Manual

About

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: Z6ZRN

Calculation Name: 3WZ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WZ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U4Q9

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2770232.529289
FMO2-HF: Nuclear repulsion 2682983.370562
FMO2-HF: Total energy -87249.158726
FMO2-MP2: Total energy -87503.840892


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:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-4.2821.0153.222-3.079-5.439-0.016
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.001
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].
3A8ASN0-0.045-0.0173.6060.0672.241-0.004-1.030-1.1400.000
4A9LEU00.0220.0046.367-0.433-0.4330.0000.0000.0000.000
5A10VAL0-0.049-0.0049.3780.0730.0730.0000.0000.0000.000
6A11LEU00.0110.00712.316-0.079-0.0790.0000.0000.0000.000
7A12PRO00.0240.02214.7330.0170.0170.0000.0000.0000.000
8A13GLU-1-0.855-0.91616.9630.1320.1320.0000.0000.0000.000
9A14VAL0-0.0110.00218.8870.0000.0000.0000.0000.0000.000
10A15GLU-1-0.882-0.93821.6560.0240.0240.0000.0000.0000.000
11A16ASN0-0.043-0.02523.808-0.008-0.0080.0000.0000.0000.000
12A17ALA00.0030.00820.927-0.004-0.0040.0000.0000.0000.000
13A18ILE00.0070.00923.010-0.013-0.0130.0000.0000.0000.000
14A19PHE00.013-0.00415.2570.0000.0000.0000.0000.0000.000
15A20ILE00.0230.01321.062-0.013-0.0130.0000.0000.0000.000
16A21GLU-1-0.780-0.85516.303-0.189-0.1890.0000.0000.0000.000
17A22GLY00.0510.02119.1260.0030.0030.0000.0000.0000.000
18A23TYR0-0.010-0.01712.433-0.021-0.0210.0000.0000.0000.000
19A24PRO0-0.042-0.01716.8820.0080.0080.0000.0000.0000.000
20A25GLY00.0390.00418.773-0.027-0.0270.0000.0000.0000.000
21A26VAL0-0.001-0.01021.4620.0140.0140.0000.0000.0000.000
22A27GLY00.0960.04625.0540.0020.0020.0000.0000.0000.000
23A28LEU0-0.051-0.02622.6920.0080.0080.0000.0000.0000.000
24A29VAL0-0.0060.01625.1600.0040.0040.0000.0000.0000.000
25A30GLY00.0560.02623.0040.0070.0070.0000.0000.0000.000
26A31HIS0-0.038-0.02820.4650.0070.0070.0000.0000.0000.000
27A32ILE00.0240.00823.0150.0120.0120.0000.0000.0000.000
28A33ALA00.0170.01026.2400.0090.0090.0000.0000.0000.000
29A34ALA00.0160.00922.3500.0080.0080.0000.0000.0000.000
30A35ASN0-0.019-0.03122.4090.0190.0190.0000.0000.0000.000
31A36PHE0-0.029-0.00725.5030.0090.0090.0000.0000.0000.000
32A37LEU00.0150.00126.7450.0060.0060.0000.0000.0000.000
33A38ALA00.0180.00324.6010.0060.0060.0000.0000.0000.000
34A39LYS10.8240.91426.7120.0110.0110.0000.0000.0000.000
35A40GLU-1-0.838-0.92529.7380.0010.0010.0000.0000.0000.000
36A41LEU0-0.071-0.02728.6690.0010.0010.0000.0000.0000.000
37A42ASP-1-0.921-0.96530.2640.0380.0380.0000.0000.0000.000
