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

tag_button

FMODB ID: 3N56L

Calculation Name: 2ICW-G-Xray311

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2603675.465846
FMO2-HF: Nuclear repulsion 2516127.60028
FMO2-HF: Total energy -87547.865566
FMO2-MP2: Total energy -87807.247824


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.
-28.762-16.8217.757-9.46-20.237-0.033
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].
3G3LEU 0-0.0050.0093.291-3.815-0.9070.072-1.272-1.707-0.002
4G4ARG 10.9140.9705.1702.0012.1250.000-0.012-0.1120.000
5G5VAL 0-0.037-0.0177.6750.3550.3550.0000.0000.0000.000
6G6GLU -1-0.856-0.9437.211-1.202-1.2020.0000.0000.0000.000
7G7ASN 0-0.033-0.0088.9930.0680.0680.0000.0000.0000.000
8G8PRO 0-0.042-0.0058.8970.0730.0730.0000.0000.0000.000
9G9LYS 10.9520.98311.9300.2700.2700.0000.0000.0000.000
10G10LYS 10.9620.97114.258-0.066-0.0660.0000.0000.0000.000
11G11ALA 0-0.0070.01713.275-0.029-0.0290.0000.0000.0000.000
12G12GLN 0-0.051-0.02915.3320.0510.0510.0000.0000.0000.000
13G13LYS 10.9570.99016.512-0.112-0.1120.0000.0000.0000.000
14G14HIS 00.013-0.00718.8520.0100.0100.0000.0000.0000.000
15G15PHE 0-0.065-0.03320.2250.0100.0100.0000.0000.0000.000
16G16VAL 00.0590.04119.5590.0010.0010.0000.0000.0000.000
17G17GLN 00.0240.00217.338-0.015-0.0150.0000.0000.0000.000
18G18ASN 0-0.023-0.01918.923-0.001-0.0010.0000.0000.0000.000
19G19LEU 0-0.0180.00921.883-0.002-0.0020.0000.0000.0000.000
20G20ASN 00.0240.00021.918-0.009-0.0090.0000.0000.0000.000
21G21ASN 0-0.039-0.02624.142-0.006-0.0060.0000.0000.0000.000
22G22VAL 00.0480.03021.0550.0020.0020.0000.0000.0000.000
23G23VAL 0-0.069-0.02321.101-0.011-0.0110.0000.0000.0000.000
24G24PHE 00.0460.02323.9070.0080.0080.0000.0000.0000.000
25G25THR 00.0180.00726.551-0.011-0.0110.0000.0000.0000.000
26G26ASN 00.049-0.00128.430-0.002-0.0020.0000.0000.0000.000
27G27LYS 10.9140.98430.4960.0780.0780.0000.0000.0000.000
28G28GLU -1-0.802-0.89329.857-0.090-0.0900.0000.0000.0000.000
29G29LEU 0-0.020-0.01026.5500.0000.0000.0000.0000.0000.000
30G30GLU -1-0.930-0.98031.113-0.112-0.1120.0000.0000.0000.000
31G31ASP -1-0.923-0.96234.311-0.074-0.0740.0000.0000.0000.000
32G32ILE 0-0.037-0.01330.9870.0030.0030.0000.0000.0000.000
33G33TYR 00.007-0.01828.495-0.001-0.0010.0000.0000.0000.000
34G34ASN 0-0.021-0.00235.2250.0000.0000.0000.0000.0000.000
35G35LEU 0-0.0100.00136.9180.0050.0050.0000.0000.0000.000
36G36SER 0-0.082-0.04136.8250.0010.0010.0000.0000.0000.000
37G37ASN 0-0.104-0.05239.168-0.001-0.0010.0000.0000.0000.000
38G38LYS 10.9620.98541.9210.0710.0710.0000.0000.0000.000
39G39GLU -1-0.880-0.93742.131-0.085-0.0850.0000.0000.0000.000
