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: R94V8

Calculation Name: 3AXL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AXL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1806789.765874
FMO2-HF: Nuclear repulsion 1732035.550359
FMO2-HF: Total energy -74754.215515
FMO2-MP2: Total energy -74968.727537


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:3:GLN)


Summations of interaction energy for fragment #1(A:3: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.
-14.951-12.53316.078-7.624-10.8720.012
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : -0.013
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].
3A5GLU-1-0.928-0.9563.826-3.507-1.772-0.018-0.748-0.9690.000
4A6GLN0-0.004-0.0315.8920.6520.6520.0000.0000.0000.000
5A7SER0-0.0500.0129.470-0.139-0.1390.0000.0000.0000.000
6A8PRO00.0750.03212.6100.0780.0780.0000.0000.0000.000
7A9ALA00.0720.00813.4130.0230.0230.0000.0000.0000.000
8A10SER0-0.047-0.02614.3250.0520.0520.0000.0000.0000.000
9A11LEU0-0.009-0.00617.885-0.020-0.0200.0000.0000.0000.000
10A12VAL00.0410.01521.0370.0150.0150.0000.0000.0000.000
11A13LEU0-0.009-0.00323.630-0.005-0.0050.0000.0000.0000.000
12A14GLN00.0320.03027.0030.0060.0060.0000.0000.0000.000
13A15GLU-1-0.878-0.96229.8190.0830.0830.0000.0000.0000.000
14A16GLY0-0.009-0.01730.680-0.006-0.0060.0000.0000.0000.000
15A17GLU-1-0.912-0.94528.0090.0920.0920.0000.0000.0000.000
16A18ASN0-0.033-0.00226.4010.0220.0220.0000.0000.0000.000
17A19ALA00.0230.00122.227-0.015-0.0150.0000.0000.0000.000
18A20GLU-1-0.863-0.93819.7220.2900.2900.0000.0000.0000.000
19A21LEU0-0.043-0.00215.496-0.035-0.0350.0000.0000.0000.000
20A22GLN00.009-0.00612.7590.1150.1150.0000.0000.0000.000
21A23CYS0-0.0060.0048.7490.0360.0360.0000.0000.0000.000
22A24THR0-0.0040.0016.7600.2990.2990.0000.0000.0000.000
23A25TYR0-0.029-0.0271.898-2.687-5.4889.787-3.095-3.8910.010
24A26SER0-0.021-0.0052.245-4.944-3.2076.068-3.233-4.572-0.002
25A27THR00.0180.0092.964-3.146-1.8140.192-0.460-1.0650.004
26A28THR00.0420.0305.467-1.124-1.170-0.0010.0000.0480.000
27A29LEU0-0.038-0.0297.8920.5410.5410.0000.0000.0000.000
28A30ASN0-0.091-0.0239.178-0.428-0.4280.0000.0000.0000.000
29A31SER00.0290.02411.760-0.254-0.2540.0000.0000.0000.000
30A32MET0-0.014-0.0099.4790.3100.3100.0000.0000.0000.000
31A40GLN0-0.0100.03311.710-0.305-0.3050.0000.0000.0000.000
32A41TRP00.0670.03812.5390.0520.0520.0000.0000.0000.000
33A42PHE0-0.021-0.01813.375-0.050-0.0500.0000.0000.0000.000
34A43TYR0-0.026-0.04116.586-0.006-0.0060.0000.0000.0000.000
35A44GLN0-0.042-0.02918.7900.0190.0190.0000.0000.0000.000
36A45ARG11.0121.01320.837-0.145-0.1450.0000.0000.0000.000
37A46PRO00.0830.03422.5850.0090.0090.0000.0000.0000.000
38A47GLY00.0220.01423.762-0.005-0.0050.0000.0000.0000.000
39A48GLY0-0.058-0.02124.8470.0020.0020.0000.0000.0000.000
40A49ARG10.9770.98522.447-0.238-0.2380.0000.0000.0000.000
41A50LEU0-0.003-0.01016.222-0.001-0.0010.0000.0000.0000.000
