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: 7G58K

Calculation Name: 2ICW-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ICW

Chain ID: G

ChEMBL ID:

UniProt ID: P01903

Base Structure: X-ray

Registration Date: 2023-06-19

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2607246.56966
FMO2-HF: Nuclear repulsion 2519695.02626
FMO2-HF: Total energy -87551.5434
FMO2-MP2: Total energy -87810.598682


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(G:1:MET)


Summations of interaction energy for fragment #1(G:1:MET)
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.
-39.937-30.83424.992-10.854-23.24-0.065
Interaction energy analysis for fragmet #1(G:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.021
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].
3G3LEU0-0.0260.0023.146-4.221-1.3860.133-1.307-1.661-0.003
4G4ARG10.7820.8514.8071.0821.224-0.001-0.010-0.1300.000
5G5VAL0-0.028-0.0207.2200.1450.1450.0000.0000.0000.000
6G6GLU-1-0.816-0.9166.937-0.019-0.0190.0000.0000.0000.000
7G7ASN0-0.092-0.0439.4640.1400.1400.0000.0000.0000.000
8G8PRO0-0.0140.0229.500-0.078-0.0780.0000.0000.0000.000
9G9LYS10.9720.97512.513-0.099-0.0990.0000.0000.0000.000
10G10LYS10.9610.99015.173-0.409-0.4090.0000.0000.0000.000
11G11ALA0-0.0050.02213.676-0.071-0.0710.0000.0000.0000.000
12G12GLN0-0.054-0.03815.7870.0140.0140.0000.0000.0000.000
13G13LYS10.8060.91116.181-0.359-0.3590.0000.0000.0000.000
14G14HIS00.031-0.00119.390-0.028-0.0280.0000.0000.0000.000
15G15PHE0-0.048-0.02520.444-0.009-0.0090.0000.0000.0000.000
16G16VAL00.0680.04019.323-0.019-0.0190.0000.0000.0000.000
17G17GLN0-0.003-0.00117.2180.0060.0060.0000.0000.0000.000
18G18ASN00.0100.00718.798-0.003-0.0030.0000.0000.0000.000
19G19LEU00.0030.01521.712-0.015-0.0150.0000.0000.0000.000
20G20ASN00.017-0.01121.532-0.003-0.0030.0000.0000.0000.000
21G21ASN00.008-0.00623.5130.0010.0010.0000.0000.0000.000
22G22VAL00.0090.01820.810-0.001-0.0010.0000.0000.0000.000
23G23VAL0-0.043-0.01120.884-0.005-0.0050.0000.0000.0000.000
24G24PHE00.0190.02223.880-0.001-0.0010.0000.0000.0000.000
25G25THR00.018-0.01926.377-0.016-0.0160.0000.0000.0000.000
26G26ASN00.014-0.01827.2640.0040.0040.0000.0000.0000.000
27G27LYS10.8150.89929.8770.0590.0590.0000.0000.0000.000
28G28GLU-1-0.735-0.84230.561-0.053-0.0530.0000.0000.0000.000
29G29LEU0-0.040-0.01726.1840.0020.0020.0000.0000.0000.000
30G30GLU-1-0.773-0.87930.702-0.089-0.0890.0000.0000.0000.000
31G31ASP-1-0.793-0.86033.812-0.050-0.0500.0000.0000.0000.000
32G32ILE0-0.030-0.02130.8430.0040.0040.0000.0000.0000.000
33G33TYR0-0.016-0.02727.9690.0000.0000.0000.0000.0000.000
34G34ASN0-0.029-0.02534.4670.0030.0030.0000.0000.0000.000
