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: 2JLGR

Calculation Name: 3ZLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLA

Chain ID: A

ChEMBL ID:

UniProt ID: P16495

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2847678.14815
FMO2-HF: Nuclear repulsion 2755031.65143
FMO2-HF: Total energy -92646.49672
FMO2-MP2: Total energy -92919.63307


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:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
-1.3980.857-0.017-1.258-0.980.005
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.015
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].
3A1MET00.008-0.0123.820-0.4221.833-0.017-1.258-0.9800.005
4A2ILE0-0.022-0.0046.8990.0440.0440.0000.0000.0000.000
5A3GLU-1-0.934-0.95510.330-0.645-0.6450.0000.0000.0000.000
6A4LEU0-0.064-0.03213.6330.0190.0190.0000.0000.0000.000
7A5GLU-1-0.900-0.94116.769-0.424-0.4240.0000.0000.0000.000
8A6PHE0-0.055-0.04220.0930.0310.0310.0000.0000.0000.000
9A7HIS00.008-0.00223.812-0.014-0.0140.0000.0000.0000.000
10A8ASP-1-0.937-0.95527.333-0.166-0.1660.0000.0000.0000.000
11A9VAL0-0.017-0.01330.937-0.001-0.0010.0000.0000.0000.000
12A10ALA0-0.022-0.01733.7740.0030.0030.0000.0000.0000.000
13A11ALA00.0360.01337.3730.0060.0060.0000.0000.0000.000
14A12ASN0-0.068-0.02938.6420.0060.0060.0000.0000.0000.000
15A13THR00.0470.03438.3190.0010.0010.0000.0000.0000.000
16A14SER0-0.032-0.02641.3140.0040.0040.0000.0000.0000.000
17A15SER0-0.028-0.01643.624-0.002-0.0020.0000.0000.0000.000
18A16THR0-0.016-0.00642.109-0.002-0.0020.0000.0000.0000.000
19A17PHE00.0550.04844.5480.0010.0010.0000.0000.0000.000
20A18ASP-1-0.886-0.95846.427-0.055-0.0550.0000.0000.0000.000
21A19PRO00.0090.01550.022-0.001-0.0010.0000.0000.0000.000
22A20GLU-1-0.740-0.87351.158-0.044-0.0440.0000.0000.0000.000
23A21VAL00.0180.01851.1690.0010.0010.0000.0000.0000.000
24A22ALA00.0220.01448.373-0.001-0.0010.0000.0000.0000.000
25A23TYR0-0.084-0.07250.2260.0000.0000.0000.0000.0000.000
26A24ALA0-0.0080.00552.9400.0010.0010.0000.0000.0000.000
27A25ASN00.0350.01748.8410.0030.0030.0000.0000.0000.000
28A26PHE00.0070.00149.6290.0000.0000.0000.0000.0000.000
29A27LYS10.8660.91051.7820.0400.0400.0000.0000.0000.000
30A28ARG10.8850.95652.4900.0570.0570.0000.0000.0000.000
31A29VAL0-0.018-0.00950.2000.0010.0010.0000.0000.0000.000
32A30HIS00.0360.01147.4310.0030.0030.0000.0000.0000.000
33A31THR0-0.113-0.06052.7350.0020.0020.0000.0000.0000.000
34A32THR00.0240.02455.7090.0020.0020.0000.0000.0000.000
35A33GLY00.0160.01556.2930.0020.0020.0000.0000.0000.000
36A34LEU0-0.048-0.02453.9350.0000.0000.0000.0000.0000.000
37A35SER00.028-0.01057.1600.0020.0020.0000.0000.0000.000
38A36TYR00.029-0.03557.866-0.001-0.0010.0000.0000.0000.000
39A37ASP-1-0.827-0.89758.670-0.024-0.0240.0000.0000.0000.000
