FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YY3L2

Calculation Name: 2WRZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WRZ

Chain ID: B

ChEMBL ID:

UniProt ID: P02924

Base Structure: X-ray

Registration Date: 2023-06-20

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 294
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3673065.364225
FMO2-HF: Nuclear repulsion 3561912.158915
FMO2-HF: Total energy -111153.20531
FMO2-MP2: Total energy -111477.81137


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(B:1:GLU)


Summations of interaction energy for fragment #1(B:1:GLU)
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.
-103.31-105.10226.884-13.761-11.330.16
Interaction energy analysis for fragmet #1(B:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.818 / q_NPA : -0.895
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].
3B3LEU00.0050.0013.38810.64113.6630.069-1.627-1.4630.003
4B4LYS10.8460.9271.706-129.664-132.82517.318-7.928-6.2290.096
5B5LEU0-0.0040.0006.1930.4390.4390.0000.0000.0000.000
6B6GLY00.0380.0079.444-0.166-0.1660.0000.0000.0000.000
7B7PHE0-0.036-0.02612.427-0.996-0.9960.0000.0000.0000.000
8B8LEU00.0010.00915.751-0.391-0.3910.0000.0000.0000.000
9B9VAL00.0360.01218.496-0.500-0.5000.0000.0000.0000.000
10B10ALA0-0.0210.00822.139-0.016-0.0160.0000.0000.0000.000
11B11GLN0-0.012-0.02725.297-0.199-0.1990.0000.0000.0000.000
12B12PRO0-0.025-0.00723.476-0.063-0.0630.0000.0000.0000.000
13B13GLU-1-0.856-0.93625.52211.55211.5520.0000.0000.0000.000
14B14GLU-1-0.867-0.93628.9139.3319.3310.0000.0000.0000.000
15B15PRO0-0.030-0.01529.4730.4080.4080.0000.0000.0000.000
16B16ALA0-0.0020.00430.0510.1800.1800.0000.0000.0000.000
17B17SER00.010-0.00225.2550.1650.1650.0000.0000.0000.000
18B18GLN0-0.0450.00324.9270.4930.4930.0000.0000.0000.000
19B19THR00.0200.00924.8470.4530.4530.0000.0000.0000.000
20B20GLN0-0.053-0.05522.2900.8530.8530.0000.0000.0000.000
21B21TRP00.015-0.01118.8700.3900.3900.0000.0000.0000.000
22B22LYS10.9140.96818.821-11.389-11.3890.0000.0000.0000.000
23B23PHE0-0.022-0.02620.1030.2310.2310.0000.0000.0000.000
24B24ALA00.0450.03716.6640.2350.2350.0000.0000.0000.000
25B25ASP-1-0.822-0.89314.63120.87020.8700.0000.0000.0000.000
26B26LYS10.7220.85015.844-14.160-14.1600.0000.0000.0000.000
27B27ALA00.0670.02017.308-0.030-0.0300.0000.0000.0000.000
28B28GLY00.0400.01713.2860.2980.2980.0000.0000.0000.000
29B29LYS10.8840.92413.114-17.675-17.6750.0000.0000.0000.000
30B30ASP-1-0.791-0.84814.72214.60814.6080.0000.0000.0000.000
31B31LEU0-0.031-0.00814.652-0.459-0.4590.0000.0000.0000.000
32B32GLY0-0.0370.00311.0900.2750.2750.0000.0000.0000.000
33B33PHE0-0.052-0.0228.6282.0442.0440.0000.0000.0000.000