35G35LEU00.0130.02336.5000.0040.0040.0000.0000.0000.000
36G36SER0-0.059-0.03835.9690.0020.0020.0000.0000.0000.000
37G37ASN0-0.087-0.04138.245-0.002-0.0020.0000.0000.0000.000
38G38LYS10.8930.92141.0310.0410.0410.0000.0000.0000.000
39G39GLU-1-0.822-0.89841.295-0.061-0.0610.0000.0000.0000.000
40G40GLU-1-0.795-0.89341.637-0.045-0.0450.0000.0000.0000.000
41G41THR0-0.031-0.03236.756-0.002-0.0020.0000.0000.0000.000
42G42LYS10.8280.90136.8430.0540.0540.0000.0000.0000.000
43G43GLU-1-0.982-0.97835.381-0.081-0.0810.0000.0000.0000.000
44G44VAL00.0320.00732.280-0.008-0.0080.0000.0000.0000.000
45G45LEU00.0310.01731.962-0.007-0.0070.0000.0000.0000.000
46G46LYS10.9340.97731.6290.0810.0810.0000.0000.0000.000
47G47LEU00.0230.01228.220-0.012-0.0120.0000.0000.0000.000
48G48PHE00.0230.01427.345-0.012-0.0120.0000.0000.0000.000
49G49LYS10.8260.90827.1020.0890.0890.0000.0000.0000.000
50G50LEU0-0.0080.00025.611-0.013-0.0130.0000.0000.0000.000
51G51LYS10.8100.87721.4980.1580.1580.0000.0000.0000.000
52G52VAL00.0550.03022.227-0.012-0.0120.0000.0000.0000.000
53G53ASN0-0.032-0.03122.230-0.020-0.0200.0000.0000.0000.000
54G54GLN0-0.057-0.00917.912-0.018-0.0180.0000.0000.0000.000
55G55PHE00.0430.00217.945-0.038-0.0380.0000.0000.0000.000
56G56TYR0-0.014-0.03617.640-0.013-0.0130.0000.0000.0000.000
57G57ARG10.8930.93416.8730.2870.2870.0000.0000.0000.000
58G58HIS0-0.016-0.00611.714-0.074-0.0740.0000.0000.0000.000
59G59ALA00.011-0.00412.878-0.045-0.0450.0000.0000.0000.000
60G60PHE00.007-0.02413.5710.0010.0010.0000.0000.0000.000
61G61GLY00.0340.02811.962-0.024-0.0240.0000.0000.0000.000
62G62ILE00.0000.0028.825-0.129-0.1290.0000.0000.0000.000
63G63VAL00.0040.0068.856-0.007-0.0070.0000.0000.0000.000
64G64ASN0-0.021-0.00710.822-0.004-0.0040.0000.0000.0000.000
65G65ASP-1-0.763-0.8546.142-1.417-1.4170.0000.0000.0000.000
66G66TYR0-0.033-0.0462.234-1.129-1.2002.100-0.410-1.6190.003
67G67ASN0-0.050-0.0266.3600.4050.4050.0000.0000.0000.000
68G68GLY00.008-0.0198.0890.0520.0520.0000.0000.0000.000
69G69LEU0-0.044-0.0055.9240.2040.2040.0000.0000.0000.000
70G70LEU00.0380.0078.505-0.178-0.1780.0000.0000.0000.000
71G71GLU-1-0.827-0.91111.1090.4720.4720.0000.0000.0000.000
72G72TYR00.0070.0159.645-0.114-0.1140.0000.0000.0000.000
73G73LYS10.8870.94711.209-0.129-0.1290.0000.0000.0000.000
74G74GLU-1-0.766-0.88114.6460.1860.1860.0000.0000.0000.000
75G75ILE0-0.002-0.00210.135-0.032-0.0320.0000.0000.0000.000
76G76PHE0-0.018-0.00814.154-0.042-0.0420.0000.0000.0000.000
77G77ASN0-0.030-0.04215.534-0.039-0.0390.0000.0000.0000.000
78G78MET0-0.010-0.00117.440-0.014-0.0140.0000.0000.0000.000
79G79MET0-0.087-0.01613.646-0.021-0.0210.0000.0000.0000.000
80G80PHE00.0420.00918.533-0.009-0.0090.0000.0000.0000.000
