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: 537KZ

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 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 294
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3663781.468159
FMO2-HF: Nuclear repulsion 3552628.820851
FMO2-HF: Total energy -111152.647308
FMO2-MP2: Total energy -111477.241487


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.
-54.215-55.39413.65-6.995-5.4730.087
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 : -0.926 / q_NPA : -0.962
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].
3B3LEU00.0250.0123.8049.54111.232-0.004-0.782-0.9040.002
4B4LYS10.8740.9381.692-117.521-120.61913.657-6.209-4.3500.085
5B5LEU0-0.007-0.0047.221-0.913-0.9130.0000.0000.0000.000
6B6GLY00.0420.01510.727-0.093-0.0930.0000.0000.0000.000
7B7PHE0-0.033-0.02313.228-0.970-0.9700.0000.0000.0000.000
8B8LEU0-0.020-0.01516.229-0.189-0.1890.0000.0000.0000.000
9B9VAL00.0590.03119.194-0.524-0.5240.0000.0000.0000.000
10B10ALA0-0.0030.01822.6690.0190.0190.0000.0000.0000.000
11B11GLN0-0.022-0.03225.684-0.137-0.1370.0000.0000.0000.000
12B12PRO0-0.024-0.00823.798-0.089-0.0890.0000.0000.0000.000
13B13GLU-1-0.858-0.93225.88711.13811.1380.0000.0000.0000.000
14B14GLU-1-0.892-0.94429.1739.0469.0460.0000.0000.0000.000
15B15PRO0-0.021-0.01629.9410.3530.3530.0000.0000.0000.000
16B16ALA0-0.004-0.00330.8430.1700.1700.0000.0000.0000.000
17B17SER00.0250.00726.1190.1280.1280.0000.0000.0000.000
18B18GLN0-0.058-0.00525.7840.4980.4980.0000.0000.0000.000
19B19THR00.0260.01125.6280.4540.4540.0000.0000.0000.000
20B20GLN0-0.046-0.05022.7020.8810.8810.0000.0000.0000.000
21B21TRP00.0220.00019.1440.4580.4580.0000.0000.0000.000
22B22LYS10.9400.98919.022-11.152-11.1520.0000.0000.0000.000
23B23PHE0-0.022-0.02520.1840.3090.3090.0000.0000.0000.000
24B24ALA00.0470.03117.2590.2550.2550.0000.0000.0000.000
25B25ASP-1-0.820-0.89914.98020.22920.2290.0000.0000.0000.000
26B26LYS10.7470.86915.720-13.644-13.6440.0000.0000.0000.000
27B27ALA00.0580.01617.4010.1140.1140.0000.0000.0000.000
28B28GLY00.0550.03913.4700.3690.3690.0000.0000.0000.000
29B29LYS10.8680.92512.585-18.373-18.3730.0000.0000.0000.000
30B30ASP-1-0.801-0.87314.27414.87414.8740.0000.0000.0000.000
31B31LEU0-0.020-0.01014.872-0.290-0.2900.0000.0000.0000.000
32B32GLY0-0.0400.00210.7990.3320.3320.0000.0000.0000.000
33B33PHE0-0.066-0.0378.7931.7421.7420.0000.0000.0000.000
34B34GLU-1-0.859-0.9076.11437.02937.0290.0000.0000.0000.000
35B35VAL00.004-0.0099.5971.1151.1150.0000.0000.0000.000
36B36ILE0-0.0100.0008.095-0.702-0.7020.0000.0000.0000.000
37B37LYS10.7850.87812.427-21.087-21.0870.0000.0000.0000.000