34B34GLU-1-0.861-0.9225.67037.84437.8440.0000.0000.0000.000
35B35VAL0-0.010-0.0109.2661.4201.4200.0000.0000.0000.000
36B36ILE00.0230.0097.955-1.598-1.5980.0000.0000.0000.000
37B37LYS10.7930.87912.254-21.376-21.3760.0000.0000.0000.000
38B38ILE0-0.002-0.00414.004-0.013-0.0130.0000.0000.0000.000
39B39ALA00.0230.01417.985-0.406-0.4060.0000.0000.0000.000
40B40VAL0-0.059-0.03519.8740.3020.3020.0000.0000.0000.000
41B41PRO00.0800.03822.875-0.262-0.2620.0000.0000.0000.000
42B42ASP-1-0.785-0.87525.83011.79611.7960.0000.0000.0000.000
43B43GLY00.0450.01625.2110.5880.5880.0000.0000.0000.000
44B44GLU-1-0.879-0.92124.40013.10713.1070.0000.0000.0000.000
45B45LYS10.8120.86822.398-11.679-11.6790.0000.0000.0000.000
46B46THR0-0.002-0.01920.7290.9610.9610.0000.0000.0000.000
47B47LEU0-0.047-0.03019.5930.9340.9340.0000.0000.0000.000
48B48ASN00.0350.00618.8141.0251.0250.0000.0000.0000.000
49B49ALA00.0090.01316.7751.2781.2780.0000.0000.0000.000
50B50ILE00.0010.00014.8261.6971.6970.0000.0000.0000.000
51B51ASP-1-0.744-0.82813.68220.41920.4190.0000.0000.0000.000
52B52SER00.0030.00212.9421.3981.3980.0000.0000.0000.000
53B53LEU0-0.051-0.00810.5342.7942.7940.0000.0000.0000.000
54B54ALA00.0310.0188.8934.8274.8270.0000.0000.0000.000
55B55ALA0-0.023-0.0118.8293.9583.9580.0000.0000.0000.000
56B56SER0-0.042-0.0237.3021.6681.6680.0000.0000.0000.000
57B57GLY00.0070.0104.57511.87712.040-0.001-0.018-0.1440.000
58B58ALA0-0.029-0.0154.12413.14513.3460.002-0.031-0.1720.000
59B59LYS10.8560.9111.836-108.122-110.1399.496-4.157-3.3220.061
60B60GLY00.0470.0127.683-3.542-3.5420.0000.0000.0000.000
61B61PHE0-0.058-0.03610.9861.3891.3890.0000.0000.0000.000
62B62VAL00.0260.02213.764-1.105-1.1050.0000.0000.0000.000
63B63ILE0-0.022-0.02017.2250.4670.4670.0000.0000.0000.000
64B64SER00.0530.04919.973-0.398-0.3980.0000.0000.0000.000
65B65THR0-0.021-0.03423.5800.1820.1820.0000.0000.0000.000
66B66PRO00.0080.01724.659-0.480-0.4800.0000.0000.0000.000
67B67ASP-1-0.802-0.90727.35410.12810.1280.0000.0000.0000.000
68B68PRO00.0090.01427.7790.4570.4570.0000.0000.0000.000
69B69LYS10.8340.91428.617-9.286-9.2860.0000.0000.0000.000
70B70LEU00.0070.02024.9760.1360.1360.0000.0000.0000.000
71B71GLY00.0470.01324.4390.5150.5150.0000.0000.0000.000
72B72SER0-0.025-0.04024.0460.2650.2650.0000.0000.0000.000
73B73ALA0-0.018-0.00324.1140.2360.2360.0000.0000.0000.000
74B74ILE00.0190.02119.3500.6600.6600.0000.0000.0000.000
75B75VAL00.0110.00219.3740.8380.8380.0000.0000.0000.000
76B76ALA0-0.076-0.03219.9970.4700.4700.0000.0000.0000.000
77B77LYS10.8340.89217.523-16.880-16.8800.0000.0000.0000.000
78B78ALA00.0110.01415.3000.9210.9210.0000.0000.0000.000
79B79ARG10.9540.97915.072-13.650-13.6500.0000.0000.0000.000
