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

tag_button

FMODB ID: 8N9NY

Calculation Name: 1XWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XWM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333516.939806
FMO2-HF: Nuclear repulsion 2251356.467569
FMO2-HF: Total energy -82160.472237
FMO2-MP2: Total energy -82396.878856


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-17.912-11.0453.319-4.698-5.486-0.042
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / 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].
3A6ALA0-0.001-0.0053.645-1.4920.052-0.007-0.629-0.9080.001
4A7ASP-1-0.880-0.9472.453-10.539-7.7252.612-2.718-2.708-0.027
5A8ASP-1-0.833-0.9122.666-9.380-7.0380.716-1.320-1.737-0.016
6A9LEU0-0.0040.0024.5441.3311.412-0.001-0.009-0.0700.000
7A10ALA0-0.0080.0017.6370.5500.5500.0000.0000.0000.000
8A11SER0-0.060-0.0396.6010.5660.5660.0000.0000.0000.000
9A12LEU00.0290.0158.6190.3620.3620.0000.0000.0000.000
10A13HIS10.8170.91210.5511.1291.1290.0000.0000.0000.000
11A14ASN00.007-0.01611.4600.2510.2510.0000.0000.0000.000
12A15LYS10.8010.89710.7631.1881.1880.0000.0000.0000.000
13A16LEU00.0270.03214.2270.1110.1110.0000.0000.0000.000
14A17ILE0-0.010-0.00416.3010.0930.0930.0000.0000.0000.000
15A18GLU-1-0.821-0.87017.037-0.500-0.5000.0000.0000.0000.000
16A19MET0-0.0290.00118.3520.0450.0450.0000.0000.0000.000
17A20GLY00.0350.01620.4330.0520.0520.0000.0000.0000.000
18A21ARG10.7920.86321.2220.5210.5210.0000.0000.0000.000
19A22LEU0-0.024-0.02021.4290.0420.0420.0000.0000.0000.000
20A23THR00.0650.02524.4940.0280.0280.0000.0000.0000.000
21A24GLU-1-0.858-0.90026.032-0.290-0.2900.0000.0000.0000.000
22A25VAL0-0.054-0.02827.2820.0280.0280.0000.0000.0000.000
23A26ALA00.0230.01328.6970.0240.0240.0000.0000.0000.000
24A27LEU00.0210.00129.8430.0220.0220.0000.0000.0000.000
25A28GLN0-0.022-0.00931.1700.0340.0340.0000.0000.0000.000
26A29GLN00.0180.00432.2900.0120.0120.0000.0000.0000.000
27A30ALA00.0090.01934.7140.0140.0140.0000.0000.0000.000
28A31ILE0-0.018-0.00636.5500.0140.0140.0000.0000.0000.000
29A32GLU-1-0.941-0.96537.974-0.167-0.1670.0000.0000.0000.000
30A33ALA0-0.0030.00939.1330.0100.0100.0000.0000.0000.000
31A34PHE00.0230.00240.7460.0100.0100.0000.0000.0000.000
32A35GLN00.002-0.00742.1640.0020.0020.0000.0000.0000.000
33A36THR0-0.089-0.06343.0710.0060.0060.0000.0000.0000.000
34A37GLN0-0.060-0.04645.5430.0060.0060.0000.0000.0000.000
35A38ASN0-0.0080.01042.6220.0040.0040.0000.0000.0000.000
36A39ALA00.0450.00542.228-0.007-0.0070.0000.0000.0000.000
37A40ASN0-0.009-0.01341.616-0.001-0.0010.0000.0000.0000.000
38A41LEU0-0.0210.00036.767-0.006-0.0060.0000.0000.0000.000
