Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: JQV59

Calculation Name: 3EXR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EXR

Chain ID: B

ChEMBL ID:

UniProt ID: Q93DA8

Base Structure: X-ray

Registration Date: 2023-09-23

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2492042.473132
FMO2-HF: Nuclear repulsion 2409614.839395
FMO2-HF: Total energy -82427.633738
FMO2-MP2: Total energy -82668.000938


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:4:GLN)


Summations of interaction energy for fragment #1(B:4:GLN)
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.
-23.37-16.4370.412-3.528-3.817-0.002
Interaction energy analysis for fragmet #1(B:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.004
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].
3B6PRO00.0460.0373.136-8.134-4.4040.272-1.961-2.041-0.001
4B7ASN0-0.059-0.0333.244-2.278-1.3600.043-0.321-0.640-0.002
5B8LEU0-0.029-0.0075.0041.0281.087-0.001-0.003-0.0560.000
6B9GLN00.005-0.0257.540-0.735-0.7350.0000.0000.0000.000
7B10VAL0-0.034-0.0209.9880.3050.3050.0000.0000.0000.000
8B11ALA00.0420.02613.317-0.076-0.0760.0000.0000.0000.000
9B12LEU0-0.074-0.03716.4660.1290.1290.0000.0000.0000.000
10B13ASP-1-0.880-0.95019.359-0.591-0.5910.0000.0000.0000.000
11B14HIS0-0.003-0.00720.7250.0260.0260.0000.0000.0000.000
12B15SER00.0520.01925.062-0.007-0.0070.0000.0000.0000.000
13B16ASN0-0.022-0.01827.4280.0160.0160.0000.0000.0000.000
14B17LEU00.1330.07025.413-0.015-0.0150.0000.0000.0000.000
15B18LYS10.9900.99125.3270.1610.1610.0000.0000.0000.000
16B19GLY0-0.0170.00825.3930.0050.0050.0000.0000.0000.000
17B20ALA00.0630.02421.552-0.003-0.0030.0000.0000.0000.000
18B21ILE00.0300.01720.656-0.025-0.0250.0000.0000.0000.000
19B22THR0-0.037-0.03721.0620.0080.0080.0000.0000.0000.000
20B23ALA0-0.0120.00019.7260.0190.0190.0000.0000.0000.000
21B24ALA00.0460.03716.742-0.001-0.0010.0000.0000.0000.000
22B25VAL00.004-0.00316.388-0.009-0.0090.0000.0000.0000.000
23B26SER0-0.117-0.06417.9500.0480.0480.0000.0000.0000.000
24B27VAL00.008-0.01713.9030.0690.0690.0000.0000.0000.000
25B28GLY00.0480.03812.742-0.026-0.0260.0000.0000.0000.000
26B29ASN00.011-0.01911.214-0.229-0.2290.0000.0000.0000.000
27B30GLU-1-0.863-0.90110.3210.5540.5540.0000.0000.0000.000
28B31VAL0-0.038-0.0038.1330.1440.1440.0000.0000.0000.000
29B32ASP-1-0.762-0.8553.311-5.547-4.5660.019-0.609-0.391-0.005
30B33VAL0-0.016-0.0046.046-0.128-0.1280.0000.0000.0000.000
31B34ILE0-0.0100.0018.9740.3940.3940.0000.0000.0000.000
32B35GLU-1-0.842-0.91412.670-1.205-1.2050.0000.0000.0000.000
33B36ALA0-0.009-0.00915.3520.1280.1280.0000.0000.0000.000
34B37GLY00.0790.03119.023-0.028-0.0280.0000.0000.0000.000
35B38THR0-0.020-0.03320.6720.0560.0560.0000.0000.0000.000
