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: V5GL1

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2354809.938281
FMO2-HF: Nuclear repulsion 2275025.887148
FMO2-HF: Total energy -79784.051132
FMO2-MP2: Total energy -80021.367652


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.
-10.324-5.1632.055-2.567-4.6490.012
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 : 0.034 / q_NPA : -0.003
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].
3B14ASN00.018-0.0092.957-2.0110.0470.040-0.835-1.2630.000
4B15GLN0-0.012-0.0012.265-0.4880.4201.479-0.881-1.5060.005
5B16GLN00.0660.0312.798-5.540-3.4030.537-0.847-1.8270.007
6B17ARG10.9441.0095.283-2.788-2.730-0.001-0.004-0.0530.000
7B18LEU00.001-0.0207.676-0.352-0.3520.0000.0000.0000.000
8B19GLY00.0150.0107.948-0.301-0.3010.0000.0000.0000.000
9B20THR00.008-0.0168.859-0.337-0.3370.0000.0000.0000.000
10B21VAL00.0020.01111.056-0.252-0.2520.0000.0000.0000.000
11B22VAL00.000-0.00212.347-0.147-0.1470.0000.0000.0000.000
12B23ALA00.0000.00412.937-0.121-0.1210.0000.0000.0000.000
13B24VAL00.008-0.00114.777-0.109-0.1090.0000.0000.0000.000
14B25LEU0-0.004-0.00916.695-0.087-0.0870.0000.0000.0000.000
15B26LYS10.8630.93616.986-0.389-0.3890.0000.0000.0000.000
16B27SER0-0.051-0.01218.805-0.068-0.0680.0000.0000.0000.000
17B28VAL0-0.017-0.00120.516-0.033-0.0330.0000.0000.0000.000
18B29ASN0-0.059-0.02822.796-0.038-0.0380.0000.0000.0000.000
19B30ALA00.0000.00822.083-0.027-0.0270.0000.0000.0000.000
20B31LYS10.9270.96422.953-0.142-0.1420.0000.0000.0000.000
21B32LYS10.8790.95124.822-0.146-0.1460.0000.0000.0000.000
22B33VAL00.0250.00119.4810.0180.0180.0000.0000.0000.000
23B34ILE00.0000.00722.813-0.026-0.0260.0000.0000.0000.000
24B35ASP-1-0.821-0.90416.6430.3820.3820.0000.0000.0000.000
25B36LEU0-0.035-0.02619.820-0.038-0.0380.0000.0000.0000.000
26B37GLY00.0250.00419.4540.0290.0290.0000.0000.0000.000
27B38CYS0-0.029-0.00516.9230.0110.0110.0000.0000.0000.000
28B39GLY00.0290.03015.766-0.006-0.0060.0000.0000.0000.000
29B40GLU-1-0.936-0.99314.048-0.057-0.0570.0000.0000.0000.000
30B41GLY00.0550.01915.510-0.046-0.0460.0000.0000.0000.000
31B42ASN0-0.055-0.0559.803-0.103-0.1030.0000.0000.0000.000
32B43LEU00.0630.04211.943-0.012-0.0120.0000.0000.0000.000
33B44LEU00.0660.02813.250-0.011-0.0110.0000.0000.0000.000
34B45SER0-0.052-0.02813.024-0.046-0.0460.0000.0000.0000.000
35B46LEU0-0.025-0.0209.152-0.068-0.0680.0000.0000.0000.000
36B47LEU00.0400.02813.550-0.010-0.0100.0000.0000.0000.000
37B48LEU00.0370.02216.785-0.021-0.0210.0000.0000.0000.000
38B49LYS10.8900.93911.6330.1800.1800.0000.0000.0000.000
39B50ASP-1-0.809-0.85416.9660.1970.1970.0000.0000.0000.000
40B51LYS10.8910.92018.6660.0080.0080.0000.0000.0000.000
41B52SER0-0.053-0.04020.6690.0010.0010.0000.0000.0000.000
42B53PHE0-0.0080.00517.3730.0090.0090.0000.0000.0000.000
43B54GLU-1-0.914-0.96722.7470.0890.0890.0000.0000.0000.000
44B55GLN0-0.036-0.02325.349-0.016-0.0160.0000.0000.0000.000
45B56ILE00.0100.01319.6350.0240.0240.0000.0000.0000.000
46B57THR00.0050.01322.745-0.026-0.0260.0000.0000.0000.000
