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: 4924N

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2590056.812882
FMO2-HF: Nuclear repulsion 2494397.30539
FMO2-HF: Total energy -95659.507491
FMO2-MP2: Total energy -95933.070039


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.
-75.056-73.723-0.012-0.477-0.8440.001
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 : 0.939 / q_NPA : 0.947
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].
3B4ARG10.9320.9623.80232.69334.026-0.012-0.477-0.8440.001
4B5THR00.031-0.0116.4162.7312.7310.0000.0000.0000.000
5B6GLN0-0.018-0.0109.1061.4771.4770.0000.0000.0000.000
6B7GLU-1-0.950-0.9878.225-24.294-24.2940.0000.0000.0000.000
7B8LEU0-0.0180.00311.8411.0551.0550.0000.0000.0000.000
8B9ARG10.9120.97314.06115.99215.9920.0000.0000.0000.000
9B27ASP-1-0.965-0.98133.415-9.025-9.0250.0000.0000.0000.000
10B28ARG10.8580.93928.01110.14910.1490.0000.0000.0000.000
11B29PHE00.002-0.01029.1370.2590.2590.0000.0000.0000.000
12B30MET0-0.041-0.02831.045-0.265-0.2650.0000.0000.0000.000
13B31ASP-1-0.835-0.92132.873-9.284-9.2840.0000.0000.0000.000
14B32GLU-1-0.859-0.93233.864-7.933-7.9330.0000.0000.0000.000
15B33PHE0-0.043-0.02331.7480.0680.0680.0000.0000.0000.000
16B34PHE0-0.012-0.03228.547-0.207-0.2070.0000.0000.0000.000
17B35GLU-1-0.882-0.91232.260-8.675-8.6750.0000.0000.0000.000
18B36GLN0-0.028-0.01934.7530.0280.0280.0000.0000.0000.000
19B37VAL0-0.020-0.00629.464-0.013-0.0130.0000.0000.0000.000
20B38GLU-1-0.937-0.97329.238-10.632-10.6320.0000.0000.0000.000
21B39GLU-1-0.896-0.94131.773-8.171-8.1710.0000.0000.0000.000
22B40ILE0-0.032-0.02833.8290.1450.1450.0000.0000.0000.000
23B41ARG10.8940.94624.68711.84911.8490.0000.0000.0000.000
24B42GLY00.0540.03431.536-0.075-0.0750.0000.0000.0000.000
25B43PHE0-0.058-0.04133.5050.1740.1740.0000.0000.0000.000
26B44ILE0-0.008-0.00331.6510.1340.1340.0000.0000.0000.000
27B45ASP-1-0.865-0.93429.527-10.874-10.8740.0000.0000.0000.000
28B46LYS10.8780.95032.3888.4928.4920.0000.0000.0000.000
29B47ILE0-0.018-0.01235.8180.1870.1870.0000.0000.0000.000
30B48ALA00.0180.00032.1320.1380.1380.0000.0000.0000.000
31B49GLU-1-0.901-0.94133.849-8.929-8.9290.0000.0000.0000.000
32B50ASN00.012-0.01334.9050.0940.0940.0000.0000.0000.000
33B51VAL0-0.014-0.00236.1000.2360.2360.0000.0000.0000.000
34B52GLU-1-0.900-0.95432.912-9.375-9.3750.0000.0000.0000.000
35B53GLU-1-0.891-0.94736.337-8.073-8.0730.0000.0000.0000.000
36B54VAL0-0.024-0.01739.3190.2090.2090.0000.0000.0000.000
37B55LYS10.8940.96035.1229.1529.1520.0000.0000.0000.000
38B56ARG10.8750.93737.2578.2968.2960.0000.0000.0000.000
39B57LYS10.9130.96440.7797.2857.2850.0000.0000.0000.000
40B58HIS10.9070.97542.5177.3977.3970.0000.0000.0000.000
41B59SER00.014-0.00341.5310.1560.1560.0000.0000.0000.000
42B60ALA0-0.0140.00244.4400.1250.1250.0000.0000.0000.000
