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: 176VZ

Calculation Name: 4AEZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AEZ

Chain ID: B

ChEMBL ID:

UniProt ID: O14417

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062529.170591
FMO2-HF: Nuclear repulsion 1988771.359354
FMO2-HF: Total energy -73757.811237
FMO2-MP2: Total energy -73972.433618


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:13:LYS)


Summations of interaction energy for fragment #1(B:13:LYS)
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.
2.6319.05099999999992.656-3.243-5.83-0.007
Interaction energy analysis for fragmet #1(B:13:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.035 / q_NPA : 0.999
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].
3B15SER00.0180.0003.4236.8658.7410.039-0.631-1.2840.002
4B16SER00.0910.0362.189-2.292-0.2772.350-1.849-2.516-0.007
5B17LYS10.9471.0073.55732.22932.5410.003-0.055-0.2610.000
6B18LEU0-0.014-0.0075.6723.7933.7930.0000.0000.0000.000
7B19VAL00.0290.0126.9862.6712.6710.0000.0000.0000.000
8B20SER00.013-0.0076.6812.5582.5580.0000.0000.0000.000
9B21GLU-1-0.927-0.9689.175-19.983-19.9830.0000.0000.0000.000
10B22PHE00.001-0.00111.1871.6321.6320.0000.0000.0000.000
11B23PHE00.0440.00910.7541.1651.1650.0000.0000.0000.000
12B24GLU-1-0.898-0.94513.417-15.867-15.8670.0000.0000.0000.000
13B25TYR0-0.020-0.02715.2230.9380.9380.0000.0000.0000.000
14B26ALA0-0.0040.01116.7290.9000.9000.0000.0000.0000.000
15B27VAL00.0380.01517.4320.7300.7300.0000.0000.0000.000
16B28ASN0-0.001-0.01019.1081.1691.1690.0000.0000.0000.000
17B29SER0-0.031-0.01521.1310.5930.5930.0000.0000.0000.000
18B30ILE00.0040.00721.1240.4640.4640.0000.0000.0000.000
19B31LEU0-0.008-0.00323.0310.4610.4610.0000.0000.0000.000
20B32PHE0-0.0150.00025.6470.4240.4240.0000.0000.0000.000
21B33GLN0-0.037-0.03625.8570.2570.2570.0000.0000.0000.000
22B34ARG10.7510.86327.4079.6369.6360.0000.0000.0000.000
23B35GLY00.0270.02429.9730.2350.2350.0000.0000.0000.000
24B36ILE0-0.057-0.01727.5390.1630.1630.0000.0000.0000.000
25B37TYR00.002-0.00726.329-0.024-0.0240.0000.0000.0000.000
26B38PRO00.0620.02630.856-0.078-0.0780.0000.0000.0000.000
27B39ALA00.015-0.00931.646-0.231-0.2310.0000.0000.0000.000
28B40GLU-1-0.958-0.97031.630-8.339-8.3390.0000.0000.0000.000
29B41ASP-1-0.846-0.90329.747-9.158-9.1580.0000.0000.0000.000
30B42PHE0-0.086-0.05424.890-0.603-0.6030.0000.0000.0000.000
31B43LYS10.9480.98524.99511.80111.8010.0000.0000.0000.000
32B44VAL00.0170.00526.315-0.373-0.3730.0000.0000.0000.000
33B45VAL0-0.046-0.02321.551-0.014-0.0140.0000.0000.0000.000
34B46ARG10.9030.95023.39111.72011.7200.0000.0000.0000.000
35B47LYS10.9190.97214.39118.62518.6250.0000.0000.0000.000
36B48TYR00.0900.04313.5780.7220.7220.0000.0000.0000.000
37B49GLY00.0010.00319.5330.4180.4180.0000.0000.0000.000
38B50LEU0-0.019-0.01621.9640.6650.6650.0000.0000.0000.000
