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

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FMODB ID: LZG79

Calculation Name: 1ZP2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZP2

Chain ID: A

ChEMBL ID:

UniProt ID: O94503

Base Structure: X-ray

Registration Date: 2023-06-22

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2790846.043464
FMO2-HF: Nuclear repulsion 2699221.816166
FMO2-HF: Total energy -91624.227298
FMO2-MP2: Total energy -91889.203677


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:TRP)


Summations of interaction energy for fragment #1(A:6:TRP)
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.
-3.089-0.8320.116-0.488-1.8840.003
Interaction energy analysis for fragmet #1(A:6:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.018
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].
3A8SER00.0510.0183.488-3.554-1.6320.118-0.459-1.5810.003
4A9SER00.0390.0364.125-0.2110.080-0.001-0.026-0.2630.000
5A10GLN00.016-0.0035.0000.3390.383-0.001-0.003-0.0400.000
6A11LEU00.0270.0257.3240.0390.0390.0000.0000.0000.000
7A12THR00.000-0.0178.273-0.030-0.0300.0000.0000.0000.000
8A13GLN00.010-0.00310.5400.0570.0570.0000.0000.0000.000
9A14LEU0-0.090-0.03011.6300.0290.0290.0000.0000.0000.000
10A15PHE0-0.028-0.02712.4100.0460.0460.0000.0000.0000.000
11A16LEU00.0130.00815.438-0.040-0.0400.0000.0000.0000.000
12A17SER0-0.0050.00317.8500.0220.0220.0000.0000.0000.000
13A18THR0-0.079-0.04516.9620.0210.0210.0000.0000.0000.000
14A19ASP-1-0.871-0.94219.2160.0440.0440.0000.0000.0000.000
15A20LEU0-0.077-0.03022.304-0.008-0.0080.0000.0000.0000.000
16A21GLU-1-0.886-0.95324.178-0.055-0.0550.0000.0000.0000.000
17A22SER0-0.065-0.02227.1360.0000.0000.0000.0000.0000.000
18A23LEU0-0.051-0.03426.6260.0060.0060.0000.0000.0000.000
19A24GLU-1-0.964-0.98526.8980.0790.0790.0000.0000.0000.000
20A25PRO0-0.037-0.02527.099-0.004-0.0040.0000.0000.0000.000
21A26THR00.0610.05526.5400.0050.0050.0000.0000.0000.000
22A27CYS0-0.079-0.02724.3000.0020.0020.0000.0000.0000.000
23A28LEU0-0.0220.00121.5050.0000.0000.0000.0000.0000.000
24A29SER00.0330.02523.419-0.005-0.0050.0000.0000.0000.000
25A30LYS10.9460.94621.4350.1600.1600.0000.0000.0000.000
26A31ASP-1-0.833-0.89526.355-0.060-0.0600.0000.0000.0000.000
27A32THR0-0.097-0.02627.6090.0090.0090.0000.0000.0000.000
28A33ILE00.1170.03823.6240.0060.0060.0000.0000.0000.000
29A34TYR0-0.014-0.00128.2980.0030.0030.0000.0000.0000.000
30A35GLN00.032-0.00331.0880.0100.0100.0000.0000.0000.000
31A36TRP00.0140.00430.1790.0030.0030.0000.0000.0000.000
32A37LYS10.9630.99327.7730.0350.0350.0000.0000.0000.000
33A38VAL0-0.0320.00333.4580.0010.0010.0000.0000.0000.000
34A39VAL0-0.030-0.02936.4660.0020.0020.0000.0000.0000.000
35A40GLN00.0120.00132.486-0.002-0.0020.0000.0000.0000.000
