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: 1N3ZZ

Calculation Name: 2ICU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ICU

Chain ID: A

ChEMBL ID:

UniProt ID: P76318

Base Structure: X-ray

Registration Date: 2023-09-23

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2704487.859913
FMO2-HF: Nuclear repulsion 2618393.120276
FMO2-HF: Total energy -86094.739637
FMO2-MP2: Total energy -86349.099725


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(A:10:GLY)


Summations of interaction energy for fragment #1(A:10:GLY)
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.
-6.281-1.7221.082-2.465-3.177-0.004
Interaction energy analysis for fragmet #1(A:10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.024
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].
3A12PHE00.0230.0203.792-0.5671.656-0.023-1.258-0.9420.003
4A13ALA00.0060.0256.967-0.091-0.0910.0000.0000.0000.000
5A14GLN0-0.052-0.03910.7510.0720.0720.0000.0000.0000.000
6A15SER0-0.044-0.05013.3890.0440.0440.0000.0000.0000.000
7A16GLN00.006-0.00416.4050.0700.0700.0000.0000.0000.000
8A17THR00.018-0.01919.361-0.016-0.0160.0000.0000.0000.000
9A18ARG10.8910.92120.4910.2430.2430.0000.0000.0000.000
10A19GLU-1-0.831-0.92121.679-0.131-0.1310.0000.0000.0000.000
11A20ASP-1-0.837-0.88721.156-0.231-0.2310.0000.0000.0000.000
12A21TYR0-0.087-0.08215.860-0.018-0.0180.0000.0000.0000.000
13A22LEU00.0120.00020.0560.0200.0200.0000.0000.0000.000
14A23ALA00.0070.02222.8100.0210.0210.0000.0000.0000.000
15A24LEU0-0.058-0.03721.3840.0150.0150.0000.0000.0000.000
16A25LEU0-0.069-0.02119.3190.0160.0160.0000.0000.0000.000
17A26ALA00.0500.01923.9580.0160.0160.0000.0000.0000.000
18A27GLU-1-0.926-0.94626.833-0.059-0.0590.0000.0000.0000.000
19A28ASP-1-0.913-0.97729.495-0.093-0.0930.0000.0000.0000.000
20A29ILE0-0.035-0.03330.663-0.001-0.0010.0000.0000.0000.000
21A30GLU-1-0.778-0.83928.772-0.034-0.0340.0000.0000.0000.000
22A31ARG10.7970.90126.0280.1080.1080.0000.0000.0000.000
23A32ASP-1-0.904-0.94326.755-0.074-0.0740.0000.0000.0000.000
24A33ILE0-0.052-0.03522.341-0.011-0.0110.0000.0000.0000.000
25A34PRO0-0.035-0.01925.853-0.004-0.0040.0000.0000.0000.000
26A35TYR0-0.013-0.00126.421-0.017-0.0170.0000.0000.0000.000
27A36ASP-1-0.838-0.92724.335-0.233-0.2330.0000.0000.0000.000
28A37PRO0-0.058-0.02025.453-0.011-0.0110.0000.0000.0000.000
29A38GLU-1-0.941-0.96123.554-0.271-0.2710.0000.0000.0000.000
30A39PRO0-0.059-0.03121.243-0.014-0.0140.0000.0000.0000.000
31A40ILE0-0.037-0.01315.773-0.014-0.0140.0000.0000.0000.000
32A41GLY0-0.0040.00517.909-0.033-0.0330.0000.0000.0000.000
33A42ARG10.8410.91311.0270.8700.8700.0000.0000.0000.000
34A43TYR00.0770.03113.033-0.045-0.0450.0000.0000.0000.000
