FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 5NJYZ

Calculation Name: 1ZK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZK8

Chain ID: A

ChEMBL ID:

UniProt ID: Q815X4

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1712300.299912
FMO2-HF: Nuclear repulsion 1644916.637396
FMO2-HF: Total energy -67383.662516
FMO2-MP2: Total energy -67583.275686


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:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
-6.014-3.6944.228-2.335-4.2110.007
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.013
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].
3A8LEU0-0.034-0.0222.998-2.742-0.3890.242-1.221-1.373-0.003
4A9THR00.0280.0054.6490.0800.232-0.001-0.010-0.1400.000
5A10LEU00.0580.0256.512-0.014-0.0140.0000.0000.0000.000
6A11GLN0-0.049-0.0357.3560.0530.0530.0000.0000.0000.000
7A12LYS11.0131.0222.196-2.515-2.7003.987-1.104-2.6980.010
8A13ILE0-0.031-0.0036.1740.0000.0000.0000.0000.0000.000
9A14VAL00.000-0.0069.0740.0070.0070.0000.0000.0000.000
10A15GLU-1-0.849-0.9186.804-0.522-0.5220.0000.0000.0000.000
11A16THR00.008-0.0088.0580.0000.0000.0000.0000.0000.000
12A17ALA0-0.033-0.02510.3230.0150.0150.0000.0000.0000.000
13A18ALA0-0.002-0.01013.0540.0150.0150.0000.0000.0000.000
14A19GLU-1-0.928-0.95010.652-0.358-0.3580.0000.0000.0000.000
15A20ILE0-0.026-0.01314.0100.0150.0150.0000.0000.0000.000
16A21ALA0-0.021-0.01316.2920.0130.0130.0000.0000.0000.000
17A22ASP-1-0.833-0.90417.527-0.154-0.1540.0000.0000.0000.000
18A23ALA0-0.055-0.00118.2120.0080.0080.0000.0000.0000.000
19A24ASN0-0.057-0.04719.5800.0010.0010.0000.0000.0000.000
20A25GLY00.0990.06321.3980.0110.0110.0000.0000.0000.000
21A26VAL00.000-0.01520.710-0.003-0.0030.0000.0000.0000.000
22A27GLN0-0.069-0.03221.5360.0000.0000.0000.0000.0000.000
23A28GLU-1-0.892-0.91920.438-0.085-0.0850.0000.0000.0000.000
24A29VAL0-0.0300.01616.463-0.005-0.0050.0000.0000.0000.000
25A30THR00.019-0.01218.2390.0140.0140.0000.0000.0000.000
26A31LEU00.008-0.00816.319-0.008-0.0080.0000.0000.0000.000
27A32ALA0-0.010-0.00316.154-0.005-0.0050.0000.0000.0000.000
28A33SER00.011-0.01517.250-0.005-0.0050.0000.0000.0000.000
29A34LEU00.0340.00811.829-0.013-0.0130.0000.0000.0000.000
30A35ALA0-0.035-0.02912.296-0.016-0.0160.0000.0000.0000.000
31A36GLN0-0.023-0.00713.081-0.007-0.0070.0000.0000.0000.000
32A37THR00.0220.01511.451-0.006-0.0060.0000.0000.0000.000
33A38LEU0-0.068-0.0326.717-0.028-0.0280.0000.0000.0000.000
34A39GLY0-0.0030.0249.077-0.038-0.0380.0000.0000.0000.000
35A40VAL0-0.0270.0009.3920.0200.0200.0000.0000.0000.000
36A41ARG10.9930.97211.6580.0230.0230.0000.0000.0000.000
37A42SER00.0600.01413.8540.0070.0070.0000.0000.0000.000
38A43PRO00.0090.00716.138-0.001-0.0010.0000.0000.0000.000
