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: L7NK9

Calculation Name: 2ZB9-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ZB9

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9RK47

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 OptAll
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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1909615.557661
FMO2-HF: Nuclear repulsion 1838029.400764
FMO2-HF: Total energy -71586.156898
FMO2-MP2: Total energy -71799.491396


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:17:GLY)


Summations of interaction energy for fragment #1(A:17:GLY)
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.
-0.732.192-0.015-1.622-1.2840.002
Interaction energy analysis for fragmet #1(A:17:GLY)
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 : 0.026
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].
3A19ARG10.8350.9103.8680.0672.827-0.013-1.588-1.1590.002
4A20PRO00.1090.0564.616-0.109-0.047-0.001-0.004-0.0560.000
5A21ALA0-0.017-0.0144.3080.0620.162-0.001-0.030-0.0690.000
6A22GLU-1-0.843-0.9086.307-1.281-1.2810.0000.0000.0000.000
7A23GLU-1-0.823-0.9108.538-0.457-0.4570.0000.0000.0000.000
8A24VAL00.0580.0279.5940.1220.1220.0000.0000.0000.000
9A25ARG10.7440.8689.8241.2371.2370.0000.0000.0000.000
10A26ALA00.0230.00511.6150.1570.1570.0000.0000.0000.000
11A27GLU-1-0.910-0.94714.257-0.417-0.4170.0000.0000.0000.000
12A28VAL0-0.036-0.02914.0860.0810.0810.0000.0000.0000.000
13A29LEU0-0.057-0.02215.5360.0650.0650.0000.0000.0000.000
14A30HIS00.000-0.00117.4740.0390.0390.0000.0000.0000.000
15A31ALA00.0250.01119.5540.0440.0440.0000.0000.0000.000
16A32VAL0-0.086-0.04419.0660.0420.0420.0000.0000.0000.000
17A33GLY00.0340.01821.7190.0340.0340.0000.0000.0000.000
18A34GLU-1-0.881-0.93523.714-0.243-0.2430.0000.0000.0000.000
19A35LEU00.0110.02424.7740.0260.0260.0000.0000.0000.000
20A36LEU0-0.059-0.02525.2290.0230.0230.0000.0000.0000.000
21A37LEU0-0.006-0.02326.9080.0190.0190.0000.0000.0000.000
22A38THR0-0.078-0.04529.1970.0180.0180.0000.0000.0000.000
23A39GLU-1-0.798-0.86130.289-0.161-0.1610.0000.0000.0000.000
24A40GLY00.0160.02730.7750.0090.0090.0000.0000.0000.000
25A41THR00.011-0.01528.464-0.004-0.0040.0000.0000.0000.000
26A42ALA0-0.0030.00829.368-0.008-0.0080.0000.0000.0000.000
27A43GLN00.006-0.00630.2490.0010.0010.0000.0000.0000.000
28A44LEU00.0000.02822.816-0.003-0.0030.0000.0000.0000.000
29A45THR00.009-0.00425.0960.0020.0020.0000.0000.0000.000
30A46PHE00.0310.00818.4070.0000.0000.0000.0000.0000.000
31A47GLU-1-0.779-0.88121.331-0.223-0.2230.0000.0000.0000.000
32A48ARG10.7940.88423.5870.1970.1970.0000.0000.0000.000
33A49VAL00.0750.02818.8780.0030.0030.0000.0000.0000.000
34A50ALA00.0050.02118.882-0.019-0.0190.0000.0000.0000.000
35A51ARG10.8990.94719.9110.1760.1760.0000.0000.0000.000
36A52VAL0-0.035-0.01522.4400.0180.0180.0000.0000.0000.000
37A53SER00.023-0.00317.262-0.014-0.0140.0000.0000.0000.000
38A54GLY00.0100.01917.775-0.014-0.0140.0000.0000.0000.000
