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

tag_button

FMODB ID: 228VR

Calculation Name: 2FPN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FPN

Chain ID: A

ChEMBL ID:

UniProt ID: O32277

Base Structure: X-ray

Registration Date: 2023-06-19

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2206875.434051
FMO2-HF: Nuclear repulsion 2118678.516155
FMO2-HF: Total energy -88196.917896
FMO2-MP2: Total energy -88452.260361


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-6.82-2.6482.78-3.267-3.685-0.017
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.023
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].
3A3PRO00.021-0.0023.865-1.910-0.106-0.014-0.958-0.8320.005
4A4LEU00.0060.0146.8280.2270.2270.0000.0000.0000.000
5A5ALA00.0130.0143.3000.0140.3650.022-0.125-0.2480.000
6A6GLN0-0.032-0.0213.3550.7081.7590.024-0.411-0.6650.001
7A7MET0-0.062-0.0325.6850.5510.5510.0000.0000.0000.000
8A8ALA00.0150.0158.6560.2140.2140.0000.0000.0000.000
9A9GLU-1-0.809-0.9015.194-0.665-0.599-0.0010.000-0.0640.000
10A10GLY0-0.067-0.0299.1190.1800.1800.0000.0000.0000.000
11A11MET0-0.052-0.02610.7940.0810.0810.0000.0000.0000.000
12A12GLU-1-0.840-0.92411.045-0.401-0.4010.0000.0000.0000.000
13A13ARG10.8090.8887.3170.4080.4080.0000.0000.0000.000
14A14GLN0-0.083-0.03614.0970.0470.0470.0000.0000.0000.000
15A15ASP-1-0.924-0.95316.861-0.105-0.1050.0000.0000.0000.000
16A16VAL0-0.079-0.03616.6310.0080.0080.0000.0000.0000.000
17A17SER00.0090.01316.679-0.041-0.0410.0000.0000.0000.000
18A18ILE0-0.025-0.02313.155-0.025-0.0250.0000.0000.0000.000
19A19ASP-1-0.835-0.89617.538-0.204-0.2040.0000.0000.0000.000
20A20LYS10.8330.89818.7090.3300.3300.0000.0000.0000.000
21A21TRP0-0.0090.00513.716-0.075-0.0750.0000.0000.0000.000
22A22THR0-0.011-0.04015.3090.0800.0800.0000.0000.0000.000
23A23LEU0-0.0210.01511.134-0.082-0.0820.0000.0000.0000.000
24A24HIS00.0190.00615.1740.0570.0570.0000.0000.0000.000
25A25ALA00.0410.03116.428-0.040-0.0400.0000.0000.0000.000
26A26LYS10.8920.93318.2630.2040.2040.0000.0000.0000.000
27A27GLN0-0.019-0.00521.3070.0000.0000.0000.0000.0000.000
28A28ASN00.005-0.00923.7730.0020.0020.0000.0000.0000.000
29A29LEU00.0280.01126.9030.0040.0040.0000.0000.0000.000
30A30SER0-0.036-0.03529.7590.0030.0030.0000.0000.0000.000
31A31LEU00.0000.00731.7720.0020.0020.0000.0000.0000.000
32A32THR00.012-0.01135.7060.0000.0000.0000.0000.0000.000
33A33GLU-1-0.759-0.84538.538-0.067-0.0670.0000.0000.0000.000
34A34LYS10.9800.98139.6670.0470.0470.0000.0000.0000.000
35A35GLU-1-0.823-0.89336.435-0.066-0.0660.0000.0000.0000.000
36A36PHE00.0150.00633.648-0.002-0.0020.0000.0000.0000.000
37A37TYR00.003-0.02835.078-0.005-0.0050.0000.0000.0000.000
38A38GLN00.0580.04436.438-0.002-0.0020.0000.0000.0000.000
39A39LYS10.9390.99326.5630.1190.1190.0000.0000.0000.000
40A40VAL00.010-0.00331.933-0.004-0.0040.0000.0000.0000.000
41A41GLN0-0.054-0.02233.332-0.001-0.0010.0000.0000.0000.000
42A42ARG10.9280.93831.5210.0760.0760.0000.0000.0000.000
43A43LEU00.0030.00927.020-0.002-0.0020.0000.0000.0000.000
44A44LYS10.9150.97029.7450.0810.0810.0000.0000.0000.000
45A45GLN0-0.036-0.01632.4850.0020.0020.0000.0000.0000.000
46A46GLU-1-0.907-0.94426.686-0.084-0.0840.0000.0000.0000.000
47A47TYR0-0.041-0.03123.989-0.006-0.0060.0000.0000.0000.000
48A48ARG10.9000.92528.0860.0770.0770.0000.0000.0000.000
49A49GLN00.0320.03624.0340.0160.0160.0000.0000.0000.000
50A50TYR0-0.061-0.02423.092-0.009-0.0090.0000.0000.0000.000
