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: M3JKZ

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2601935.220674
FMO2-HF: Nuclear repulsion 2514384.590512
FMO2-HF: Total energy -87550.630162
FMO2-MP2: Total energy -87809.822054


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.
-31.976-21.35518.518-8.8-20.337-0.036
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 : -0.034 / q_NPA : -0.012
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].
3G3LEU0-0.0150.0093.212-3.729-0.6650.099-1.349-1.814-0.002
4G4ARG10.7820.8615.0681.2901.405-0.001-0.008-0.1060.000
5G5VAL0-0.031-0.0177.5930.1630.1630.0000.0000.0000.000
6G6GLU-1-0.856-0.9447.125-0.295-0.2950.0000.0000.0000.000
7G7ASN0-0.051-0.0199.0640.1260.1260.0000.0000.0000.000
8G8PRO0-0.0220.0109.090-0.052-0.0520.0000.0000.0000.000
9G9LYS10.9540.97812.211-0.060-0.0600.0000.0000.0000.000
10G10LYS10.9760.98214.820-0.344-0.3440.0000.0000.0000.000
11G11ALA0-0.0100.01513.755-0.063-0.0630.0000.0000.0000.000
12G12GLN0-0.058-0.03215.8600.0280.0280.0000.0000.0000.000
13G13LYS10.8560.92516.053-0.380-0.3800.0000.0000.0000.000
14G14HIS00.005-0.02219.348-0.019-0.0190.0000.0000.0000.000
15G15PHE0-0.049-0.01920.686-0.008-0.0080.0000.0000.0000.000
16G16VAL00.0530.02719.869-0.018-0.0180.0000.0000.0000.000
17G17GLN00.002-0.00117.745-0.001-0.0010.0000.0000.0000.000
18G18ASN0-0.001-0.00819.216-0.003-0.0030.0000.0000.0000.000
19G19LEU0-0.0120.01422.119-0.012-0.0120.0000.0000.0000.000
20G20ASN00.014-0.01022.085-0.010-0.0100.0000.0000.0000.000
21G21ASN0-0.018-0.01324.268-0.002-0.0020.0000.0000.0000.000
22G22VAL00.0520.03121.2690.0030.0030.0000.0000.0000.000
23G23VAL0-0.066-0.02021.128-0.006-0.0060.0000.0000.0000.000
24G24PHE00.0180.02223.9640.0030.0030.0000.0000.0000.000
25G25THR00.010-0.02026.542-0.016-0.0160.0000.0000.0000.000
26G26ASN00.035-0.00728.0140.0000.0000.0000.0000.0000.000
27G27LYS10.8230.90530.4280.0680.0680.0000.0000.0000.000
28G28GLU-1-0.755-0.85730.465-0.066-0.0660.0000.0000.0000.000
29G29LEU0-0.028-0.01226.5060.0020.0020.0000.0000.0000.000
30G30GLU-1-0.835-0.93031.043-0.105-0.1050.0000.0000.0000.000
31G31ASP-1-0.831-0.88134.182-0.059-0.0590.0000.0000.0000.000
32G32ILE0-0.025-0.01031.0130.0050.0050.0000.0000.0000.000
33G33TYR00.016-0.01028.4310.0000.0000.0000.0000.0000.000
34G34ASN0-0.041-0.02334.8990.0020.0020.0000.0000.0000.000
35G35LEU00.0080.02036.7140.0050.0050.0000.0000.0000.000
36G36SER0-0.081-0.05836.5030.0020.0020.0000.0000.0000.000
37G37ASN0-0.096-0.05438.751-0.002-0.0020.0000.0000.0000.000
38G38LYS10.9440.95941.4990.0500.0500.0000.0000.0000.000