39A55VAL0-0.028-0.00112.9110.0050.0050.0000.0000.0000.000
40A56SER00.0360.01214.060-0.001-0.0010.0000.0000.0000.000
41A57LYS10.9310.93115.1610.1570.1570.0000.0000.0000.000
42A58THR0-0.033-0.01514.454-0.035-0.0350.0000.0000.0000.000
43A59THR0-0.053-0.0209.718-0.019-0.0190.0000.0000.0000.000
44A60LEU00.0570.02512.383-0.095-0.0950.0000.0000.0000.000
45A61TYR00.003-0.01314.926-0.015-0.0150.0000.0000.0000.000
46A62LYS10.8630.9419.9400.5350.5350.0000.0000.0000.000
47A63TRP0-0.0130.0007.2180.0400.0400.0000.0000.0000.000
48A64TRP0-0.005-0.00812.751-0.008-0.0080.0000.0000.0000.000
49A65PRO00.0220.01715.9670.0510.0510.0000.0000.0000.000
50A66SER00.0290.00818.3390.0450.0450.0000.0000.0000.000
51A67LYS10.8730.92921.3860.1990.1990.0000.0000.0000.000
52A68GLY00.0560.02823.897-0.003-0.0030.0000.0000.0000.000
53A69ALA00.0220.00219.013-0.009-0.0090.0000.0000.0000.000
54A70LEU0-0.029-0.01518.572-0.035-0.0350.0000.0000.0000.000
55A71ALA00.007-0.00420.412-0.012-0.0120.0000.0000.0000.000
56A72LEU00.0130.00922.9280.0050.0050.0000.0000.0000.000
57A73ASP-1-0.691-0.82116.463-0.715-0.7150.0000.0000.0000.000
58A74GLY00.0300.00420.119-0.013-0.0130.0000.0000.0000.000
59A75TYR00.0160.00321.2290.0180.0180.0000.0000.0000.000
60A76PHE0-0.009-0.01320.9240.0230.0230.0000.0000.0000.000
61A77HIS10.8050.88718.0810.5700.5700.0000.0000.0000.000
62A78ALA0-0.0030.02621.3730.0010.0010.0000.0000.0000.000
63A79VAL0-0.064-0.03524.5000.0280.0280.0000.0000.0000.000
64A80GLU-1-0.893-0.94920.233-0.447-0.4470.0000.0000.0000.000
65A81ASP-1-0.885-0.94523.288-0.310-0.3100.0000.0000.0000.000
66A82THR0-0.029-0.02125.8620.0240.0240.0000.0000.0000.000
67A83LEU0-0.042-0.00428.1100.0210.0210.0000.0000.0000.000
68A84ALA00.0360.03626.782-0.002-0.0020.0000.0000.0000.000
69A85PHE0-0.010-0.01428.1950.0160.0160.0000.0000.0000.000
70A86PRO0-0.039-0.00630.292-0.002-0.0020.0000.0000.0000.000
71A87ASP-1-0.833-0.92431.542-0.142-0.1420.0000.0000.0000.000
72A88THR0-0.056-0.05733.4800.0060.0060.0000.0000.0000.000
73A89GLY00.0250.02236.5100.0060.0060.0000.0000.0000.000
74A90ASP-1-0.855-0.91838.423-0.087-0.0870.0000.0000.0000.000
75A91VAL00.0400.02037.685-0.005-0.0050.0000.0000.0000.000
76A92ARG10.8040.86539.2250.0770.0770.0000.0000.0000.000
77A93ALA00.005-0.00240.783-0.003-0.0030.0000.0000.0000.000
78A94ASP-1-0.766-0.84635.675-0.131-0.1310.0000.0000.0000.000
79A95LEU00.011-0.00636.322-0.009-0.0090.0000.0000.0000.000
80A96LEU0-0.019-0.00538.162-0.003-0.0030.0000.0000.0000.000
81A97ALA0-0.027-0.00736.894-0.001-0.0010.0000.0000.0000.000
82A98GLN00.0120.01131.2060.0030.0030.0000.0000.0000.000
83A99LEU00.0380.01135.314-0.006-0.0060.0000.0000.0000.000
84A100ARG10.8200.89037.7010.1030.1030.0000.0000.0000.000
85A101ALA00.0150.01633.7860.0000.0000.0000.0000.0000.000
86A102PHE0-0.009-0.02032.825-0.006-0.0060.0000.0000.0000.000
87A103THR00.0450.00234.881-0.001-0.0010.0000.0000.0000.000
88A104HIS0-0.0200.00935.5600.0080.0080.0000.0000.0000.000
89A105VAL00.006-0.01131.1510.0010.0010.0000.0000.0000.000