39B51ASN0-0.031-0.02224.050-0.421-0.4210.0000.0000.0000.000
40B52MET00.0060.02319.5240.1820.1820.0000.0000.0000.000
41B53LEU00.0450.02323.6830.1540.1540.0000.0000.0000.000
42B54VAL0-0.029-0.02620.637-0.465-0.4650.0000.0000.0000.000
43B55SER00.0530.02923.2660.3760.3760.0000.0000.0000.000
44B56VAL0-0.085-0.06824.424-0.457-0.4570.0000.0000.0000.000
45B57ASP-1-0.779-0.87526.956-9.695-9.6950.0000.0000.0000.000
46B58GLU-1-0.831-0.91325.559-11.715-11.7150.0000.0000.0000.000
47B59GLU-1-0.909-0.94825.323-9.913-9.9130.0000.0000.0000.000
48B60VAL0-0.0020.00423.898-0.479-0.4790.0000.0000.0000.000
49B61LYS10.7980.87621.91811.12911.1290.0000.0000.0000.000
50B62THR0-0.024-0.01620.592-0.851-0.8510.0000.0000.0000.000
51B63TYR0-0.0220.00320.608-0.541-0.5410.0000.0000.0000.000
52B64ILE00.0280.00517.530-0.596-0.5960.0000.0000.0000.000
53B65ARG10.9180.96016.52413.93813.9380.0000.0000.0000.000
54B66LYS10.9530.98215.69810.95310.9530.0000.0000.0000.000
55B67ILE00.0330.02515.781-0.847-0.8470.0000.0000.0000.000
56B68VAL00.0230.00111.770-0.952-0.9520.0000.0000.0000.000
57B69SER0-0.043-0.01711.296-1.870-1.8700.0000.0000.0000.000
58B70GLN00.0220.00510.936-1.335-1.3350.0000.0000.0000.000
59B71LEU00.0130.00511.015-1.027-1.0270.0000.0000.0000.000
60B72HIS0-0.012-0.0034.113-1.669-1.532-0.001-0.010-0.1250.000
61B73LYS10.9150.9576.35016.81516.8150.0000.0000.0000.000
62B74TRP00.0300.0087.916-1.730-1.7300.0000.0000.0000.000
63B75MET0-0.0150.0125.185-0.302-0.3020.0000.0000.0000.000
64B76PHE0-0.145-0.0622.880-6.412-4.9160.264-0.598-1.161-0.002
65B77ALA0-0.017-0.0114.404-1.971-1.873-0.001-0.012-0.0840.000
66B78LYS10.8810.9325.72434.53634.5360.0000.0000.0000.000
67B79LYS10.8780.9288.29619.98319.9830.0000.0000.0000.000
68B80ILE0-0.0230.0029.4851.2641.2640.0000.0000.0000.000
69B81GLN0-0.018-0.02411.757-0.134-0.1340.0000.0000.0000.000
70B82LYS10.8620.93514.55914.01014.0100.0000.0000.0000.000
71B83LEU00.0000.01414.482-0.137-0.1370.0000.0000.0000.000
72B84ILE0-0.054-0.02316.4660.2690.2690.0000.0000.0000.000
73B85LEU0-0.0130.00320.181-0.116-0.1160.0000.0000.0000.000
74B86VAL00.0030.00522.2860.1710.1710.0000.0000.0000.000
75B87ILE0-0.0010.00225.955-0.066-0.0660.0000.0000.0000.000
76B88THR00.003-0.04028.7970.0410.0410.0000.0000.0000.000
77B89SER00.031-0.01231.998-0.042-0.0420.0000.0000.0000.000
78B90LYS10.8970.93133.8138.1498.1490.0000.0000.0000.000
79B91CYS0-0.060-0.01036.5890.1210.1210.0000.0000.0000.000
80B92SER00.0470.02238.9990.0640.0640.0000.0000.0000.000
81B93GLY0-0.026-0.00336.0560.0380.0380.0000.0000.0000.000
82B94GLU-1-0.935-0.96635.318-7.636-7.6360.0000.0000.0000.000
83B95ASP-1-0.843-0.89030.593-9.230-9.2300.0000.0000.0000.000
84B96LEU00.004-0.00932.2060.1190.1190.0000.0000.0000.000
85B97GLU-1-0.744-0.86028.103-9.623-9.6230.0000.0000.0000.000
86B98ARG10.8100.90423.63010.93410.9340.0000.0000.0000.000
