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

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FMODB ID: YZ3L2

Calculation Name: 3C98-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C98

Chain ID: B

ChEMBL ID:

UniProt ID: P32851

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptAll
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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2607232.534533
FMO2-HF: Nuclear repulsion 2511570.593198
FMO2-HF: Total energy -95661.941335
FMO2-MP2: Total energy -95935.642021


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:2:LYS)


Summations of interaction energy for fragment #1(B:2: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.
-75.007-73.561-0.011-0.653-0.7820.002
Interaction energy analysis for fragmet #1(B:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.964
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].
3B4ARG10.8200.8613.86430.35931.805-0.011-0.653-0.7820.002
4B5THR00.011-0.0116.7614.1034.1030.0000.0000.0000.000
5B6GLN0-0.018-0.0079.0951.3701.3700.0000.0000.0000.000
6B7GLU-1-0.838-0.8848.236-25.633-25.6330.0000.0000.0000.000
7B8LEU00.0160.01911.8911.4741.4740.0000.0000.0000.000
8B9ARG10.8620.94814.05517.28217.2820.0000.0000.0000.000
9B27ASP-1-0.999-1.00332.920-8.973-8.9730.0000.0000.0000.000
10B28ARG10.7230.81328.3019.9149.9140.0000.0000.0000.000
11B29PHE0-0.007-0.02028.8830.2980.2980.0000.0000.0000.000
12B30MET0-0.031-0.01230.595-0.315-0.3150.0000.0000.0000.000
13B31ASP-1-0.752-0.84632.439-9.514-9.5140.0000.0000.0000.000
14B32GLU-1-0.875-0.93433.464-8.047-8.0470.0000.0000.0000.000
15B33PHE0-0.033-0.01832.1080.0810.0810.0000.0000.0000.000
16B34PHE0-0.010-0.01527.792-0.206-0.2060.0000.0000.0000.000
17B35GLU-1-0.876-0.93031.848-8.621-8.6210.0000.0000.0000.000
18B36GLN0-0.028-0.00934.2140.2000.2000.0000.0000.0000.000
19B37VAL0-0.025-0.00729.3630.0010.0010.0000.0000.0000.000
20B38GLU-1-0.838-0.89828.861-10.621-10.6210.0000.0000.0000.000
21B39GLU-1-0.817-0.88631.556-8.066-8.0660.0000.0000.0000.000
22B40ILE0-0.008-0.01034.3190.1060.1060.0000.0000.0000.000
23B41ARG10.8060.86825.47011.50611.5060.0000.0000.0000.000
24B42GLY00.0180.01132.040-0.070-0.0700.0000.0000.0000.000
25B43PHE0-0.046-0.03633.5240.1570.1570.0000.0000.0000.000
26B44ILE00.0180.00632.1420.1360.1360.0000.0000.0000.000
27B45ASP-1-0.786-0.85929.435-10.864-10.8640.0000.0000.0000.000
28B46LYS10.8420.91932.7468.4038.4030.0000.0000.0000.000
29B47ILE0-0.016-0.01136.2850.1940.1940.0000.0000.0000.000
30B48ALA00.0260.00232.4230.1170.1170.0000.0000.0000.000
31B49GLU-1-0.890-0.92334.483-8.635-8.6350.0000.0000.0000.000
32B50ASN0-0.035-0.04235.4260.0620.0620.0000.0000.0000.000
33B51VAL00.0020.00736.4140.2380.2380.0000.0000.0000.000
34B52GLU-1-0.797-0.88833.460-9.047-9.0470.0000.0000.0000.000
35B53GLU-1-0.823-0.88236.937-7.774-7.7740.0000.0000.0000.000
