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: J2MJ9

Calculation Name: 2D8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D8N

Chain ID: A

ChEMBL ID:

UniProt ID: P35243

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2278055.613862
FMO2-HF: Nuclear repulsion 2197845.869815
FMO2-HF: Total energy -80209.744048
FMO2-MP2: Total energy -80443.800348


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-24.194-26.59918.38-7.458-8.5170.03
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.037
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].
3A3ASN0-0.0030.0113.469-2.234-0.476-0.002-0.750-1.0060.000
4A4SER00.005-0.0192.336-4.784-3.9002.862-1.331-2.416-0.007
5A5LYS10.8590.9122.239-16.236-21.31115.521-5.367-5.0790.037
6A6SER00.0580.0375.728-0.779-0.751-0.001-0.010-0.0160.000
7A7GLY00.0270.0057.127-0.526-0.5260.0000.0000.0000.000
8A8ALA0-0.043-0.0108.576-0.149-0.1490.0000.0000.0000.000
9A9LEU00.0560.0399.975-0.143-0.1430.0000.0000.0000.000
10A10SER00.001-0.02013.718-0.052-0.0520.0000.0000.0000.000
11A11LYS10.9520.95811.535-0.835-0.8350.0000.0000.0000.000
12A12GLU-1-0.866-0.90317.3800.2670.2670.0000.0000.0000.000
13A13ILE00.0190.00917.541-0.014-0.0140.0000.0000.0000.000
14A14LEU0-0.051-0.02716.167-0.010-0.0100.0000.0000.0000.000
15A15GLU-1-0.944-0.96719.7060.1920.1920.0000.0000.0000.000
16A16GLU-1-0.835-0.92622.7530.2570.2570.0000.0000.0000.000
17A17LEU0-0.038-0.03520.611-0.018-0.0180.0000.0000.0000.000
18A18GLN0-0.017-0.00521.8100.0010.0010.0000.0000.0000.000
19A19LEU0-0.0330.00025.114-0.027-0.0270.0000.0000.0000.000
20A20ASN0-0.116-0.05827.805-0.027-0.0270.0000.0000.0000.000
21A21THR0-0.025-0.00726.0920.0020.0020.0000.0000.0000.000
22A22LYS10.9080.94328.720-0.188-0.1880.0000.0000.0000.000
23A23PHE00.0120.01823.679-0.005-0.0050.0000.0000.0000.000
24A24SER0-0.016-0.01622.2480.0080.0080.0000.0000.0000.000
25A25GLU-1-0.861-0.94916.7140.4860.4860.0000.0000.0000.000
26A26GLU-1-0.965-0.98616.3300.4450.4450.0000.0000.0000.000
27A27GLU-1-0.861-0.92317.7510.3590.3590.0000.0000.0000.000
28A28LEU00.0060.01319.2740.0460.0460.0000.0000.0000.000
29A29CYS0-0.029-0.00614.0140.0980.0980.0000.0000.0000.000
30A30SER0-0.018-0.01114.9960.1480.1480.0000.0000.0000.000
31A31TRP00.0360.01616.5410.0290.0290.0000.0000.0000.000
32A32TYR0-0.023-0.01412.167-0.044-0.0440.0000.0000.0000.000
33A33GLN0-0.037-0.0259.3770.1160.1160.0000.0000.0000.000
34A34SER00.0230.00113.8350.0250.0250.0000.0000.0000.000
35A35PHE00.0480.02616.565-0.034-0.0340.0000.0000.0000.000
36A36LEU0-0.033-0.01911.5870.0250.0250.0000.0000.0000.000
37A37LYS10.7690.89710.604-1.354-1.3540.0000.0000.0000.000
38A38ASP-1-0.883-0.92715.4450.4070.4070.0000.0000.0000.000
39A39CYS0-0.096-0.04017.792-0.076-0.0760.0000.0000.0000.000
40A40PRO00.0420.02514.6690.0610.0610.0000.0000.0000.000
41A41THR0-0.045-0.02014.5010.0920.0920.0000.0000.0000.000
42A42GLY0-0.011-0.01816.6750.0320.0320.0000.0000.0000.000
43A43ARG10.8980.95017.199-0.461-0.4610.0000.0000.0000.000
44A44ILE0-0.028-0.00121.0030.0000.0000.0000.0000.0000.000