36A41THR0-0.0040.00136.6790.0000.0000.0000.0000.0000.000
37A42PHE0-0.030-0.02338.8650.0020.0020.0000.0000.0000.000
38A43GLY00.012-0.00240.6840.0020.0020.0000.0000.0000.000
39A44ASP-1-0.903-0.95838.2190.0010.0010.0000.0000.0000.000
40A45ARG10.7530.89641.7740.0170.0170.0000.0000.0000.000
41A46LEU0-0.079-0.03444.7490.0010.0010.0000.0000.0000.000
42A47ARG10.9210.95544.5820.0040.0040.0000.0000.0000.000
43A48LEU00.0150.02743.6060.0030.0030.0000.0000.0000.000
44A49ARG10.9500.97942.620-0.025-0.0250.0000.0000.0000.000
45A50GLN00.0950.02534.889-0.006-0.0060.0000.0000.0000.000
46A51ARG10.8420.89338.889-0.031-0.0310.0000.0000.0000.000
47A52VAL00.0240.01540.9130.0000.0000.0000.0000.0000.000
48A53LEU00.0290.04938.074-0.002-0.0020.0000.0000.0000.000
49A54ALA00.0490.03136.710-0.002-0.0020.0000.0000.0000.000
50A55THR0-0.010-0.03637.7020.0010.0010.0000.0000.0000.000
51A56ALA00.0190.01640.551-0.001-0.0010.0000.0000.0000.000
52A57ILE0-0.025-0.01234.051-0.003-0.0030.0000.0000.0000.000
53A58VAL00.001-0.01135.507-0.001-0.0010.0000.0000.0000.000
54A59LEU0-0.034-0.01137.456-0.001-0.0010.0000.0000.0000.000
55A60LEU00.0350.01437.426-0.002-0.0020.0000.0000.0000.000
56A61ARG10.7490.86931.502-0.004-0.0040.0000.0000.0000.000
57A62ARG10.8780.92936.216-0.029-0.0290.0000.0000.0000.000
58A63TYR0-0.069-0.06138.599-0.002-0.0020.0000.0000.0000.000
59A64MET0-0.026-0.01636.390-0.004-0.0040.0000.0000.0000.000
60A65LEU0-0.0050.01234.593-0.002-0.0020.0000.0000.0000.000
61A66LYS10.8250.90737.304-0.013-0.0130.0000.0000.0000.000
62A67LYS10.7930.88038.8850.0230.0230.0000.0000.0000.000
63A68ASN00.0180.00640.418-0.002-0.0020.0000.0000.0000.000
64A69GLU-1-0.870-0.93642.358-0.014-0.0140.0000.0000.0000.000
65A70GLU-1-0.887-0.93039.737-0.036-0.0360.0000.0000.0000.000
66A71LYS10.8450.92643.5520.0120.0120.0000.0000.0000.000
67A72GLY0-0.018-0.00245.0190.0000.0000.0000.0000.0000.000
68A73PHE00.0070.00344.8170.0000.0000.0000.0000.0000.000
69A74SER0-0.028-0.03843.0110.0000.0000.0000.0000.0000.000
70A75LEU00.0700.03736.1210.0040.0040.0000.0000.0000.000
71A76GLU-1-0.828-0.88940.316-0.034-0.0340.0000.0000.0000.000
72A77ALA00.0280.01342.4760.0040.0040.0000.0000.0000.000
73A78LEU00.0000.01140.7380.0040.0040.0000.0000.0000.000
74A79VAL00.0240.02538.8970.0040.0040.0000.0000.0000.000
75A80ALA0-0.005-0.01141.9040.0030.0030.0000.0000.0000.000
76A81THR0-0.031-0.02945.3960.0030.0030.0000.0000.0000.000
77A82CYS0-0.059-0.02642.0880.0030.0030.0000.0000.0000.000
78A83ILE00.0230.02041.5050.0040.0040.0000.0000.0000.000
79A84TYR0-0.007-0.01144.7940.0030.0030.0000.0000.0000.000
80A85LEU0-0.007-0.00946.3980.0020.0020.0000.0000.0000.000
81A86SER00.003-0.01143.0240.0030.0030.0000.0000.0000.000
82A87CYS0-0.058-0.01845.8250.0020.0020.0000.0000.0000.000