80B80GLY0-0.036-0.01416.6860.2280.2280.0000.0000.0000.000
81B81TYR0-0.095-0.07911.7360.4090.4090.0000.0000.0000.000
82B82ASP-1-0.944-0.96011.34525.42425.4240.0000.0000.0000.000
83B83MET0-0.0530.00110.1441.6741.6740.0000.0000.0000.000
84B84LYS10.8270.90812.399-22.852-22.8520.0000.0000.0000.000
85B85VAL0-0.005-0.01014.2290.7390.7390.0000.0000.0000.000
86B86ILE0-0.045-0.01217.027-0.929-0.9290.0000.0000.0000.000
87B87ALA0-0.0020.00919.4760.3640.3640.0000.0000.0000.000
88B88VAL00.032-0.00821.762-0.214-0.2140.0000.0000.0000.000
89B89ASP-1-0.752-0.84124.16112.31212.3120.0000.0000.0000.000
90B90ASN0-0.049-0.03626.723-0.798-0.7980.0000.0000.0000.000
91B91GLN0-0.017-0.01526.7180.2150.2150.0000.0000.0000.000
92B92PHE00.0220.02321.565-0.202-0.2020.0000.0000.0000.000
93B93VAL0-0.002-0.01127.725-0.313-0.3130.0000.0000.0000.000
94B94ASN00.0510.02230.284-0.031-0.0310.0000.0000.0000.000
95B95ALA00.0570.02331.467-0.264-0.2640.0000.0000.0000.000
96B96LYS10.9390.95633.623-8.731-8.7310.0000.0000.0000.000
97B97GLY00.0040.00335.041-0.259-0.2590.0000.0000.0000.000
98B98LYS10.8540.93033.884-9.427-9.4270.0000.0000.0000.000
99B99PRO00.0310.02031.8960.2590.2590.0000.0000.0000.000
100B100MET0-0.057-0.01925.578-0.217-0.2170.0000.0000.0000.000
101B101ASP-1-0.788-0.89227.50310.33510.3350.0000.0000.0000.000
102B102THR0-0.022-0.00925.9360.0510.0510.0000.0000.0000.000
103B103VAL0-0.027-0.00821.9760.4830.4830.0000.0000.0000.000
104B104PRO0-0.0110.00420.766-0.491-0.4910.0000.0000.0000.000
105B105LEU0-0.0090.00622.9950.4500.4500.0000.0000.0000.000
106B106VAL0-0.027-0.02122.748-0.314-0.3140.0000.0000.0000.000
107B107MET0-0.014-0.00725.5270.3290.3290.0000.0000.0000.000
108B108GLU-1-0.741-0.88628.41011.19611.1960.0000.0000.0000.000
109B109ALA0-0.013-0.01230.831-0.157-0.1570.0000.0000.0000.000
110B110ALA00.0150.01634.492-0.111-0.1110.0000.0000.0000.000
111B111THR0-0.047-0.01736.504-0.116-0.1160.0000.0000.0000.000
112B112LYS10.8310.91236.768-8.438-8.4380.0000.0000.0000.000
113B113ILE00.018-0.00941.121-0.173-0.1730.0000.0000.0000.000
114B114GLY00.0130.01242.893-0.135-0.1350.0000.0000.0000.000
115B115GLU-1-0.809-0.90242.9477.4467.4460.0000.0000.0000.000
116B116ARG10.8250.90139.642-7.892-7.8920.0000.0000.0000.000
117B117GLN00.0170.00544.672-0.113-0.1130.0000.0000.0000.000
118B118GLY00.0520.02947.836-0.108-0.1080.0000.0000.0000.000
119B119GLN0-0.001-0.01643.265-0.021-0.0210.0000.0000.0000.000
120B120GLU-1-0.781-0.86944.1337.1517.1510.0000.0000.0000.000
121B121LEU0-0.027-0.00548.158-0.101-0.1010.0000.0000.0000.000
122B122TYR00.024-0.00451.297-0.149-0.1490.0000.0000.0000.000
123B123LYS10.8380.90244.282-7.224-7.2240.0000.0000.0000.000
124B124GLU-1-0.771-0.86750.6266.0486.0480.0000.0000.0000.000
