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: 39Z7L

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2792002.253922
FMO2-HF: Nuclear repulsion 2700379.905808
FMO2-HF: Total energy -91622.348114
FMO2-MP2: Total energy -91887.548104


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.
-2.144-1.1070.2520.765-2.0530.004
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 : -0.002 / q_NPA : -0.012
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].
3A8SER00.0490.0173.194-2.517-1.8150.2540.793-1.7490.004
4A9SER00.0210.0144.266-0.2450.028-0.001-0.025-0.2470.000
5A10GLN00.002-0.0055.0100.2600.322-0.001-0.003-0.0570.000
6A11LEU00.0310.0267.3520.0110.0110.0000.0000.0000.000
7A12THR00.0180.0038.544-0.052-0.0520.0000.0000.0000.000
8A13GLN00.012-0.00810.5470.0300.0300.0000.0000.0000.000
9A14LEU0-0.089-0.02811.6520.0210.0210.0000.0000.0000.000
10A15PHE0-0.014-0.01712.8570.0340.0340.0000.0000.0000.000
11A16LEU00.0020.00615.454-0.044-0.0440.0000.0000.0000.000
12A17SER00.0100.02217.8660.0240.0240.0000.0000.0000.000
13A18THR0-0.067-0.04317.1610.0260.0260.0000.0000.0000.000
14A19ASP-1-0.886-0.94819.2410.0800.0800.0000.0000.0000.000
15A20LEU0-0.080-0.03322.324-0.011-0.0110.0000.0000.0000.000
16A21GLU-1-0.931-0.98224.196-0.033-0.0330.0000.0000.0000.000
17A22SER0-0.053-0.01927.152-0.001-0.0010.0000.0000.0000.000
18A23LEU0-0.046-0.03426.8480.0040.0040.0000.0000.0000.000
19A24GLU-1-0.967-0.98326.9230.1030.1030.0000.0000.0000.000
20A25PRO0-0.019-0.02027.122-0.003-0.0030.0000.0000.0000.000
21A26THR00.0580.05826.6010.0050.0050.0000.0000.0000.000
22A27CYS0-0.065-0.03324.2630.0020.0020.0000.0000.0000.000
23A28LEU0-0.0140.00421.3250.0010.0010.0000.0000.0000.000
24A29SER00.0610.05723.423-0.006-0.0060.0000.0000.0000.000
25A30LYS11.0490.98922.7500.1170.1170.0000.0000.0000.000
26A31ASP-1-0.886-0.93226.347-0.040-0.0400.0000.0000.0000.000
27A32THR0-0.108-0.01527.5090.0080.0080.0000.0000.0000.000
28A33ILE00.0920.01723.7670.0040.0040.0000.0000.0000.000
29A34TYR0-0.0210.00028.2930.0010.0010.0000.0000.0000.000
30A35GLN00.024-0.02031.0790.0080.0080.0000.0000.0000.000
31A36TRP00.0240.00830.1710.0020.0020.0000.0000.0000.000
32A37LYS11.0331.02528.8210.0180.0180.0000.0000.0000.000
33A38VAL0-0.033-0.01033.4480.0000.0000.0000.0000.0000.000
34A39VAL0-0.031-0.03236.4560.0010.0010.0000.0000.0000.000
35A40GLN00.007-0.00332.358-0.003-0.0030.0000.0000.0000.000
36A41THR00.0170.02236.714-0.001-0.0010.0000.0000.0000.000
37A42PHE0-0.047-0.02938.8520.0010.0010.0000.0000.0000.000
38A43GLY00.017-0.00240.6740.0010.0010.0000.0000.0000.000
39A44ASP-1-0.900-0.96238.2740.0110.0110.0000.0000.0000.000
40A45ARG10.8140.94441.7630.0090.0090.0000.0000.0000.000
