Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 17Q6Z

Calculation Name: 4PN7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PN7

Chain ID: A

ChEMBL ID:

UniProt ID: G0RXV8

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2298051.226115
FMO2-HF: Nuclear repulsion 2220720.012917
FMO2-HF: Total energy -77331.213198
FMO2-MP2: Total energy -77560.830705


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:17:ASN)


Summations of interaction energy for fragment #1(A:17:ASN)
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.
-1.5731.5090.106-1.124-2.0650.002
Interaction energy analysis for fragmet #1(A:17:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.002
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].
3A19ASP-1-0.846-0.9252.896-5.349-2.5860.107-1.100-1.7700.002
4A20ASP-1-0.916-0.9544.5285.7886.107-0.001-0.024-0.2950.000
5A21ILE0-0.049-0.0326.185-0.271-0.2710.0000.0000.0000.000
6A22PRO00.0020.0058.278-0.534-0.5340.0000.0000.0000.000
7A23SER00.0040.00810.6480.1400.1400.0000.0000.0000.000
8A24LEU0-0.0060.00412.368-0.153-0.1530.0000.0000.0000.000
9A25ARG10.9460.97112.1830.7370.7370.0000.0000.0000.000
10A26THR0-0.026-0.02016.777-0.008-0.0080.0000.0000.0000.000
11A27ILE00.0110.00219.107-0.006-0.0060.0000.0000.0000.000
12A28ILE0-0.011-0.01522.1880.0230.0230.0000.0000.0000.000
13A29ILE00.014-0.00925.653-0.018-0.0180.0000.0000.0000.000
14A30ASP-1-0.752-0.87427.822-0.127-0.1270.0000.0000.0000.000
15A31THR0-0.0100.00030.895-0.018-0.0180.0000.0000.0000.000
16A32ASN0-0.019-0.02033.6090.0040.0040.0000.0000.0000.000
17A33PRO00.0440.02736.536-0.010-0.0100.0000.0000.0000.000
18A34ARG10.9750.99238.9660.0940.0940.0000.0000.0000.000
19A35ALA0-0.035-0.00535.842-0.004-0.0040.0000.0000.0000.000
20A36TRP0-0.020-0.05929.440-0.018-0.0180.0000.0000.0000.000
21A37ALA0-0.034-0.01336.135-0.008-0.0080.0000.0000.0000.000
22A38ALA0-0.052-0.03038.294-0.002-0.0020.0000.0000.0000.000
23A39LEU0-0.0040.00932.192-0.003-0.0030.0000.0000.0000.000
24A40ALA00.0060.01135.548-0.015-0.0150.0000.0000.0000.000
25A41ASP-1-0.889-0.93337.403-0.197-0.1970.0000.0000.0000.000
26A42VAL0-0.047-0.02633.123-0.013-0.0130.0000.0000.0000.000
27A43LEU0-0.093-0.06628.707-0.025-0.0250.0000.0000.0000.000
28A44PRO00.0610.03232.7700.0060.0060.0000.0000.0000.000
29A45LEU00.0710.03930.995-0.021-0.0210.0000.0000.0000.000
30A46SER0-0.003-0.01031.055-0.019-0.0190.0000.0000.0000.000
31A47LYS11.0020.99127.8050.3790.3790.0000.0000.0000.000
32A48ALA00.0060.00927.668-0.035-0.0350.0000.0000.0000.000
33A49ILE00.0130.00626.265-0.031-0.0310.0000.0000.0000.000
34A50ALA00.0180.01025.709-0.031-0.0310.0000.0000.0000.000