39A42ALA00.0290.00537.407-0.009-0.0090.0000.0000.0000.000
40A43MET0-0.043-0.02037.313-0.003-0.0030.0000.0000.0000.000
41A44ALA0-0.014-0.00134.819-0.006-0.0060.0000.0000.0000.000
42A45VAL0-0.0050.01132.592-0.012-0.0120.0000.0000.0000.000
43A46ILE0-0.041-0.04032.383-0.008-0.0080.0000.0000.0000.000
44A47ASP-1-0.945-0.98033.098-0.173-0.1730.0000.0000.0000.000
45A48GLY0-0.043-0.01829.656-0.005-0.0050.0000.0000.0000.000
46A49ASP-1-0.863-0.94627.945-0.274-0.2740.0000.0000.0000.000
47A50GLY00.0550.03427.038-0.018-0.0180.0000.0000.0000.000
48A51SER0-0.080-0.04122.938-0.012-0.0120.0000.0000.0000.000
49A52ILE0-0.050-0.03022.498-0.043-0.0430.0000.0000.0000.000
50A53ASP-1-0.845-0.92622.063-0.305-0.3050.0000.0000.0000.000
51A54ALA0-0.006-0.00320.848-0.017-0.0170.0000.0000.0000.000
52A55LEU0-0.015-0.00817.490-0.043-0.0430.0000.0000.0000.000
53A56GLU-1-0.774-0.88317.441-0.397-0.3970.0000.0000.0000.000
54A57GLU-1-0.962-0.96918.352-0.333-0.3330.0000.0000.0000.000
55A58GLU-1-0.827-0.90314.104-0.862-0.8620.0000.0000.0000.000
56A59VAL0-0.056-0.03013.821-0.116-0.1160.0000.0000.0000.000
57A60ASN0-0.038-0.03814.263-0.058-0.0580.0000.0000.0000.000
58A61ASP-1-0.873-0.93314.623-0.382-0.3820.0000.0000.0000.000
59A62PHE0-0.093-0.0425.7040.0820.0820.0000.0000.0000.000
60A63ALA00.0250.00410.511-0.091-0.0910.0000.0000.0000.000
61A64LEU0-0.012-0.01912.6880.0800.0800.0000.0000.0000.000
62A65TRP0-0.023-0.0095.1810.1730.1730.0000.0000.0000.000
63A66LEU0-0.008-0.0066.0280.1580.1580.0000.0000.0000.000
64A67ILE0-0.040-0.0349.8820.2490.2490.0000.0000.0000.000
65A68ALA0-0.047-0.01613.3630.1200.1200.0000.0000.0000.000
66A69ALA0-0.045-0.01310.1880.1210.1210.0000.0000.0000.000
67A70GLN0-0.078-0.0524.0221.5081.594-0.001-0.022-0.0630.000
68A71GLN0-0.074-0.0358.8930.1250.1250.0000.0000.0000.000
69A72PRO00.0410.03910.9120.0990.0990.0000.0000.0000.000
70A73VAL00.0190.01512.397-0.003-0.0030.0000.0000.0000.000
71A74ALA0-0.002-0.01714.700-0.105-0.1050.0000.0000.0000.000
72A75THR0-0.029-0.01714.922-0.036-0.0360.0000.0000.0000.000
73A76ASP-1-0.809-0.89911.278-0.305-0.3050.0000.0000.0000.000
74A77LEU0-0.020-0.00913.688-0.102-0.1020.0000.0000.0000.000
75A78ARG10.9310.96915.5020.1050.1050.0000.0000.0000.000
76A79ARG10.8170.86314.4180.4060.4060.0000.0000.0000.000
77A80ILE00.0060.01910.725-0.050-0.0500.0000.0000.0000.000
78A81VAL0-0.011-0.01114.4090.0120.0120.0000.0000.0000.000
79A82ALA0-0.021-0.01718.0870.0170.0170.0000.0000.0000.000
80A83ALA00.0070.00515.1260.0110.0110.0000.0000.0000.000
81A84ILE00.0230.01316.6400.0160.0160.0000.0000.0000.000
82A85LYS10.7930.89218.7410.2570.2570.0000.0000.0000.000
