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: 9GK52

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2604010.877695
FMO2-HF: Nuclear repulsion 2516462.441592
FMO2-HF: Total energy -87548.436103
FMO2-MP2: Total energy -87807.839579


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.
-28.25-16.45317.785-9.355-20.225-0.033
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 : -0.028 / q_NPA : -0.004
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].
3G3LEU00.0000.0123.291-3.878-0.9160.068-1.294-1.735-0.002
4G4ARG10.9100.9685.1701.9802.105-0.001-0.010-0.1140.000
5G5VAL0-0.036-0.0167.6750.3440.3440.0000.0000.0000.000
6G6GLU-1-0.856-0.9447.218-1.245-1.2450.0000.0000.0000.000
7G7ASN0-0.035-0.0088.9970.0560.0560.0000.0000.0000.000
8G8PRO0-0.040-0.0058.8970.0750.0750.0000.0000.0000.000
9G9LYS10.9540.98511.9300.2770.2770.0000.0000.0000.000
10G10LYS10.9640.97114.258-0.055-0.0550.0000.0000.0000.000
11G11ALA0-0.0070.01613.275-0.028-0.0280.0000.0000.0000.000
12G12GLN0-0.050-0.02915.3320.0510.0510.0000.0000.0000.000
13G13LYS10.9550.98916.512-0.103-0.1030.0000.0000.0000.000
14G14HIS00.014-0.00618.8520.0110.0110.0000.0000.0000.000
15G15PHE0-0.064-0.03220.2250.0100.0100.0000.0000.0000.000
16G16VAL00.0590.04119.5590.0020.0020.0000.0000.0000.000
17G17GLN00.0240.00117.338-0.015-0.0150.0000.0000.0000.000
18G18ASN0-0.024-0.02018.923-0.002-0.0020.0000.0000.0000.000
19G19LEU0-0.0160.01021.883-0.001-0.0010.0000.0000.0000.000
20G20ASN00.0220.00021.918-0.009-0.0090.0000.0000.0000.000
21G21ASN0-0.037-0.02624.142-0.005-0.0050.0000.0000.0000.000
22G22VAL00.0490.03021.0550.0020.0020.0000.0000.0000.000
23G23VAL0-0.071-0.02521.101-0.010-0.0100.0000.0000.0000.000
24G24PHE00.0470.02523.9070.0080.0080.0000.0000.0000.000
25G25THR00.0170.00726.551-0.010-0.0100.0000.0000.0000.000
26G26ASN00.047-0.00228.430-0.002-0.0020.0000.0000.0000.000
27G27LYS10.9150.98430.4960.0780.0780.0000.0000.0000.000
28G28GLU-1-0.803-0.89429.857-0.092-0.0920.0000.0000.0000.000
29G29LEU0-0.021-0.01026.5500.0000.0000.0000.0000.0000.000
30G30GLU-1-0.931-0.98031.113-0.113-0.1130.0000.0000.0000.000
31G31ASP-1-0.922-0.96234.311-0.075-0.0750.0000.0000.0000.000
32G32ILE0-0.035-0.01230.9870.0030.0030.0000.0000.0000.000
33G33TYR00.006-0.01828.495-0.001-0.0010.0000.0000.0000.000
34G34ASN0-0.023-0.00335.2250.0000.0000.0000.0000.0000.000
35G35LEU0-0.0090.00236.9180.0050.0050.0000.0000.0000.000
36G36SER0-0.082-0.04136.8250.0010.0010.0000.0000.0000.000
37G37ASN0-0.104-0.05339.168-0.001-0.0010.0000.0000.0000.000
38G38LYS10.9640.98841.9200.0720.0720.0000.0000.0000.000