43B61ILE00.0440.02246.4650.1570.1570.0000.0000.0000.000
44B62LEU0-0.020-0.02246.1960.1540.1540.0000.0000.0000.000
45B63ALA0-0.051-0.01047.0780.0670.0670.0000.0000.0000.000
46B64SER0-0.029-0.00749.1540.1150.1150.0000.0000.0000.000
47B65PRO0-0.007-0.01152.5870.0130.0130.0000.0000.0000.000
48B66ASN0-0.016-0.02055.8880.0830.0830.0000.0000.0000.000
49B67PRO0-0.062-0.01252.3180.0010.0010.0000.0000.0000.000
50B68ASP-1-0.815-0.91152.400-6.053-6.0530.0000.0000.0000.000
51B69GLU-1-0.904-0.96954.257-5.683-5.6830.0000.0000.0000.000
52B70LYS10.9320.98650.4586.2216.2210.0000.0000.0000.000
53B71THR0-0.057-0.04648.614-0.121-0.1210.0000.0000.0000.000
54B72LYS10.9620.98049.2675.6725.6720.0000.0000.0000.000
55B73GLU-1-0.917-0.94251.375-5.925-5.9250.0000.0000.0000.000
56B74GLU-1-0.928-0.98946.921-6.844-6.8440.0000.0000.0000.000
57B75LEU0-0.041-0.02145.582-0.167-0.1670.0000.0000.0000.000
58B76GLU-1-0.852-0.94747.108-6.115-6.1150.0000.0000.0000.000
59B77GLU-1-0.931-0.94947.247-6.522-6.5220.0000.0000.0000.000
60B78LEU0-0.014-0.01041.831-0.120-0.1200.0000.0000.0000.000
61B79MET0-0.025-0.00744.076-0.154-0.1540.0000.0000.0000.000
62B80SER00.0020.00745.920-0.011-0.0110.0000.0000.0000.000
63B81ASP-1-0.882-0.94143.085-7.162-7.1620.0000.0000.0000.000
64B82ILE0-0.049-0.02740.518-0.145-0.1450.0000.0000.0000.000
65B83LYS10.9320.99042.3946.3996.3990.0000.0000.0000.000
66B84LYS10.9090.94344.9676.4276.4270.0000.0000.0000.000
67B85THR0-0.053-0.02839.258-0.003-0.0030.0000.0000.0000.000
68B86ALA00.0580.02940.541-0.143-0.1430.0000.0000.0000.000
69B87ASN0-0.025-0.01641.610-0.084-0.0840.0000.0000.0000.000
70B88LYS10.9230.97241.8257.4187.4180.0000.0000.0000.000
71B89VAL00.0260.03136.813-0.020-0.0200.0000.0000.0000.000
72B90ARG10.8970.94839.6126.9476.9470.0000.0000.0000.000
73B91SER0-0.037-0.01541.560-0.001-0.0010.0000.0000.0000.000
74B92LYS10.9150.94839.0887.9427.9420.0000.0000.0000.000
75B93LEU00.0140.00735.131-0.075-0.0750.0000.0000.0000.000
76B94LYS10.9100.96338.8667.2727.2720.0000.0000.0000.000
77B95SER0-0.022-0.00541.7720.0330.0330.0000.0000.0000.000
78B96ILE0-0.004-0.01435.6250.0110.0110.0000.0000.0000.000
79B97GLU-1-0.864-0.93039.297-7.737-7.7370.0000.0000.0000.000
80B98GLN00.0280.00440.169-0.004-0.0040.0000.0000.0000.000
81B99SER0-0.044-0.01040.388-0.010-0.0100.0000.0000.0000.000
82B100ILE0-0.011-0.00735.831-0.042-0.0420.0000.0000.0000.000
83B101GLU-1-0.906-0.94239.817-7.213-7.2130.0000.0000.0000.000
84B102GLN0-0.029-0.01542.8850.0940.0940.0000.0000.0000.000
85B103GLU-1-0.898-0.95739.716-7.706-7.7060.0000.0000.0000.000
86B104GLU-1-0.861-0.94138.541-8.194-8.1940.0000.0000.0000.000
87B105GLY0-0.0120.00941.9480.0810.0810.0000.0000.0000.000
88B106LEU0-0.112-0.05244.1560.1900.1900.0000.0000.0000.000
89B107ASN0-0.055-0.03143.019-0.127-0.1270.0000.0000.0000.000
90B108ARG10.8270.92939.6457.4127.4120.0000.0000.0000.000
