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: 527KZ

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2592837.980588
FMO2-HF: Nuclear repulsion 2497176.593436
FMO2-HF: Total energy -95661.387152
FMO2-MP2: Total energy -95935.026289


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.
-73.757-72.22-0.007-0.628-0.9020
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 : 0.966 / q_NPA : 0.967
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].
3B4ARG10.8240.8703.73332.22133.758-0.007-0.628-0.9020.000
4B5THR00.019-0.0146.4163.9123.9120.0000.0000.0000.000
5B6GLN0-0.013-0.0099.1171.6201.6200.0000.0000.0000.000
6B7GLU-1-0.845-0.8908.169-25.642-25.6420.0000.0000.0000.000
7B8LEU00.0110.02011.8631.3301.3300.0000.0000.0000.000
8B9ARG10.8770.95114.07817.13617.1360.0000.0000.0000.000
9B27ASP-1-1.019-1.01333.339-9.002-9.0020.0000.0000.0000.000
10B28ARG10.7090.81828.32310.10710.1070.0000.0000.0000.000
11B29PHE0-0.009-0.01529.0460.2820.2820.0000.0000.0000.000
12B30MET0-0.043-0.02730.956-0.267-0.2670.0000.0000.0000.000
13B31ASP-1-0.714-0.84232.778-9.628-9.6280.0000.0000.0000.000
14B32GLU-1-0.878-0.93833.775-8.014-8.0140.0000.0000.0000.000
15B33PHE0-0.029-0.02031.7600.0660.0660.0000.0000.0000.000
16B34PHE0-0.001-0.02228.169-0.191-0.1910.0000.0000.0000.000
17B35GLU-1-0.891-0.91732.182-8.708-8.7080.0000.0000.0000.000
18B36GLN0-0.033-0.02134.7100.1530.1530.0000.0000.0000.000
19B37VAL0-0.0120.00029.3060.0060.0060.0000.0000.0000.000
20B38GLU-1-0.855-0.90529.035-10.766-10.7660.0000.0000.0000.000
21B39GLU-1-0.804-0.88331.553-8.142-8.1420.0000.0000.0000.000
22B40ILE0-0.015-0.01733.7820.1450.1450.0000.0000.0000.000
23B41ARG10.8050.86624.73911.69011.6900.0000.0000.0000.000
24B42GLY00.0310.02331.331-0.083-0.0830.0000.0000.0000.000
25B43PHE0-0.039-0.03533.2300.1490.1490.0000.0000.0000.000
26B44ILE0-0.005-0.00131.4730.1410.1410.0000.0000.0000.000
27B45ASP-1-0.791-0.86728.810-11.030-11.0300.0000.0000.0000.000
28B46LYS10.8460.91932.1078.5568.5560.0000.0000.0000.000
29B47ILE00.000-0.00535.5610.1820.1820.0000.0000.0000.000
30B48ALA00.0160.00231.8390.1360.1360.0000.0000.0000.000
31B49GLU-1-0.878-0.91033.762-8.849-8.8490.0000.0000.0000.000
32B50ASN0-0.035-0.04134.7420.0550.0550.0000.0000.0000.000
33B51VAL0-0.011-0.00235.8590.2330.2330.0000.0000.0000.000
34B52GLU-1-0.813-0.90032.737-9.226-9.2260.0000.0000.0000.000
35B53GLU-1-0.841-0.88636.193-7.986-7.9860.0000.0000.0000.000
36B54VAL0-0.028-0.02139.2660.2100.2100.0000.0000.0000.000
37B55LYS10.8210.90534.6049.2149.2140.0000.0000.0000.000
38B56ARG10.7990.86737.1218.3188.3180.0000.0000.0000.000
39B57LYS10.8790.92740.7937.3647.3640.0000.0000.0000.000
40B58HIS10.8880.95542.6417.3687.3680.0000.0000.0000.000
41B59SER00.0230.00241.4370.1610.1610.0000.0000.0000.000
42B60ALA0-0.0170.00044.4300.1270.1270.0000.0000.0000.000