47B58GLY00.0110.02220.7720.0290.0290.0000.0000.0000.000
48B59VAL0-0.005-0.00521.443-0.025-0.0250.0000.0000.0000.000
49B60ASP-1-0.768-0.90019.8820.1890.1890.0000.0000.0000.000
50B61VAL00.0450.02322.649-0.017-0.0170.0000.0000.0000.000
51B62SER0-0.0230.00322.991-0.019-0.0190.0000.0000.0000.000
52B63TYR00.1090.02624.072-0.002-0.0020.0000.0000.0000.000
53B64SER00.0020.00524.674-0.006-0.0060.0000.0000.0000.000
54B65VAL0-0.0280.00318.845-0.018-0.0180.0000.0000.0000.000
55B66LEU00.015-0.00420.531-0.013-0.0130.0000.0000.0000.000
56B67GLU-1-0.905-0.94522.599-0.008-0.0080.0000.0000.0000.000
57B68ARG10.9880.99418.531-0.026-0.0260.0000.0000.0000.000
58B69ALA00.0100.01918.136-0.025-0.0250.0000.0000.0000.000
59B70LYS10.8830.95219.191-0.038-0.0380.0000.0000.0000.000
60B71ASP-1-0.887-0.94320.674-0.099-0.0990.0000.0000.0000.000
61B72ARG10.8390.93612.8010.1070.1070.0000.0000.0000.000
62B73LEU0-0.098-0.05616.680-0.029-0.0290.0000.0000.0000.000
63B74LYS10.9230.96618.8480.2260.2260.0000.0000.0000.000
64B75ILE00.032-0.00122.220-0.001-0.0010.0000.0000.0000.000
65B76ASP-1-0.891-0.94124.254-0.025-0.0250.0000.0000.0000.000
66B77ARG10.8810.94025.2320.1130.1130.0000.0000.0000.000
67B78LEU0-0.0540.00421.973-0.009-0.0090.0000.0000.0000.000
68B79PRO00.0260.00425.4490.0090.0090.0000.0000.0000.000
69B80GLU-1-0.880-0.93127.9960.0010.0010.0000.0000.0000.000
70B81MET0-0.005-0.02627.0770.0070.0070.0000.0000.0000.000
71B82GLN00.002-0.01620.9520.0260.0260.0000.0000.0000.000
72B83ARG10.9920.98925.2010.0270.0270.0000.0000.0000.000
73B84LYS10.9140.98627.060-0.024-0.0240.0000.0000.0000.000
74B85ARG10.7660.89121.036-0.065-0.0650.0000.0000.0000.000
75B86ILE0-0.024-0.00120.5790.0170.0170.0000.0000.0000.000
76B87SER0-0.0120.01224.240-0.017-0.0170.0000.0000.0000.000
77B88LEU0-0.016-0.01320.9230.0130.0130.0000.0000.0000.000
78B89PHE0-0.011-0.00324.831-0.012-0.0120.0000.0000.0000.000
79B90GLN0-0.022-0.01825.4890.0060.0060.0000.0000.0000.000
80B91SER0-0.019-0.03426.9180.0000.0000.0000.0000.0000.000
81B92SER00.0120.00326.8130.0100.0100.0000.0000.0000.000
82B93LEU00.0210.01322.8920.0070.0070.0000.0000.0000.000
83B94VAL00.0430.02427.5420.0110.0110.0000.0000.0000.000
84B95TYR0-0.029-0.01130.562-0.008-0.0080.0000.0000.0000.000
85B96ARG10.9670.98431.748-0.126-0.1260.0000.0000.0000.000
86B97ASP-1-0.736-0.84530.5800.1080.1080.0000.0000.0000.000
87B98LYS11.0000.98632.040-0.095-0.0950.0000.0000.0000.000
88B99ARG10.8000.89530.522-0.103-0.1030.0000.0000.0000.000
89B100PHE0-0.001-0.01827.6290.0030.0030.0000.0000.0000.000
90B101SER0-0.0080.00529.3160.0110.0110.0000.0000.0000.000
91B102GLY00.0010.00131.325-0.005-0.0050.0000.0000.0000.000
92B103TYR0-0.072-0.05025.810-0.006-0.0060.0000.0000.0000.000
93B104ASP-1-0.819-0.90225.6240.1990.1990.0000.0000.0000.000
94B105ALA0-0.035-0.03822.2910.0180.0180.0000.0000.0000.000
95B106ALA00.0100.01422.499-0.023-0.0230.0000.0000.0000.000
96B107THR0-0.089-0.07416.9350.0260.0260.0000.0000.0000.000
97B108VAL00.0280.00418.353-0.045-0.0450.0000.0000.0000.000
98B109ILE0-0.033-0.02411.8530.0670.0670.0000.0000.0000.000