45A45THR00.0410.01023.566-0.029-0.0290.0000.0000.0000.000
46A46GLN00.1070.05526.8030.0030.0030.0000.0000.0000.000
47A47GLN0-0.027-0.00629.0790.0080.0080.0000.0000.0000.000
48A48GLN00.0590.01622.8630.0000.0000.0000.0000.0000.000
49A49PHE00.0510.03127.7850.0010.0010.0000.0000.0000.000
50A50GLN0-0.008-0.02629.134-0.017-0.0170.0000.0000.0000.000
51A51SER0-0.092-0.05029.667-0.016-0.0160.0000.0000.0000.000
52A52ILE0-0.035-0.00126.166-0.005-0.0050.0000.0000.0000.000
53A53TYR00.0460.01330.244-0.004-0.0040.0000.0000.0000.000
54A54ALA0-0.025-0.01833.694-0.010-0.0100.0000.0000.0000.000
55A55LYS10.8750.94627.766-0.253-0.2530.0000.0000.0000.000
56A56PHE0-0.027-0.02428.9400.0010.0010.0000.0000.0000.000
57A57PHE00.0010.01334.906-0.003-0.0030.0000.0000.0000.000
58A58PRO0-0.038-0.01038.500-0.001-0.0010.0000.0000.0000.000
59A59ASP-1-0.884-0.94440.3010.1060.1060.0000.0000.0000.000
60A60THR0-0.127-0.06442.090-0.004-0.0040.0000.0000.0000.000
61A61ASP-1-0.883-0.95640.6820.1350.1350.0000.0000.0000.000
62A62PRO0-0.0120.00637.082-0.002-0.0020.0000.0000.0000.000
63A63LYS10.9520.98234.694-0.160-0.1600.0000.0000.0000.000
64A64ALA00.0300.01537.4390.0050.0050.0000.0000.0000.000
65A65TYR00.0880.03637.2030.0060.0060.0000.0000.0000.000
66A66ALA00.001-0.00933.7890.0050.0050.0000.0000.0000.000
67A67GLN0-0.032-0.01734.3960.0150.0150.0000.0000.0000.000
68A68HIS00.0140.01735.7540.0080.0080.0000.0000.0000.000
69A69VAL00.0240.02432.8860.0020.0020.0000.0000.0000.000
70A70PHE0-0.0610.02527.7850.0060.0060.0000.0000.0000.000
71A71ARG10.8520.89332.201-0.136-0.1360.0000.0000.0000.000
72A72SER0-0.065-0.04534.2320.0000.0000.0000.0000.0000.000
73A73PHE0-0.011-0.02229.475-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.782-0.86829.7170.2390.2390.0000.0000.0000.000
75A75SER00.0100.00029.535-0.018-0.0180.0000.0000.0000.000
76A76ASN0-0.091-0.03426.799-0.018-0.0180.0000.0000.0000.000
77A77LEU00.000-0.01330.922-0.009-0.0090.0000.0000.0000.000
78A78ASP-1-0.918-0.93326.6180.2540.2540.0000.0000.0000.000
79A79GLY0-0.076-0.04929.737-0.004-0.0040.0000.0000.0000.000
80A80THR0-0.124-0.11424.5840.0240.0240.0000.0000.0000.000
81A81LEU00.0530.04225.332-0.007-0.0070.0000.0000.0000.000
82A82ASP-1-0.888-0.94920.2590.4630.4630.0000.0000.0000.000
83A83PHE00.023-0.00818.636-0.007-0.0070.0000.0000.0000.000
84A84LYS10.9550.97920.685-0.352-0.3520.0000.0000.0000.000
85A85GLU-1-0.824-0.91422.5820.2850.2850.0000.0000.0000.000
86A86TYR0-0.0100.00122.288-0.017-0.0170.0000.0000.0000.000
87A87VAL0-0.007-0.00722.208-0.023-0.0230.0000.0000.0000.000
88A88ILE00.001-0.00325.348-0.027-0.0270.0000.0000.0000.000
89A89ALA00.0160.01228.208-0.022-0.0220.0000.0000.0000.000
90A90LEU0-0.058-0.03326.447-0.016-0.0160.0000.0000.0000.000
91A91HIS0-0.079-0.05427.291-0.021-0.0210.0000.0000.0000.000
92A92MET0-0.0520.00031.500-0.021-0.0210.0000.0000.0000.000
93A93THR0-0.0090.03033.408-0.012-0.0120.0000.0000.0000.000
94A94THR00.005-0.01634.627-0.009-0.0090.0000.0000.0000.000
95A95ALA00.0380.02335.7920.0040.0040.0000.0000.0000.000
96A96GLY0-0.0230.00835.0110.0070.0070.0000.0000.0000.000
