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: 3JYKL

Calculation Name: 3ZLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLC

Chain ID: A

ChEMBL ID:

UniProt ID: Q04651

Base Structure: X-ray

Registration Date: 2023-09-24

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2840088.356988
FMO2-HF: Nuclear repulsion 2748927.2855
FMO2-HF: Total energy -91161.071488
FMO2-MP2: Total energy -91428.522525


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:51:ILE)


Summations of interaction energy for fragment #1(A:51:ILE)
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.
-9.638-3.9364.18-3.851-6.032-0.016
Interaction energy analysis for fragmet #1(A:51:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.023
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].
3A53GLN0-0.037-0.0213.388-1.1211.6250.053-1.326-1.4740.002
4A54GLN0-0.055-0.0245.4380.5290.5290.0000.0000.0000.000
5A55TYR00.0230.0159.1710.1330.1330.0000.0000.0000.000
6A56VAL0-0.049-0.02012.3420.0320.0320.0000.0000.0000.000
7A57VAL00.0230.00214.8730.0090.0090.0000.0000.0000.000
8A58ASP-1-0.808-0.88117.107-0.224-0.2240.0000.0000.0000.000
9A59SER0-0.086-0.05118.3440.0300.0300.0000.0000.0000.000
10A60GLN0-0.057-0.04318.9950.0180.0180.0000.0000.0000.000
11A61VAL00.0340.03120.7300.0080.0080.0000.0000.0000.000
12A62ARG10.8380.92816.5800.0330.0330.0000.0000.0000.000
13A63ASP-1-0.894-0.95323.021-0.055-0.0550.0000.0000.0000.000
14A64THR0-0.064-0.03425.574-0.001-0.0010.0000.0000.0000.000
15A65VAL0-0.020-0.00721.208-0.002-0.0020.0000.0000.0000.000
16A66GLN00.0290.01622.622-0.001-0.0010.0000.0000.0000.000
17A67ILE00.0070.00722.698-0.015-0.0150.0000.0000.0000.000
18A68ASN0-0.0290.00420.6120.0220.0220.0000.0000.0000.000
19A69MET00.0090.00324.102-0.020-0.0200.0000.0000.0000.000
20A70ASP-1-0.823-0.88226.1530.0080.0080.0000.0000.0000.000
21A71ILE00.0200.00227.389-0.009-0.0090.0000.0000.0000.000
22A72TYR00.0340.02730.1150.0070.0070.0000.0000.0000.000
23A73VAL00.017-0.00633.281-0.008-0.0080.0000.0000.0000.000
24A74ASN0-0.045-0.01536.0340.0030.0030.0000.0000.0000.000
25A75THR0-0.013-0.02839.2130.0000.0000.0000.0000.0000.000
26A76LYS10.8750.94240.6120.0120.0120.0000.0000.0000.000
27A77CYS0-0.0140.02637.8580.0020.0020.0000.0000.0000.000
28A78ASP-1-0.831-0.90541.444-0.014-0.0140.0000.0000.0000.000
29A79TRP0-0.069-0.06544.143-0.001-0.0010.0000.0000.0000.000
30A80LEU0-0.024-0.00638.065-0.003-0.0030.0000.0000.0000.000
31A81GLN0-0.053-0.03540.4770.0040.0040.0000.0000.0000.000
32A82ILE00.0550.02733.972-0.004-0.0040.0000.0000.0000.000
33A83ASN0-0.038-0.02535.9970.0050.0050.0000.0000.0000.000
34A84VAL00.0470.02631.416-0.005-0.0050.0000.0000.0000.000
35A85ARG10.8390.92333.6240.0830.0830.0000.0000.0000.000