35A51ASN0-0.006-0.01423.646-0.064-0.0640.0000.0000.0000.000
36A52ILE00.0160.01021.826-0.065-0.0650.0000.0000.0000.000
37A53LEU00.0040.00121.051-0.044-0.0440.0000.0000.0000.000
38A54ILE0-0.016-0.00319.088-0.051-0.0510.0000.0000.0000.000
39A55PHE00.004-0.00214.969-0.080-0.0800.0000.0000.0000.000
40A56VAL0-0.005-0.00116.123-0.115-0.1150.0000.0000.0000.000
41A57ASN0-0.008-0.00616.199-0.131-0.1310.0000.0000.0000.000
42A58ALA00.0150.01213.711-0.082-0.0820.0000.0000.0000.000
43A59HIS0-0.004-0.00611.815-0.415-0.4150.0000.0000.0000.000
44A60LEU0-0.064-0.03811.641-0.177-0.1770.0000.0000.0000.000
45A61ALA00.0020.00811.615-0.010-0.0100.0000.0000.0000.000
46A62PHE0-0.057-0.0167.576-0.146-0.1460.0000.0000.0000.000
47A63SER00.0460.0275.872-0.924-0.9240.0000.0000.0000.000
48A64ASN00.0200.0227.2830.4270.4270.0000.0000.0000.000
49A65SER0-0.097-0.0357.4050.0830.0830.0000.0000.0000.000
50A66ASN00.0090.0039.2740.3600.3600.0000.0000.0000.000
51A67GLN0-0.058-0.04511.4400.1370.1370.0000.0000.0000.000
52A68VAL0-0.033-0.01415.227-0.044-0.0440.0000.0000.0000.000
53A69ALA0-0.019-0.01218.2780.0550.0550.0000.0000.0000.000
54A70ILE0-0.0190.00321.868-0.024-0.0240.0000.0000.0000.000
55A71ILE0-0.006-0.00724.5020.0260.0260.0000.0000.0000.000
56A72ALA00.0520.03627.639-0.021-0.0210.0000.0000.0000.000
57A73SER0-0.088-0.07530.5230.0250.0250.0000.0000.0000.000
58A74HIS00.0970.05932.129-0.016-0.0160.0000.0000.0000.000
59A75THR0-0.006-0.00735.6280.0050.0050.0000.0000.0000.000
60A76ASN00.0520.03238.6880.0020.0020.0000.0000.0000.000
61A77ARG10.9220.95237.0880.0960.0960.0000.0000.0000.000
62A78ALA00.0020.01632.057-0.010-0.0100.0000.0000.0000.000
63A79VAL00.000-0.01132.5730.0120.0120.0000.0000.0000.000
64A80TRP0-0.021-0.00424.959-0.017-0.0170.0000.0000.0000.000
65A81LEU0-0.030-0.00827.745-0.001-0.0010.0000.0000.0000.000
66A82TYR00.0490.03021.263-0.009-0.0090.0000.0000.0000.000
67A83PRO00.006-0.02223.584-0.011-0.0110.0000.0000.0000.000
68A84GLN0-0.008-0.00826.1970.0000.0000.0000.0000.0000.000
69A85PRO00.0240.03229.2860.0010.0010.0000.0000.0000.000
70A106ILE0-0.028-0.02919.764-0.009-0.0090.0000.0000.0000.000
71A107GLY00.0230.00919.0140.0200.0200.0000.0000.0000.000
72A108LYS11.0021.01412.6640.0140.0140.0000.0000.0000.000
73A109TYR00.0760.04613.5780.0620.0620.0000.0000.0000.000
74A110PRO00.0200.00415.1840.0220.0220.0000.0000.0000.000
75A111GLN0-0.042-0.02918.1290.0510.0510.0000.0000.0000.000
76A112PHE00.0690.03718.7780.0280.0280.0000.0000.0000.000
77A113ALA00.0470.02020.6490.0290.0290.0000.0000.0000.000
78A114GLN0-0.071-0.04223.5790.0290.0290.0000.0000.0000.000
