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: 8NN7Y

Calculation Name: 4JKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JKZ

Chain ID: A

ChEMBL ID:

UniProt ID: A0R6I8

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 OptHSide
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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1692304.09079
FMO2-HF: Nuclear repulsion 1624958.717562
FMO2-HF: Total energy -67345.373228
FMO2-MP2: Total energy -67544.4216


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:11:SER)


Summations of interaction energy for fragment #1(A:11:SER)
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.
-25.028-15.1614.189-5.859-8.1970.047
Interaction energy analysis for fragmet #1(A:11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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].
3A13LYS10.9880.9952.559-6.253-1.1541.002-2.886-3.2150.023
4A14SER0-0.033-0.0182.365-5.791-3.5671.743-1.629-2.3380.010
5A15ARG11.0051.0163.904-3.540-3.1940.004-0.098-0.2520.000
6A16VAL00.0400.0156.103-0.641-0.6410.0000.0000.0000.000
7A17ALA00.0670.0437.332-0.432-0.4320.0000.0000.0000.000
8A18ILE00.0130.0166.746-0.385-0.3850.0000.0000.0000.000
9A19VAL0-0.0090.0109.931-0.282-0.2820.0000.0000.0000.000
10A20GLU-1-0.926-0.97311.6810.5840.5840.0000.0000.0000.000
11A21ALA0-0.023-0.01012.483-0.157-0.1570.0000.0000.0000.000
12A22THR0-0.025-0.03913.572-0.132-0.1320.0000.0000.0000.000
13A23ARG10.8120.88115.899-0.667-0.6670.0000.0000.0000.000
14A24ALA0-0.001-0.00217.286-0.070-0.0700.0000.0000.0000.000
15A25LEU0-0.029-0.02016.686-0.054-0.0540.0000.0000.0000.000
16A26LEU00.0360.02819.674-0.050-0.0500.0000.0000.0000.000
17A27LEU0-0.080-0.02421.861-0.045-0.0450.0000.0000.0000.000
18A28GLU-1-0.818-0.89421.7660.2770.2770.0000.0000.0000.000
19A29ARG10.9300.96523.486-0.241-0.2410.0000.0000.0000.000
20A30GLY0-0.0400.00024.773-0.014-0.0140.0000.0000.0000.000
21A31PHE00.023-0.00423.9100.0180.0180.0000.0000.0000.000
22A32ASP-1-0.850-0.92424.6670.2400.2400.0000.0000.0000.000
23A33GLY0-0.030-0.00224.573-0.005-0.0050.0000.0000.0000.000
24A34LEU00.0150.01818.3330.0150.0150.0000.0000.0000.000
25A35SER00.0300.01520.1980.0220.0220.0000.0000.0000.000
26A36ILE00.0750.02414.0250.0200.0200.0000.0000.0000.000
27A37GLU-1-0.782-0.86715.4370.4660.4660.0000.0000.0000.000
28A38ALA0-0.008-0.00116.680-0.006-0.0060.0000.0000.0000.000
29A39VAL00.0290.01512.579-0.009-0.0090.0000.0000.0000.000
30A40ALA0-0.014-0.01011.8380.0820.0820.0000.0000.0000.000
31A41ALA0-0.0120.00012.285-0.006-0.0060.0000.0000.0000.000
32A42LYS10.8030.90014.547-0.417-0.4170.0000.0000.0000.000
33A43ALA0-0.014-0.0069.192-0.017-0.0170.0000.0000.0000.000
34A44GLY0-0.0110.0079.5740.0070.0070.0000.0000.0000.000
35A45VAL0-0.074-0.0296.385-0.086-0.0860.0000.0000.0000.000
36A46GLY00.0580.0248.898-0.139-0.1390.0000.0000.0000.000