36A86ASP-1-0.731-0.84131.442-0.076-0.0760.0000.0000.0000.000
37A87GLN0-0.044-0.03031.299-0.003-0.0030.0000.0000.0000.000
38A88THR0-0.119-0.06633.3440.0040.0040.0000.0000.0000.000
39A89MET0-0.074-0.02333.6220.0080.0080.0000.0000.0000.000
40A90ASP-1-0.873-0.93737.166-0.055-0.0550.0000.0000.0000.000
41A91ARG10.8290.89237.9860.0560.0560.0000.0000.0000.000
42A92LYS10.9020.96833.0490.0340.0340.0000.0000.0000.000
43A93LEU0-0.027-0.02137.187-0.002-0.0020.0000.0000.0000.000
44A94VAL0-0.038-0.01733.2940.0020.0020.0000.0000.0000.000
45A95LEU0-0.069-0.04836.4950.0000.0000.0000.0000.0000.000
46A96GLU-1-0.960-0.97236.4570.0050.0050.0000.0000.0000.000
47A97GLU-1-0.822-0.91231.745-0.015-0.0150.0000.0000.0000.000
48A98LEU0-0.046-0.02130.425-0.002-0.0020.0000.0000.0000.000
49A99GLN0-0.050-0.01133.2760.0020.0020.0000.0000.0000.000
50A100LEU0-0.014-0.03034.644-0.006-0.0060.0000.0000.0000.000
51A101GLU-1-0.882-0.93536.7340.0180.0180.0000.0000.0000.000
52A102GLU-1-0.842-0.93238.317-0.013-0.0130.0000.0000.0000.000
53A103MET0-0.049-0.00534.9970.0030.0030.0000.0000.0000.000
54A104PRO0-0.041-0.00739.913-0.003-0.0030.0000.0000.0000.000
55A105PHE0-0.010-0.02134.9920.0010.0010.0000.0000.0000.000
56A106PHE0-0.028-0.02533.0680.0000.0000.0000.0000.0000.000
57A107ILE00.0570.03031.408-0.003-0.0030.0000.0000.0000.000
58A108PRO00.0190.02328.9920.0030.0030.0000.0000.0000.000
59A109TYR00.000-0.01229.699-0.006-0.0060.0000.0000.0000.000
60A110ASP-1-0.940-0.96524.400-0.011-0.0110.0000.0000.0000.000
61A111THR0-0.035-0.00424.546-0.006-0.0060.0000.0000.0000.000
62A112LYS10.7760.88320.0910.1540.1540.0000.0000.0000.000
63A113VAL00.0510.01526.1240.0020.0020.0000.0000.0000.000
64A114ASN00.026-0.00524.9110.0000.0000.0000.0000.0000.000
65A115ASP-1-0.812-0.89628.900-0.095-0.0950.0000.0000.0000.000
66A116ILE00.0040.01130.6770.0050.0050.0000.0000.0000.000
67A117ASN0-0.061-0.02232.1320.0060.0060.0000.0000.0000.000
68A118GLU-1-0.990-0.98835.574-0.064-0.0640.0000.0000.0000.000
69A129GLY0-0.035-0.03633.8170.0010.0010.0000.0000.0000.000
70A130GLU-1-0.787-0.87033.114-0.040-0.0400.0000.0000.0000.000
71A131ALA0-0.035-0.02333.309-0.002-0.0020.0000.0000.0000.000
72A132ILE0-0.029-0.00132.729-0.002-0.0020.0000.0000.0000.000
73A133PRO00.0240.01835.9980.0030.0030.0000.0000.0000.000
74A134ALA00.0210.01239.1020.0020.0020.0000.0000.0000.000
75A135GLU-1-0.895-0.95440.581-0.024-0.0240.0000.0000.0000.000
76A136PHE0-0.005-0.00837.7430.0020.0020.0000.0000.0000.000
77A137ARG10.8070.89331.7540.0320.0320.0000.0000.0000.000
78A138GLU-1-0.917-0.96234.6870.0110.0110.0000.0000.0000.000
79A139LYS10.7800.89237.3900.0140.0140.0000.0000.0000.000
80A140LEU0-0.0110.00137.2310.0020.0020.0000.0000.0000.000
81A141ASP-1-0.801-0.91441.2410.0180.0180.0000.0000.0000.000
