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: ZYZRN

Calculation Name: 2Y2C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y2C

Chain ID: A

ChEMBL ID:

UniProt ID: P82974

Base Structure: X-ray

Registration Date: 2023-03-14

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1937889.577808
FMO2-HF: Nuclear repulsion 1868134.184222
FMO2-HF: Total energy -69755.393585
FMO2-MP2: Total energy -69960.110354


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:2:LEU)


Summations of interaction energy for fragment #1(A:2: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.
-7.097-21.29330.98-5.933-10.8490.01
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.021
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].
3A4ASP-1-0.864-0.9163.790-2.882-0.991-0.021-0.814-1.0550.001
4A5GLU-1-0.938-0.9766.1960.8210.8210.0000.0000.0000.000
5A6GLY00.0270.0368.5100.0850.0850.0000.0000.0000.000
6A7TRP0-0.048-0.0407.2410.1570.1570.0000.0000.0000.000
7A8LEU0-0.015-0.0162.472-0.9670.4820.894-0.968-1.3750.004
8A9ALA0-0.003-0.0201.795-0.296-13.26323.301-5.916-4.4170.003
9A10GLU-1-0.965-0.9892.719-3.430-4.5580.2592.216-1.3470.001
10A11ALA0-0.0500.0034.683-0.933-0.883-0.001-0.007-0.0420.000
11A12ARG10.8530.9137.332-0.804-0.8040.0000.0000.0000.000
12A13ARG10.8970.9546.566-1.561-1.5610.0000.0000.0000.000
13A14VAL0-0.018-0.00611.941-0.175-0.1750.0000.0000.0000.000
14A15PRO0-0.017-0.01814.4150.0040.0040.0000.0000.0000.000
15A16SER00.006-0.02016.142-0.093-0.0930.0000.0000.0000.000
16A17PRO0-0.013-0.01418.9520.0070.0070.0000.0000.0000.000
17A18HIS0-0.068-0.02821.288-0.052-0.0520.0000.0000.0000.000
18A19TYR00.0080.00217.4550.0360.0360.0000.0000.0000.000
19A20ASP-1-0.783-0.85620.6260.2480.2480.0000.0000.0000.000
20A21CYS0-0.009-0.02019.9940.0400.0400.0000.0000.0000.000
21A22ARG10.8060.90714.052-0.466-0.4660.0000.0000.0000.000
22A23PRO0-0.027-0.01920.589-0.015-0.0150.0000.0000.0000.000
23A24ASP-1-0.920-0.96522.7350.1260.1260.0000.0000.0000.000
24A25ASP-1-0.958-0.95720.0160.1310.1310.0000.0000.0000.000
25A26GLU-1-0.834-0.88119.2670.1620.1620.0000.0000.0000.000
26A27ASN0-0.034-0.03114.8760.0500.0500.0000.0000.0000.000
27A28PRO0-0.0120.00212.783-0.022-0.0220.0000.0000.0000.000
28A29SER0-0.025-0.02814.401-0.016-0.0160.0000.0000.0000.000
29A30LEU0-0.032-0.00716.010-0.022-0.0220.0000.0000.0000.000
30A31LEU00.0000.02111.9920.0500.0500.0000.0000.0000.000
31A32VAL0-0.019-0.02614.850-0.059-0.0590.0000.0000.0000.000
32A33VAL00.005-0.00515.5230.0600.0600.0000.0000.0000.000
33A34HIS10.8350.92017.708-0.419-0.4190.0000.0000.0000.000
34A35ASN0-0.102-0.04919.3860.0230.0230.0000.0000.0000.000
35A36ILE00.0650.03420.589-0.013-0.0130.0000.0000.0000.000
36A37SER0-0.003-0.00722.866-0.001-0.0010.0000.0000.0000.000
37A38LEU0-0.0430.01524.628-0.014-0.0140.0000.0000.0000.000