35A44ASN0-0.045-0.0278.393-0.706-0.7060.0000.0000.0000.000
36A45VAL00.0040.0247.6110.0440.0440.0000.0000.0000.000
37A46ALA00.006-0.0145.536-1.261-1.2610.0000.0000.0000.000
38A47PRO00.0110.0003.2950.3200.8340.045-0.165-0.394-0.001
39A48GLY0-0.0210.0006.0680.0020.0020.0000.0000.0000.000
40A49THR0-0.062-0.0249.2630.1140.1140.0000.0000.0000.000
41A50LYS10.8600.90910.9340.2350.2350.0000.0000.0000.000
42A51VAL0-0.036-0.0288.916-0.127-0.1270.0000.0000.0000.000
43A52LEU00.0020.01512.4070.0920.0920.0000.0000.0000.000
44A53LEU0-0.029-0.01912.272-0.041-0.0410.0000.0000.0000.000
45A54LEU00.0220.01615.1050.0130.0130.0000.0000.0000.000
46A55SER00.004-0.01417.5140.0370.0370.0000.0000.0000.000
47A56GLU-1-0.793-0.89520.082-0.002-0.0020.0000.0000.0000.000
48A57ARG10.7610.84622.0650.0710.0710.0000.0000.0000.000
49A58ASP-1-0.920-0.96026.351-0.021-0.0210.0000.0000.0000.000
50A59GLU-1-0.976-0.97829.481-0.008-0.0080.0000.0000.0000.000
51A60HIS0-0.045-0.01628.104-0.007-0.0070.0000.0000.0000.000
52A61LEU0-0.034-0.03122.4810.0030.0030.0000.0000.0000.000
53A62HIS00.0710.03722.857-0.018-0.0180.0000.0000.0000.000
54A63LEU0-0.007-0.01417.392-0.009-0.0090.0000.0000.0000.000
55A64ASP-1-0.774-0.84918.609-0.092-0.0920.0000.0000.0000.000
56A65PRO0-0.048-0.02016.303-0.033-0.0330.0000.0000.0000.000
57A66VAL00.0150.00813.9190.0360.0360.0000.0000.0000.000
58A67PHE00.0020.00912.298-0.104-0.1040.0000.0000.0000.000
59A68TRP0-0.029-0.0122.821-1.163-0.5620.441-0.379-0.663-0.005
60A69GLY00.014-0.0058.486-0.058-0.0580.0000.0000.0000.000
61A70TYR0-0.012-0.0019.740-0.057-0.0570.0000.0000.0000.000
62A71ALA0-0.0070.00012.6790.1200.1200.0000.0000.0000.000
63A72PRO00.0300.01615.031-0.046-0.0460.0000.0000.0000.000
64A73GLY00.0320.00718.072-0.022-0.0220.0000.0000.0000.000
65A74TRP0-0.002-0.00220.8620.0080.0080.0000.0000.0000.000
66A75TRP00.005-0.00117.0730.0050.0050.0000.0000.0000.000
67A76ASP-1-0.787-0.87015.1100.2740.2740.0000.0000.0000.000
68A77LYS10.7020.85014.626-0.242-0.2420.0000.0000.0000.000
69A78PRO0-0.017-0.0079.5710.0180.0180.0000.0000.0000.000
70A79PRO00.018-0.00910.2330.1180.1180.0000.0000.0000.000
71A80LEU0-0.0070.0089.2060.2470.2470.0000.0000.0000.000
72A81ILE00.0530.0142.480-0.646-0.0440.612-0.514-0.700-0.001
73A82ASN00.0100.0073.813-1.183-1.0300.000-0.025-0.1280.000
74A83ALA00.0180.0167.288-0.171-0.1710.0000.0000.0000.000
75A84ARG10.8370.92210.962-1.072-1.0720.0000.0000.0000.000
76A85VAL00.1040.04712.560-0.106-0.1060.0000.0000.0000.000
77A86GLU-1-0.812-0.87914.3400.7490.7490.0000.0000.0000.000
78A87THR0-0.029-0.02816.383-0.033-0.0330.0000.0000.0000.000
79A88ALA00.0140.01914.730-0.045-0.0450.0000.0000.0000.000