38A43MET0-0.073-0.00125.3300.0060.0060.0000.0000.0000.000
39A44ASP-1-0.819-0.89325.1730.0620.0620.0000.0000.0000.000
40A45LEU0-0.047-0.04019.066-0.006-0.0060.0000.0000.0000.000
41A46ILE00.0000.00519.1040.0200.0200.0000.0000.0000.000
42A47GLY00.0250.00316.3890.0300.0300.0000.0000.0000.000
43A48TYR0-0.084-0.04112.224-0.052-0.0520.0000.0000.0000.000
44A49VAL0-0.0060.0088.4400.0390.0390.0000.0000.0000.000
45A50ASP-1-0.855-0.9227.5391.3741.3740.0000.0000.0000.000
46A51SER00.017-0.0273.907-0.1440.3770.000-0.293-0.2280.001
47A52LEU0-0.0120.0004.416-0.209-0.032-0.001-0.011-0.1650.000
48A53PHE0-0.041-0.0192.507-0.946-0.3401.099-0.398-1.307-0.001
49A54ILE0-0.0150.0086.986-0.076-0.0760.0000.0000.0000.000
50A55PRO0-0.016-0.0029.6590.0880.0880.0000.0000.0000.000
51A56PRO00.0030.00112.5680.0120.0120.0000.0000.0000.000
52A57MET0-0.005-0.00614.173-0.023-0.0230.0000.0000.0000.000
53A58SER0-0.048-0.03416.5270.0330.0330.0000.0000.0000.000
54A59LEU0-0.0140.01019.114-0.012-0.0120.0000.0000.0000.000
55A60ILE0-0.0110.00321.8210.0100.0100.0000.0000.0000.000
56A61LEU00.0180.01123.046-0.011-0.0110.0000.0000.0000.000
57A62GLU-1-0.800-0.88126.5090.0490.0490.0000.0000.0000.000
58A63GLY0-0.012-0.00128.9530.0030.0030.0000.0000.0000.000
59A64ARG10.8220.88425.023-0.052-0.0520.0000.0000.0000.000
60A65PRO0-0.015-0.00221.256-0.010-0.0100.0000.0000.0000.000
61A66THR0-0.010-0.01119.6500.0090.0090.0000.0000.0000.000
62A67PRO00.0660.03614.478-0.010-0.0100.0000.0000.0000.000
63A68PRO00.0260.00514.002-0.015-0.0150.0000.0000.0000.000
64A69LEU0-0.007-0.00710.491-0.044-0.0440.0000.0000.0000.000
65A70ARG10.7860.85014.2690.0440.0440.0000.0000.0000.000
66A71PHE00.0120.00212.422-0.045-0.0450.0000.0000.0000.000
67A72TYR00.0380.03018.0130.0240.0240.0000.0000.0000.000
68A73GLY00.054-0.00121.517-0.010-0.0100.0000.0000.0000.000
69A74LYS10.8230.91423.694-0.035-0.0350.0000.0000.0000.000
70A75ASN0-0.011-0.00527.151-0.003-0.0030.0000.0000.0000.000
71A76ASN00.0220.00925.3620.0080.0080.0000.0000.0000.000
72A77ILE0-0.0120.01224.433-0.007-0.0070.0000.0000.0000.000
73A78ILE00.005-0.00618.3760.0100.0100.0000.0000.0000.000
74A79ILE0-0.006-0.00921.140-0.016-0.0160.0000.0000.0000.000
75A80ALA0-0.029-0.00815.7250.0140.0140.0000.0000.0000.000
76A81ILE0-0.018-0.01317.360-0.019-0.0190.0000.0000.0000.000
77A82ALA0-0.006-0.00614.8190.0010.0010.0000.0000.0000.000
78A83ASP-1-0.768-0.85916.596-0.033-0.0330.0000.0000.0000.000
79A84ILE0-0.042-0.02512.8990.0070.0070.0000.0000.0000.000
80A85PHE00.0170.01115.155-0.030-0.0300.0000.0000.0000.000
81A86LEU00.0080.0029.515-0.001-0.0010.0000.0000.0000.000
82A87PRO00.0410.0238.9860.0020.0020.0000.0000.0000.000
83A88PRO00.0690.0199.959-0.098-0.0980.0000.0000.0000.000
