.91116.172-0.246-0.2460.0000.0000.0000.000
107A104THR0-0.045-0.03219.3610.0280.0280.0000.0000.0000.000
108A105GLY0-0.029-0.01622.8140.0170.0170.0000.0000.0000.000
109A106ALA0-0.016-0.01725.3900.0120.0120.0000.0000.0000.000
110A107PHE0-0.005-0.00327.3320.0050.0050.0000.0000.0000.000
111A108PRO00.0710.03429.250-0.001-0.0010.0000.0000.0000.000
112A109ASP-1-0.837-0.91529.413-0.089-0.0890.0000.0000.0000.000
113A110GLU-1-0.869-0.93730.532-0.097-0.0970.0000.0000.0000.000
114A111LEU00.0110.02132.070-0.006-0.0060.0000.0000.0000.000
115A112PHE0-0.006-0.01522.597-0.009-0.0090.0000.0000.0000.000
116A113ARG10.9680.99428.1310.0930.0930.0000.0000.0000.000
117A114MET0-0.0030.01529.600-0.009-0.0090.0000.0000.0000.000
118A115VAL00.0270.00727.514-0.006-0.0060.0000.0000.0000.000
119A116CYS0-0.025-0.00324.988-0.017-0.0170.0000.0000.0000.000
120A117GLU-1-0.937-0.96826.933-0.138-0.1380.0000.0000.0000.000
121A118SER00.0110.00929.576-0.003-0.0030.0000.0000.0000.000
122A119VAL0-0.037-0.01424.245-0.005-0.0050.0000.0000.0000.000
123A120VAL0-0.067-0.05224.335-0.013-0.0130.0000.0000.0000.000
124A121LYS10.8830.93226.7510.1290.1290.0000.0000.0000.000
125A122GLU-1-0.947-0.96530.369-0.125-0.1250.0000.0000.0000.000
126A123GLY00.0170.02727.6370.0000.0000.0000.0000.0000.000
127A124ALA0-0.026-0.00628.6850.0010.0010.0000.0000.0000.000
128A125LEU0-0.005-0.00925.947-0.015-0.0150.0000.0000.0000.000
129A126ILE0-0.009-0.01825.7870.0180.0180.0000.0000.0000.000
130A127ASN00.0640.02326.523-0.015-0.0150.0000.0000.0000.000
131A128SER0-0.029-0.00727.6170.0130.0130.0000.0000.0000.000
132A129CYS0-0.026-0.01429.202-0.004-0.0040.0000.0000.0000.000
133A130ALA00.0310.01231.6420.0060.0060.0000.0000.0000.000
134A131THR00.0060.00531.5300.0050.0050.0000.0000.0000.000
135A132GLU-1-0.697-0.82934.344-0.052-0.0520.0000.0000.0000.000
136A133PRO00.0050.01537.9550.0030.0030.0000.0000.0000.000
137A144PRO0-0.044-0.04137.9990.0000.0000.0000.0000.0000.000
138A145GLU-1-0.938-0.96340.463-0.032-0.0320.0000.0000.0000.000
139A146THR0-0.057-0.04240.263-0.001-0.0010.0000.0000.0000.000
140A147THR0-0.037-0.00842.4230.0020.0020.0000.0000.0000.000
141A148ALA0-0.025-0.01942.450-0.003-0.0030.0000.0000.0000.000
142A149VAL00.0210.01144.5360.0030.0030.0000.0000.0000.000
143A150LYS10.9060.97245.8300.0380.0380.0000.0000.0000.000
144A151VAL0-0.013-0.01248.0480.0020.0020.0000.0000.0000.000
145A152PRO0-0.012-0.03349.217-0.001-0.0010.0000.0000.0000.000
146A153GLY00.0270.01948.040-0.001-0.0010.0000.0000.0000.000
147A154GLY0-0.002-0.00244.883-0.003-0.0030.0000.0000.0000.000
148A155TYR00.0080.00243.0720.0050.0050.0000.0000.0000.000
149A156ARG10.8890.95244.9710.0460.0460.0000.0000.0000.000
150A157ILE00.0060.00040.1880.0020.0020.0000.0000.0000.000
151A158THR00.004-0.00544.083-0.002-0.0020.0000.0000.0000.000
152A159GLY00.0220.00942.8570.0020.0020.0000.0000.0000.000
153A160ARG10.8020.89940.8510.0580.0580.0000.0000.0000.000
154A161LYS10.7620.89635.5530.0630.0630.0000.0000.0000.000
155A162THR0-0.037-0.02634.847-0.001-0.0010.0000.0000.0000.000
156A163PHE0-0.017-0.00531.021-0.002-0.0020.0000.0000.0000.000
157A164SER00.0780.03530.665-0.006-0.0060.0000.0000.0000.000
158A165THR0-0.003-0.00826.753-0.003-0.0030.0000.0000.0000.000
159A166LEU00.0430.01626.007-0.002-0.0020.0000.0000.0000.000
160A167SER0-0.024-0.02229.4090.0010.0010.0000.0000.0000.000
