Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 399RL

Calculation Name: 5DSS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DSS

Chain ID: B

ChEMBL ID:

UniProt ID: A0A158

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1909334.370854
FMO2-HF: Nuclear repulsion 1838320.660766
FMO2-HF: Total energy -71013.710087
FMO2-MP2: Total energy -71220.677202


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:LYS)


Summations of interaction energy for fragment #1(B:1: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.
-66.241-57.3930.927-4.385-5.39-0.018
Interaction energy analysis for fragmet #1(B:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.911 / q_NPA : 0.922
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].
3B3ASP-1-0.838-0.9042.303-37.431-28.9420.910-4.454-4.945-0.019
4B4ALA0-0.050-0.0233.5831.1461.5050.0170.069-0.4450.001
5B5GLU-1-0.836-0.9096.037-18.396-18.3960.0000.0000.0000.000
6B6PRO0-0.079-0.0579.409-0.502-0.5020.0000.0000.0000.000
7B7VAL00.0150.00812.0090.4390.4390.0000.0000.0000.000
8B8ILE00.0260.04014.5800.9020.9020.0000.0000.0000.000
9B9ASP-1-0.898-0.97717.746-12.381-12.3810.0000.0000.0000.000
10B10THR0-0.068-0.05818.892-0.125-0.1250.0000.0000.0000.000
11B11ASP-1-0.893-0.92521.315-10.805-10.8050.0000.0000.0000.000
12B12GLY0-0.052-0.03821.9660.3270.3270.0000.0000.0000.000
13B13ASN0-0.038-0.01621.279-0.393-0.3930.0000.0000.0000.000
14B14PRO00.0040.00516.730-0.127-0.1270.0000.0000.0000.000
15B15LEU00.0100.02517.5250.7760.7760.0000.0000.0000.000
16B16LEU0-0.060-0.04118.144-0.494-0.4940.0000.0000.0000.000
17B17HIS0-0.020-0.02116.444-0.275-0.2750.0000.0000.0000.000
18B18ARG10.9360.96921.13711.19211.1920.0000.0000.0000.000
19B19GLY0-0.001-0.03023.3660.6540.6540.0000.0000.0000.000
20B20LYS10.8500.92624.2379.2839.2830.0000.0000.0000.000
21B21TYR00.1340.07321.9010.3410.3410.0000.0000.0000.000
22B22TYR00.0300.03825.6220.2950.2950.0000.0000.0000.000
23B23ILE00.027-0.00221.848-0.327-0.3270.0000.0000.0000.000
24B24MET00.0240.02624.6700.3650.3650.0000.0000.0000.000
25B25PRO0-0.0690.00924.845-0.516-0.5160.0000.0000.0000.000
26B26SER0-0.019-0.01922.3630.1200.1200.0000.0000.0000.000
27B27ASN00.0160.00124.4380.3450.3450.0000.0000.0000.000
28B28TRP00.033-0.00126.799-0.038-0.0380.0000.0000.0000.000
29B29GLY00.0490.05227.1300.1890.1890.0000.0000.0000.000
30B30PRO0-0.0110.03227.441-0.275-0.2750.0000.0000.0000.000
31B31PRO00.019-0.02830.325-0.078-0.0780.0000.0000.0000.000
32B32GLY0-0.016-0.02229.773-0.059-0.0590.0000.0000.0000.000
33B33GLY00.0880.04929.8860.2960.2960.0000.0000.0000.000
34B34GLY00.0380.01729.166-0.389-0.3890.0000.0000.0000.000
35B35LEU00.006-0.00324.7730.0490.0490.0000.0000.0000.000
36B36ARG10.9520.99829.4869.2219.2210.0000.0000.0000.000
37B37LEU00.0120.04031.349-0.205-0.2050.0000.0000.0000.000
38B38GLY0-0.001-0.00333.3510.2290.2290.0000.0000.0000.000
39B39LYS10.9340.95735.4527.2867.2860.0000.0000.0000.000