40G40GLU -1-0.867-0.95442.370-0.077-0.0770.0000.0000.0000.000
41G41THR 0-0.045-0.03937.648-0.004-0.0040.0000.0000.0000.000
42G42LYS 10.9220.95437.7130.0740.0740.0000.0000.0000.000
43G43GLU -1-0.949-0.95836.206-0.118-0.1180.0000.0000.0000.000
44G44VAL 00.0700.00133.187-0.009-0.0090.0000.0000.0000.000
45G45LEU 00.0230.01832.838-0.011-0.0110.0000.0000.0000.000
46G46LYS 10.9380.97032.3320.1060.1060.0000.0000.0000.000
47G47LEU 0-0.0070.01929.759-0.012-0.0120.0000.0000.0000.000
48G48PHE 00.0100.00128.247-0.016-0.0160.0000.0000.0000.000
49G49LYS 10.9510.97527.7030.1090.1090.0000.0000.0000.000
50G50LEU 0-0.021-0.00425.960-0.012-0.0120.0000.0000.0000.000
51G51LYS 10.8460.90621.4920.2750.2750.0000.0000.0000.000
52G52VAL 00.0360.03722.778-0.022-0.0220.0000.0000.0000.000
53G53ASN 00.0060.00222.704-0.012-0.0120.0000.0000.0000.000
54G54GLN 00.0080.01218.2370.0150.0150.0000.0000.0000.000
55G55PHE 00.016-0.00218.469-0.046-0.0460.0000.0000.0000.000
56G56TYR 0-0.008-0.03818.184-0.025-0.0250.0000.0000.0000.000
57G57ARG 10.9130.95717.1470.3050.3050.0000.0000.0000.000
58G58HIS 0-0.036-0.01912.262-0.015-0.0150.0000.0000.0000.000
59G59ALA 0-0.002-0.01313.367-0.059-0.0590.0000.0000.0000.000
60G60PHE 0-0.001-0.03913.609-0.013-0.0130.0000.0000.0000.000
61G61GLY 00.0230.01912.457-0.003-0.0030.0000.0000.0000.000
62G62ILE 00.0050.0058.849-0.107-0.1070.0000.0000.0000.000
63G63VAL 0-0.0120.0209.1270.0210.0210.0000.0000.0000.000
64G64ASN 0-0.058-0.05111.1180.1220.1220.0000.0000.0000.000
65G65ASP -1-0.797-0.9056.379-1.006-1.0060.0000.0000.0000.000
66G66TYR 0-0.026-0.0302.283-0.811-0.4970.975-0.208-1.081-0.001
67G67ASN 0-0.106-0.0366.8100.2950.2950.0000.0000.0000.000
68G68GLY 00.0180.0008.1900.0540.0540.0000.0000.0000.000
69G69LEU 0-0.066-0.0175.5860.1770.1770.0000.0000.0000.000
70G70LEU 00.0610.0038.146-0.176-0.1760.0000.0000.0000.000
71G71GLU -1-0.936-0.96810.7770.2660.2660.0000.0000.0000.000
72G72TYR 00.0080.0149.507-0.092-0.0920.0000.0000.0000.000
73G73LYS 10.9530.98211.068-0.035-0.0350.0000.0000.0000.000
74G74GLU -1-0.802-0.90514.555-0.057-0.0570.0000.0000.0000.000
75G75ILE 00.0030.00710.060-0.020-0.0200.0000.0000.0000.000
76G76PHE 0-0.012-0.00414.078-0.029-0.0290.0000.0000.0000.000
77G77ASN 00.014-0.02615.370-0.021-0.0210.0000.0000.0000.000
78G78MET 0-0.026-0.00317.3290.0060.0060.0000.0000.0000.000
79G79MET 0-0.0620.01113.914-0.013-0.0130.0000.0000.0000.000
80G80PHE 00.0470.00318.6450.0030.0030.0000.0000.0000.000
81G81LEU 0-0.0070.00821.5790.0130.0130.0000.0000.0000.000
82G82LYS 10.9220.96118.5720.1900.1900.0000.0000.0000.000
83G83LEU 0-0.0010.01822.7490.0060.0060.0000.0000.0000.000
