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: 5N2LZ

Calculation Name: 1AN8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AN8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NKX2

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2554005.962451
FMO2-HF: Nuclear repulsion 2469980.721561
FMO2-HF: Total energy -84025.24089
FMO2-MP2: Total energy -84273.418087


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-104.104-99.2050.55-2.604-2.845-0.012
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.009 / q_NPA : 1.008
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].
3A5ASP-1-0.826-0.9162.848-57.420-52.7310.551-2.589-2.651-0.012
4A6ILE00.0230.0134.2433.9774.187-0.001-0.015-0.1940.000
5A7SER0-0.052-0.0315.6215.5195.5190.0000.0000.0000.000
6A8ASN00.0320.0127.1555.4625.4620.0000.0000.0000.000
7A9VAL0-0.0050.0146.0313.0903.0900.0000.0000.0000.000
8A10LYS10.8360.9328.81029.63329.6330.0000.0000.0000.000
9A11SER00.0340.02511.3282.7402.7400.0000.0000.0000.000
10A12ASP-1-0.810-0.89411.052-23.643-23.6430.0000.0000.0000.000
11A13LEU0-0.057-0.03210.7652.0482.0480.0000.0000.0000.000
12A14LEU00.0170.01514.6421.5521.5520.0000.0000.0000.000
13A15TYR00.0020.05216.8601.7311.7310.0000.0000.0000.000
14A16ALA0-0.037-0.02116.9171.0751.0750.0000.0000.0000.000
15A17TYR00.006-0.03015.7910.6150.6150.0000.0000.0000.000
16A18THR0-0.049-0.04919.9540.6710.6710.0000.0000.0000.000
17A19ILE0-0.093-0.04322.4930.2850.2850.0000.0000.0000.000
18A20THR0-0.028-0.02725.2010.1410.1410.0000.0000.0000.000
19A21PRO0-0.0140.01127.0440.0220.0220.0000.0000.0000.000
20A22TYR00.0020.00728.4590.3630.3630.0000.0000.0000.000
21A23ASP-1-0.906-0.96931.077-9.695-9.6950.0000.0000.0000.000
22A24TYR0-0.104-0.07933.4220.3320.3320.0000.0000.0000.000
23A25LYS10.9620.97836.3008.5998.5990.0000.0000.0000.000
24A26ASP-1-0.854-0.89938.735-7.165-7.1650.0000.0000.0000.000
25A27CYS0-0.049-0.00738.1850.1760.1760.0000.0000.0000.000
26A28ARG10.9610.99640.0777.0037.0030.0000.0000.0000.000
27A29VAL00.0130.01937.365-0.124-0.1240.0000.0000.0000.000
28A30ASN0-0.015-0.02439.3030.3740.3740.0000.0000.0000.000
29A31PHE0-0.064-0.05537.0320.2310.2310.0000.0000.0000.000
30A32SER00.0560.03935.650-0.159-0.1590.0000.0000.0000.000
31A33THR0-0.0140.00432.0450.1500.1500.0000.0000.0000.000
32A34THR0-0.006-0.02130.3960.0720.0720.0000.0000.0000.000
33A35HIS00.0400.02627.252-0.061-0.0610.0000.0000.0000.000
34A36THR0-0.025-0.00828.602-0.275-0.2750.0000.0000.0000.000
35A37LEU00.0220.01330.7920.3130.3130.0000.0000.0000.000
36A38ASN0-0.0060.01133.153-0.029-0.0290.0000.0000.0000.000
37A39ILE00.008-0.01333.8780.2270.2270.0000.0000.0000.000
38A40ASP-1-0.810-0.89837.232-7.398-7.3980.0000.0000.0000.000
39A41THR00.0270.00636.0570.0570.0570.0000.0000.0000.000
40A42GLN00.0340.03139.4530.0810.0810.0000.0000.0000.000
41A43LYS10.8230.91542.1457.4837.4830.0000.0000.0000.000
42A44TYR0-0.096-0.08639.3090.0550.0550.0000.0000.0000.000
43A45ARG10.8520.91733.6519.0119.0110.0000.0000.0000.000
44A46GLY00.0160.03340.2760.0370.0370.0000.0000.0000.000
45A47LYS10.8940.93042.7016.4846.4840.0000.0000.0000.000
46A48ASP-1-0.857-0.95642.081-7.053-7.0530.0000.0000.0000.000
47A49TYR0-0.058-0.01436.765-0.101-0.1010.0000.0000.0000.000