161A168PRO00.0200.01732.5620.0030.0030.0000.0000.0000.000
162A169ALA00.0030.00030.5790.0030.0030.0000.0000.0000.000
163A170LEU0-0.099-0.02829.012-0.007-0.0070.0000.0000.0000.000
164A171THR00.0250.01231.5870.0040.0040.0000.0000.0000.000
165A172TRP0-0.013-0.03030.3600.0160.0160.0000.0000.0000.000
166A173ILE00.028-0.00431.362-0.008-0.0080.0000.0000.0000.000
167A174MET0-0.059-0.00127.5430.0020.0020.0000.0000.0000.000
168A175VAL00.0330.02232.302-0.001-0.0010.0000.0000.0000.000
169A176THR00.005-0.00533.5130.0020.0020.0000.0000.0000.000
170A177ALA00.0220.00036.186-0.001-0.0010.0000.0000.0000.000
171A178THR00.0160.01239.8490.0010.0010.0000.0000.0000.000
172A179VAL00.0110.00242.196-0.002-0.0020.0000.0000.0000.000
173A180ALA0-0.003-0.00544.6330.0030.0030.0000.0000.0000.000
174A181ASP-1-0.930-0.97748.211-0.024-0.0240.0000.0000.0000.000
175A182GLU-1-0.977-0.99445.713-0.027-0.0270.0000.0000.0000.000
176A183ASP-1-0.969-0.97345.845-0.018-0.0180.0000.0000.0000.000
177A184VAL0-0.0260.00741.5580.0010.0010.0000.0000.0000.000
178A185VAL00.004-0.00136.835-0.003-0.0030.0000.0000.0000.000
179A186GLY00.0060.00037.6540.0010.0010.0000.0000.0000.000
180A187GLN0-0.033-0.02230.050-0.006-0.0060.0000.0000.0000.000
181A188PHE00.0310.00635.3310.0010.0010.0000.0000.0000.000
182A189LEU0-0.016-0.00331.618-0.004-0.0040.0000.0000.0000.000
183A190VAL00.0270.00935.0290.0040.0040.0000.0000.0000.000
184A191ARG10.8500.90935.6310.0740.0740.0000.0000.0000.000
185A192LYS10.9570.98135.1300.1130.1130.0000.0000.0000.000
186A193GLU-1-0.985-1.00137.169-0.084-0.0840.0000.0000.0000.000
187A194ASP-1-0.824-0.88940.288-0.072-0.0720.0000.0000.0000.000
188A195VAL0-0.088-0.04238.2740.0040.0040.0000.0000.0000.000
189A196GLU-1-0.943-0.96441.534-0.064-0.0640.0000.0000.0000.000
190A197ILE0-0.021-0.01336.765-0.001-0.0010.0000.0000.0000.000
191A198VAL0-0.024-0.01539.7820.0030.0030.0000.0000.0000.000
192A199GLU-1-0.894-0.94039.211-0.087-0.0870.0000.0000.0000.000
193A200THR0-0.073-0.04138.0410.0050.0050.0000.0000.0000.000
194A201TRP0-0.037-0.01939.7540.0000.0000.0000.0000.0000.000
195A202ASP-1-0.831-0.90337.024-0.081-0.0810.0000.0000.0000.000
196A203THR0-0.039-0.05032.3020.0050.0050.0000.0000.0000.000
197A204LEU0-0.057-0.02531.613-0.001-0.0010.0000.0000.0000.000
198A205GLY00.0570.00429.990-0.001-0.0010.0000.0000.0000.000
199A206MET0-0.103-0.04923.1260.0000.0000.0000.0000.0000.000
200A207ARG10.8430.92928.7830.0990.0990.0000.0000.0000.000
201A208ALA00.0220.04129.6950.0040.0040.0000.0000.0000.000
202A209THR0-0.002-0.01727.6460.0000.0000.0000.0000.0000.000
203A210GLY00.0260.03330.8780.0060.0060.0000.0000.0000.000
204A211SER0-0.032-0.02632.118-0.007-0.0070.0000.0000.0000.000
205A212HIS0-0.016-0.00733.8610.0090.0090.0000.0000.0000.000
206A213ASP-1-0.758-0.86135.422-0.070-0.0700.0000.0000.0000.000
207A214ILE0-0.054-0.01935.586-0.003-0.0030.0000.0000.0000.000
208A215VAL00.008-0.01338.5820.0050.0050.0000.0000.0000.000
209A216LEU00.0000.00939.078-0.002-0.0020.0000.0000.0000.000
210A217LYS10.9710.96543.2210.0570.0570.0000.0000.0000.000
211A218ASP-1-0.873-0.92546.898-0.048-0.0480.0000.0000.0000.000
212A219VAL00.0140.01841.304-0.001-0.0010.0000.0000.0000.000
213A220PHE0-0.0070.00144.3640.0020.0020.0000.0000.0000.000
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