FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2JRRR

Calculation Name: 2I81-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I81

Chain ID: A

ChEMBL ID:

UniProt ID: A5K421

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2107986.912449
FMO2-HF: Nuclear repulsion 2033024.306693
FMO2-HF: Total energy -74962.605757
FMO2-MP2: Total energy -75183.583693


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
0.4942.5020.169-0.858-1.3180.002
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : -0.003
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].
3A4TYR00.0580.0183.898-1.866-0.545-0.008-0.631-0.6820.001
4A5VAL0-0.020-0.0066.7010.4090.4090.0000.0000.0000.000
5A6GLY0-0.0040.0047.341-0.101-0.1010.0000.0000.0000.000
6A7LYS10.7950.8892.6893.5874.2740.177-0.227-0.6360.001
7A8GLU-1-0.923-0.9568.818-0.682-0.6820.0000.0000.0000.000
8A9ALA00.003-0.0039.457-0.252-0.2520.0000.0000.0000.000
9A10PRO00.0080.0118.5210.0510.0510.0000.0000.0000.000
10A11PHE00.0300.02011.2540.1510.1510.0000.0000.0000.000
11A12PHE00.0260.01014.6500.0160.0160.0000.0000.0000.000
12A13LYS10.8020.87017.1450.1990.1990.0000.0000.0000.000
13A14ALA00.0020.01720.7440.0040.0040.0000.0000.0000.000
14A15GLU-1-0.806-0.88522.837-0.075-0.0750.0000.0000.0000.000
15A16ALA0-0.005-0.01125.523-0.003-0.0030.0000.0000.0000.000
16A17VAL0-0.055-0.02727.7350.0070.0070.0000.0000.0000.000
17A18PHE00.0460.03728.939-0.004-0.0040.0000.0000.0000.000
18A19GLY00.0960.05432.1210.0070.0070.0000.0000.0000.000
19A20ASP-1-0.866-0.92334.433-0.059-0.0590.0000.0000.0000.000
20A21ASN0-0.101-0.07135.2870.0050.0050.0000.0000.0000.000
21A22SER0-0.028-0.02435.4660.0000.0000.0000.0000.0000.000
22A23PHE0-0.015-0.03032.517-0.001-0.0010.0000.0000.0000.000
23A24GLY00.0190.00530.9140.0010.0010.0000.0000.0000.000
24A25GLU-1-0.818-0.87925.369-0.167-0.1670.0000.0000.0000.000
25A26VAL0-0.009-0.00223.1250.0030.0030.0000.0000.0000.000
26A27ASN0-0.036-0.03321.248-0.019-0.0190.0000.0000.0000.000
27A28LEU00.0180.02515.4830.0190.0190.0000.0000.0000.000
28A29THR00.0630.00819.7400.0010.0010.0000.0000.0000.000
29A30GLN0-0.0030.02321.4500.0110.0110.0000.0000.0000.000
30A31PHE00.0350.00922.0590.0220.0220.0000.0000.0000.000
31A32ILE00.0230.02618.2610.0090.0090.0000.0000.0000.000
32A33GLY0-0.007-0.01122.0810.0180.0180.0000.0000.0000.000
33A34LYS10.7760.89524.3410.1960.1960.0000.0000.0000.000
34A35LYS10.8350.92024.8510.1550.1550.0000.0000.0000.000
35A36TYR0-0.027-0.02820.884-0.016-0.0160.0000.0000.0000.000
36A37VAL0-0.018-0.01319.4010.0200.0200.0000.0000.0000.000
37A38LEU0-0.0070.01019.216-0.026-0.0260.0000.0000.0000.000
38A39LEU00.0080.01116.0810.0220.0220.0000.0000.0000.000
39A40TYR0-0.074-0.06018.2380.0080.0080.0000.0000.0000.000
40A41PHE00.0210.01015.1240.0080.0080.0000.0000.0000.000
41A42TYR0-0.045-0.05019.7720.0150.0150.0000.0000.0000.000
42A43PRO00.0040.01521.903-0.008-0.0080.0000.0000.0000.000
43A44LEU00.026-0.00122.882-0.002-0.0020.0000.0000.0000.000
44A45ASP-1-0.707-0.83526.244-0.032-0.0320.0000.0000.0000.000
