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: P98V2

Calculation Name: 3CZZ-A-Xray21

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CZZ

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -942100.648154
FMO2-HF: Nuclear repulsion 894863.24109
FMO2-HF: Total energy -47237.407064
FMO2-MP2: Total energy -47369.933598


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-144.646-147.52136.749-18.288-15.578-0.156
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.752 / q_NPA : 0.854
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].
3A3LYS10.8540.9013.41368.29270.081-0.012-0.737-1.040-0.001
4A4PHE00.0350.0216.3994.1114.1110.0000.0000.0000.000
5A5SER0-0.040-0.0318.9223.1323.1320.0000.0000.0000.000
6A6GLN00.0180.0097.8000.6850.6850.0000.0000.0000.000
7A7THR00.0200.01410.1571.9391.9390.0000.0000.0000.000
8A22CYS0-0.091-0.00912.648-0.059-0.0590.0000.0000.0000.000
9A9TYR00.0350.03214.6260.2650.2650.0000.0000.0000.000
10A10ASN00.006-0.00417.8850.1550.1550.0000.0000.0000.000
11A11SER0-0.008-0.00715.9720.1430.1430.0000.0000.0000.000
12A12ALA0-0.0080.00418.5410.7560.7560.0000.0000.0000.000
13A13ILE00.0160.00916.371-0.784-0.7840.0000.0000.0000.000
14A14GLN00.0330.03420.0150.9600.9600.0000.0000.0000.000
15A15GLY00.0410.02722.046-0.138-0.1380.0000.0000.0000.000
16A16SER0-0.015-0.02118.557-0.152-0.1520.0000.0000.0000.000
17A17VAL0-0.014-0.00117.531-1.124-1.1240.0000.0000.0000.000
18A18LEU00.0090.02412.8290.4200.4200.0000.0000.0000.000
19A19THR0-0.022-0.00716.654-0.075-0.0750.0000.0000.0000.000
20A20SER00.013-0.01615.165-0.191-0.1910.0000.0000.0000.000
21A21THR00.0040.02417.3150.5580.5580.0000.0000.0000.000
22A23GLU-1-0.890-0.94514.946-16.668-16.6680.0000.0000.0000.000
23A24ARG10.8350.91414.25914.70014.7000.0000.0000.0000.000
24A25THR00.016-0.02113.630-0.588-0.5880.0000.0000.0000.000
25A26ASN0-0.046-0.00715.014-0.230-0.2300.0000.0000.0000.000
26A27GLY00.0690.06117.9631.0051.0050.0000.0000.0000.000
27A28GLY0-0.0020.00919.8370.1930.1930.0000.0000.0000.000
28A29TYR00.008-0.00318.223-0.916-0.9160.0000.0000.0000.000
29A30ASN0-0.027-0.01617.2211.7411.7410.0000.0000.0000.000
30A31THR00.0060.00518.039-0.628-0.6280.0000.0000.0000.000
31A32SER0-0.0170.01015.5080.1360.1360.0000.0000.0000.000
32A33SER00.0510.00117.0010.1850.1850.0000.0000.0000.000
33A34ILE00.0100.01810.769-0.381-0.3810.0000.0000.0000.000
34A35ASP-1-0.710-0.82315.057-14.843-14.8430.0000.0000.0000.000
35A36LEU00.0390.00212.242-0.739-0.7390.0000.0000.0000.000
36A37ASN0-0.015-0.01614.667-0.428-0.4280.0000.0000.0000.000
37A38SER0-0.034-0.01414.4960.8340.8340.0000.0000.0000.000
38A39VAL0-0.061-0.01110.075-0.205-0.2050.0000.0000.0000.000
39A40ILE00.0530.04411.290-1.343-1.3430.0000.0000.0000.000