40B40THR00.025-0.00634.582-0.100-0.1000.0000.0000.0000.000
41B41ARG10.8440.94136.4978.4258.4250.0000.0000.0000.000
42B42ASN0-0.050-0.06439.2290.2130.2130.0000.0000.0000.000
43B43LEU00.0240.00140.353-0.183-0.1830.0000.0000.0000.000
44B44ASN00.0400.07539.6450.1040.1040.0000.0000.0000.000
45B45CYS0-0.050-0.05437.420-0.061-0.0610.0000.0000.0000.000
46B46PRO0-0.0070.00536.010-0.218-0.2180.0000.0000.0000.000
47B47VAL00.0520.10530.358-0.096-0.0960.0000.0000.0000.000
48B48THR0-0.035-0.02830.598-0.406-0.4060.0000.0000.0000.000
49B49VAL00.0280.02326.7790.3360.3360.0000.0000.0000.000
50B50LEU0-0.067-0.01729.146-0.147-0.1470.0000.0000.0000.000
51B51GLN00.0480.01225.700-0.549-0.5490.0000.0000.0000.000
52B52ASP-1-0.932-0.99130.157-8.666-8.6660.0000.0000.0000.000
53B53TYR0-0.071-0.02232.655-0.252-0.2520.0000.0000.0000.000
54B54ASN0-0.024-0.02835.0410.1940.1940.0000.0000.0000.000
55B55GLU-1-0.855-0.94233.555-8.751-8.7510.0000.0000.0000.000
56B56ALA0-0.0130.02734.940-0.028-0.0280.0000.0000.0000.000
57B57ILE0-0.053-0.01634.7450.0650.0650.0000.0000.0000.000
58B58ASN00.0680.03830.896-0.031-0.0310.0000.0000.0000.000
59B59GLY00.006-0.04630.404-0.326-0.3260.0000.0000.0000.000
60B60LEU0-0.091-0.03830.4980.2190.2190.0000.0000.0000.000
61B61PRO0-0.019-0.01028.576-0.347-0.3470.0000.0000.0000.000
62B62VAL0-0.019-0.01522.7020.0710.0710.0000.0000.0000.000
63B63LYS10.8550.93023.92810.54810.5480.0000.0000.0000.000
64B64PHE00.1260.06517.4530.0230.0230.0000.0000.0000.000
65B65ASN00.0600.05719.8450.0220.0220.0000.0000.0000.000
66B66ILE00.1500.09314.334-0.113-0.1130.0000.0000.0000.000
67B67ARG10.7800.86318.47313.07413.0740.0000.0000.0000.000
68B68GLU-1-0.923-0.92721.983-11.120-11.1200.0000.0000.0000.000
69B69ILE00.0240.00718.9740.0670.0670.0000.0000.0000.000
70B70LEU0-0.019-0.02422.8840.4430.4430.0000.0000.0000.000
71B71PRO0-0.0410.00117.9570.0670.0670.0000.0000.0000.000
72B72ARG10.9930.97618.49013.03513.0350.0000.0000.0000.000
73B73THR0-0.004-0.01013.9070.7040.7040.0000.0000.0000.000
74B74ILE00.0020.02013.645-0.493-0.4930.0000.0000.0000.000
75B75PHE00.0560.0179.3930.5420.5420.0000.0000.0000.000
76B76THR0-0.012-0.0147.455-0.010-0.0100.0000.0000.0000.000
77B77ASP-1-0.935-0.9595.471-38.895-38.8950.0000.0000.0000.000
78B78THR0-0.051-0.0247.481-0.715-0.7150.0000.0000.0000.000
79B79GLU-1-0.919-0.93910.413-18.978-18.9780.0000.0000.0000.000
80B80LEU00.008-0.02913.2431.2091.2090.0000.0000.0000.000
81B81ASN0-0.071-0.03716.735-0.381-0.3810.0000.0000.0000.000
82B82ILE00.0310.02719.6490.4990.4990.0000.0000.0000.000
83B83GLU-1-0.855-0.95921.884-11.245-11.2450.0000.0000.0000.000
84B84PHE0-0.0100.00725.663-0.026-0.0260.0000.0000.0000.000
85B85THR0-0.040-0.05428.425-0.014-0.0140.0000.0000.0000.000
86B86GLU-1-0.952-0.97830.730-8.076-8.0760.0000.0000.0000.000
87B87LYS10.8770.97033.1978.6188.6180.0000.0000.0000.000
88B88PRO00.0720.03434.2550.2270.2270.0000.0000.0000.000
