FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8N9KY

Calculation Name: 2GAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GAI

Chain ID: A

ChEMBL ID:

UniProt ID: P46799

Base Structure: X-ray

Registration Date: 2023-09-27

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 580
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12262514.421354
FMO2-HF: Nuclear repulsion 12029081.968145
FMO2-HF: Total energy -233432.453209
FMO2-MP2: Total energy -234118.332945


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-5.9680.5729999999999727.211-15.69-18.062-0.139
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.887 / q_NPA : 0.939
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].
3A9ILE00.0120.0053.8130.4002.963-0.017-1.263-1.2840.006
4A10VAL0-0.023-0.0045.9371.7941.7940.0000.0000.0000.000
5A11VAL0-0.019-0.0059.4430.3400.3400.0000.0000.0000.000
6A12GLU-1-0.743-0.87012.574-16.604-16.6040.0000.0000.0000.000
7A13SER0-0.041-0.06116.2460.2620.2620.0000.0000.0000.000
8A14PRO00.0500.00816.204-0.917-0.9170.0000.0000.0000.000
9A15ALA00.0140.01517.030-0.608-0.6080.0000.0000.0000.000
10A16LYS10.8450.90314.53517.05117.0510.0000.0000.0000.000
11A17ALA0-0.036-0.02112.518-1.223-1.2230.0000.0000.0000.000
12A18LYS10.8290.90612.72913.18513.1850.0000.0000.0000.000
13A19THR00.011-0.00114.758-0.699-0.6990.0000.0000.0000.000
14A20ILE00.008-0.0099.036-0.794-0.7940.0000.0000.0000.000
15A21LYS10.8080.8877.50531.20631.2060.0000.0000.0000.000
16A22SER0-0.029-0.02911.113-0.568-0.5680.0000.0000.0000.000
17A23ILE0-0.0570.00111.0780.1670.1670.0000.0000.0000.000
18A24LEU0-0.014-0.0046.0290.0830.0830.0000.0000.0000.000
19A25GLY00.0490.0477.849-3.209-3.2090.0000.0000.0000.000
20A26ASN0-0.014-0.0247.998-2.642-2.6420.0000.0000.0000.000
21A27GLU-1-0.806-0.8701.688-115.178-122.45721.182-8.322-5.581-0.091
22A28TYR00.0180.0062.404-26.153-19.8234.811-3.914-7.226-0.040
23A29GLU-1-0.839-0.9093.704-20.000-19.5140.000-0.095-0.3910.000
24A30VAL0-0.033-0.0195.754-0.660-0.6600.0000.0000.0000.000
25A31PHE00.015-0.0018.6472.5022.5020.0000.0000.0000.000
26A32ALA00.0270.01410.9570.0410.0410.0000.0000.0000.000
27A33SER0-0.010-0.02014.1740.3190.3190.0000.0000.0000.000
28A34MET0-0.003-0.00515.9561.0871.0870.0000.0000.0000.000
29A35GLY00.0300.03818.6490.8430.8430.0000.0000.0000.000
30A36HIS0-0.022-0.00818.947-0.646-0.6460.0000.0000.0000.000
31A37ILE00.0600.02016.3630.2180.2180.0000.0000.0000.000
32A38ILE0-0.017-0.00319.3110.4370.4370.0000.0000.0000.000
33A39ASP-1-0.777-0.86022.442-10.275-10.2750.0000.0000.0000.000
34A40LEU00.0190.01725.6400.0710.0710.0000.0000.0000.000