40A41ALA0-0.030-0.00113.7481.0881.0880.0000.0000.0000.000
41A42ALA00.0360.00016.577-0.622-0.6220.0000.0000.0000.000
42A43VAL0-0.006-0.00418.3110.5620.5620.0000.0000.0000.000
43A44ASP-1-0.726-0.85020.688-11.449-11.4490.0000.0000.0000.000
44A45GLY00.0170.01723.2320.1550.1550.0000.0000.0000.000
45A46SER0-0.008-0.01718.350-0.281-0.2810.0000.0000.0000.000
46A47LEU0-0.024-0.00215.908-0.134-0.1340.0000.0000.0000.000
47A48LYS10.9050.97613.37917.68917.6890.0000.0000.0000.000
48A49TRP00.0160.0078.564-0.468-0.4680.0000.0000.0000.000
49A50GLN0-0.019-0.0176.7022.3912.3910.0000.0000.0000.000
50A51GLY00.000-0.01211.1161.4431.4430.0000.0000.0000.000
51A52SER0-0.0260.01213.536-0.609-0.6090.0000.0000.0000.000
52A53ASN00.0770.01516.1880.4980.4980.0000.0000.0000.000
53A54PHE00.0770.03416.8820.6920.6920.0000.0000.0000.000
54A55ILE0-0.031-0.01119.5200.5000.5000.0000.0000.0000.000
55A56GLU-1-0.888-0.90222.108-10.799-10.7990.0000.0000.0000.000
56A57ALA00.0040.02023.1830.5670.5670.0000.0000.0000.000
57A73CYS0-0.127-0.05121.903-0.126-0.1260.0000.0000.0000.000
58A59ARG10.8710.92624.39310.52810.5280.0000.0000.0000.000
59A60ASN0-0.022-0.02624.942-0.419-0.4190.0000.0000.0000.000
60A61THR0-0.001-0.01420.674-0.045-0.0450.0000.0000.0000.000
61A62GLN00.0290.02821.1300.5060.5060.0000.0000.0000.000
62A63LEU00.0270.02816.307-0.694-0.6940.0000.0000.0000.000
63A64ALA00.0030.00618.3210.9710.9710.0000.0000.0000.000
64A65GLY00.011-0.00117.660-1.051-1.0510.0000.0000.0000.000
65A66SER0-0.015-0.00914.4710.4340.4340.0000.0000.0000.000
66A67SER00.0320.00111.533-0.111-0.1110.0000.0000.0000.000
67A68GLU-1-0.766-0.85312.723-19.856-19.8560.0000.0000.0000.000
68A69LEU00.0100.02614.8041.0191.0190.0000.0000.0000.000
69A70ALA0-0.025-0.01616.500-0.212-0.2120.0000.0000.0000.000
70A71ALA00.016-0.00319.7050.2060.2060.0000.0000.0000.000
71A72GLU-1-0.753-0.82122.236-10.894-10.8940.0000.0000.0000.000
72A74LYS10.9390.98224.66310.10310.1030.0000.0000.0000.000
73A75THR00.0140.02726.020-0.179-0.1790.0000.0000.0000.000
74A76ALA00.0330.00127.3490.2730.2730.0000.0000.0000.000
75A77ALA0-0.009-0.00128.9450.3320.3320.0000.0000.0000.000
76A78GLY00.0220.02130.8220.3920.3920.0000.0000.0000.000
77A79GLN0-0.0090.00231.836-0.146-0.1460.0000.0000.0000.000
78A80PHE0-0.001-0.00727.534-0.209-0.2090.0000.0000.0000.000
79A81VAL00.0070.01824.2670.2990.2990.0000.0000.0000.000
80A82SER0-0.038-0.02524.073-0.391-0.3910.0000.0000.0000.000
81A83THR00.0820.03818.800-0.273-0.2730.0000.0000.0000.000
82A84LYS10.8890.94117.20716.26816.2680.0000.0000.0000.000
83A85ILE00.0140.02211.508-0.065-0.0650.0000.0000.0000.000
84A86ASN00.0430.02110.0890.8220.8220.0000.0000.0000.000
85A87LEU00.0420.0119.260-2.582-2.5820.0000.0000.0000.000