36B54VAL0-0.022-0.01239.9150.2210.2210.0000.0000.0000.000
37B55LYS10.7840.88335.3609.0769.0760.0000.0000.0000.000
38B56ARG10.8040.87137.2558.1978.1970.0000.0000.0000.000
39B57LYS10.8490.91840.8537.4417.4410.0000.0000.0000.000
40B58HIS10.8820.94843.0147.3097.3090.0000.0000.0000.000
41B59SER00.0420.01241.3800.1640.1640.0000.0000.0000.000
42B60ALA0-0.032-0.00344.3900.1110.1110.0000.0000.0000.000
43B61ILE00.0320.00946.4060.1570.1570.0000.0000.0000.000
44B62LEU00.0120.01046.2570.1530.1530.0000.0000.0000.000
45B63ALA0-0.0240.01347.2600.0620.0620.0000.0000.0000.000
46B64SER0-0.017-0.01449.2260.1330.1330.0000.0000.0000.000
47B65PRO0-0.012-0.00952.697-0.015-0.0150.0000.0000.0000.000
48B66ASN00.007-0.00755.8650.1020.1020.0000.0000.0000.000
49B67PRO0-0.0250.00652.396-0.010-0.0100.0000.0000.0000.000
50B68ASP-1-0.793-0.87452.205-6.058-6.0580.0000.0000.0000.000
51B69GLU-1-0.799-0.91854.156-5.679-5.6790.0000.0000.0000.000
52B70LYS10.8170.92750.3156.2736.2730.0000.0000.0000.000
53B71THR0-0.031-0.06348.477-0.116-0.1160.0000.0000.0000.000
54B72LYS10.8290.91849.1675.6215.6210.0000.0000.0000.000
55B73GLU-1-0.843-0.90551.041-6.106-6.1060.0000.0000.0000.000
56B74GLU-1-0.884-0.94546.661-6.907-6.9070.0000.0000.0000.000
57B75LEU0-0.019-0.00745.626-0.165-0.1650.0000.0000.0000.000
58B76GLU-1-0.853-0.92447.226-6.096-6.0960.0000.0000.0000.000
59B77GLU-1-0.791-0.89747.735-6.587-6.5870.0000.0000.0000.000
60B78LEU0-0.034-0.01041.920-0.117-0.1170.0000.0000.0000.000
61B79MET0-0.0220.00544.228-0.135-0.1350.0000.0000.0000.000
62B80SER0-0.064-0.03645.976-0.028-0.0280.0000.0000.0000.000
63B81ASP-1-0.857-0.94542.479-7.527-7.5270.0000.0000.0000.000
64B82ILE00.0000.00740.514-0.136-0.1360.0000.0000.0000.000
65B83LYS10.8380.90842.7076.2156.2150.0000.0000.0000.000
66B84LYS10.8270.92145.4416.6216.6210.0000.0000.0000.000
67B85THR0-0.011-0.00939.4720.0150.0150.0000.0000.0000.000
68B86ALA00.0560.02740.829-0.125-0.1250.0000.0000.0000.000
69B87ASN0-0.021-0.00741.885-0.037-0.0370.0000.0000.0000.000
70B88LYS10.8380.92941.6247.4947.4940.0000.0000.0000.000
71B89VAL00.0170.01937.046-0.045-0.0450.0000.0000.0000.000
72B90ARG10.7890.85739.7206.9176.9170.0000.0000.0000.000
73B91SER0-0.037-0.00641.7320.0200.0200.0000.0000.0000.000
74B92LYS10.8380.87939.5517.8957.8950.0000.0000.0000.000
75B93LEU00.0150.01135.376-0.081-0.0810.0000.0000.0000.000
76B94LYS10.8340.91939.2327.3627.3620.0000.0000.0000.000
77B95SER0-0.029-0.00942.2170.0400.0400.0000.0000.0000.000
78B96ILE00.002-0.00835.9750.0100.0100.0000.0000.0000.000
79B97GLU-1-0.825-0.91539.722-7.707-7.7070.0000.0000.0000.000
80B98GLN00.0440.02340.7960.0140.0140.0000.0000.0000.000
81B99SER0-0.056-0.02240.3990.0290.0290.0000.0000.0000.000
82B100ILE0-0.043-0.01836.571-0.067-0.0670.0000.0000.0000.000
83B101GLU-1-0.896-0.94840.271-7.049-7.0490.0000.0000.0000.000
84B102GLN0-0.029-0.01043.6000.2020.2020.0000.0000.0000.000