91B109SER00.0590.02336.264-0.212-0.2120.0000.0000.0000.000
92B110SER0-0.034-0.03033.9430.0150.0150.0000.0000.0000.000
93B111ALA00.0250.00129.493-0.082-0.0820.0000.0000.0000.000
94B112ASP-1-0.828-0.89431.133-9.176-9.1760.0000.0000.0000.000
95B113LEU00.0490.02533.570-0.078-0.0780.0000.0000.0000.000
96B114ARG10.9930.98726.65311.18511.1850.0000.0000.0000.000
97B115ILE0-0.0060.00627.861-0.189-0.1890.0000.0000.0000.000
98B116ARG10.8910.93330.1128.6108.6100.0000.0000.0000.000
99B117LYS10.9360.96432.6258.8078.8070.0000.0000.0000.000
100B118THR0-0.014-0.01927.714-0.103-0.1030.0000.0000.0000.000
101B119GLN00.013-0.00126.375-0.052-0.0520.0000.0000.0000.000
102B120HIS00.0010.01829.896-0.182-0.1820.0000.0000.0000.000
103B121SER00.0580.04030.2780.1270.1270.0000.0000.0000.000
104B122THR00.002-0.01025.917-0.011-0.0110.0000.0000.0000.000
105B123LEU0-0.008-0.00828.9370.0180.0180.0000.0000.0000.000
106B124SER00.007-0.01031.3670.2670.2670.0000.0000.0000.000
107B125ARG10.9140.96029.20710.42610.4260.0000.0000.0000.000
108B126LYS10.9050.95825.37411.87311.8730.0000.0000.0000.000
109B127PHE00.0210.00030.5660.1440.1440.0000.0000.0000.000
110B128VAL00.0410.01134.2860.1840.1840.0000.0000.0000.000
111B129GLU-1-0.938-0.96528.287-11.144-11.1440.0000.0000.0000.000
112B130VAL0-0.013-0.01032.0040.0870.0870.0000.0000.0000.000
113B131MET0-0.014-0.01034.0840.1810.1810.0000.0000.0000.000
114B132SER0-0.0100.00435.0050.3380.3380.0000.0000.0000.000
115B133GLU-1-0.851-0.92533.653-9.197-9.1970.0000.0000.0000.000
116B134TYR0-0.036-0.01535.7870.1880.1880.0000.0000.0000.000
117B135ASN00.018-0.00339.0310.3850.3850.0000.0000.0000.000
118B136ALA00.0090.00537.5070.1990.1990.0000.0000.0000.000
119B137THR0-0.038-0.02038.1150.0680.0680.0000.0000.0000.000
120B138GLN0-0.018-0.02140.3440.1470.1470.0000.0000.0000.000
121B139SER0-0.009-0.00542.4820.2320.2320.0000.0000.0000.000
122B140ASP-1-0.857-0.92741.134-7.624-7.6240.0000.0000.0000.000
123B141TYR0-0.118-0.06443.2670.0990.0990.0000.0000.0000.000
124B142ARG10.8790.94045.5356.3626.3620.0000.0000.0000.000
125B143GLU-1-0.906-0.94146.049-6.460-6.4600.0000.0000.0000.000
126B144ARG10.8960.94642.0497.5977.5970.0000.0000.0000.000
127B145CYS0-0.076-0.02548.0560.1380.1380.0000.0000.0000.000
128B146LYS10.9630.99151.1736.2696.2690.0000.0000.0000.000
129B147GLY00.0340.01751.1050.1100.1100.0000.0000.0000.000
130B148ARG10.8410.92050.3176.2936.2930.0000.0000.0000.000
131B149ILE00.0230.00454.0500.1100.1100.0000.0000.0000.000
132B150GLN00.0520.03154.9130.1860.1860.0000.0000.0000.000
133B151ARG10.8800.93654.6535.7005.7000.0000.0000.0000.000
134B152GLN0-0.025-0.01856.7210.1880.1880.0000.0000.0000.000
135B153LEU00.0240.01959.9020.1310.1310.0000.0000.0000.000
136B154GLU-1-0.840-0.91158.620-5.461-5.4610.0000.0000.0000.000
137B155ILE0-0.111-0.03959.8400.0710.0710.0000.0000.0000.000