48A50TYR0-0.0260.00833.768-0.008-0.0080.0000.0000.0000.000
49A51ILE00.0040.01431.362-0.204-0.2040.0000.0000.0000.000
50A52SER0-0.057-0.02330.2820.2080.2080.0000.0000.0000.000
51A53SER0-0.022-0.02528.781-0.349-0.3490.0000.0000.0000.000
52A54GLU-1-0.856-0.93623.735-11.668-11.6680.0000.0000.0000.000
53A55MET0-0.051-0.03625.874-0.354-0.3540.0000.0000.0000.000
54A56SER00.0000.00324.9930.2340.2340.0000.0000.0000.000
55A57TYR00.0690.03226.4690.3430.3430.0000.0000.0000.000
56A58GLU-1-0.879-0.94526.979-10.477-10.4770.0000.0000.0000.000
57A59ALA0-0.060-0.01528.2130.2620.2620.0000.0000.0000.000
58A60SER0-0.018-0.03530.2410.3200.3200.0000.0000.0000.000
59A61GLN00.0100.00332.3850.1750.1750.0000.0000.0000.000
60A62LYS10.8650.94632.8939.2089.2080.0000.0000.0000.000
61A63PHE0-0.044-0.01732.4720.0960.0960.0000.0000.0000.000
62A64LYS10.8170.88537.3267.1847.1840.0000.0000.0000.000
63A65ARG10.9690.97240.2837.0777.0770.0000.0000.0000.000
64A66ASP-1-0.863-0.94942.328-6.687-6.6870.0000.0000.0000.000
65A67ASP-1-0.854-0.88640.054-7.506-7.5060.0000.0000.0000.000
66A68HIS0-0.071-0.04241.2760.0480.0480.0000.0000.0000.000
67A69VAL0-0.028-0.02235.525-0.077-0.0770.0000.0000.0000.000
68A70ASP-1-0.799-0.89035.521-8.318-8.3180.0000.0000.0000.000
69A71VAL0-0.025-0.03431.439-0.204-0.2040.0000.0000.0000.000
70A72PHE0-0.001-0.01126.2510.0500.0500.0000.0000.0000.000
71A73GLY0-0.0130.00226.474-0.272-0.2720.0000.0000.0000.000
72A74LEU0-0.035-0.00221.6290.2720.2720.0000.0000.0000.000
73A75PHE0-0.017-0.00624.271-0.223-0.2230.0000.0000.0000.000
74A76TYR00.0300.00221.104-0.544-0.5440.0000.0000.0000.000
75A77ILE0-0.028-0.00522.642-0.251-0.2510.0000.0000.0000.000
76A78LEU0-0.009-0.00825.0890.1570.1570.0000.0000.0000.000
77A79ASN0-0.046-0.02427.8660.2770.2770.0000.0000.0000.000
78A80SER00.0380.01229.928-0.087-0.0870.0000.0000.0000.000
79A81HIS0-0.009-0.00631.981-0.021-0.0210.0000.0000.0000.000
80A82THR00.0230.00535.752-0.078-0.0780.0000.0000.0000.000
81A83GLY00.0140.02133.8240.1020.1020.0000.0000.0000.000
82A84GLU-1-0.795-0.86231.140-9.536-9.5360.0000.0000.0000.000
83A85TYR00.010-0.01727.1790.0600.0600.0000.0000.0000.000
84A86ILE00.0200.00925.569-0.397-0.3970.0000.0000.0000.000
85A87TYR00.0220.02519.8550.2950.2950.0000.0000.0000.000
86A88GLY00.0290.01824.724-0.150-0.1500.0000.0000.0000.000
87A89GLY00.0330.00726.6930.1980.1980.0000.0000.0000.000
88A90ILE0-0.040-0.00628.1600.3200.3200.0000.0000.0000.000
89A91THR00.0270.00931.548-0.223-0.2230.0000.0000.0000.000
90A92PRO0-0.019-0.01433.9010.1370.1370.0000.0000.0000.000
91A93ALA00.0000.01637.617-0.110-0.1100.0000.0000.0000.000
92A94GLN0-0.018-0.00438.107-0.080-0.0800.0000.0000.0000.000
93A95ASN00.0160.00540.0270.1070.1070.0000.0000.0000.000
94A96ASN0-0.085-0.02842.7740.1560.1560.0000.0000.0000.000
95A97LYS10.9920.97542.1116.7386.7380.0000.0000.0000.000
96A98VAL0-0.006-0.00237.6090.1270.1270.0000.0000.0000.000
97A99ASN0-0.013-0.01537.304-0.180-0.1800.0000.0000.0000.000
98A100HIS0-0.036-0.00233.7190.0540.0540.0000.0000.0000.000
99A101LYS10.9740.99433.3828.1898.1890.0000.0000.0000.000
100A102LEU0-0.001-0.00127.4460.0650.0650.0000.0000.0000.000
101A103LEU0-0.0030.00029.9240.0280.0280.0000.0000.0000.000