39G39GLU-1-0.830-0.89441.710-0.073-0.0730.0000.0000.0000.000
40G40GLU-1-0.824-0.91841.965-0.056-0.0560.0000.0000.0000.000
41G41THR0-0.041-0.03437.195-0.002-0.0020.0000.0000.0000.000
42G42LYS10.8300.89637.2720.0640.0640.0000.0000.0000.000
43G43GLU-1-0.963-0.96835.756-0.096-0.0960.0000.0000.0000.000
44G44VAL00.0580.01632.741-0.009-0.0090.0000.0000.0000.000
45G45LEU00.0110.01532.390-0.008-0.0080.0000.0000.0000.000
46G46LYS10.9510.97531.9590.0960.0960.0000.0000.0000.000
47G47LEU00.0030.00428.842-0.013-0.0130.0000.0000.0000.000
48G48PHE00.0120.00227.846-0.014-0.0140.0000.0000.0000.000
49G49LYS10.8900.94427.2920.1000.1000.0000.0000.0000.000
50G50LEU0-0.0130.00925.699-0.015-0.0150.0000.0000.0000.000
51G51LYS10.8240.88521.5680.1960.1960.0000.0000.0000.000
52G52VAL00.0600.04422.372-0.017-0.0170.0000.0000.0000.000
53G53ASN0-0.036-0.02822.379-0.021-0.0210.0000.0000.0000.000
54G54GLN0-0.0170.00417.896-0.003-0.0030.0000.0000.0000.000
55G55PHE00.038-0.00218.172-0.043-0.0430.0000.0000.0000.000
56G56TYR0-0.020-0.04317.886-0.016-0.0160.0000.0000.0000.000
57G57ARG10.8870.93717.1250.3100.3100.0000.0000.0000.000
58G58HIS0-0.010-0.00312.198-0.079-0.0790.0000.0000.0000.000
59G59ALA00.0100.00513.126-0.048-0.0480.0000.0000.0000.000
60G60PHE00.011-0.02113.610-0.011-0.0110.0000.0000.0000.000
61G61GLY00.0300.02612.383-0.035-0.0350.0000.0000.0000.000
62G62ILE00.0090.0048.820-0.158-0.1580.0000.0000.0000.000
63G63VAL00.0000.0209.085-0.007-0.0070.0000.0000.0000.000
64G64ASN0-0.035-0.03410.9760.0480.0480.0000.0000.0000.000
65G65ASP-1-0.743-0.8746.261-1.539-1.5390.0000.0000.0000.000
66G66TYR0-0.024-0.0462.221-1.137-0.9481.643-0.369-1.4620.002
67G67ASN0-0.102-0.0336.7540.3890.3890.0000.0000.0000.000
68G68GLY00.022-0.0058.1050.0640.0640.0000.0000.0000.000
69G69LEU0-0.064-0.0216.2710.2160.2160.0000.0000.0000.000
70G70LEU00.0540.0068.381-0.202-0.2020.0000.0000.0000.000
71G71GLU-1-0.866-0.92411.2520.5100.5100.0000.0000.0000.000
72G72TYR00.0240.0269.801-0.112-0.1120.0000.0000.0000.000
73G73LYS10.9050.95711.321-0.115-0.1150.0000.0000.0000.000
74G74GLU-1-0.775-0.87614.9980.1350.1350.0000.0000.0000.000
75G75ILE00.0030.00210.484-0.030-0.0300.0000.0000.0000.000
76G76PHE0-0.011-0.00314.200-0.044-0.0440.0000.0000.0000.000
77G77ASN0-0.031-0.05015.571-0.037-0.0370.0000.0000.0000.000
78G78MET00.0000.00917.635-0.012-0.0120.0000.0000.0000.000
79G79MET0-0.075-0.00813.812-0.021-0.0210.0000.0000.0000.000
80G80PHE00.0520.00718.823-0.009-0.0090.0000.0000.0000.000
81G81LEU00.0000.01221.7710.0040.0040.0000.0000.0000.000
82G82LYS10.9330.96618.227-0.012-0.0120.0000.0000.0000.000
83G83LEU0-0.0040.01522.5870.0000.0000.0000.0000.0000.000