40A38HIS00.0240.02754.0050.0000.0000.0000.0000.0000.000
41A39ILE00.0200.02053.598-0.001-0.0010.0000.0000.0000.000
42A40ARG10.9110.94954.0650.0220.0220.0000.0000.0000.000
43A41ILE0-0.028-0.01250.9190.0010.0010.0000.0000.0000.000
44A42PHE0-0.0200.00146.6760.0000.0000.0000.0000.0000.000
45A43TYR00.014-0.01249.8210.0000.0000.0000.0000.0000.000
46A44ILE0-0.029-0.00651.5630.0010.0010.0000.0000.0000.000
47A45LYS10.8340.89848.1520.0250.0250.0000.0000.0000.000
48A46GLY00.0710.04347.129-0.002-0.0020.0000.0000.0000.000
49A47ARG10.9330.95545.5040.0150.0150.0000.0000.0000.000
50A48GLU-1-0.803-0.88943.932-0.025-0.0250.0000.0000.0000.000
51A49ILE00.0270.02542.447-0.002-0.0020.0000.0000.0000.000
52A50LYS10.9850.99940.3620.0370.0370.0000.0000.0000.000
53A51THR0-0.021-0.01338.944-0.002-0.0020.0000.0000.0000.000
54A52SER0-0.043-0.04537.615-0.003-0.0030.0000.0000.0000.000
55A53LEU00.0230.00437.094-0.002-0.0020.0000.0000.0000.000
56A54ALA0-0.003-0.00235.078-0.005-0.0050.0000.0000.0000.000
57A55LYS10.8850.94433.1650.0300.0300.0000.0000.0000.000
58A56ARG10.9450.98431.7300.0500.0500.0000.0000.0000.000
59A57SER00.0310.01028.049-0.002-0.0020.0000.0000.0000.000
60A58GLU-1-0.849-0.92329.928-0.095-0.0950.0000.0000.0000.000
61A59TRP00.0800.02431.1170.0090.0090.0000.0000.0000.000
62A60GLU-1-0.874-0.92632.822-0.094-0.0940.0000.0000.0000.000
63A61VAL0-0.015-0.00635.9390.0010.0010.0000.0000.0000.000
64A62THR00.0130.00938.3460.0010.0010.0000.0000.0000.000
65A63LEU0-0.071-0.03841.9930.0030.0030.0000.0000.0000.000
66A64ASN00.0170.00044.618-0.002-0.0020.0000.0000.0000.000
67A65LEU0-0.041-0.00847.4360.0030.0030.0000.0000.0000.000
68A66GLY00.0340.00550.1860.0010.0010.0000.0000.0000.000
69A67GLY0-0.019-0.02051.706-0.001-0.0010.0000.0000.0000.000
70A68TRP00.0410.03050.763-0.001-0.0010.0000.0000.0000.000
71A69LYS10.9670.97945.2890.0550.0550.0000.0000.0000.000
72A70ILE00.0040.00446.162-0.001-0.0010.0000.0000.0000.000
73A71THR00.0140.01840.7210.0030.0030.0000.0000.0000.000
74A72VAL0-0.089-0.04640.7670.0010.0010.0000.0000.0000.000
75A73TYR00.0330.01936.4620.0000.0000.0000.0000.0000.000
76A74ASN0-0.057-0.02634.0720.0090.0090.0000.0000.0000.000
77A75THR00.032-0.01034.386-0.006-0.0060.0000.0000.0000.000
78A76ASN0-0.137-0.05435.5700.0000.0000.0000.0000.0000.000
79A77PHE00.0150.01627.2410.0040.0040.0000.0000.0000.000
80A78PRO0-0.029-0.03329.257-0.006-0.0060.0000.0000.0000.000
81A79GLY00.0170.00627.267-0.003-0.0030.0000.0000.0000.000
82A80ASN00.0040.01427.903-0.017-0.0170.0000.0000.0000.000
83A81ARG10.8600.95130.5090.0760.0760.0000.0000.0000.000
84A82ASN0-0.049-0.02930.696-0.002-0.0020.0000.0000.0000.000
85A83ASN00.0740.04230.070-0.015-0.0150.0000.0000.0000.000
86A84PRO0-0.008-0.00332.1240.0080.0080.0000.0000.0000.000