45A46PHE0-0.058-0.04029.3200.0070.0070.0000.0000.0000.000
46A47THR0-0.0070.00828.6460.0060.0060.0000.0000.0000.000
47A48PHE00.010-0.01430.826-0.005-0.0050.0000.0000.0000.000
48A49VAL00.0150.01827.014-0.004-0.0040.0000.0000.0000.000
49A50CYS0-0.0160.04226.773-0.002-0.0020.0000.0000.0000.000
50A51PRO00.0560.04228.103-0.008-0.0080.0000.0000.0000.000
51A52SER0-0.065-0.04430.469-0.004-0.0040.0000.0000.0000.000
52A53GLU-1-0.733-0.86024.7840.0060.0060.0000.0000.0000.000
53A54ILE00.0220.02127.261-0.007-0.0070.0000.0000.0000.000
54A55ILE0-0.006-0.01629.063-0.006-0.0060.0000.0000.0000.000
55A56ALA0-0.043-0.01730.249-0.002-0.0020.0000.0000.0000.000
56A57LEU00.0220.00625.130-0.003-0.0030.0000.0000.0000.000
57A58ASP-1-0.767-0.86829.309-0.060-0.0600.0000.0000.0000.000
58A59LYS10.8760.93731.9760.0230.0230.0000.0000.0000.000
59A60ALA00.0350.03130.5230.0020.0020.0000.0000.0000.000
60A61LEU0-0.015-0.00829.943-0.006-0.0060.0000.0000.0000.000
61A62ASP-1-0.811-0.91031.901-0.062-0.0620.0000.0000.0000.000
62A63ALA00.0330.02831.953-0.002-0.0020.0000.0000.0000.000
63A64PHE0-0.010-0.02125.413-0.005-0.0050.0000.0000.0000.000
64A65HIS0-0.0060.00029.170-0.013-0.0130.0000.0000.0000.000
65A66GLU-1-0.891-0.92331.793-0.064-0.0640.0000.0000.0000.000
66A67ARG10.7450.86527.3550.0690.0690.0000.0000.0000.000
67A68ASN00.013-0.00527.222-0.010-0.0100.0000.0000.0000.000
68A69VAL00.0290.01424.109-0.014-0.0140.0000.0000.0000.000
69A70GLU-1-0.920-0.96423.715-0.120-0.1200.0000.0000.0000.000
70A71LEU0-0.042-0.02023.912-0.009-0.0090.0000.0000.0000.000
71A72LEU0-0.001-0.00321.2060.0100.0100.0000.0000.0000.000
72A73GLY00.0650.02522.108-0.005-0.0050.0000.0000.0000.000
73A74CYS0-0.061-0.03019.690-0.014-0.0140.0000.0000.0000.000
74A75SER0-0.003-0.02921.2470.0080.0080.0000.0000.0000.000
75A76VAL00.0310.00920.324-0.012-0.0120.0000.0000.0000.000
76A77ASP-1-0.789-0.84822.641-0.015-0.0150.0000.0000.0000.000
77A78SER00.0080.02426.180-0.012-0.0120.0000.0000.0000.000
78A79LYS10.8850.92228.2580.0720.0720.0000.0000.0000.000
79A80TYR00.0260.00229.8370.0000.0000.0000.0000.0000.000
80A81THR0-0.0070.00329.6770.0040.0040.0000.0000.0000.000
81A82HIS10.8450.89825.5240.0570.0570.0000.0000.0000.000
82A83LEU0-0.0090.00931.1970.0020.0020.0000.0000.0000.000
83A84ALA0-0.003-0.00734.6110.0020.0020.0000.0000.0000.000
84A85TRP0-0.002-0.00628.7750.0020.0020.0000.0000.0000.000
85A86LYS10.8120.90832.7890.0550.0550.0000.0000.0000.000
86A87LYS10.9150.96435.7390.0340.0340.0000.0000.0000.000
87A88THR0-0.0330.00237.3880.0040.0040.0000.0000.0000.000
88A89PRO0-0.001-0.00538.719-0.001-0.0010.0000.0000.0000.000
89A90LEU00.0590.02037.1700.0030.0030.0000.0000.0000.000
90A91ALA0-0.018-0.00839.6220.0030.0030.0000.0000.0000.000
91A92LYS10.8800.93740.9670.0020.0020.0000.0000.0000.000
92A93GLY00.0440.03837.1510.0010.0010.0000.0000.0000.000
93A94GLY0-0.010-0.00235.5270.0000.0000.0000.0000.0000.000
94A95ILE0-0.006-0.00231.0590.0020.0020.0000.0000.0000.000
95A96GLY00.0120.01634.872-0.002-0.0020.0000.0000.0000.000