87B99TRP0-0.006-0.01722.143-0.303-0.3030.0000.0000.0000.000
88B100GLN00.0110.00120.0990.0560.0560.0000.0000.0000.000
89B101PHE0-0.027-0.02615.667-0.083-0.0830.0000.0000.0000.000
90B102ASN0-0.024-0.01216.366-0.068-0.0680.0000.0000.0000.000
91B103VAL0-0.011-0.01510.087-0.800-0.8000.0000.0000.0000.000
92B104GLU-1-0.905-0.94513.168-15.872-15.8720.0000.0000.0000.000
93B105MET0-0.064-0.0408.814-2.654-2.6540.0000.0000.0000.000
94B106VAL0-0.030-0.01211.5961.3321.3320.0000.0000.0000.000
95B107ASP-1-0.950-0.96413.248-18.210-18.2100.0000.0000.0000.000
96B117ASN00.0410.01010.169-1.524-1.5240.0000.0000.0000.000
97B118LYS10.9900.97110.81321.96921.9690.0000.0000.0000.000
98B119GLU-1-0.905-0.94812.552-16.336-16.3360.0000.0000.0000.000
99B120ASP-1-0.802-0.89510.924-23.416-23.4160.0000.0000.0000.000
100B121GLU-1-0.988-0.9839.073-29.195-29.1950.0000.0000.0000.000
101B122LEU0-0.020-0.01512.0121.0861.0860.0000.0000.0000.000
102B123ARG10.8050.88812.24722.28822.2880.0000.0000.0000.000
103B124VAL00.0090.00611.0350.6700.6700.0000.0000.0000.000
104B125GLN0-0.027-0.01813.2282.2422.2420.0000.0000.0000.000
105B126LYS10.8740.93116.27114.58414.5840.0000.0000.0000.000
106B127GLU-1-0.803-0.89616.236-17.800-17.8000.0000.0000.0000.000
107B128ILE0-0.0010.00812.7890.6170.6170.0000.0000.0000.000
108B129GLN0-0.0170.00117.2810.9120.9120.0000.0000.0000.000
109B130ALA0-0.021-0.01620.5910.6760.6760.0000.0000.0000.000
110B131LEU0-0.0140.00217.1360.5720.5720.0000.0000.0000.000
111B132ILE00.0300.00617.8480.4590.4590.0000.0000.0000.000
112B133ALA0-0.009-0.00621.4860.5480.5480.0000.0000.0000.000
113B134GLN00.005-0.01124.0020.2310.2310.0000.0000.0000.000
114B135ILE00.0270.01820.0260.3300.3300.0000.0000.0000.000
115B136THR0-0.0120.01324.5070.3770.3770.0000.0000.0000.000
116B137ALA0-0.023-0.01227.1270.3770.3770.0000.0000.0000.000
117B138THR0-0.021-0.02326.8430.3810.3810.0000.0000.0000.000
118B139VAL0-0.0020.00229.7110.2370.2370.0000.0000.0000.000
119B140THR0-0.104-0.05832.2520.3230.3230.0000.0000.0000.000
120B141PHE00.0060.00129.5970.1360.1360.0000.0000.0000.000
121B142LEU0-0.0470.00028.9610.1110.1110.0000.0000.0000.000
122B143PRO00.0250.03033.7120.1210.1210.0000.0000.0000.000
123B144GLN00.000-0.01635.046-0.148-0.1480.0000.0000.0000.000
124B145LEU0-0.031-0.01031.5360.0980.0980.0000.0000.0000.000
125B146GLU-1-0.926-0.96136.189-7.054-7.0540.0000.0000.0000.000
126B147GLU-1-0.866-0.89538.041-7.149-7.1490.0000.0000.0000.000
127B148GLN0-0.024-0.00833.307-0.051-0.0510.0000.0000.0000.000
128B149CYS0-0.018-0.00332.0300.0780.0780.0000.0000.0000.000
129B150THR0-0.020-0.01929.716-0.111-0.1110.0000.0000.0000.000
130B151PHE0-0.004-0.01222.228-0.127-0.1270.0000.0000.0000.000
131B152ASN0-0.020-0.00524.9020.1860.1860.0000.0000.0000.000
132B153VAL0-0.004-0.00918.302-0.145-0.1450.0000.0000.0000.000
133B154LEU0-0.0040.00520.5390.0880.0880.0000.0000.0000.000