102A104GLY00.0390.00125.878-0.239-0.2390.0000.0000.0000.000
103A105ASN0-0.067-0.02023.9500.7460.7460.0000.0000.0000.000
104A106LEU0-0.0060.00018.873-0.562-0.5620.0000.0000.0000.000
105A107PHE0-0.018-0.00818.7100.6340.6340.0000.0000.0000.000
106A108ILE00.0210.01916.517-1.230-1.2300.0000.0000.0000.000
107A109SER00.029-0.00314.3230.5160.5160.0000.0000.0000.000
108A110GLY0-0.042-0.02616.5060.0820.0820.0000.0000.0000.000
109A111GLU-1-0.926-0.94519.441-14.240-14.2400.0000.0000.0000.000
110A112SER0-0.023-0.01421.850-0.159-0.1590.0000.0000.0000.000
111A113GLN0-0.007-0.00823.682-0.245-0.2450.0000.0000.0000.000
112A114GLN00.0340.02822.4860.7230.7230.0000.0000.0000.000
113A115ASN0-0.0020.00325.433-0.216-0.2160.0000.0000.0000.000
114A116LEU00.013-0.00822.9900.0990.0990.0000.0000.0000.000
115A117ASN00.0560.02027.463-0.270-0.2700.0000.0000.0000.000
116A118ASN0-0.099-0.06030.4850.1660.1660.0000.0000.0000.000
117A119LYS10.9420.99028.02210.66910.6690.0000.0000.0000.000
118A120ILE00.0210.02124.8140.0170.0170.0000.0000.0000.000
119A121ILE00.003-0.00629.2510.1810.1810.0000.0000.0000.000
120A122LEU0-0.023-0.00928.662-0.176-0.1760.0000.0000.0000.000
121A123GLU-1-0.958-0.98732.627-8.505-8.5050.0000.0000.0000.000
122A124LYS10.8970.95932.2109.8919.8910.0000.0000.0000.000
123A125ASP-1-0.843-0.91734.599-8.425-8.4250.0000.0000.0000.000
124A126ILE0-0.044-0.02533.132-0.176-0.1760.0000.0000.0000.000
125A127VAL00.0300.01928.5870.0670.0670.0000.0000.0000.000
126A128THR00.0860.04726.644-0.284-0.2840.0000.0000.0000.000
127A129PHE00.051-0.00121.3210.0290.0290.0000.0000.0000.000
128A130GLN00.0300.01622.590-0.587-0.5870.0000.0000.0000.000
129A131GLU-1-0.789-0.87423.581-10.732-10.7320.0000.0000.0000.000
130A132ILE0-0.041-0.03023.284-0.045-0.0450.0000.0000.0000.000
131A133ASP-1-0.781-0.85918.478-17.434-17.4340.0000.0000.0000.000
132A134PHE00.0050.00220.718-0.254-0.2540.0000.0000.0000.000
133A135LYS10.8680.90822.40710.60910.6090.0000.0000.0000.000
134A136ILE00.0150.01319.7970.1360.1360.0000.0000.0000.000
135A137ARG10.8790.92813.64419.82719.8270.0000.0000.0000.000
136A138LYS10.8850.94119.51111.97711.9770.0000.0000.0000.000
137A139TYR00.0180.01822.3560.3780.3780.0000.0000.0000.000
138A140LEU00.014-0.00817.1480.1320.1320.0000.0000.0000.000
139A141MET0-0.063-0.01618.231-0.447-0.4470.0000.0000.0000.000
140A142ASP-1-0.832-0.91120.041-12.633-12.6330.0000.0000.0000.000
141A143ASN0-0.112-0.06123.1200.6130.6130.0000.0000.0000.000
142A144TYR0-0.048-0.03519.0150.2840.2840.0000.0000.0000.000
143A145LYS10.9080.97518.67114.62514.6250.0000.0000.0000.000
144A146ILE0-0.013-0.02014.361-0.837-0.8370.0000.0000.0000.000
145A147TYR0-0.014-0.03412.131-0.895-0.8950.0000.0000.0000.000
146A148ASP-1-0.828-0.90614.864-16.582-16.5820.0000.0000.0000.000
147A149ALA0-0.002-0.01913.980-1.282-1.2820.0000.0000.0000.000
148A150THR0-0.046-0.03213.973-1.133-1.1330.0000.0000.0000.000
149A151SER0-0.063-0.00513.556-0.062-0.0620.0000.0000.0000.000
150A152PRO00.0350.00112.983-1.243-1.2430.0000.0000.0000.000
151A153TYR0-0.058-0.03011.382-0.951-0.9510.0000.0000.0000.000
152A154VAL00.0360.0005.861-1.250-1.2500.0000.0000.0000.000
153A155SER0-0.025-0.0236.121-7.153-7.1530.0000.0000.0000.000
154A156GLY00.0650.0248.0773.1863.1860.0000.0000.0000.000
