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: 17LKZ

Calculation Name: 3JWI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JWI

Chain ID: B

ChEMBL ID:

UniProt ID: A3DJ37

Base Structure: X-ray

Registration Date: 2023-09-19

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2356632.588484
FMO2-HF: Nuclear repulsion 2276847.417018
FMO2-HF: Total energy -79785.171465
FMO2-MP2: Total energy -80022.457502


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:12:ASN)


Summations of interaction energy for fragment #1(B:12:ASN)
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.
-11.708-11.7999.827-4.024-5.7130.028
Interaction energy analysis for fragmet #1(B:12:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.008
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].
3B14ASN00.027-0.0012.943-1.7970.1150.033-0.743-1.2010.000
4B15GLN0-0.020-0.0072.346-0.0420.8601.091-0.673-1.3210.002
5B16GLN00.0410.0201.867-10.357-13.3278.704-2.604-3.1300.026
6B17ARG10.8840.9635.589-2.164-2.099-0.001-0.004-0.0610.000
7B18LEU00.003-0.0197.677-0.221-0.2210.0000.0000.0000.000
8B19GLY00.0070.0097.953-0.206-0.2060.0000.0000.0000.000
9B20THR00.009-0.0129.188-0.207-0.2070.0000.0000.0000.000
10B21VAL0-0.0050.00811.339-0.201-0.2010.0000.0000.0000.000
11B22VAL00.001-0.00212.780-0.110-0.1100.0000.0000.0000.000
12B23ALA00.0070.00913.188-0.086-0.0860.0000.0000.0000.000
13B24VAL00.0150.00115.028-0.081-0.0810.0000.0000.0000.000
14B25LEU0-0.012-0.01216.716-0.074-0.0740.0000.0000.0000.000
15B26LYS10.8020.87917.601-0.212-0.2120.0000.0000.0000.000
16B27SER0-0.0170.00219.006-0.027-0.0270.0000.0000.0000.000
17B28VAL0-0.066-0.02620.758-0.023-0.0230.0000.0000.0000.000
18B29ASN0-0.067-0.03023.045-0.037-0.0370.0000.0000.0000.000
19B30ALA0-0.0010.01222.076-0.024-0.0240.0000.0000.0000.000
20B31LYS10.8880.92922.952-0.077-0.0770.0000.0000.0000.000
21B32LYS10.8320.91724.816-0.091-0.0910.0000.0000.0000.000
22B33VAL00.020-0.00619.4570.0200.0200.0000.0000.0000.000
23B34ILE0-0.0060.00622.776-0.029-0.0290.0000.0000.0000.000
24B35ASP-1-0.822-0.90716.5600.1990.1990.0000.0000.0000.000
25B36LEU0-0.018-0.01819.815-0.035-0.0350.0000.0000.0000.000
26B37GLY00.0300.00519.4440.0290.0290.0000.0000.0000.000
27B38CYS0-0.048-0.01116.9200.0040.0040.0000.0000.0000.000
28B39GLY00.0470.04315.763-0.030-0.0300.0000.0000.0000.000
29B40GLU-1-0.851-0.93714.241-0.217-0.2170.0000.0000.0000.000
30B41GLY00.0610.03015.511-0.052-0.0520.0000.0000.0000.000
31B42ASN0-0.005-0.0229.798-0.091-0.0910.0000.0000.0000.000
32B43LEU00.0580.03911.946-0.051-0.0510.0000.0000.0000.000
33B44LEU00.0740.03213.250-0.007-0.0070.0000.0000.0000.000
34B45SER0-0.074-0.03013.015-0.049-0.0490.0000.0000.0000.000
35B46LEU0-0.024-0.0169.034-0.066-0.0660.0000.0000.0000.000
36B47LEU00.0560.03613.5370.0060.0060.0000.0000.0000.000
37B48LEU00.0300.02816.775-0.003-0.0030.0000.0000.0000.000
38B49LYS10.9390.97111.6190.5660.5660.0000.0000.0000.000
39B50ASP-1-0.764-0.82216.8880.0620.0620.0000.0000.0000.000
40B51LYS10.8260.89518.6630.1470.1470.0000.0000.0000.000
41B52SER0-0.029-0.02620.7470.0140.0140.0000.0000.0000.000
42B53PHE0-0.0100.00917.5240.0110.0110.0000.0000.0000.000