82A142THR0-0.119-0.06542.6380.0030.0030.0000.0000.0000.000
83A143ARG10.8650.92442.613-0.025-0.0250.0000.0000.0000.000
84A144SER00.0610.03938.5050.0000.0000.0000.0000.0000.000
85A145PHE0-0.0080.01835.5050.0020.0020.0000.0000.0000.000
86A154ALA0-0.045-0.03647.124-0.001-0.0010.0000.0000.0000.000
87A155HIS00.0170.00845.0460.0000.0000.0000.0000.0000.000
88A156LEU00.0420.02447.5280.0000.0000.0000.0000.0000.000
89A157PRO00.0630.02946.6600.0000.0000.0000.0000.0000.000
90A158GLU-1-0.933-0.96644.587-0.025-0.0250.0000.0000.0000.000
91A159PHE00.006-0.00241.716-0.001-0.0010.0000.0000.0000.000
92A160ASN0-0.060-0.03942.5300.0050.0050.0000.0000.0000.000
93A161GLY00.0130.00039.486-0.003-0.0030.0000.0000.0000.000
94A163HIS00.023-0.01130.373-0.004-0.0040.0000.0000.0000.000
95A164VAL0-0.029-0.02632.4310.0030.0030.0000.0000.0000.000
96A165PHE00.0030.00129.343-0.004-0.0040.0000.0000.0000.000
97A166GLY00.0100.00528.5200.0050.0050.0000.0000.0000.000
98A167SER0-0.022-0.02424.800-0.003-0.0030.0000.0000.0000.000
99A168ILE0-0.016-0.00127.3490.0050.0050.0000.0000.0000.000
100A169PRO0-0.0130.00927.447-0.008-0.0080.0000.0000.0000.000
101A170VAL0-0.039-0.02526.5560.0000.0000.0000.0000.0000.000
102A171ASN0-0.005-0.02927.5690.0050.0050.0000.0000.0000.000
103A172ARG10.8500.94918.2340.1490.1490.0000.0000.0000.000
104A173VAL0-0.049-0.03425.572-0.012-0.0120.0000.0000.0000.000
105A174SER00.004-0.00627.690-0.001-0.0010.0000.0000.0000.000
106A175GLY00.024-0.01128.7360.0130.0130.0000.0000.0000.000
107A176GLU-1-0.800-0.86529.888-0.096-0.0960.0000.0000.0000.000
108A177LEU00.0440.04028.9040.0080.0080.0000.0000.0000.000
109A178GLN0-0.065-0.04931.653-0.001-0.0010.0000.0000.0000.000
110A179ILE00.0700.04831.9340.0060.0060.0000.0000.0000.000
111A180THR0-0.013-0.01235.995-0.002-0.0020.0000.0000.0000.000
112A181ALA00.0720.03639.6080.0040.0040.0000.0000.0000.000
113A182LYS10.7910.91443.1580.0160.0160.0000.0000.0000.000
114A183SER00.006-0.02645.3860.0000.0000.0000.0000.0000.000
115A184LEU0-0.050-0.01047.7870.0000.0000.0000.0000.0000.000
116A185GLY00.0450.02650.571-0.001-0.0010.0000.0000.0000.000
117A186TYR00.0350.00253.6920.0010.0010.0000.0000.0000.000
118A187VAL00.0240.01957.0770.0010.0010.0000.0000.0000.000
119A188ALA00.019-0.00958.083-0.001-0.0010.0000.0000.0000.000
120A189SER0-0.0280.00954.218-0.001-0.0010.0000.0000.0000.000
121A190ARG10.8350.91253.1720.0220.0220.0000.0000.0000.000
122A191LYS10.9750.98448.3900.0340.0340.0000.0000.0000.000
123A192ALA00.0440.04246.6570.0010.0010.0000.0000.0000.000
124A193PRO0-0.022-0.01548.740-0.002-0.0020.0000.0000.0000.000
125A194LEU0-0.019-0.02447.5790.0000.0000.0000.0000.0000.000
126A195GLU-1-0.910-0.93047.528-0.025-0.0250.0000.0000.0000.000
127A196GLU-1-0.824-0.89147.035-0.020-0.0200.0000.0000.0000.000
