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: R9128

Calculation Name: 1R8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8N

Chain ID: A

ChEMBL ID:

UniProt ID: P83667

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1940361.697891
FMO2-HF: Nuclear repulsion 1868952.743134
FMO2-HF: Total energy -71408.954757
FMO2-MP2: Total energy -71615.231448


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-9.328-10.64812.761-4.92-6.52-0.007
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.034
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].
3A3ALA0-0.057-0.0383.878-1.2910.281-0.008-0.903-0.6610.003
4A4GLU-1-0.838-0.8956.333-0.174-0.1740.0000.0000.0000.000
5A5LYS10.8740.9505.232-0.181-0.1810.0000.0000.0000.000
6A6VAL00.0200.0196.8200.4070.4070.0000.0000.0000.000
7A7TYR0-0.032-0.0239.5700.1650.1650.0000.0000.0000.000
8A8ASP-1-0.806-0.92112.369-0.423-0.4230.0000.0000.0000.000
9A9ILE0-0.049-0.04215.8330.0250.0250.0000.0000.0000.000
10A10GLU-1-0.960-0.96318.577-0.174-0.1740.0000.0000.0000.000
11A11GLY0-0.025-0.00216.3070.0550.0550.0000.0000.0000.000
12A12TYR0-0.062-0.03114.0330.0630.0630.0000.0000.0000.000
13A13PRO0-0.046-0.0348.559-0.079-0.0790.0000.0000.0000.000
14A14VAL00.0070.01310.2820.1380.1380.0000.0000.0000.000
15A15PHE0-0.027-0.0229.382-0.236-0.2360.0000.0000.0000.000
16A16LEU00.0240.0198.0310.0720.0720.0000.0000.0000.000
17A17GLY0-0.019-0.00711.5400.1760.1760.0000.0000.0000.000
18A18SER0-0.063-0.03714.5530.1050.1050.0000.0000.0000.000
19A19GLH0-0.027-0.01916.313-0.059-0.0590.0000.0000.0000.000
20A20TYR0-0.024-0.01314.0070.0100.0100.0000.0000.0000.000
21A21TYR00.0100.01018.6880.0050.0050.0000.0000.0000.000
22A22ILE00.0000.00317.866-0.043-0.0430.0000.0000.0000.000
23A23VAL0-0.004-0.01320.4150.0450.0450.0000.0000.0000.000
24A24SER00.0080.01022.105-0.041-0.0410.0000.0000.0000.000
25A25ALA0-0.0160.00321.3970.0150.0150.0000.0000.0000.000
26A26ILE00.0220.00323.1800.0240.0240.0000.0000.0000.000
27A27ILE0-0.0010.00922.2670.0240.0240.0000.0000.0000.000
28A28GLY00.0220.01425.974-0.014-0.0140.0000.0000.0000.000
29A29ALA0-0.0070.00326.5720.0260.0260.0000.0000.0000.000
30A30GLY00.0260.01229.3800.0140.0140.0000.0000.0000.000
31A31GLY00.0200.01329.200-0.017-0.0170.0000.0000.0000.000
32A32GLY00.0070.01428.054-0.006-0.0060.0000.0000.0000.000
33A33GLY0-0.007-0.00424.927-0.029-0.0290.0000.0000.0000.000
34A34VAL0-0.025-0.01022.7310.0180.0180.0000.0000.0000.000
35A35ARG10.8740.93025.8780.2500.2500.0000.0000.0000.000
36A36PRO00.0800.04827.180-0.004-0.0040.0000.0000.0000.000
37A37GLY00.004-0.00129.4300.0180.0180.0000.0000.0000.000
38A38ARG10.8800.92932.5280.1790.1790.0000.0000.0000.000
39A39THR00.0580.03934.609-0.006-0.0060.0000.0000.0000.000
40A40ARG10.9200.97036.0640.2180.2180.0000.0000.0000.000
41A41GLY00.0310.01139.0730.0050.0050.0000.0000.0000.000