43B54GLU-1-0.825-0.90622.7410.0240.0240.0000.0000.0000.000
44B55GLN0-0.046-0.02525.364-0.019-0.0190.0000.0000.0000.000
45B56ILE0-0.0070.00719.6350.0200.0200.0000.0000.0000.000
46B57THR00.019-0.00322.731-0.028-0.0280.0000.0000.0000.000
47B58GLY0-0.0010.01220.7590.0230.0230.0000.0000.0000.000
48B59VAL0-0.016-0.01021.442-0.015-0.0150.0000.0000.0000.000
49B60ASP-1-0.764-0.88919.8890.0630.0630.0000.0000.0000.000
50B61VAL00.0500.02322.644-0.009-0.0090.0000.0000.0000.000
51B62SER0-0.029-0.01022.961-0.012-0.0120.0000.0000.0000.000
52B63TYR00.0870.01924.069-0.011-0.0110.0000.0000.0000.000
53B64SER0-0.0090.00324.403-0.014-0.0140.0000.0000.0000.000
54B65VAL0-0.024-0.00318.757-0.022-0.0220.0000.0000.0000.000
55B66LEU00.0280.00520.532-0.023-0.0230.0000.0000.0000.000
56B67GLU-1-0.822-0.89022.602-0.096-0.0960.0000.0000.0000.000
57B68ARG10.8930.93518.1810.0970.0970.0000.0000.0000.000
58B69ALA0-0.0030.01418.147-0.039-0.0390.0000.0000.0000.000
59B70LYS10.8310.90719.1950.0560.0560.0000.0000.0000.000
60B71ASP-1-0.894-0.94920.723-0.227-0.2270.0000.0000.0000.000
61B72ARG10.7910.88613.3200.3520.3520.0000.0000.0000.000
62B73LEU0-0.093-0.05616.534-0.045-0.0450.0000.0000.0000.000
63B74LYS10.9140.96418.7810.4110.4110.0000.0000.0000.000
64B75ILE00.0230.00021.9260.0050.0050.0000.0000.0000.000
65B76ASP-1-0.896-0.94724.263-0.115-0.1150.0000.0000.0000.000
66B77ARG10.9100.95425.3550.2210.2210.0000.0000.0000.000
67B78LEU0-0.0320.01421.843-0.010-0.0100.0000.0000.0000.000
68B79PRO00.0260.00125.3830.0170.0170.0000.0000.0000.000
69B80GLU-1-0.886-0.93327.979-0.067-0.0670.0000.0000.0000.000
70B81MET0-0.010-0.01927.3280.0050.0050.0000.0000.0000.000
71B82GLN00.020-0.00421.2700.0330.0330.0000.0000.0000.000
72B83ARG10.9730.97925.1850.1070.1070.0000.0000.0000.000
73B84LYS10.9100.97427.0690.0590.0590.0000.0000.0000.000
74B85ARG10.7480.86020.9230.0640.0640.0000.0000.0000.000
75B86ILE0-0.036-0.01220.2470.0110.0110.0000.0000.0000.000
76B87SER00.0100.02224.258-0.008-0.0080.0000.0000.0000.000
77B88LEU0-0.007-0.00720.8220.0050.0050.0000.0000.0000.000
78B89PHE0-0.022-0.01124.832-0.003-0.0030.0000.0000.0000.000
79B90GLN0-0.010-0.00625.4870.0030.0030.0000.0000.0000.000
80B91SER0-0.028-0.04626.9100.0050.0050.0000.0000.0000.000
81B92SER00.0170.00526.8060.0050.0050.0000.0000.0000.000
82B93LEU00.0190.01122.9130.0070.0070.0000.0000.0000.000
83B94VAL00.0300.01627.5320.0120.0120.0000.0000.0000.000
84B95TYR0-0.023-0.00330.550-0.003-0.0030.0000.0000.0000.000
85B96ARG10.8930.94031.739-0.102-0.1020.0000.0000.0000.000
86B97ASP-1-0.745-0.83430.5560.0510.0510.0000.0000.0000.000
87B98LYS11.0000.99132.033-0.058-0.0580.0000.0000.0000.000
88B99ARG10.7970.87830.511-0.040-0.0400.0000.0000.0000.000
89B100PHE0-0.006-0.02327.654-0.002-0.0020.0000.0000.0000.000
90B101SER0-0.0010.00729.3100.0100.0100.0000.0000.0000.000
91B102GLY0-0.001-0.00131.321-0.007-0.0070.0000.0000.0000.000
92B103TYR0-0.033-0.00425.781-0.010-0.0100.0000.0000.0000.000
93B104ASP-1-0.796-0.88025.5650.1370.1370.0000.0000.0000.000
94B105ALA0-0.034-0.03522.2620.0220.0220.0000.0000.0000.000
95B106ALA00.0070.01222.474-0.027-0.0270.0000.0000.0000.000