89B89ASN0-0.001-0.03237.087-0.216-0.2160.0000.0000.0000.000
90B91ALA00.0230.05534.1030.0020.0020.0000.0000.0000.000
91B92GLU-1-0.893-0.95533.252-8.820-8.8200.0000.0000.0000.000
92B93ASN00.000-0.01328.1040.1880.1880.0000.0000.0000.000
93B94ARG10.9240.94529.24510.29610.2960.0000.0000.0000.000
94B95ALA0-0.025-0.00525.074-0.181-0.1810.0000.0000.0000.000
95B96TRP0-0.048-0.00722.1030.1240.1240.0000.0000.0000.000
96B97SER00.0360.01423.076-0.637-0.6370.0000.0000.0000.000
97B98LEU00.0120.00520.0850.2840.2840.0000.0000.0000.000
98B99PHE00.0030.06223.973-0.119-0.1190.0000.0000.0000.000
99B100LYS10.9400.95624.12511.67811.6780.0000.0000.0000.000
100B101GLY0-0.115-0.06526.2690.2740.2740.0000.0000.0000.000
101B102ASP-1-0.782-0.88127.041-10.031-10.0310.0000.0000.0000.000
102B103ASP-1-0.885-0.95730.690-9.037-9.0370.0000.0000.0000.000
103B104ARG10.8920.96033.3168.3788.3780.0000.0000.0000.000
104B105GLY0-0.092-0.08430.8420.1190.1190.0000.0000.0000.000
105B106HIS0-0.006-0.01829.424-0.108-0.1080.0000.0000.0000.000
106B107LYS11.0041.02223.12912.43712.4370.0000.0000.0000.000
107B108ALA0-0.021-0.00222.1960.3880.3880.0000.0000.0000.000
108B109ARG10.8600.99923.90710.59110.5910.0000.0000.0000.000
109B110VAL00.0210.03224.405-0.168-0.1680.0000.0000.0000.000
110B111GLY0-0.007-0.08725.9440.4950.4950.0000.0000.0000.000
111B112ILE00.0100.03027.307-0.334-0.3340.0000.0000.0000.000
112B113GLY00.024-0.00929.7210.2990.2990.0000.0000.0000.000
113B114GLY00.0100.00730.243-0.324-0.3240.0000.0000.0000.000
114B115SER00.0380.01731.6850.0550.0550.0000.0000.0000.000
115B116ASN0-0.047-0.02832.972-0.180-0.1800.0000.0000.0000.000
116B117GLY00.0330.02434.7510.2510.2510.0000.0000.0000.000
117B118HIS0-0.002-0.01936.543-0.286-0.2860.0000.0000.0000.000
118B119PRO0-0.0070.01234.297-0.002-0.0020.0000.0000.0000.000
119B120GLY0-0.003-0.05431.657-0.243-0.2430.0000.0000.0000.000
120B121GLY00.0000.00031.0650.2310.2310.0000.0000.0000.000
121B122GLU-1-0.863-0.93128.419-10.494-10.4940.0000.0000.0000.000
122B123MET0-0.027-0.01526.456-0.257-0.2570.0000.0000.0000.000
123B124LEU0-0.078-0.06020.699-0.113-0.1130.0000.0000.0000.000
124B125ARG10.9200.98521.30812.63712.6370.0000.0000.0000.000
125B126GLY00.0900.02217.805-0.429-0.4290.0000.0000.0000.000
126B127GLY0-0.0010.02716.0391.0801.0800.0000.0000.0000.000
127B128PHE0-0.079-0.07015.029-0.623-0.6230.0000.0000.0000.000
128B129TYR00.0670.0229.435-1.171-1.1710.0000.0000.0000.000
129B130GLY0-0.104-0.06311.1101.9011.9010.0000.0000.0000.000
130B131GLU-1-0.733-0.85310.727-19.530-19.5300.0000.0000.0000.000
131B132GLN0-0.097-0.03910.991-2.153-2.1530.0000.0000.0000.000
132B133HIS00.0210.0337.4580.6580.6580.0000.0000.0000.000
133B134GLY0-0.050-0.06611.3630.9830.9830.0000.0000.0000.000
134B135LEU00.008-0.01813.776-0.080-0.0800.0000.0000.0000.000
135B136ARG10.9560.99116.38712.91912.9190.0000.0000.0000.000
136B137ASN0-0.013-0.03219.3330.6840.6840.0000.0000.0000.000
