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

tag_button

FMODB ID: YVMZ2

Calculation Name: 1N7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N7K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y948

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2664261.69288
FMO2-HF: Nuclear repulsion 2579988.363883
FMO2-HF: Total energy -84273.328997
FMO2-MP2: Total energy -84523.976397


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-5.7040.1789.511-5.278-10.115-0.03
Interaction energy analysis for fragmet #1(A:2:PRO)
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 : 0.009
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].
3A4ALA00.043-0.0023.555-1.1860.9630.007-1.123-1.0320.006
4A5ARG10.9630.9655.8750.7110.7110.0000.0000.0000.000
5A6ASP-1-0.787-0.8752.614-3.514-0.3711.922-2.407-2.658-0.024
6A7ILE0-0.014-0.0062.568-0.3350.3760.378-0.249-0.8410.000
7A8LEU0-0.020-0.0125.0870.1600.201-0.001-0.005-0.0350.000
8A9GLN0-0.035-0.0097.6690.0650.0650.0000.0000.0000.000
9A10GLN0-0.028-0.0243.488-0.1420.2790.004-0.112-0.3140.000
10A11GLY00.012-0.0027.9650.0460.0460.0000.0000.0000.000
11A12LEU0-0.063-0.04010.3880.0350.0350.0000.0000.0000.000
12A13ASP-1-0.888-0.94210.6130.0750.0750.0000.0000.0000.000
13A14ARG10.8000.9027.356-0.114-0.1140.0000.0000.0000.000
14A15LEU0-0.064-0.03013.7660.0050.0050.0000.0000.0000.000
15A16GLY00.0560.04716.162-0.016-0.0160.0000.0000.0000.000
16A17SER0-0.017-0.00318.727-0.007-0.0070.0000.0000.0000.000
17A18PRO0-0.009-0.02520.977-0.006-0.0060.0000.0000.0000.000
18A19GLU-1-0.830-0.91922.966-0.045-0.0450.0000.0000.0000.000
19A20ASP-1-0.842-0.91518.859-0.016-0.0160.0000.0000.0000.000
20A21LEU0-0.063-0.03217.784-0.003-0.0030.0000.0000.0000.000
21A22ALA00.0200.00319.926-0.003-0.0030.0000.0000.0000.000
22A23SER00.0740.03022.2440.0040.0040.0000.0000.0000.000
23A24ARG10.8400.92515.3120.0160.0160.0000.0000.0000.000
24A25ILE0-0.045-0.01519.153-0.011-0.0110.0000.0000.0000.000
25A26ASP-1-0.759-0.86821.048-0.042-0.0420.0000.0000.0000.000
26A27SER00.0180.00222.956-0.015-0.0150.0000.0000.0000.000
27A28THR0-0.064-0.04524.2260.0060.0060.0000.0000.0000.000
28A29LEU00.0280.02126.510-0.006-0.0060.0000.0000.0000.000
29A30LEU0-0.016-0.00625.9740.0050.0050.0000.0000.0000.000
30A31SER00.0030.00829.865-0.004-0.0040.0000.0000.0000.000
31A32PRO00.020-0.00332.2060.0040.0040.0000.0000.0000.000
32A33ARG10.9380.95035.0460.0730.0730.0000.0000.0000.000
33A34ALA0-0.0190.02533.9920.0020.0020.0000.0000.0000.000
34A35THR00.0150.02036.0960.0040.0040.0000.0000.0000.000
35A36GLU-1-0.830-0.95638.149-0.034-0.0340.0000.0000.0000.000
36A37GLU-1-0.890-0.92139.389-0.038-0.0380.0000.0000.0000.000
37A38ASP-1-0.820-0.91035.378-0.057-0.0570.0000.0000.0000.000
38A39VAL00.007-0.00634.735-0.002-0.0020.0000.0000.0000.000
39A40ARG10.8460.90435.4350.0350.0350.0000.0000.0000.000
40A41ASN00.0060.00635.8890.0040.0040.0000.0000.0000.000
