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: N9M6Q

Calculation Name: 3E9N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E9N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NMW9

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1969088.870207
FMO2-HF: Nuclear repulsion 1898494.793272
FMO2-HF: Total energy -70594.076935
FMO2-MP2: Total energy -70804.181331


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:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-279.911-263.2256.391-9.317-13.761-0.085
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.913 / q_NPA : 0.962
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].
3A6ALA00.0000.0103.751-4.167-1.979-0.039-1.061-1.087-0.001
4A7VAL0-0.0020.0056.1504.2104.2100.0000.0000.0000.000
5A8VAL00.0120.0029.856-0.594-0.5940.0000.0000.0000.000
6A9THR00.0360.02312.5161.4241.4240.0000.0000.0000.000
7A10GLY00.0240.00616.205-0.204-0.2040.0000.0000.0000.000
8A11ALA00.003-0.00315.4940.0980.0980.0000.0000.0000.000
9A12THR00.0420.02517.0820.1170.1170.0000.0000.0000.000
10A13GLY0-0.049-0.01220.3840.8260.8260.0000.0000.0000.000
11A14GLY00.019-0.00320.386-0.472-0.4720.0000.0000.0000.000
12A15MET00.016-0.00517.306-0.574-0.5740.0000.0000.0000.000
13A16GLY00.0670.04415.643-1.116-1.1160.0000.0000.0000.000
14A17ILE00.0310.03415.233-1.346-1.3460.0000.0000.0000.000
15A18GLU-1-0.902-0.97015.614-18.324-18.3240.0000.0000.0000.000
16A19ILE0-0.039-0.02410.660-1.324-1.3240.0000.0000.0000.000
17A20VAL00.0030.00411.020-2.717-2.7170.0000.0000.0000.000
18A21LYS10.9310.96510.82315.88115.8810.0000.0000.0000.000
19A22ASP-1-0.865-0.9078.791-33.090-33.0900.0000.0000.0000.000
20A23LEU00.025-0.0095.699-1.985-1.9850.0000.0000.0000.000
21A24SER0-0.0060.0136.031-4.093-4.0930.0000.0000.0000.000
22A25ARG10.8070.9047.83531.74831.7480.0000.0000.0000.000
23A26ASP-1-0.826-0.9033.691-62.757-62.0070.013-0.264-0.499-0.001
24A27HIS0-0.031-0.0152.480-36.556-30.2153.649-3.732-6.258-0.038
25A28ILE00.0120.0223.3406.6117.3410.021-0.106-0.6460.000
26A29VAL0-0.035-0.0285.364-2.912-2.952-0.001-0.0060.0470.000
27A30TYR0-0.008-0.0027.7553.3953.3950.0000.0000.0000.000
28A31ALA00.0180.00611.138-0.571-0.5710.0000.0000.0000.000
29A32LEU00.0110.00413.8601.3031.3030.0000.0000.0000.000
30A33GLY0-0.054-0.03716.893-0.263-0.2630.0000.0000.0000.000
31A34ARG10.9210.97920.04112.23212.2320.0000.0000.0000.000
32A35ASN0-0.029-0.02523.2720.4500.4500.0000.0000.0000.000
33A36PRO00.1040.03223.087-0.468-0.4680.0000.0000.0000.000
34A37GLU-1-0.885-0.92823.713-11.316-11.3160.0000.0000.0000.000
35A38HIS0-0.033-0.02421.138-0.510-0.5100.0000.0000.0000.000
36A39LEU0-0.0180.00718.309-0.763-0.7630.0000.0000.0000.000
37A40ALA00.0000.01418.784-0.573-0.5730.0000.0000.0000.000
38A41ALA00.002-0.00919.858-0.302-0.3020.0000.0000.0000.000
39A42LEU0-0.076-0.05315.295-0.577-0.5770.0000.0000.0000.000
40A43ALA0-0.002-0.00715.302-0.960-0.9600.0000.0000.0000.000
41A44GLU-1-0.972-0.95816.214-13.242-13.2420.0000.0000.0000.000