41A46LEU0-0.085-0.03544.7360.0000.0000.0000.0000.0000.000
42A47ARG10.9230.95744.583-0.004-0.0040.0000.0000.0000.000
43A48LEU00.0160.02543.5240.0020.0020.0000.0000.0000.000
44A49ARG10.9480.98142.616-0.034-0.0340.0000.0000.0000.000
45A50GLN00.0860.01334.695-0.006-0.0060.0000.0000.0000.000
46A51ARG10.8390.89838.891-0.039-0.0390.0000.0000.0000.000
47A52VAL00.0290.01640.9170.0010.0010.0000.0000.0000.000
48A53LEU00.0360.04838.126-0.001-0.0010.0000.0000.0000.000
49A54ALA00.0520.03236.705-0.002-0.0020.0000.0000.0000.000
50A55THR0-0.019-0.02537.7070.0020.0020.0000.0000.0000.000
51A56ALA00.0150.01240.559-0.001-0.0010.0000.0000.0000.000
52A57ILE0-0.032-0.00233.966-0.003-0.0030.0000.0000.0000.000
53A58VAL00.003-0.01635.591-0.001-0.0010.0000.0000.0000.000
54A59LEU0-0.016-0.00637.4660.0000.0000.0000.0000.0000.000
55A60LEU00.0510.01537.299-0.002-0.0020.0000.0000.0000.000
56A61ARG10.8020.91631.319-0.022-0.0220.0000.0000.0000.000
57A62ARG10.9100.94836.225-0.042-0.0420.0000.0000.0000.000
58A63TYR0-0.073-0.05538.612-0.002-0.0020.0000.0000.0000.000
59A64MET0-0.055-0.02636.348-0.004-0.0040.0000.0000.0000.000
60A65LEU0-0.0080.01134.847-0.001-0.0010.0000.0000.0000.000
61A66LYS10.9430.96937.318-0.028-0.0280.0000.0000.0000.000
62A67LYS10.8880.96439.4990.0100.0100.0000.0000.0000.000
63A68ASN00.0240.01240.430-0.002-0.0020.0000.0000.0000.000
64A69GLU-1-0.934-0.96942.370-0.004-0.0040.0000.0000.0000.000
65A70GLU-1-0.953-1.01139.514-0.026-0.0260.0000.0000.0000.000
66A71LYS10.9160.97743.5560.0040.0040.0000.0000.0000.000
67A72GLY0-0.0040.00245.0170.0000.0000.0000.0000.0000.000
68A73PHE00.0220.01244.671-0.001-0.0010.0000.0000.0000.000
69A74SER00.0420.02643.0340.0000.0000.0000.0000.0000.000
70A75LEU00.0860.04636.3210.0030.0030.0000.0000.0000.000
71A76GLU-1-0.888-0.94540.236-0.022-0.0220.0000.0000.0000.000
72A77ALA0-0.0030.00042.4680.0030.0030.0000.0000.0000.000
73A78LEU00.0070.02140.5670.0030.0030.0000.0000.0000.000
74A79VAL00.0030.01639.0310.0040.0040.0000.0000.0000.000
75A80ALA0-0.002-0.01441.9010.0030.0030.0000.0000.0000.000
76A81THR0-0.027-0.04245.3910.0020.0020.0000.0000.0000.000
77A82CYS0-0.032-0.01142.0560.0030.0030.0000.0000.0000.000
78A83ILE00.0040.01641.4640.0040.0040.0000.0000.0000.000
79A84TYR0-0.017-0.02944.7930.0020.0020.0000.0000.0000.000
80A85LEU00.002-0.00846.4920.0020.0020.0000.0000.0000.000
81A86SER0-0.005-0.00943.0810.0030.0030.0000.0000.0000.000
82A87CYS0-0.042-0.00645.8300.0020.0020.0000.0000.0000.000
83A88LYS10.8350.92848.396-0.012-0.0120.0000.0000.0000.000
84A89VAL00.0110.00547.1310.0010.0010.0000.0000.0000.000
85A90GLU-1-0.850-0.89244.4300.0400.0400.0000.0000.0000.000
86A91GLU-1-0.936-0.97547.7740.0300.0300.0000.0000.0000.000