84G84SER 00.012-0.00324.5460.0090.0090.0000.0000.0000.000
85G85VAL 0-0.0160.00826.8690.0070.0070.0000.0000.0000.000
86G86VAL 0-0.026-0.00625.6600.0050.0050.0000.0000.0000.000
87G87PHE 00.012-0.00927.2830.0040.0040.0000.0000.0000.000
88G88ASP -1-0.899-0.95630.666-0.075-0.0750.0000.0000.0000.000
89G89THR 0-0.034-0.01032.1560.0080.0080.0000.0000.0000.000
90G90GLN 00.0390.02631.848-0.002-0.0020.0000.0000.0000.000
91G91ARG 10.8660.92431.7580.0910.0910.0000.0000.0000.000
92G92LYS 10.9030.95936.4770.0720.0720.0000.0000.0000.000
93G93GLU -1-0.877-0.93136.482-0.073-0.0730.0000.0000.0000.000
94G94ALA 00.0180.02237.055-0.005-0.0050.0000.0000.0000.000
95G95ASN 00.0270.01238.125-0.006-0.0060.0000.0000.0000.000
96G96ASN 0-0.0250.01137.831-0.002-0.0020.0000.0000.0000.000
97G97VAL 00.0790.01736.806-0.006-0.0060.0000.0000.0000.000
98G98GLU -1-0.822-0.92135.229-0.115-0.1150.0000.0000.0000.000
99G99GLN 00.0000.00233.076-0.012-0.0120.0000.0000.0000.000
100G100ILE 0-0.008-0.00332.170-0.008-0.0080.0000.0000.0000.000
101G101LYS 10.8980.95330.7760.1050.1050.0000.0000.0000.000
102G102ARG 10.8990.95726.3150.1390.1390.0000.0000.0000.000
103G103ASN 00.0630.00528.122-0.011-0.0110.0000.0000.0000.000
104G104ILE 0-0.033-0.00525.544-0.015-0.0150.0000.0000.0000.000
105G105ALA 00.0000.00124.582-0.019-0.0190.0000.0000.0000.000
106G106ILE 0-0.0160.00123.582-0.016-0.0160.0000.0000.0000.000
107G107LEU 00.0120.00122.261-0.014-0.0140.0000.0000.0000.000
108G108ASP -1-0.818-0.90819.747-0.329-0.3290.0000.0000.0000.000
109G109GLU -1-0.890-0.94218.472-0.232-0.2320.0000.0000.0000.000
110G110ILE 0-0.068-0.02418.354-0.015-0.0150.0000.0000.0000.000
111G111MET 0-0.0310.00715.774-0.022-0.0220.0000.0000.0000.000
112G112ALA 00.0330.02214.135-0.067-0.0670.0000.0000.0000.000
113G113LYS 10.7720.87813.8670.1710.1710.0000.0000.0000.000
114G114ALA 00.0220.00713.1270.0190.0190.0000.0000.0000.000
115G115ASP -1-0.798-0.9039.744-0.871-0.8710.0000.0000.0000.000
116G116ASN 0-0.044-0.0319.087-0.125-0.1250.0000.0000.0000.000
117G117ASP -1-0.824-0.93610.347-0.199-0.1990.0000.0000.0000.000
118G118LEU 00.0020.0025.6360.1490.1490.0000.0000.0000.000
119G119SER 00.001-0.0105.618-0.004-0.0040.0000.0000.0000.000
120G120TYR 00.0410.0186.7050.2650.2650.0000.0000.0000.000
121G121PHE 00.0360.0108.8610.1530.1530.0000.0000.0000.000
122G122ILE 00.0060.0192.380-0.5020.0611.953-0.359-2.1560.004
123G123SER 0-0.094-0.0465.7460.6680.6680.0000.0000.0000.000
124G124GLN 0-0.058-0.0276.829-0.088-0.0880.0000.0000.0000.000
125G125ASN 00.0060.0267.683-0.033-0.0330.0000.0000.0000.000
126G126LYS 10.9900.9814.9900.0550.0550.0000.0000.0000.000
127G127ASN 00.0210.0266.4860.4640.4640.0000.0000.0000.000