42A42SER0-0.005-0.00237.897-0.005-0.0050.0000.0000.0000.000
43A43MET00.003-0.00539.9870.0010.0010.0000.0000.0000.000
44A44CYS0-0.091-0.02935.0110.0000.0000.0000.0000.0000.000
45A45PRO0-0.070-0.04733.494-0.003-0.0030.0000.0000.0000.000
46A46MET00.0530.03031.072-0.010-0.0100.0000.0000.0000.000
47A47SER0-0.011-0.00630.135-0.019-0.0190.0000.0000.0000.000
48A48ILE00.0270.02524.3260.0100.0100.0000.0000.0000.000
49A49ILE0-0.046-0.02128.1540.0090.0090.0000.0000.0000.000
50A50GLN00.0210.02126.632-0.008-0.0080.0000.0000.0000.000
51A51GLU-1-0.853-0.92428.700-0.222-0.2220.0000.0000.0000.000
52A52GLN0-0.035-0.03430.869-0.007-0.0070.0000.0000.0000.000
53A53SER0-0.044-0.02832.7850.0060.0060.0000.0000.0000.000
54A54ASP-1-0.858-0.94029.698-0.220-0.2200.0000.0000.0000.000
55A55LEU0-0.0020.00329.688-0.005-0.0050.0000.0000.0000.000
56A56GLN0-0.0100.01130.8160.0070.0070.0000.0000.0000.000
57A57MET00.0550.02125.468-0.018-0.0180.0000.0000.0000.000
58A58GLY0-0.0050.01125.581-0.030-0.0300.0000.0000.0000.000
59A59LEU0-0.041-0.02325.8690.0200.0200.0000.0000.0000.000
60A60PRO00.002-0.00322.061-0.031-0.0310.0000.0000.0000.000
61A61VAL00.0140.00817.9490.0210.0210.0000.0000.0000.000
62A62ARG10.8450.91917.1060.4070.4070.0000.0000.0000.000
63A63PHE00.0330.01712.458-0.022-0.0220.0000.0000.0000.000
64A64SER0-0.028-0.02312.5670.0900.0900.0000.0000.0000.000
65A65SER00.1000.0477.5240.0180.0180.0000.0000.0000.000
66A66PRO0-0.026-0.01210.0600.2910.2910.0000.0000.0000.000
67A67GLU-1-0.947-0.9565.915-2.157-2.1570.0000.0000.0000.000
68A68GLU-1-0.882-0.9455.785-1.552-1.5520.0000.0000.0000.000
69A69LYS10.8500.8979.2670.6890.6890.0000.0000.0000.000
70A70GLN0-0.027-0.01710.5480.0900.0900.0000.0000.0000.000
71A71GLY00.0800.0527.1460.1700.1700.0000.0000.0000.000
72A72LYS10.8650.9385.265-0.358-0.3580.0000.0000.0000.000
73A73ILE00.0800.0364.608-1.275-1.216-0.001-0.004-0.0540.000
74A74TYR0-0.017-0.0012.149-1.935-4.99112.772-4.000-5.716-0.010
75A75THR0-0.015-0.0085.3080.4150.473-0.001-0.001-0.0550.000
76A76ASP-1-0.831-0.9127.433-2.751-2.7510.0000.0000.0000.000
77A77THR0-0.043-0.0114.4780.0540.101-0.001-0.012-0.0340.000
78A78GLU-1-0.947-0.9757.857-0.890-0.8900.0000.0000.0000.000
79A79LEU0-0.025-0.0238.813-0.068-0.0680.0000.0000.0000.000
80A80GLU-1-0.850-0.91112.025-0.498-0.4980.0000.0000.0000.000
81A81ILE0-0.0070.00114.999-0.049-0.0490.0000.0000.0000.000
82A82GLU-1-0.832-0.90017.479-0.393-0.3930.0000.0000.0000.000
83A83PHE0-0.007-0.01020.517-0.017-0.0170.0000.0000.0000.000
84A84VAL0-0.058-0.03421.6770.0090.0090.0000.0000.0000.000
85A85GLU-1-0.796-0.88523.817-0.203-0.2030.0000.0000.0000.000
86A86LYS10.7860.88427.2510.1950.1950.0000.0000.0000.000
87A87PRO0-0.034-0.00629.3950.0160.0160.0000.0000.0000.000
88A88ASP-1-0.855-0.94332.842-0.181-0.1810.0000.0000.0000.000
89A90ALA00.0490.02430.914-0.001-0.0010.0000.0000.0000.000