39G39GLU-1-0.879-0.93742.131-0.085-0.0850.0000.0000.0000.000
40G40GLU-1-0.866-0.95442.370-0.077-0.0770.0000.0000.0000.000
41G41THR0-0.046-0.03937.648-0.004-0.0040.0000.0000.0000.000
42G42LYS10.9210.95437.7130.0740.0740.0000.0000.0000.000
43G43GLU-1-0.948-0.95836.206-0.118-0.1180.0000.0000.0000.000
44G44VAL00.0680.00133.187-0.009-0.0090.0000.0000.0000.000
45G45LEU00.0220.01732.838-0.011-0.0110.0000.0000.0000.000
46G46LYS10.9410.97032.3320.1060.1060.0000.0000.0000.000
47G47LEU0-0.0100.01829.759-0.012-0.0120.0000.0000.0000.000
48G48PHE00.0130.00328.247-0.016-0.0160.0000.0000.0000.000
49G49LYS10.9530.97627.7030.1100.1100.0000.0000.0000.000
50G50LEU0-0.022-0.00525.960-0.012-0.0120.0000.0000.0000.000
51G51LYS10.8400.90421.4920.2770.2770.0000.0000.0000.000
52G52VAL00.0460.04122.778-0.022-0.0220.0000.0000.0000.000
53G53ASN00.000-0.00122.704-0.011-0.0110.0000.0000.0000.000
54G54GLN00.0050.01018.2370.0160.0160.0000.0000.0000.000
55G55PHE00.0220.00118.469-0.046-0.0460.0000.0000.0000.000
56G56TYR0-0.007-0.03718.184-0.026-0.0260.0000.0000.0000.000
57G57ARG10.9070.95517.1470.3040.3040.0000.0000.0000.000
58G58HIS0-0.038-0.02012.262-0.012-0.0120.0000.0000.0000.000
59G59ALA00.005-0.01113.367-0.061-0.0610.0000.0000.0000.000
60G60PHE0-0.004-0.03913.609-0.014-0.0140.0000.0000.0000.000
61G61GLY00.0200.01712.4570.0000.0000.0000.0000.0000.000
62G62ILE00.0060.0058.849-0.104-0.1040.0000.0000.0000.000
63G63VAL0-0.0070.0239.1270.0150.0150.0000.0000.0000.000
64G64ASN0-0.062-0.05211.1180.1220.1220.0000.0000.0000.000
65G65ASP-1-0.801-0.9086.379-0.984-0.9840.0000.0000.0000.000
66G66TYR0-0.026-0.0282.283-0.826-0.5110.975-0.209-1.080-0.001
67G67ASN0-0.102-0.0356.8100.2810.2810.0000.0000.0000.000
68G68GLY00.017-0.0018.1900.0490.0490.0000.0000.0000.000
69G69LEU0-0.066-0.0165.5860.1730.1730.0000.0000.0000.000
70G70LEU00.0600.0038.146-0.168-0.1680.0000.0000.0000.000
71G71GLU-1-0.937-0.96710.7770.2500.2500.0000.0000.0000.000
72G72TYR00.0110.0159.506-0.087-0.0870.0000.0000.0000.000
73G73LYS10.9500.98111.068-0.028-0.0280.0000.0000.0000.000
74G74GLU-1-0.802-0.90514.555-0.066-0.0660.0000.0000.0000.000
75G75ILE00.0010.00610.059-0.018-0.0180.0000.0000.0000.000
76G76PHE0-0.012-0.00514.078-0.028-0.0280.0000.0000.0000.000
77G77ASN00.015-0.02515.370-0.021-0.0210.0000.0000.0000.000
78G78MET0-0.026-0.00217.3290.0070.0070.0000.0000.0000.000
79G79MET0-0.0610.01013.914-0.013-0.0130.0000.0000.0000.000
80G80PHE00.0480.00318.6450.0030.0030.0000.0000.0000.000
81G81LEU0-0.0070.00921.5790.0130.0130.0000.0000.0000.000
82G82LYS10.9220.96118.5720.1980.1980.0000.0000.0000.000
83G83LEU0-0.0020.01822.7490.0060.0060.0000.0000.0000.000