43B61ILE00.0420.01746.4590.1590.1590.0000.0000.0000.000
44B62LEU0-0.011-0.00346.0140.1570.1570.0000.0000.0000.000
45B63ALA0-0.036-0.00247.0170.0740.0740.0000.0000.0000.000
46B64SER0-0.013-0.00249.1110.1150.1150.0000.0000.0000.000
47B65PRO0-0.019-0.00852.5460.0090.0090.0000.0000.0000.000
48B66ASN0-0.029-0.03255.8550.0870.0870.0000.0000.0000.000
49B67PRO0-0.0200.01652.266-0.001-0.0010.0000.0000.0000.000
50B68ASP-1-0.788-0.87652.197-6.068-6.0680.0000.0000.0000.000
51B69GLU-1-0.817-0.91754.295-5.709-5.7090.0000.0000.0000.000
52B70LYS10.8210.91650.7136.2506.2500.0000.0000.0000.000
53B71THR0-0.040-0.06248.590-0.112-0.1120.0000.0000.0000.000
54B72LYS10.8440.91049.2455.6375.6370.0000.0000.0000.000
55B73GLU-1-0.843-0.90051.257-6.041-6.0410.0000.0000.0000.000
56B74GLU-1-0.889-0.94946.906-6.866-6.8660.0000.0000.0000.000
57B75LEU0-0.035-0.01845.363-0.160-0.1600.0000.0000.0000.000
58B76GLU-1-0.840-0.92646.897-6.125-6.1250.0000.0000.0000.000
59B77GLU-1-0.845-0.89947.335-6.584-6.5840.0000.0000.0000.000
60B78LEU0-0.034-0.01441.445-0.107-0.1070.0000.0000.0000.000
61B79MET0-0.010-0.00243.789-0.144-0.1440.0000.0000.0000.000
62B80SER0-0.053-0.04145.655-0.030-0.0300.0000.0000.0000.000
63B81ASP-1-0.860-0.93442.120-7.559-7.5590.0000.0000.0000.000
64B82ILE00.000-0.00240.068-0.129-0.1290.0000.0000.0000.000
65B83LYS10.8560.93542.1866.2806.2800.0000.0000.0000.000
66B84LYS10.8740.93544.7816.6326.6320.0000.0000.0000.000
67B85THR0-0.015-0.01439.1820.0150.0150.0000.0000.0000.000
68B86ALA00.0610.04040.381-0.140-0.1400.0000.0000.0000.000
69B87ASN0-0.025-0.01541.444-0.071-0.0710.0000.0000.0000.000
70B88LYS10.8720.94841.3977.5367.5360.0000.0000.0000.000
71B89VAL00.0170.02336.627-0.027-0.0270.0000.0000.0000.000
72B90ARG10.7910.85639.4806.9106.9100.0000.0000.0000.000
73B91SER0-0.042-0.01241.4830.0200.0200.0000.0000.0000.000
74B92LYS10.8290.88339.0358.0058.0050.0000.0000.0000.000
75B93LEU00.0160.00834.909-0.080-0.0800.0000.0000.0000.000
76B94LYS10.8640.92838.8267.4007.4000.0000.0000.0000.000
77B95SER0-0.024-0.00341.7750.0270.0270.0000.0000.0000.000
78B96ILE0-0.001-0.01435.5790.0100.0100.0000.0000.0000.000
79B97GLU-1-0.834-0.90439.326-7.751-7.7510.0000.0000.0000.000
80B98GLN00.0340.01340.2290.0260.0260.0000.0000.0000.000
81B99SER0-0.045-0.01340.3300.0170.0170.0000.0000.0000.000
82B100ILE0-0.032-0.02136.067-0.034-0.0340.0000.0000.0000.000
83B101GLU-1-0.894-0.93839.930-7.166-7.1660.0000.0000.0000.000
84B102GLN0-0.040-0.02243.0320.1430.1430.0000.0000.0000.000
85B103GLU-1-0.847-0.92539.903-7.694-7.6940.0000.0000.0000.000
86B104GLU-1-0.808-0.89238.299-8.276-8.2760.0000.0000.0000.000
87B105GLY0-0.0150.00942.1540.0790.0790.0000.0000.0000.000
88B106LEU0-0.099-0.04844.4620.1840.1840.0000.0000.0000.000
89B107ASN0-0.066-0.03343.291-0.075-0.0750.0000.0000.0000.000
90B108ARG10.8030.91339.9217.3947.3940.0000.0000.0000.000