84G84SER00.0260.00624.434-0.001-0.0010.0000.0000.0000.000
85G85VAL0-0.026-0.00226.8570.0020.0020.0000.0000.0000.000
86G86VAL0-0.026-0.00725.4270.0000.0000.0000.0000.0000.000
87G87PHE00.007-0.01727.129-0.002-0.0020.0000.0000.0000.000
88G88ASP-1-0.843-0.90330.483-0.025-0.0250.0000.0000.0000.000
89G89THR0-0.027-0.01132.0450.0040.0040.0000.0000.0000.000
90G90GLN00.0380.02731.553-0.001-0.0010.0000.0000.0000.000
91G91ARG10.8460.89232.0540.0440.0440.0000.0000.0000.000
92G92LYS10.8930.95935.9620.0240.0240.0000.0000.0000.000
93G93GLU-1-0.840-0.89136.203-0.036-0.0360.0000.0000.0000.000
94G94ALA00.0300.02936.732-0.005-0.0050.0000.0000.0000.000
95G95ASN00.0280.02337.770-0.008-0.0080.0000.0000.0000.000
96G96ASN0-0.0160.00237.796-0.002-0.0020.0000.0000.0000.000
97G97VAL00.0600.00736.499-0.003-0.0030.0000.0000.0000.000
98G98GLU-1-0.757-0.86934.939-0.071-0.0710.0000.0000.0000.000
99G99GLN0-0.030-0.01833.541-0.005-0.0050.0000.0000.0000.000
100G100ILE0-0.016-0.00631.887-0.004-0.0040.0000.0000.0000.000
101G101LYS10.8220.89730.4810.0640.0640.0000.0000.0000.000
102G102ARG10.8560.91025.8190.0540.0540.0000.0000.0000.000
103G103ASN00.0460.00227.9540.0020.0020.0000.0000.0000.000
104G104ILE0-0.029-0.00425.392-0.010-0.0100.0000.0000.0000.000
105G105ALA00.0070.00324.312-0.013-0.0130.0000.0000.0000.000
106G106ILE0-0.024-0.00223.432-0.004-0.0040.0000.0000.0000.000
107G107LEU00.0070.00621.9270.0000.0000.0000.0000.0000.000
108G108ASP-1-0.800-0.88219.466-0.233-0.2330.0000.0000.0000.000
109G109GLU-1-0.846-0.90018.301-0.081-0.0810.0000.0000.0000.000
110G110ILE0-0.043-0.01818.3340.0150.0150.0000.0000.0000.000
111G111MET0-0.0140.02115.436-0.003-0.0030.0000.0000.0000.000
112G112ALA00.0140.01113.990-0.026-0.0260.0000.0000.0000.000
113G113LYS10.7600.85513.912-0.115-0.1150.0000.0000.0000.000
114G114ALA00.0250.00513.0910.0680.0680.0000.0000.0000.000
115G115ASP-1-0.743-0.8569.659-0.536-0.5360.0000.0000.0000.000
116G116ASN0-0.049-0.0319.2320.0570.0570.0000.0000.0000.000
117G117ASP-1-0.796-0.89210.7460.3270.3270.0000.0000.0000.000
118G118LEU0-0.014-0.0015.9750.2150.2150.0000.0000.0000.000
119G119SER00.016-0.0156.0980.3820.3820.0000.0000.0000.000
120G120TYR00.015-0.0067.1750.4740.4740.0000.0000.0000.000
121G121PHE00.0340.0049.5540.1580.1580.0000.0000.0000.000
122G122ILE00.0000.0182.8570.155-0.3033.096-0.452-2.1860.005
123G123SER0-0.074-0.0395.8670.5690.5690.0000.0000.0000.000
124G124GLN0-0.038-0.0186.834-0.636-0.6360.0000.0000.0000.000
125G125ASN00.0010.0147.766-0.351-0.3510.0000.0000.0000.000
126G126LYS10.9700.9675.113-0.523-0.5230.0000.0000.0000.000
127G127ASN00.0430.0316.5220.2220.2220.0000.0000.0000.000