37A47LYS10.8680.8909.786-0.138-0.1380.0000.0000.0000.000
38A48GLN00.0410.01010.5760.0850.0850.0000.0000.0000.000
39A49THR0-0.038-0.0174.749-0.0310.043-0.001-0.003-0.0700.000
40A50ILE00.0140.0077.3380.6910.6910.0000.0000.0000.000
41A51TYR00.0100.0069.5480.0350.0350.0000.0000.0000.000
42A52ARG10.8450.9522.858-8.732-7.6240.698-0.615-1.1910.006
43A53TRP0-0.053-0.0502.705-0.3860.6300.743-0.628-1.1310.008
44A54TRP0-0.031-0.0269.104-0.067-0.0670.0000.0000.0000.000
45A55PRO00.0220.02113.4540.0380.0380.0000.0000.0000.000
46A56SER00.005-0.02816.213-0.050-0.0500.0000.0000.0000.000
47A57ARG10.8720.93416.768-0.367-0.3670.0000.0000.0000.000
48A58HIS00.0390.01218.1050.0270.0270.0000.0000.0000.000
49A59ALA00.0360.02817.409-0.003-0.0030.0000.0000.0000.000
50A60LEU0-0.023-0.01012.6590.0100.0100.0000.0000.0000.000
51A61VAL0-0.021-0.02415.998-0.011-0.0110.0000.0000.0000.000
52A62ALA00.004-0.00618.898-0.028-0.0280.0000.0000.0000.000
53A63ASP-1-0.866-0.92115.3820.8010.8010.0000.0000.0000.000
54A64VAL0-0.006-0.00715.526-0.016-0.0160.0000.0000.0000.000
55A65LEU0-0.036-0.03617.995-0.055-0.0550.0000.0000.0000.000
56A66LEU00.0160.00720.638-0.042-0.0420.0000.0000.0000.000
57A67GLU-1-0.892-0.92115.5760.7400.7400.0000.0000.0000.000
58A68ASP-1-0.835-0.89820.5860.3610.3610.0000.0000.0000.000
59A69ALA00.0070.00323.725-0.031-0.0310.0000.0000.0000.000
60A70ASP-1-0.880-0.93226.4450.2410.2410.0000.0000.0000.000
61A71LYS10.8020.88224.601-0.303-0.3030.0000.0000.0000.000
62A72ILE0-0.095-0.03525.021-0.010-0.0100.0000.0000.0000.000
63A73LEU0-0.0270.00829.418-0.015-0.0150.0000.0000.0000.000
64A74ALA0-0.037-0.02732.212-0.007-0.0070.0000.0000.0000.000
65A75ARG10.9650.97034.091-0.153-0.1530.0000.0000.0000.000
66A76MET0-0.0080.01738.772-0.002-0.0020.0000.0000.0000.000
67A77PRO0-0.062-0.02242.236-0.002-0.0020.0000.0000.0000.000
68A78LYS10.8470.89044.146-0.098-0.0980.0000.0000.0000.000
69A79THR0-0.053-0.04747.763-0.004-0.0040.0000.0000.0000.000
70A80ASP-1-0.901-0.94951.3560.0660.0660.0000.0000.0000.000
71A81ASP-1-0.818-0.90953.2430.0720.0720.0000.0000.0000.000
72A82VAL00.0660.03049.9610.0040.0040.0000.0000.0000.000
73A83THR0-0.031-0.01950.3830.0050.0050.0000.0000.0000.000
74A84ALA0-0.042-0.02250.8560.0040.0040.0000.0000.0000.000
75A85ASP-1-0.746-0.83447.4470.0920.0920.0000.0000.0000.000
76A86LEU00.0520.01045.9380.0070.0070.0000.0000.0000.000
77A87ALA0-0.026-0.01146.0510.0050.0050.0000.0000.0000.000
78A88SER0-0.029-0.01046.0920.0050.0050.0000.0000.0000.000
79A89TRP00.0290.00738.5120.0040.0040.0000.0000.0000.000
80A90ALA00.0230.01341.6250.0080.0080.0000.0000.0000.000
81A91GLY00.010-0.00142.3600.0050.0050.0000.0000.0000.000
82A92THR0-0.047-0.04239.1960.0020.0020.0000.0000.0000.000
83A93LEU00.0130.02635.7040.0080.0080.0000.0000.0000.000
84A94ALA00.0280.00337.8420.0080.0080.0000.0000.0000.000
85A95ALA0-0.039-0.00639.2990.0040.0040.0000.0000.0000.000