91B109SER00.0540.02036.464-0.204-0.2040.0000.0000.0000.000
92B110SER0-0.029-0.02634.1880.0140.0140.0000.0000.0000.000
93B111ALA00.0320.00229.635-0.073-0.0730.0000.0000.0000.000
94B112ASP-1-0.782-0.86031.306-9.116-9.1160.0000.0000.0000.000
95B113LEU00.0370.02133.682-0.073-0.0730.0000.0000.0000.000
96B114ARG10.9840.98727.27811.04811.0480.0000.0000.0000.000
97B115ILE0-0.0040.00627.941-0.176-0.1760.0000.0000.0000.000
98B116ARG10.8490.89930.2088.6288.6280.0000.0000.0000.000
99B117LYS10.8780.91633.0058.6028.6020.0000.0000.0000.000
100B118THR00.006-0.00927.840-0.088-0.0880.0000.0000.0000.000
101B119GLN0-0.011-0.00826.075-0.034-0.0340.0000.0000.0000.000
102B120HIS00.0000.01129.921-0.168-0.1680.0000.0000.0000.000
103B121SER00.0530.02830.3690.0140.0140.0000.0000.0000.000
104B122THR0-0.006-0.01425.860-0.021-0.0210.0000.0000.0000.000
105B123LEU0-0.009-0.00228.9630.0150.0150.0000.0000.0000.000
106B124SER0-0.001-0.01631.3200.2620.2620.0000.0000.0000.000
107B125ARG10.8220.91029.30210.40410.4040.0000.0000.0000.000
108B126LYS10.8220.89525.72311.64711.6470.0000.0000.0000.000
109B127PHE00.014-0.00230.4930.1400.1400.0000.0000.0000.000
110B128VAL00.0390.00834.2140.1830.1830.0000.0000.0000.000
111B129GLU-1-0.857-0.90528.249-11.149-11.1490.0000.0000.0000.000
112B130VAL0-0.010-0.00831.7260.0860.0860.0000.0000.0000.000
113B131MET0-0.010-0.00833.9410.1840.1840.0000.0000.0000.000
114B132SER00.0190.01534.9340.2950.2950.0000.0000.0000.000
115B133GLU-1-0.867-0.92533.311-9.020-9.0200.0000.0000.0000.000
116B134TYR0-0.025-0.01135.6430.1810.1810.0000.0000.0000.000
117B135ASN00.002-0.00938.8560.3430.3430.0000.0000.0000.000
118B136ALA00.0170.01137.3720.1990.1990.0000.0000.0000.000
119B137THR0-0.035-0.02137.8670.0790.0790.0000.0000.0000.000
120B138GLN00.002-0.00340.1510.1210.1210.0000.0000.0000.000
121B139SER00.0310.01242.4220.1860.1860.0000.0000.0000.000
122B140ASP-1-0.846-0.89641.003-7.545-7.5450.0000.0000.0000.000
123B141TYR0-0.087-0.07743.1010.0920.0920.0000.0000.0000.000
124B142ARG10.8060.87245.3236.3146.3140.0000.0000.0000.000
125B143GLU-1-0.821-0.89946.075-6.344-6.3440.0000.0000.0000.000
126B144ARG10.8030.88541.5747.5897.5890.0000.0000.0000.000
127B145CYS0-0.080-0.02947.8440.1320.1320.0000.0000.0000.000
128B146LYS10.8610.92350.9926.3396.3390.0000.0000.0000.000
129B147GLY00.0300.01650.9240.1080.1080.0000.0000.0000.000
130B148ARG10.7990.88951.0046.2146.2140.0000.0000.0000.000
131B149ILE00.011-0.00253.8310.1070.1070.0000.0000.0000.000
132B150GLN00.0310.01354.6520.1520.1520.0000.0000.0000.000
133B151ARG10.8660.91654.6375.6585.6580.0000.0000.0000.000
134B152GLN0-0.042-0.03957.1590.1760.1760.0000.0000.0000.000
135B153LEU00.0040.01259.7200.1260.1260.0000.0000.0000.000
136B154GLU-1-0.846-0.90358.417-5.418-5.4180.0000.0000.0000.000
137B155ILE0-0.103-0.03760.0640.0760.0760.0000.0000.0000.000