81G81LEU00.0100.00621.382-0.001-0.0010.0000.0000.0000.000
82G82LYS10.9260.96817.933-0.064-0.0640.0000.0000.0000.000
83G83LEU00.0030.01522.262-0.003-0.0030.0000.0000.0000.000
84G84SER00.0350.01424.114-0.004-0.0040.0000.0000.0000.000
85G85VAL0-0.0100.00526.866-0.001-0.0010.0000.0000.0000.000
86G86VAL00.0020.00525.129-0.001-0.0010.0000.0000.0000.000
87G87PHE0-0.006-0.01726.672-0.004-0.0040.0000.0000.0000.000
88G88ASP-1-0.843-0.90130.100-0.010-0.0100.0000.0000.0000.000
89G89THR0-0.0110.01331.4890.0040.0040.0000.0000.0000.000
90G90GLN00.0390.01831.2020.0000.0000.0000.0000.0000.000
91G91ARG10.8450.89331.4980.0260.0260.0000.0000.0000.000
92G92LYS10.8420.92735.7630.0120.0120.0000.0000.0000.000
93G93GLU-1-0.799-0.88235.717-0.023-0.0230.0000.0000.0000.000
94G94ALA00.0070.02436.183-0.003-0.0030.0000.0000.0000.000
95G95ASN00.0460.02937.270-0.008-0.0080.0000.0000.0000.000
96G96ASN0-0.018-0.00237.725-0.003-0.0030.0000.0000.0000.000
97G97VAL00.040-0.00336.162-0.002-0.0020.0000.0000.0000.000
98G98GLU-1-0.761-0.86534.760-0.053-0.0530.0000.0000.0000.000
99G99GLN0-0.029-0.01933.445-0.002-0.0020.0000.0000.0000.000
100G100ILE0-0.028-0.00831.512-0.003-0.0030.0000.0000.0000.000
101G101LYS10.8300.89730.2340.0480.0480.0000.0000.0000.000
102G102ARG10.8220.88925.4290.0300.0300.0000.0000.0000.000
103G103ASN00.039-0.00227.7810.0040.0040.0000.0000.0000.000
104G104ILE0-0.024-0.01625.555-0.007-0.0070.0000.0000.0000.000
105G105ALA00.0340.02224.229-0.012-0.0120.0000.0000.0000.000
106G106ILE0-0.0150.00523.1890.0000.0000.0000.0000.0000.000
107G107LEU0-0.026-0.00621.7110.0020.0020.0000.0000.0000.000
108G108ASP-1-0.788-0.87119.162-0.190-0.1900.0000.0000.0000.000
109G109GLU-1-0.832-0.89818.266-0.038-0.0380.0000.0000.0000.000
110G110ILE0-0.064-0.02718.0340.0220.0220.0000.0000.0000.000
111G111MET0-0.0260.02115.3590.0000.0000.0000.0000.0000.000
112G112ALA00.0370.02613.766-0.021-0.0210.0000.0000.0000.000
113G113LYS10.7780.87513.758-0.173-0.1730.0000.0000.0000.000
114G114ALA00.0180.00112.9870.0730.0730.0000.0000.0000.000
115G115ASP-1-0.725-0.8359.492-0.426-0.4260.0000.0000.0000.000
116G116ASN0-0.044-0.0319.1340.0820.0820.0000.0000.0000.000
117G117ASP-1-0.796-0.89410.7610.4180.4180.0000.0000.0000.000
118G118LEU0-0.010-0.0076.0390.2130.2130.0000.0000.0000.000
119G119SER00.021-0.0076.2090.4360.4360.0000.0000.0000.000
120G120TYR0-0.002-0.0107.2710.4830.4830.0000.0000.0000.000
121G121PHE00.0350.0059.4330.2110.2110.0000.0000.0000.000
122G122ILE0-0.0060.0012.8270.126-0.4453.165-0.405-2.1900.005
123G123SER0-0.066-0.0385.9460.2390.360-0.001-0.009-0.1100.000
124G124GLN0-0.036-0.0147.066-0.479-0.4790.0000.0000.0000.000