80A89ALA00.0730.03516.784-0.038-0.0380.0000.0000.0000.000
81A90THR0-0.051-0.03420.115-0.028-0.0280.0000.0000.0000.000
82A91SER0-0.0270.01217.270-0.035-0.0350.0000.0000.0000.000
83A92ARG10.9190.93820.070-0.278-0.2780.0000.0000.0000.000
84A93MET00.0060.01616.443-0.010-0.0100.0000.0000.0000.000
85A94PHE00.0500.00512.634-0.006-0.0060.0000.0000.0000.000
86A95LYS10.9671.00917.785-0.256-0.2560.0000.0000.0000.000
87A96PRO00.007-0.01220.800-0.019-0.0190.0000.0000.0000.000
88A97LEU00.0440.02715.800-0.017-0.0170.0000.0000.0000.000
89A98TRP0-0.029-0.00915.5140.0030.0030.0000.0000.0000.000
90A99GLN0-0.072-0.04919.157-0.025-0.0250.0000.0000.0000.000
91A100HIS00.0200.01021.853-0.020-0.0200.0000.0000.0000.000
92A101GLY00.0400.03318.776-0.022-0.0220.0000.0000.0000.000
93A102ARG10.7810.88817.142-0.108-0.1080.0000.0000.0000.000
94A103ALA00.0240.02115.064-0.029-0.0290.0000.0000.0000.000
95A104ILE00.0030.00114.5290.0450.0450.0000.0000.0000.000
96A105CYS0-0.034-0.00610.396-0.106-0.1060.0000.0000.0000.000
97A106PHE00.0490.02812.1270.0000.0000.0000.0000.0000.000
98A107ALA0-0.001-0.00210.594-0.114-0.1140.0000.0000.0000.000
99A108ASP-1-0.738-0.80712.537-0.465-0.4650.0000.0000.0000.000
100A109GLY00.021-0.00311.1410.1130.1130.0000.0000.0000.000
101A110TRP0-0.029-0.0235.231-0.150-0.1500.0000.0000.0000.000
102A111PHE0-0.030-0.0185.7320.2940.2940.0000.0000.0000.000
103A112GLU-1-0.854-0.9074.6680.3790.561-0.001-0.014-0.1670.000
104A113TRP0-0.065-0.0483.301-0.0330.2510.008-0.110-0.1830.000
105A114LYS10.9490.9937.9530.2680.2680.0000.0000.0000.000
106A115LYS10.7700.87511.273-0.276-0.2760.0000.0000.0000.000
107A116GLU-1-0.776-0.88313.1300.0070.0070.0000.0000.0000.000
108A117GLY00.0660.04015.836-0.019-0.0190.0000.0000.0000.000
109A118ASP-1-0.835-0.89416.6380.1340.1340.0000.0000.0000.000
110A119LYS10.7530.86315.657-0.024-0.0240.0000.0000.0000.000
111A120LYS10.9170.9427.602-0.289-0.2890.0000.0000.0000.000
112A121GLN00.018-0.00511.611-0.006-0.0060.0000.0000.0000.000
113A122PRO0-0.0010.0218.9170.0830.0830.0000.0000.0000.000
114A123PHE00.020-0.0019.6190.1160.1160.0000.0000.0000.000
115A124PHE00.0350.0229.518-0.205-0.2050.0000.0000.0000.000
116A125ILE0-0.029-0.0218.9170.1620.1620.0000.0000.0000.000
117A126TYR00.0320.00711.387-0.064-0.0640.0000.0000.0000.000
118A127ARG10.8290.89114.1330.1560.1560.0000.0000.0000.000
119A128ALA00.0030.00117.240-0.022-0.0220.0000.0000.0000.000
120A129ASP-1-0.837-0.89420.367-0.118-0.1180.0000.0000.0000.000
121A130GLY0-0.016-0.00919.7820.0030.0030.0000.0000.0000.000
122A131GLN0-0.0170.00420.101-0.027-0.0270.0000.0000.0000.000
123A132PRO00.0420.02116.468-0.020-0.0200.0000.0000.0000.000
124A133ILE0-0.076-0.02710.0070.0620.0620.0000.0000.0000.000