42A45ILE0-0.129-0.06211.678-0.158-0.1580.0000.0000.0000.000
43A46GLU-1-0.904-0.95010.473-18.753-18.7530.0000.0000.0000.000
44A47GLY00.008-0.0028.238-1.824-1.8240.0000.0000.0000.000
45A48VAL0-0.036-0.0228.481-2.538-2.5380.0000.0000.0000.000
46A49GLU-1-0.850-0.93710.922-15.814-15.8140.0000.0000.0000.000
47A50PRO0-0.014-0.00512.586-0.493-0.4930.0000.0000.0000.000
48A51ILE0-0.048-0.02614.1360.6800.6800.0000.0000.0000.000
49A52GLU-1-0.898-0.96717.775-12.867-12.8670.0000.0000.0000.000
50A53SER0-0.062-0.07220.159-0.011-0.0110.0000.0000.0000.000
51A54ASP-1-0.921-0.96422.226-11.305-11.3050.0000.0000.0000.000
52A55ILE00.0470.00018.6290.0770.0770.0000.0000.0000.000
53A56VAL00.0230.01422.517-0.187-0.1870.0000.0000.0000.000
54A57LYS10.8940.96425.21211.36111.3610.0000.0000.0000.000
55A58GLU-1-0.810-0.88421.943-13.208-13.2080.0000.0000.0000.000
56A59VAL0-0.064-0.04019.679-0.064-0.0640.0000.0000.0000.000
57A60LEU0-0.028-0.02522.401-0.003-0.0030.0000.0000.0000.000
58A61GLU-1-0.985-0.98725.826-9.873-9.8730.0000.0000.0000.000
59A62GLU-1-0.884-0.94025.258-11.063-11.0630.0000.0000.0000.000
60A63GLY0-0.039-0.00524.336-0.048-0.0480.0000.0000.0000.000
61A64GLY0-0.013-0.00720.357-0.410-0.4100.0000.0000.0000.000
62A65VAL00.0390.01517.3600.4270.4270.0000.0000.0000.000
63A66ASP-1-0.816-0.91117.568-13.476-13.4760.0000.0000.0000.000
64A67LYS10.8630.92215.75314.85814.8580.0000.0000.0000.000
65A68LEU0-0.029-0.00912.154-0.924-0.9240.0000.0000.0000.000
66A69LYS10.8550.92213.49112.59712.5970.0000.0000.0000.000
67A70ASN0-0.085-0.03112.315-0.290-0.2900.0000.0000.0000.000
68A71LEU00.0000.0278.420-0.468-0.4680.0000.0000.0000.000
69A72ASP-1-0.825-0.8899.313-22.043-22.0430.0000.0000.0000.000
70A73HIS10.8050.8555.90026.91226.9120.0000.0000.0000.000
71A74VAL00.0110.0056.290-0.437-0.4370.0000.0000.0000.000
72A75ASP-1-0.815-0.9042.586-67.467-61.3842.750-4.058-4.775-0.045
73A76THR0-0.028-0.0043.637-0.2610.0450.000-0.056-0.2500.000
74A77LEU00.0140.0225.8683.2733.2730.0000.0000.0000.000
75A78VAL0-0.013-0.0139.3520.6630.6630.0000.0000.0000.000
76A79HIS00.001-0.00911.8061.3821.3820.0000.0000.0000.000
77A80ALA00.019-0.00615.5280.5330.5330.0000.0000.0000.000
78A81ALA0-0.049-0.00217.4691.1631.1630.0000.0000.0000.000
79A92GLY00.0710.03140.6450.1150.1150.0000.0000.0000.000
80A93SER00.043-0.00939.079-0.224-0.2240.0000.0000.0000.000
81A94VAL0-0.0280.01037.858-0.201-0.2010.0000.0000.0000.000
82A95ALA00.0350.01236.836-0.211-0.2110.0000.0000.0000.000
83A96GLU-1-0.887-0.95134.756-9.085-9.0850.0000.0000.0000.000
84A97TRP0-0.017-0.02832.988-0.372-0.3720.0000.0000.0000.000
85A98HIS00.0170.00932.196-0.444-0.4440.0000.0000.0000.000
86A99ALA00.0510.03830.788-0.338-0.3380.0000.0000.0000.000
87A100HIS00.016-0.01028.694-0.651-0.6510.0000.0000.0000.000
88A101LEU0-0.039-0.00927.328-0.473-0.4730.0000.0000.0000.000
89A102ASP-1-0.841-0.92126.787-11.205-11.2050.0000.0000.0000.000
90A103LEU0-0.048-0.02623.176-0.556-0.5560.0000.0000.0000.000
91A104ASN0-0.030-0.02522.943-0.896-0.8960.0000.0000.0000.000