138B156THR0-0.104-0.06262.9360.0980.0980.0000.0000.0000.000
139B157GLY00.0030.00965.1490.0910.0910.0000.0000.0000.000
140B158ARG10.8220.90363.6615.0385.0380.0000.0000.0000.000
141B159THR00.003-0.00961.850-0.047-0.0470.0000.0000.0000.000
142B160THR00.0060.01860.2150.0990.0990.0000.0000.0000.000
143B161THR0-0.0320.00158.538-0.127-0.1270.0000.0000.0000.000
144B162SER00.020-0.01452.7240.0200.0200.0000.0000.0000.000
145B163GLU-1-0.874-0.94155.935-5.680-5.6800.0000.0000.0000.000
146B164GLU-1-0.817-0.89657.539-5.060-5.0600.0000.0000.0000.000
147B165LEU0-0.043-0.02955.6410.0610.0610.0000.0000.0000.000
148B166GLU-1-0.747-0.85853.128-6.043-6.0430.0000.0000.0000.000
149B167ASP-1-0.828-0.90457.307-5.193-5.1930.0000.0000.0000.000
150B168MET0-0.152-0.07260.7390.0600.0600.0000.0000.0000.000
151B169LEU0-0.063-0.03155.2120.0200.0200.0000.0000.0000.000
152B170GLU-1-0.954-0.96556.900-5.620-5.6200.0000.0000.0000.000
153B171SER0-0.076-0.03058.5820.0740.0740.0000.0000.0000.000
154B172GLY00.0260.02061.8790.0430.0430.0000.0000.0000.000
155B173ASN0-0.032-0.03762.6860.1260.1260.0000.0000.0000.000
156B174PRO0-0.030-0.01364.764-0.053-0.0530.0000.0000.0000.000
157B175ALA00.0290.01265.211-0.059-0.0590.0000.0000.0000.000
158B176ILE0-0.0120.00663.1320.0960.0960.0000.0000.0000.000
159B177PHE00.0700.02759.4400.0290.0290.0000.0000.0000.000
160B178ALA0-0.071-0.04565.1070.0310.0310.0000.0000.0000.000
161B179SER0-0.022-0.00168.0210.0770.0770.0000.0000.0000.000
162B180GLY00.0040.01069.1570.0730.0730.0000.0000.0000.000
163B181ILE0-0.040-0.01465.6990.0540.0540.0000.0000.0000.000
164B182ILE00.0630.03369.5970.0400.0400.0000.0000.0000.000
165B183MET0-0.053-0.06270.530-0.081-0.0810.0000.0000.0000.000
166B184ASP-1-0.923-0.95372.359-4.298-4.2980.0000.0000.0000.000
167B185SER00.0530.03269.472-0.032-0.0320.0000.0000.0000.000
168B186SER00.0310.00068.726-0.016-0.0160.0000.0000.0000.000
169B187ILE00.0180.00563.934-0.072-0.0720.0000.0000.0000.000
170B188SER00.0420.02465.080-0.094-0.0940.0000.0000.0000.000
171B189LYS10.8640.94067.1344.6914.6910.0000.0000.0000.000
172B190GLN00.0210.03159.8870.0170.0170.0000.0000.0000.000
173B191ALA00.0190.00361.166-0.085-0.0850.0000.0000.0000.000
174B192LEU00.0060.00261.458-0.042-0.0420.0000.0000.0000.000
175B193SER00.0100.01061.655-0.007-0.0070.0000.0000.0000.000
176B194GLU-1-0.778-0.85654.837-5.908-5.9080.0000.0000.0000.000
177B195ILE0-0.024-0.01957.942-0.091-0.0910.0000.0000.0000.000
178B196GLU-1-0.867-0.93859.010-5.270-5.2700.0000.0000.0000.000
179B197THR0-0.045-0.01755.293-0.053-0.0530.0000.0000.0000.000
180B198ARG10.7400.82551.9105.9735.9730.0000.0000.0000.000
181B199HIS00.0610.03754.463-0.177-0.1770.0000.0000.0000.000
182B200SER00.0020.00456.588-0.058-0.0580.0000.0000.0000.000
183B201GLU-1-0.837-0.90650.664-6.330-6.3300.0000.0000.0000.000
184B202ILE00.0280.00451.691-0.119-0.1190.0000.0000.0000.000