36B39VAL0-0.028-0.01023.7680.0380.0380.0000.0000.0000.000
37B40CYS0-0.0260.00023.1910.0350.0350.0000.0000.0000.000
38B41LEU00.0120.00221.1380.0340.0340.0000.0000.0000.000
39B42LEU0-0.023-0.01525.3070.0290.0290.0000.0000.0000.000
40B43GLN0-0.101-0.03628.2050.0340.0340.0000.0000.0000.000
41B44VAL0-0.068-0.04125.8420.0250.0250.0000.0000.0000.000
42B45GLY00.0110.02227.9940.0130.0130.0000.0000.0000.000
43B46SER00.021-0.01224.534-0.009-0.0090.0000.0000.0000.000
44B47GLU-1-0.827-0.89123.995-0.346-0.3460.0000.0000.0000.000
45B48LEU0-0.005-0.00721.344-0.004-0.0040.0000.0000.0000.000
46B49VAL00.000-0.00718.506-0.023-0.0230.0000.0000.0000.000
47B50GLU-1-0.805-0.87919.479-0.445-0.4450.0000.0000.0000.000
48B51VAL0-0.060-0.03521.3500.0090.0090.0000.0000.0000.000
49B52LEU0-0.021-0.02316.8980.0210.0210.0000.0000.0000.000
50B53ARG10.8000.87012.7171.1291.1290.0000.0000.0000.000
51B54SER0-0.015-0.00717.4850.0150.0150.0000.0000.0000.000
52B55LEU0-0.104-0.04818.2610.0460.0460.0000.0000.0000.000
53B56PHE0-0.022-0.01613.1920.0620.0620.0000.0000.0000.000
54B57PRO00.0380.02114.095-0.149-0.1490.0000.0000.0000.000
55B58ASP-1-0.975-0.96211.446-0.675-0.6750.0000.0000.0000.000
56B59LYS10.8460.9218.1610.7880.7880.0000.0000.0000.000
57B60ILE0-0.0010.0115.8510.2040.2040.0000.0000.0000.000
58B61ILE0-0.0060.0219.6860.1590.1590.0000.0000.0000.000
59B62VAL00.0180.01012.140-0.006-0.0060.0000.0000.0000.000
60B63ALA00.0070.00014.6710.1390.1390.0000.0000.0000.000
61B64ASP-1-0.744-0.85418.141-0.759-0.7590.0000.0000.0000.000
62B65THR0-0.001-0.01719.5940.0920.0920.0000.0000.0000.000
63B66LYS10.7590.88920.9660.7440.7440.0000.0000.0000.000
64B67CYS0-0.0340.01123.5160.0580.0580.0000.0000.0000.000
65B68ALA00.0530.01225.498-0.021-0.0210.0000.0000.0000.000
66B69ASP-1-0.853-0.94428.503-0.330-0.3300.0000.0000.0000.000
67B70ALA0-0.048-0.02729.452-0.017-0.0170.0000.0000.0000.000
68B71GLY00.0380.00526.744-0.014-0.0140.0000.0000.0000.000
69B72GLY00.0170.01326.061-0.029-0.0290.0000.0000.0000.000
70B73THR0-0.006-0.01127.158-0.012-0.0120.0000.0000.0000.000
71B74VAL00.0150.00524.549-0.005-0.0050.0000.0000.0000.000
72B75ALA00.0510.02822.560-0.027-0.0270.0000.0000.0000.000
73B76LYS10.8970.95122.9010.3870.3870.0000.0000.0000.000
74B77ASN0-0.024-0.02024.7220.0050.0050.0000.0000.0000.000
75B78ASN0-0.024-0.03220.9350.0080.0080.0000.0000.0000.000
76B79ALA00.0260.01720.003-0.038-0.0380.0000.0000.0000.000
77B80VAL0-0.041-0.02621.016-0.006-0.0060.0000.0000.0000.000
78B81ARG10.7370.85522.1730.4190.4190.0000.0000.0000.000
79B82GLY00.0330.02518.9840.0070.0070.0000.0000.0000.000
80B83ALA0-0.033-0.00916.501-0.102-0.1020.0000.0000.0000.000
81B84ASP-1-0.750-0.84811.915-1.589-1.5890.0000.0000.0000.000
82B85TRP00.0070.0027.176-0.075-0.0750.0000.0000.0000.000