125G125ASN00.0010.0137.738-0.312-0.3120.0000.0000.0000.000
126G126LYS10.9510.9585.841-0.763-0.7630.0000.0000.0000.000
127G127ASN00.0130.0146.6330.1020.1020.0000.0000.0000.000
128G128PHE0-0.001-0.0022.345-1.267-0.4010.633-0.313-1.1860.001
129G129GLN00.0790.0331.940-4.251-3.9507.677-3.013-4.9660.011
130G130GLU-1-0.867-0.9243.697-1.544-2.280-0.0131.179-0.430-0.001
131G131LEU0-0.049-0.0265.973-0.617-0.6170.0000.0000.0000.000
132G132TRP0-0.004-0.0062.606-5.972-3.7464.275-1.378-5.123-0.011
133G133ASP-1-0.784-0.9071.999-22.928-18.9657.025-5.184-5.803-0.070
134G134LYS10.7630.8665.0880.5240.551-0.001-0.004-0.0220.000
135G135ALA00.0120.0007.7380.0400.0400.0000.0000.0000.000
136G136VAL00.0210.0215.4280.1860.1860.0000.0000.0000.000
137G137LYS10.8870.9498.3610.7060.7060.0000.0000.0000.000
138G138LEU0-0.032-0.02310.7740.1390.1390.0000.0000.0000.000
139G139THR00.0060.00111.2010.1330.1330.0000.0000.0000.000
140G140LYS10.8290.8989.4551.2021.2020.0000.0000.0000.000
141G141GLU-1-0.838-0.91213.759-0.257-0.2570.0000.0000.0000.000
142G142MET0-0.045-0.00414.9080.0830.0830.0000.0000.0000.000
143G143LYS10.9030.96616.0320.4790.4790.0000.0000.0000.000
144G144ILE0-0.0180.00318.0770.0410.0410.0000.0000.0000.000
145G145LYS10.8580.91719.1620.3050.3050.0000.0000.0000.000
146G146LEU00.014-0.00219.3680.0250.0250.0000.0000.0000.000
147G147LYS10.9460.98622.9200.2160.2160.0000.0000.0000.000
148G148GLY00.0340.01824.8550.0060.0060.0000.0000.0000.000
149G149GLN0-0.0420.00824.7080.0310.0310.0000.0000.0000.000
150G150LYS10.9750.98227.0360.1220.1220.0000.0000.0000.000
151G151LEU00.0250.00522.5730.0000.0000.0000.0000.0000.000
152G152ASP-1-0.753-0.84826.548-0.168-0.1680.0000.0000.0000.000
153G153LEU0-0.065-0.05823.013-0.017-0.0170.0000.0000.0000.000
154G154ARG10.8020.87726.3750.1610.1610.0000.0000.0000.000
155G155ASP-1-0.854-0.92328.597-0.111-0.1110.0000.0000.0000.000
156G156GLY00.0090.00927.887-0.012-0.0120.0000.0000.0000.000
157G157GLU-1-0.891-0.93523.842-0.137-0.1370.0000.0000.0000.000
158G158VAL00.0110.00124.229-0.009-0.0090.0000.0000.0000.000
159G159ALA00.0180.01519.694-0.007-0.0070.0000.0000.0000.000
160G160ILE00.021-0.00718.673-0.014-0.0140.0000.0000.0000.000
161G161ASN0-0.029-0.01121.1850.0130.0130.0000.0000.0000.000
162G162LYS10.8620.89422.3360.1830.1830.0000.0000.0000.000
163G163VAL00.0030.00217.177-0.006-0.0060.0000.0000.0000.000
164G164ARG10.8900.93319.8360.1010.1010.0000.0000.0000.000
165G165GLU-1-0.841-0.89022.527-0.156-0.1560.0000.0000.0000.000
166G166LEU0-0.023-0.00920.4610.0040.0040.0000.0000.0000.000
167G167PHE0-0.004-0.01517.190-0.012-0.0120.0000.0000.0000.000
168G168GLY0-0.0120.00820.0140.0170.0170.0000.0000.0000.000
169G169SER0-0.021-0.01121.9770.0170.0170.0000.0000.0000.000