39A44SER0-0.007-0.01611.1940.0230.0230.0000.0000.0000.000
40A45LEU00.003-0.00310.7260.0010.0010.0000.0000.0000.000
41A46TYR0-0.014-0.01012.609-0.003-0.0030.0000.0000.0000.000
42A47ASN0-0.079-0.01212.0310.0230.0230.0000.0000.0000.000
43A48HIS0-0.031-0.0098.785-0.009-0.0090.0000.0000.0000.000
44A49VAL0-0.0030.00712.442-0.009-0.0090.0000.0000.0000.000
45A50LYS10.9760.97415.1210.0060.0060.0000.0000.0000.000
46A51GLY00.0370.00318.0320.0050.0050.0000.0000.0000.000
47A52LEU0-0.0110.00518.349-0.005-0.0050.0000.0000.0000.000
48A53GLN00.0500.03419.718-0.008-0.0080.0000.0000.0000.000
49A54ASP-1-0.820-0.91317.493-0.040-0.0400.0000.0000.0000.000
50A55VAL00.0120.01614.522-0.007-0.0070.0000.0000.0000.000
51A56ARG10.8910.93016.7290.0650.0650.0000.0000.0000.000
52A57LYS10.8450.92019.6960.0350.0350.0000.0000.0000.000
53A58ASN0-0.057-0.04815.065-0.005-0.0050.0000.0000.0000.000
54A59LEU00.0090.01515.158-0.012-0.0120.0000.0000.0000.000
55A60GLY00.0600.03116.933-0.007-0.0070.0000.0000.0000.000
56A61ILE0-0.038-0.02818.319-0.001-0.0010.0000.0000.0000.000
57A62TYR0-0.006-0.00311.4290.0090.0090.0000.0000.0000.000
58A63GLY00.0460.01116.712-0.010-0.0100.0000.0000.0000.000
59A64ILE00.0050.00919.0460.0010.0010.0000.0000.0000.000
60A65LYS10.9320.96617.6180.0970.0970.0000.0000.0000.000
61A66LYS10.8740.94415.3850.2140.2140.0000.0000.0000.000
62A67LEU0-0.020-0.00419.0890.0010.0010.0000.0000.0000.000
63A68HIS0-0.081-0.07022.7280.0020.0020.0000.0000.0000.000
64A69ASN00.0300.01518.5130.0150.0150.0000.0000.0000.000
65A70ARG10.8720.93420.9360.1380.1380.0000.0000.0000.000
66A71LEU0-0.026-0.01123.9040.0060.0060.0000.0000.0000.000
67A72GLU-1-0.834-0.92825.024-0.060-0.0600.0000.0000.0000.000
68A73GLU-1-0.846-0.91221.297-0.135-0.1350.0000.0000.0000.000
69A74ALA0-0.036-0.01426.1860.0040.0040.0000.0000.0000.000
70A75ALA0-0.017-0.01229.0480.0050.0050.0000.0000.0000.000
71A76GLU-1-0.922-0.94326.933-0.072-0.0720.0000.0000.0000.000
72A77ASP-1-0.936-0.96130.889-0.052-0.0520.0000.0000.0000.000
73A78LYS10.7680.89031.3050.0700.0700.0000.0000.0000.000
74A79ARG10.9390.94736.0200.0360.0360.0000.0000.0000.000
75A80MET0-0.003-0.00338.8090.0000.0000.0000.0000.0000.000
76A81ASP-1-0.732-0.83939.475-0.040-0.0400.0000.0000.0000.000
77A82GLU-1-0.896-0.94437.740-0.045-0.0450.0000.0000.0000.000
78A83ALA0-0.0020.00535.167-0.004-0.0040.0000.0000.0000.000
79A84ILE0-0.0050.00134.988-0.003-0.0030.0000.0000.0000.000
80A85HIS00.0240.01635.924-0.005-0.0050.0000.0000.0000.000
81A86ALA00.0090.01532.275-0.003-0.0030.0000.0000.0000.000
82A87LEU00.000-0.00530.472-0.005-0.0050.0000.0000.0000.000
83A88GLY00.012-0.00731.070-0.004-0.0040.0000.0000.0000.000
84A89GLU-1-0.847-0.90930.998-0.078-0.0780.0000.0000.0000.000
85A90ALA0-0.003-0.00127.362-0.005-0.0050.0000.0000.0000.000