42A51VAL0-0.021-0.00719.8410.0150.0150.0000.0000.0000.000
43A52SER0-0.055-0.04818.3500.0110.0110.0000.0000.0000.000
44A53LEU0-0.029-0.01218.446-0.034-0.0340.0000.0000.0000.000
45A54LEU00.015-0.00717.513-0.023-0.0230.0000.0000.0000.000
46A55TYR0-0.046-0.02515.7500.1090.1090.0000.0000.0000.000
47A56SER0-0.001-0.00614.955-0.084-0.0840.0000.0000.0000.000
48A57PRO0-0.0060.00116.3250.1240.1240.0000.0000.0000.000
49A58SER00.000-0.02918.8360.0070.0070.0000.0000.0000.000
50A59TRP0-0.060-0.01714.543-0.068-0.0680.0000.0000.0000.000
51A60ALA00.0090.00317.971-0.037-0.0370.0000.0000.0000.000
52A61GLU-1-0.718-0.83019.1220.5190.5190.0000.0000.0000.000
53A62GLN0-0.062-0.04121.264-0.057-0.0570.0000.0000.0000.000
54A63ARG10.9190.95121.069-0.431-0.4310.0000.0000.0000.000
55A64GLY0-0.0340.00124.604-0.019-0.0190.0000.0000.0000.000
56A70GLY0-0.021-0.02526.805-0.017-0.0170.0000.0000.0000.000
57A71ARG10.8430.92327.546-0.186-0.1860.0000.0000.0000.000
58A72LEU00.0220.01221.303-0.007-0.0070.0000.0000.0000.000
59A80THR0-0.028-0.02422.3160.0110.0110.0000.0000.0000.000
60A81SER0-0.013-0.00517.1440.0250.0250.0000.0000.0000.000
61A82SER0-0.015-0.00117.454-0.043-0.0430.0000.0000.0000.000
62A83ALA00.0570.05014.3510.0680.0680.0000.0000.0000.000
63A84ALA0-0.013-0.02314.526-0.123-0.1230.0000.0000.0000.000
64A84SER00.0130.00714.8060.1340.1340.0000.0000.0000.000
65A84ASN0-0.053-0.02712.726-0.135-0.1350.0000.0000.0000.000
66A84GLU-1-0.855-0.9199.2112.4452.4450.0000.0000.0000.000
67A85SER00.006-0.0208.291-0.436-0.4360.0000.0000.0000.000
68A86ARG10.8600.9399.356-0.575-0.5750.0000.0000.0000.000
69A87SER00.0450.01011.097-0.108-0.1080.0000.0000.0000.000
70A88SER00.0150.00212.950-0.072-0.0720.0000.0000.0000.000
71A89LEU0-0.032-0.00915.6020.0280.0280.0000.0000.0000.000
72A90HIS10.8710.95218.054-0.406-0.4060.0000.0000.0000.000
73A91ILE0-0.027-0.01921.1760.0190.0190.0000.0000.0000.000
74A92SER00.0030.01024.064-0.024-0.0240.0000.0000.0000.000
75A93SER0-0.014-0.01627.729-0.002-0.0020.0000.0000.0000.000
76A94SER0-0.031-0.02426.101-0.004-0.0040.0000.0000.0000.000
77A95GLN00.0450.01728.112-0.010-0.0100.0000.0000.0000.000
78A96ILE00.1240.04428.5780.0080.0080.0000.0000.0000.000
79A97THR0-0.033-0.01328.445-0.004-0.0040.0000.0000.0000.000
80A98ASP-1-0.787-0.85224.7670.1900.1900.0000.0000.0000.000
81A99SER00.0120.04623.6910.0120.0120.0000.0000.0000.000
82A100GLY0-0.0450.00522.1070.0080.0080.0000.0000.0000.000
83A101THR0-0.0050.02115.865-0.025-0.0250.0000.0000.0000.000
84A102TYR0-0.042-0.07316.5040.0540.0540.0000.0000.0000.000
85A103LEU0-0.0030.00212.065-0.018-0.0180.0000.0000.0000.000
86A105ALA00.0070.0108.3740.1330.1330.0000.0000.0000.000
87A106ILE00.0110.0195.343-0.203-0.2030.0000.0000.0000.000
88A107ALA00.0360.0137.3170.2120.2120.0000.0000.0000.000
89A108SER00.0270.0046.950-0.468-0.4680.0000.0000.0000.000
90A109SER00.0190.0109.074-0.265-0.2650.0000.0000.0000.000
91A110SER0-0.0110.00412.5500.0010.0010.0000.0000.0000.000
92A113PHE00.015-0.00714.042-0.075-0.0750.0000.0000.0000.000