86A96ALA00.0090.00734.8590.0040.0040.0000.0000.0000.000
87A97LEU00.006-0.00533.1650.0130.0130.0000.0000.0000.000
88A98THR00.0000.00235.3570.0040.0040.0000.0000.0000.000
89A99THR00.0150.03034.017-0.002-0.0020.0000.0000.0000.000
90A100ARG10.8710.90231.191-0.175-0.1750.0000.0000.0000.000
91A101ARG10.8880.93125.154-0.260-0.2600.0000.0000.0000.000
92A102GLY00.0480.03229.5530.0180.0180.0000.0000.0000.000
93A103HIS00.0560.03931.3560.0100.0100.0000.0000.0000.000
94A104ALA0-0.031-0.02128.1270.0070.0070.0000.0000.0000.000
95A105MET00.0040.02225.9670.0190.0190.0000.0000.0000.000
96A106LEU00.0270.02127.4480.0180.0180.0000.0000.0000.000
97A107LYS10.9070.94729.504-0.206-0.2060.0000.0000.0000.000
98A108THR0-0.044-0.02922.8630.0140.0140.0000.0000.0000.000
99A109LEU00.0350.02524.1530.0250.0250.0000.0000.0000.000
100A110MET0-0.0030.01926.1260.0100.0100.0000.0000.0000.000
101A111ALA0-0.010-0.01625.8330.0010.0010.0000.0000.0000.000
102A112ALA00.008-0.00522.1740.0090.0090.0000.0000.0000.000
103A113SER0-0.041-0.04123.8430.0090.0090.0000.0000.0000.000
104A114LEU0-0.042-0.01826.343-0.008-0.0080.0000.0000.0000.000
105A115GLU-1-0.877-0.90821.5460.4820.4820.0000.0000.0000.000
106A116HIS0-0.014-0.01021.6970.0010.0010.0000.0000.0000.000
107A117GLU-1-0.876-0.92624.8570.2340.2340.0000.0000.0000.000
108A118ASP-1-0.860-0.93723.2190.3310.3310.0000.0000.0000.000
109A119THR0-0.091-0.06121.3730.0240.0240.0000.0000.0000.000
110A120ALA00.0410.01923.495-0.004-0.0040.0000.0000.0000.000
111A121ALA0-0.031-0.00627.020-0.013-0.0130.0000.0000.0000.000
112A122ARG10.9340.98218.906-0.545-0.5450.0000.0000.0000.000
113A123LEU00.009-0.00322.567-0.004-0.0040.0000.0000.0000.000
114A124ARG10.9530.97926.063-0.212-0.2120.0000.0000.0000.000
115A125GLU-1-0.840-0.88727.5100.2070.2070.0000.0000.0000.000
116A126GLY00.0120.01026.522-0.010-0.0100.0000.0000.0000.000
117A127PHE0-0.002-0.03024.463-0.012-0.0120.0000.0000.0000.000
118A128SER0-0.059-0.02329.750-0.018-0.0180.0000.0000.0000.000
119A129ARG10.8390.87131.130-0.207-0.2070.0000.0000.0000.000
120A130PRO00.0560.03231.391-0.015-0.0150.0000.0000.0000.000
121A131LEU0-0.042-0.00534.055-0.013-0.0130.0000.0000.0000.000
122A132ILE00.012-0.00136.661-0.010-0.0100.0000.0000.0000.000
123A133GLU-1-0.810-0.89236.5860.1450.1450.0000.0000.0000.000
124A134SER0-0.0220.00237.875-0.009-0.0090.0000.0000.0000.000
125A135VAL0-0.047-0.02740.367-0.008-0.0080.0000.0000.0000.000
126A136ARG10.8740.91839.688-0.137-0.1370.0000.0000.0000.000
127A137ASP-1-0.906-0.96141.7640.1120.1120.0000.0000.0000.000
128A138ARG10.6840.82544.512-0.091-0.0910.0000.0000.0000.000
129A139LEU0-0.004-0.00846.523-0.005-0.0050.0000.0000.0000.000
130A140ARG10.8850.93746.711-0.092-0.0920.0000.0000.0000.000
131A141ASP-1-0.820-0.88647.7900.0890.0890.0000.0000.0000.000
132A142GLU-1-0.910-0.93950.2930.0720.0720.0000.0000.0000.000