86A91TYR0-0.014-0.01227.055-0.006-0.0060.0000.0000.0000.000
87A92VAL00.0360.00327.668-0.005-0.0050.0000.0000.0000.000
88A93ALA00.0030.00526.857-0.004-0.0040.0000.0000.0000.000
89A94PHE0-0.012-0.01020.045-0.011-0.0110.0000.0000.0000.000
90A95VAL0-0.024-0.00623.542-0.008-0.0080.0000.0000.0000.000
91A96ARG10.7920.88425.4020.0780.0780.0000.0000.0000.000
92A97LYS10.8520.93119.4600.1660.1660.0000.0000.0000.000
93A98HIS0-0.056-0.03316.990-0.021-0.0210.0000.0000.0000.000
94A99PRO00.1110.07121.2620.0050.0050.0000.0000.0000.000
95A100GLY00.0400.02021.1010.0080.0080.0000.0000.0000.000
96A101LEU0-0.026-0.02516.6460.0040.0040.0000.0000.0000.000
97A102TYR00.0160.00019.8930.0090.0090.0000.0000.0000.000
98A103GLU-1-0.867-0.91723.376-0.079-0.0790.0000.0000.0000.000
99A104ALA00.003-0.00520.4290.0080.0080.0000.0000.0000.000
100A105THR0-0.107-0.06522.0910.0070.0070.0000.0000.0000.000
101A106PHE0-0.055-0.02023.8370.0080.0080.0000.0000.0000.000
102A107LEU0-0.068-0.01122.5880.0070.0070.0000.0000.0000.000
103A108ARG10.9430.95826.1040.0410.0410.0000.0000.0000.000
104A109ASP-1-0.829-0.92724.777-0.038-0.0380.0000.0000.0000.000
105A110GLU-1-0.960-0.98827.227-0.024-0.0240.0000.0000.0000.000
106A111GLU-1-0.792-0.88521.435-0.038-0.0380.0000.0000.0000.000
107A112VAL0-0.016-0.00322.175-0.004-0.0040.0000.0000.0000.000
108A113ARG10.9620.98124.3360.0300.0300.0000.0000.0000.000
109A114LYS10.9390.97625.9240.0300.0300.0000.0000.0000.000
110A115ALA0-0.037-0.02122.5290.0000.0000.0000.0000.0000.000
111A116GLY00.0540.02624.564-0.005-0.0050.0000.0000.0000.000
112A117ASP-1-0.895-0.94926.844-0.036-0.0360.0000.0000.0000.000
113A118GLY0-0.036-0.01927.1690.0030.0030.0000.0000.0000.000
114A119ILE00.0720.04525.1350.0010.0010.0000.0000.0000.000
115A120VAL0-0.033-0.01429.0580.0020.0020.0000.0000.0000.000
116A121LYS10.8530.91630.6110.0390.0390.0000.0000.0000.000
117A122LEU00.0360.04528.8370.0030.0030.0000.0000.0000.000
118A123CYS0-0.044-0.03732.1440.0010.0010.0000.0000.0000.000
119A124LEU00.003-0.00234.7120.0020.0020.0000.0000.0000.000
120A125GLN0-0.0060.00433.1890.0040.0040.0000.0000.0000.000
121A126VAL00.006-0.00235.1540.0020.0020.0000.0000.0000.000
122A127LEU0-0.014-0.01137.9130.0020.0020.0000.0000.0000.000
123A128GLN00.000-0.00539.6490.0030.0030.0000.0000.0000.000
124A129GLN0-0.046-0.00937.7370.0020.0020.0000.0000.0000.000
125A130TYR0-0.092-0.07141.1460.0000.0000.0000.0000.0000.000
126A131GLY00.0120.01645.4080.0010.0010.0000.0000.0000.000
127A132LEU0-0.047-0.00843.4830.0010.0010.0000.0000.0000.000
128A133GLU-1-0.873-0.95844.662-0.021-0.0210.0000.0000.0000.000
129A134GLY0-0.013-0.01543.7760.0000.0000.0000.0000.0000.000
130A135GLU-1-0.850-0.92343.374-0.023-0.0230.0000.0000.0000.000
131A136ASN00.0410.00944.234-0.002-0.0020.0000.0000.0000.000