87A92CYS0-0.114-0.04848.4680.0000.0000.0000.0000.0000.000
88A93PRO00.0020.00250.267-0.002-0.0020.0000.0000.0000.000
89A94VAL00.0620.02449.525-0.001-0.0010.0000.0000.0000.000
90A95HIS0-0.048-0.03452.575-0.002-0.0020.0000.0000.0000.000
91A96ILE00.0600.01854.055-0.001-0.0010.0000.0000.0000.000
92A97ARG10.9610.98253.958-0.002-0.0020.0000.0000.0000.000
93A98THR00.003-0.00952.086-0.002-0.0020.0000.0000.0000.000
94A99ILE00.0660.04848.380-0.001-0.0010.0000.0000.0000.000
95A100CYS0-0.030-0.00449.975-0.002-0.0020.0000.0000.0000.000
96A101ASN0-0.032-0.00551.687-0.002-0.0020.0000.0000.0000.000
97A102GLU-1-0.785-0.90248.171-0.007-0.0070.0000.0000.0000.000
98A103ALA0-0.0040.01047.039-0.002-0.0020.0000.0000.0000.000
99A104ASN0-0.040-0.04847.343-0.004-0.0040.0000.0000.0000.000
100A105ASP-1-0.961-0.97949.413-0.014-0.0140.0000.0000.0000.000
101A106LEU0-0.064-0.02742.8550.0000.0000.0000.0000.0000.000
102A107TRP00.010-0.00140.608-0.001-0.0010.0000.0000.0000.000
103A108SER00.0080.01445.4900.0010.0010.0000.0000.0000.000
104A109LEU0-0.014-0.01645.110-0.003-0.0030.0000.0000.0000.000
105A110LYS10.9210.95845.4550.0420.0420.0000.0000.0000.000
106A111VAL00.0130.00049.4140.0000.0000.0000.0000.0000.000
107A112LYS10.9560.99250.3010.0140.0140.0000.0000.0000.000
108A113LEU00.0230.02247.4700.0010.0010.0000.0000.0000.000
109A114SER0-0.042-0.04852.0530.0010.0010.0000.0000.0000.000
110A115ARG10.9480.94554.4840.0000.0000.0000.0000.0000.000
111A116SER00.0390.01455.6940.0010.0010.0000.0000.0000.000
112A117ASN00.0870.07551.9380.0000.0000.0000.0000.0000.000
113A118ILE00.0770.02150.0630.0000.0000.0000.0000.0000.000
114A119SER0-0.025-0.00251.4010.0020.0020.0000.0000.0000.000
115A120GLU-1-0.928-0.95552.834-0.006-0.0060.0000.0000.0000.000
116A121ILE0-0.0060.00546.8640.0010.0010.0000.0000.0000.000
117A122GLU-1-0.868-0.95248.9350.0110.0110.0000.0000.0000.000
118A123PHE0-0.027-0.00750.0820.0020.0020.0000.0000.0000.000
119A124GLU-1-0.811-0.87847.0050.0030.0030.0000.0000.0000.000
120A125ILE0-0.024-0.01644.6300.0010.0010.0000.0000.0000.000
121A126ILE0-0.016-0.01746.9880.0020.0020.0000.0000.0000.000
122A127SER0-0.038-0.02049.3220.0020.0020.0000.0000.0000.000
123A128VAL00.0150.01944.3510.0020.0020.0000.0000.0000.000
124A129LEU0-0.109-0.06142.1960.0020.0020.0000.0000.0000.000
125A130ASP-1-0.883-0.92945.9500.0240.0240.0000.0000.0000.000
126A131ALA0-0.081-0.04349.1930.0020.0020.0000.0000.0000.000
127A132PHE0-0.048-0.01745.2140.0020.0020.0000.0000.0000.000
128A133LEU0-0.040-0.03945.1040.0000.0000.0000.0000.0000.000
129A134ILE00.0080.02044.8650.0010.0010.0000.0000.0000.000
130A135VAL0-0.032-0.02539.1380.0010.0010.0000.0000.0000.000
131A136HIS0-0.0100.01539.8480.0010.0010.0000.0000.0000.000