83A86ILE00.0280.01120.2140.0190.0190.0000.0000.0000.000
84A87ALA00.0100.00718.5120.0080.0080.0000.0000.0000.000
85A88SER00.0210.00320.6340.0270.0270.0000.0000.0000.000
86A89ASP-1-0.821-0.89323.767-0.239-0.2390.0000.0000.0000.000
87A90ILE0-0.007-0.01921.4870.0170.0170.0000.0000.0000.000
88A91GLU-1-0.799-0.86824.058-0.240-0.2400.0000.0000.0000.000
89A92ARG10.7700.84925.6650.2330.2330.0000.0000.0000.000
90A93ILE0-0.006-0.01527.5610.0170.0170.0000.0000.0000.000
91A94ALA00.0070.02427.0460.0120.0120.0000.0000.0000.000
92A95ASP-1-0.739-0.86729.176-0.166-0.1660.0000.0000.0000.000
93A96PHE0-0.056-0.03231.7120.0220.0220.0000.0000.0000.000
94A97ALA00.0470.02832.0650.0150.0150.0000.0000.0000.000
95A98VAL00.0110.01732.4540.0170.0170.0000.0000.0000.000
96A99ASN0-0.085-0.05034.4640.0230.0230.0000.0000.0000.000
97A100ILE00.0050.01237.0530.0130.0130.0000.0000.0000.000
98A101ALA00.0200.02336.9350.0090.0090.0000.0000.0000.000
99A102LYS10.8690.91835.3350.1760.1760.0000.0000.0000.000
100A103ALA0-0.059-0.01540.6010.0100.0100.0000.0000.0000.000
101A104CYS00.0110.01142.0820.0070.0070.0000.0000.0000.000
102A105ILE0-0.034-0.01441.9960.0070.0070.0000.0000.0000.000
103A106ARG10.8370.91642.1730.1250.1250.0000.0000.0000.000
104A107ILE0-0.0430.00146.7530.0060.0060.0000.0000.0000.000
105A108GLY00.0300.03247.7710.0050.0050.0000.0000.0000.000
106A109GLY00.0450.01548.895-0.003-0.0030.0000.0000.0000.000
107A110GLN0-0.079-0.04851.0660.0010.0010.0000.0000.0000.000
108A111PRO0-0.0020.00152.734-0.001-0.0010.0000.0000.0000.000
109A112PHE00.0470.03446.8590.0040.0040.0000.0000.0000.000
110A113VAL0-0.055-0.02752.8940.0030.0030.0000.0000.0000.000
111A114MET0-0.050-0.02050.8740.0060.0060.0000.0000.0000.000
112A115ASP-1-0.823-0.91351.235-0.104-0.1040.0000.0000.0000.000
113A116ILE00.0020.00346.0620.0000.0000.0000.0000.0000.000
114A117GLY00.0330.02046.761-0.006-0.0060.0000.0000.0000.000
115A118PRO00.014-0.00346.123-0.006-0.0060.0000.0000.0000.000
116A119LEU00.0550.02443.868-0.004-0.0040.0000.0000.0000.000
117A120VAL0-0.037-0.01641.834-0.008-0.0080.0000.0000.0000.000
118A121LEU0-0.020-0.01141.221-0.009-0.0090.0000.0000.0000.000
119A122MET0-0.0210.02141.098-0.004-0.0040.0000.0000.0000.000
120A123TYR0-0.012-0.03534.989-0.003-0.0030.0000.0000.0000.000
121A124ARG10.9060.95136.8670.1640.1640.0000.0000.0000.000
122A125LEU00.0280.02836.269-0.008-0.0080.0000.0000.0000.000
123A126ALA00.0510.01735.522-0.008-0.0080.0000.0000.0000.000
124A127THR0-0.060-0.04232.164-0.013-0.0130.0000.0000.0000.000
125A128ASP-1-0.871-0.93231.588-0.218-0.2180.0000.0000.0000.000
126A129MET0-0.087-0.01131.661-0.011-0.0110.0000.0000.0000.000