125B125MET0-0.018-0.00652.637-0.131-0.1310.0000.0000.0000.000
126B126GLN0-0.021-0.01853.180-0.171-0.1710.0000.0000.0000.000
127B127LYS10.8150.90549.742-6.409-6.4090.0000.0000.0000.000
128B128ARG10.7480.86954.323-5.768-5.7680.0000.0000.0000.000
129B129GLY0-0.0040.01057.578-0.106-0.1060.0000.0000.0000.000
130B130TRP0-0.043-0.02559.421-0.097-0.0970.0000.0000.0000.000
131B131ASP-1-0.779-0.86561.4274.8704.8700.0000.0000.0000.000
132B132VAL00.0510.02660.679-0.035-0.0350.0000.0000.0000.000
133B133LYS10.8070.87863.067-4.775-4.7750.0000.0000.0000.000
134B134GLU-1-0.811-0.86466.2154.6564.6560.0000.0000.0000.000
135B135SER00.011-0.01461.9020.0160.0160.0000.0000.0000.000
136B136ALA0-0.037-0.00462.365-0.016-0.0160.0000.0000.0000.000
137B137VAL0-0.0100.00456.7270.0700.0700.0000.0000.0000.000
138B138MET00.0050.03159.679-0.041-0.0410.0000.0000.0000.000
139B139ALA0-0.006-0.01657.0500.1170.1170.0000.0000.0000.000
140B140ILE00.0020.01157.336-0.060-0.0600.0000.0000.0000.000
141B141THR0-0.029-0.01955.8810.1090.1090.0000.0000.0000.000
142B142ALA00.0670.01754.532-0.084-0.0840.0000.0000.0000.000
143B143ASN0-0.010-0.00854.5400.2050.2050.0000.0000.0000.000
144B144GLU-1-0.865-0.93354.6235.7015.7010.0000.0000.0000.000
145B145LEU00.0020.01751.0590.1190.1190.0000.0000.0000.000
146B146ASP-1-0.718-0.84348.2416.7606.7600.0000.0000.0000.000
147B147THR0-0.016-0.02045.0320.0760.0760.0000.0000.0000.000
148B148ALA00.0420.02347.4960.0660.0660.0000.0000.0000.000
149B149ARG10.8860.95449.956-6.417-6.4170.0000.0000.0000.000
150B150ARG10.8250.91044.906-7.094-7.0940.0000.0000.0000.000
151B151ARG10.8030.89243.366-7.150-7.1500.0000.0000.0000.000
152B152THR00.034-0.00348.269-0.024-0.0240.0000.0000.0000.000
153B153THR0-0.022-0.01450.731-0.105-0.1050.0000.0000.0000.000
154B154GLY00.0440.02247.873-0.031-0.0310.0000.0000.0000.000
155B155SER0-0.037-0.02848.8840.0030.0030.0000.0000.0000.000
156B156MET0-0.008-0.01450.363-0.109-0.1090.0000.0000.0000.000
157B157ASP-1-0.860-0.94350.5866.0976.0970.0000.0000.0000.000
158B158ALA0-0.018-0.00447.999-0.006-0.0060.0000.0000.0000.000
159B159LEU0-0.013-0.00449.909-0.029-0.0290.0000.0000.0000.000
160B160LYS10.8520.94753.115-5.908-5.9080.0000.0000.0000.000
161B161ALA0-0.048-0.01649.988-0.050-0.0500.0000.0000.0000.000
162B162ALA0-0.020-0.00150.7730.0300.0300.0000.0000.0000.000
163B163GLY00.0070.01552.110-0.046-0.0460.0000.0000.0000.000
164B164PHE0-0.047-0.02055.731-0.127-0.1270.0000.0000.0000.000
165B165PRO00.003-0.01457.7360.0030.0030.0000.0000.0000.000
166B166GLU-1-0.836-0.93559.2055.4305.4300.0000.0000.0000.000
167B167LYS10.8650.93560.731-4.952-4.9520.0000.0000.0000.000
168B168GLN0-0.036-0.01662.846-0.132-0.1320.0000.0000.0000.000