86A88ASP-1-0.763-0.8577.755-35.772-35.7720.0000.0000.0000.000
87A89ASP-1-0.801-0.8405.059-44.078-44.0780.0000.0000.0000.000
88A90HIS10.7770.8723.08033.40434.5930.110-0.377-0.921-0.001
89A91ILE00.0410.0494.7151.6881.835-0.001-0.004-0.1420.000
90A92ALA0-0.052-0.0234.489-3.079-3.059-0.001-0.011-0.0080.000
91A93ASN00.029-0.0096.5365.1665.1660.0000.0000.0000.000
92A94ILE0-0.043-0.0078.640-2.070-2.0700.0000.0000.0000.000
93A95ASP-1-0.775-0.88810.046-16.387-16.3870.0000.0000.0000.000
94A96GLY00.0800.03713.0381.6791.6790.0000.0000.0000.000
95A97THR0-0.044-0.01513.1841.7641.7640.0000.0000.0000.000
96A98LEU00.0010.00911.085-2.327-2.3270.0000.0000.0000.000
97A99LYS10.8890.9405.75634.71934.7190.0000.0000.0000.000
98A100TYR0-0.001-0.0027.097-3.288-3.2880.0000.0000.0000.000
99A101GLU-2-1.507-1.7122.403-127.445-120.8402.733-3.817-5.520-0.045
100A102HOH0-0.017-0.00915.2120.4420.4420.0000.0000.0000.000
101A103HOH0-0.029-0.02919.198-0.157-0.1570.0000.0000.0000.000
102A104HOH0-0.017-0.0259.0090.5580.5580.0000.0000.0000.000
103A106HOH00.0370.0275.7503.0293.0290.0000.0000.0000.000
104A107HOH0-0.037-0.0333.5360.6420.8080.003-0.048-0.1210.000
105A108HOH0-0.003-0.00423.753-0.133-0.1330.0000.0000.0000.000
106A109HOH00.0070.00016.218-0.228-0.2280.0000.0000.0000.000
107A110HOH0-0.0030.0067.641-0.354-0.3540.0000.0000.0000.000
108A111HOH0-0.043-0.04020.1620.3170.3170.0000.0000.0000.000
109A112HOH0-0.023-0.01623.304-0.211-0.2110.0000.0000.0000.000
110A113HOH0-0.039-0.0169.0350.7310.7310.0000.0000.0000.000
111A115HOH0-0.027-0.01618.3280.2140.2140.0000.0000.0000.000
112A116HOH0-0.018-0.02122.257-0.063-0.0630.0000.0000.0000.000
113A117HOH0-0.048-0.02813.5730.2330.2330.0000.0000.0000.000
114A118HOH00.0290.02122.873-0.311-0.3110.0000.0000.0000.000
115A119HOH00.0040.00515.0150.1970.1970.0000.0000.0000.000
116A121HOH00.0170.01314.8130.3390.3390.0000.0000.0000.000
117A122HOH0-0.039-0.02122.130-0.132-0.1320.0000.0000.0000.000
118A123HOH0-0.011-0.01617.5780.1440.1440.0000.0000.0000.000
119A125HOH0-0.018-0.0077.8541.5941.5940.0000.0000.0000.000
120A127HOH00.0330.02125.678-0.113-0.1130.0000.0000.0000.000
121A128HOH0-0.022-0.01620.148-0.224-0.2240.0000.0000.0000.000
122A129HOH00.000-0.00517.413-0.312-0.3120.0000.0000.0000.000
123A130HOH0-0.019-0.02028.0420.1380.1380.0000.0000.0000.000
124A131HOH00.0460.0388.711-1.472-1.4720.0000.0000.0000.000
125A133HOH00.0070.00320.491-0.159-0.1590.0000.0000.0000.000
126A134HOH00.0170.01322.0630.0700.0700.0000.0000.0000.000
127A135HOH00.0060.00423.6400.0000.0000.0000.0000.0000.000
128A136HOH00.0210.01219.774-0.035-0.0350.0000.0000.0000.000
129A139HOH00.001-0.01015.8820.2770.2770.0000.0000.0000.000