38B38ILE00.0160.00214.130-0.047-0.0470.0000.0000.0000.000
39B39ALA00.0260.01618.137-0.322-0.3220.0000.0000.0000.000
40B40VAL0-0.059-0.03820.4280.3630.3630.0000.0000.0000.000
41B41PRO00.0680.02823.200-0.305-0.3050.0000.0000.0000.000
42B42ASP-1-0.762-0.86426.15111.40111.4010.0000.0000.0000.000
43B43GLY00.0580.02125.5830.5330.5330.0000.0000.0000.000
44B44GLU-1-0.875-0.92424.89912.44812.4480.0000.0000.0000.000
45B45LYS10.8080.86322.636-11.283-11.2830.0000.0000.0000.000
46B46THR0-0.008-0.01320.9800.8380.8380.0000.0000.0000.000
47B47LEU0-0.042-0.03019.9300.8860.8860.0000.0000.0000.000
48B48ASN00.0330.01419.2470.8720.8720.0000.0000.0000.000
49B49ALA00.0070.01816.9751.1551.1550.0000.0000.0000.000
50B50ILE0-0.012-0.01015.2391.4561.4560.0000.0000.0000.000
51B51ASP-1-0.742-0.83614.35218.95918.9590.0000.0000.0000.000
52B52SER00.0220.01212.9521.2821.2820.0000.0000.0000.000
53B53LEU0-0.057-0.02310.8252.6942.6940.0000.0000.0000.000
54B54ALA00.0380.0259.3613.7013.7010.0000.0000.0000.000
55B55ALA0-0.022-0.0039.1653.3523.3520.0000.0000.0000.000
56B56SER0-0.057-0.0317.4082.3772.3770.0000.0000.0000.000
57B57GLY00.0020.0034.87710.25710.386-0.001-0.002-0.1240.000
58B58ALA0-0.042-0.0255.5954.0314.047-0.0010.001-0.0160.000
59B59LYS10.9390.9624.768-54.974-54.891-0.001-0.003-0.0790.000
60B60GLY00.0440.0119.590-2.553-2.5530.0000.0000.0000.000
61B61PHE0-0.042-0.02812.2791.2521.2520.0000.0000.0000.000
62B62VAL00.0170.01614.987-0.927-0.9270.0000.0000.0000.000
63B63ILE0-0.027-0.01318.3740.3400.3400.0000.0000.0000.000
64B64SER00.0580.04720.889-0.423-0.4230.0000.0000.0000.000
65B65THR0-0.027-0.04324.3920.1970.1970.0000.0000.0000.000
66B66PRO00.0050.02425.292-0.436-0.4360.0000.0000.0000.000
67B67ASP-1-0.787-0.91128.1359.6069.6060.0000.0000.0000.000
68B68PRO00.0140.02828.6890.4210.4210.0000.0000.0000.000
69B69LYS10.8240.91829.943-8.900-8.9000.0000.0000.0000.000
70B70LEU0-0.0030.01126.0160.0500.0500.0000.0000.0000.000
71B71GLY00.0380.01426.1050.4640.4640.0000.0000.0000.000
72B72SER0-0.035-0.05025.5280.2580.2580.0000.0000.0000.000
73B73ALA0-0.0110.00825.2940.2250.2250.0000.0000.0000.000
74B74ILE00.0470.02820.5840.5980.5980.0000.0000.0000.000
75B75VAL0-0.0010.00120.7980.6840.6840.0000.0000.0000.000
76B76ALA0-0.055-0.02621.4850.4520.4520.0000.0000.0000.000
77B77LYS10.8230.89418.806-15.937-15.9370.0000.0000.0000.000
78B78ALA00.0110.01316.7990.8850.8850.0000.0000.0000.000
79B79ARG10.9370.97316.730-12.885-12.8850.0000.0000.0000.000
80B80GLY0-0.031-0.00718.0080.3870.3870.0000.0000.0000.000
81B81TYR0-0.084-0.07613.2660.5170.5170.0000.0000.0000.000
82B82ASP-1-0.967-0.97013.00423.06823.0680.0000.0000.0000.000
