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: KG283

Calculation Name: 2I9I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I9I

Chain ID: A

ChEMBL ID:

UniProt ID: O25234

Base Structure: X-ray

Registration Date: 2023-09-22

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2610464.510061
FMO2-HF: Nuclear repulsion 2520910.998508
FMO2-HF: Total energy -89553.511553
FMO2-MP2: Total energy -89816.671684


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:51:GLU)


Summations of interaction energy for fragment #1(A:51:GLU)
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.
-167.016-176.3250.448-22.601-18.5440.157
Interaction energy analysis for fragmet #1(A:51:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.823 / q_NPA : -0.878
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].
3A53MET0-0.018-0.0013.4730.7213.111-0.010-0.859-1.5220.004
4A54LYS10.9820.9885.794-24.361-24.3610.0000.0000.0000.000
5A55THR0-0.001-0.0209.4481.4221.4220.0000.0000.0000.000
6A56SER0-0.042-0.02112.107-0.947-0.9470.0000.0000.0000.000
7A57SER00.0500.01315.5780.1250.1250.0000.0000.0000.000
8A58GLU-1-0.901-0.92218.73614.85914.8590.0000.0000.0000.000
9A59HIS0-0.001-0.00616.570-1.216-1.2160.0000.0000.0000.000
10A60VAL00.0060.02216.3591.0021.0020.0000.0000.0000.000
11A61THR0-0.046-0.04810.9870.0020.0020.0000.0000.0000.000
12A62PRO00.0070.00514.2900.0430.0430.0000.0000.0000.000
13A63LEU0-0.025-0.00613.7371.5601.5600.0000.0000.0000.000
14A64ASP-1-0.934-0.97212.57120.96520.9650.0000.0000.0000.000
15A65PHE0-0.074-0.03212.7661.2991.2990.0000.0000.0000.000
16A66ASN00.0370.00613.821-2.087-2.0870.0000.0000.0000.000
17A67TYR0-0.0010.0069.8602.6702.6700.0000.0000.0000.000
18A68PRO0-0.001-0.00214.017-1.392-1.3920.0000.0000.0000.000
19A69ILE00.0010.01016.0530.7410.7410.0000.0000.0000.000
20A70HIS00.000-0.00117.674-1.465-1.4650.0000.0000.0000.000
21A71ILE0-0.019-0.00920.6970.0000.0000.0000.0000.0000.000
22A72VAL00.004-0.00123.573-0.230-0.2300.0000.0000.0000.000
23A73GLN0-0.047-0.02127.2650.2480.2480.0000.0000.0000.000
24A74ALA00.0330.03029.517-0.358-0.3580.0000.0000.0000.000
25A75PRO00.001-0.00931.272-0.081-0.0810.0000.0000.0000.000
26A76GLN00.0070.00532.9440.0810.0810.0000.0000.0000.000
27A77ASN00.0390.01531.720-0.399-0.3990.0000.0000.0000.000
28A78HIS0-0.010-0.00235.858-0.034-0.0340.0000.0000.0000.000
29A79HIS10.7970.89033.869-9.075-9.0750.0000.0000.0000.000
30A80VAL0-0.003-0.00133.5410.1390.1390.0000.0000.0000.000
31A81VAL00.0180.01128.012-0.114-0.1140.0000.0000.0000.000
32A82GLY00.0200.01330.371-0.120-0.1200.0000.0000.0000.000
33A83ILE0-0.015-0.01224.2210.3390.3390.0000.0000.0000.000
34A84LEU0-0.031-0.01126.666-0.372-0.3720.0000.0000.0000.000