83A88LYS10.7800.87148.393-0.004-0.0040.0000.0000.0000.000
84A89VAL00.0140.00546.9310.0010.0010.0000.0000.0000.000
85A90GLU-1-0.831-0.85144.1310.0310.0310.0000.0000.0000.000
86A91GLU-1-0.938-0.97447.7670.0240.0240.0000.0000.0000.000
87A92CYS0-0.115-0.05348.4160.0010.0010.0000.0000.0000.000
88A93PRO00.0090.00750.267-0.002-0.0020.0000.0000.0000.000
89A94VAL00.0480.01449.5940.0000.0000.0000.0000.0000.000
90A95HIS0-0.049-0.02952.578-0.002-0.0020.0000.0000.0000.000
91A96ILE00.0690.02654.057-0.001-0.0010.0000.0000.0000.000
92A97ARG10.9480.97253.9640.0040.0040.0000.0000.0000.000
93A98THR00.000-0.00852.127-0.002-0.0020.0000.0000.0000.000
94A99ILE00.0680.04748.643-0.001-0.0010.0000.0000.0000.000
95A100CYS0-0.026-0.00749.985-0.002-0.0020.0000.0000.0000.000
96A101ASN0-0.044-0.01451.698-0.002-0.0020.0000.0000.0000.000
97A102GLU-1-0.756-0.87448.267-0.015-0.0150.0000.0000.0000.000
98A103ALA00.0200.01547.056-0.002-0.0020.0000.0000.0000.000
99A104ASN0-0.036-0.03647.357-0.004-0.0040.0000.0000.0000.000
100A105ASP-1-0.965-0.98349.430-0.021-0.0210.0000.0000.0000.000
101A106LEU0-0.053-0.01442.4450.0000.0000.0000.0000.0000.000
102A107TRP0-0.003-0.01040.869-0.002-0.0020.0000.0000.0000.000
103A108SER00.0060.01145.6140.0010.0010.0000.0000.0000.000
104A109LEU0-0.004-0.00645.016-0.003-0.0030.0000.0000.0000.000
105A110LYS10.9220.95545.7190.0520.0520.0000.0000.0000.000
106A111VAL00.0130.00149.4210.0010.0010.0000.0000.0000.000
107A112LYS10.9500.99250.3120.0210.0210.0000.0000.0000.000
108A113LEU00.0290.02147.4540.0010.0010.0000.0000.0000.000
109A114SER0-0.019-0.03952.0610.0020.0020.0000.0000.0000.000
110A115ARG10.9720.96254.4890.0060.0060.0000.0000.0000.000
111A116SER0-0.015-0.01755.6960.0010.0010.0000.0000.0000.000
112A117ASN00.0640.06051.9550.0000.0000.0000.0000.0000.000
113A118ILE00.0820.02849.9640.0000.0000.0000.0000.0000.000
114A119SER0-0.027-0.00251.4000.0020.0020.0000.0000.0000.000
115A120GLU-1-0.904-0.94052.920-0.013-0.0130.0000.0000.0000.000
116A121ILE00.0170.01146.8250.0010.0010.0000.0000.0000.000
117A122GLU-1-0.818-0.89848.9300.0040.0040.0000.0000.0000.000
118A123PHE0-0.023-0.00650.0740.0020.0020.0000.0000.0000.000
119A124GLU-1-0.784-0.86646.976-0.008-0.0080.0000.0000.0000.000
120A125ILE0-0.014-0.01044.6610.0010.0010.0000.0000.0000.000
121A126ILE0-0.018-0.01546.9790.0020.0020.0000.0000.0000.000
122A127SER0-0.001-0.00249.3110.0020.0020.0000.0000.0000.000
123A128VAL0-0.0040.01044.3920.0020.0020.0000.0000.0000.000
124A129LEU0-0.073-0.03742.1920.0020.0020.0000.0000.0000.000
125A130ASP-1-0.842-0.91345.9340.0160.0160.0000.0000.0000.000
126A131ALA0-0.065-0.03949.1750.0020.0020.0000.0000.0000.000
127A132PHE0-0.034-0.00645.2750.0020.0020.0000.0000.0000.000
128A133LEU0-0.030-0.03145.0880.0000.0000.0000.0000.0000.000
129A134ILE00.0160.01744.8520.0000.0000.0000.0000.0000.000