83B83MET0-0.062-0.00711.5481.6001.6000.0000.0000.0000.000
84B84LYS10.8210.91013.969-20.783-20.7830.0000.0000.0000.000
85B85VAL00.005-0.00315.8290.5350.5350.0000.0000.0000.000
86B86ILE0-0.0160.00318.602-0.774-0.7740.0000.0000.0000.000
87B87ALA0-0.0120.00820.6660.4350.4350.0000.0000.0000.000
88B88VAL00.036-0.00722.882-0.232-0.2320.0000.0000.0000.000
89B89ASP-1-0.772-0.84625.07311.66111.6610.0000.0000.0000.000
90B90ASN0-0.047-0.04227.679-0.713-0.7130.0000.0000.0000.000
91B91GLN0-0.002-0.00527.9180.2030.2030.0000.0000.0000.000
92B92PHE00.0120.00922.805-0.228-0.2280.0000.0000.0000.000
93B93VAL00.0080.00429.084-0.271-0.2710.0000.0000.0000.000
94B94ASN00.0490.02031.581-0.015-0.0150.0000.0000.0000.000
95B95ALA00.0810.02732.844-0.189-0.1890.0000.0000.0000.000
96B96LYS10.9070.94135.115-8.441-8.4410.0000.0000.0000.000
97B97GLY00.001-0.00136.601-0.221-0.2210.0000.0000.0000.000
98B98LYS10.8820.94336.036-8.909-8.9090.0000.0000.0000.000
99B99PRO00.0310.02333.4730.2360.2360.0000.0000.0000.000
100B100MET0-0.062-0.02927.142-0.152-0.1520.0000.0000.0000.000
101B101ASP-1-0.826-0.92229.2609.7299.7290.0000.0000.0000.000
102B102THR0-0.031-0.01327.8540.1330.1330.0000.0000.0000.000
103B103VAL0-0.024-0.00423.3410.3860.3860.0000.0000.0000.000
104B104PRO0-0.0130.00522.391-0.397-0.3970.0000.0000.0000.000
105B105LEU0-0.0070.00124.4190.4110.4110.0000.0000.0000.000
106B106VAL0-0.021-0.02324.061-0.259-0.2590.0000.0000.0000.000
107B107MET0-0.019-0.00526.8710.2820.2820.0000.0000.0000.000
108B108GLU-1-0.773-0.89029.44010.65310.6530.0000.0000.0000.000
109B109ALA0-0.009-0.00631.699-0.170-0.1700.0000.0000.0000.000
110B110ALA0-0.0030.00635.247-0.056-0.0560.0000.0000.0000.000
111B111THR0-0.065-0.03337.435-0.113-0.1130.0000.0000.0000.000
112B112LYS10.9110.95738.238-8.130-8.1300.0000.0000.0000.000
113B113ILE00.011-0.00641.767-0.142-0.1420.0000.0000.0000.000
114B114GLY00.0280.01043.739-0.113-0.1130.0000.0000.0000.000
115B115GLU-1-0.830-0.90543.8957.2127.2120.0000.0000.0000.000
116B116ARG10.8310.89840.517-7.746-7.7460.0000.0000.0000.000
117B117GLN00.002-0.01045.577-0.100-0.1000.0000.0000.0000.000
118B118GLY00.0480.03148.579-0.122-0.1220.0000.0000.0000.000
119B119GLN00.002-0.01644.514-0.023-0.0230.0000.0000.0000.000
120B120GLU-1-0.794-0.87545.0227.0037.0030.0000.0000.0000.000
121B121LEU0-0.0130.00549.200-0.089-0.0890.0000.0000.0000.000
122B122TYR00.0180.00552.451-0.139-0.1390.0000.0000.0000.000
123B123LYS10.8470.90045.374-7.066-7.0660.0000.0000.0000.000
124B124GLU-1-0.786-0.86951.8005.9655.9650.0000.0000.0000.000
125B125MET00.0030.00153.397-0.123-0.1230.0000.0000.0000.000