35A85THR00.000-0.00125.5040.4850.4850.0000.0000.0000.000
36A86PRO0-0.028-0.00421.058-0.104-0.1040.0000.0000.0000.000
37A87ARG10.8700.92522.992-12.224-12.2240.0000.0000.0000.000
38A88ILE00.0000.00416.8190.2240.2240.0000.0000.0000.000
39A89GLN0-0.0160.00620.422-0.660-0.6600.0000.0000.0000.000
40A90VAL00.010-0.00517.2300.8680.8680.0000.0000.0000.000
41A91SER00.024-0.01316.393-0.586-0.5860.0000.0000.0000.000
42A92ASP-1-0.811-0.90918.64513.15313.1530.0000.0000.0000.000
43A93ASN0-0.015-0.00615.417-0.187-0.1870.0000.0000.0000.000
44A94LEU00.002-0.01213.6030.5820.5820.0000.0000.0000.000
45A95LYS10.8270.90117.701-12.918-12.9180.0000.0000.0000.000
46A96PRO00.0000.00720.129-0.251-0.2510.0000.0000.0000.000
47A97TYR0-0.008-0.00516.7370.2060.2060.0000.0000.0000.000
48A98ILE0-0.022-0.00317.3100.6310.6310.0000.0000.0000.000
49A99ASP-1-0.840-0.91919.16413.72513.7250.0000.0000.0000.000
50A100LYS10.9640.99216.920-17.907-17.9070.0000.0000.0000.000
51A101PHE0-0.043-0.02811.7350.2720.2720.0000.0000.0000.000
52A102GLN00.048-0.00817.1310.5560.5560.0000.0000.0000.000
53A103ASP-1-0.858-0.92119.56413.35513.3550.0000.0000.0000.000
54A104ALA0-0.068-0.03117.542-0.364-0.3640.0000.0000.0000.000
55A105LEU00.0220.01114.1630.0050.0050.0000.0000.0000.000
56A106ILE0-0.012-0.00118.108-0.291-0.2910.0000.0000.0000.000
57A107ASN00.0270.02521.701-0.968-0.9680.0000.0000.0000.000
58A108GLN00.0550.03216.4820.7280.7280.0000.0000.0000.000
59A109ILE00.0420.01817.924-0.281-0.2810.0000.0000.0000.000
60A110GLN0-0.006-0.00120.835-0.300-0.3000.0000.0000.0000.000
61A111THR0-0.010-0.01921.913-0.281-0.2810.0000.0000.0000.000
62A112ILE0-0.032-0.00818.148-0.303-0.3030.0000.0000.0000.000
63A113PHE00.001-0.00722.758-0.434-0.4340.0000.0000.0000.000
64A114GLU-1-0.818-0.90025.88911.22811.2280.0000.0000.0000.000
65A115LYS10.8790.94424.436-12.346-12.3460.0000.0000.0000.000
66A116ARG10.8680.92721.100-14.438-14.4380.0000.0000.0000.000
67A117GLY0-0.021-0.00327.711-0.289-0.2890.0000.0000.0000.000
68A118TYR0-0.079-0.05928.656-0.338-0.3380.0000.0000.0000.000
69A119GLN00.008-0.00230.8930.1740.1740.0000.0000.0000.000
70A120VAL0-0.005-0.00527.3370.1170.1170.0000.0000.0000.000
71A121LEU0-0.019-0.00230.620-0.211-0.2110.0000.0000.0000.000
72A122ARG10.8620.91425.772-12.049-12.0490.0000.0000.0000.000
73A123PHE0-0.004-0.00630.089-0.392-0.3920.0000.0000.0000.000
74A124GLN0-0.018-0.00730.0450.3360.3360.0000.0000.0000.000
75A125ASP-1-0.808-0.92230.1499.9859.9850.0000.0000.0000.000
76A126GLU-1-0.802-0.90731.5819.1819.1810.0000.0000.0000.000
77A127LYS10.9270.95233.096-8.986-8.9860.0000.0000.0000.000
78A128ALA0-0.0230.01234.561-0.269-0.2690.0000.0000.0000.000
79A129LEU0-0.0370.00632.934-0.123-0.1230.0000.0000.0000.000