128A197LEU0-0.062-0.03143.2540.0000.0000.0000.0000.0000.000
129A198LYS10.8290.92241.7310.0280.0280.0000.0000.0000.000
130A199PHE00.0170.00237.2670.0030.0030.0000.0000.0000.000
131A200ASN00.0210.01336.131-0.009-0.0090.0000.0000.0000.000
132A201HIS0-0.038-0.01930.637-0.001-0.0010.0000.0000.0000.000
133A202VAL00.0230.00828.727-0.005-0.0050.0000.0000.0000.000
134A203ILE0-0.025-0.00724.8030.0050.0050.0000.0000.0000.000
135A204ASN00.002-0.01125.355-0.012-0.0120.0000.0000.0000.000
136A205GLU-1-0.848-0.90621.039-0.036-0.0360.0000.0000.0000.000
137A206PHE0-0.007-0.01121.7800.0020.0020.0000.0000.0000.000
138A207SER0-0.008-0.01018.275-0.024-0.0240.0000.0000.0000.000
139A208PHE00.009-0.01018.7350.0080.0080.0000.0000.0000.000
140A209GLY0-0.0060.00618.000-0.012-0.0120.0000.0000.0000.000
141A210ASP-1-0.880-0.92816.7770.0770.0770.0000.0000.0000.000
142A211PHE00.0480.01516.136-0.020-0.0200.0000.0000.0000.000
143A212TYR0-0.063-0.0589.6140.0430.0430.0000.0000.0000.000
144A213PRO0-0.035-0.04010.270-0.039-0.0390.0000.0000.0000.000
145A214TYR0-0.080-0.0426.7070.2440.2440.0000.0000.0000.000
146A215ILE0-0.0250.0179.423-0.132-0.1320.0000.0000.0000.000
147A216ASP-1-0.913-0.95912.323-0.237-0.2370.0000.0000.0000.000
148A217ASN0-0.047-0.03014.097-0.070-0.0700.0000.0000.0000.000
149A218PRO0-0.014-0.01216.6280.0240.0240.0000.0000.0000.000
150A219LEU00.0040.00119.1990.0110.0110.0000.0000.0000.000
151A220ASP-1-0.741-0.83118.728-0.074-0.0740.0000.0000.0000.000
152A221ASN0-0.021-0.01020.754-0.002-0.0020.0000.0000.0000.000
153A222THR0-0.057-0.02723.460-0.009-0.0090.0000.0000.0000.000
154A223ALA00.0450.01025.9440.0120.0120.0000.0000.0000.000
155A224GLN0-0.070-0.03029.156-0.010-0.0100.0000.0000.0000.000
156A225PHE0-0.038-0.03532.2660.0090.0090.0000.0000.0000.000
157A226ASN00.0720.03536.0250.0010.0010.0000.0000.0000.000
158A227GLN0-0.009-0.01439.2680.0040.0040.0000.0000.0000.000
159A228ASP-1-0.896-0.93342.457-0.045-0.0450.0000.0000.0000.000
160A229GLU-1-0.957-0.98441.809-0.060-0.0600.0000.0000.0000.000
161A230PRO00.0630.04841.044-0.003-0.0030.0000.0000.0000.000
162A231LEU0-0.046-0.03541.1520.0000.0000.0000.0000.0000.000
163A232THR0-0.063-0.03937.041-0.002-0.0020.0000.0000.0000.000
164A233THR0-0.043-0.00636.7170.0030.0030.0000.0000.0000.000
165A234TYR0-0.008-0.01232.565-0.004-0.0040.0000.0000.0000.000
166A235VAL0-0.048-0.03531.3880.0040.0040.0000.0000.0000.000
167A236TYR00.0280.01426.403-0.012-0.0120.0000.0000.0000.000
168A237TYR0-0.049-0.03326.9600.0110.0110.0000.0000.0000.000
169A238THR0-0.029-0.03022.203-0.015-0.0150.0000.0000.0000.000
170A239SER0-0.079-0.07120.5460.0260.0260.0000.0000.0000.000
171A240VAL0-0.0090.00118.222-0.034-0.0340.0000.0000.0000.000