134B155VAL00.0170.00115.223-0.507-0.5070.0000.0000.0000.000
135B156TYR0-0.030-0.00417.2040.7380.7380.0000.0000.0000.000
136B157ALA00.0370.00315.376-0.880-0.8800.0000.0000.0000.000
137B158ASP-1-0.825-0.89614.316-16.745-16.7450.0000.0000.0000.000
138B159LYS10.9310.95116.76411.88911.8890.0000.0000.0000.000
139B160ASP-1-0.861-0.89015.750-16.400-16.4000.0000.0000.0000.000
140B161SER0-0.003-0.02014.860-0.963-0.9630.0000.0000.0000.000
141B162GLU-1-0.934-0.95514.696-14.488-14.4880.0000.0000.0000.000
142B163VAL00.002-0.00915.824-0.652-0.6520.0000.0000.0000.000
143B164PRO0-0.033-0.01416.4980.5090.5090.0000.0000.0000.000
144B165THR00.0520.01119.2730.1330.1330.0000.0000.0000.000
145B166ASP-1-0.973-0.97420.445-11.692-11.6920.0000.0000.0000.000
146B167TRP0-0.075-0.04016.446-0.179-0.1790.0000.0000.0000.000
147B168VAL00.0070.00321.1000.1310.1310.0000.0000.0000.000
148B169ASP-1-0.939-0.96123.530-11.278-11.2780.0000.0000.0000.000
149B170SER0-0.019-0.02824.4600.3620.3620.0000.0000.0000.000
150B171ASP-1-0.875-0.91725.825-9.614-9.6140.0000.0000.0000.000
151B172PRO0-0.009-0.01024.933-0.187-0.1870.0000.0000.0000.000
152B173ARG10.8970.92025.9269.3449.3440.0000.0000.0000.000
153B174ILE0-0.026-0.00927.188-0.108-0.1080.0000.0000.0000.000
154B175LEU0-0.048-0.01129.0750.2730.2730.0000.0000.0000.000
155B176ARG10.9120.95831.6348.4528.4520.0000.0000.0000.000
156B177ASP-1-0.920-0.96535.144-7.523-7.5230.0000.0000.0000.000
157B178ALA0-0.041-0.01832.2390.0500.0500.0000.0000.0000.000
158B179GLU-1-0.909-0.94133.720-8.070-8.0700.0000.0000.0000.000
159B180GLN0-0.023-0.03228.858-0.323-0.3230.0000.0000.0000.000
160B181VAL0-0.0180.00227.6030.1190.1190.0000.0000.0000.000
161B182GLN0-0.0260.00121.674-0.076-0.0760.0000.0000.0000.000
162B183LEU0-0.017-0.01322.7150.1880.1880.0000.0000.0000.000
163B184ARG10.9200.95721.60912.12812.1280.0000.0000.0000.000
164B185SER00.0290.00717.2760.0060.0060.0000.0000.0000.000
165B186PHE0-0.054-0.02311.1280.2330.2330.0000.0000.0000.000
166B187SER00.0270.01513.077-0.213-0.2130.0000.0000.0000.000
167B188THR0-0.042-0.0457.758-0.010-0.0100.0000.0000.0000.000
168B189SER0-0.016-0.0185.5380.4440.4440.0000.0000.0000.000
169B190MET0-0.055-0.0243.977-0.988-0.6170.003-0.079-0.2950.000
170B191HIS00.1170.0714.3380.9111.026-0.001-0.009-0.1040.000
171B192LYS11.0001.0229.63816.27016.2700.0000.0000.0000.000
172B193ILE0-0.0080.00610.0780.3350.3350.0000.0000.0000.000
173B194ASP-1-0.834-0.92214.008-14.223-14.2230.0000.0000.0000.000
174B195CYS0-0.0380.00017.607-0.065-0.0650.0000.0000.0000.000
175B196GLN00.008-0.01020.0770.3570.3570.0000.0000.0000.000
176B197VAL00.0190.01123.367-0.202-0.2020.0000.0000.0000.000
177B198ALA00.0020.00725.9600.2470.2470.0000.0000.0000.000
178B199TYR00.029-0.00428.874-0.036-0.0360.0000.0000.0000.000
179B200ARG10.9790.99731.8397.9347.9340.0000.0000.0000.000
180B201VAL00.0160.02435.4610.0750.0750.0000.0000.0000.000