125A134PHE00.0670.02413.990-0.052-0.0520.0000.0000.0000.000
126A135MET0-0.040-0.0158.2600.0950.0950.0000.0000.0000.000
127A136ALA00.0430.02911.933-0.027-0.0270.0000.0000.0000.000
128A137ALA00.000-0.00211.3090.1000.1000.0000.0000.0000.000
129A138ILE0-0.019-0.01312.325-0.014-0.0140.0000.0000.0000.000
130A139GLY00.012-0.02013.0620.0470.0470.0000.0000.0000.000
131A140SER0-0.053-0.02015.312-0.004-0.0040.0000.0000.0000.000
132A141THR00.0230.04218.336-0.022-0.0220.0000.0000.0000.000
133A142PRO0-0.025-0.01721.1370.0130.0130.0000.0000.0000.000
134A143PHE00.0530.00215.7070.0010.0010.0000.0000.0000.000
135A144GLU-1-0.840-0.92219.597-0.045-0.0450.0000.0000.0000.000
136A145ARG10.7030.84020.476-0.066-0.0660.0000.0000.0000.000
137A146GLY0-0.0120.00519.225-0.004-0.0040.0000.0000.0000.000
138A147ASP-1-0.779-0.87517.8740.0390.0390.0000.0000.0000.000
139A148GLU-1-0.866-0.92617.105-0.175-0.1750.0000.0000.0000.000
140A149ALA0-0.067-0.02815.511-0.004-0.0040.0000.0000.0000.000
141A150GLU-1-0.926-0.94714.8980.2040.2040.0000.0000.0000.000
142A151GLY00.0410.02013.388-0.035-0.0350.0000.0000.0000.000
143A152PHE0-0.005-0.0168.5850.0490.0490.0000.0000.0000.000
144A153LEU0-0.063-0.0338.5010.0430.0430.0000.0000.0000.000
145A154ILE00.0340.0235.967-0.159-0.1590.0000.0000.0000.000
146A155VAL0-0.002-0.0068.1530.3930.3930.0000.0000.0000.000
147A156THR0-0.0040.0096.8030.0090.0090.0000.0000.0000.000
148A157ALA00.018-0.0039.780-0.120-0.1200.0000.0000.0000.000
149A158ALA0-0.005-0.01211.2430.1270.1270.0000.0000.0000.000
150A159ALA0-0.026-0.00311.927-0.073-0.0730.0000.0000.0000.000
151A160ASP-1-0.759-0.87413.3550.1710.1710.0000.0000.0000.000
152A161GLN0-0.026-0.04216.477-0.048-0.0480.0000.0000.0000.000
153A162GLY00.0560.02418.1980.0170.0170.0000.0000.0000.000
154A163LEU00.0100.00912.012-0.008-0.0080.0000.0000.0000.000
155A164VAL0-0.041-0.01413.4280.0440.0440.0000.0000.0000.000
156A165ASP-1-0.932-0.94715.4440.1500.1500.0000.0000.0000.000
157A166ILE0-0.101-0.05510.448-0.042-0.0420.0000.0000.0000.000
158A167HIS0-0.001-0.0166.706-0.161-0.1610.0000.0000.0000.000
159A168ASP-1-0.864-0.93511.0011.1211.1210.0000.0000.0000.000
160A169ARG10.7390.8567.775-1.209-1.2090.0000.0000.0000.000
161A170ARG10.8020.8907.864-0.383-0.3830.0000.0000.0000.000
162A171PRO00.0430.0206.0570.2240.2240.0000.0000.0000.000
163A172LEU0-0.015-0.0068.496-0.110-0.1100.0000.0000.0000.000
164A173VAL0-0.031-0.01811.294-0.051-0.0510.0000.0000.0000.000
165A174LEU00.0300.02213.5700.0280.0280.0000.0000.0000.000
166A175SER00.0060.00617.113-0.037-0.0370.0000.0000.0000.000
167A176PRO00.0630.01720.2150.0080.0080.0000.0000.0000.000
168A177GLU-1-0.930-0.95121.8440.0210.0210.0000.0000.0000.000