97A97LYS10.8800.90734.777-0.135-0.1350.0000.0000.0000.000
98A98THR00.0530.05437.2960.0000.0000.0000.0000.0000.000
99A99ASN0-0.021-0.01840.656-0.004-0.0040.0000.0000.0000.000
100A100GLN0-0.076-0.05436.607-0.009-0.0090.0000.0000.0000.000
101A101LYS10.9660.99833.477-0.161-0.1610.0000.0000.0000.000
102A102LEU00.0280.01637.4220.0020.0020.0000.0000.0000.000
103A103GLU-1-0.898-0.95334.5930.1560.1560.0000.0000.0000.000
104A104TRP00.011-0.00634.807-0.002-0.0020.0000.0000.0000.000
105A105ALA00.0310.01036.894-0.001-0.0010.0000.0000.0000.000
106A106PHE00.0070.00140.305-0.005-0.0050.0000.0000.0000.000
107A107SER00.0540.02236.877-0.002-0.0020.0000.0000.0000.000
108A108LEU0-0.058-0.01437.8430.0010.0010.0000.0000.0000.000
109A109TYR0-0.026-0.03139.418-0.004-0.0040.0000.0000.0000.000
110A110ASP-1-0.789-0.86541.5590.1070.1070.0000.0000.0000.000
111A111VAL0-0.072-0.04741.2840.0060.0060.0000.0000.0000.000
112A112ASP-1-0.942-0.97940.9670.1070.1070.0000.0000.0000.000
113A113GLY0-0.0230.00740.1110.0020.0020.0000.0000.0000.000
114A114ASN0-0.100-0.04940.986-0.002-0.0020.0000.0000.0000.000
115A115GLY00.015-0.00543.169-0.005-0.0050.0000.0000.0000.000
116A116THR0-0.158-0.08444.075-0.006-0.0060.0000.0000.0000.000
117A117ILE00.0250.02544.6110.0020.0020.0000.0000.0000.000
118A118SER0-0.018-0.02147.733-0.006-0.0060.0000.0000.0000.000
119A119LYS10.9630.98149.931-0.067-0.0670.0000.0000.0000.000
120A120ASN00.005-0.01050.8880.0000.0000.0000.0000.0000.000
121A121GLU-1-0.752-0.86245.7090.1010.1010.0000.0000.0000.000
122A122VAL00.0100.00646.7080.0040.0040.0000.0000.0000.000
123A123LEU0-0.058-0.03348.1180.0020.0020.0000.0000.0000.000
124A124GLU-1-0.876-0.93444.7460.1090.1090.0000.0000.0000.000
125A125ILE00.0170.01841.7050.0040.0040.0000.0000.0000.000
126A126VAL0-0.030-0.02144.8400.0020.0020.0000.0000.0000.000
127A127MET0-0.019-0.01847.4100.0000.0000.0000.0000.0000.000
128A128ALA0-0.037-0.01342.0670.0010.0010.0000.0000.0000.000
129A129ILE00.007-0.00142.7120.0030.0030.0000.0000.0000.000
130A130PHE0-0.033-0.02744.318-0.001-0.0010.0000.0000.0000.000
131A131LYS10.8750.96044.099-0.113-0.1130.0000.0000.0000.000
132A132MET00.0220.02639.6710.0050.0050.0000.0000.0000.000
133A133ILE0-0.0170.01643.0710.0020.0020.0000.0000.0000.000
134A134THR00.0180.01145.876-0.004-0.0040.0000.0000.0000.000
135A135PRO00.009-0.02048.568-0.002-0.0020.0000.0000.0000.000
136A136GLU-1-0.930-0.97751.5540.0700.0700.0000.0000.0000.000
137A137ASP-1-0.816-0.91347.1420.0980.0980.0000.0000.0000.000
138A138VAL0-0.018-0.01350.750-0.002-0.0020.0000.0000.0000.000
139A139LYS10.8800.94552.876-0.071-0.0710.0000.0000.0000.000
140A140LEU0-0.021-0.00851.853-0.003-0.0030.0000.0000.0000.000
141A141LEU0-0.020-0.00950.8380.0000.0000.0000.0000.0000.000
142A142PRO0-0.064-0.01954.763-0.003-0.0030.0000.0000.0000.000
143A143ASP-1-0.840-0.93757.5720.0610.0610.0000.0000.0000.000
144A144ASP-1-0.856-0.91559.2490.0640.0640.0000.0000.0000.000
145A145GLU-1-0.850-0.91954.2700.0760.0760.0000.0000.0000.000
146A146ASN00.0190.02954.1140.0030.0030.0000.0000.0000.000
147A147THR00.0450.02654.2190.0000.0000.0000.0000.0000.000