99B110GLU-1-0.902-0.96411.2100.9630.9630.0000.0000.0000.000
100B111VAL00.0150.01114.621-0.073-0.0730.0000.0000.0000.000
101B112ILE00.008-0.01418.200-0.038-0.0380.0000.0000.0000.000
102B113GLU-1-0.831-0.90315.3380.5470.5470.0000.0000.0000.000
103B114HIS0-0.061-0.02615.436-0.058-0.0580.0000.0000.0000.000
104B115LEU0-0.109-0.04420.791-0.042-0.0420.0000.0000.0000.000
105B116ASP-1-0.852-0.91824.1810.1910.1910.0000.0000.0000.000
106B117GLU-1-0.860-0.96127.3620.2060.2060.0000.0000.0000.000
107B118ASN0-0.036-0.01329.6810.0000.0000.0000.0000.0000.000
108B119ARG10.9180.94726.990-0.168-0.1680.0000.0000.0000.000
109B120LEU00.0370.04524.3970.0020.0020.0000.0000.0000.000
110B121GLN00.0220.01327.327-0.007-0.0070.0000.0000.0000.000
111B122ALA0-0.037-0.02230.675-0.004-0.0040.0000.0000.0000.000
112B123PHE00.0140.00122.775-0.004-0.0040.0000.0000.0000.000
113B124GLU-1-0.813-0.90027.4000.2670.2670.0000.0000.0000.000
114B125LYS10.9660.99328.747-0.163-0.1630.0000.0000.0000.000
115B126VAL0-0.029-0.00428.925-0.007-0.0070.0000.0000.0000.000
116B127LEU00.0010.00523.926-0.007-0.0070.0000.0000.0000.000
117B128PHE00.0410.00324.658-0.001-0.0010.0000.0000.0000.000
118B129GLU-1-0.960-0.97829.8420.1560.1560.0000.0000.0000.000
119B130PHE0-0.107-0.05831.955-0.013-0.0130.0000.0000.0000.000
120B131THR0-0.094-0.04827.952-0.007-0.0070.0000.0000.0000.000
121B132ARG10.8060.91630.280-0.209-0.2090.0000.0000.0000.000
122B133PRO00.0310.02426.078-0.007-0.0070.0000.0000.0000.000
123B134GLN00.0420.02727.416-0.005-0.0050.0000.0000.0000.000
124B135THR00.017-0.00821.9240.0180.0180.0000.0000.0000.000
125B136VAL0-0.0070.00422.414-0.011-0.0110.0000.0000.0000.000
126B137ILE0-0.027-0.00316.2020.0300.0300.0000.0000.0000.000
127B138VAL00.0050.00418.319-0.020-0.0200.0000.0000.0000.000
128B139SER0-0.008-0.00613.3080.0430.0430.0000.0000.0000.000
129B140THR0-0.0090.00314.967-0.090-0.0900.0000.0000.0000.000
130B141PRO00.0460.02612.3100.1090.1090.0000.0000.0000.000
131B142ASN0-0.026-0.01313.956-0.210-0.2100.0000.0000.0000.000
132B143LYS10.9620.97315.450-0.352-0.3520.0000.0000.0000.000
133B144GLU-1-0.824-0.89317.9330.4660.4660.0000.0000.0000.000
134B145TYR00.0380.0319.7650.0330.0330.0000.0000.0000.000
135B146ASN00.020-0.03012.2170.0810.0810.0000.0000.0000.000
136B147PHE0-0.047-0.01414.536-0.072-0.0720.0000.0000.0000.000
137B148HIS10.8640.94016.855-0.473-0.4730.0000.0000.0000.000
138B149TYR0-0.039-0.03311.984-0.055-0.0550.0000.0000.0000.000
139B150GLN0-0.040-0.0148.9770.0450.0450.0000.0000.0000.000
140B151ASN0-0.0050.04013.659-0.077-0.0770.0000.0000.0000.000
141B152LEU00.0360.00817.411-0.038-0.0380.0000.0000.0000.000
142B153PHE0-0.136-0.08318.849-0.045-0.0450.0000.0000.0000.000
143B154GLU-1-0.855-0.91615.8540.1830.1830.0000.0000.0000.000
144B155GLY0-0.058-0.01419.877-0.017-0.0170.0000.0000.0000.000
145B156ASN00.0020.00220.7320.0110.0110.0000.0000.0000.000
146B157LEU00.0820.05620.987-0.010-0.0100.0000.0000.0000.000
147B158ARG10.8480.92722.892-0.116-0.1160.0000.0000.0000.000
148B159HIS00.048-0.01719.0070.0340.0340.0000.0000.0000.000