128G128PHE 00.014-0.0072.430-0.5850.1870.392-0.232-0.933-0.001
129G129GLN 00.033-0.0012.038-3.275-1.9046.072-3.279-4.1640.020
130G130GLU -1-0.891-0.9363.6650.162-0.3630.1231.462-1.060-0.007
131G131LEU 0-0.049-0.0285.845-0.356-0.3560.0000.0000.0000.000
132G132TRP 00.004-0.0052.621-4.787-4.4717.223-2.150-5.388-0.009
133G133ASP -1-0.803-0.9182.681-12.938-6.8600.947-3.403-3.622-0.037
134G134LYS 10.7270.8365.150-0.848-0.8270.000-0.007-0.0140.000
135G135ALA 00.0100.0048.147-0.231-0.2310.0000.0000.0000.000
136G136VAL 00.0330.0315.438-0.144-0.1440.0000.0000.0000.000
137G137LYS 10.9180.9738.428-0.282-0.2820.0000.0000.0000.000
138G138LEU 0-0.055-0.04710.476-0.021-0.0210.0000.0000.0000.000
139G139THR 0-0.007-0.01811.565-0.018-0.0180.0000.0000.0000.000
140G140LYS 10.8540.92410.2030.4190.4190.0000.0000.0000.000
141G141GLU -1-0.923-0.97513.8460.1130.1130.0000.0000.0000.000
142G142MET 0-0.025-0.00116.0840.0140.0140.0000.0000.0000.000
143G143LYS 10.9861.01116.4430.2090.2090.0000.0000.0000.000
144G144ILE 0-0.0010.04718.3560.0030.0030.0000.0000.0000.000
145G145LYS 10.8980.96219.457-0.049-0.0490.0000.0000.0000.000
146G146LEU 00.026-0.01819.7460.0060.0060.0000.0000.0000.000
147G147LYS 10.9240.98223.4890.0440.0440.0000.0000.0000.000
148G148GLY 00.0370.02125.224-0.006-0.0060.0000.0000.0000.000
149G149GLN 0-0.061-0.01025.8120.0140.0140.0000.0000.0000.000
150G150LYS 10.9850.98727.7230.0230.0230.0000.0000.0000.000
151G151LEU 00.0260.00423.3420.0060.0060.0000.0000.0000.000
152G152ASP -1-0.872-0.92927.156-0.060-0.0600.0000.0000.0000.000
153G153LEU 0-0.003-0.02623.7390.0020.0020.0000.0000.0000.000
154G154ARG 10.8990.95526.9380.0760.0760.0000.0000.0000.000
155G155ASP -1-0.890-0.91928.840-0.026-0.0260.0000.0000.0000.000
156G156GLY 00.0700.02428.4320.0020.0020.0000.0000.0000.000
157G157GLU -1-0.940-0.96724.576-0.011-0.0110.0000.0000.0000.000
158G158VAL 00.0150.00924.8960.0080.0080.0000.0000.0000.000
159G159ALA 00.011-0.00120.0200.0060.0060.0000.0000.0000.000
160G160ILE 00.0310.00219.4500.0150.0150.0000.0000.0000.000
161G161ASN 00.0400.02321.5480.0270.0270.0000.0000.0000.000
162G162LYS 10.9180.95322.6530.0230.0230.0000.0000.0000.000
163G163VAL 0-0.0220.00117.5550.0080.0080.0000.0000.0000.000
164G164ARG 10.8890.92620.471-0.070-0.0700.0000.0000.0000.000
165G165GLU -1-0.891-0.92222.7910.0180.0180.0000.0000.0000.000
166G166LEU 0-0.026-0.00820.4440.0060.0060.0000.0000.0000.000
167G167PHE 0-0.007-0.02017.2870.0140.0140.0000.0000.0000.000
168G168GLY 00.0090.01420.1880.0260.0260.0000.0000.0000.000
169G169SER 0-0.091-0.04321.9770.0080.0080.0000.0000.0000.000
170G170ASP -1-0.802-0.89615.7330.3330.3330.0000.0000.0000.000