84A89THR00.0080.0006.6940.0050.0050.0000.0000.0000.000
85A90LEU00.0260.0274.474-0.355-0.265-0.001-0.010-0.0790.000
86A91VAL00.0100.0086.588-0.098-0.0980.0000.0000.0000.000
87A92ASN0-0.014-0.0228.5690.0760.0760.0000.0000.0000.000
88A93GLU-1-0.825-0.8982.630-5.775-4.3652.132-1.319-2.224-0.016
89A94ILE00.0150.0055.3110.1140.161-0.001-0.002-0.0430.000
90A95ALA00.0310.0077.4600.1810.1810.0000.0000.0000.000
91A96LYS10.7540.8764.2792.1172.226-0.001-0.006-0.1010.000
92A97GLU-1-0.809-0.9054.690-0.776-0.613-0.001-0.010-0.1520.000
93A98ILE0-0.0020.0088.1670.1720.1720.0000.0000.0000.000
94A99VAL00.0280.00911.6370.0720.0720.0000.0000.0000.000
95A100ASN0-0.086-0.0637.9180.0630.0630.0000.0000.0000.000
96A101TYR0-0.030-0.03911.6070.0430.0430.0000.0000.0000.000
97A102LEU00.004-0.00713.2530.0180.0180.0000.0000.0000.000
98A103LYS10.8760.94512.5390.2330.2330.0000.0000.0000.000
99A104LYS10.8160.91914.005-0.179-0.1790.0000.0000.0000.000
100A105VAL0-0.032-0.01716.9820.0090.0090.0000.0000.0000.000
101A106ASN0-0.072-0.03219.309-0.010-0.0100.0000.0000.0000.000
102A107ALA0-0.018-0.00519.7090.0040.0040.0000.0000.0000.000
103A108GLU-1-0.895-0.93821.641-0.035-0.0350.0000.0000.0000.000
104A109LYS10.8330.91324.0400.0390.0390.0000.0000.0000.000
105A110VAL0-0.0070.00018.3340.0020.0020.0000.0000.0000.000
106A111ILE0-0.011-0.01221.438-0.010-0.0100.0000.0000.0000.000
107A112SER0-0.020-0.03118.9190.0010.0010.0000.0000.0000.000
108A113LEU0-0.037-0.01221.5640.0100.0100.0000.0000.0000.000
109A114ALA00.0210.00222.719-0.009-0.0090.0000.0000.0000.000
110A115GLY00.0280.01524.3500.0120.0120.0000.0000.0000.000
111A116MET0-0.047-0.02826.387-0.010-0.0100.0000.0000.0000.000
112A117GLY00.014-0.00828.8820.0070.0070.0000.0000.0000.000
113A118ILE0-0.030-0.00930.563-0.002-0.0020.0000.0000.0000.000
114A119GLY0-0.0150.00533.6920.0010.0010.0000.0000.0000.000
115A120PHE0-0.074-0.04234.8400.0040.0040.0000.0000.0000.000
116A121PHE00.0010.00037.522-0.002-0.0020.0000.0000.0000.000
117A122LYS10.8390.89738.1820.0540.0540.0000.0000.0000.000
118A123ASP-1-0.885-0.94140.793-0.036-0.0360.0000.0000.0000.000
119A124THR0-0.066-0.04540.5310.0030.0030.0000.0000.0000.000
120A125PHE0-0.0030.01435.602-0.002-0.0020.0000.0000.0000.000
121A126GLU-1-0.867-0.92036.683-0.047-0.0470.0000.0000.0000.000
122A127VAL0-0.019-0.01731.138-0.003-0.0030.0000.0000.0000.000
123A128TRP0-0.070-0.03731.3070.0030.0030.0000.0000.0000.000
124A129GLY00.0410.00628.893-0.001-0.0010.0000.0000.0000.000
125A130ILE0-0.067-0.02425.3180.0010.0010.0000.0000.0000.000
126A131GLY00.0620.02526.500-0.001-0.0010.0000.0000.0000.000
127A132GLY0-0.023-0.02423.970-0.007-0.0070.0000.0000.0000.000
128A133SER0-0.042-0.04924.642-0.001-0.0010.0000.0000.0000.000