128G128PHE00.0120.0012.529-1.118-0.2250.323-0.251-0.9640.000
129G129GLN00.0760.0331.876-4.375-4.1777.934-3.254-4.8780.010
130G130GLU-1-0.902-0.9403.601-0.789-1.5000.0191.308-0.617-0.003
131G131LEU0-0.053-0.0265.789-0.652-0.6520.0000.0000.0000.000
132G132TRP0-0.001-0.0062.573-5.575-3.8074.484-1.356-4.896-0.013
133G133ASP-1-0.807-0.9192.697-15.314-9.7750.922-3.067-3.393-0.035
134G134LYS10.7490.8445.1790.0940.118-0.001-0.002-0.0210.000
135G135ALA00.0120.0097.8750.0220.0220.0000.0000.0000.000
136G136VAL00.0330.0325.4640.1600.1600.0000.0000.0000.000
137G137LYS10.8650.9338.4890.5110.5110.0000.0000.0000.000
138G138LEU0-0.047-0.04210.5980.1020.1020.0000.0000.0000.000
139G139THR00.011-0.00911.3350.1090.1090.0000.0000.0000.000
140G140LYS10.8370.9169.9881.1491.1490.0000.0000.0000.000
141G141GLU-1-0.849-0.91713.985-0.190-0.1900.0000.0000.0000.000
142G142MET0-0.031-0.00815.3280.0780.0780.0000.0000.0000.000
143G143LYS10.9290.98416.5060.4920.4920.0000.0000.0000.000
144G144ILE00.0000.02218.4390.0370.0370.0000.0000.0000.000
145G145LYS10.8720.94719.0920.2550.2550.0000.0000.0000.000
146G146LEU00.022-0.01819.6110.0160.0160.0000.0000.0000.000
147G147LYS10.9340.98623.3400.1990.1990.0000.0000.0000.000
148G148GLY00.0360.02225.240-0.001-0.0010.0000.0000.0000.000
149G149GLN0-0.053-0.01125.0200.0300.0300.0000.0000.0000.000
150G150LYS10.9820.98627.2160.1150.1150.0000.0000.0000.000
151G151LEU00.004-0.00722.6930.0000.0000.0000.0000.0000.000
152G152ASP-1-0.788-0.86826.724-0.160-0.1600.0000.0000.0000.000
153G153LEU00.000-0.01823.331-0.003-0.0030.0000.0000.0000.000
154G154ARG10.7930.87526.6520.1650.1650.0000.0000.0000.000
155G155ASP-1-0.923-0.95728.545-0.108-0.1080.0000.0000.0000.000
156G156GLY00.0700.03228.031-0.006-0.0060.0000.0000.0000.000
157G157GLU-1-0.945-0.97323.911-0.128-0.1280.0000.0000.0000.000
158G158VAL00.0510.02824.523-0.003-0.0030.0000.0000.0000.000
159G159ALA00.0060.00019.694-0.005-0.0050.0000.0000.0000.000
160G160ILE00.037-0.00418.735-0.006-0.0060.0000.0000.0000.000
161G161ASN00.0110.01221.0890.0180.0180.0000.0000.0000.000
162G162LYS10.8650.89922.1750.1720.1720.0000.0000.0000.000
163G163VAL0-0.018-0.00317.179-0.008-0.0080.0000.0000.0000.000
164G164ARG10.8890.93119.9600.0770.0770.0000.0000.0000.000
165G165GLU-1-0.845-0.87622.400-0.135-0.1350.0000.0000.0000.000
166G166LEU0-0.031-0.00620.5330.0070.0070.0000.0000.0000.000
167G167PHE0-0.004-0.02217.2870.0010.0010.0000.0000.0000.000
168G168GLY00.0160.01720.3280.0220.0220.0000.0000.0000.000
169G169SER0-0.079-0.03822.2160.0160.0160.0000.0000.0000.000
170G170ASP-1-0.816-0.91516.2210.0160.0160.0000.0000.0000.000