35A41PRO0-0.0050.00228.9940.0220.0220.0000.0000.0000.000
36A42LYS10.8770.92429.1259.7359.7350.0000.0000.0000.000
37A43SER0-0.001-0.00933.3270.1250.1250.0000.0000.0000.000
38A44LYS10.8830.94235.0438.3568.3560.0000.0000.0000.000
39A45PHE00.039-0.00335.542-0.185-0.1850.0000.0000.0000.000
40A46GLY0-0.012-0.00533.283-0.153-0.1530.0000.0000.0000.000
41A47VAL00.0300.03132.566-0.273-0.2730.0000.0000.0000.000
42A48ASP-1-0.824-0.90634.524-7.581-7.5810.0000.0000.0000.000
43A49LEU0-0.042-0.04236.533-0.110-0.1100.0000.0000.0000.000
44A50GLU-1-0.867-0.91539.146-6.724-6.7240.0000.0000.0000.000
45A51LYS10.8010.89634.7658.0648.0640.0000.0000.0000.000
46A52ASP-1-0.758-0.85534.991-8.328-8.3280.0000.0000.0000.000
47A53PHE00.0010.00034.327-0.279-0.2790.0000.0000.0000.000
48A54GLU-1-0.843-0.91629.645-9.811-9.8110.0000.0000.0000.000
49A55PRO0-0.049-0.00627.8260.1310.1310.0000.0000.0000.000
50A56GLU-1-0.823-0.88729.420-8.590-8.5900.0000.0000.0000.000
51A57PHE0-0.029-0.03924.735-0.053-0.0530.0000.0000.0000.000
52A58ALA00.0090.00325.9570.0750.0750.0000.0000.0000.000
53A59VAL00.0040.00021.524-0.170-0.1700.0000.0000.0000.000
54A60ILE0-0.050-0.01923.4150.4960.4960.0000.0000.0000.000
55A61LYS10.9090.94524.8789.6739.6730.0000.0000.0000.000
56A62GLY00.0170.01225.7270.0940.0940.0000.0000.0000.000
57A63LYS10.7840.88720.10512.93312.9330.0000.0000.0000.000
58A64GLU-1-0.765-0.89720.280-11.552-11.5520.0000.0000.0000.000
59A65LYS10.9900.99319.76511.60011.6000.0000.0000.0000.000
60A66VAL0-0.0110.00715.927-0.661-0.6610.0000.0000.0000.000
61A67VAL00.0170.00715.312-0.974-0.9740.0000.0000.0000.000
62A68GLU-1-0.803-0.88915.523-14.625-14.6250.0000.0000.0000.000
63A69LYS10.8700.9569.75222.99922.9990.0000.0000.0000.000
64A70LEU0-0.006-0.01210.901-1.349-1.3490.0000.0000.0000.000
65A71LYS10.8480.89710.69513.02013.0200.0000.0000.0000.000
66A72ASP-1-0.882-0.93011.755-20.620-20.6200.0000.0000.0000.000
67A73LEU0-0.008-0.0087.036-0.398-0.3980.0000.0000.0000.000
68A74ALA0-0.018-0.0076.768-2.151-2.1510.0000.0000.0000.000
69A75LYS10.9050.9698.38917.34617.3460.0000.0000.0000.000
70A76LYS10.8170.9017.08321.61421.6140.0000.0000.0000.000
71A77GLY00.0170.0083.642-2.303-2.1380.004-0.043-0.1250.000
72A78GLU-1-0.827-0.8702.715-29.610-28.3280.472-0.557-1.198-0.002
73A79LEU0-0.007-0.0012.848-6.783-4.7660.497-1.291-1.223-0.012
74A80LEU0-0.008-0.0132.9342.1413.1180.262-0.205-1.0340.000
75A81ILE0-0.003-0.0045.4890.6270.6270.0000.0000.0000.000
76A82ALA00.0080.0069.0770.4770.4770.0000.0000.0000.000
77A83SER00.018-0.00310.7800.4630.4630.0000.0000.0000.000
78A84ASP-1-0.774-0.84414.319-15.404-15.4040.0000.0000.0000.000
79A85MET0-0.0350.00817.326-0.005-0.0050.0000.0000.0000.000