129A134GLU-1-0.826-0.92427.958-0.069-0.0690.0000.0000.0000.000
130A135GLU-1-0.890-0.92030.634-0.050-0.0500.0000.0000.0000.000
131A136GLU-1-0.780-0.84326.507-0.082-0.0820.0000.0000.0000.000
132A137ASN0-0.006-0.02529.754-0.001-0.0010.0000.0000.0000.000
133A138LYS10.9210.95131.7530.0620.0620.0000.0000.0000.000
134A139GLU-1-0.761-0.84430.370-0.052-0.0520.0000.0000.0000.000
135A140LEU00.0120.01928.6550.0040.0040.0000.0000.0000.000
136A141GLU-1-0.865-0.93233.205-0.058-0.0580.0000.0000.0000.000
137A142SER0-0.123-0.06736.3040.0040.0040.0000.0000.0000.000
138A143LEU0-0.015-0.00633.3410.0030.0030.0000.0000.0000.000
139A144GLY0-0.025-0.00637.1840.0010.0010.0000.0000.0000.000
140A145VAL0-0.046-0.01731.886-0.001-0.0010.0000.0000.0000.000
141A146LYS10.8490.90835.1470.0500.0500.0000.0000.0000.000
142A147ILE00.0050.00131.158-0.004-0.0040.0000.0000.0000.000
143A148LEU0-0.010-0.00828.0310.0030.0030.0000.0000.0000.000
144A149LYS10.8240.90430.6490.0650.0650.0000.0000.0000.000
145A150TYR0-0.008-0.00531.073-0.001-0.0010.0000.0000.0000.000
146A151GLY00.0310.01729.1920.0050.0050.0000.0000.0000.000
147A152SER0-0.042-0.01824.402-0.005-0.0050.0000.0000.0000.000
148A153ILE00.0340.02520.9440.0060.0060.0000.0000.0000.000
149A154THR0-0.019-0.01319.121-0.015-0.0150.0000.0000.0000.000
150A155GLY00.0320.01115.7940.0120.0120.0000.0000.0000.000
151A156MET00.0030.01110.786-0.025-0.0250.0000.0000.0000.000
152A157SER00.023-0.01014.923-0.009-0.0090.0000.0000.0000.000
153A158GLY0-0.0170.00418.2290.0090.0090.0000.0000.0000.000
154A159LYS10.8080.91011.5400.5630.5630.0000.0000.0000.000
155A160LEU00.018-0.00413.294-0.008-0.0080.0000.0000.0000.000
156A161LEU00.0270.03416.0580.0130.0130.0000.0000.0000.000
157A162TRP00.0380.01916.9820.0180.0180.0000.0000.0000.000
158A163GLU-1-0.798-0.89213.073-0.420-0.4200.0000.0000.0000.000
159A164ALA00.0230.01316.1220.0120.0120.0000.0000.0000.000
160A165SER0-0.020-0.00618.0410.0200.0200.0000.0000.0000.000
161A166ARG10.8000.88115.0400.3100.3100.0000.0000.0000.000
162A167ALA0-0.087-0.03516.9210.0060.0060.0000.0000.0000.000
163A168GLY0-0.0060.00319.0010.0180.0180.0000.0000.0000.000
164A169LEU0-0.033-0.00717.9570.0110.0110.0000.0000.0000.000
165A170LYS10.8050.88022.2050.0510.0510.0000.0000.0000.000
166A171SER0-0.026-0.01020.7700.0010.0010.0000.0000.0000.000
167A172TYR0-0.012-0.05622.8080.0060.0060.0000.0000.0000.000
168A173VAL0-0.042-0.01521.820-0.011-0.0110.0000.0000.0000.000
169A174LEU00.0230.02024.4650.0070.0070.0000.0000.0000.000
170A175LEU0-0.039-0.03025.783-0.008-0.0080.0000.0000.0000.000
171A176GLY00.0510.02528.2560.0070.0070.0000.0000.0000.000
172A177GLU-1-0.799-0.86730.288-0.065-0.0650.0000.0000.0000.000