185B203ILE00.0350.02952.775-0.036-0.0360.0000.0000.0000.000
186B204LYS10.7850.88852.1365.9295.9290.0000.0000.0000.000
187B205LEU0-0.061-0.01247.435-0.088-0.0880.0000.0000.0000.000
188B206GLU-1-0.797-0.90549.267-6.133-6.1330.0000.0000.0000.000
189B207ASN0-0.037-0.01551.2340.0330.0330.0000.0000.0000.000
190B208SER0-0.0040.01147.183-0.067-0.0670.0000.0000.0000.000
191B209ILE00.0360.01345.702-0.099-0.0990.0000.0000.0000.000
192B210ARG10.9470.97247.7585.8045.8040.0000.0000.0000.000
193B211GLU-1-0.907-0.94149.922-6.202-6.2020.0000.0000.0000.000
194B212LEU0-0.010-0.01643.774-0.051-0.0510.0000.0000.0000.000
195B213HIS00.0110.01946.117-0.176-0.1760.0000.0000.0000.000
196B214ASP-1-0.821-0.90947.275-6.613-6.6130.0000.0000.0000.000
197B215MET0-0.0170.01542.379-0.096-0.0960.0000.0000.0000.000
198B216PHE00.001-0.02039.954-0.139-0.1390.0000.0000.0000.000
199B217MET00.0120.01042.992-0.107-0.1070.0000.0000.0000.000
200B218ASP-1-0.873-0.92044.061-7.196-7.1960.0000.0000.0000.000
201B219MET0-0.007-0.01538.556-0.115-0.1150.0000.0000.0000.000
202B220ALA0-0.0020.00139.479-0.234-0.2340.0000.0000.0000.000
203B221MET00.0190.01041.1920.0130.0130.0000.0000.0000.000
204B222LEU0-0.034-0.00539.193-0.037-0.0370.0000.0000.0000.000
205B223VAL0-0.029-0.01935.587-0.141-0.1410.0000.0000.0000.000
206B224GLU-1-0.945-0.95737.400-7.519-7.5190.0000.0000.0000.000
207B225SER0-0.081-0.04140.117-0.034-0.0340.0000.0000.0000.000
208B226GLN0-0.039-0.00534.520-0.331-0.3310.0000.0000.0000.000
209B227GLY00.0330.03635.739-0.143-0.1430.0000.0000.0000.000
210B228GLU-1-0.877-0.96331.156-9.312-9.3120.0000.0000.0000.000
211B229MET0-0.020-0.01330.196-0.488-0.4880.0000.0000.0000.000
212B230ILE0-0.0090.00629.327-0.401-0.4010.0000.0000.0000.000
213B231ASP-1-0.830-0.90827.131-11.631-11.6310.0000.0000.0000.000
214B232ARG10.7850.88925.07511.25311.2530.0000.0000.0000.000
215B233ILE00.0470.00419.2670.1490.1490.0000.0000.0000.000
216B234GLU-1-0.845-0.91923.098-12.561-12.5610.0000.0000.0000.000
217B235TYR00.0290.01924.1670.2660.2660.0000.0000.0000.000
218B236ASN0-0.069-0.04525.6650.5900.5900.0000.0000.0000.000
219B237VAL0-0.082-0.04722.1300.1230.1230.0000.0000.0000.000
220B238GLU-1-0.915-0.94825.593-10.483-10.4830.0000.0000.0000.000
221B239HIS0-0.053-0.02028.0430.5170.5170.0000.0000.0000.000
222B240ALA0-0.089-0.02628.1270.2780.2780.0000.0000.0000.000
223B241VAL0-0.010-0.00530.210-0.081-0.0810.0000.0000.0000.000
224B242ASP-1-0.920-0.95830.773-10.483-10.4830.0000.0000.0000.000
225B243TYR0-0.047-0.03431.4430.3340.3340.0000.0000.0000.000
226B244VAL00.010-0.00233.1130.0920.0920.0000.0000.0000.000
227B245GLU-1-0.974-0.98235.879-8.682-8.6820.0000.0000.0000.000
228B246ARG10.9480.98337.6478.3798.3790.0000.0000.0000.000
229B247ALA00.0090.00140.395-0.030-0.0300.0000.0000.0000.000
230B248VAL0-0.020-0.00342.1130.1460.1460.0000.0000.0000.000