127A130VAL00.0390.02027.584-0.014-0.0140.0000.0000.0000.000
128A131SER0-0.002-0.02827.344-0.017-0.0170.0000.0000.0000.000
129A132THR0-0.110-0.06726.814-0.025-0.0250.0000.0000.0000.000
130A133ALA00.0170.00626.895-0.014-0.0140.0000.0000.0000.000
131A134ILE0-0.0030.01121.809-0.030-0.0300.0000.0000.0000.000
132A135ALA0-0.006-0.00922.217-0.044-0.0440.0000.0000.0000.000
133A136ALA0-0.049-0.02123.235-0.016-0.0160.0000.0000.0000.000
134A137TYR00.0430.00815.645-0.047-0.0470.0000.0000.0000.000
135A138ASP-1-0.901-0.94317.992-0.722-0.7220.0000.0000.0000.000
136A139ARG10.8270.89718.2050.3090.3090.0000.0000.0000.000
137A140GLU-1-0.795-0.86717.620-0.439-0.4390.0000.0000.0000.000
138A141ASP-1-0.763-0.84720.731-0.219-0.2190.0000.0000.0000.000
139A142ALA00.011-0.00124.3960.0130.0130.0000.0000.0000.000
140A143SER0-0.169-0.10626.4490.0320.0320.0000.0000.0000.000
141A144LEU00.0470.01727.0800.0110.0110.0000.0000.0000.000
142A145ALA00.0210.02229.3920.0060.0060.0000.0000.0000.000
143A146ALA00.004-0.00230.9980.0080.0080.0000.0000.0000.000
144A147GLN0-0.027-0.01633.1680.0080.0080.0000.0000.0000.000
145A148ILE00.019-0.00329.3210.0040.0040.0000.0000.0000.000
146A149ALA00.0300.02233.9030.0060.0060.0000.0000.0000.000
147A150ASP-1-0.875-0.95036.506-0.120-0.1200.0000.0000.0000.000
148A151MET0-0.104-0.04534.3250.0020.0020.0000.0000.0000.000
149A152ASP-1-0.766-0.87636.232-0.157-0.1570.0000.0000.0000.000
150A153HIS0-0.038-0.00438.6070.0070.0070.0000.0000.0000.000
151A154ARG10.7720.85641.0580.1250.1250.0000.0000.0000.000
152A155VAL0-0.016-0.00438.1250.0020.0020.0000.0000.0000.000
153A156ASP-1-0.905-0.95341.516-0.103-0.1030.0000.0000.0000.000
154A157GLU-1-0.859-0.91943.919-0.101-0.1010.0000.0000.0000.000
155A158GLN0-0.054-0.01844.1710.0020.0020.0000.0000.0000.000
156A159TYR00.025-0.02543.0990.0050.0050.0000.0000.0000.000
157A160GLY0-0.018-0.00346.3080.0040.0040.0000.0000.0000.000
158A161GLU-1-0.920-0.95049.374-0.093-0.0930.0000.0000.0000.000
159A162MET0-0.0200.00747.2360.0010.0010.0000.0000.0000.000
160A163MET0-0.022-0.01947.7620.0040.0040.0000.0000.0000.000
161A164ALA0-0.032-0.01151.6190.0040.0040.0000.0000.0000.000
162A165SER0-0.032-0.03652.4590.0020.0020.0000.0000.0000.000
163A166LEU0-0.021-0.00750.3020.0020.0020.0000.0000.0000.000
164A167LEU0-0.036-0.02753.9970.0030.0030.0000.0000.0000.000
165A168ALA00.0030.01456.5950.0030.0030.0000.0000.0000.000
166A169VAL0-0.049-0.01756.7660.0030.0030.0000.0000.0000.000
167A170ALA0-0.012-0.01659.7470.0000.0000.0000.0000.0000.000
168A171LYS10.8690.92958.8090.0740.0740.0000.0000.0000.000
169A172THR0-0.005-0.00761.348-0.001-0.0010.0000.0000.0000.000