79A115ILE00.0150.00219.8790.0260.0260.0000.0000.0000.000
80A116GLU-1-0.930-0.96224.033-0.410-0.4100.0000.0000.0000.000
81A117LYS10.9310.95325.8030.2860.2860.0000.0000.0000.000
82A118SER00.0160.00727.1570.0230.0230.0000.0000.0000.000
83A119LEU0-0.0060.01925.2250.0200.0200.0000.0000.0000.000
84A120LEU0-0.015-0.01428.7350.0150.0150.0000.0000.0000.000
85A121SER0-0.039-0.01531.3370.0180.0180.0000.0000.0000.000
86A122SER00.028-0.00431.0060.0180.0180.0000.0000.0000.000
87A123ILE0-0.0100.00130.1300.0110.0110.0000.0000.0000.000
88A124ARG10.9130.95733.5580.2110.2110.0000.0000.0000.000
89A125ALA00.0910.04636.7520.0070.0070.0000.0000.0000.000
90A126LEU0-0.022-0.00933.7610.0090.0090.0000.0000.0000.000
91A127MET0-0.080-0.04836.5710.0060.0060.0000.0000.0000.000
92A128ASP-1-0.932-0.95739.187-0.131-0.1310.0000.0000.0000.000
93A129ASP-1-0.964-0.96441.365-0.091-0.0910.0000.0000.0000.000
94A130THR0-0.105-0.04840.7350.0040.0040.0000.0000.0000.000
95A131THR0-0.014-0.00543.0080.0040.0040.0000.0000.0000.000
96A132PRO00.031-0.02045.791-0.003-0.0030.0000.0000.0000.000
97A133SER00.0460.02346.7580.0000.0000.0000.0000.0000.000
98A134ASP-1-0.804-0.89341.913-0.086-0.0860.0000.0000.0000.000
99A135LEU0-0.048-0.02342.521-0.007-0.0070.0000.0000.0000.000
100A136ASP-1-0.935-0.96044.459-0.082-0.0820.0000.0000.0000.000
101A137THR0-0.063-0.02940.5710.0070.0070.0000.0000.0000.000
102A138THR00.0010.00240.499-0.006-0.0060.0000.0000.0000.000
103A139THR0-0.0110.00437.755-0.006-0.0060.0000.0000.0000.000
104A140THR00.0940.05232.763-0.002-0.0020.0000.0000.0000.000
105A141GLN0-0.0330.00835.2940.0100.0100.0000.0000.0000.000
106A142ILE00.0690.02028.1130.0000.0000.0000.0000.0000.000
107A143SER0-0.0140.00030.7040.0020.0020.0000.0000.0000.000
108A144GLY00.0410.03032.1000.0110.0110.0000.0000.0000.000
109A145ALA00.0290.00028.9610.0050.0050.0000.0000.0000.000
110A146LEU00.011-0.00425.858-0.001-0.0010.0000.0000.0000.000
111A147THR0-0.008-0.00127.6160.0200.0200.0000.0000.0000.000
112A148LEU0-0.038-0.01429.3300.0150.0150.0000.0000.0000.000
113A149ALA00.0290.00624.0870.0070.0070.0000.0000.0000.000
114A150LEU0-0.016-0.00924.0980.0160.0160.0000.0000.0000.000
115A151ALA0-0.0080.00725.8480.0300.0300.0000.0000.0000.000
116A152HIS00.001-0.00521.6010.0370.0370.0000.0000.0000.000
117A153ILE00.0220.01420.1570.0160.0160.0000.0000.0000.000
118A154ASN00.0150.01721.7160.0680.0680.0000.0000.0000.000
119A155LYS10.9610.97723.835-0.003-0.0030.0000.0000.0000.000
120A156THR0-0.042-0.03218.5740.0010.0010.0000.0000.0000.000
121A157ALA00.0050.00419.2110.0370.0370.0000.0000.0000.000
122A158LEU00.0140.00620.2770.0500.0500.0000.0000.0000.000