132A137HIS00.0630.02636.8580.0050.0050.0000.0000.0000.000
133A138PRO0-0.030-0.01532.5980.0010.0010.0000.0000.0000.000
134A139TYR0-0.008-0.03934.4650.0020.0020.0000.0000.0000.000
135A140THR00.0270.01337.1810.0010.0010.0000.0000.0000.000
136A141SER00.0190.00735.4990.0010.0010.0000.0000.0000.000
137A142LEU0-0.0310.00432.0750.0030.0030.0000.0000.0000.000
138A143GLU-1-0.913-0.96635.9990.0740.0740.0000.0000.0000.000
139A144GLN00.0440.03639.405-0.003-0.0030.0000.0000.0000.000
140A145ALA00.0210.01035.7990.0010.0010.0000.0000.0000.000
141A146PHE0-0.078-0.04137.7900.0020.0020.0000.0000.0000.000
142A147HIS0-0.029-0.00538.865-0.002-0.0020.0000.0000.0000.000
143A148ASP-1-0.958-0.98440.4740.0920.0920.0000.0000.0000.000
144A149GLY0-0.044-0.02640.5070.0030.0030.0000.0000.0000.000
145A150ILE0-0.091-0.03034.7580.0070.0070.0000.0000.0000.000
146A151ILE0-0.041-0.00733.1550.0100.0100.0000.0000.0000.000
147A152ASN00.0530.02233.703-0.006-0.0060.0000.0000.0000.000
148A153GLN00.033-0.00535.3940.0000.0000.0000.0000.0000.000
149A154LYS10.9710.97228.947-0.133-0.1330.0000.0000.0000.000
150A155GLN00.016-0.01230.068-0.011-0.0110.0000.0000.0000.000
151A156LEU00.0290.01331.1790.0010.0010.0000.0000.0000.000
152A157GLU-1-0.952-0.96832.2940.0780.0780.0000.0000.0000.000
153A158PHE00.0510.04123.689-0.004-0.0040.0000.0000.0000.000
154A159ALA00.039-0.00228.699-0.001-0.0010.0000.0000.0000.000
155A160TRP0-0.011-0.02829.727-0.004-0.0040.0000.0000.0000.000
156A161SER0-0.026-0.01629.243-0.010-0.0100.0000.0000.0000.000
157A162ILE00.0560.04525.072-0.006-0.0060.0000.0000.0000.000
158A163VAL0-0.026-0.00127.729-0.005-0.0050.0000.0000.0000.000
159A164ASN00.0560.07830.445-0.003-0.0030.0000.0000.0000.000
160A165ASP-1-0.771-0.83926.6470.0500.0500.0000.0000.0000.000
161A166SER0-0.101-0.07627.027-0.006-0.0060.0000.0000.0000.000
162A167TYR0-0.070-0.05728.083-0.001-0.0010.0000.0000.0000.000
163A168ALA00.0560.02227.289-0.009-0.0090.0000.0000.0000.000
164A169SER00.031-0.02125.529-0.004-0.0040.0000.0000.0000.000
165A170SER0-0.057-0.04027.146-0.001-0.0010.0000.0000.0000.000
166A171LEU00.1170.03825.2170.0020.0020.0000.0000.0000.000
167A172CYS0-0.053-0.00828.9470.0020.0020.0000.0000.0000.000
168A173LEU0-0.044-0.01931.830-0.002-0.0020.0000.0000.0000.000
169A174MET0-0.059-0.00925.6860.0000.0000.0000.0000.0000.000
170A175ALA0-0.008-0.01129.3530.0100.0100.0000.0000.0000.000
171A176HIS0-0.0020.01931.481-0.010-0.0100.0000.0000.0000.000
172A177PRO00.0470.00333.1810.0080.0080.0000.0000.0000.000
173A178HIS00.0520.02333.729-0.001-0.0010.0000.0000.0000.000
174A179GLN0-0.019-0.01630.2100.0050.0050.0000.0000.0000.000
175A180LEU00.0490.00927.6900.0120.0120.0000.0000.0000.000
176A181ALA0-0.013-0.00929.0160.0060.0060.0000.0000.0000.000