80A130ASN00.0070.00037.077-0.287-0.2870.0000.0000.0000.000
81A131ALA00.029-0.01240.3040.1030.1030.0000.0000.0000.000
82A132GLN00.0160.00242.286-0.004-0.0040.0000.0000.0000.000
83A133ASP-1-0.793-0.89537.6148.3638.3630.0000.0000.0000.000
84A134LYS10.7970.90335.840-8.790-8.7900.0000.0000.0000.000
85A135ARG10.9080.96338.348-7.236-7.2360.0000.0000.0000.000
86A136LYS10.9030.95539.136-7.979-7.9790.0000.0000.0000.000
87A137ILE0-0.037-0.00233.2300.0910.0910.0000.0000.0000.000
88A138PHE0-0.017-0.00930.873-0.111-0.1110.0000.0000.0000.000
89A139SER00.007-0.02429.722-0.008-0.0080.0000.0000.0000.000
90A140VAL0-0.033-0.00728.6320.0100.0100.0000.0000.0000.000
91A141LEU0-0.0130.00221.2260.1720.1720.0000.0000.0000.000
92A142ASP-1-0.777-0.86024.72212.45112.4510.0000.0000.0000.000
93A143LEU00.0200.01217.3220.4350.4350.0000.0000.0000.000
94A144LYS10.8560.90420.582-13.117-13.1170.0000.0000.0000.000
95A145GLY00.0400.00717.9940.8850.8850.0000.0000.0000.000
96A146TRP0-0.0370.01016.090-1.100-1.1000.0000.0000.0000.000
97A147VAL00.012-0.00812.6311.1121.1120.0000.0000.0000.000
98A148GLY00.0550.02413.076-1.163-1.1630.0000.0000.0000.000
99A149ILE0-0.024-0.01910.6742.1072.1070.0000.0000.0000.000
100A150LEU0-0.039-0.00511.910-1.451-1.4510.0000.0000.0000.000
101A151GLU-1-0.788-0.88912.59017.72817.7280.0000.0000.0000.000
102A152ASP-1-0.806-0.89514.93014.52114.5210.0000.0000.0000.000
103A153LEU0-0.027-0.01811.366-0.978-0.9780.0000.0000.0000.000
104A154LYS10.9130.96214.201-13.805-13.8050.0000.0000.0000.000
105A155MET0-0.050-0.0229.6280.3540.3540.0000.0000.0000.000
106A156ASN00.0670.03814.0630.3990.3990.0000.0000.0000.000
107A157LEU0-0.012-0.01010.6701.2801.2800.0000.0000.0000.000
108A158LYS10.8660.91611.403-17.885-17.8850.0000.0000.0000.000
109A159ASP-1-0.792-0.86713.51016.97316.9730.0000.0000.0000.000
110A160PRO0-0.005-0.00814.563-0.761-0.7610.0000.0000.0000.000
111A161ASN0-0.060-0.03716.389-1.330-1.3300.0000.0000.0000.000
112A162ASN0-0.101-0.06016.793-1.049-1.0490.0000.0000.0000.000
113A163PRO00.0530.03417.6740.5280.5280.0000.0000.0000.000
114A164ASN0-0.033-0.01819.5640.1020.1020.0000.0000.0000.000
115A165LEU0-0.0080.00215.585-0.211-0.2110.0000.0000.0000.000
116A166ASP-1-0.780-0.87316.02814.83114.8310.0000.0000.0000.000
117A167THR0-0.047-0.04411.2070.4370.4370.0000.0000.0000.000
118A168LEU0-0.0210.01614.624-0.300-0.3000.0000.0000.0000.000
119A169VAL0-0.061-0.0489.5250.9680.9680.0000.0000.0000.000
120A170ASP-1-0.775-0.88210.72618.92118.9210.0000.0000.0000.000
121A171GLN0-0.063-0.0425.6022.7772.7770.0000.0000.0000.000
122A172SER00.003-0.0176.798-1.302-1.3020.0000.0000.0000.000
123A173SER0-0.021-0.0158.476-0.025-0.0250.0000.0000.0000.000
124A174GLY00.0530.02810.666-0.460-0.4600.0000.0000.0000.000