123A159SER00.0060.00521.6950.0070.0070.0000.0000.0000.000
124A160LEU0-0.0200.00314.894-0.004-0.0040.0000.0000.0000.000
125A161THR0-0.041-0.03419.0090.0420.0420.0000.0000.0000.000
126A162ALA00.0050.00620.2020.0130.0130.0000.0000.0000.000
127A163SER0-0.022-0.02118.511-0.020-0.0200.0000.0000.0000.000
128A164ASN0-0.028-0.00414.924-0.005-0.0050.0000.0000.0000.000
129A165THR0-0.057-0.03418.9110.0160.0160.0000.0000.0000.000
130A166ALA0-0.0320.01022.160-0.024-0.0240.0000.0000.0000.000
131A167ALA00.0040.00219.9090.0080.0080.0000.0000.0000.000
132A168ALA0-0.028-0.00921.872-0.020-0.0200.0000.0000.0000.000
133A198ALA00.0090.00610.396-0.030-0.0300.0000.0000.0000.000
134A199GLY0-0.006-0.00712.162-0.208-0.2080.0000.0000.0000.000
135A200LEU0-0.029-0.02012.9240.0890.0890.0000.0000.0000.000
136A201HIS0-0.0030.01611.8550.0500.0500.0000.0000.0000.000
137A202ALA0-0.006-0.01413.830-0.148-0.1480.0000.0000.0000.000
138A203ARG10.8500.90613.7220.1830.1830.0000.0000.0000.000
139A204ILE00.0050.00716.988-0.057-0.0570.0000.0000.0000.000
140A205LEU0-0.0090.01218.656-0.011-0.0110.0000.0000.0000.000
141A206ILE0-0.017-0.00620.8050.0080.0080.0000.0000.0000.000
142A207ILE00.0010.00222.986-0.019-0.0190.0000.0000.0000.000
143A208SER0-0.021-0.01525.9970.0210.0210.0000.0000.0000.000
144A209VAL0-0.001-0.01029.167-0.013-0.0130.0000.0000.0000.000
145A210SER0-0.003-0.01032.4590.0100.0100.0000.0000.0000.000
146A211ASP-1-0.871-0.91634.373-0.108-0.1080.0000.0000.0000.000
147A212SER0-0.039-0.02534.4230.0030.0030.0000.0000.0000.000
148A213SER00.0470.01336.7770.0030.0030.0000.0000.0000.000
149A214ALA00.0690.02439.3860.0030.0030.0000.0000.0000.000
150A215ALA00.0130.01341.0350.0060.0060.0000.0000.0000.000
151A216GLN0-0.018-0.01336.6370.0010.0010.0000.0000.0000.000
152A217TYR0-0.0050.01435.9200.0040.0040.0000.0000.0000.000
153A218ILE00.0550.02136.0940.0030.0030.0000.0000.0000.000
154A219PRO00.006-0.00436.1510.0070.0070.0000.0000.0000.000
155A220THR0-0.012-0.03331.5490.0000.0000.0000.0000.0000.000
156A221MET00.0110.00331.5070.0060.0060.0000.0000.0000.000
157A222ASN0-0.0120.01131.8660.0210.0210.0000.0000.0000.000
158A223ALA00.0170.01229.3570.0130.0130.0000.0000.0000.000
159A224VAL0-0.002-0.00427.1930.0080.0080.0000.0000.0000.000
160A225PHE00.010-0.01326.8990.0140.0140.0000.0000.0000.000
161A226ALA0-0.0040.01528.2500.0240.0240.0000.0000.0000.000
162A227ALA00.0150.00523.3820.0280.0280.0000.0000.0000.000
163A228ALA00.0180.00823.1480.0310.0310.0000.0000.0000.000
164A229HIS0-0.0220.00523.6290.0370.0370.0000.0000.0000.000
165A230ALA0-0.046-0.01722.7760.0400.0400.0000.0000.0000.000
166A231ARG10.8630.93018.445-0.441-0.4410.0000.0000.0000.000