96B107THR0-0.079-0.06416.9180.0330.0330.0000.0000.0000.000
97B108VAL00.016-0.00618.339-0.045-0.0450.0000.0000.0000.000
98B109ILE0-0.026-0.02411.8350.0650.0650.0000.0000.0000.000
99B110GLU-1-0.832-0.91111.1620.8020.8020.0000.0000.0000.000
100B111VAL00.0060.00614.605-0.069-0.0690.0000.0000.0000.000
101B112ILE00.007-0.00818.186-0.031-0.0310.0000.0000.0000.000
102B113GLU-1-0.809-0.87515.4900.4520.4520.0000.0000.0000.000
103B114HIS0-0.068-0.03015.490-0.056-0.0560.0000.0000.0000.000
104B115LEU0-0.095-0.03220.775-0.039-0.0390.0000.0000.0000.000
105B116ASP-1-0.792-0.88724.1650.1560.1560.0000.0000.0000.000
106B117GLU-1-0.867-0.95627.3450.1860.1860.0000.0000.0000.000
107B118ASN0-0.062-0.03229.663-0.002-0.0020.0000.0000.0000.000
108B119ARG10.8900.92627.220-0.121-0.1210.0000.0000.0000.000
109B120LEU00.0390.04224.225-0.001-0.0010.0000.0000.0000.000
110B121GLN00.0490.03027.311-0.005-0.0050.0000.0000.0000.000
111B122ALA0-0.024-0.01630.658-0.003-0.0030.0000.0000.0000.000
112B123PHE00.0310.00922.358-0.005-0.0050.0000.0000.0000.000
113B124GLU-1-0.761-0.85727.5490.2340.2340.0000.0000.0000.000
114B125LYS10.9100.96428.732-0.139-0.1390.0000.0000.0000.000
115B126VAL0-0.0110.00029.042-0.006-0.0060.0000.0000.0000.000
116B127LEU0-0.0070.00623.832-0.008-0.0080.0000.0000.0000.000
117B128PHE00.0460.00724.459-0.002-0.0020.0000.0000.0000.000
118B129GLU-1-0.879-0.93329.8290.1300.1300.0000.0000.0000.000
119B130PHE0-0.093-0.05632.260-0.010-0.0100.0000.0000.0000.000
120B131THR0-0.086-0.04428.012-0.008-0.0080.0000.0000.0000.000
121B132ARG10.7820.89930.264-0.179-0.1790.0000.0000.0000.000
122B133PRO00.0430.03526.075-0.007-0.0070.0000.0000.0000.000
123B134GLN00.0400.01927.766-0.001-0.0010.0000.0000.0000.000
124B135THR00.013-0.00822.1730.0250.0250.0000.0000.0000.000
125B136VAL0-0.0090.00122.314-0.019-0.0190.0000.0000.0000.000
126B137ILE0-0.027-0.00416.4200.0370.0370.0000.0000.0000.000
127B138VAL0-0.0010.00218.308-0.033-0.0330.0000.0000.0000.000
128B139SER0-0.043-0.03813.0100.0530.0530.0000.0000.0000.000
129B140THR00.001-0.01314.946-0.094-0.0940.0000.0000.0000.000
130B141PRO00.0380.02212.6080.1250.1250.0000.0000.0000.000
131B142ASN0-0.040-0.01214.012-0.217-0.2170.0000.0000.0000.000
132B143LYS10.8750.92715.506-0.350-0.3500.0000.0000.0000.000
133B144GLU-1-0.801-0.88217.9880.5300.5300.0000.0000.0000.000
134B145TYR00.0390.02810.0490.0290.0290.0000.0000.0000.000
135B146ASN00.018-0.02512.2220.1190.1190.0000.0000.0000.000
136B147PHE0-0.045-0.00814.588-0.069-0.0690.0000.0000.0000.000
137B148HIS10.8970.96716.890-0.575-0.5750.0000.0000.0000.000
138B149TYR0-0.039-0.02912.030-0.050-0.0500.0000.0000.0000.000
139B150GLN0-0.053-0.0228.9960.0990.0990.0000.0000.0000.000
140B151ASN0-0.0430.00513.704-0.107-0.1070.0000.0000.0000.000
141B152LEU00.0570.00917.455-0.038-0.0380.0000.0000.0000.000
142B153PHE0-0.136-0.08318.849-0.049-0.0490.0000.0000.0000.000
143B154GLU-1-0.844-0.91915.7040.2900.2900.0000.0000.0000.000
144B155GLY0-0.063-0.01419.913-0.016-0.0160.0000.0000.0000.000
145B156ASN00.0110.00120.7580.0250.0250.0000.0000.0000.000
146B157LEU00.0740.05521.057-0.005-0.0050.0000.0000.0000.000