84G84SER00.011-0.00324.5460.0090.0090.0000.0000.0000.000
85G85VAL0-0.0150.00926.8690.0070.0070.0000.0000.0000.000
86G86VAL0-0.026-0.00625.6600.0050.0050.0000.0000.0000.000
87G87PHE00.013-0.00927.2830.0040.0040.0000.0000.0000.000
88G88ASP-1-0.899-0.95630.666-0.077-0.0770.0000.0000.0000.000
89G89THR0-0.033-0.00932.1560.0080.0080.0000.0000.0000.000
90G90GLN00.0390.02531.848-0.002-0.0020.0000.0000.0000.000
91G91ARG10.8650.92231.7580.0920.0920.0000.0000.0000.000
92G92LYS10.9040.95936.4770.0740.0740.0000.0000.0000.000
93G93GLU-1-0.876-0.93036.482-0.074-0.0740.0000.0000.0000.000
94G94ALA00.0170.02137.055-0.005-0.0050.0000.0000.0000.000
95G95ASN00.0280.01238.125-0.006-0.0060.0000.0000.0000.000
96G96ASN0-0.0250.01337.831-0.001-0.0010.0000.0000.0000.000
97G97VAL00.0790.01736.806-0.006-0.0060.0000.0000.0000.000
98G98GLU-1-0.820-0.92035.229-0.116-0.1160.0000.0000.0000.000
99G99GLN0-0.0010.00233.076-0.012-0.0120.0000.0000.0000.000
100G100ILE0-0.009-0.00332.170-0.008-0.0080.0000.0000.0000.000
101G101LYS10.8990.95430.7760.1060.1060.0000.0000.0000.000
102G102ARG10.8980.95726.3150.1420.1420.0000.0000.0000.000
103G103ASN00.0630.00528.122-0.011-0.0110.0000.0000.0000.000
104G104ILE0-0.033-0.00625.544-0.015-0.0150.0000.0000.0000.000
105G105ALA00.0000.00124.582-0.019-0.0190.0000.0000.0000.000
106G106ILE0-0.0160.00123.582-0.017-0.0170.0000.0000.0000.000
107G107LEU00.0160.00422.261-0.014-0.0140.0000.0000.0000.000
108G108ASP-1-0.822-0.91119.747-0.330-0.3300.0000.0000.0000.000
109G109GLU-1-0.892-0.94318.472-0.237-0.2370.0000.0000.0000.000
110G110ILE0-0.066-0.02318.354-0.016-0.0160.0000.0000.0000.000
111G111MET0-0.0280.00815.774-0.021-0.0210.0000.0000.0000.000
112G112ALA00.0260.01914.135-0.067-0.0670.0000.0000.0000.000
113G113LYS10.7740.87813.8670.1800.1800.0000.0000.0000.000
114G114ALA00.0250.00913.1290.0170.0170.0000.0000.0000.000
115G115ASP-1-0.802-0.9059.745-0.880-0.8800.0000.0000.0000.000
116G116ASN0-0.046-0.0319.087-0.133-0.1330.0000.0000.0000.000
117G117ASP-1-0.820-0.93410.347-0.223-0.2230.0000.0000.0000.000
118G118LEU00.0000.0025.6360.1440.1440.0000.0000.0000.000
119G119SER00.001-0.0125.618-0.017-0.0170.0000.0000.0000.000
120G120TYR00.0470.0216.7050.2430.2430.0000.0000.0000.000
121G121PHE00.0330.0098.8610.1440.1440.0000.0000.0000.000
122G122ILE00.0030.0172.380-0.4910.0551.955-0.349-2.1520.004
123G123SER0-0.096-0.0485.7460.6690.6690.0000.0000.0000.000
124G124GLN0-0.052-0.0246.829-0.073-0.0730.0000.0000.0000.000
125G125ASN00.0060.0287.683-0.028-0.0280.0000.0000.0000.000
126G126LYS10.9900.9814.9840.0810.0810.0000.0000.0000.000
127G127ASN00.0230.0276.4860.4650.4650.0000.0000.0000.000