172A241VAL0-0.0150.00013.3770.0010.0010.0000.0000.0000.000
173A242PRO00.0350.02514.569-0.008-0.0080.0000.0000.0000.000
174A243THR0-0.025-0.0269.408-0.057-0.0570.0000.0000.0000.000
175A244LEU00.0100.0189.8470.1020.1020.0000.0000.0000.000
176A245PHE00.0710.0205.347-0.111-0.1110.0000.0000.0000.000
177A246LYS10.9210.9486.1250.3990.3990.0000.0000.0000.000
178A247LYS10.8610.9352.774-5.552-4.6540.227-0.288-0.8380.003
179A248LEU0-0.044-0.0176.3390.0250.0250.0000.0000.0000.000
180A249GLY00.0270.0229.698-0.019-0.0190.0000.0000.0000.000
181A250ALA0-0.027-0.02811.458-0.061-0.0610.0000.0000.0000.000
182A251GLU-1-0.898-0.93914.1660.2190.2190.0000.0000.0000.000
183A252VAL00.0060.01612.949-0.024-0.0240.0000.0000.0000.000
184A253ASP-1-0.832-0.93015.285-0.111-0.1110.0000.0000.0000.000
185A254THR0-0.0180.00211.4490.0140.0140.0000.0000.0000.000
186A255ASN0-0.003-0.00713.827-0.072-0.0720.0000.0000.0000.000
187A256GLN00.0290.0389.8220.0130.0130.0000.0000.0000.000
188A257TYR0-0.023-0.03314.313-0.003-0.0030.0000.0000.0000.000
189A258SER00.0010.01916.902-0.011-0.0110.0000.0000.0000.000
190A259VAL00.041-0.00518.6730.0270.0270.0000.0000.0000.000
191A260ASN0-0.084-0.03322.250-0.003-0.0030.0000.0000.0000.000
192A261ASP-1-0.779-0.89925.444-0.147-0.1470.0000.0000.0000.000
193A262TYR0-0.066-0.03428.5150.0030.0030.0000.0000.0000.000
194A263ARG10.9050.95931.0380.1190.1190.0000.0000.0000.000
195A264TYR0-0.030-0.01634.831-0.003-0.0030.0000.0000.0000.000
196A265LEU00.0600.04238.8920.0030.0030.0000.0000.0000.000
197A266TYR00.0750.03641.9860.0010.0010.0000.0000.0000.000
198A267LYS10.8430.89544.3620.0720.0720.0000.0000.0000.000
199A268ASP-1-0.826-0.90142.808-0.072-0.0720.0000.0000.0000.000
200A269VAL00.0350.01741.0740.0000.0000.0000.0000.0000.000
201A270ALA00.0040.00743.8000.0020.0020.0000.0000.0000.000
202A271ALA0-0.033-0.02346.9580.0030.0030.0000.0000.0000.000
203A272LYS10.7850.87744.1220.0670.0670.0000.0000.0000.000
204A273GLY00.0750.05741.804-0.002-0.0020.0000.0000.0000.000
205A274ASP-1-0.884-0.94938.756-0.077-0.0770.0000.0000.0000.000
206A275LYS10.8090.90841.7750.0550.0550.0000.0000.0000.000
207A276MET0-0.054-0.01641.7580.0040.0040.0000.0000.0000.000
208A277PRO00.0170.01540.869-0.003-0.0030.0000.0000.0000.000
209A278GLY00.023-0.00638.0520.0040.0040.0000.0000.0000.000
210A279ILE0-0.0140.01431.735-0.004-0.0040.0000.0000.0000.000
211A280PHE0-0.065-0.03332.6040.0050.0050.0000.0000.0000.000
212A281PHE00.0660.02826.541-0.007-0.0070.0000.0000.0000.000
213A282LYS10.8470.91928.8340.1060.1060.0000.0000.0000.000
214A283TYR00.0440.03224.747-0.009-0.0090.0000.0000.0000.000
215A284ASN00.016-0.00224.2270.0170.0170.0000.0000.0000.000
216A285PHE00.0460.02220.804-0.013-0.0130.0000.0000.0000.000
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