171G171LYS 10.9680.96817.943-0.207-0.2070.0000.0000.0000.000
172G172ASN 00.0900.05813.0710.0400.0400.0000.0000.0000.000
173G173VAL 00.0160.01815.469-0.005-0.0050.0000.0000.0000.000
174G174LYS 10.8660.93017.013-0.180-0.1800.0000.0000.0000.000
175G175GLU -1-0.912-0.95717.6940.2740.2740.0000.0000.0000.000
176G176LEU 0-0.0270.00312.2260.0040.0040.0000.0000.0000.000
177G177TRP 00.0080.00914.986-0.004-0.0040.0000.0000.0000.000
178G178TRP 00.0870.0236.963-0.134-0.1340.0000.0000.0000.000
179G179PHE 00.0550.0369.989-0.043-0.0430.0000.0000.0000.000
180G180ARG 10.9270.95512.124-0.223-0.2230.0000.0000.0000.000
181G181SER 0-0.021-0.02113.125-0.060-0.0600.0000.0000.0000.000
182G182LEU 00.0450.0218.032-0.063-0.0630.0000.0000.0000.000
183G183LEU 00.0150.01211.640-0.071-0.0710.0000.0000.0000.000
184G184VAL 0-0.025-0.00814.232-0.044-0.0440.0000.0000.0000.000
185G185LYS 10.9550.97611.9410.2820.2820.0000.0000.0000.000
186G186GLY 00.0460.03213.996-0.044-0.0440.0000.0000.0000.000
187G187VAL 0-0.0040.01314.526-0.011-0.0110.0000.0000.0000.000
188G188TYR 0-0.058-0.04017.7530.0020.0020.0000.0000.0000.000
189G189LEU 0-0.015-0.00512.609-0.005-0.0050.0000.0000.0000.000
190G190ILE 00.014-0.00515.644-0.003-0.0030.0000.0000.0000.000
191G191LYS 10.7760.89218.5650.1040.1040.0000.0000.0000.000
192G192ARG 10.9730.98718.5960.2040.2040.0000.0000.0000.000
193G193TYR 00.0260.02418.6350.0010.0010.0000.0000.0000.000
194G194TYR 0-0.118-0.11020.5280.0100.0100.0000.0000.0000.000
195G195GLU -1-0.951-0.97023.356-0.112-0.1120.0000.0000.0000.000
196G196GLY 0-0.035-0.00124.7940.0050.0050.0000.0000.0000.000
197G197ASP -1-0.830-0.93220.937-0.258-0.2580.0000.0000.0000.000
198G198ILE 0-0.067-0.04619.279-0.027-0.0270.0000.0000.0000.000
199G199GLU -1-0.861-0.91918.646-0.337-0.3370.0000.0000.0000.000
200G200LEU 0-0.062-0.03915.813-0.056-0.0560.0000.0000.0000.000
201G201LYS 10.9150.96314.2990.2770.2770.0000.0000.0000.000
202G202THR 0-0.022-0.00912.901-0.120-0.1200.0000.0000.0000.000
203G203THR 0-0.0220.00413.4850.0530.0530.0000.0000.0000.000
204G204SER 0-0.039-0.0369.8080.0510.0510.0000.0000.0000.000
205G205ASP -1-0.801-0.9044.975-2.268-2.2680.0000.0000.0000.000
206G206PHE 0-0.048-0.0256.282-0.320-0.3200.0000.0000.0000.000
207G207ALA 0-0.001-0.0057.4480.0860.0860.0000.0000.0000.000
208G208LYS 10.9300.9788.7621.3551.3550.0000.0000.0000.000
209G209ALA 00.0000.0165.9540.0460.0460.0000.0000.0000.000
210G210VAL 00.000-0.0087.8260.3050.3050.0000.0000.0000.000
211G211PHE 0-0.146-0.07110.5530.1660.1660.0000.0000.0000.000
212G212GLU -1-0.900-0.9629.303-0.917-0.9170.0000.0000.0000.000
213G213ASP -2-1.855-1.90811.136-0.490-0.4900.0000.0000.0000.000