128G128PHE00.014-0.0072.430-0.5870.1830.391-0.231-0.930-0.001
129G129GLN00.0380.0002.038-3.227-1.8736.100-3.285-4.1690.019
130G130GLU-1-0.898-0.9393.6650.324-0.2190.1221.475-1.054-0.007
131G131LEU0-0.046-0.0265.845-0.340-0.3400.0000.0000.0000.000
132G132TRP00.010-0.0022.621-4.809-4.5287.231-2.119-5.393-0.008
133G133ASP-1-0.812-0.9212.681-12.649-6.6850.945-3.327-3.583-0.037
134G134LYS10.7270.8355.150-0.875-0.852-0.001-0.006-0.0150.000
135G135ALA00.0160.0088.147-0.235-0.2350.0000.0000.0000.000
136G136VAL00.0270.0285.437-0.156-0.1560.0000.0000.0000.000
137G137LYS10.9090.9668.428-0.314-0.3140.0000.0000.0000.000
138G138LEU0-0.049-0.04310.476-0.028-0.0280.0000.0000.0000.000
139G139THR00.004-0.01211.565-0.023-0.0230.0000.0000.0000.000
140G140LYS10.8290.91010.2040.3890.3890.0000.0000.0000.000
141G141GLU-1-0.918-0.97313.8460.1200.1200.0000.0000.0000.000
142G142MET0-0.0160.00516.0850.0120.0120.0000.0000.0000.000
143G143LYS10.9671.00416.4440.1930.1930.0000.0000.0000.000
144G144ILE0-0.0020.04418.3560.0000.0000.0000.0000.0000.000
145G145LYS10.9010.96419.461-0.060-0.0600.0000.0000.0000.000
146G146LEU00.030-0.01519.7470.0050.0050.0000.0000.0000.000
147G147LYS10.9230.98023.4890.0370.0370.0000.0000.0000.000
148G148GLY00.0390.02225.224-0.006-0.0060.0000.0000.0000.000
149G149GLN0-0.059-0.00925.8120.0130.0130.0000.0000.0000.000
150G150LYS10.9860.98827.7230.0200.0200.0000.0000.0000.000
151G151LEU00.0250.00323.3420.0060.0060.0000.0000.0000.000
152G152ASP-1-0.866-0.92627.156-0.056-0.0560.0000.0000.0000.000
153G153LEU0-0.013-0.03123.7390.0020.0020.0000.0000.0000.000
154G154ARG10.9030.95426.9380.0720.0720.0000.0000.0000.000
155G155ASP-1-0.892-0.91928.840-0.024-0.0240.0000.0000.0000.000
156G156GLY00.0720.02528.4320.0020.0020.0000.0000.0000.000
157G157GLU-1-0.942-0.96824.576-0.008-0.0080.0000.0000.0000.000
158G158VAL00.0300.01824.8980.0090.0090.0000.0000.0000.000
159G159ALA00.005-0.00620.0200.0060.0060.0000.0000.0000.000
160G160ILE00.0300.00219.4500.0150.0150.0000.0000.0000.000
161G161ASN00.0410.02321.5480.0270.0270.0000.0000.0000.000
162G162LYS10.9190.95322.6530.0170.0170.0000.0000.0000.000
163G163VAL0-0.025-0.00117.5550.0080.0080.0000.0000.0000.000
164G164ARG10.8910.92720.471-0.075-0.0750.0000.0000.0000.000
165G165GLU-1-0.888-0.92122.7910.0240.0240.0000.0000.0000.000
166G166LEU0-0.027-0.01020.4440.0050.0050.0000.0000.0000.000
167G167PHE0-0.011-0.02217.2870.0130.0130.0000.0000.0000.000
168G168GLY00.0100.01620.1880.0250.0250.0000.0000.0000.000
169G169SER0-0.090-0.04321.9770.0070.0070.0000.0000.0000.000
170G170ASP-1-0.801-0.89515.7330.3400.3400.0000.0000.0000.000