87A85VAL0-0.022-0.00735.347-0.001-0.0010.0000.0000.0000.000
88A86PRO00.0570.04037.9380.0020.0020.0000.0000.0000.000
89A87ASP-1-0.838-0.92440.733-0.079-0.0790.0000.0000.0000.000
90A88ASP-1-0.946-0.97843.729-0.079-0.0790.0000.0000.0000.000
91A89GLY00.0240.02242.0760.0010.0010.0000.0000.0000.000
92A90LEU0-0.036-0.01142.7890.0040.0040.0000.0000.0000.000
93A91THR00.0790.02739.994-0.001-0.0010.0000.0000.0000.000
94A92LEU00.0450.00741.5990.0040.0040.0000.0000.0000.000
95A93HIS0-0.059-0.03343.2380.0030.0030.0000.0000.0000.000
96A94ARG10.8610.91642.8750.0770.0770.0000.0000.0000.000
97A95LEU00.0100.02246.1910.0020.0020.0000.0000.0000.000
98A96SER0-0.006-0.02847.7560.0030.0030.0000.0000.0000.000
99A97GLY00.0420.02649.4000.0020.0020.0000.0000.0000.000
100A98PHE0-0.013-0.01648.7260.0020.0020.0000.0000.0000.000
101A99LEU0-0.013-0.00451.1950.0020.0020.0000.0000.0000.000
102A100ALA00.0270.02753.8790.0020.0020.0000.0000.0000.000
103A101ARG10.7630.86555.4300.0420.0420.0000.0000.0000.000
104A102TYR00.013-0.00556.5350.0020.0020.0000.0000.0000.000
105A103LEU0-0.030-0.01557.6500.0010.0010.0000.0000.0000.000
106A104LEU00.0140.01459.9300.0010.0010.0000.0000.0000.000
107A105GLU-1-0.754-0.83460.248-0.037-0.0370.0000.0000.0000.000
108A106LYS10.8810.93461.4550.0330.0330.0000.0000.0000.000
109A107MET0-0.048-0.03163.8870.0010.0010.0000.0000.0000.000
110A108LEU00.0030.02165.7840.0010.0010.0000.0000.0000.000
111A109LYS10.9120.96965.2800.0310.0310.0000.0000.0000.000
112A110VAL0-0.060-0.01866.9280.0000.0000.0000.0000.0000.000
113A111SER00.0500.01369.9520.0010.0010.0000.0000.0000.000
114A112GLU-1-0.757-0.88271.600-0.021-0.0210.0000.0000.0000.000
115A113PRO00.0110.01072.9280.0000.0000.0000.0000.0000.000
116A114GLU-1-0.835-0.90466.759-0.026-0.0260.0000.0000.0000.000
117A115LYS10.8580.90667.9330.0220.0220.0000.0000.0000.000
118A116LEU00.0110.01667.7870.0000.0000.0000.0000.0000.000
119A117ILE0-0.0080.01365.1990.0000.0000.0000.0000.0000.000
120A118ILE0-0.034-0.01462.4760.0000.0000.0000.0000.0000.000
121A119LYS10.8760.92663.4890.0210.0210.0000.0000.0000.000
122A120SER0-0.038-0.01264.9080.0000.0000.0000.0000.0000.000
123A121LYS10.8080.90061.2510.0230.0230.0000.0000.0000.000
124A122ILE0-0.016-0.01157.7790.0000.0000.0000.0000.0000.000
125A123ILE00.0360.03057.6840.0010.0010.0000.0000.0000.000
126A124ASN00.021-0.00355.204-0.002-0.0020.0000.0000.0000.000
127A125PRO0-0.020-0.01152.4440.0010.0010.0000.0000.0000.000
128A126LEU0-0.008-0.00650.0190.0020.0020.0000.0000.0000.000
129A127ALA00.0330.03254.2190.0010.0010.0000.0000.0000.000
130A128GLU-1-0.751-0.85157.824-0.017-0.0170.0000.0000.0000.000
131A129LYS10.7540.88653.9160.0150.0150.0000.0000.0000.000
132A130ASN0-0.141-0.08454.5340.0020.0020.0000.0000.0000.000