171G171LYS10.9810.98118.024-0.056-0.0560.0000.0000.0000.000
172G172ASN00.0870.06113.535-0.003-0.0030.0000.0000.0000.000
173G173VAL00.0190.02115.6770.0020.0020.0000.0000.0000.000
174G174LYS10.9140.95716.850-0.029-0.0290.0000.0000.0000.000
175G175GLU-1-0.913-0.94817.5530.1440.1440.0000.0000.0000.000
176G176LEU0-0.0150.00512.0240.0180.0180.0000.0000.0000.000
177G177TRP00.0320.02414.778-0.041-0.0410.0000.0000.0000.000
178G178TRP00.0810.0246.853-0.128-0.1280.0000.0000.0000.000
179G179PHE00.0430.02910.446-0.126-0.1260.0000.0000.0000.000
180G180ARG10.8370.90111.808-0.084-0.0840.0000.0000.0000.000
181G181SER0-0.017-0.01912.680-0.042-0.0420.0000.0000.0000.000
182G182LEU00.0120.0087.712-0.016-0.0160.0000.0000.0000.000
183G183LEU00.0300.01911.169-0.068-0.0680.0000.0000.0000.000
184G184VAL0-0.017-0.00113.777-0.014-0.0140.0000.0000.0000.000
185G185LYS10.8340.91811.6180.6120.6120.0000.0000.0000.000
186G186GLY00.0430.02413.598-0.027-0.0270.0000.0000.0000.000
187G187VAL0-0.0020.00514.1140.0170.0170.0000.0000.0000.000
188G188TYR0-0.036-0.02017.4380.0300.0300.0000.0000.0000.000
189G189LEU0-0.0070.00212.4730.0170.0170.0000.0000.0000.000
190G190ILE0-0.017-0.01715.0350.0150.0150.0000.0000.0000.000
191G191LYS10.7640.86718.1220.2740.2740.0000.0000.0000.000
192G192ARG10.9960.98718.5950.4020.4020.0000.0000.0000.000
193G193TYR00.0130.03318.2020.0060.0060.0000.0000.0000.000
194G194TYR0-0.087-0.08320.2000.0220.0220.0000.0000.0000.000
195G195GLU-1-0.854-0.89222.950-0.228-0.2280.0000.0000.0000.000
196G196GLY0-0.0280.00324.4840.0150.0150.0000.0000.0000.000
197G197ASP-1-0.822-0.92421.205-0.384-0.3840.0000.0000.0000.000
198G198ILE0-0.074-0.05319.288-0.050-0.0500.0000.0000.0000.000
199G199GLU-1-0.843-0.90618.488-0.453-0.4530.0000.0000.0000.000
200G200LEU0-0.057-0.03615.665-0.077-0.0770.0000.0000.0000.000
201G201LYS10.8420.91214.1370.5290.5290.0000.0000.0000.000
202G202THR0-0.033-0.01412.802-0.159-0.1590.0000.0000.0000.000
203G203THR0-0.0140.00313.4000.1000.1000.0000.0000.0000.000
204G204SER0-0.055-0.0539.3300.0810.0810.0000.0000.0000.000
205G205ASP-1-0.733-0.8235.146-2.311-2.3110.0000.0000.0000.000
206G206PHE0-0.062-0.0316.091-0.520-0.5200.0000.0000.0000.000
207G207ALA00.001-0.0047.2310.0510.0510.0000.0000.0000.000
208G208LYS10.9040.9588.7191.5761.5760.0000.0000.0000.000
209G209ALA0-0.0010.0145.6760.1050.1050.0000.0000.0000.000
210G210VAL00.001-0.0077.7630.3390.3390.0000.0000.0000.000
211G211PHE0-0.063-0.02410.5150.2310.2310.0000.0000.0000.000
212G212GLU-1-0.810-0.8949.058-1.239-1.2390.0000.0000.0000.000
213G213ASP-1-0.937-0.94711.231-0.571-0.5710.0000.0000.0000.000