138B156THR0-0.107-0.06763.0690.0980.0980.0000.0000.0000.000
139B157GLY00.0040.00965.3490.0910.0910.0000.0000.0000.000
140B158ARG10.8760.95364.6495.0185.0180.0000.0000.0000.000
141B159THR00.0190.00261.821-0.043-0.0430.0000.0000.0000.000
142B160THR0-0.008-0.01559.9680.0800.0800.0000.0000.0000.000
143B161THR00.0090.02058.633-0.124-0.1240.0000.0000.0000.000
144B162SER0-0.003-0.02552.8670.0210.0210.0000.0000.0000.000
145B163GLU-1-0.902-0.96156.018-5.616-5.6160.0000.0000.0000.000
146B164GLU-1-0.862-0.92057.588-5.042-5.0420.0000.0000.0000.000
147B165LEU0-0.057-0.03856.0700.0500.0500.0000.0000.0000.000
148B166GLU-1-0.814-0.92253.319-6.063-6.0630.0000.0000.0000.000
149B167ASP-1-0.803-0.88657.393-5.282-5.2820.0000.0000.0000.000
150B168MET0-0.159-0.08360.8460.0650.0650.0000.0000.0000.000
151B169LEU0-0.065-0.03755.3270.0150.0150.0000.0000.0000.000
152B170GLU-1-0.952-0.96357.146-5.641-5.6410.0000.0000.0000.000
153B171SER0-0.085-0.03858.6600.0730.0730.0000.0000.0000.000
154B172GLY00.0220.01861.9590.0430.0430.0000.0000.0000.000
155B173ASN0-0.001-0.02062.8130.1000.1000.0000.0000.0000.000
156B174PRO0-0.057-0.02664.934-0.052-0.0520.0000.0000.0000.000
157B175ALA00.0310.01265.413-0.060-0.0600.0000.0000.0000.000
158B176ILE0-0.0200.00663.3100.0960.0960.0000.0000.0000.000
159B177PHE00.0640.02559.5630.0300.0300.0000.0000.0000.000
160B178ALA0-0.073-0.04765.2980.0320.0320.0000.0000.0000.000
161B179SER0-0.0210.00168.2380.0820.0820.0000.0000.0000.000
162B180GLY00.0110.01569.3440.0730.0730.0000.0000.0000.000
163B181ILE0-0.040-0.01666.0570.0530.0530.0000.0000.0000.000
164B182ILE00.0570.03069.8110.0410.0410.0000.0000.0000.000
165B183MET0-0.061-0.06270.701-0.081-0.0810.0000.0000.0000.000
166B184ASP-1-0.927-0.94772.496-4.275-4.2750.0000.0000.0000.000
167B185SER00.0400.02369.449-0.027-0.0270.0000.0000.0000.000
168B186SER00.0370.00268.540-0.020-0.0200.0000.0000.0000.000
169B187ILE00.0120.00064.111-0.068-0.0680.0000.0000.0000.000
170B188SER00.0170.00865.125-0.091-0.0910.0000.0000.0000.000
171B189LYS10.9210.95867.1864.6634.6630.0000.0000.0000.000
172B190GLN00.0080.02260.0090.0250.0250.0000.0000.0000.000
173B191ALA00.0290.00861.243-0.079-0.0790.0000.0000.0000.000
174B192LEU00.0010.00561.599-0.041-0.0410.0000.0000.0000.000
175B193SER00.0030.00161.505-0.007-0.0070.0000.0000.0000.000
176B194GLU-1-0.861-0.93155.194-5.867-5.8670.0000.0000.0000.000
177B195ILE0-0.026-0.02058.112-0.091-0.0910.0000.0000.0000.000
178B196GLU-1-0.871-0.93959.251-5.301-5.3010.0000.0000.0000.000
179B197THR0-0.045-0.01155.366-0.059-0.0590.0000.0000.0000.000
180B198ARG10.7570.86451.9665.9795.9790.0000.0000.0000.000
181B199HIS00.0700.04654.694-0.175-0.1750.0000.0000.0000.000
182B200SER0-0.0070.00356.803-0.062-0.0620.0000.0000.0000.000
183B201GLU-1-0.881-0.96550.968-6.345-6.3450.0000.0000.0000.000
184B202ILE00.0150.00151.799-0.122-0.1220.0000.0000.0000.000