80A86ASP-1-0.792-0.89118.496-11.866-11.8660.0000.0000.0000.000
81A87ARG10.8260.87420.5019.8529.8520.0000.0000.0000.000
82A88GLU-1-0.835-0.90421.697-11.958-11.9580.0000.0000.0000.000
83A89GLY00.0390.01918.385-0.248-0.2480.0000.0000.0000.000
84A90GLU-1-0.782-0.87416.597-16.711-16.7110.0000.0000.0000.000
85A91ALA0-0.008-0.00817.760-0.260-0.2600.0000.0000.0000.000
86A92ILE0-0.0120.00115.562-0.102-0.1020.0000.0000.0000.000
87A93ALA00.0190.01113.549-0.451-0.4510.0000.0000.0000.000
88A94TRP00.0530.01814.511-0.201-0.2010.0000.0000.0000.000
89A95HIS0-0.047-0.03217.051-0.170-0.1700.0000.0000.0000.000
90A96ILE00.0160.00611.5430.1450.1450.0000.0000.0000.000
91A97ALA00.0490.03812.976-0.362-0.3620.0000.0000.0000.000
92A98ARG10.9050.96413.91612.40512.4050.0000.0000.0000.000
93A99VAL0-0.069-0.02715.5270.2730.2730.0000.0000.0000.000
94A100THR0-0.039-0.03411.371-0.058-0.0580.0000.0000.0000.000
95A101ASN0-0.042-0.00613.343-0.091-0.0910.0000.0000.0000.000
96A102THR00.008-0.0119.883-0.488-0.4880.0000.0000.0000.000
97A103LEU0-0.036-0.02912.860-0.546-0.5460.0000.0000.0000.000
98A104GLY00.0420.02815.1010.4030.4030.0000.0000.0000.000
99A105ARG10.8190.8917.25625.11125.1110.0000.0000.0000.000
100A106LYS10.9380.9699.61420.02320.0230.0000.0000.0000.000
101A107ASN00.0350.0187.532-1.539-1.5390.0000.0000.0000.000
102A108ARG10.7980.8708.50317.17917.1790.0000.0000.0000.000
103A109ILE0-0.015-0.0066.4750.3180.3180.0000.0000.0000.000
104A110VAL0-0.018-0.00810.4191.3611.3610.0000.0000.0000.000
105A111PHE00.0230.00911.458-0.449-0.4490.0000.0000.0000.000
106A112SER00.0440.01015.9200.4680.4680.0000.0000.0000.000
107A113GLU-1-0.759-0.86917.840-14.036-14.0360.0000.0000.0000.000
108A114ILE0-0.0170.00914.227-1.065-1.0650.0000.0000.0000.000
109A115THR00.014-0.01216.396-0.037-0.0370.0000.0000.0000.000
110A116PRO00.0890.02314.140-1.014-1.0140.0000.0000.0000.000
111A117ARG10.9280.97113.52814.17514.1750.0000.0000.0000.000
112A118VAL00.0060.00714.126-0.853-0.8530.0000.0000.0000.000
113A119ILE00.0040.00410.219-0.893-0.8930.0000.0000.0000.000
114A120ARG10.9210.9439.27023.07723.0770.0000.0000.0000.000
115A121GLU-1-0.826-0.8849.049-26.845-26.8450.0000.0000.0000.000
116A122ALA0-0.0030.00310.344-0.718-0.7180.0000.0000.0000.000
117A123VAL0-0.037-0.0275.2670.2270.2270.0000.0000.0000.000
118A124LYS10.8390.9085.76125.93625.9360.0000.0000.0000.000
119A125ASN0-0.106-0.0477.4141.8651.8650.0000.0000.0000.000
120A126PRO0-0.0200.0116.4152.2412.2410.0000.0000.0000.000
121A127ARG10.9270.9459.44518.29218.2920.0000.0000.0000.000
122A128GLU-1-0.900-0.94611.999-16.133-16.1330.0000.0000.0000.000