38A39PRO00.054-0.00226.7450.0090.0090.0000.0000.0000.000
39A40PRO00.0100.00628.8700.0040.0040.0000.0000.0000.000
40A41GLY0-0.024-0.01228.588-0.012-0.0120.0000.0000.0000.000
41A42GLU-1-0.977-0.97228.3990.1490.1490.0000.0000.0000.000
42A43PHE0-0.008-0.02523.3310.0200.0200.0000.0000.0000.000
43A44GLY00.001-0.00422.423-0.018-0.0180.0000.0000.0000.000
44A45GLY0-0.0090.00923.3240.0030.0030.0000.0000.0000.000
45A46PRO00.0320.01222.4460.0320.0320.0000.0000.0000.000
46A47TRP00.0340.00123.3080.0210.0210.0000.0000.0000.000
47A48ILE00.0540.03519.705-0.005-0.0050.0000.0000.0000.000
48A49ASP-1-0.771-0.86918.1960.5480.5480.0000.0000.0000.000
49A50ALA00.0040.01720.5500.0040.0040.0000.0000.0000.000
50A51LEU0-0.010-0.00223.776-0.010-0.0100.0000.0000.0000.000
51A52PHE0-0.023-0.01018.444-0.013-0.0130.0000.0000.0000.000
52A53THR0-0.049-0.01419.7410.0150.0150.0000.0000.0000.000
53A54GLY00.0020.00022.213-0.019-0.0190.0000.0000.0000.000
54A55THR0-0.071-0.03324.671-0.027-0.0270.0000.0000.0000.000
55A56ILE0-0.053-0.01326.934-0.010-0.0100.0000.0000.0000.000
56A57ASP-1-0.809-0.91628.5090.1430.1430.0000.0000.0000.000
57A58PRO0-0.026-0.02131.9600.0000.0000.0000.0000.0000.000
58A59ASN0-0.024-0.03434.292-0.008-0.0080.0000.0000.0000.000
59A60ALA0-0.0320.00932.206-0.006-0.0060.0000.0000.0000.000
60A61HIS00.0540.02632.893-0.003-0.0030.0000.0000.0000.000
61A62PRO00.0140.00534.8090.0020.0020.0000.0000.0000.000
62A63TYR0-0.018-0.02429.983-0.004-0.0040.0000.0000.0000.000
63A64PHE00.020-0.00629.1810.0080.0080.0000.0000.0000.000
64A65ALA00.0400.03032.8240.0050.0050.0000.0000.0000.000
65A66GLY0-0.029-0.01235.504-0.001-0.0010.0000.0000.0000.000
66A67ILE0-0.009-0.01928.5090.0010.0010.0000.0000.0000.000
67A68ALA00.0190.02230.5230.0130.0130.0000.0000.0000.000
68A69HIS0-0.072-0.02431.6480.0040.0040.0000.0000.0000.000
69A70LEU0-0.066-0.02227.7780.0000.0000.0000.0000.0000.000
70A71ARG10.9540.98026.792-0.222-0.2220.0000.0000.0000.000
71A72VAL0-0.015-0.00523.580-0.003-0.0030.0000.0000.0000.000
72A73SER00.005-0.00618.9020.0070.0070.0000.0000.0000.000
73A74ALA00.0410.02316.445-0.035-0.0350.0000.0000.0000.000
74A75HIS00.0100.00211.7760.0140.0140.0000.0000.0000.000
75A76CYS0-0.028-0.0248.9440.2240.2240.0000.0000.0000.000
76A77LEU00.0390.04012.588-0.163-0.1630.0000.0000.0000.000
77A78ILE0-0.036-0.00511.2830.1130.1130.0000.0000.0000.000
78A79ARG10.8520.90214.179-0.489-0.4890.0000.0000.0000.000
79A80ARG10.8540.90716.508-0.241-0.2410.0000.0000.0000.000
80A81ASP-1-0.875-0.93316.4370.3240.3240.0000.0000.0000.000
81A82GLY0-0.026-0.01813.920-0.034-0.0340.0000.0000.0000.000
82A83GLU-1-0.844-0.91811.9410.6860.6860.0000.0000.0000.000
83A84ILE0-0.015-0.0047.9110.0110.0110.0000.0000.0000.000
84A85VAL00.0050.01710.1570.1430.1430.0000.0000.0000.000
85A86GLN00.022-0.0027.8400.8490.8490.0000.0000.0000.000
86A87TYR0-0.023-0.03611.376-0.078-0.0780.0000.0000.0000.000