155A157ARG10.8370.92411.06419.60919.6090.0000.0000.0000.000
156A158ILE0-0.0020.00113.6861.0861.0860.0000.0000.0000.000
157A159GLU-1-0.843-0.92317.402-17.228-17.2280.0000.0000.0000.000
158A160ILE0-0.021-0.01519.6650.7090.7090.0000.0000.0000.000
159A161GLY00.0680.03622.991-0.084-0.0840.0000.0000.0000.000
160A162THR0-0.038-0.06125.6120.2920.2920.0000.0000.0000.000
161A163LYS10.8540.91128.7859.0549.0540.0000.0000.0000.000
162A164ASP-1-0.871-0.89529.793-10.350-10.3500.0000.0000.0000.000
163A165GLY0-0.020-0.00929.1560.0620.0620.0000.0000.0000.000
164A166LYS10.9080.96025.80910.44010.4400.0000.0000.0000.000
165A167HIS00.0260.00121.3440.2250.2250.0000.0000.0000.000
166A168GLU-1-0.859-0.88521.006-14.035-14.0350.0000.0000.0000.000
167A169GLN0-0.014-0.01314.799-0.960-0.9600.0000.0000.0000.000
168A170ILE0-0.0140.00115.6750.1300.1300.0000.0000.0000.000
169A171ASP-1-0.795-0.8988.973-32.199-32.1990.0000.0000.0000.000
170A172LEU0-0.040-0.02311.2921.4081.4080.0000.0000.0000.000
171A173PHE0-0.078-0.0327.4271.0561.0560.0000.0000.0000.000
172A174ASP-1-0.867-0.9237.269-34.408-34.4080.0000.0000.0000.000
173A175SER0-0.091-0.0657.8343.8133.8130.0000.0000.0000.000
174A176PRO00.0390.0137.973-2.203-2.2030.0000.0000.0000.000
175A177ASN0-0.061-0.0288.3680.7190.7190.0000.0000.0000.000
176A178GLU-1-0.900-0.9638.737-19.413-19.4130.0000.0000.0000.000
177A179GLY0-0.0540.00311.172-0.230-0.2300.0000.0000.0000.000
178A180THR00.0080.00711.8921.0941.0940.0000.0000.0000.000
179A181ARG10.9070.94615.60513.83313.8330.0000.0000.0000.000
180A182SER0-0.0050.00818.1480.1120.1120.0000.0000.0000.000
181A183ASP-1-0.771-0.89212.830-18.310-18.3100.0000.0000.0000.000
182A184ILE0-0.006-0.01112.928-0.272-0.2720.0000.0000.0000.000
183A185PHE0-0.022-0.02414.955-0.037-0.0370.0000.0000.0000.000
184A186ALA00.0610.04416.5620.6620.6620.0000.0000.0000.000
185A187LYS10.8380.91714.71719.95319.9530.0000.0000.0000.000
186A188TYR0-0.053-0.05717.8670.2540.2540.0000.0000.0000.000
187A189LYS10.9140.96620.72513.92613.9260.0000.0000.0000.000
188A190ASP-1-0.869-0.93121.601-13.127-13.1270.0000.0000.0000.000
189A191ASN0-0.028-0.02423.9900.3450.3450.0000.0000.0000.000
190A192ARG10.8470.91322.63113.58113.5810.0000.0000.0000.000
191A193ILE0-0.038-0.02125.919-0.017-0.0170.0000.0000.0000.000
192A194ILE0-0.021-0.01327.089-0.030-0.0300.0000.0000.0000.000
193A195ASN0-0.028-0.01129.5850.4240.4240.0000.0000.0000.000
194A196MET00.1040.05130.879-0.218-0.2180.0000.0000.0000.000
195A197LYS10.8920.95933.3008.2218.2210.0000.0000.0000.000
196A198ASN00.005-0.02031.9600.3110.3110.0000.0000.0000.000
197A199PHE00.0170.02626.106-0.248-0.2480.0000.0000.0000.000
198A200SER0-0.045-0.01228.8340.3140.3140.0000.0000.0000.000
199A201HIS10.8360.90725.31512.18712.1870.0000.0000.0000.000
200A202PHE00.0160.01222.317-0.151-0.1510.0000.0000.0000.000
201A203ASP-1-0.808-0.89720.962-12.892-12.8920.0000.0000.0000.000
202A204ILE00.006-0.00117.111-0.593-0.5930.0000.0000.0000.000
203A205TYR0-0.0110.00614.7970.5600.5600.0000.0000.0000.000
204A206LEU0-0.0040.01113.169-1.407-1.4070.0000.0000.0000.000
205A207GLU-1-0.851-0.93410.281-24.901-24.9010.0000.0000.0000.000
206A208LYS10.9140.97010.70016.52016.5200.0000.0000.0000.000