90A91GLU-1-0.841-0.91530.791-0.202-0.2020.0000.0000.0000.000
91A92SER0-0.083-0.03725.170-0.019-0.0190.0000.0000.0000.000
92A93SER00.0290.00224.2500.0030.0030.0000.0000.0000.000
93A94LYS10.8330.89519.2240.5670.5670.0000.0000.0000.000
94A95TRP0-0.020-0.01720.4090.0140.0140.0000.0000.0000.000
95A96VAL0-0.028-0.00821.535-0.041-0.0410.0000.0000.0000.000
96A97ILE00.0020.00722.1840.0130.0130.0000.0000.0000.000
97A98VAL00.0050.00525.2050.0180.0180.0000.0000.0000.000
98A99LYS10.7980.87929.0090.3300.3300.0000.0000.0000.000
99A100ASP-1-0.761-0.84631.051-0.261-0.2610.0000.0000.0000.000
100A101SER0-0.042-0.04034.3610.0140.0140.0000.0000.0000.000
101A102GLY0-0.0060.01535.2070.0060.0060.0000.0000.0000.000
102A103GLU-1-0.760-0.88830.384-0.359-0.3590.0000.0000.0000.000
103A104ALA0-0.046-0.02627.6860.0070.0070.0000.0000.0000.000
104A105ARG10.8780.92528.0360.2650.2650.0000.0000.0000.000
105A106VAL00.0160.00623.137-0.009-0.0090.0000.0000.0000.000
106A107ALA0-0.062-0.03325.9340.0350.0350.0000.0000.0000.000
107A108ILE0-0.0030.00025.102-0.037-0.0370.0000.0000.0000.000
108A109GLY00.0580.03926.3280.0290.0290.0000.0000.0000.000
109A110GLY0-0.015-0.02026.557-0.028-0.0280.0000.0000.0000.000
110A111SER0-0.067-0.07127.4530.0030.0030.0000.0000.0000.000
111A112GLU-1-0.891-0.92829.731-0.243-0.2430.0000.0000.0000.000
112A113ASP-1-0.792-0.86729.875-0.258-0.2580.0000.0000.0000.000
113A114HIS10.7700.86529.4580.3030.3030.0000.0000.0000.000
114A115PRO00.0300.02732.3680.0000.0000.0000.0000.0000.000
115A116GLN00.0310.00528.557-0.033-0.0330.0000.0000.0000.000
116A117GLY0-0.025-0.01130.462-0.017-0.0170.0000.0000.0000.000
117A118GLU-1-0.860-0.92631.382-0.268-0.2680.0000.0000.0000.000
118A119LEU0-0.026-0.00526.652-0.021-0.0210.0000.0000.0000.000
119A120VAL0-0.0010.00024.1200.0010.0010.0000.0000.0000.000
120A121ARG10.9380.96221.6550.4030.4030.0000.0000.0000.000
121A122GLY00.0280.00719.2960.0220.0220.0000.0000.0000.000
122A123PHE0-0.0560.00314.1780.0350.0350.0000.0000.0000.000
123A124PHE00.010-0.00715.2220.0680.0680.0000.0000.0000.000
124A125LYS10.8570.92610.7871.8831.8830.0000.0000.0000.000
125A126ILE0-0.034-0.01911.1310.2920.2920.0000.0000.0000.000
126A127GLU-1-0.760-0.89511.295-2.180-2.1800.0000.0000.0000.000
127A128LYS10.8210.89412.3931.0161.0160.0000.0000.0000.000
128A129LEU0-0.023-0.00614.1860.0630.0630.0000.0000.0000.000
129A130GLY00.0280.01417.6570.0830.0830.0000.0000.0000.000
130A131SER0-0.015-0.03117.121-0.068-0.0680.0000.0000.0000.000
131A132LEU0-0.021-0.01218.6430.0160.0160.0000.0000.0000.000
132A133ALA0-0.014-0.00718.5880.0300.0300.0000.0000.0000.000
133A134TYR00.0040.01112.168-0.093-0.0930.0000.0000.0000.000
134A135LYS10.8030.89316.2360.8530.8530.0000.0000.0000.000
135A136LEU00.0020.01315.937-0.129-0.1290.0000.0000.0000.000
136A137VAL00.0330.01915.3010.1010.1010.0000.0000.0000.000