169A178ALA00.0300.01220.7390.0070.0070.0000.0000.0000.000
170A179ALA0-0.036-0.02618.6860.0160.0160.0000.0000.0000.000
171A180ARG10.8340.87620.0530.0330.0330.0000.0000.0000.000
172A181GLU-1-0.826-0.90323.2750.0450.0450.0000.0000.0000.000
173A182TRP0-0.089-0.05815.6380.0380.0380.0000.0000.0000.000
174A183MET0-0.057-0.02919.3240.0070.0070.0000.0000.0000.000
175A184ARG10.8070.91021.495-0.038-0.0380.0000.0000.0000.000
176A185GLN0-0.033-0.03624.8600.0170.0170.0000.0000.0000.000
177A186GLU-1-0.918-0.93526.5080.0380.0380.0000.0000.0000.000
178A187ILE0-0.0350.01924.3840.0060.0060.0000.0000.0000.000
179A188SER0-0.047-0.06425.6530.0150.0150.0000.0000.0000.000
180A189GLY00.042-0.00723.0690.0090.0090.0000.0000.0000.000
181A190LYS10.9030.95023.458-0.124-0.1240.0000.0000.0000.000
182A191GLU-1-0.765-0.84825.6110.1020.1020.0000.0000.0000.000
183A192ALA00.0550.03720.8200.0010.0010.0000.0000.0000.000
184A193SER0-0.085-0.05421.1170.0150.0150.0000.0000.0000.000
185A194GLU-1-0.929-0.94422.1470.1260.1260.0000.0000.0000.000
186A195ILE00.0890.05720.9740.0040.0040.0000.0000.0000.000
187A196ALA0-0.065-0.03317.7760.0010.0010.0000.0000.0000.000
188A197ALA0-0.078-0.03918.7360.0150.0150.0000.0000.0000.000
189A198SER0-0.064-0.05221.038-0.004-0.0040.0000.0000.0000.000
190A199GLY00.0580.02921.092-0.016-0.0160.0000.0000.0000.000
191A200CYS0-0.080-0.03516.118-0.010-0.0100.0000.0000.0000.000
192A201VAL00.0010.00216.081-0.018-0.0180.0000.0000.0000.000
193A202PRO00.0100.01616.2000.0250.0250.0000.0000.0000.000
194A203ALA00.045-0.00615.915-0.036-0.0360.0000.0000.0000.000
195A204ASN0-0.0150.00217.042-0.017-0.0170.0000.0000.0000.000
196A205GLN0-0.021-0.01118.773-0.006-0.0060.0000.0000.0000.000
197A206PHE0-0.012-0.00713.772-0.031-0.0310.0000.0000.0000.000
198A207SER0-0.033-0.00616.6380.0280.0280.0000.0000.0000.000
199A208TRP00.0260.00013.804-0.028-0.0280.0000.0000.0000.000
200A209HIS0-0.0160.00914.6940.0950.0950.0000.0000.0000.000
201A210PRO0-0.017-0.00414.223-0.075-0.0750.0000.0000.0000.000
202A211VAL00.0570.03311.7040.0150.0150.0000.0000.0000.000
203A212SER00.0440.01614.3370.0240.0240.0000.0000.0000.000
204A213ARG10.9030.92112.3620.1910.1910.0000.0000.0000.000
205A214ALA0-0.0160.00412.184-0.078-0.0780.0000.0000.0000.000
206A215VAL00.1010.0688.329-0.015-0.0150.0000.0000.0000.000
207A216GLY0-0.0080.0058.017-0.359-0.3590.0000.0000.0000.000
208A217ASN0-0.010-0.0068.667-0.172-0.1720.0000.0000.0000.000
209A218VAL00.0770.0327.6690.0310.0310.0000.0000.0000.000
210A219LYS10.9260.96410.3140.6160.6160.0000.0000.0000.000
211A220ASN0-0.066-0.03013.2080.1650.1650.0000.0000.0000.000
212A221GLN0-0.021-0.04511.080-0.134-0.1340.0000.0000.0000.000
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