126B126GLN0-0.026-0.01954.367-0.160-0.1600.0000.0000.0000.000
127B127LYS10.8250.90950.375-6.324-6.3240.0000.0000.0000.000
128B128ARG10.7640.87855.352-5.703-5.7030.0000.0000.0000.000
129B129GLY0-0.0090.01158.499-0.102-0.1020.0000.0000.0000.000
130B130TRP0-0.058-0.02860.191-0.094-0.0940.0000.0000.0000.000
131B131ASP-1-0.780-0.86662.5484.8094.8090.0000.0000.0000.000
132B132VAL00.0680.02561.986-0.033-0.0330.0000.0000.0000.000
133B133LYS10.8310.89264.146-4.711-4.7110.0000.0000.0000.000
134B134GLU-1-0.815-0.86667.2884.6104.6100.0000.0000.0000.000
135B135SER0-0.020-0.02462.7830.0240.0240.0000.0000.0000.000
136B136ALA0-0.020-0.00363.551-0.035-0.0350.0000.0000.0000.000
137B137VAL0-0.0070.01257.8490.0650.0650.0000.0000.0000.000
138B138MET00.0140.03960.549-0.063-0.0630.0000.0000.0000.000
139B139ALA0-0.024-0.02857.7110.1090.1090.0000.0000.0000.000
140B140ILE00.0130.01258.059-0.058-0.0580.0000.0000.0000.000
141B141THR0-0.047-0.03356.6840.1110.1110.0000.0000.0000.000
142B142ALA00.0680.02755.000-0.083-0.0830.0000.0000.0000.000
143B143ASN00.002-0.02155.0420.2040.2040.0000.0000.0000.000
144B144GLU-1-0.875-0.92455.5195.6155.6150.0000.0000.0000.000
145B145LEU0-0.0120.00851.2400.1220.1220.0000.0000.0000.000
146B146ASP-1-0.743-0.85848.3516.5996.5990.0000.0000.0000.000
147B147THR0-0.038-0.03145.6010.0550.0550.0000.0000.0000.000
148B148ALA00.0650.03647.9480.0450.0450.0000.0000.0000.000
149B149ARG10.9090.96350.376-6.281-6.2810.0000.0000.0000.000
150B150ARG10.8570.91645.626-6.955-6.9550.0000.0000.0000.000
151B151ARG10.8150.90943.921-6.985-6.9850.0000.0000.0000.000
152B152THR00.0430.00749.087-0.021-0.0210.0000.0000.0000.000
153B153THR0-0.024-0.01951.776-0.105-0.1050.0000.0000.0000.000
154B154GLY00.0290.02148.782-0.017-0.0170.0000.0000.0000.000
155B155SER0-0.037-0.03149.7410.0070.0070.0000.0000.0000.000
156B156MET0-0.024-0.02551.303-0.099-0.0990.0000.0000.0000.000
157B157ASP-1-0.845-0.92651.2466.0176.0170.0000.0000.0000.000
158B158ALA0-0.0130.00049.080-0.021-0.0210.0000.0000.0000.000
159B159LEU0-0.006-0.00751.000-0.029-0.0290.0000.0000.0000.000
160B160LYS10.8500.93954.257-5.840-5.8400.0000.0000.0000.000
161B161ALA0-0.050-0.02151.435-0.055-0.0550.0000.0000.0000.000
162B162ALA0-0.030-0.00352.2330.0280.0280.0000.0000.0000.000
163B163GLY00.0060.00953.579-0.037-0.0370.0000.0000.0000.000
164B164PHE0-0.044-0.01757.049-0.120-0.1200.0000.0000.0000.000
165B165PRO00.001-0.01159.0340.0050.0050.0000.0000.0000.000
166B166GLU-1-0.866-0.94560.4595.2935.2930.0000.0000.0000.000
167B167LYS10.8840.94761.933-4.859-4.8590.0000.0000.0000.000
168B168GLN0-0.042-0.02564.039-0.115-0.1150.0000.0000.0000.000
169B169ILE0-0.0120.00158.0860.0490.0490.0000.0000.0000.000