171G171LYS10.9700.96917.943-0.211-0.2110.0000.0000.0000.000
172G172ASN00.0910.05813.0710.0400.0400.0000.0000.0000.000
173G173VAL00.0140.01615.469-0.004-0.0040.0000.0000.0000.000
174G174LYS10.8710.93117.013-0.183-0.1830.0000.0000.0000.000
175G175GLU-1-0.909-0.95617.6940.2740.2740.0000.0000.0000.000
176G176LEU0-0.0280.00412.2260.0030.0030.0000.0000.0000.000
177G177TRP00.0090.01014.9860.0000.0000.0000.0000.0000.000
178G178TRP00.0880.0236.963-0.129-0.1290.0000.0000.0000.000
179G179PHE00.0540.0359.989-0.042-0.0420.0000.0000.0000.000
180G180ARG10.9290.95612.124-0.221-0.2210.0000.0000.0000.000
181G181SER0-0.023-0.02213.125-0.057-0.0570.0000.0000.0000.000
182G182LEU00.0460.0218.032-0.062-0.0620.0000.0000.0000.000
183G183LEU00.0130.01111.640-0.069-0.0690.0000.0000.0000.000
184G184VAL0-0.022-0.00714.232-0.043-0.0430.0000.0000.0000.000
185G185LYS10.9540.97611.9410.2730.2730.0000.0000.0000.000
186G186GLY00.0360.02813.996-0.044-0.0440.0000.0000.0000.000
187G187VAL00.0020.01414.526-0.013-0.0130.0000.0000.0000.000
188G188TYR0-0.053-0.03717.7530.0020.0020.0000.0000.0000.000
189G189LEU0-0.017-0.00612.610-0.006-0.0060.0000.0000.0000.000
190G190ILE00.006-0.01015.644-0.005-0.0050.0000.0000.0000.000
191G191LYS10.7830.89518.5650.0970.0970.0000.0000.0000.000
192G192ARG10.9760.99018.5960.1960.1960.0000.0000.0000.000
193G193TYR00.0230.02218.6350.0020.0020.0000.0000.0000.000
194G194TYR0-0.120-0.11220.5280.0080.0080.0000.0000.0000.000
195G195GLU-1-0.945-0.96723.356-0.108-0.1080.0000.0000.0000.000
196G196GLY0-0.0310.00124.7940.0050.0050.0000.0000.0000.000
197G197ASP-1-0.826-0.92920.937-0.250-0.2500.0000.0000.0000.000
198G198ILE0-0.071-0.04819.279-0.025-0.0250.0000.0000.0000.000
199G199GLU-1-0.855-0.91718.646-0.329-0.3290.0000.0000.0000.000
200G200LEU0-0.065-0.04015.813-0.054-0.0540.0000.0000.0000.000
201G201LYS10.9120.95914.2990.2680.2680.0000.0000.0000.000
202G202THR0-0.027-0.01212.901-0.115-0.1150.0000.0000.0000.000
203G203THR0-0.0140.00913.4880.0490.0490.0000.0000.0000.000
204G204SER0-0.032-0.0329.8080.0540.0540.0000.0000.0000.000
205G205ASP-1-0.802-0.9044.975-2.241-2.2410.0000.0000.0000.000
206G206PHE0-0.044-0.0226.282-0.309-0.3090.0000.0000.0000.000
207G207ALA00.001-0.0047.4480.0820.0820.0000.0000.0000.000
208G208LYS10.9350.9818.7621.3371.3370.0000.0000.0000.000
209G209ALA00.0030.0185.9540.0630.0630.0000.0000.0000.000
210G210VAL00.011-0.0037.8260.2970.2970.0000.0000.0000.000
211G211PHE0-0.144-0.06610.5530.1590.1590.0000.0000.0000.000
212G212GLU-1-0.857-0.9409.303-0.870-0.8700.0000.0000.0000.000
213G213ASP-1-0.952-0.95811.134-0.234-0.2340.0000.0000.0000.000