41A42LEU0-0.0220.00128.960-0.001-0.0010.0000.0000.0000.000
42A43VAL0-0.006-0.01532.0350.0000.0000.0000.0000.0000.000
43A44ARG10.9360.96133.7660.0350.0350.0000.0000.0000.000
44A45GLU-1-0.875-0.93232.018-0.059-0.0590.0000.0000.0000.000
45A46ALA0-0.046-0.02929.560-0.001-0.0010.0000.0000.0000.000
46A47SER0-0.001-0.00430.2170.0030.0030.0000.0000.0000.000
47A48ASP-1-0.979-0.97632.610-0.036-0.0360.0000.0000.0000.000
48A49TYR0-0.103-0.06727.9650.0000.0000.0000.0000.0000.000
49A50GLY00.0100.02827.991-0.001-0.0010.0000.0000.0000.000
50A51PHE0-0.067-0.04024.802-0.002-0.0020.0000.0000.0000.000
51A52ARG10.8880.97221.2410.0230.0230.0000.0000.0000.000
52A53CYS0-0.095-0.05624.4570.0070.0070.0000.0000.0000.000
53A54ALA00.0220.02726.655-0.008-0.0080.0000.0000.0000.000
54A55VAL0-0.018-0.02324.2270.0040.0040.0000.0000.0000.000
55A56LEU00.003-0.01127.653-0.006-0.0060.0000.0000.0000.000
56A57THR00.0220.00530.4410.0020.0020.0000.0000.0000.000
57A58PRO00.0770.04032.2570.0020.0020.0000.0000.0000.000
58A59VAL00.0150.00634.7700.0020.0020.0000.0000.0000.000
59A60TYR0-0.026-0.03734.9930.0030.0030.0000.0000.0000.000
60A61THR0-0.0060.01132.9900.0010.0010.0000.0000.0000.000
61A62VAL00.0390.01435.1460.0020.0020.0000.0000.0000.000
62A63LYS10.8700.94738.6730.0290.0290.0000.0000.0000.000
63A64ILE00.0040.01235.1770.0010.0010.0000.0000.0000.000
64A65SER00.0130.00037.3580.0010.0010.0000.0000.0000.000
65A66GLY00.0530.03938.3640.0010.0010.0000.0000.0000.000
66A67LEU0-0.054-0.03138.4360.0010.0010.0000.0000.0000.000
67A68ALA00.013-0.01134.8480.0000.0000.0000.0000.0000.000
68A69GLU-1-0.912-0.94036.508-0.006-0.0060.0000.0000.0000.000
69A70LYS10.8950.95038.4460.0190.0190.0000.0000.0000.000
70A71LEU0-0.069-0.05036.7400.0010.0010.0000.0000.0000.000
71A72GLY00.0250.04035.6110.0000.0000.0000.0000.0000.000
72A73VAL0-0.045-0.01630.852-0.001-0.0010.0000.0000.0000.000
73A74LYS10.9100.96124.9990.0080.0080.0000.0000.0000.000
74A75LEU00.0240.00930.074-0.005-0.0050.0000.0000.0000.000
75A76CYS0-0.026-0.00524.7670.0040.0040.0000.0000.0000.000
76A77SER00.0640.03228.505-0.005-0.0050.0000.0000.0000.000
77A78VAL0-0.073-0.02826.0670.0010.0010.0000.0000.0000.000
78A79ILE00.0270.00127.9610.0030.0030.0000.0000.0000.000
79A80GLY0-0.013-0.02328.648-0.002-0.0020.0000.0000.0000.000
80A81PHE0-0.0290.02424.296-0.005-0.0050.0000.0000.0000.000
81A82PRO0-0.023-0.03926.7730.0030.0030.0000.0000.0000.000
82A83LEU00.018-0.01826.756-0.004-0.0040.0000.0000.0000.000
83A84GLY00.0680.04528.4330.0010.0010.0000.0000.0000.000
84A85GLN0-0.052-0.02829.4340.0010.0010.0000.0000.0000.000
85A86ALA00.0220.03432.2970.0010.0010.0000.0000.0000.000
86A87PRO00.0350.00033.8090.0000.0000.0000.0000.0000.000
87A88LEU00.0550.02032.408-0.001-0.0010.0000.0000.0000.000
88A89GLU-1-0.912-0.95634.839-0.010-0.0100.0000.0000.0000.000
89A90VAL00.0190.00436.7010.0000.0000.0000.0000.0000.000
90A91LYS10.7180.83529.0740.0300.0300.0000.0000.0000.000