93A114SER0-0.033-0.0039.541-0.166-0.1660.0000.0000.0000.000
94A115LYS10.9650.9797.410-0.386-0.3860.0000.0000.0000.000
95A116LEU00.0170.0028.7050.2860.2860.0000.0000.0000.000
96A117VAL0-0.051-0.0193.025-0.814-0.3530.050-0.088-0.4230.000
97A118PHE0-0.021-0.0266.1180.2190.2190.0000.0000.0000.000
98A119GLY00.0310.0096.3250.2770.2770.0000.0000.0000.000
99A120GLN0-0.008-0.0237.298-0.040-0.0400.0000.0000.0000.000
100A121GLY0-0.041-0.0069.195-0.068-0.0680.0000.0000.0000.000
101A122THR0-0.0240.00212.355-0.058-0.0580.0000.0000.0000.000
102A123SER0-0.018-0.02814.8350.0510.0510.0000.0000.0000.000
103A124LEU0-0.0150.00018.194-0.020-0.0200.0000.0000.0000.000
104A125SER00.0240.00720.9170.0020.0020.0000.0000.0000.000
105A126VAL0-0.043-0.01224.404-0.006-0.0060.0000.0000.0000.000
106A127VAL0-0.003-0.00727.272-0.003-0.0030.0000.0000.0000.000
107A128PRO00.0310.00930.4650.0030.0030.0000.0000.0000.000
108A129ASN0-0.035-0.00534.036-0.012-0.0120.0000.0000.0000.000
109A130ILE0-0.037-0.01136.3960.0020.0020.0000.0000.0000.000
110A131GLN00.0200.01039.310-0.005-0.0050.0000.0000.0000.000
111A132ASN0-0.057-0.03342.3710.0000.0000.0000.0000.0000.000
112A133PRO0-0.018-0.00841.6140.0010.0010.0000.0000.0000.000
113A134ASP-1-0.932-0.97243.4980.0120.0120.0000.0000.0000.000
114A135PRO00.0080.02143.030-0.001-0.0010.0000.0000.0000.000
115A136ALA00.0470.03744.552-0.001-0.0010.0000.0000.0000.000
116A137VAL0-0.009-0.01544.305-0.001-0.0010.0000.0000.0000.000
117A138TYR00.0030.01046.745-0.001-0.0010.0000.0000.0000.000
118A139GLN00.004-0.01947.900-0.001-0.0010.0000.0000.0000.000
119A140LEU0-0.017-0.01046.2240.0020.0020.0000.0000.0000.000
120A141ARG10.9090.94849.766-0.001-0.0010.0000.0000.0000.000
121A142ASP-1-0.942-0.95450.8580.0070.0070.0000.0000.0000.000
122A150VAL0-0.015-0.01744.139-0.001-0.0010.0000.0000.0000.000
123A151CYS0-0.068-0.01745.092-0.001-0.0010.0000.0000.0000.000
124A152LEU00.0110.00341.902-0.001-0.0010.0000.0000.0000.000
125A153PHE00.0210.02539.0400.0000.0000.0000.0000.0000.000
126A154THR00.012-0.04041.0090.0030.0030.0000.0000.0000.000
127A155ASP-1-0.833-0.90041.4070.0190.0190.0000.0000.0000.000
128A156PHE00.0320.03635.9970.0000.0000.0000.0000.0000.000
129A157ASP-1-0.830-0.93837.9450.0120.0120.0000.0000.0000.000
130A158SER0-0.001-0.02933.125-0.006-0.0060.0000.0000.0000.000
131A159GLN0-0.046-0.00133.437-0.006-0.0060.0000.0000.0000.000
132A160THR0-0.0040.01133.575-0.009-0.0090.0000.0000.0000.000
133A161ASN0-0.085-0.05430.1710.0020.0020.0000.0000.0000.000
134A162VAL00.0390.02833.026-0.003-0.0030.0000.0000.0000.000
135A163SER0-0.051-0.01733.015-0.006-0.0060.0000.0000.0000.000
136A164GLN00.0530.01631.4870.0050.0050.0000.0000.0000.000
137A165SER00.0290.02535.178-0.005-0.0050.0000.0000.0000.000
138A166LYS10.9050.93936.3890.0860.0860.0000.0000.0000.000
139A167ASP-1-0.929-0.96338.580-0.050-0.0500.0000.0000.0000.000
140A168SER0-0.041-0.04939.3140.0000.0000.0000.0000.0000.000