123A129ILE0-0.031-0.02513.2060.4320.4320.0000.0000.0000.000
124A130ASP-1-0.816-0.89315.818-12.274-12.2740.0000.0000.0000.000
125A131MET00.014-0.02619.3450.1820.1820.0000.0000.0000.000
126A132LYS10.9741.00221.73310.79810.7980.0000.0000.0000.000
127A133LYS10.8610.94519.84113.38113.3810.0000.0000.0000.000
128A134VAL0-0.044-0.02019.6810.2870.2870.0000.0000.0000.000
129A135ARG10.8840.91322.57110.63810.6380.0000.0000.0000.000
130A136ALA00.0390.03826.0880.3770.3770.0000.0000.0000.000
131A137GLN0-0.008-0.00423.6750.4710.4710.0000.0000.0000.000
132A138LEU0-0.059-0.03924.3020.2920.2920.0000.0000.0000.000
133A139ALA00.0690.03327.3800.2770.2770.0000.0000.0000.000
134A140ARG10.8500.91329.3989.4059.4050.0000.0000.0000.000
135A141ARG10.8060.88326.53410.30010.3000.0000.0000.0000.000
136A142ILE00.0090.00330.5070.2320.2320.0000.0000.0000.000
137A143LEU00.0310.02633.0510.2550.2550.0000.0000.0000.000
138A144ASP-1-0.868-0.93033.419-8.292-8.2920.0000.0000.0000.000
139A145ARG10.7650.88632.5518.7888.7880.0000.0000.0000.000
140A146ILE00.0500.02635.7970.1830.1830.0000.0000.0000.000
141A147VAL00.0310.03838.7990.2050.2050.0000.0000.0000.000
142A148GLY0-0.010-0.00938.6710.1630.1630.0000.0000.0000.000
143A149TYR0-0.055-0.05936.1700.0930.0930.0000.0000.0000.000
144A150SER0-0.0120.01440.7410.1450.1450.0000.0000.0000.000
145A151LEU00.0310.01243.4230.1430.1430.0000.0000.0000.000
146A152SER0-0.070-0.04341.6940.1040.1040.0000.0000.0000.000
147A153PRO00.000-0.00143.6150.0850.0850.0000.0000.0000.000
148A154VAL00.0510.04246.6390.1120.1120.0000.0000.0000.000
149A155LEU00.001-0.00745.7580.1290.1290.0000.0000.0000.000
150A156TRP0-0.0290.00346.9830.0450.0450.0000.0000.0000.000
151A157ARG10.9300.96348.9865.5985.5980.0000.0000.0000.000
152A158ASN0-0.032-0.03152.0760.2330.2330.0000.0000.0000.000
153A159PHE00.0460.03351.0570.0940.0940.0000.0000.0000.000
154A160LYS10.8660.96050.2595.6005.6000.0000.0000.0000.000
155A161SER0-0.030-0.02046.940-0.073-0.0730.0000.0000.0000.000
156A162ASN00.0410.02140.4860.0820.0820.0000.0000.0000.000
157A163LEU00.0370.04042.233-0.016-0.0160.0000.0000.0000.000
158A164SER00.0510.02736.917-0.078-0.0780.0000.0000.0000.000
159A165ALA0-0.046-0.04735.5850.0760.0760.0000.0000.0000.000
160A166GLY00.0520.02636.539-0.019-0.0190.0000.0000.0000.000
161A167ARG10.8980.96034.6218.3038.3030.0000.0000.0000.000
162A168VAL00.0710.03635.6690.1160.1160.0000.0000.0000.000
163A169GLN0-0.014-0.00638.8760.0520.0520.0000.0000.0000.000
164A170SER0-0.001-0.02440.4810.1560.1560.0000.0000.0000.000
165A171ALA00.0590.04241.8660.1520.1520.0000.0000.0000.000
166A172THR0-0.003-0.03040.7100.0710.0710.0000.0000.0000.000