130A135VAL0-0.007-0.00639.0720.0010.0010.0000.0000.0000.000
131A136HIS0-0.0120.01739.8200.0010.0010.0000.0000.0000.000
132A137HIS00.0550.01936.8380.0040.0040.0000.0000.0000.000
133A138PRO0-0.018-0.00632.6690.0020.0020.0000.0000.0000.000
134A139TYR0-0.002-0.03034.8440.0030.0030.0000.0000.0000.000
135A140THR00.0240.01037.1680.0020.0020.0000.0000.0000.000
136A141SER00.0250.01135.6200.0010.0010.0000.0000.0000.000
137A142LEU0-0.0320.00332.0270.0040.0040.0000.0000.0000.000
138A143GLU-1-0.871-0.93735.9830.0660.0660.0000.0000.0000.000
139A144GLN0-0.024-0.01539.395-0.003-0.0030.0000.0000.0000.000
140A145ALA00.0340.01435.7570.0020.0020.0000.0000.0000.000
141A146PHE0-0.071-0.03937.6800.0030.0030.0000.0000.0000.000
142A147HIS0-0.058-0.02938.850-0.001-0.0010.0000.0000.0000.000
143A148ASP-1-0.919-0.94340.4360.0840.0840.0000.0000.0000.000
144A149GLY0-0.026-0.01540.4910.0040.0040.0000.0000.0000.000
145A150ILE0-0.073-0.03234.7280.0070.0070.0000.0000.0000.000
146A151ILE00.0050.00232.8040.0100.0100.0000.0000.0000.000
147A152ASN00.0160.00433.339-0.011-0.0110.0000.0000.0000.000
148A153GLN00.057-0.00135.385-0.001-0.0010.0000.0000.0000.000
149A154LYS10.9770.99028.904-0.121-0.1210.0000.0000.0000.000
150A155GLN0-0.002-0.01830.094-0.010-0.0100.0000.0000.0000.000
151A156LEU00.0300.02231.1710.0000.0000.0000.0000.0000.000
152A157GLU-1-0.923-0.96431.9870.0680.0680.0000.0000.0000.000
153A158PHE00.0440.03623.544-0.004-0.0040.0000.0000.0000.000
154A159ALA00.033-0.00228.685-0.002-0.0020.0000.0000.0000.000
155A160TRP0-0.018-0.02829.719-0.004-0.0040.0000.0000.0000.000
156A161SER0-0.034-0.01429.475-0.010-0.0100.0000.0000.0000.000
157A162ILE00.0510.04524.922-0.007-0.0070.0000.0000.0000.000
158A163VAL0-0.0050.00327.725-0.006-0.0060.0000.0000.0000.000
159A164ASN00.0120.03230.438-0.005-0.0050.0000.0000.0000.000
160A165ASP-1-0.773-0.86126.6890.0290.0290.0000.0000.0000.000
161A166SER0-0.080-0.05527.030-0.006-0.0060.0000.0000.0000.000
162A167TYR0-0.067-0.04728.077-0.002-0.0020.0000.0000.0000.000
163A168ALA00.0700.03127.266-0.008-0.0080.0000.0000.0000.000
164A169SER00.017-0.01625.574-0.006-0.0060.0000.0000.0000.000
165A170SER0-0.034-0.02927.139-0.002-0.0020.0000.0000.0000.000
166A171LEU00.1180.05225.1960.0020.0020.0000.0000.0000.000
167A172CYS0-0.062-0.01328.9300.0030.0030.0000.0000.0000.000
168A173LEU0-0.032-0.01231.816-0.001-0.0010.0000.0000.0000.000
169A174MET0-0.048-0.01225.419-0.002-0.0020.0000.0000.0000.000
170A175ALA00.0180.00829.3130.0110.0110.0000.0000.0000.000
171A176HIS00.0180.02631.455-0.010-0.0100.0000.0000.0000.000
172A177PRO00.0370.00033.1560.0080.0080.0000.0000.0000.000
173A178HIS00.016-0.00533.707-0.003-0.0030.0000.0000.0000.000
174A179GLN0-0.026-0.02930.1860.0040.0040.0000.0000.0000.000