133A143ASP-1-0.963-0.97352.6900.0660.0660.0000.0000.0000.000
134A144ILE0-0.0350.00551.115-0.001-0.0010.0000.0000.0000.000
135A145ASP-1-0.790-0.87651.3750.0830.0830.0000.0000.0000.000
136A146ALA00.003-0.03147.3700.0030.0030.0000.0000.0000.000
137A147ASP-1-0.888-0.93447.5170.0960.0960.0000.0000.0000.000
138A148HIS0-0.062-0.06548.7900.0030.0030.0000.0000.0000.000
139A149ALA0-0.0080.00347.1100.0030.0030.0000.0000.0000.000
140A150GLN0-0.052-0.04140.9180.0050.0050.0000.0000.0000.000
141A151ALA00.0350.02544.5950.0050.0050.0000.0000.0000.000
142A152ALA0-0.0050.00046.7640.0020.0020.0000.0000.0000.000
143A153ALA00.000-0.01042.2630.0030.0030.0000.0000.0000.000
144A154ASP-1-0.878-0.93441.7130.1380.1380.0000.0000.0000.000
145A155ALA0-0.026-0.00542.5430.0040.0040.0000.0000.0000.000
146A156LEU0-0.019-0.00343.7590.0010.0010.0000.0000.0000.000
147A157LEU0-0.003-0.00436.1980.0040.0040.0000.0000.0000.000
148A158GLY00.0150.00639.8890.0060.0060.0000.0000.0000.000
149A159ALA0-0.026-0.01641.0920.0020.0020.0000.0000.0000.000
150A160VAL0-0.015-0.00738.7360.0010.0010.0000.0000.0000.000
151A161VAL00.0190.00235.1120.0050.0050.0000.0000.0000.000
152A162ASN00.0220.01337.4930.0100.0100.0000.0000.0000.000
153A163ALA00.0140.02439.5060.0000.0000.0000.0000.0000.000
154A164VAL0-0.014-0.00735.7350.0000.0000.0000.0000.0000.000
155A165LEU0-0.052-0.03632.8000.0060.0060.0000.0000.0000.000
156A166SER0-0.063-0.02336.5210.0010.0010.0000.0000.0000.000
157A167GLU-1-0.815-0.88539.7530.1140.1140.0000.0000.0000.000
158A168GLY0-0.0190.00537.492-0.002-0.0020.0000.0000.0000.000
159A169ARG10.7940.85535.503-0.151-0.1510.0000.0000.0000.000
160A170SER00.0140.02239.208-0.002-0.0020.0000.0000.0000.000
161A171TYR00.0130.02041.180-0.006-0.0060.0000.0000.0000.000
162A172SER00.0300.00442.6200.0020.0020.0000.0000.0000.000
163A173ARG10.9010.95143.122-0.108-0.1080.0000.0000.0000.000
164A174GLN00.0570.01745.1480.0020.0020.0000.0000.0000.000
165A175ARG10.8430.90045.870-0.112-0.1120.0000.0000.0000.000
166A176ALA00.0500.04543.979-0.002-0.0020.0000.0000.0000.000
167A177GLU-1-0.832-0.91445.9230.0930.0930.0000.0000.0000.000
168A178THR0-0.049-0.03348.481-0.004-0.0040.0000.0000.0000.000
169A179SER0-0.022-0.02647.257-0.002-0.0020.0000.0000.0000.000
170A180ALA00.0110.00747.299-0.001-0.0010.0000.0000.0000.000
171A181ARG10.9070.94048.962-0.086-0.0860.0000.0000.0000.000
172A182ILE0-0.031-0.01052.406-0.003-0.0030.0000.0000.0000.000
173A183ILE00.0020.00447.469-0.002-0.0020.0000.0000.0000.000
174A184VAL00.0340.01950.351-0.001-0.0010.0000.0000.0000.000
175A185ALA0-0.058-0.03052.740-0.003-0.0030.0000.0000.0000.000
176A186GLY0-0.038-0.02254.865-0.003-0.0030.0000.0000.0000.000
177A187LEU0-0.0020.00250.6380.0000.0000.0000.0000.0000.000
178A188ARG10.8990.96055.342-0.068-0.0680.0000.0000.0000.000
179A189PRO00.0200.02857.6390.0000.0000.0000.0000.0000.000