83B86MET0-0.0180.01114.5710.1240.1240.0000.0000.0000.000
84B87THR00.009-0.00717.259-0.007-0.0070.0000.0000.0000.000
85B88CYS0-0.030-0.00819.2090.0760.0760.0000.0000.0000.000
86B89ILE0-0.0020.00422.049-0.042-0.0420.0000.0000.0000.000
87B90CYS00.0060.00623.9250.0170.0170.0000.0000.0000.000
88B91SER0-0.022-0.00625.2460.0110.0110.0000.0000.0000.000
89B92ALA0-0.0100.00926.3250.0350.0350.0000.0000.0000.000
90B93THR0-0.0020.00227.936-0.010-0.0100.0000.0000.0000.000
91B94ILE00.0780.02526.153-0.023-0.0230.0000.0000.0000.000
92B95PRO0-0.012-0.02027.796-0.024-0.0240.0000.0000.0000.000
93B96THR00.0170.03227.4650.0010.0010.0000.0000.0000.000
94B97MET00.0380.01823.716-0.033-0.0330.0000.0000.0000.000
95B98LYS10.9330.98223.9150.4010.4010.0000.0000.0000.000
96B99ALA0-0.051-0.02025.453-0.009-0.0090.0000.0000.0000.000
97B100ALA00.011-0.00123.0460.0010.0010.0000.0000.0000.000
98B101ARG10.7900.86419.3730.6950.6950.0000.0000.0000.000
99B102LYS10.9650.98421.4190.4670.4670.0000.0000.0000.000
100B103ALA0-0.028-0.00123.9060.0120.0120.0000.0000.0000.000
101B104ILE0-0.022-0.00917.4290.0230.0230.0000.0000.0000.000
102B105GLU-1-0.816-0.89319.049-0.747-0.7470.0000.0000.0000.000
103B106ASP-1-0.926-0.96020.399-0.408-0.4080.0000.0000.0000.000
104B107ILE0-0.069-0.03021.0100.0340.0340.0000.0000.0000.000
105B108ASN0-0.054-0.03014.8570.0060.0060.0000.0000.0000.000
106B109PRO00.0260.01617.231-0.105-0.1050.0000.0000.0000.000
107B110ASP-1-0.942-0.96014.024-0.759-0.7590.0000.0000.0000.000
108B111LYS10.8410.89310.1741.4681.4680.0000.0000.0000.000
109B112GLY0-0.0090.01413.083-0.168-0.1680.0000.0000.0000.000
110B113GLU-1-0.787-0.84511.746-2.096-2.0960.0000.0000.0000.000
111B114ILE0-0.038-0.02215.7290.0430.0430.0000.0000.0000.000
112B115GLN0-0.021-0.02412.0470.0840.0840.0000.0000.0000.000
113B116VAL00.0120.00216.7530.1110.1110.0000.0000.0000.000
114B117GLU-1-0.732-0.87219.079-0.825-0.8250.0000.0000.0000.000
115B118LEU0-0.042-0.01420.1290.0790.0790.0000.0000.0000.000
116B119TYR0-0.082-0.06522.0210.0410.0410.0000.0000.0000.000
117B120GLY00.0140.00326.0480.0060.0060.0000.0000.0000.000
118B121ASP-1-0.942-0.96828.446-0.333-0.3330.0000.0000.0000.000
119B122TRP0-0.0240.00022.668-0.006-0.0060.0000.0000.0000.000
120B123THR0-0.023-0.04427.9320.0060.0060.0000.0000.0000.000
121B124TYR00.044-0.01121.889-0.008-0.0080.0000.0000.0000.000
122B125ASP-1-0.841-0.89625.243-0.368-0.3680.0000.0000.0000.000
123B126GLN00.0110.00427.002-0.031-0.0310.0000.0000.0000.000
124B127ALA00.012-0.00521.688-0.025-0.0250.0000.0000.0000.000
125B128GLN0-0.014-0.01922.037-0.058-0.0580.0000.0000.0000.000
126B129GLN0-0.003-0.00723.639-0.005-0.0050.0000.0000.0000.000
127B130TRP00.002-0.00521.155-0.020-0.0200.0000.0000.0000.000