90A106MET0-0.034-0.01133.887-0.008-0.0080.0000.0000.0000.000
91A107THR0-0.042-0.02936.3170.0090.0090.0000.0000.0000.000
92A108ARG10.8660.93738.3500.1200.1200.0000.0000.0000.000
93A109THR0-0.006-0.00633.030-0.005-0.0050.0000.0000.0000.000
94A110PRO00.0150.00933.0050.0010.0010.0000.0000.0000.000
95A111GLY00.0420.01731.592-0.002-0.0020.0000.0000.0000.000
96A112GLY00.0660.04532.493-0.004-0.0040.0000.0000.0000.000
97A113ARG10.7970.88432.2090.1680.1680.0000.0000.0000.000
98A114ILE0-0.067-0.03629.084-0.001-0.0010.0000.0000.0000.000
99A115LEU0-0.011-0.00428.891-0.004-0.0040.0000.0000.0000.000
100A116THR00.007-0.01631.8630.0020.0020.0000.0000.0000.000
101A117GLU-1-0.770-0.85034.284-0.147-0.1470.0000.0000.0000.000
102A118LEU0-0.075-0.03027.833-0.002-0.0020.0000.0000.0000.000
103A119ILE0-0.0020.00531.563-0.002-0.0020.0000.0000.0000.000
104A120GLY00.0340.01933.3850.0060.0060.0000.0000.0000.000
105A121ALA0-0.005-0.01132.4120.0050.0050.0000.0000.0000.000
106A122ALA0-0.033-0.01730.7070.0020.0020.0000.0000.0000.000
107A123GLN0-0.061-0.03232.3160.0080.0080.0000.0000.0000.000
108A124THR0-0.040-0.02034.9600.0100.0100.0000.0000.0000.000
109A125ASP-1-0.868-0.91929.410-0.191-0.1910.0000.0000.0000.000
110A126ALA00.0640.02430.363-0.010-0.0100.0000.0000.0000.000
111A127ASP-1-0.905-0.93625.386-0.217-0.2170.0000.0000.0000.000
112A128LEU0-0.045-0.01825.463-0.030-0.0300.0000.0000.0000.000
113A129ALA00.0400.01026.860-0.016-0.0160.0000.0000.0000.000
114A130THR0-0.073-0.05023.482-0.001-0.0010.0000.0000.0000.000
115A131ALA00.0190.00722.392-0.020-0.0200.0000.0000.0000.000
116A132TYR00.0220.00723.317-0.024-0.0240.0000.0000.0000.000
117A133ARG10.8770.96025.7540.2130.2130.0000.0000.0000.000
118A134GLN0-0.023-0.03020.091-0.012-0.0120.0000.0000.0000.000
119A135LEU0-0.032-0.00317.688-0.035-0.0350.0000.0000.0000.000
120A136TYR00.0450.01521.122-0.005-0.0050.0000.0000.0000.000
121A137SER0-0.004-0.00824.3850.0090.0090.0000.0000.0000.000
122A138ALA0-0.010-0.00323.9830.0160.0160.0000.0000.0000.000
123A139GLN00.0220.00918.8360.0110.0110.0000.0000.0000.000
124A140ARG10.8920.93623.8960.2670.2670.0000.0000.0000.000
125A141ARG10.8040.87127.1680.1790.1790.0000.0000.0000.000
126A142ALA0-0.018-0.00124.8320.0140.0140.0000.0000.0000.000
127A143LEU00.0210.00023.1670.0130.0130.0000.0000.0000.000
128A144ALA00.0210.01527.0760.0130.0130.0000.0000.0000.000
129A145ALA0-0.016-0.01929.8480.0140.0140.0000.0000.0000.000
130A146GLU-1-0.848-0.89825.598-0.200-0.2000.0000.0000.0000.000
131A147ARG10.8260.92829.4510.1480.1480.0000.0000.0000.000
132A148LEU0-0.002-0.01332.0080.0120.0120.0000.0000.0000.000
133A149ARG10.7910.88028.3390.1750.1750.0000.0000.0000.000
134A150HIS0-0.025-0.01831.7550.0160.0160.0000.0000.0000.000
135A151ALA00.012-0.00433.7690.0090.0090.0000.0000.0000.000
136A152ARG10.8360.92136.2210.1110.1110.0000.0000.0000.000
137A153GLU-1-0.936-0.97132.843-0.121-0.1210.0000.0000.0000.000
138A154LEU0-0.046-0.01536.2020.0070.0070.0000.0000.0000.000
139A155GLY0-0.038-0.01339.0480.0050.0050.0000.0000.0000.000