185B203ILE00.0440.03552.974-0.036-0.0360.0000.0000.0000.000
186B204LYS10.8270.91552.5685.8525.8520.0000.0000.0000.000
187B205LEU0-0.0100.00547.142-0.089-0.0890.0000.0000.0000.000
188B206GLU-1-0.875-0.95249.438-6.126-6.1260.0000.0000.0000.000
189B207ASN0-0.068-0.03951.3810.0390.0390.0000.0000.0000.000
190B208SER00.0070.01447.422-0.068-0.0680.0000.0000.0000.000
191B209ILE00.0430.01545.731-0.098-0.0980.0000.0000.0000.000
192B210ARG10.9530.98447.8845.8395.8390.0000.0000.0000.000
193B211GLU-1-0.961-0.98450.004-6.260-6.2600.0000.0000.0000.000
194B212LEU0-0.021-0.02443.739-0.048-0.0480.0000.0000.0000.000
195B213HIS00.0130.02046.184-0.196-0.1960.0000.0000.0000.000
196B214ASP-1-0.857-0.94747.292-6.590-6.5900.0000.0000.0000.000
197B215MET0-0.057-0.00942.377-0.104-0.1040.0000.0000.0000.000
198B216PHE00.005-0.02040.279-0.144-0.1440.0000.0000.0000.000
199B217MET00.0040.00642.969-0.113-0.1130.0000.0000.0000.000
200B218ASP-1-0.902-0.95044.348-7.167-7.1670.0000.0000.0000.000
201B219MET0-0.017-0.01238.439-0.125-0.1250.0000.0000.0000.000
202B220ALA0-0.0010.00039.419-0.239-0.2390.0000.0000.0000.000
203B221MET00.0190.00741.0730.0070.0070.0000.0000.0000.000
204B222LEU0-0.031-0.00539.019-0.058-0.0580.0000.0000.0000.000
205B223VAL0-0.025-0.02135.689-0.146-0.1460.0000.0000.0000.000
206B224GLU-1-0.959-0.96637.222-7.626-7.6260.0000.0000.0000.000
207B225SER0-0.096-0.03439.930-0.012-0.0120.0000.0000.0000.000
208B226GLN0-0.045-0.02034.489-0.285-0.2850.0000.0000.0000.000
209B227GLY00.0330.03535.501-0.152-0.1520.0000.0000.0000.000
210B228GLU-1-0.896-0.97230.865-9.461-9.4610.0000.0000.0000.000
211B229MET0-0.015-0.01029.942-0.477-0.4770.0000.0000.0000.000
212B230ILE0-0.0130.00629.025-0.419-0.4190.0000.0000.0000.000
213B231ASP-1-0.930-0.96926.392-12.176-12.1760.0000.0000.0000.000
214B232ARG10.9270.97824.54711.61811.6180.0000.0000.0000.000
215B233ILE00.032-0.00318.9450.1530.1530.0000.0000.0000.000
216B234GLU-1-0.945-0.98922.647-12.984-12.9840.0000.0000.0000.000
217B235TYR00.0230.01523.7540.3290.3290.0000.0000.0000.000
218B236ASN0-0.058-0.03525.3100.7800.7800.0000.0000.0000.000
219B237VAL0-0.096-0.05221.7850.1290.1290.0000.0000.0000.000
220B238GLU-1-0.944-0.96325.199-10.746-10.7460.0000.0000.0000.000
221B239HIS0-0.0160.00627.5850.4050.4050.0000.0000.0000.000
222B240ALA0-0.083-0.02727.7560.2980.2980.0000.0000.0000.000
223B241VAL0-0.014-0.00329.832-0.090-0.0900.0000.0000.0000.000
224B242ASP-1-0.915-0.95730.502-10.585-10.5850.0000.0000.0000.000
225B243TYR0-0.056-0.04031.2680.3230.3230.0000.0000.0000.000
226B244VAL00.010-0.00132.9670.0890.0890.0000.0000.0000.000
227B245GLU-1-0.967-0.97635.776-8.607-8.6070.0000.0000.0000.000
228B246ARG10.9460.98137.5308.2998.2990.0000.0000.0000.000
229B247ALA00.0110.00340.283-0.023-0.0230.0000.0000.0000.000
230B248VAL0-0.025-0.00642.1310.1520.1520.0000.0000.0000.000