125A175SER00.0190.01211.6291.4191.4190.0000.0000.0000.000
126A176VAL0-0.034-0.01213.594-1.247-1.2470.0000.0000.0000.000
127A177TRP0-0.017-0.01615.7950.3080.3080.0000.0000.0000.000
128A178PHE00.014-0.00115.080-0.520-0.5200.0000.0000.0000.000
129A179ASN0-0.045-0.02620.197-0.599-0.5990.0000.0000.0000.000
130A180PHE00.004-0.00123.629-0.115-0.1150.0000.0000.0000.000
131A181TYR0-0.005-0.01125.938-0.089-0.0890.0000.0000.0000.000
132A182GLU-1-0.661-0.79629.5358.8058.8050.0000.0000.0000.000
133A183PRO0-0.027-0.01733.026-0.089-0.0890.0000.0000.0000.000
134A184GLU-1-0.884-0.94634.7267.7157.7150.0000.0000.0000.000
135A185SER0-0.066-0.07436.503-0.083-0.0830.0000.0000.0000.000
136A186ASN0-0.056-0.02733.4270.1420.1420.0000.0000.0000.000
137A187ARG10.9030.96332.388-9.274-9.2740.0000.0000.0000.000
138A188VAL00.0570.02026.5560.0970.0970.0000.0000.0000.000
139A189VAL0-0.057-0.01927.942-0.117-0.1170.0000.0000.0000.000
140A190HIS0-0.009-0.02020.202-0.647-0.6470.0000.0000.0000.000
141A191ASP-1-0.908-0.93622.25513.44113.4410.0000.0000.0000.000
142A192PHE0-0.010-0.00716.1540.3610.3610.0000.0000.0000.000
143A193ALA00.0430.02016.054-0.268-0.2680.0000.0000.0000.000
144A194VAL0-0.050-0.0359.7960.8180.8180.0000.0000.0000.000
145A195GLU-1-0.867-0.9319.83321.67121.6710.0000.0000.0000.000
146A196VAL0-0.004-0.0138.2683.4913.4910.0000.0000.0000.000
147A197GLY00.0190.0297.8781.4391.4390.0000.0000.0000.000
148A198THR0-0.017-0.0013.740-3.792-3.1300.003-0.250-0.415-0.001
149A199PHE0-0.032-0.0111.858-7.213-8.14913.926-6.425-6.565-0.011
150A200GLN00.0150.0063.574-5.361-4.6430.003-0.148-0.5730.000
151A201ALA0-0.0020.0025.2563.6593.6590.0000.0000.0000.000
152A202MET0-0.013-0.0167.872-2.426-2.4260.0000.0000.0000.000
153A203THR00.0250.02810.706-0.215-0.2150.0000.0000.0000.000
154A204TYR00.006-0.00713.930-0.759-0.7590.0000.0000.0000.000
155A205THR0-0.051-0.01813.5490.4960.4960.0000.0000.0000.000
156A206TYR00.0080.00116.034-0.571-0.5710.0000.0000.0000.000
157A207LYS10.9640.97818.839-11.891-11.8910.0000.0000.0000.000
158A208HIS00.0190.01721.156-0.899-0.8990.0000.0000.0000.000
159A209ASN00.0290.02124.1030.3010.3010.0000.0000.0000.000
160A210ASN00.003-0.01526.7910.3370.3370.0000.0000.0000.000
161A211SER0-0.0020.00528.224-0.027-0.0270.0000.0000.0000.000
162A212GLY00.0010.02027.968-0.182-0.1820.0000.0000.0000.000
163A213GLY0-0.019-0.01729.048-0.106-0.1060.0000.0000.0000.000
164A214LEU00.0130.00828.5050.3270.3270.0000.0000.0000.000
165A215ASN0-0.053-0.04925.328-0.081-0.0810.0000.0000.0000.000
166A216SER00.0440.01527.7950.1740.1740.0000.0000.0000.000
167A217SER00.0020.02521.9700.3520.3520.0000.0000.0000.000
168A218ASN0-0.021-0.03522.8210.2020.2020.0000.0000.0000.000