92A105VAL0-0.048-0.03022.556-0.444-0.4440.0000.0000.0000.000
93A106ILE0-0.008-0.00822.784-0.480-0.4800.0000.0000.0000.000
94A107VAL00.0570.04820.145-0.389-0.3890.0000.0000.0000.000
95A108PRO00.0010.00718.099-0.653-0.6530.0000.0000.0000.000
96A109ALA00.0100.02218.195-0.854-0.8540.0000.0000.0000.000
97A110GLU-1-0.765-0.83320.009-13.749-13.7490.0000.0000.0000.000
98A111LEU00.0130.00115.015-0.179-0.1790.0000.0000.0000.000
99A112SER0-0.022-0.04115.243-1.437-1.4370.0000.0000.0000.000
100A113ARG10.8000.86916.20413.23813.2380.0000.0000.0000.000
101A114GLN0-0.101-0.07217.908-0.653-0.6530.0000.0000.0000.000
102A115LEU00.0140.00811.673-0.051-0.0510.0000.0000.0000.000
103A116LEU00.0110.01513.111-1.457-1.4570.0000.0000.0000.000
104A117PRO0-0.051-0.03714.258-0.920-0.9200.0000.0000.0000.000
105A118ALA00.0830.0469.767-0.388-0.3880.0000.0000.0000.000
106A119LEU0-0.0310.0039.252-2.505-2.5050.0000.0000.0000.000
107A120ARG10.8300.9009.92515.71915.7190.0000.0000.0000.000
108A121ALA0-0.058-0.01010.340-0.550-0.5500.0000.0000.0000.000
109A122ALA0-0.042-0.0265.6390.5190.5190.0000.0000.0000.000
110A123SER0-0.048-0.0076.383-3.160-3.1600.0000.0000.0000.000
111A124GLY00.0320.0265.806-3.486-3.4860.0000.0000.0000.000
112A125CYS0-0.097-0.0425.5375.0125.0120.0000.0000.0000.000
113A126VAL00.0240.0097.602-0.725-0.7250.0000.0000.0000.000
114A127ILE0-0.023-0.0238.4421.4451.4450.0000.0000.0000.000
115A128TYR0-0.013-0.01912.1830.5990.5990.0000.0000.0000.000
116A129ILE0-0.0130.00214.671-0.042-0.0420.0000.0000.0000.000
117A130ASN0-0.011-0.01717.7011.2511.2510.0000.0000.0000.000
118A141ASN00.0310.00234.8480.0040.0040.0000.0000.0000.000
119A142THR00.0230.00934.850-0.218-0.2180.0000.0000.0000.000
120A143ILE00.0320.02131.997-0.180-0.1800.0000.0000.0000.000
121A144TYR0-0.019-0.01430.226-0.296-0.2960.0000.0000.0000.000
122A145ALA0-0.036-0.00829.590-0.369-0.3690.0000.0000.0000.000
123A146ALA00.0490.02630.227-0.259-0.2590.0000.0000.0000.000
124A147SER00.0460.02827.141-0.345-0.3450.0000.0000.0000.000
125A148LYS11.0161.00925.31510.86210.8620.0000.0000.0000.000
126A149HIS0-0.083-0.04225.297-0.432-0.4320.0000.0000.0000.000
127A150ALA0-0.015-0.01126.585-0.204-0.2040.0000.0000.0000.000
128A151LEU00.0010.01419.722-0.253-0.2530.0000.0000.0000.000
129A152ARG10.9000.95321.65613.67313.6730.0000.0000.0000.000
130A153GLY00.0130.00422.507-0.286-0.2860.0000.0000.0000.000
131A154LEU0-0.0140.00320.1760.0100.0100.0000.0000.0000.000
132A155ALA00.0200.00418.017-0.408-0.4080.0000.0000.0000.000
133A156ASP-1-0.823-0.91018.596-15.414-15.4140.0000.0000.0000.000
134A157ALA0-0.071-0.09120.9280.0920.0920.0000.0000.0000.000
135A158PHE00.1050.07114.1890.0800.0800.0000.0000.0000.000
136A159ARG10.8340.89315.76817.98217.9820.0000.0000.0000.000
137A160LYS10.8240.95017.42912.94012.9400.0000.0000.0000.000
138A161GLU-1-0.961-0.98020.199-13.879-13.8790.0000.0000.0000.000
139A162GLU-1-0.743-0.84715.202-17.790-17.7900.0000.0000.0000.000
140A163ALA0-0.0210.00315.300-0.947-0.9470.0000.0000.0000.000