96A97ASN0-0.020-0.01235.903-0.002-0.0020.0000.0000.0000.000
97A98ILE0-0.028-0.00230.5620.0000.0000.0000.0000.0000.000
98A99LYS10.8430.89434.3740.0520.0520.0000.0000.0000.000
99A100HIS0-0.042-0.00927.225-0.005-0.0050.0000.0000.0000.000
100A101THR0-0.0100.00626.7420.0080.0080.0000.0000.0000.000
101A102LEU0-0.023-0.00726.091-0.004-0.0040.0000.0000.0000.000
102A103LEU00.0570.01620.6280.0040.0040.0000.0000.0000.000
103A104SER0-0.058-0.04724.0870.0150.0150.0000.0000.0000.000
104A105ASP-1-0.677-0.82617.626-0.145-0.1450.0000.0000.0000.000
105A106ILE0-0.011-0.00320.9610.0150.0150.0000.0000.0000.000
106A107THR0-0.032-0.03419.5910.0180.0180.0000.0000.0000.000
107A108LYS10.7920.90717.815-0.014-0.0140.0000.0000.0000.000
108A109SER00.0350.02815.4340.0130.0130.0000.0000.0000.000
109A110ILE00.0080.00413.784-0.035-0.0350.0000.0000.0000.000
110A111SER0-0.014-0.04413.243-0.039-0.0390.0000.0000.0000.000
111A112LYS10.7710.88011.747-0.012-0.0120.0000.0000.0000.000
112A113ASP-1-0.894-0.9409.268-0.424-0.4240.0000.0000.0000.000
113A114TYR0-0.046-0.0538.393-0.246-0.2460.0000.0000.0000.000
114A115ASN0-0.104-0.0446.024-0.081-0.0810.0000.0000.0000.000
115A116VAL00.0280.0179.4970.1430.1430.0000.0000.0000.000
116A117LEU0-0.067-0.02013.146-0.003-0.0030.0000.0000.0000.000
117A118PHE0-0.0050.00214.5980.0720.0720.0000.0000.0000.000
118A119ASP-1-0.845-0.93317.3700.1810.1810.0000.0000.0000.000
119A120ASP-1-0.848-0.90516.5710.0950.0950.0000.0000.0000.000
120A121SER0-0.041-0.02518.429-0.037-0.0370.0000.0000.0000.000
121A122VAL0-0.005-0.00920.173-0.025-0.0250.0000.0000.0000.000
122A123SER00.0240.00417.5980.0200.0200.0000.0000.0000.000
123A124LEU00.003-0.00414.632-0.001-0.0010.0000.0000.0000.000
124A125ARG10.7600.83618.216-0.069-0.0690.0000.0000.0000.000
125A126ALA00.0220.01515.3580.0110.0110.0000.0000.0000.000
126A127PHE00.002-0.00616.898-0.010-0.0100.0000.0000.0000.000
127A128VAL00.0320.00712.819-0.006-0.0060.0000.0000.0000.000
128A129LEU0-0.0130.00315.7030.0130.0130.0000.0000.0000.000
129A130ILE00.0010.00615.001-0.043-0.0430.0000.0000.0000.000
130A131ASP-1-0.726-0.85716.616-0.310-0.3100.0000.0000.0000.000
131A132MET0-0.009-0.00818.660-0.011-0.0110.0000.0000.0000.000
132A133ASN0-0.047-0.02917.3470.0290.0290.0000.0000.0000.000
133A134GLY00.0100.01216.240-0.022-0.0220.0000.0000.0000.000
134A135ILE0-0.008-0.00311.749-0.100-0.1000.0000.0000.0000.000
135A136VAL0-0.031-0.00910.7440.1020.1020.0000.0000.0000.000
136A137GLN0-0.004-0.01111.826-0.037-0.0370.0000.0000.0000.000
137A138HIS0-0.025-0.01914.4920.0340.0340.0000.0000.0000.000
138A139LEU00.0100.0099.748-0.047-0.0470.0000.0000.0000.000
139A140LEU0-0.041-0.00213.6340.0530.0530.0000.0000.0000.000
140A141VAL00.025-0.00112.657-0.029-0.0290.0000.0000.0000.000
141A142ASN0-0.027-0.00415.8380.0450.0450.0000.0000.0000.000
142A143ASN00.0470.01719.113-0.002-0.0020.0000.0000.0000.000
143A144LEU00.0770.02220.552-0.023-0.0230.0000.0000.0000.000
144A145ALA0-0.032-0.00223.333-0.016-0.0160.0000.0000.0000.000