170B170TYR0-0.014-0.01562.041-0.052-0.0520.0000.0000.0000.000
171B171GLN00.0200.00259.5820.0820.0820.0000.0000.0000.000
172B172VAL0-0.023-0.01261.669-0.096-0.0960.0000.0000.0000.000
173B173PRO00.0270.02660.8240.0740.0740.0000.0000.0000.000
174B174THR0-0.042-0.04057.940-0.142-0.1420.0000.0000.0000.000
175B175LYS10.8550.93060.893-5.025-5.0250.0000.0000.0000.000
176B176SER0-0.003-0.01659.177-0.035-0.0350.0000.0000.0000.000
177B177GLU-1-0.923-0.95753.8625.7395.7390.0000.0000.0000.000
178B178ASP-1-0.842-0.90754.8305.5125.5120.0000.0000.0000.000
179B179ILE00.0230.00555.542-0.051-0.0510.0000.0000.0000.000
180B180PRO00.0070.00458.585-0.052-0.0520.0000.0000.0000.000
181B181GLY00.0870.05861.024-0.079-0.0790.0000.0000.0000.000
182B182ALA00.0150.00058.545-0.057-0.0570.0000.0000.0000.000
183B183PHE0-0.0080.00460.668-0.047-0.0470.0000.0000.0000.000
184B184ASP-1-0.901-0.95563.3754.7814.7810.0000.0000.0000.000
185B185ALA0-0.078-0.04362.409-0.066-0.0660.0000.0000.0000.000
186B186ALA00.0690.02062.627-0.038-0.0380.0000.0000.0000.000
187B187ASN0-0.0050.00464.482-0.082-0.0820.0000.0000.0000.000
188B188SER0-0.047-0.01867.104-0.068-0.0680.0000.0000.0000.000
189B189MET0-0.0080.00764.749-0.075-0.0750.0000.0000.0000.000
190B190LEU0-0.020-0.01865.928-0.037-0.0370.0000.0000.0000.000
191B191VAL0-0.030-0.01669.077-0.057-0.0570.0000.0000.0000.000
192B192GLN0-0.089-0.04069.659-0.052-0.0520.0000.0000.0000.000
193B193HIS10.7870.88268.717-4.689-4.6890.0000.0000.0000.000
194B194PRO00.0390.02470.5000.0540.0540.0000.0000.0000.000
195B195GLU-1-0.845-0.90771.3464.5374.5370.0000.0000.0000.000
196B196VAL0-0.051-0.01066.2160.0200.0200.0000.0000.0000.000
197B197LYS10.8530.91068.365-4.592-4.5920.0000.0000.0000.000
198B198HIS10.7580.85763.180-4.912-4.9120.0000.0000.0000.000
199B199TRP00.0380.01662.3720.0240.0240.0000.0000.0000.000
200B200LEU0-0.010-0.00456.6820.0730.0730.0000.0000.0000.000
201B201ILE0-0.021-0.02056.990-0.043-0.0430.0000.0000.0000.000
202B202VAL00.0020.00153.7280.1230.1230.0000.0000.0000.000
203B203GLY00.0430.00753.522-0.117-0.1170.0000.0000.0000.000
204B204MET0-0.0010.01250.7660.1820.1820.0000.0000.0000.000
205B205ASN00.0350.02649.2530.0870.0870.0000.0000.0000.000
206B206ASP-1-0.649-0.81948.6936.5296.5290.0000.0000.0000.000
207B207SER00.001-0.00451.137-0.095-0.0950.0000.0000.0000.000
208B208THR0-0.013-0.02353.826-0.135-0.1350.0000.0000.0000.000
209B209VAL0-0.0130.00452.838-0.119-0.1190.0000.0000.0000.000
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211B211GLY00.0160.02456.789-0.104-0.1040.0000.0000.0000.000
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