128B131LEU00.0370.03217.277-0.032-0.0320.0000.0000.0000.000
129B132ASP-1-0.869-0.91220.409-0.477-0.4770.0000.0000.0000.000
130B133ALA0-0.135-0.07623.1620.0420.0420.0000.0000.0000.000
131B134GLY0-0.005-0.01019.6740.0090.0090.0000.0000.0000.000
132B135ILE0-0.056-0.01718.192-0.078-0.0780.0000.0000.0000.000
133B136SER00.0810.04214.378-0.019-0.0190.0000.0000.0000.000
134B137GLN00.0160.02510.650-0.213-0.2130.0000.0000.0000.000
135B138ALA0-0.009-0.00314.7740.1990.1990.0000.0000.0000.000
136B139ILE0-0.0060.00114.406-0.155-0.1550.0000.0000.0000.000
137B140TYR0-0.023-0.04316.8660.1410.1410.0000.0000.0000.000
138B141HIS10.7990.88318.2710.6780.6780.0000.0000.0000.000
139B142GLN00.0130.01320.8980.0450.0450.0000.0000.0000.000
140B143SER0-0.073-0.06222.5970.0120.0120.0000.0000.0000.000
141B144ARG10.9080.94524.2480.4100.4100.0000.0000.0000.000
142B145ASP-1-0.894-0.94728.497-0.180-0.1800.0000.0000.0000.000
143B146ALA00.0510.04231.5630.0100.0100.0000.0000.0000.000
144B147LEU0-0.056-0.02227.507-0.003-0.0030.0000.0000.0000.000
145B148LEU00.0180.00031.6720.0140.0140.0000.0000.0000.000
146B149ALA0-0.041-0.02333.284-0.008-0.0080.0000.0000.0000.000
147B150GLY00.026-0.00429.736-0.015-0.0150.0000.0000.0000.000
148B151GLU-1-0.905-0.94126.188-0.121-0.1210.0000.0000.0000.000
149B152THR0-0.0170.00322.462-0.012-0.0120.0000.0000.0000.000
150B153TRP0-0.062-0.04718.742-0.008-0.0080.0000.0000.0000.000
151B154GLY00.0760.03823.0800.0170.0170.0000.0000.0000.000
152B155GLU-1-0.772-0.90722.774-0.312-0.3120.0000.0000.0000.000
153B156LYS10.8010.90124.5150.1850.1850.0000.0000.0000.000
154B157ASP-1-0.764-0.84222.187-0.423-0.4230.0000.0000.0000.000
155B158LEU00.0670.04218.611-0.070-0.0700.0000.0000.0000.000
156B159ASN0-0.049-0.04119.668-0.059-0.0590.0000.0000.0000.000
157B160LYS10.8990.97021.1140.3860.3860.0000.0000.0000.000
158B161VAL00.0150.00315.758-0.046-0.0460.0000.0000.0000.000
159B162LYS10.8720.93816.3710.2620.2620.0000.0000.0000.000
160B163LYS11.0011.01817.0930.3660.3660.0000.0000.0000.000
161B164LEU0-0.059-0.03117.3600.0010.0010.0000.0000.0000.000
162B165ILE00.0320.01611.933-0.032-0.0320.0000.0000.0000.000
163B166GLU-1-0.961-0.98214.354-0.528-0.5280.0000.0000.0000.000
164B167MET0-0.112-0.05216.5180.0420.0420.0000.0000.0000.000
165B168GLY00.0150.02114.3330.0530.0530.0000.0000.0000.000
166B169PHE0-0.085-0.04014.068-0.097-0.0970.0000.0000.0000.000
167B170ARG10.7950.8598.4622.3682.3680.0000.0000.0000.000
168B171VAL0-0.002-0.01011.2710.0940.0940.0000.0000.0000.000
169B172SER00.0220.01411.763-0.333-0.3330.0000.0000.0000.000
170B173VAL0-0.0140.00912.8020.2390.2390.0000.0000.0000.000
171B174THR00.021-0.00414.4780.0030.0030.0000.0000.0000.000
172B175GLY00.0250.01617.1270.0530.0530.0000.0000.0000.000
173B176GLY00.0440.01619.610-0.002-0.0020.0000.0000.0000.000