145A146ILE0-0.034-0.01323.029-0.006-0.0060.0000.0000.0000.000
146A147GLY00.0500.03423.796-0.003-0.0030.0000.0000.0000.000
147A148ARG10.7580.86320.6810.0340.0340.0000.0000.0000.000
148A149SER0-0.045-0.02824.792-0.008-0.0080.0000.0000.0000.000
149A150VAL00.0610.02124.982-0.006-0.0060.0000.0000.0000.000
150A151ASP-1-0.820-0.90926.749-0.026-0.0260.0000.0000.0000.000
151A152GLU-1-0.799-0.85922.207-0.029-0.0290.0000.0000.0000.000
152A153ILE00.009-0.00520.612-0.008-0.0080.0000.0000.0000.000
153A154LEU00.0050.01123.244-0.016-0.0160.0000.0000.0000.000
154A155ARG10.7800.85922.4530.0250.0250.0000.0000.0000.000
155A156ILE0-0.023-0.01119.290-0.005-0.0050.0000.0000.0000.000
156A157ILE00.0070.00422.058-0.015-0.0150.0000.0000.0000.000
157A158ASP-1-0.818-0.89923.446-0.078-0.0780.0000.0000.0000.000
158A159ALA0-0.007-0.02722.6120.0010.0010.0000.0000.0000.000
159A160ILE0-0.009-0.00618.158-0.003-0.0030.0000.0000.0000.000
160A161GLN0-0.011-0.01421.5350.0100.0100.0000.0000.0000.000
161A162HIS0-0.074-0.04124.7420.0030.0030.0000.0000.0000.000
162A163HIS0-0.065-0.04319.416-0.012-0.0120.0000.0000.0000.000
163A164GLU-1-0.817-0.89821.418-0.190-0.1900.0000.0000.0000.000
164A165LYS10.8580.95123.5200.0980.0980.0000.0000.0000.000
165A166TYR0-0.016-0.01526.3820.0060.0060.0000.0000.0000.000
166A167GLY00.0040.02323.5680.0050.0050.0000.0000.0000.000
167A168ASP-1-0.847-0.92223.729-0.056-0.0560.0000.0000.0000.000
168A169VAL00.0130.01321.407-0.011-0.0110.0000.0000.0000.000
169A170CYS0-0.0170.01122.9790.0080.0080.0000.0000.0000.000
170A171PRO0-0.0120.01823.0830.0020.0020.0000.0000.0000.000
171A172ALA00.0450.00624.508-0.002-0.0020.0000.0000.0000.000
172A173ASN0-0.005-0.01325.299-0.002-0.0020.0000.0000.0000.000
173A174TRP00.0050.01426.115-0.001-0.0010.0000.0000.0000.000
174A175GLN00.0620.02027.386-0.005-0.0050.0000.0000.0000.000
175A176LYS10.8750.95928.4380.0810.0810.0000.0000.0000.000
176A177GLY00.001-0.00431.6000.0030.0030.0000.0000.0000.000
177A178LYS10.8120.90329.8640.0140.0140.0000.0000.0000.000
178A179VAL00.0250.02431.832-0.005-0.0050.0000.0000.0000.000
179A180SER0-0.058-0.05827.6190.0030.0030.0000.0000.0000.000
180A181MET0-0.0090.00425.8920.0070.0070.0000.0000.0000.000
181A182LYS10.9170.96626.2220.0330.0330.0000.0000.0000.000
182A183PRO0-0.0070.00322.7810.0090.0090.0000.0000.0000.000
183A184SER0-0.025-0.02324.592-0.002-0.0020.0000.0000.0000.000
184A185GLU-1-0.899-0.95326.849-0.005-0.0050.0000.0000.0000.000
185A186GLU-1-0.809-0.89628.852-0.031-0.0310.0000.0000.0000.000
186A187GLY0-0.012-0.00729.8060.0020.0020.0000.0000.0000.000
187A188VAL00.060-0.00326.1620.0010.0010.0000.0000.0000.000
188A189ALA0-0.0090.00028.4720.0040.0040.0000.0000.0000.000
189A190GLN0-0.0220.01131.8320.0000.0000.0000.0000.0000.000
190A191TYR00.005-0.00928.9240.0000.0000.0000.0000.0000.000
191A192LEU0-0.043-0.02628.5740.0030.0030.0000.0000.0000.000
192A193SER0-0.048-0.01932.2830.0050.0050.0000.0000.0000.000
193A194THR0-0.075-0.01934.214-0.001-0.0010.0000.0000.0000.000