137B138GLY0-0.0010.02119.553-0.067-0.0670.0000.0000.0000.000
138B139THR00.0160.01316.330-0.313-0.3130.0000.0000.0000.000
139B140TYR0-0.080-0.04014.7960.2530.2530.0000.0000.0000.000
140B141LYS10.9811.00012.09020.97020.9700.0000.0000.0000.000
141B142LEU00.0710.04714.074-0.790-0.7900.0000.0000.0000.000
142B143VAL0-0.011-0.00611.3310.5080.5080.0000.0000.0000.000
143B144PHE0-0.016-0.00214.2320.4630.4630.0000.0000.0000.000
144B145CYS0-0.025-0.06210.327-1.221-1.2210.0000.0000.0000.000
145B146ARG10.8450.93313.70617.13417.1340.0000.0000.0000.000
146B147ASP-1-0.784-0.90315.473-16.891-16.8910.0000.0000.0000.000
147B148GLY0-0.066-0.02517.971-0.061-0.0610.0000.0000.0000.000
148B149SER0-0.011-0.05916.7130.3360.3360.0000.0000.0000.000
149B150SER0-0.084-0.00614.9010.0090.0090.0000.0000.0000.000
150B151THR00.1070.0899.729-1.506-1.5060.0000.0000.0000.000
151B153LEU0-0.0030.01811.634-0.812-0.8120.0000.0000.0000.000
152B154ASP-1-0.843-0.92414.394-20.553-20.5530.0000.0000.0000.000
153B155VAL00.010-0.01315.7250.8440.8440.0000.0000.0000.000
154B156GLY0-0.003-0.04419.0210.0660.0660.0000.0000.0000.000
155B157ARG10.7100.81021.56012.27212.2720.0000.0000.0000.000
156B158TYR0-0.0100.01325.2890.0660.0660.0000.0000.0000.000
157B159GLY00.0530.01928.3890.0790.0790.0000.0000.0000.000
158B160ASN0-0.065-0.05631.836-0.064-0.0640.0000.0000.0000.000
159B161ARG10.9460.97534.8788.0278.0270.0000.0000.0000.000
160B162GLU-1-0.845-0.92036.098-8.185-8.1850.0000.0000.0000.000
161B163GLY00.0750.01334.6360.1210.1210.0000.0000.0000.000
162B164ARG10.8450.92228.57310.17910.1790.0000.0000.0000.000
163B165ARG10.9400.99629.3749.5259.5250.0000.0000.0000.000
164B166LEU00.0790.03223.030-0.073-0.0730.0000.0000.0000.000
165B167GLY0-0.029-0.02023.4400.4100.4100.0000.0000.0000.000
166B168LEU00.0000.02117.744-0.107-0.1070.0000.0000.0000.000
167B169SER0-0.068-0.00219.6850.6270.6270.0000.0000.0000.000
168B170GLU-1-0.922-0.96918.443-14.985-14.9850.0000.0000.0000.000
169B171ALA0-0.0230.00117.387-0.658-0.6580.0000.0000.0000.000
170B172GLY00.0620.04016.255-1.063-1.0630.0000.0000.0000.000
171B173GLU-1-0.920-0.94817.385-12.079-12.0790.0000.0000.0000.000
172B174LEU0-0.037-0.00819.044-0.328-0.3280.0000.0000.0000.000
173B175GLY00.0460.04719.234-0.731-0.7310.0000.0000.0000.000
174B176VAL0-0.045-0.03318.3110.7140.7140.0000.0000.0000.000
175B177GLY00.0280.03219.654-0.416-0.4160.0000.0000.0000.000
176B178PHE0-0.030-0.02017.4560.3370.3370.0000.0000.0000.000
177B179GLU-1-0.770-0.88122.674-9.847-9.8470.0000.0000.0000.000
178B180LYS10.8890.95925.23110.82910.8290.0000.0000.0000.000
179B181ALA0-0.085-0.04426.2800.2670.2670.0000.0000.0000.000
180B182GLY00.0240.02329.3200.3500.3500.0000.0000.0000.000
181B183GLY0-0.069-0.06030.078-0.268-0.2680.0000.0000.0000.000
182B184GLY00.0750.04631.4110.0260.0260.0000.0000.0000.000
183B185ASN0-0.025-0.01328.674-0.168-0.1680.0000.0000.0000.000