169B169ILE0-0.0100.00656.9710.0560.0560.0000.0000.0000.000
170B170TYR0-0.030-0.03160.943-0.068-0.0680.0000.0000.0000.000
171B171GLN00.0320.00158.5460.0480.0480.0000.0000.0000.000
172B172VAL0-0.033-0.01060.738-0.098-0.0980.0000.0000.0000.000
173B173PRO00.0350.02560.4480.0720.0720.0000.0000.0000.000
174B174THR00.0350.00057.272-0.140-0.1400.0000.0000.0000.000
175B175LYS10.7840.88960.616-5.170-5.1700.0000.0000.0000.000
176B176SER00.006-0.01458.507-0.053-0.0530.0000.0000.0000.000
177B177GLU-1-0.923-0.96053.2085.8295.8290.0000.0000.0000.000
178B178ASP-1-0.834-0.90354.1695.5895.5890.0000.0000.0000.000
179B179ILE00.0220.01055.698-0.049-0.0490.0000.0000.0000.000
180B180PRO00.004-0.00458.482-0.056-0.0560.0000.0000.0000.000
181B181GLY00.0720.05460.613-0.072-0.0720.0000.0000.0000.000
182B182ALA00.0290.00058.155-0.054-0.0540.0000.0000.0000.000
183B183PHE00.0040.00960.280-0.039-0.0390.0000.0000.0000.000
184B184ASP-1-0.889-0.93862.9734.8224.8220.0000.0000.0000.000
185B185ALA0-0.084-0.03661.889-0.062-0.0620.0000.0000.0000.000
186B186ALA00.0610.02161.973-0.054-0.0540.0000.0000.0000.000
187B187ASN0-0.023-0.02163.871-0.096-0.0960.0000.0000.0000.000
188B188SER0-0.070-0.03766.474-0.064-0.0640.0000.0000.0000.000
189B189MET0-0.0100.00863.873-0.068-0.0680.0000.0000.0000.000
190B190LEU0-0.008-0.01165.249-0.042-0.0420.0000.0000.0000.000
191B191VAL0-0.025-0.01568.357-0.057-0.0570.0000.0000.0000.000
192B192GLN0-0.093-0.04268.817-0.064-0.0640.0000.0000.0000.000
193B193HIS10.8080.88767.762-4.744-4.7440.0000.0000.0000.000
194B194PRO00.0380.02469.5300.0530.0530.0000.0000.0000.000
195B195GLU-1-0.834-0.90270.3754.5984.5980.0000.0000.0000.000
196B196VAL0-0.069-0.02065.0320.0250.0250.0000.0000.0000.000
197B197LYS10.8720.91467.691-4.626-4.6260.0000.0000.0000.000
198B198HIS10.7540.85562.526-4.972-4.9720.0000.0000.0000.000
199B199TRP00.0240.00961.4470.0260.0260.0000.0000.0000.000
200B200LEU00.0070.00555.5510.0680.0680.0000.0000.0000.000
201B201ILE0-0.030-0.01756.250-0.068-0.0680.0000.0000.0000.000
202B202VAL00.0100.00952.8170.1230.1230.0000.0000.0000.000
203B203GLY00.0260.00152.686-0.131-0.1310.0000.0000.0000.000
204B204MET0-0.0020.01850.4600.1840.1840.0000.0000.0000.000
205B205ASN00.0490.03148.9350.1000.1000.0000.0000.0000.000
206B206ASP-1-0.668-0.81948.3996.6186.6180.0000.0000.0000.000
207B207SER0-0.003-0.01750.907-0.094-0.0940.0000.0000.0000.000
208B208THR0-0.017-0.01653.507-0.154-0.1540.0000.0000.0000.000
209B209VAL0-0.028-0.00452.258-0.123-0.1230.0000.0000.0000.000
210B210LEU00.004-0.00653.100-0.113-0.1130.0000.0000.0000.000
211B211GLY00.0190.01856.573-0.106-0.1060.0000.0000.0000.000
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