149B160ARG10.8360.91720.628-0.227-0.2270.0000.0000.0000.000
150B161ASP-1-0.825-0.91519.3520.2960.2960.0000.0000.0000.000
151B162HIS0-0.023-0.04512.850-0.061-0.0610.0000.0000.0000.000
152B163ARG10.8900.93317.745-0.219-0.2190.0000.0000.0000.000
153B164PHE0-0.029-0.02116.403-0.020-0.0200.0000.0000.0000.000
154B165GLU-1-0.796-0.85014.5520.7210.7210.0000.0000.0000.000
155B166TRP00.0520.01818.841-0.031-0.0310.0000.0000.0000.000
156B167THR0-0.035-0.02019.3750.0610.0610.0000.0000.0000.000
157B168ARG10.8600.90018.151-0.574-0.5740.0000.0000.0000.000
158B169LYS10.9941.00621.051-0.339-0.3390.0000.0000.0000.000
159B170GLU-1-0.867-0.91923.5060.3510.3510.0000.0000.0000.000
160B171PHE0-0.0010.01219.357-0.018-0.0180.0000.0000.0000.000
161B172GLU-1-0.918-0.97021.7190.4900.4900.0000.0000.0000.000
162B173THR0-0.064-0.04624.145-0.035-0.0350.0000.0000.0000.000
163B174TRP0-0.064-0.04922.617-0.017-0.0170.0000.0000.0000.000
164B175ALA00.019-0.00423.412-0.020-0.0200.0000.0000.0000.000
165B176VAL00.0350.02625.534-0.015-0.0150.0000.0000.0000.000
166B177LYS10.8910.95428.557-0.277-0.2770.0000.0000.0000.000
167B178VAL0-0.020-0.01326.837-0.024-0.0240.0000.0000.0000.000
168B179ALA0-0.005-0.00427.849-0.014-0.0140.0000.0000.0000.000
169B180GLU-1-0.940-0.97529.6660.2190.2190.0000.0000.0000.000
170B181LYS10.8570.94032.927-0.226-0.2260.0000.0000.0000.000
171B182TYR0-0.033-0.02430.753-0.018-0.0180.0000.0000.0000.000
172B183GLY00.0330.03233.348-0.006-0.0060.0000.0000.0000.000
173B184TYR0-0.078-0.04727.608-0.004-0.0040.0000.0000.0000.000
174B185SER0-0.0240.00127.8760.0040.0040.0000.0000.0000.000
175B186VAL00.0400.00522.8890.0140.0140.0000.0000.0000.000
176B187ARG10.9360.98419.379-0.500-0.5000.0000.0000.0000.000
177B188PHE00.0350.00719.4540.0320.0320.0000.0000.0000.000
178B189LEU0-0.051-0.03214.299-0.001-0.0010.0000.0000.0000.000
179B190GLN00.0220.01013.6160.0150.0150.0000.0000.0000.000
180B191ILE0-0.015-0.0057.6490.1280.1280.0000.0000.0000.000
181B192GLY00.0590.0076.5500.0900.0900.0000.0000.0000.000
182B193GLU-1-0.961-0.9947.4830.6440.6440.0000.0000.0000.000
183B194ILE0-0.041-0.0199.307-0.090-0.0900.0000.0000.0000.000
184B195ASP-1-0.789-0.85612.9150.4730.4730.0000.0000.0000.000
185B196ASP-1-0.916-0.97215.6210.4780.4780.0000.0000.0000.000
186B197GLU-1-0.970-0.96419.0240.3080.3080.0000.0000.0000.000
187B198PHE0-0.058-0.05416.571-0.005-0.0050.0000.0000.0000.000
188B199GLY00.0200.01416.1160.0280.0280.0000.0000.0000.000
189B200SER00.0000.01511.125-0.059-0.0590.0000.0000.0000.000
190B201PRO00.0030.0168.007-0.158-0.1580.0000.0000.0000.000
191B202THR0-0.042-0.0329.917-0.070-0.0700.0000.0000.0000.000
192B203GLN0-0.0060.00411.8970.0030.0030.0000.0000.0000.000
193B204MET0-0.005-0.01811.821-0.003-0.0030.0000.0000.0000.000
194B205GLY00.0190.01915.965-0.032-0.0320.0000.0000.0000.000
195B206VAL0-0.052-0.02818.033-0.003-0.0030.0000.0000.0000.000
196B207PHE00.001-0.00620.582-0.026-0.0260.0000.0000.0000.000
197B208THR0-0.020-0.01423.9750.0070.0070.0000.0000.0000.000
198B209LEU00.0030.01926.539-0.007-0.0070.0000.0000.0000.000