177A182TYR00.0280.00929.8630.0020.0020.0000.0000.0000.000
178A183ALA00.0160.01925.0530.0130.0130.0000.0000.0000.000
179A184ALA00.0170.01325.7040.0130.0130.0000.0000.0000.000
180A185LEU00.003-0.01127.0740.0040.0040.0000.0000.0000.000
181A186LEU0-0.031-0.01024.9020.0060.0060.0000.0000.0000.000
182A187ILE0-0.001-0.00421.6180.0140.0140.0000.0000.0000.000
183A188SER0-0.062-0.03323.5810.0100.0100.0000.0000.0000.000
184A189CYS0-0.067-0.02925.866-0.001-0.0010.0000.0000.0000.000
185A190CYS0-0.061-0.02522.0190.0130.0130.0000.0000.0000.000
186A191ASN00.020-0.00321.8550.0440.0440.0000.0000.0000.000
187A192ASP-1-0.919-0.93724.6510.1830.1830.0000.0000.0000.000
188A193GLU-1-0.903-0.96027.8210.2610.2610.0000.0000.0000.000
189A194ASN0-0.038-0.02528.8280.0020.0020.0000.0000.0000.000
190A195THR00.001-0.00130.438-0.004-0.0040.0000.0000.0000.000
191A196ILE00.0380.03325.009-0.007-0.0070.0000.0000.0000.000
192A197PRO0-0.011-0.00329.364-0.004-0.0040.0000.0000.0000.000
193A198LYS11.0061.00231.586-0.146-0.1460.0000.0000.0000.000
194A199LEU0-0.013-0.01229.431-0.008-0.0080.0000.0000.0000.000
195A200LEU0-0.052-0.04127.056-0.001-0.0010.0000.0000.0000.000
196A201ASP-1-0.913-0.93430.9850.1570.1570.0000.0000.0000.000
197A202LEU0-0.082-0.04333.960-0.006-0.0060.0000.0000.0000.000
198A203ILE0-0.068-0.01628.675-0.006-0.0060.0000.0000.0000.000
199A204LYS11.0261.02832.581-0.110-0.1100.0000.0000.0000.000
200A205SER00.0230.00031.1610.0000.0000.0000.0000.0000.000
201A206THR0-0.009-0.01431.2950.0050.0050.0000.0000.0000.000
202A207ASP-1-0.846-0.93831.4710.1280.1280.0000.0000.0000.000
203A208ALA0-0.0010.00627.5870.0040.0040.0000.0000.0000.000
204A209PHE00.0420.02623.4520.0100.0100.0000.0000.0000.000
205A210LYS10.9741.00125.301-0.112-0.1120.0000.0000.0000.000
206A211VAL00.0370.02825.656-0.003-0.0030.0000.0000.0000.000
207A212ILE00.0220.00720.7360.0040.0040.0000.0000.0000.000
208A213LEU0-0.043-0.02321.9320.0050.0050.0000.0000.0000.000
209A214CYS0-0.068-0.03222.788-0.014-0.0140.0000.0000.0000.000
210A215VAL00.0270.00019.730-0.009-0.0090.0000.0000.0000.000
211A216GLN0-0.0080.00717.415-0.017-0.0170.0000.0000.0000.000
212A217ARG10.9450.96519.090-0.144-0.1440.0000.0000.0000.000
213A218ILE00.0370.02821.323-0.018-0.0180.0000.0000.0000.000
214A219ILE00.0200.01515.634-0.011-0.0110.0000.0000.0000.000
215A220SER0-0.050-0.03816.897-0.022-0.0220.0000.0000.0000.000
216A221ILE0-0.038-0.03317.922-0.029-0.0290.0000.0000.0000.000
217A222TYR0-0.030-0.06119.483-0.008-0.0080.0000.0000.0000.000
218A223TYR0-0.042-0.01213.7550.0030.0030.0000.0000.0000.000
219A224PHE0-0.048-0.02316.050-0.030-0.0300.0000.0000.0000.000
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