137A138PHE00.0140.00116.967-0.080-0.0800.0000.0000.0000.000
138A139CYS00.0440.02816.241-0.057-0.0570.0000.0000.0000.000
139A140PRO00.0140.00318.456-0.009-0.0090.0000.0000.0000.000
140A141LYS10.9850.97618.5200.5650.5650.0000.0000.0000.000
141A142SER0-0.033-0.02520.6720.0080.0080.0000.0000.0000.000
142A143ASP-1-0.888-0.90822.235-0.481-0.4810.0000.0000.0000.000
143A144SER0-0.003-0.00418.924-0.071-0.0710.0000.0000.0000.000
144A145GLY0-0.052-0.03819.0620.0400.0400.0000.0000.0000.000
145A146SER0-0.105-0.06019.8600.0000.0000.0000.0000.0000.000
146A148SER0-0.0120.00120.0220.0650.0650.0000.0000.0000.000
147A149ASP-1-0.707-0.85120.518-0.742-0.7420.0000.0000.0000.000
148A150ILE0-0.043-0.01719.1120.0640.0640.0000.0000.0000.000
149A151GLY00.0440.01722.421-0.014-0.0140.0000.0000.0000.000
150A152ILE0-0.058-0.01725.3680.0110.0110.0000.0000.0000.000
151A153ASN0-0.028-0.01928.2130.0110.0110.0000.0000.0000.000
152A154TYR00.0290.00229.9700.0050.0050.0000.0000.0000.000
153A155GLU-1-0.765-0.86534.137-0.248-0.2480.0000.0000.0000.000
154A156GLY0-0.012-0.01937.2160.0100.0100.0000.0000.0000.000
155A157ARG10.8270.90434.2250.2140.2140.0000.0000.0000.000
156A158ARG10.8070.91729.7600.2760.2760.0000.0000.0000.000
157A159SER0-0.009-0.01929.975-0.021-0.0210.0000.0000.0000.000
158A160LEU00.0410.02023.303-0.004-0.0040.0000.0000.0000.000
159A161VAL0-0.054-0.02226.7680.0130.0130.0000.0000.0000.000
160A162LEU00.0040.00422.977-0.031-0.0310.0000.0000.0000.000
161A163LYS10.8150.92425.5750.3760.3760.0000.0000.0000.000
162A164SER0-0.021-0.02425.763-0.021-0.0210.0000.0000.0000.000
163A165SER0-0.027-0.03826.9040.0140.0140.0000.0000.0000.000
164A166ASP-1-0.852-0.91921.461-0.611-0.6110.0000.0000.0000.000
165A167ASP-1-0.921-0.93524.246-0.354-0.3540.0000.0000.0000.000
166A168VAL0-0.080-0.03826.5290.0180.0180.0000.0000.0000.000
167A169PRO00.0150.01421.624-0.003-0.0030.0000.0000.0000.000
168A170PHE0-0.071-0.04822.4930.0410.0410.0000.0000.0000.000
169A171ARG10.9100.95121.1900.3310.3310.0000.0000.0000.000
170A172VAL0-0.0090.00217.7660.0460.0460.0000.0000.0000.000
171A173VAL00.015-0.00117.885-0.038-0.0380.0000.0000.0000.000
172A174PHE00.0370.02214.0110.0190.0190.0000.0000.0000.000
173A175VAL00.0330.01217.6660.0430.0430.0000.0000.0000.000
174A176LYS11.0301.02218.1120.1990.1990.0000.0000.0000.000
175A177PRO0-0.009-0.00920.1350.0310.0310.0000.0000.0000.000
176A178ARG10.8740.95222.9640.2360.2360.0000.0000.0000.000
177A179SER0-0.004-0.00424.138-0.003-0.0030.0000.0000.0000.000
178A180GLY00.013-0.00826.7870.0110.0110.0000.0000.0000.000
179A181SER0-0.063-0.02826.861-0.001-0.0010.0000.0000.0000.000
180A182GLU-1-0.831-0.90428.184-0.104-0.1040.0000.0000.0000.000
181A183THR0-0.129-0.09524.186-0.012-0.0120.0000.0000.0000.000
182A184GLU-1-0.916-0.93826.838-0.132-0.1320.0000.0000.0000.000
183A185SER0-0.054-0.02425.293-0.015-0.0150.0000.0000.0000.000