148A148PRO00.0570.03550.7720.0000.0000.0000.0000.0000.000
149A149GLU-1-0.838-0.93652.6020.0770.0770.0000.0000.0000.000
150A150LYS10.7820.89155.728-0.066-0.0660.0000.0000.0000.000
151A151ARG10.9350.97548.904-0.092-0.0920.0000.0000.0000.000
152A152ALA00.0440.02552.0030.0000.0000.0000.0000.0000.000
153A153GLU-1-0.915-0.96153.2980.0630.0630.0000.0000.0000.000
154A154LYS10.7730.86755.770-0.069-0.0690.0000.0000.0000.000
155A155ILE0-0.009-0.02249.661-0.001-0.0010.0000.0000.0000.000
156A156TRP0-0.011-0.01150.8490.0020.0020.0000.0000.0000.000
157A157LYS10.9750.99455.251-0.059-0.0590.0000.0000.0000.000
158A158TYR0-0.114-0.06955.079-0.003-0.0030.0000.0000.0000.000
159A159PHE0-0.027-0.01148.8910.0000.0000.0000.0000.0000.000
160A160GLY0-0.034-0.01354.926-0.001-0.0010.0000.0000.0000.000
161A161LYS10.8240.92854.089-0.069-0.0690.0000.0000.0000.000
162A162ASN0-0.020-0.01157.774-0.001-0.0010.0000.0000.0000.000
163A163ASP-1-0.848-0.94457.7900.0640.0640.0000.0000.0000.000
164A164ASP-1-0.969-0.97256.7830.0640.0640.0000.0000.0000.000
165A165ASP-1-0.948-0.95856.3210.0600.0600.0000.0000.0000.000
166A166LYS10.9190.95150.966-0.070-0.0700.0000.0000.0000.000
167A167LEU0-0.047-0.00948.842-0.003-0.0030.0000.0000.0000.000
168A168THR00.0310.00748.2700.0040.0040.0000.0000.0000.000
169A169GLU-1-0.830-0.92041.1160.1130.1130.0000.0000.0000.000
170A170LYS10.9110.94845.905-0.069-0.0690.0000.0000.0000.000
171A171GLU-1-0.800-0.91048.0690.0700.0700.0000.0000.0000.000
172A172PHE00.0330.02743.246-0.001-0.0010.0000.0000.0000.000
173A173ILE0-0.007-0.00843.4320.0000.0000.0000.0000.0000.000
174A174GLU-1-0.950-0.98446.8730.0670.0670.0000.0000.0000.000
175A175GLY00.0130.01850.455-0.002-0.0020.0000.0000.0000.000
176A176THR0-0.053-0.03346.5420.0000.0000.0000.0000.0000.000
177A177LEU0-0.033-0.01645.9530.0000.0000.0000.0000.0000.000
178A178ALA0-0.049-0.01849.623-0.003-0.0030.0000.0000.0000.000
179A179ASN00.018-0.00152.805-0.002-0.0020.0000.0000.0000.000
180A180LYS10.9970.99048.959-0.082-0.0820.0000.0000.0000.000
181A181GLU-1-0.838-0.92851.4230.0740.0740.0000.0000.0000.000
182A182ILE00.0070.01649.8170.0020.0020.0000.0000.0000.000
183A183LEU00.0200.02544.7500.0030.0030.0000.0000.0000.000
184A184ARG10.6680.80747.320-0.075-0.0750.0000.0000.0000.000
185A185LEU0-0.052-0.01248.3770.0030.0030.0000.0000.0000.000
186A186ILE00.0610.02644.6550.0020.0020.0000.0000.0000.000
187A187GLN00.0050.01942.8430.0090.0090.0000.0000.0000.000
188A188PHE0-0.054-0.05644.365-0.003-0.0030.0000.0000.0000.000
189A189GLU-1-0.831-0.92641.0020.1380.1380.0000.0000.0000.000
190A190PRO0-0.104-0.05644.0910.0010.0010.0000.0000.0000.000
191A191GLN00.0660.01841.628-0.010-0.0100.0000.0000.0000.000
192A192LYS10.9640.99845.267-0.090-0.0900.0000.0000.0000.000
193A193VAL0-0.067-0.00346.640-0.005-0.0050.0000.0000.0000.000
194A194LYS10.8900.94249.233-0.084-0.0840.0000.0000.0000.000
195A195GLU-1-0.821-0.88948.7040.0890.0890.0000.0000.0000.000
196A196LYS10.8730.92551.498-0.069-0.0690.0000.0000.0000.000
197A197MET0-0.0130.00654.124-0.003-0.0030.0000.0000.0000.000