130A140HOH00.0330.02026.650-0.040-0.0400.0000.0000.0000.000
131A142HOH00.0390.02413.1730.0600.0600.0000.0000.0000.000
132A145HOH00.0340.03611.875-0.702-0.7020.0000.0000.0000.000
133A146HOH0-0.018-0.0396.693-3.063-3.0630.0000.0000.0000.000
134A147HOH00.0030.00224.1650.1060.1060.0000.0000.0000.000
135A148HOH0-0.027-0.02223.4490.1890.1890.0000.0000.0000.000
136A149HOH0-0.008-0.0142.766-4.488-3.5960.164-0.500-0.555-0.004
137A151HOH0-0.022-0.01420.645-0.065-0.0650.0000.0000.0000.000
138A152HOH0-0.001-0.01417.4580.0260.0260.0000.0000.0000.000
139A154HOH0-0.001-0.00421.5980.0180.0180.0000.0000.0000.000
140A158HOH00.0390.02528.008-0.064-0.0640.0000.0000.0000.000
141A159HOH0-0.049-0.0362.5800.0660.9210.327-0.568-0.613-0.004
142A160HOH0-0.055-0.04329.4200.0530.0530.0000.0000.0000.000
143A161HOH0-0.032-0.03117.7580.0970.0970.0000.0000.0000.000
144A164HOH0-0.0090.00823.555-0.080-0.0800.0000.0000.0000.000
145A165HOH0-0.015-0.00623.3840.0870.0870.0000.0000.0000.000
146A166HOH0-0.009-0.01512.6070.6930.6930.0000.0000.0000.000
147A168HOH00.0260.01823.004-0.155-0.1550.0000.0000.0000.000
148A169HOH0-0.058-0.03920.4460.3340.3340.0000.0000.0000.000
149A170HOH00.0210.01831.677-0.060-0.0600.0000.0000.0000.000
150A171HOH00.0130.00021.7950.2250.2250.0000.0000.0000.000
151A173HOH0-0.051-0.04024.158-0.190-0.1900.0000.0000.0000.000
152A176HOH00.006-0.00415.540-0.269-0.2690.0000.0000.0000.000
153A177HOH0-0.010-0.01013.0070.2480.2480.0000.0000.0000.000
154A179HOH0-0.038-0.03125.832-0.017-0.0170.0000.0000.0000.000
155A181HOH00.0040.00819.4450.1160.1160.0000.0000.0000.000
156A182HOH0-0.034-0.02625.2320.1230.1230.0000.0000.0000.000
157A183HOH0-0.056-0.03916.082-0.387-0.3870.0000.0000.0000.000
158A187HOH0-0.0060.00922.613-0.228-0.2280.0000.0000.0000.000
159A188HOH00.000-0.0034.2442.5642.5990.000-0.005-0.0290.000
160A189HOH0-0.007-0.00322.8610.1590.1590.0000.0000.0000.000
161A190HOH0-0.013-0.02226.7200.1720.1720.0000.0000.0000.000
162A191HOH00.0080.00323.964-0.197-0.1970.0000.0000.0000.000
163A193HOH00.0080.00424.091-0.012-0.0120.0000.0000.0000.000
164A194HOH0-0.040-0.02214.3670.3250.3250.0000.0000.0000.000
165A195HOH0-0.042-0.02825.8840.1750.1750.0000.0000.0000.000
166A199HOH0-0.038-0.02435.2940.0100.0100.0000.0000.0000.000
167A202HOH0-0.028-0.02314.559-0.325-0.3250.0000.0000.0000.000
168A203HOH0-0.0100.00020.004-0.135-0.1350.0000.0000.0000.000
169A204HOH0-0.016-0.0136.591-0.771-0.7710.0000.0000.0000.000
170A205HOH00.0110.01620.299-0.071-0.0710.0000.0000.0000.000
171A206HOH00.0200.03015.3520.3170.3170.0000.0000.0000.000
172A208HOH0-0.026-0.01329.6110.0480.0480.0000.0000.0000.000
173A209HOH0-0.029-0.02228.5170.0780.0780.0000.0000.0000.000
174A212HOH0-0.066-0.05021.6700.1960.1960.0000.0000.0000.000