132A137ALA00.0260.03042.070-0.001-0.0010.0000.0000.0000.000
133A138LEU0-0.002-0.00538.690-0.002-0.0020.0000.0000.0000.000
134A139HIS0-0.067-0.04440.205-0.004-0.0040.0000.0000.0000.000
135A140ALA00.0490.02941.619-0.002-0.0020.0000.0000.0000.000
136A141THR0-0.059-0.03336.218-0.003-0.0030.0000.0000.0000.000
137A142ARG10.9210.96136.8030.0280.0280.0000.0000.0000.000
138A143GLY00.0410.04038.043-0.002-0.0020.0000.0000.0000.000
139A144PHE00.0480.02533.224-0.001-0.0010.0000.0000.0000.000
140A145ARG10.9730.97631.0640.0490.0490.0000.0000.0000.000
141A146SER0-0.045-0.03434.456-0.002-0.0020.0000.0000.0000.000
142A147ILE0-0.0050.00836.909-0.001-0.0010.0000.0000.0000.000
143A148CYS0-0.027-0.00532.382-0.002-0.0020.0000.0000.0000.000
144A149HIS00.001-0.00431.016-0.005-0.0050.0000.0000.0000.000
145A150GLY0-0.0070.00032.957-0.001-0.0010.0000.0000.0000.000
146A151PHE00.0260.00334.6560.0000.0000.0000.0000.0000.000
147A152ALA00.0490.02130.284-0.001-0.0010.0000.0000.0000.000
148A153SER0-0.037-0.01131.828-0.003-0.0030.0000.0000.0000.000
149A154ILE00.000-0.00232.7930.0000.0000.0000.0000.0000.000
150A155GLU-1-0.841-0.90132.033-0.076-0.0760.0000.0000.0000.000
151A156GLN0-0.034-0.01028.067-0.004-0.0040.0000.0000.0000.000
152A157GLN0-0.061-0.02731.604-0.004-0.0040.0000.0000.0000.000
153A158GLY00.0060.01734.0920.0020.0020.0000.0000.0000.000
154A159GLY0-0.036-0.02336.2550.0030.0030.0000.0000.0000.000
155A160PHE0-0.048-0.02736.7760.0030.0030.0000.0000.0000.000
156A161GLY00.0200.01240.350-0.001-0.0010.0000.0000.0000.000
157A162LEU0-0.018-0.01642.8140.0010.0010.0000.0000.0000.000
158A163PRO00.0100.02943.334-0.002-0.0020.0000.0000.0000.000
159A164LEU0-0.053-0.04243.5890.0010.0010.0000.0000.0000.000
160A165ASP-1-0.814-0.90939.768-0.060-0.0600.0000.0000.0000.000
161A166LEU00.0320.00835.4970.0020.0020.0000.0000.0000.000
162A167ASP-1-0.802-0.90334.794-0.072-0.0720.0000.0000.0000.000
163A168ILE0-0.047-0.03037.5030.0020.0020.0000.0000.0000.000
164A169SER0-0.035-0.02840.2720.0020.0020.0000.0000.0000.000
165A170LEU0-0.0200.01334.1860.0020.0020.0000.0000.0000.000
166A171HIS10.7880.86135.2930.0630.0630.0000.0000.0000.000
167A172VAL00.0650.04340.0630.0020.0020.0000.0000.0000.000
168A173LEU0-0.0090.00939.7080.0020.0020.0000.0000.0000.000
169A174LEU0-0.019-0.01736.3390.0020.0020.0000.0000.0000.000
170A175GLU-1-0.870-0.93840.929-0.037-0.0370.0000.0000.0000.000
171A176THR0-0.090-0.04244.2110.0020.0020.0000.0000.0000.000
172A177PHE00.005-0.01039.9430.0020.0020.0000.0000.0000.000
173A178ILE00.0050.00740.8840.0020.0020.0000.0000.0000.000
174A179LYS10.8260.88944.5540.0370.0370.0000.0000.0000.000
175A180GLY0-0.0170.00347.4840.0010.0010.0000.0000.0000.000
176A181LEU0-0.072-0.01642.5060.0010.0010.0000.0000.0000.000
177A182ARG10.8410.92545.4630.0350.0350.0000.0000.0000.000