91A92LEU0-0.016-0.00633.9790.0010.0010.0000.0000.0000.000
92A93VAL00.0080.02035.8670.0010.0010.0000.0000.0000.000
93A94GLU-1-0.829-0.90932.903-0.033-0.0330.0000.0000.0000.000
94A95ALA00.016-0.00932.661-0.001-0.0010.0000.0000.0000.000
95A96GLN00.0530.07934.3090.0010.0010.0000.0000.0000.000
96A97THR0-0.0150.00137.5200.0000.0000.0000.0000.0000.000
97A98VAL0-0.023-0.01432.9140.0000.0000.0000.0000.0000.000
98A99LEU0-0.060-0.03132.1930.0000.0000.0000.0000.0000.000
99A100GLU-1-0.951-0.97235.753-0.005-0.0050.0000.0000.0000.000
100A101ALA0-0.061-0.02837.6530.0000.0000.0000.0000.0000.000
101A102GLY00.0300.02136.638-0.001-0.0010.0000.0000.0000.000
102A103ALA0-0.080-0.02731.7100.0000.0000.0000.0000.0000.000
103A104THR00.0380.00830.1530.0030.0030.0000.0000.0000.000
104A105GLU-1-0.830-0.90924.254-0.008-0.0080.0000.0000.0000.000
105A106LEU00.0250.01126.564-0.005-0.0050.0000.0000.0000.000
106A107ASP-1-0.755-0.88022.593-0.055-0.0550.0000.0000.0000.000
107A108VAL00.023-0.01124.581-0.005-0.0050.0000.0000.0000.000
108A109VAL0-0.0110.01824.020-0.005-0.0050.0000.0000.0000.000
109A110PRO0-0.0090.00423.7610.0040.0040.0000.0000.0000.000
110A111HIS00.0330.01226.604-0.010-0.0100.0000.0000.0000.000
111A112LEU0-0.022-0.02921.8540.0050.0050.0000.0000.0000.000
112A113SER00.0010.00225.3040.0060.0060.0000.0000.0000.000
113A114LEU0-0.0070.00527.0340.0030.0030.0000.0000.0000.000
114A115GLY0-0.0070.00825.7230.0060.0060.0000.0000.0000.000
115A116PRO0-0.010-0.02622.3930.0010.0010.0000.0000.0000.000
116A117GLU-1-0.827-0.91224.4550.0300.0300.0000.0000.0000.000
117A118ALA00.0060.00327.6610.0020.0020.0000.0000.0000.000
118A119VAL00.0380.01923.3810.0000.0000.0000.0000.0000.000
119A120TYR0-0.0120.00825.7660.0020.0020.0000.0000.0000.000
120A121ARG10.8980.96226.881-0.014-0.0140.0000.0000.0000.000
121A122GLU-1-0.774-0.86828.832-0.021-0.0210.0000.0000.0000.000
122A123VAL00.007-0.00424.446-0.001-0.0010.0000.0000.0000.000
123A124SER00.007-0.02227.6770.0040.0040.0000.0000.0000.000
124A125GLY0-0.068-0.01929.4920.0020.0020.0000.0000.0000.000
125A126ILE00.0200.00227.5480.0010.0010.0000.0000.0000.000
126A127VAL00.0070.01926.3680.0000.0000.0000.0000.0000.000
127A128LYS10.9200.96429.310-0.020-0.0200.0000.0000.0000.000
128A129LEU00.0100.01032.7130.0010.0010.0000.0000.0000.000
129A130ALA00.0570.03729.7810.0000.0000.0000.0000.0000.000
130A131LYS10.9500.97127.654-0.039-0.0390.0000.0000.0000.000
131A132SER0-0.117-0.06032.1150.0010.0010.0000.0000.0000.000
132A133TYR0-0.027-0.07533.9950.0000.0000.0000.0000.0000.000
133A134GLY0-0.058-0.02031.886-0.001-0.0010.0000.0000.0000.000
134A135ALA0-0.025-0.00829.9070.0000.0000.0000.0000.0000.000
135A136VAL0-0.045-0.02223.1270.0030.0030.0000.0000.0000.000
136A137VAL0-0.020-0.01224.263-0.009-0.0090.0000.0000.0000.000
137A138LYS10.7670.88220.0050.0300.0300.0000.0000.0000.000
138A139VAL00.015-0.00620.439-0.007-0.0070.0000.0000.0000.000