173A178THR0-0.033-0.05629.6130.0030.0030.0000.0000.0000.000
174A179PHE00.0420.02633.010-0.002-0.0020.0000.0000.0000.000
175A180GLY0-0.006-0.01629.601-0.003-0.0030.0000.0000.0000.000
176A181ASP-1-0.870-0.91528.837-0.068-0.0680.0000.0000.0000.000
177A182ARG10.7950.88730.2520.0530.0530.0000.0000.0000.000
178A183PRO0-0.033-0.01328.285-0.005-0.0050.0000.0000.0000.000
179A184ASP-1-0.743-0.83829.448-0.049-0.0490.0000.0000.0000.000
180A185PRO00.023-0.00331.162-0.002-0.0020.0000.0000.0000.000
181A186ARG10.9410.97932.3110.0350.0350.0000.0000.0000.000
182A187ALA00.0340.02031.5840.0010.0010.0000.0000.0000.000
183A188ALA0-0.028-0.01329.289-0.002-0.0020.0000.0000.0000.000
184A189ALA00.0200.00830.5560.0010.0010.0000.0000.0000.000
185A190ASN0-0.0010.00233.6520.0040.0040.0000.0000.0000.000
186A191VAL00.0080.00427.5260.0000.0000.0000.0000.0000.000
187A192VAL0-0.019-0.00329.4220.0000.0000.0000.0000.0000.000
188A193GLU-1-0.798-0.89031.354-0.026-0.0260.0000.0000.0000.000
189A194VAL0-0.037-0.01231.9140.0020.0020.0000.0000.0000.000
190A195LEU00.016-0.00226.8640.0010.0010.0000.0000.0000.000
191A196ASN0-0.005-0.00530.8540.0050.0050.0000.0000.0000.000
192A197LYS10.7900.87733.5110.0330.0330.0000.0000.0000.000
193A198MET0-0.050-0.01727.9400.0000.0000.0000.0000.0000.000
194A199LEU0-0.021-0.00727.5500.0000.0000.0000.0000.0000.000
195A200GLY0-0.0150.01132.1060.0040.0040.0000.0000.0000.000
196A201LEU0-0.045-0.00930.1740.0040.0040.0000.0000.0000.000
197A202ASN0-0.036-0.03534.912-0.001-0.0010.0000.0000.0000.000
198A203VAL00.0230.01632.0860.0020.0020.0000.0000.0000.000
199A204SER00.0000.00335.478-0.004-0.0040.0000.0000.0000.000
200A205VAL00.0670.01334.4900.0010.0010.0000.0000.0000.000
201A206GLU-1-0.912-0.95236.717-0.018-0.0180.0000.0000.0000.000
202A207PRO0-0.035-0.02136.2920.0000.0000.0000.0000.0000.000
203A208LEU00.0170.02931.6380.0000.0000.0000.0000.0000.000
204A209LEU00.003-0.01135.345-0.002-0.0020.0000.0000.0000.000
205A210LYS10.9020.95738.1610.0060.0060.0000.0000.0000.000
206A211GLU-1-0.952-0.98235.464-0.007-0.0070.0000.0000.0000.000
207A212ALA0-0.017-0.01134.979-0.001-0.0010.0000.0000.0000.000
208A213GLU-1-0.948-0.96835.245-0.022-0.0220.0000.0000.0000.000
209A214MET00.0080.00334.242-0.001-0.0010.0000.0000.0000.000
210A215ILE0-0.017-0.01430.268-0.001-0.0010.0000.0000.0000.000
211A216GLU-1-0.870-0.93331.037-0.045-0.0450.0000.0000.0000.000
212A217GLU-1-0.805-0.90831.761-0.031-0.0310.0000.0000.0000.000
213A218GLN0-0.069-0.03129.2360.0010.0010.0000.0000.0000.000
214A219LEU0-0.018-0.01825.6640.0000.0000.0000.0000.0000.000
215A220ARG10.8130.89727.3060.0280.0280.0000.0000.0000.000
216A221ARG10.9590.98625.3840.0200.0200.0000.0000.0000.000
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