175A180LEU00.0320.00827.9920.0110.0110.0000.0000.0000.000
176A181ALA0-0.003-0.00428.9970.0050.0050.0000.0000.0000.000
177A182TYR0-0.007-0.00929.8720.0020.0020.0000.0000.0000.000
178A183ALA00.0170.02425.0650.0120.0120.0000.0000.0000.000
179A184ALA00.0150.01125.6840.0120.0120.0000.0000.0000.000
180A185LEU0-0.007-0.01627.0600.0030.0030.0000.0000.0000.000
181A186LEU0-0.032-0.01724.7660.0070.0070.0000.0000.0000.000
182A187ILE00.000-0.00821.5280.0150.0150.0000.0000.0000.000
183A188SER0-0.053-0.02423.5650.0110.0110.0000.0000.0000.000
184A189CYS0-0.049-0.02125.8560.0000.0000.0000.0000.0000.000
185A190CYS0-0.047-0.01621.9790.0140.0140.0000.0000.0000.000
186A191ASN00.001-0.01021.7900.0410.0410.0000.0000.0000.000
187A192ASP-1-0.915-0.94124.6370.1740.1740.0000.0000.0000.000
188A193GLU-1-0.898-0.95927.9080.2530.2530.0000.0000.0000.000
189A194ASN0-0.050-0.02228.807-0.002-0.0020.0000.0000.0000.000
190A195THR0-0.006-0.01430.546-0.003-0.0030.0000.0000.0000.000
191A196ILE00.0400.03424.979-0.007-0.0070.0000.0000.0000.000
192A197PRO00.0090.00429.338-0.005-0.0050.0000.0000.0000.000
193A198LYS10.9330.97931.555-0.136-0.1360.0000.0000.0000.000
194A199LEU0-0.035-0.01929.345-0.008-0.0080.0000.0000.0000.000
195A200LEU0-0.055-0.04326.841-0.002-0.0020.0000.0000.0000.000
196A201ASP-1-0.896-0.92730.9520.1490.1490.0000.0000.0000.000
197A202LEU0-0.072-0.03734.074-0.007-0.0070.0000.0000.0000.000
198A203ILE0-0.064-0.01728.475-0.007-0.0070.0000.0000.0000.000
199A204LYS11.0231.03032.546-0.100-0.1000.0000.0000.0000.000
200A205SER00.0400.00731.1140.0000.0000.0000.0000.0000.000
201A206THR0-0.027-0.02031.2540.0040.0040.0000.0000.0000.000
202A207ASP-1-0.821-0.90331.4010.1120.1120.0000.0000.0000.000
203A208ALA00.0000.00427.5040.0030.0030.0000.0000.0000.000
204A209PHE00.0440.02623.2930.0090.0090.0000.0000.0000.000
205A210LYS10.9520.97925.265-0.091-0.0910.0000.0000.0000.000
206A211VAL00.0380.03125.819-0.004-0.0040.0000.0000.0000.000
207A212ILE00.0120.00320.7330.0030.0030.0000.0000.0000.000
208A213LEU0-0.019-0.01321.9020.0030.0030.0000.0000.0000.000
209A214CYS0-0.088-0.05422.763-0.015-0.0150.0000.0000.0000.000
210A215VAL00.0300.00119.596-0.009-0.0090.0000.0000.0000.000
211A216GLN00.0190.03417.225-0.033-0.0330.0000.0000.0000.000
212A217ARG10.9070.92919.073-0.108-0.1080.0000.0000.0000.000
213A218ILE00.0250.01121.313-0.019-0.0190.0000.0000.0000.000
214A219ILE00.0190.01315.645-0.012-0.0120.0000.0000.0000.000
215A220SER0-0.005-0.01016.902-0.020-0.0200.0000.0000.0000.000
216A221ILE0-0.065-0.03417.916-0.031-0.0310.0000.0000.0000.000
217A222TYR0-0.025-0.05219.482-0.011-0.0110.0000.0000.0000.000
218A223TYR0-0.078-0.02914.3170.0080.0080.0000.0000.0000.000
219A224PHE0-0.026-0.02016.059-0.041-0.0410.0000.0000.0000.000
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