133A131GLY0-0.031-0.01758.5850.0000.0000.0000.0000.0000.000
134A132ILE00.0260.04260.5380.0000.0000.0000.0000.0000.000
135A133THR0-0.042-0.03761.7080.0000.0000.0000.0000.0000.000
136A134TRP00.031-0.02461.349-0.001-0.0010.0000.0000.0000.000
137A135ASN0-0.036-0.01465.275-0.001-0.0010.0000.0000.0000.000
138A136ASP-1-0.808-0.89065.182-0.016-0.0160.0000.0000.0000.000
139A137GLY00.0400.02366.6720.0000.0000.0000.0000.0000.000
140A138GLU-1-0.867-0.94264.563-0.023-0.0230.0000.0000.0000.000
141A139GLU-1-0.847-0.91562.712-0.027-0.0270.0000.0000.0000.000
142A140VAL00.0320.02761.208-0.001-0.0010.0000.0000.0000.000
143A141TYR0-0.030-0.03660.082-0.001-0.0010.0000.0000.0000.000
144A142LEU00.001-0.01058.324-0.001-0.0010.0000.0000.0000.000
145A143SER0-0.015-0.02456.688-0.001-0.0010.0000.0000.0000.000
146A144PHE0-0.0150.00055.342-0.001-0.0010.0000.0000.0000.000
147A145PHE0-0.070-0.01052.8240.0000.0000.0000.0000.0000.000
148A146PRO00.0070.00647.819-0.001-0.0010.0000.0000.0000.000
149A147GLY00.0360.01749.034-0.001-0.0010.0000.0000.0000.000
150A148SER0-0.011-0.01849.804-0.002-0.0020.0000.0000.0000.000
151A149GLU-1-0.724-0.85348.541-0.046-0.0460.0000.0000.0000.000
152A150MET0-0.090-0.03148.537-0.002-0.0020.0000.0000.0000.000
153A151PHE00.0140.00651.645-0.001-0.0010.0000.0000.0000.000
154A152LEU00.0090.00554.3810.0020.0020.0000.0000.0000.000
155A153GLY00.0180.00657.1150.0020.0020.0000.0000.0000.000
156A154THR00.001-0.00558.7450.0010.0010.0000.0000.0000.000
157A155PHE0-0.015-0.00955.7850.0010.0010.0000.0000.0000.000
158A156ARG10.8750.92060.3320.0270.0270.0000.0000.0000.000
159A157PHE00.0290.00558.1580.0010.0010.0000.0000.0000.000
160A158TYR00.0560.03759.4180.0000.0000.0000.0000.0000.000
161A159PRO0-0.0210.00054.2950.0010.0010.0000.0000.0000.000
162A160LEU0-0.016-0.00554.3610.0000.0000.0000.0000.0000.000
163A161ALA00.0230.02155.9670.0010.0010.0000.0000.0000.000
164A162ILE00.0070.00455.3340.0010.0010.0000.0000.0000.000
165A163GLY00.007-0.00653.6640.0010.0010.0000.0000.0000.000
166A164ILE0-0.006-0.01254.2890.0010.0010.0000.0000.0000.000
167A165TYR0-0.0040.00056.3400.0020.0020.0000.0000.0000.000
168A166LYS10.9100.96052.3880.0240.0240.0000.0000.0000.000
169A167VAL0-0.035-0.01651.1610.0010.0010.0000.0000.0000.000
170A168GLN00.0030.00953.6960.0020.0020.0000.0000.0000.000
171A169ARG10.8150.91556.7230.0160.0160.0000.0000.0000.000
172A170LYS10.9320.94953.4590.0100.0100.0000.0000.0000.000
173A171GLU-1-0.836-0.89152.220-0.016-0.0160.0000.0000.0000.000
174A172MET0-0.059-0.01948.949-0.001-0.0010.0000.0000.0000.000
175A173GLU-1-0.784-0.89343.763-0.026-0.0260.0000.0000.0000.000
176A174PRO00.050-0.00747.895-0.002-0.0020.0000.0000.0000.000
177A175LYS10.9200.96840.4600.0320.0320.0000.0000.0000.000
178A176TYR0-0.076-0.04342.783-0.004-0.0040.0000.0000.0000.000