141A164ASN0-0.051-0.04515.480-0.816-0.8160.0000.0000.0000.000
142A165ASN0-0.090-0.05815.3950.6160.6160.0000.0000.0000.000
143A166GLY00.0290.03212.125-0.800-0.8000.0000.0000.0000.000
144A167ILE0-0.0230.00510.337-2.660-2.6600.0000.0000.0000.000
145A168ARG10.8310.9175.82441.64541.6450.0000.0000.0000.000
146A169VAL0-0.0070.00610.724-0.828-0.8280.0000.0000.0000.000
147A170SER0-0.058-0.03912.0551.3951.3950.0000.0000.0000.000
148A171THR0-0.031-0.02913.907-0.010-0.0100.0000.0000.0000.000
149A172VAL00.0410.02913.7220.3730.3730.0000.0000.0000.000
150A173SER0-0.008-0.02816.7500.3800.3800.0000.0000.0000.000
151A174PRO00.0020.01619.8130.4240.4240.0000.0000.0000.000
152A175GLY00.0080.00622.3210.3530.3530.0000.0000.0000.000
153A176PRO0-0.046-0.03726.1040.0170.0170.0000.0000.0000.000
154A177THR0-0.028-0.03029.1470.0960.0960.0000.0000.0000.000
155A194ARG10.9230.95932.2229.2869.2860.0000.0000.0000.000
156A195PRO00.0370.01530.875-0.200-0.2000.0000.0000.0000.000
157A196GLU-1-0.837-0.94724.646-12.737-12.7370.0000.0000.0000.000
158A197ILE00.0230.02025.847-0.349-0.3490.0000.0000.0000.000
159A198TYR0-0.050-0.02426.8950.0360.0360.0000.0000.0000.000
160A199ILE0-0.067-0.01721.4510.0620.0620.0000.0000.0000.000
161A200GLU-1-0.883-0.94121.756-13.276-13.2760.0000.0000.0000.000
162A201PRO00.0180.00419.562-0.707-0.7070.0000.0000.0000.000
163A202LYS10.9330.96913.45020.66520.6650.0000.0000.0000.000
164A203GLU-1-0.952-0.98316.064-16.935-16.9350.0000.0000.0000.000
165A204ILE00.0050.00015.290-0.689-0.6890.0000.0000.0000.000
166A205ALA00.0220.01912.641-1.393-1.3930.0000.0000.0000.000
167A206ASN00.0180.00911.455-3.100-3.1000.0000.0000.0000.000
168A207ALA0-0.0250.00412.033-1.207-1.2070.0000.0000.0000.000
169A208ILE00.021-0.0038.410-0.805-0.8050.0000.0000.0000.000
170A209ARG10.7120.8444.70244.91944.975-0.0010.000-0.0550.000
171A210PHE0-0.016-0.0237.798-2.036-2.0360.0000.0000.0000.000
172A211VAL0-0.043-0.0188.727-0.149-0.1490.0000.0000.0000.000
173A212ILE0-0.046-0.0343.6880.5020.7110.000-0.032-0.1780.000
174A213ASP-1-0.868-0.9365.017-52.906-52.843-0.001-0.002-0.0600.000
175A214ALA0-0.073-0.0146.4613.4143.4140.0000.0000.0000.000
176A215GLY00.0320.0098.082-2.504-2.5040.0000.0000.0000.000
177A216GLU-1-0.872-0.9567.330-34.452-34.4520.0000.0000.0000.000
178A217THR0-0.092-0.02310.4110.8540.8540.0000.0000.0000.000
179A218THR0-0.063-0.03812.2421.7321.7320.0000.0000.0000.000
180A219GLN00.1220.04711.675-2.334-2.3340.0000.0000.0000.000
181A220ILE00.0200.02712.1062.0992.0990.0000.0000.0000.000
182A221THR0-0.007-0.00713.367-0.838-0.8380.0000.0000.0000.000
183A222ASN0-0.0110.00615.8900.0390.0390.0000.0000.0000.000
184A223VAL00.0260.03014.7070.0980.0980.0000.0000.0000.000
185A224ASP-1-0.894-0.92917.918-14.040-14.0400.0000.0000.0000.000
186A225VAL00.0140.00518.4270.1540.1540.0000.0000.0000.000
187A226ARG10.8790.93121.68813.08413.0840.0000.0000.0000.000
188A227PRO00.0230.02824.939-0.206-0.2060.0000.0000.0000.000
189A228ARG10.9871.01326.14511.88011.8800.0000.0000.0000.000