139A140ILE0-0.041-0.01719.321-0.009-0.0090.0000.0000.0000.000
140A141LEU00.0340.00016.3160.0070.0070.0000.0000.0000.000
141A142GLU-1-0.850-0.91218.831-0.122-0.1220.0000.0000.0000.000
142A143ALA00.0490.02213.533-0.001-0.0010.0000.0000.0000.000
143A144PRO0-0.066-0.04115.033-0.005-0.0050.0000.0000.0000.000
144A145LEU0-0.0140.00616.079-0.006-0.0060.0000.0000.0000.000
145A146TRP0-0.019-0.00117.0080.0190.0190.0000.0000.0000.000
146A147ASP-1-0.799-0.87614.926-0.112-0.1120.0000.0000.0000.000
147A148ASP-1-0.785-0.91110.173-0.224-0.2240.0000.0000.0000.000
148A149LYS10.9330.97613.1200.0110.0110.0000.0000.0000.000
149A150THR0-0.013-0.02416.0170.0250.0250.0000.0000.0000.000
150A151LEU00.0180.01212.0980.0080.0080.0000.0000.0000.000
151A152SER00.0320.01513.9410.0160.0160.0000.0000.0000.000
152A153LEU0-0.0150.00015.3060.0130.0130.0000.0000.0000.000
153A154LEU0-0.008-0.00418.4040.0070.0070.0000.0000.0000.000
154A155VAL00.0200.01813.9970.0000.0000.0000.0000.0000.000
155A156ASP-1-0.867-0.93917.1500.1280.1280.0000.0000.0000.000
156A157SER0-0.093-0.04919.2490.0030.0030.0000.0000.0000.000
157A158SER00.017-0.00719.509-0.005-0.0050.0000.0000.0000.000
158A159ARG10.9480.97619.042-0.113-0.1130.0000.0000.0000.000
159A160ARG10.8600.92921.143-0.083-0.0830.0000.0000.0000.000
160A161ALA0-0.0060.00624.379-0.001-0.0010.0000.0000.0000.000
161A162GLY0-0.051-0.02424.569-0.004-0.0040.0000.0000.0000.000
162A163ALA0-0.019-0.00422.013-0.003-0.0030.0000.0000.0000.000
163A164ASP-1-0.827-0.91221.4360.0470.0470.0000.0000.0000.000
164A165ILE0-0.066-0.03516.8220.0090.0090.0000.0000.0000.000
165A166VAL00.0260.03715.450-0.005-0.0050.0000.0000.0000.000
166A167LYS10.8130.89415.8090.0810.0810.0000.0000.0000.000
167A168THR00.0060.02213.3340.0070.0070.0000.0000.0000.000
168A169SER0-0.042-0.04215.332-0.003-0.0030.0000.0000.0000.000
169A170THR00.042-0.00418.5310.0060.0060.0000.0000.0000.000
170A171GLY0-0.081-0.03820.9850.0060.0060.0000.0000.0000.000
171A172VAL0-0.061-0.03821.945-0.001-0.0010.0000.0000.0000.000
172A173TYR00.0260.00724.084-0.003-0.0030.0000.0000.0000.000
173A174THR00.0430.06118.916-0.016-0.0160.0000.0000.0000.000
174A175LYS10.8790.92218.4150.1960.1960.0000.0000.0000.000
175A176GLY00.0650.02114.677-0.021-0.0210.0000.0000.0000.000
176A177GLY0-0.006-0.01613.6900.0020.0020.0000.0000.0000.000
177A178ASP-1-0.790-0.87411.520-0.577-0.5770.0000.0000.0000.000
178A179PRO00.0610.0047.0270.0120.0120.0000.0000.0000.000
179A180VAL00.0380.0326.809-0.136-0.1360.0000.0000.0000.000
180A181THR0-0.029-0.0437.8830.0450.0450.0000.0000.0000.000
181A182VAL0-0.066-0.0327.8690.0790.0790.0000.0000.0000.000
182A183PHE00.0410.0202.446-1.526-2.1097.201-1.382-5.235-0.012
183A184ARG10.7790.8775.6480.5410.5410.0000.0000.0000.000
184A185LEU0-0.0010.0118.1840.1310.1310.0000.0000.0000.000
185A186ALA0-0.003-0.0086.7760.0940.0940.0000.0000.0000.000
186A187SER0-0.079-0.0405.3860.1560.1560.0000.0000.0000.000