85B103GLU-1-0.841-0.91840.190-7.637-7.6370.0000.0000.0000.000
86B104GLU-1-0.813-0.89838.400-8.258-8.2580.0000.0000.0000.000
87B105GLY0-0.0020.00742.5030.0900.0900.0000.0000.0000.000
88B106LEU0-0.092-0.04245.0140.1890.1890.0000.0000.0000.000
89B107ASN0-0.063-0.03043.833-0.057-0.0570.0000.0000.0000.000
90B108ARG10.8100.91640.3237.3307.3300.0000.0000.0000.000
91B109SER00.0650.02736.604-0.213-0.2130.0000.0000.0000.000
92B110SER0-0.027-0.03034.4990.1350.1350.0000.0000.0000.000
93B111ALA00.0220.00229.481-0.064-0.0640.0000.0000.0000.000
94B112ASP-1-0.763-0.85531.423-9.068-9.0680.0000.0000.0000.000
95B113LEU00.0520.03233.405-0.104-0.1040.0000.0000.0000.000
96B114ARG10.9760.99027.70510.98910.9890.0000.0000.0000.000
97B115ILE0-0.0070.01828.297-0.204-0.2040.0000.0000.0000.000
98B116ARG10.8280.88230.7358.5298.5290.0000.0000.0000.000
99B117LYS10.8780.91133.5278.5298.5290.0000.0000.0000.000
100B118THR0-0.003-0.02028.280-0.086-0.0860.0000.0000.0000.000
101B119GLN0-0.0060.00426.542-0.078-0.0780.0000.0000.0000.000
102B120HIS00.0150.01830.641-0.179-0.1790.0000.0000.0000.000
103B121SER00.0480.02231.138-0.006-0.0060.0000.0000.0000.000
104B122THR0-0.021-0.02726.598-0.016-0.0160.0000.0000.0000.000
105B123LEU0-0.019-0.00329.620-0.039-0.0390.0000.0000.0000.000
106B124SER0-0.001-0.02231.8270.2470.2470.0000.0000.0000.000
107B125ARG10.7950.88330.10210.15210.1520.0000.0000.0000.000
108B126LYS10.8150.88926.40611.43011.4300.0000.0000.0000.000
109B127PHE00.016-0.00331.1460.1140.1140.0000.0000.0000.000
110B128VAL00.0510.01334.6700.1540.1540.0000.0000.0000.000
111B129GLU-1-0.863-0.90528.715-10.968-10.9680.0000.0000.0000.000
112B130VAL0-0.002-0.00232.0980.1260.1260.0000.0000.0000.000
113B131MET0-0.006-0.00334.3680.2080.2080.0000.0000.0000.000
114B132SER00.0210.01335.4230.2870.2870.0000.0000.0000.000
115B133GLU-1-0.859-0.91833.640-8.877-8.8770.0000.0000.0000.000
116B134TYR0-0.011-0.00536.0910.1860.1860.0000.0000.0000.000
117B135ASN00.003-0.00439.2540.3280.3280.0000.0000.0000.000
118B136ALA00.0110.00837.6040.1950.1950.0000.0000.0000.000
119B137THR0-0.023-0.02238.0240.1200.1200.0000.0000.0000.000
120B138GLN0-0.011-0.00940.3540.1170.1170.0000.0000.0000.000
121B139SER00.0400.00842.7520.1850.1850.0000.0000.0000.000
122B140ASP-1-0.854-0.90741.305-7.489-7.4890.0000.0000.0000.000
123B141TYR0-0.084-0.07943.4010.1010.1010.0000.0000.0000.000
124B142ARG10.7900.86445.6946.3296.3290.0000.0000.0000.000
125B143GLU-1-0.790-0.88146.688-6.276-6.2760.0000.0000.0000.000
126B144ARG10.7960.87541.9517.5587.5580.0000.0000.0000.000
127B145CYS0-0.069-0.02748.0420.1390.1390.0000.0000.0000.000
128B146LYS10.8370.89951.1986.2656.2650.0000.0000.0000.000
129B147GLY00.0140.00551.1880.1170.1170.0000.0000.0000.000
130B148ARG10.7720.86951.0436.2046.2040.0000.0000.0000.000
131B149ILE00.0100.01154.0730.1160.1160.0000.0000.0000.000
132B150GLN0-0.026-0.02755.1110.1050.1050.0000.0000.0000.000