170G170ASP-1-0.817-0.91015.960-0.067-0.0670.0000.0000.0000.000
171G171LYS10.9370.97817.531-0.002-0.0020.0000.0000.0000.000
172G172ASN00.0840.04913.568-0.014-0.0140.0000.0000.0000.000
173G173VAL00.0170.02415.6560.0020.0020.0000.0000.0000.000
174G174LYS10.9000.96017.0430.0100.0100.0000.0000.0000.000
175G175GLU-1-0.860-0.93117.2370.1020.1020.0000.0000.0000.000
176G176LEU0-0.023-0.00912.1970.0110.0110.0000.0000.0000.000
177G177TRP00.0270.00714.620-0.039-0.0390.0000.0000.0000.000
178G178TRP00.0680.0416.635-0.152-0.1520.0000.0000.0000.000
179G179PHE00.0320.02210.313-0.139-0.1390.0000.0000.0000.000
180G180ARG10.8540.91211.580-0.066-0.0660.0000.0000.0000.000
181G181SER0-0.001-0.00212.360-0.033-0.0330.0000.0000.0000.000
182G182LEU00.0020.0047.535-0.020-0.0200.0000.0000.0000.000
183G183LEU00.0250.01710.990-0.078-0.0780.0000.0000.0000.000
184G184VAL0-0.030-0.01613.5080.0000.0000.0000.0000.0000.000
185G185LYS10.8140.89510.8630.7640.7640.0000.0000.0000.000
186G186GLY00.0480.01513.245-0.022-0.0220.0000.0000.0000.000
187G187VAL0-0.019-0.00913.8950.0200.0200.0000.0000.0000.000
188G188TYR0-0.023-0.01617.1420.0280.0280.0000.0000.0000.000
189G189LEU0-0.0350.00212.0430.0150.0150.0000.0000.0000.000
190G190ILE0-0.009-0.01714.7680.0290.0290.0000.0000.0000.000
191G191LYS10.7760.87517.9460.2850.2850.0000.0000.0000.000
192G192ARG10.9920.99718.2130.4160.4160.0000.0000.0000.000
193G193TYR00.0400.03018.1240.0200.0200.0000.0000.0000.000
194G194TYR0-0.076-0.06120.2180.0230.0230.0000.0000.0000.000
195G195GLU-1-0.850-0.89923.153-0.232-0.2320.0000.0000.0000.000
196G196GLY0-0.0020.00923.8960.0200.0200.0000.0000.0000.000
197G197ASP-1-0.893-0.94820.707-0.408-0.4080.0000.0000.0000.000
198G198ILE0-0.016-0.03419.609-0.052-0.0520.0000.0000.0000.000
199G199GLU-1-0.854-0.91618.291-0.439-0.4390.0000.0000.0000.000
200G200LEU0-0.049-0.02215.390-0.082-0.0820.0000.0000.0000.000
201G201LYS10.8590.91713.7410.5030.5030.0000.0000.0000.000
202G202THR0-0.022-0.01312.855-0.138-0.1380.0000.0000.0000.000
203G203THR0-0.038-0.00813.9260.0710.0710.0000.0000.0000.000
204G204SER0-0.078-0.0739.1260.0810.0810.0000.0000.0000.000
205G205ASP-1-0.736-0.8175.156-2.108-2.1080.0000.0000.0000.000
206G206PHE0-0.010-0.0165.652-0.385-0.3850.0000.0000.0000.000
207G207ALA00.000-0.0016.7910.1110.1110.0000.0000.0000.000
208G208LYS10.8810.9378.5591.5191.5190.0000.0000.0000.000
209G209ALA00.000-0.0025.7060.1740.1740.0000.0000.0000.000
210G210VAL0-0.011-0.0097.6930.3380.3380.0000.0000.0000.000
211G211PHE0-0.056-0.01910.5230.2220.2220.0000.0000.0000.000
212G212GLU-1-0.789-0.8518.662-1.071-1.0710.0000.0000.0000.000
213G213ASP-1-0.892-0.9379.597-0.525-0.5250.0000.0000.0000.000