187A188LEU00.0120.0047.2900.1260.1260.0000.0000.0000.000
188A189ALA00.0220.00010.7900.0280.0280.0000.0000.0000.000
189A190LYS10.9530.9898.272-0.191-0.1910.0000.0000.0000.000
190A191PRO0-0.039-0.0049.8310.0000.0000.0000.0000.0000.000
191A192LEU0-0.022-0.00912.542-0.017-0.0170.0000.0000.0000.000
192A193GLY0-0.045-0.02814.871-0.029-0.0290.0000.0000.0000.000
193A194MET0-0.073-0.01015.567-0.023-0.0230.0000.0000.0000.000
194A195GLY00.0190.01914.4520.0140.0140.0000.0000.0000.000
195A196VAL00.002-0.01310.701-0.017-0.0170.0000.0000.0000.000
196A197LYS10.7480.86613.7130.0660.0660.0000.0000.0000.000
197A198ALA00.0270.01712.470-0.016-0.0160.0000.0000.0000.000
198A199SER00.012-0.01814.4700.0320.0320.0000.0000.0000.000
199A200GLY00.0430.01617.027-0.014-0.0140.0000.0000.0000.000
200A201GLY0-0.038-0.02617.668-0.025-0.0250.0000.0000.0000.000
201A202ILE00.0200.05014.988-0.011-0.0110.0000.0000.0000.000
202A203ARG10.8980.95518.6830.1840.1840.0000.0000.0000.000
203A204SER00.0220.02018.6300.0240.0240.0000.0000.0000.000
204A205GLY00.0880.04118.325-0.009-0.0090.0000.0000.0000.000
205A206ILE00.018-0.00215.351-0.005-0.0050.0000.0000.0000.000
206A207ASP-1-0.820-0.90613.987-0.336-0.3360.0000.0000.0000.000
207A208ALA0-0.016-0.01813.603-0.027-0.0270.0000.0000.0000.000
208A209VAL00.0480.01612.0970.0000.0000.0000.0000.0000.000
209A210LEU0-0.017-0.0069.193-0.019-0.0190.0000.0000.0000.000
210A211ALA0-0.0020.0078.776-0.074-0.0740.0000.0000.0000.000
211A212VAL00.0400.0189.5390.0170.0170.0000.0000.0000.000
212A213GLY00.0240.0178.0160.0840.0840.0000.0000.0000.000
213A214ALA0-0.082-0.0294.9200.0870.0870.0000.0000.0000.000
214A215GLY0-0.055-0.0445.6410.0650.0650.0000.0000.0000.000
215A216ALA0-0.0070.0027.8140.0480.0480.0000.0000.0000.000
216A217ASP-1-0.865-0.92611.2390.0760.0760.0000.0000.0000.000
217A218ILE0-0.043-0.03014.190-0.001-0.0010.0000.0000.0000.000
218A219ILE00.0100.00815.170-0.026-0.0260.0000.0000.0000.000
219A220GLY0-0.0010.00417.2760.0170.0170.0000.0000.0000.000
220A221THR0-0.032-0.04319.470-0.017-0.0170.0000.0000.0000.000
221A222SER0-0.014-0.00521.9490.0120.0120.0000.0000.0000.000
222A223SER0-0.087-0.04324.0060.0040.0040.0000.0000.0000.000
223A224ALA00.0700.04623.752-0.007-0.0070.0000.0000.0000.000
224A225VAL00.1050.06124.746-0.005-0.0050.0000.0000.0000.000
225A226LYS10.9340.95725.6760.0990.0990.0000.0000.0000.000
226A227VAL0-0.0060.00619.797-0.007-0.0070.0000.0000.0000.000
227A228LEU00.0250.01421.837-0.009-0.0090.0000.0000.0000.000
228A229GLU-1-0.833-0.95123.756-0.080-0.0800.0000.0000.0000.000
229A230SER0-0.059-0.01522.145-0.009-0.0090.0000.0000.0000.000
230A231PHE0-0.046-0.03017.285-0.015-0.0150.0000.0000.0000.000
231A232LYS10.8630.95721.2960.0730.0730.0000.0000.0000.000
232A233SER0-0.020-0.02924.3080.0030.0030.0000.0000.0000.000
233A234LEU0-0.0130.00620.687-0.003-0.0030.0000.0000.0000.000
234A235VAL0-0.0090.01623.734-0.001-0.0010.0000.0000.0000.000