141A169ASP-1-0.905-0.92940.287-0.044-0.0440.0000.0000.0000.000
142A170VAL0-0.010-0.02141.0840.0050.0050.0000.0000.0000.000
143A171TYR0-0.083-0.03638.189-0.003-0.0030.0000.0000.0000.000
144A172ILE00.0110.00436.9360.0040.0040.0000.0000.0000.000
145A173THR0-0.071-0.02234.636-0.003-0.0030.0000.0000.0000.000
146A174ASP-1-0.876-0.94129.334-0.021-0.0210.0000.0000.0000.000
147A175LYS10.8590.92731.0260.0040.0040.0000.0000.0000.000
148A176CYS0-0.065-0.03632.0940.0040.0040.0000.0000.0000.000
149A177VAL00.0330.01532.431-0.002-0.0020.0000.0000.0000.000
150A178LEU0-0.046-0.01134.9060.0070.0070.0000.0000.0000.000
151A179ASP-1-0.861-0.95736.4970.0790.0790.0000.0000.0000.000
152A180MET0-0.027-0.01638.4440.0020.0020.0000.0000.0000.000
153A181ARG10.9830.97338.011-0.086-0.0860.0000.0000.0000.000
154A182SER0-0.076-0.03341.7380.0020.0020.0000.0000.0000.000
155A183MET0-0.042-0.00945.5320.0000.0000.0000.0000.0000.000
156A184ASP-1-0.946-0.96541.2100.0700.0700.0000.0000.0000.000
157A185PHE00.0390.02242.438-0.002-0.0020.0000.0000.0000.000
158A186LYS10.8910.94935.160-0.072-0.0720.0000.0000.0000.000
159A187SER00.0000.01638.956-0.004-0.0040.0000.0000.0000.000
160A188ASN0-0.048-0.02635.1760.0060.0060.0000.0000.0000.000
161A189SER0-0.017-0.01036.840-0.002-0.0020.0000.0000.0000.000
162A190ALA00.0230.02136.4420.0000.0000.0000.0000.0000.000
163A191VAL0-0.0060.00138.1200.0000.0000.0000.0000.0000.000
164A192ALA00.0300.01839.276-0.004-0.0040.0000.0000.0000.000
165A193TRP0-0.016-0.03038.4600.0030.0030.0000.0000.0000.000
166A194SER00.0360.03942.896-0.004-0.0040.0000.0000.0000.000
167A195ASN0-0.049-0.03245.3750.0040.0040.0000.0000.0000.000
168A196LYS10.9420.97646.5170.0330.0330.0000.0000.0000.000
169A197SER00.0010.00950.2180.0010.0010.0000.0000.0000.000
170A198ASP-1-0.921-0.96450.497-0.031-0.0310.0000.0000.0000.000
171A199PHE0-0.039-0.00644.5520.0000.0000.0000.0000.0000.000
172A200ALA00.0640.01948.9070.0030.0030.0000.0000.0000.000
173A202ALA00.0160.01347.8140.0000.0000.0000.0000.0000.000
174A203ASN0-0.014-0.01946.966-0.001-0.0010.0000.0000.0000.000
175A204ALA0-0.035-0.01143.770-0.003-0.0030.0000.0000.0000.000
176A205PHE00.0500.01039.513-0.002-0.0020.0000.0000.0000.000
177A206ASN00.0350.02641.2570.0000.0000.0000.0000.0000.000
178A207ASN0-0.041-0.02137.372-0.001-0.0010.0000.0000.0000.000
179A208SER0-0.026-0.00437.154-0.004-0.0040.0000.0000.0000.000
180A209ILE00.0010.00736.0530.0000.0000.0000.0000.0000.000
181A210ILE0-0.028-0.02338.3060.0020.0020.0000.0000.0000.000
182A211PRO00.0070.00740.080-0.002-0.0020.0000.0000.0000.000
183A212GLU-1-0.926-0.97342.751-0.014-0.0140.0000.0000.0000.000
184A213ASP-1-0.934-0.95745.868-0.003-0.0030.0000.0000.0000.000
185A214THR0-0.039-0.01644.3940.0030.0030.0000.0000.0000.000
186A215PHE0-0.011-0.02146.774-0.002-0.0020.0000.0000.0000.000
187A216PHE0-0.010-0.02046.1400.0010.0010.0000.0000.0000.000
188A217PRO0-0.038-0.00150.8390.0000.0000.0000.0000.0000.000
189A218SER0-0.043-0.01953.946-0.001-0.0010.0000.0000.0000.000