169A219SER0-0.0200.00623.887-0.139-0.1390.0000.0000.0000.000
170A220ILE0-0.011-0.01219.9000.2760.2760.0000.0000.0000.000
171A221ILE00.0010.00823.483-0.252-0.2520.0000.0000.0000.000
172A222HIS00.0740.02819.7040.6170.6170.0000.0000.0000.000
173A223GLU-1-0.891-0.94123.14311.39411.3940.0000.0000.0000.000
174A224TYR0-0.056-0.02724.129-0.237-0.2370.0000.0000.0000.000
175A225LEU0-0.038-0.01418.6580.4660.4660.0000.0000.0000.000
176A226GLU-1-0.916-0.94819.08713.10913.1090.0000.0000.0000.000
177A227LYS10.8510.90219.271-13.427-13.4270.0000.0000.0000.000
178A228ASN00.0240.01315.6190.1550.1550.0000.0000.0000.000
179A229LYS10.9070.93314.379-13.475-13.4750.0000.0000.0000.000
180A230GLU-1-0.864-0.92714.94017.03717.0370.0000.0000.0000.000
181A231ASP-1-0.700-0.83212.78524.75524.7550.0000.0000.0000.000
182A232ALA0-0.003-0.00210.4382.3972.3970.0000.0000.0000.000
183A233ILE00.0060.01610.0452.8992.8990.0000.0000.0000.000
184A234HIS10.8000.89111.534-17.829-17.8290.0000.0000.0000.000
185A235LYS10.7900.8737.682-25.536-25.5360.0000.0000.0000.000
186A236ILE00.000-0.0016.3666.1596.1590.0000.0000.0000.000
187A237LEU00.0320.0177.6922.9332.9330.0000.0000.0000.000
188A238ASN00.001-0.0108.651-1.045-1.0450.0000.0000.0000.000
189A239ARG10.7770.8541.669-136.711-149.06136.528-14.910-9.2680.165
190A240MET0-0.0020.0025.5940.5540.601-0.0010.000-0.0460.000
191A241TYR0-0.010-0.0228.114-1.806-1.8060.0000.0000.0000.000
192A242ALA0-0.004-0.0037.009-1.733-1.7330.0000.0000.0000.000
193A243VAL0-0.035-0.0154.561-1.625-1.460-0.001-0.009-0.1550.000
194A244VAL00.0260.0217.538-3.530-3.5300.0000.0000.0000.000
195A245MET0-0.0100.00511.200-2.710-2.7100.0000.0000.0000.000
196A246LYS10.9660.9918.199-35.224-35.2240.0000.0000.0000.000
197A247LYS10.8470.93211.034-23.330-23.3300.0000.0000.0000.000
198A248ALA00.0200.00812.674-1.765-1.7650.0000.0000.0000.000
199A249VAL0-0.019-0.02114.785-1.410-1.4100.0000.0000.0000.000
200A250THR0-0.107-0.06113.509-0.804-0.8040.0000.0000.0000.000
201A251GLU-1-0.782-0.86816.09916.82516.8250.0000.0000.0000.000
202A252LEU0-0.0290.01318.489-1.181-1.1810.0000.0000.0000.000
203A253THR0-0.017-0.02220.590-0.258-0.2580.0000.0000.0000.000
204A254LYS10.9000.92322.872-10.737-10.7370.0000.0000.0000.000
205A255GLU-1-0.853-0.92225.11412.12312.1230.0000.0000.0000.000
206A256ASN0-0.033-0.01621.537-0.857-0.8570.0000.0000.0000.000
207A257ILE0-0.030-0.00924.041-0.293-0.2930.0000.0000.0000.000
208A258ASP-1-0.771-0.87026.9969.7789.7780.0000.0000.0000.000
209A259LYS10.8110.92424.850-12.796-12.7960.0000.0000.0000.000
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218A268LYS10.8130.90336.712-8.670-8.6700.0000.0000.0000.000
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