87A88VAL0-0.035-0.01613.359-0.107-0.1070.0000.0000.0000.000
88A89PRO00.0240.04311.0690.1940.1940.0000.0000.0000.000
89A90PHE00.029-0.0215.878-0.275-0.2750.0000.0000.0000.000
90A91ASP-1-0.834-0.91711.1320.4350.4350.0000.0000.0000.000
91A92LYS10.8720.95213.680-0.490-0.4900.0000.0000.0000.000
92A93ARG10.7810.87115.894-0.204-0.2040.0000.0000.0000.000
93A94ALA00.0190.02116.387-0.011-0.0110.0000.0000.0000.000
94A95TRP0-0.114-0.07218.398-0.044-0.0440.0000.0000.0000.000
95A96HIS00.1110.05618.079-0.018-0.0180.0000.0000.0000.000
96A97ALA00.0040.00621.265-0.021-0.0210.0000.0000.0000.000
97A98GLY0-0.011-0.00423.120-0.024-0.0240.0000.0000.0000.000
98A99VAL0-0.003-0.00926.5800.0000.0000.0000.0000.0000.000
99A100SER0-0.006-0.00525.6790.0050.0050.0000.0000.0000.000
100A101SER00.013-0.00127.417-0.006-0.0060.0000.0000.0000.000
101A102TYR00.0440.00521.1610.0090.0090.0000.0000.0000.000
102A103GLN0-0.033-0.01923.699-0.005-0.0050.0000.0000.0000.000
103A104GLY00.0170.01627.187-0.007-0.0070.0000.0000.0000.000
104A105ARG10.7940.88222.445-0.165-0.1650.0000.0000.0000.000
105A106GLU-1-0.918-0.97426.7060.1320.1320.0000.0000.0000.000
106A107ARG10.9310.95726.220-0.140-0.1400.0000.0000.0000.000
107A108CYS00.0750.04121.9300.0050.0050.0000.0000.0000.000
108A109ASN00.0090.04020.4150.0370.0370.0000.0000.0000.000
109A110ASP-1-0.839-0.91919.6890.2420.2420.0000.0000.0000.000
110A111PHE00.0270.02718.7930.0170.0170.0000.0000.0000.000
111A112SER0-0.038-0.04516.7130.0120.0120.0000.0000.0000.000
112A113ILE00.010-0.00410.4720.0290.0290.0000.0000.0000.000
113A114GLY0-0.0040.01114.351-0.050-0.0500.0000.0000.0000.000
114A115ILE0-0.017-0.02110.7790.1130.1130.0000.0000.0000.000
115A116GLU-1-0.861-0.95714.3910.3170.3170.0000.0000.0000.000
116A117LEU0-0.010-0.00515.1720.0610.0610.0000.0000.0000.000
117A118GLU-1-0.733-0.85318.0110.2920.2920.0000.0000.0000.000
118A119GLY0-0.002-0.00720.288-0.017-0.0170.0000.0000.0000.000
119A120THR00.0050.00723.3890.0010.0010.0000.0000.0000.000
120A121ASP-1-0.726-0.84825.7040.1830.1830.0000.0000.0000.000
121A122THR0-0.048-0.03327.528-0.006-0.0060.0000.0000.0000.000
122A123LEU0-0.0310.00726.218-0.013-0.0130.0000.0000.0000.000
123A124ALA00.0150.01024.4410.0110.0110.0000.0000.0000.000
124A125TYR0-0.019-0.02019.5970.0160.0160.0000.0000.0000.000
125A126THR0-0.021-0.02718.634-0.022-0.0220.0000.0000.0000.000
126A127ASP-1-0.848-0.93918.2830.1010.1010.0000.0000.0000.000
127A128ALA00.0030.00514.954-0.005-0.0050.0000.0000.0000.000
128A129GLN0-0.005-0.01213.769-0.001-0.0010.0000.0000.0000.000
129A130TYR00.0070.01513.9030.0570.0570.0000.0000.0000.000
130A131GLN0-0.011-0.00611.709-0.011-0.0110.0000.0000.0000.000
131A132GLN00.0210.0138.819-0.113-0.1130.0000.0000.0000.000
132A133LEU00.0220.0119.0560.2040.2040.0000.0000.0000.000
133A134ALA00.0000.0109.4880.1110.1110.0000.0000.0000.000