167A173LEU0-0.045-0.02043.2860.0860.0860.0000.0000.0000.000
168A174LYS10.8790.92845.9696.0836.0830.0000.0000.0000.000
169A175LEU00.0020.01143.8750.1130.1130.0000.0000.0000.000
170A176VAL0-0.037-0.02446.2620.1080.1080.0000.0000.0000.000
171A177CYS0-0.034-0.02648.9900.1230.1230.0000.0000.0000.000
172A178ASP-1-0.769-0.88251.178-5.774-5.7740.0000.0000.0000.000
173A179ARG10.7790.89950.1626.1236.1230.0000.0000.0000.000
174A180GLU-1-0.787-0.86552.989-5.518-5.5180.0000.0000.0000.000
175A181ARG10.8020.89953.4895.7145.7140.0000.0000.0000.000
176A182GLU-1-0.810-0.87554.043-5.646-5.6460.0000.0000.0000.000
177A183ILE0-0.073-0.04354.8650.0810.0810.0000.0000.0000.000
178A184LEU0-0.059-0.02158.8230.0790.0790.0000.0000.0000.000
179A185ARG10.9130.93758.1775.2695.2690.0000.0000.0000.000
180A186PHE0-0.052-0.00961.3240.0530.0530.0000.0000.0000.000
181A187VAL00.0350.01963.3420.0380.0380.0000.0000.0000.000
182A188PRO0-0.063-0.02665.429-0.008-0.0080.0000.0000.0000.000
183A189LYS10.8570.92467.2274.5194.5190.0000.0000.0000.000
184A190LYS10.9140.95269.1434.2554.2550.0000.0000.0000.000
185A191TYR0-0.085-0.07165.921-0.017-0.0170.0000.0000.0000.000
186A192HIS00.0660.03671.781-0.024-0.0240.0000.0000.0000.000
187A193ARG10.7990.89064.7584.8584.8580.0000.0000.0000.000
188A194ILE00.0200.00370.2350.0360.0360.0000.0000.0000.000
189A195THR0-0.034-0.01368.034-0.050-0.0500.0000.0000.0000.000
190A196VAL00.0060.01271.2800.0630.0630.0000.0000.0000.000
191A197ASN0-0.026-0.01769.732-0.149-0.1490.0000.0000.0000.000
192A198PHE00.0590.02470.5370.0750.0750.0000.0000.0000.000
193A199ASP-1-0.876-0.93771.203-4.598-4.5980.0000.0000.0000.000
194A200GLY0-0.0120.00567.923-0.055-0.0550.0000.0000.0000.000
195A201LEU0-0.058-0.01265.990-0.106-0.1060.0000.0000.0000.000
196A202THR0-0.006-0.02666.2980.0320.0320.0000.0000.0000.000
197A203ALA0-0.047-0.02467.463-0.053-0.0530.0000.0000.0000.000
198A204GLU-1-0.823-0.89865.939-4.770-4.7700.0000.0000.0000.000
199A205ILE0-0.013-0.00169.2730.0120.0120.0000.0000.0000.000
200A206ASP-1-0.832-0.89170.593-4.575-4.5750.0000.0000.0000.000
201A207VAL0-0.026-0.01570.3620.0810.0810.0000.0000.0000.000
202A208LYS10.9500.97070.2324.1934.1930.0000.0000.0000.000
203A209GLU-1-0.833-0.89868.971-4.533-4.5330.0000.0000.0000.000
204A210LYS10.9070.94864.3404.9144.9140.0000.0000.0000.000
205A211LYS10.9951.00669.8344.1184.1180.0000.0000.0000.000
206A212PHE0-0.0090.01473.443-0.033-0.0330.0000.0000.0000.000
207A213PHE0-0.023-0.03274.1080.0510.0510.0000.0000.0000.000
208A214ASP-1-0.796-0.87578.641-3.867-3.8670.0000.0000.0000.000
209A215ALA00.039-0.00782.186-0.014-0.0140.0000.0000.0000.000
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