167A232ILE0-0.012-0.00218.4220.0260.0260.0000.0000.0000.000
168A233ALA00.0040.00417.081-0.029-0.0290.0000.0000.0000.000
169A234ILE00.004-0.01119.116-0.033-0.0330.0000.0000.0000.000
170A235ASP-1-0.792-0.88116.930-0.294-0.2940.0000.0000.0000.000
171A236THR0-0.020-0.02020.5030.0070.0070.0000.0000.0000.000
172A237LEU0-0.0020.00822.583-0.015-0.0150.0000.0000.0000.000
173A238ALA0-0.023-0.01424.4040.0100.0100.0000.0000.0000.000
174A239LEU0-0.005-0.00126.707-0.010-0.0100.0000.0000.0000.000
175A240ARG10.9490.97329.6950.1580.1580.0000.0000.0000.000
176A241GLY00.0130.03032.7020.0010.0010.0000.0000.0000.000
177A242SER0-0.037-0.03633.936-0.007-0.0070.0000.0000.0000.000
178A243ALA00.0360.01330.9870.0110.0110.0000.0000.0000.000
179A244THR00.0320.00531.255-0.002-0.0020.0000.0000.0000.000
180A245PHE00.0200.00131.6210.0050.0050.0000.0000.0000.000
181A246LEU00.021-0.00227.6250.0100.0100.0000.0000.0000.000
182A247GLU-1-0.924-0.94126.914-0.109-0.1090.0000.0000.0000.000
183A248GLN0-0.035-0.03327.3150.0100.0100.0000.0000.0000.000
184A249ALA00.0260.01426.6220.0180.0180.0000.0000.0000.000
185A250SER0-0.0220.03222.6840.0120.0120.0000.0000.0000.000
186A251PHE0-0.0080.01222.9500.0180.0180.0000.0000.0000.000
187A252ILE0-0.018-0.00624.7070.0240.0240.0000.0000.0000.000
188A253THR0-0.068-0.07221.8980.0220.0220.0000.0000.0000.000
189A254ARG10.9100.95818.977-0.230-0.2300.0000.0000.0000.000
190A255GLY0-0.021-0.00418.5800.0030.0030.0000.0000.0000.000
191A256THR0-0.027-0.01317.6570.0030.0030.0000.0000.0000.000
192A257PHE00.0250.00320.071-0.016-0.0160.0000.0000.0000.000
193A258ILE0-0.0090.00219.942-0.006-0.0060.0000.0000.0000.000
194A259ARG10.9660.98124.2740.1430.1430.0000.0000.0000.000
195A260ALA0-0.020-0.00726.371-0.008-0.0080.0000.0000.0000.000
196A261ALA00.0080.01227.6750.0190.0190.0000.0000.0000.000
197A262GLU-1-0.913-0.96028.826-0.290-0.2900.0000.0000.0000.000
198A263PRO00.0200.00728.370-0.033-0.0330.0000.0000.0000.000
199A264ARG10.9300.96528.4690.2480.2480.0000.0000.0000.000
200A265GLY00.0070.01925.888-0.023-0.0230.0000.0000.0000.000
201A266LEU0-0.009-0.00523.783-0.039-0.0390.0000.0000.0000.000
202A267LEU00.000-0.00919.323-0.023-0.0230.0000.0000.0000.000
203A268GLN00.010-0.00119.712-0.040-0.0400.0000.0000.0000.000
204A269TYR00.0430.01819.232-0.043-0.0430.0000.0000.0000.000
205A270LEU0-0.042-0.02518.653-0.023-0.0230.0000.0000.0000.000
206A271MET0-0.046-0.01113.293-0.021-0.0210.0000.0000.0000.000
207A272PHE0-0.041-0.02514.288-0.144-0.1440.0000.0000.0000.000
208A273GLY00.0040.02115.7970.0230.0230.0000.0000.0000.000
209A274PHE0-0.032-0.01412.3050.0680.0680.0000.0000.0000.000