179A177LEU0-0.0140.00346.622-0.001-0.0010.0000.0000.0000.000
180A178GLU-1-0.889-0.93842.861-0.051-0.0510.0000.0000.0000.000
181A179LYS10.8070.88644.7120.0520.0520.0000.0000.0000.000
182A180THR00.0340.00346.741-0.002-0.0020.0000.0000.0000.000
183A181MET00.0240.01149.8510.0000.0000.0000.0000.0000.000
184A182ARG10.8880.96242.4280.0580.0580.0000.0000.0000.000
185A183GLN0-0.025-0.00647.661-0.003-0.0030.0000.0000.0000.000
186A184ARG10.9170.95749.4640.0580.0580.0000.0000.0000.000
187A185TYR0-0.010-0.00954.8460.0010.0010.0000.0000.0000.000
188A186MET0-0.009-0.00658.3800.0010.0010.0000.0000.0000.000
189A187GLY00.0140.00958.501-0.001-0.0010.0000.0000.0000.000
190A188LEU0-0.030-0.00457.646-0.001-0.0010.0000.0000.0000.000
191A189GLU-1-0.757-0.88552.915-0.052-0.0520.0000.0000.0000.000
192A190ALA00.0430.02952.4180.0020.0020.0000.0000.0000.000
193A191ALA00.0270.02754.5340.0020.0020.0000.0000.0000.000
194A192THR0-0.038-0.02656.3850.0020.0020.0000.0000.0000.000
195A193TRP0-0.020-0.03554.5250.0030.0030.0000.0000.0000.000
196A194THR0-0.041-0.02756.7130.0020.0020.0000.0000.0000.000
197A195VAL00.0310.00859.0590.0010.0010.0000.0000.0000.000
198A196SER0-0.0300.00562.6080.0010.0010.0000.0000.0000.000
199A197LYS10.8260.89162.4840.0290.0290.0000.0000.0000.000
200A198LEU00.0380.02962.4090.0000.0000.0000.0000.0000.000
201A199THR00.035-0.00563.9350.0010.0010.0000.0000.0000.000
202A200GLU-1-0.802-0.87964.521-0.026-0.0260.0000.0000.0000.000
203A201VAL00.0340.01959.9420.0010.0010.0000.0000.0000.000
204A202GLN0-0.036-0.00662.9480.0020.0020.0000.0000.0000.000
205A203SER0-0.030-0.00465.4820.0010.0010.0000.0000.0000.000
206A204ALA00.0320.00962.7110.0010.0010.0000.0000.0000.000
207A205LEU00.006-0.01261.2380.0000.0000.0000.0000.0000.000
208A206THR0-0.007-0.00863.4830.0010.0010.0000.0000.0000.000
209A207VAL00.0050.01665.8500.0010.0010.0000.0000.0000.000
210A208VAL0-0.012-0.00460.7340.0010.0010.0000.0000.0000.000
211A209SER0-0.082-0.05263.8160.0010.0010.0000.0000.0000.000
212A210SER0-0.058-0.04264.9320.0010.0010.0000.0000.0000.000
213A211LEU0-0.0100.00063.3840.0010.0010.0000.0000.0000.000
214A212GLY00.0120.02265.2960.0010.0010.0000.0000.0000.000
215A213TRP00.0010.00156.9890.0000.0000.0000.0000.0000.000
216A214LYS10.9150.96260.2670.0110.0110.0000.0000.0000.000
217A215LYS10.9740.99354.7570.0080.0080.0000.0000.0000.000
218A216THR0-0.010-0.01657.3000.0000.0000.0000.0000.0000.000
219A217ASN00.0480.01756.153-0.001-0.0010.0000.0000.0000.000
220A218VAL00.0130.01259.8000.0010.0010.0000.0000.0000.000
221A219SER00.0530.01963.169-0.001-0.0010.0000.0000.0000.000
222A220ALA00.0620.02366.8580.0000.0000.0000.0000.0000.000
223A221ALA00.0780.02669.4800.0000.0000.0000.0000.0000.000
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