170A173ASP-1-0.747-0.84360.566-0.065-0.0650.0000.0000.0000.000
171A174ALA00.0090.01059.419-0.002-0.0020.0000.0000.0000.000
172A175ALA0-0.007-0.00257.038-0.003-0.0030.0000.0000.0000.000
173A176THR0-0.023-0.05155.791-0.004-0.0040.0000.0000.0000.000
174A177LEU00.0190.00955.528-0.003-0.0030.0000.0000.0000.000
175A178ALA0-0.0170.00953.174-0.003-0.0030.0000.0000.0000.000
176A179GLN00.0630.01751.303-0.005-0.0050.0000.0000.0000.000
177A180MET0-0.019-0.00650.721-0.003-0.0030.0000.0000.0000.000
178A181ASN0-0.053-0.03550.124-0.003-0.0030.0000.0000.0000.000
179A182VAL0-0.0100.00645.685-0.004-0.0040.0000.0000.0000.000
180A183LEU00.0000.00445.863-0.006-0.0060.0000.0000.0000.000
181A184ALA00.0210.01346.212-0.004-0.0040.0000.0000.0000.000
182A185LEU0-0.051-0.02242.259-0.003-0.0030.0000.0000.0000.000
183A186VAL00.008-0.00141.604-0.007-0.0070.0000.0000.0000.000
184A187ALA00.0310.01541.298-0.007-0.0070.0000.0000.0000.000
185A188ARG10.8090.87441.3570.1110.1110.0000.0000.0000.000
186A189TYR0-0.008-0.02136.5370.0000.0000.0000.0000.0000.000
187A190ILE00.0050.03336.858-0.010-0.0100.0000.0000.0000.000
188A191GLU-1-0.751-0.83337.256-0.127-0.1270.0000.0000.0000.000
189A192ARG10.8730.94635.2310.1380.1380.0000.0000.0000.000
190A193THR00.000-0.00432.253-0.012-0.0120.0000.0000.0000.000
191A194ALA00.0200.01432.637-0.013-0.0130.0000.0000.0000.000
192A195ASP-1-0.877-0.92933.656-0.171-0.1710.0000.0000.0000.000
193A196HIS0-0.026-0.03529.585-0.007-0.0070.0000.0000.0000.000
194A197ALA0-0.0040.01029.080-0.019-0.0190.0000.0000.0000.000
195A198THR00.012-0.01229.350-0.014-0.0140.0000.0000.0000.000
196A199ASN0-0.070-0.05428.5080.0080.0080.0000.0000.0000.000
197A200ILE00.002-0.00423.912-0.010-0.0100.0000.0000.0000.000
198A201ALA00.004-0.00125.364-0.016-0.0160.0000.0000.0000.000
199A202GLU-1-0.826-0.89927.682-0.162-0.1620.0000.0000.0000.000
200A203HIS00.0050.01623.3810.0130.0130.0000.0000.0000.000
201A204LEU0-0.0100.01421.411-0.006-0.0060.0000.0000.0000.000
202A205VAL0-0.010-0.00923.9620.0050.0050.0000.0000.0000.000
203A206TYR0-0.018-0.00823.2360.0110.0110.0000.0000.0000.000
204A207LEU0-0.067-0.03118.6680.0200.0200.0000.0000.0000.000
205A208VAL0-0.056-0.01821.4990.0130.0130.0000.0000.0000.000
206A209LYS10.8780.92423.4500.1980.1980.0000.0000.0000.000
207A210GLY0-0.0420.01126.5000.0220.0220.0000.0000.0000.000
208A211LYS10.7330.83827.9160.1210.1210.0000.0000.0000.000
209A212HIS0-0.035-0.03130.4310.0020.0020.0000.0000.0000.000
210A213TYR00.020-0.00930.7170.0030.0030.0000.0000.0000.000
211A214ASP-1-0.922-0.95932.623-0.101-0.1010.0000.0000.0000.000
212A215PHE0-0.0150.00736.203-0.004-0.0040.0000.0000.0000.000