133B151ARG10.8740.91454.9135.6305.6300.0000.0000.0000.000
134B152GLN0-0.024-0.02557.4550.1770.1770.0000.0000.0000.000
135B153LEU00.0180.01559.8730.1210.1210.0000.0000.0000.000
136B154GLU-1-0.835-0.89058.802-5.425-5.4250.0000.0000.0000.000
137B155ILE0-0.083-0.03160.0190.0700.0700.0000.0000.0000.000
138B156THR0-0.115-0.07462.8270.0960.0960.0000.0000.0000.000
139B157GLY0-0.0040.00465.1920.0900.0900.0000.0000.0000.000
140B158ARG10.8010.87563.7725.0335.0330.0000.0000.0000.000
141B159THR00.014-0.00761.781-0.046-0.0460.0000.0000.0000.000
142B160THR0-0.0080.02260.1960.1020.1020.0000.0000.0000.000
143B161THR0-0.0130.00758.645-0.104-0.1040.0000.0000.0000.000
144B162SER00.029-0.00452.7860.0200.0200.0000.0000.0000.000
145B163GLU-1-0.878-0.93455.940-5.708-5.7080.0000.0000.0000.000
146B164GLU-1-0.807-0.88257.844-5.048-5.0480.0000.0000.0000.000
147B165LEU0-0.023-0.02056.2660.0510.0510.0000.0000.0000.000
148B166GLU-1-0.738-0.84153.297-6.020-6.0200.0000.0000.0000.000
149B167ASP-1-0.864-0.92157.289-5.106-5.1060.0000.0000.0000.000
150B168MET0-0.109-0.04060.7300.0630.0630.0000.0000.0000.000
151B169LEU0-0.056-0.02655.3250.0160.0160.0000.0000.0000.000
152B170GLU-1-0.929-0.96557.135-5.573-5.5730.0000.0000.0000.000
153B171SER0-0.066-0.03659.1630.0790.0790.0000.0000.0000.000
154B172GLY00.0060.00261.5720.0920.0920.0000.0000.0000.000
155B173ASN0-0.062-0.03962.7190.1350.1350.0000.0000.0000.000
156B174PRO0-0.035-0.03065.369-0.042-0.0420.0000.0000.0000.000
157B175ALA00.0300.01966.299-0.027-0.0270.0000.0000.0000.000
158B176ILE0-0.0010.01363.2900.0630.0630.0000.0000.0000.000
159B177PHE00.0710.03359.5870.0560.0560.0000.0000.0000.000
160B178ALA0-0.052-0.03065.1020.0260.0260.0000.0000.0000.000
161B179SER0-0.052-0.03268.1450.0880.0880.0000.0000.0000.000
162B180GLY00.0130.00369.8280.0730.0730.0000.0000.0000.000
163B181ILE0-0.0410.00765.7150.0350.0350.0000.0000.0000.000
164B182ILE00.0320.01269.5970.0390.0390.0000.0000.0000.000
165B183MET0-0.027-0.04270.791-0.072-0.0720.0000.0000.0000.000
166B184ASP-1-0.891-0.93972.999-4.327-4.3270.0000.0000.0000.000
167B185SER00.0210.02269.730-0.043-0.0430.0000.0000.0000.000
168B186SER00.0490.00468.735-0.033-0.0330.0000.0000.0000.000
169B187ILE00.0190.02364.157-0.073-0.0730.0000.0000.0000.000
170B188SER00.0410.01765.083-0.100-0.1000.0000.0000.0000.000
171B189LYS10.7950.90666.9344.6934.6930.0000.0000.0000.000
172B190GLN00.0170.01960.175-0.004-0.0040.0000.0000.0000.000
173B191ALA00.0300.01261.360-0.082-0.0820.0000.0000.0000.000
174B192LEU00.0100.00161.570-0.051-0.0510.0000.0000.0000.000
175B193SER00.0020.00761.368-0.023-0.0230.0000.0000.0000.000
176B194GLU-1-0.755-0.83054.645-5.930-5.9300.0000.0000.0000.000
177B195ILE0-0.019-0.01958.033-0.082-0.0820.0000.0000.0000.000
178B196GLU-1-0.867-0.93559.014-5.278-5.2780.0000.0000.0000.000
179B197THR0-0.043-0.02655.289-0.067-0.0670.0000.0000.0000.000
180B198ARG10.7400.83551.9515.9695.9690.0000.0000.0000.000