175A213HOH0-0.029-0.01726.110-0.057-0.0570.0000.0000.0000.000
176A215HOH00.007-0.0017.1970.9820.9820.0000.0000.0000.000
177A221HOH0-0.021-0.01116.4330.2980.2980.0000.0000.0000.000
178A222HOH0-0.005-0.00614.495-0.599-0.5990.0000.0000.0000.000
179A227HOH0-0.044-0.02735.1600.0720.0720.0000.0000.0000.000
180A228HOH0-0.020-0.01222.3450.2710.2710.0000.0000.0000.000
181A229HOH00.0330.0201.929-19.984-21.9207.086-2.645-2.504-0.031
182A243HOH0-0.031-0.02121.0420.0350.0350.0000.0000.0000.000
183A246HOH0-0.033-0.0239.0381.2121.2120.0000.0000.0000.000
184A247HOH0-0.039-0.02326.3370.1760.1760.0000.0000.0000.000
185A248HOH0-0.014-0.02130.0860.1080.1080.0000.0000.0000.000
186A249HOH0-0.076-0.05021.4000.1870.1870.0000.0000.0000.000
187A251HOH0-0.028-0.0419.1750.2200.2200.0000.0000.0000.000
188A252HOH00.0320.0286.822-0.354-0.3540.0000.0000.0000.000
189A253HOH0-0.027-0.0215.3572.7852.7850.0000.0000.0000.000
190A255HOH0-0.0030.00020.450-0.203-0.2030.0000.0000.0000.000
191A257HOH00.0120.0113.230-5.516-4.6070.021-0.529-0.400-0.004
192A258HOH00.0080.0071.574-23.532-39.12626.261-7.693-2.973-0.058
193A259HOH00.0010.03022.4000.2800.2800.0000.0000.0000.000
194A268HOH00.0290.0196.575-2.112-2.1120.0000.0000.0000.000
195A277HOH00.0130.00027.9000.1150.1150.0000.0000.0000.000
196A278HOH0-0.044-0.03316.1330.2380.2380.0000.0000.0000.000
197A282HOH0-0.048-0.03317.0830.4310.4310.0000.0000.0000.000
198A283HOH00.002-0.00811.254-0.603-0.6030.0000.0000.0000.000
199A285HOH00.005-0.00217.1000.0860.0860.0000.0000.0000.000
200A286HOH0-0.013-0.0083.406-7.114-5.2990.043-1.251-0.607-0.008
201A288HOH0-0.041-0.0193.025-1.839-1.6060.015-0.103-0.1450.000
202A289HOH0-0.034-0.0209.291-0.281-0.2810.0000.0000.0000.000
203A290HOH00.0300.03013.714-0.163-0.1630.0000.0000.0000.000
204A291HOH0-0.052-0.03719.3080.2910.2910.0000.0000.0000.000
205A294HOH0-0.052-0.05223.3060.2300.2300.0000.0000.0000.000
206A295HOH0-0.032-0.0265.948-2.963-2.9630.0000.0000.0000.000
207A296HOH0-0.015-0.0138.9681.0111.0110.0000.0000.0000.000
208A305HOH00.0200.01322.625-0.287-0.2870.0000.0000.0000.000
209A307HOH00.0000.00421.982-0.186-0.1860.0000.0000.0000.000
210A309HOH0-0.043-0.04914.427-0.354-0.3540.0000.0000.0000.000
211A310HOH0-0.027-0.01623.4450.1210.1210.0000.0000.0000.000
212A317HOH0-0.042-0.02722.3140.2240.2240.0000.0000.0000.000
213A318HOH00.0260.00616.8910.0210.0210.0000.0000.0000.000
214A319HOH0-0.052-0.04227.6780.1680.1680.0000.0000.0000.000
215A320HOH0-0.062-0.06722.7490.2170.2170.0000.0000.0000.000
216A325HOH0-0.020-0.02010.4870.5280.5280.0000.0000.0000.000
217B241HOH0-0.021-0.01321.2780.0580.0580.0000.0000.0000.000
218B245HOH0-0.018-0.01217.6420.1340.1340.0000.0000.0000.000