134A135ALA00.0000.0165.511-0.023-0.0230.0000.0000.0000.000
135A136VAL00.007-0.0024.4810.0880.281-0.001-0.009-0.1840.000
136A137THR00.001-0.0205.7680.1310.1310.0000.0000.0000.000
137A138ASN00.0140.0045.219-0.013-0.0130.0000.0000.0000.000
138A139ALA0-0.0020.0072.0821.256-1.9216.526-1.162-2.1870.001
139A140LEU0-0.020-0.0133.384-0.056-0.6490.0240.729-0.1600.000
140A141ILE0-0.0180.0006.554-0.223-0.2230.0000.0000.0000.000
141A142THR0-0.020-0.0044.675-0.281-0.195-0.001-0.002-0.0820.000
142A143ARG10.8910.9636.833-0.156-0.1560.0000.0000.0000.000
143A144TYR0-0.030-0.0298.231-0.077-0.0770.0000.0000.0000.000
144A145PRO00.0700.04211.2150.0550.0550.0000.0000.0000.000
145A146ALA0-0.010-0.01212.4380.0060.0060.0000.0000.0000.000
146A147ILE00.0370.01810.5030.0040.0040.0000.0000.0000.000
147A148ALA0-0.0070.00312.7140.0100.0100.0000.0000.0000.000
148A149ASN0-0.072-0.03213.909-0.019-0.0190.0000.0000.0000.000
149A150ASN0-0.067-0.01316.371-0.016-0.0160.0000.0000.0000.000
150A151MET00.0190.01113.8630.0570.0570.0000.0000.0000.000
151A152THR0-0.028-0.00917.079-0.038-0.0380.0000.0000.0000.000
152A153GLY00.0870.04119.1110.0400.0400.0000.0000.0000.000
153A154HIS00.008-0.03521.520-0.006-0.0060.0000.0000.0000.000
154A155CYS0-0.022-0.01223.087-0.014-0.0140.0000.0000.0000.000
155A156ASN0-0.060-0.02223.694-0.002-0.0020.0000.0000.0000.000
156A157ILE0-0.0150.02422.282-0.009-0.0090.0000.0000.0000.000
157A158ALA0-0.029-0.02025.927-0.004-0.0040.0000.0000.0000.000
158A159PRO00.0570.04128.3640.0030.0030.0000.0000.0000.000
159A160GLU-1-0.939-0.97730.5950.1050.1050.0000.0000.0000.000
160A161ARG10.8480.93027.481-0.184-0.1840.0000.0000.0000.000
161A162LYS10.8500.92426.195-0.217-0.2170.0000.0000.0000.000
162A163THR0-0.011-0.03328.461-0.007-0.0070.0000.0000.0000.000
163A164ASP-1-0.808-0.87023.3040.2590.2590.0000.0000.0000.000
164A165PRO0-0.054-0.04120.427-0.002-0.0020.0000.0000.0000.000
165A166GLY00.0990.05723.096-0.006-0.0060.0000.0000.0000.000
166A167PRO0-0.043-0.04025.0910.0030.0030.0000.0000.0000.000
167A168SER0-0.0310.00225.181-0.005-0.0050.0000.0000.0000.000
168A169PHE0-0.036-0.01416.4740.0050.0050.0000.0000.0000.000
169A170ASP-1-0.831-0.92420.8220.0830.0830.0000.0000.0000.000
170A171TRP00.040-0.00417.1340.0040.0040.0000.0000.0000.000
171A172ALA0-0.0280.00418.799-0.003-0.0030.0000.0000.0000.000
172A173ARG10.9150.95917.198-0.108-0.1080.0000.0000.0000.000
173A174PHE0-0.013-0.01411.585-0.020-0.0200.0000.0000.0000.000
174A175ARG10.9570.96314.189-0.120-0.1200.0000.0000.0000.000
175A176ALA0-0.0260.00315.135-0.020-0.0200.0000.0000.0000.000
176A177LEU0-0.039-0.01611.851-0.033-0.0330.0000.0000.0000.000
177A178VAL0-0.012-0.00710.322-0.023-0.0230.0000.0000.0000.000
178A179THR0-0.085-0.0409.662-0.040-0.0400.0000.0000.0000.000
179A180PRO0-0.0060.0098.987-0.021-0.0210.0000.0000.0000.000