181B199HIS00.0510.03354.844-0.171-0.1710.0000.0000.0000.000
182B200SER00.0050.00356.618-0.080-0.0800.0000.0000.0000.000
183B201GLU-1-0.819-0.89151.010-6.310-6.3100.0000.0000.0000.000
184B202ILE00.0260.01051.962-0.125-0.1250.0000.0000.0000.000
185B203ILE00.0440.02852.935-0.055-0.0550.0000.0000.0000.000
186B204LYS10.7780.88152.1495.9355.9350.0000.0000.0000.000
187B205LEU0-0.055-0.00947.549-0.077-0.0770.0000.0000.0000.000
188B206GLU-1-0.779-0.89249.362-6.128-6.1280.0000.0000.0000.000
189B207ASN0-0.053-0.02751.4190.0220.0220.0000.0000.0000.000
190B208SER0-0.013-0.00347.473-0.048-0.0480.0000.0000.0000.000
191B209ILE00.0200.01045.787-0.090-0.0900.0000.0000.0000.000
192B210ARG10.8980.94147.9025.7855.7850.0000.0000.0000.000
193B211GLU-1-0.863-0.91650.612-6.117-6.1170.0000.0000.0000.000
194B212LEU0-0.018-0.01344.314-0.035-0.0350.0000.0000.0000.000
195B213HIS00.0160.01646.471-0.177-0.1770.0000.0000.0000.000
196B214ASP-1-0.823-0.90647.404-6.625-6.6250.0000.0000.0000.000
197B215MET0-0.0190.01842.716-0.098-0.0980.0000.0000.0000.000
198B216PHE0-0.003-0.01540.325-0.170-0.1700.0000.0000.0000.000
199B217MET00.0000.00643.316-0.111-0.1110.0000.0000.0000.000
200B218ASP-1-0.813-0.90444.298-7.215-7.2150.0000.0000.0000.000
201B219MET00.003-0.00639.278-0.147-0.1470.0000.0000.0000.000
202B220ALA00.0050.01239.838-0.213-0.2130.0000.0000.0000.000
203B221MET00.0370.01841.172-0.036-0.0360.0000.0000.0000.000
204B222LEU0-0.0630.00339.248-0.062-0.0620.0000.0000.0000.000
205B223VAL0-0.018-0.01635.654-0.173-0.1730.0000.0000.0000.000
206B224GLU-1-0.958-0.97137.555-7.462-7.4620.0000.0000.0000.000
207B225SER0-0.092-0.06640.098-0.055-0.0550.0000.0000.0000.000
208B226GLN0-0.0210.01035.161-0.318-0.3180.0000.0000.0000.000
209B227GLY00.0370.03735.588-0.181-0.1810.0000.0000.0000.000
210B228GLU-1-0.883-0.95931.229-9.292-9.2920.0000.0000.0000.000
211B229MET0-0.041-0.02530.263-0.506-0.5060.0000.0000.0000.000
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216B234GLU-1-0.833-0.89823.055-12.455-12.4550.0000.0000.0000.000
217B235TYR00.0430.02924.2160.2060.2060.0000.0000.0000.000
218B236ASN0-0.067-0.05925.9340.5310.5310.0000.0000.0000.000
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220B238GLU-1-0.905-0.94726.146-10.279-10.2790.0000.0000.0000.000
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222B240ALA0-0.112-0.04728.1490.2600.2600.0000.0000.0000.000
223B241VAL0-0.019-0.00530.139-0.152-0.1520.0000.0000.0000.000
224B242ASP-1-0.916-0.95431.220-10.323-10.3230.0000.0000.0000.000
225B243TYR0-0.041-0.02631.7370.3080.3080.0000.0000.0000.000
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227B245GLU-1-0.961-0.98336.384-8.605-8.6050.0000.0000.0000.000
228B246ARG10.9010.96038.1458.4538.4530.0000.0000.0000.000
229B247ALA00.0120.00740.5750.0000.0000.0000.0000.0000.000
230B248VAL0-0.031-0.00642.3400.1020.1020.0000.0000.0000.000