140A156GLN0-0.064-0.04839.910-0.001-0.0010.0000.0000.0000.000
141A157ILE0-0.004-0.00138.490-0.001-0.0010.0000.0000.0000.000
142A158ARG10.8720.91642.1470.0750.0750.0000.0000.0000.000
143A159PRO00.0500.01141.178-0.004-0.0040.0000.0000.0000.000
144A160ASP-1-0.857-0.91340.922-0.076-0.0760.0000.0000.0000.000
145A161VAL0-0.0110.00340.535-0.001-0.0010.0000.0000.0000.000
146A162ASP-1-0.813-0.91036.431-0.127-0.1270.0000.0000.0000.000
147A163VAL00.0110.00333.3170.0010.0010.0000.0000.0000.000
148A164GLN00.0130.00430.586-0.007-0.0070.0000.0000.0000.000
149A165VAL00.0070.00435.230-0.002-0.0020.0000.0000.0000.000
150A166LEU00.0130.01137.7810.0010.0010.0000.0000.0000.000
151A167VAL0-0.019-0.01132.568-0.002-0.0020.0000.0000.0000.000
152A168ASP-1-0.846-0.90235.945-0.145-0.1450.0000.0000.0000.000
153A169GLN0-0.004-0.01537.9100.0020.0020.0000.0000.0000.000
154A170LEU00.0130.02837.9730.0040.0040.0000.0000.0000.000
155A171TRP00.010-0.01434.3680.0020.0020.0000.0000.0000.000
156A172GLY0-0.0060.00536.826-0.002-0.0020.0000.0000.0000.000
157A173ALA00.0260.01737.8730.0030.0030.0000.0000.0000.000
158A174VAL0-0.009-0.00538.5720.0040.0040.0000.0000.0000.000
159A175TYR0-0.003-0.02331.954-0.005-0.0050.0000.0000.0000.000
160A176HIS00.0050.01038.199-0.002-0.0020.0000.0000.0000.000
161A177ARG10.8080.89441.3530.0930.0930.0000.0000.0000.000
162A178LEU0-0.041-0.01637.5440.0010.0010.0000.0000.0000.000
163A179LEU0-0.053-0.03136.687-0.002-0.0020.0000.0000.0000.000
164A180ILE0-0.036-0.01040.8420.0030.0030.0000.0000.0000.000
165A181PRO0-0.0150.01244.1210.0020.0020.0000.0000.0000.000
166A182ASP-1-0.929-0.97246.325-0.081-0.0810.0000.0000.0000.000
167A183GLU-1-0.903-0.94148.498-0.074-0.0740.0000.0000.0000.000
168A184PRO0-0.027-0.01147.647-0.005-0.0050.0000.0000.0000.000
169A185VAL00.0240.01741.4490.0000.0000.0000.0000.0000.000
170A186ASP-1-0.869-0.94544.728-0.091-0.0910.0000.0000.0000.000
171A187ASP-1-0.751-0.85244.352-0.101-0.1010.0000.0000.0000.000
172A188ALA00.0000.02145.6900.0000.0000.0000.0000.0000.000
173A189PHE00.008-0.00242.9830.0000.0000.0000.0000.0000.000
174A190VAL00.002-0.00541.325-0.001-0.0010.0000.0000.0000.000
175A191THR0-0.034-0.03943.793-0.001-0.0010.0000.0000.0000.000
176A192ALA0-0.0050.00545.9480.0010.0010.0000.0000.0000.000
177A193LEU0-0.047-0.01542.0590.0010.0010.0000.0000.0000.000
178A194VAL00.0080.01141.478-0.001-0.0010.0000.0000.0000.000
179A195THR00.0380.00944.1150.0010.0010.0000.0000.0000.000
180A196ASN0-0.041-0.02847.7650.0040.0040.0000.0000.0000.000
181A197LEU0-0.051-0.01742.0610.0020.0020.0000.0000.0000.000
182A198LEU0-0.038-0.01741.9530.0000.0000.0000.0000.0000.000
183A199ASP-1-0.847-0.87745.947-0.073-0.0730.0000.0000.0000.000
184A200GLY0-0.0230.00749.5200.0030.0030.0000.0000.0000.000
185A201VAL00.003-0.01250.8180.0000.0000.0000.0000.0000.000
186A202CYS0-0.042-0.01853.4580.0020.0020.0000.0000.0000.000
187A203PRO00.0450.02356.5180.0000.0000.0000.0000.0000.000
188A204ARG10.9330.97357.0460.0480.0480.0000.0000.0000.000