174B177LEU0-0.0300.00914.1340.0280.0280.0000.0000.0000.000
175B178SER0-0.019-0.02017.2340.0230.0230.0000.0000.0000.000
176B179VAL00.0780.02015.344-0.012-0.0120.0000.0000.0000.000
177B180ASP-1-0.904-0.96116.7040.1550.1550.0000.0000.0000.000
178B181THR0-0.024-0.02618.8440.0100.0100.0000.0000.0000.000
179B182LEU00.0150.02912.209-0.046-0.0460.0000.0000.0000.000
180B183LYS10.8720.92915.416-0.240-0.2400.0000.0000.0000.000
181B184LEU0-0.044-0.01517.271-0.004-0.0040.0000.0000.0000.000
182B185PHE0-0.022-0.01814.595-0.076-0.0760.0000.0000.0000.000
183B186GLU-1-0.909-0.94814.0730.1950.1950.0000.0000.0000.000
184B187GLY0-0.012-0.00713.237-0.025-0.0250.0000.0000.0000.000
185B188VAL0-0.046-0.02113.264-0.075-0.0750.0000.0000.0000.000
186B189ASP-1-0.922-0.9517.447-2.374-2.3740.0000.0000.0000.000
187B190VAL0-0.065-0.0369.599-0.286-0.2860.0000.0000.0000.000
188B191PHE00.0380.0225.767-0.452-0.4520.0000.0000.0000.000
189B192THR0-0.030-0.0196.723-1.336-1.3360.0000.0000.0000.000
190B193PHE00.0360.0198.7580.4220.4220.0000.0000.0000.000
191B194ILE00.0130.00710.487-0.071-0.0710.0000.0000.0000.000
192B195ALA0-0.0040.00413.0950.1810.1810.0000.0000.0000.000
193B196GLY00.1070.04015.030-0.076-0.0760.0000.0000.0000.000
194B197ARG10.8140.86817.7700.2930.2930.0000.0000.0000.000
195B198GLY0-0.0080.01219.5520.0390.0390.0000.0000.0000.000
196B199ILE00.0350.00713.4690.0640.0640.0000.0000.0000.000
197B200THR00.029-0.00317.4570.0330.0330.0000.0000.0000.000
198B201GLU-1-0.888-0.90419.323-0.197-0.1970.0000.0000.0000.000
199B202ALA0-0.0080.01820.0710.0310.0310.0000.0000.0000.000
200B203LYS10.9720.96822.020-0.088-0.0880.0000.0000.0000.000
201B204ASN0-0.033-0.01819.903-0.006-0.0060.0000.0000.0000.000
202B205PRO00.0550.04018.7710.0370.0370.0000.0000.0000.000
203B206ALA00.0780.04515.543-0.005-0.0050.0000.0000.0000.000
204B207GLY0-0.028-0.01114.8690.0670.0670.0000.0000.0000.000
205B208ALA0-0.023-0.01616.0340.0740.0740.0000.0000.0000.000
206B209ALA00.0130.00311.9890.0200.0200.0000.0000.0000.000
207B210ARG10.8470.89411.323-0.484-0.4840.0000.0000.0000.000
208B211ALA00.0030.00111.8930.2200.2200.0000.0000.0000.000
209B212PHE0-0.0120.00010.5230.0740.0740.0000.0000.0000.000
210B213LYS10.8500.9022.592-2.524-1.2790.079-0.634-0.6890.006
211B214ASP-1-0.888-0.9428.4332.3312.3310.0000.0000.0000.000
212B215GLU-1-0.775-0.85810.7960.6990.6990.0000.0000.0000.000
213B216ILE0-0.015-0.0056.496-0.001-0.0010.0000.0000.0000.000
214B217LYS10.8460.9077.243-2.845-2.8450.0000.0000.0000.000
215B218ARG10.8020.8898.140-0.736-0.7360.0000.0000.0000.000
216B219ILE0-0.056-0.02311.481-0.068-0.0680.0000.0000.0000.000
217B220TRP0-0.007-0.0116.980-0.106-0.1060.0000.0000.0000.000
218B221GLY0-0.061-0.0086.714-0.142-0.1420.0000.0000.0000.000