147B158ARG10.8560.93222.936-0.162-0.1620.0000.0000.0000.000
148B159HIS00.0480.01718.9490.0290.0290.0000.0000.0000.000
149B160ARG10.8510.91420.807-0.230-0.2300.0000.0000.0000.000
150B161ASP-1-0.805-0.89619.1020.3040.3040.0000.0000.0000.000
151B162HIS0-0.027-0.03912.595-0.060-0.0600.0000.0000.0000.000
152B163ARG10.8790.91717.724-0.216-0.2160.0000.0000.0000.000
153B164PHE0-0.008-0.01316.084-0.013-0.0130.0000.0000.0000.000
154B165GLU-1-0.775-0.84814.5000.6960.6960.0000.0000.0000.000
155B166TRP00.0260.00718.820-0.030-0.0300.0000.0000.0000.000
156B167THR0-0.029-0.04519.3530.0660.0660.0000.0000.0000.000
157B168ARG10.8240.88218.527-0.647-0.6470.0000.0000.0000.000
158B169LYS10.9360.96921.105-0.405-0.4050.0000.0000.0000.000
159B170GLU-1-0.819-0.86323.5820.3490.3490.0000.0000.0000.000
160B171PHE0-0.0180.00119.198-0.027-0.0270.0000.0000.0000.000
161B172GLU-1-0.864-0.93622.5400.4610.4610.0000.0000.0000.000
162B173THR0-0.052-0.04924.375-0.034-0.0340.0000.0000.0000.000
163B174TRP0-0.032-0.02422.717-0.021-0.0210.0000.0000.0000.000
164B175ALA00.014-0.00823.668-0.022-0.0220.0000.0000.0000.000
165B176VAL00.0280.01925.806-0.015-0.0150.0000.0000.0000.000
166B177LYS10.8760.93828.815-0.264-0.2640.0000.0000.0000.000
167B178VAL0-0.042-0.02526.739-0.024-0.0240.0000.0000.0000.000
168B179ALA0-0.020-0.01028.075-0.016-0.0160.0000.0000.0000.000
169B180GLU-1-0.919-0.96629.9510.2190.2190.0000.0000.0000.000
170B181LYS10.7870.89531.736-0.214-0.2140.0000.0000.0000.000
171B182TYR0-0.021-0.01530.613-0.014-0.0140.0000.0000.0000.000
172B183GLY00.0410.04033.479-0.008-0.0080.0000.0000.0000.000
173B184TYR0-0.073-0.04527.868-0.005-0.0050.0000.0000.0000.000
174B185SER0-0.0170.00328.1370.0090.0090.0000.0000.0000.000
175B186VAL00.025-0.00223.2800.0100.0100.0000.0000.0000.000
176B187ARG10.9460.98719.550-0.489-0.4890.0000.0000.0000.000
177B188PHE00.0250.00919.6930.0230.0230.0000.0000.0000.000
178B189LEU0-0.043-0.03114.6100.0080.0080.0000.0000.0000.000
179B190GLN00.0250.01213.792-0.012-0.0120.0000.0000.0000.000
180B191ILE0-0.015-0.0117.8640.1410.1410.0000.0000.0000.000
181B192GLY00.0730.0216.6810.0200.0200.0000.0000.0000.000
182B193GLU-1-0.966-0.9867.2241.6211.6210.0000.0000.0000.000
183B194ILE0-0.037-0.0209.297-0.193-0.1930.0000.0000.0000.000
184B195ASP-1-0.792-0.85712.9360.6970.6970.0000.0000.0000.000
185B196ASP-1-0.913-0.96715.6360.6540.6540.0000.0000.0000.000
186B197GLU-1-0.935-0.96019.0380.3880.3880.0000.0000.0000.000
187B198PHE0-0.079-0.05616.575-0.027-0.0270.0000.0000.0000.000
188B199GLY00.0260.01416.1960.0060.0060.0000.0000.0000.000
189B200SER0-0.0060.00111.074-0.035-0.0350.0000.0000.0000.000
190B201PRO00.0130.0188.127-0.201-0.2010.0000.0000.0000.000
191B202THR0-0.052-0.0329.867-0.241-0.2410.0000.0000.0000.000
192B203GLN0-0.0080.00912.0600.0510.0510.0000.0000.0000.000
193B204MET00.000-0.01912.497-0.024-0.0240.0000.0000.0000.000
194B205GLY00.0150.02316.243-0.010-0.0100.0000.0000.0000.000
195B206VAL0-0.055-0.03418.321-0.019-0.0190.0000.0000.0000.000
196B207PHE00.003-0.00520.873-0.016-0.0160.0000.0000.0000.000
197B208THR0-0.023-0.01624.2820.0000.0000.0000.0000.0000.000
198B209LEU00.0020.02326.832-0.001-0.0010.0000.0000.0000.000