51A51ASP-1-0.850-0.90529.227-0.091-0.0910.0000.0000.0000.000
52A52TRP0-0.034-0.04128.871-0.008-0.0080.0000.0000.0000.000
53A53VAL0-0.0040.01133.4610.0080.0080.0000.0000.0000.000
54A54ILE0-0.030-0.03134.448-0.004-0.0040.0000.0000.0000.000
55A55ALA00.0000.00436.2530.0030.0030.0000.0000.0000.000
56A56ARG10.8360.87737.8850.0660.0660.0000.0000.0000.000
57A57GLU-1-0.734-0.82936.921-0.097-0.0970.0000.0000.0000.000
58A58ASP-1-0.785-0.87240.704-0.066-0.0660.0000.0000.0000.000
59A59LYS10.7590.86842.2130.0660.0660.0000.0000.0000.000
60A60MET0-0.029-0.01935.100-0.003-0.0030.0000.0000.0000.000
61A61ILE0-0.007-0.00237.1500.0030.0030.0000.0000.0000.000
62A62LYS10.8170.87632.2480.1060.1060.0000.0000.0000.000
63A63ALA0-0.0100.00032.5600.0070.0070.0000.0000.0000.000
64A64ILE0-0.002-0.01129.195-0.009-0.0090.0000.0000.0000.000
65A65GLY00.0410.03528.9050.0090.0090.0000.0000.0000.000
66A66THR00.004-0.02127.038-0.018-0.0180.0000.0000.0000.000
67A67TYR0-0.003-0.00722.7140.0170.0170.0000.0000.0000.000
68A68THR0-0.018-0.01224.340-0.012-0.0120.0000.0000.0000.000
69A69ASP-1-0.784-0.87121.207-0.152-0.1520.0000.0000.0000.000
70A70LYS10.9700.95622.4440.0920.0920.0000.0000.0000.000
71A71LYS10.8810.95020.0270.1360.1360.0000.0000.0000.000
72A72ASN0-0.054-0.04017.9700.0130.0130.0000.0000.0000.000
73A73ARG10.8130.90216.2270.1950.1950.0000.0000.0000.000
74A74THR00.0000.02417.541-0.034-0.0340.0000.0000.0000.000
75A75SER0-0.038-0.02119.6130.0430.0430.0000.0000.0000.000
76A76PHE00.0230.01417.691-0.027-0.0270.0000.0000.0000.000
77A77ARG10.7640.85422.0620.2360.2360.0000.0000.0000.000
78A78LEU00.0110.01523.019-0.016-0.0160.0000.0000.0000.000
79A79GLN0-0.0130.00325.1360.0100.0100.0000.0000.0000.000
80A80LEU0-0.009-0.00427.087-0.005-0.0050.0000.0000.0000.000
81A81VAL0-0.024-0.01429.8020.0070.0070.0000.0000.0000.000
82A82THR00.0170.00432.166-0.001-0.0010.0000.0000.0000.000
83A83THR0-0.020-0.01834.9980.0020.0020.0000.0000.0000.000
84A84LEU00.0310.02737.6710.0030.0030.0000.0000.0000.000
85A85LYS10.9430.97440.9240.0580.0580.0000.0000.0000.000
86A86LYS10.8970.92736.8550.0830.0830.0000.0000.0000.000
87A87HIS00.0190.01941.555-0.003-0.0030.0000.0000.0000.000
88A88ASN00.0030.00437.304-0.001-0.0010.0000.0000.0000.000
89A89PRO00.0160.03037.302-0.003-0.0030.0000.0000.0000.000
90A90THR00.0420.04033.155-0.001-0.0010.0000.0000.0000.000
91A91SER0-0.029-0.03632.1080.0020.0020.0000.0000.0000.000
92A92TYR0-0.011-0.01626.580-0.006-0.0060.0000.0000.0000.000
93A93LEU00.0110.01624.5190.0110.0110.0000.0000.0000.000
94A94LEU0-0.027-0.01721.767-0.006-0.0060.0000.0000.0000.000
95A95TYR0-0.048-0.03817.1940.0330.0330.0000.0000.0000.000
96A96GLU-1-0.797-0.88419.176-0.282-0.2820.0000.0000.0000.000
97A97GLN00.0370.01814.439-0.028-0.0280.0000.0000.0000.000
98A98MET0-0.0210.00517.357-0.038-0.0380.0000.0000.0000.000
99A99SER00.021-0.02317.1940.0290.0290.0000.0000.0000.000
100A100LEU00.0060.00018.593-0.023-0.0230.0000.0000.0000.000
101A101GLU-1-0.818-0.88418.561-0.171-0.1710.0000.0000.0000.000
102A102THR00.0400.02414.118-0.036-0.0360.0000.0000.0000.000
103A103PRO0-0.038-0.01110.9690.0660.0660.0000.0000.0000.000
104A104ASP-1-0.870-0.93212.482-0.229-0.2290.0000.0000.0000.000
105A105SER0-0.012-0.0417.512-0.028-0.0280.0000.0000.0000.000
106A106TRP0-0.001-0.0096.422-0.075-0.0750.0000.0000.0000.000
107A107ASN00.0360.0302.237-6.244-5.4172.750-1.771-1.807-0.023
108A108ASP-1-0.804-0.8755.311-0.297-0.224-0.001-0.002-0.0690.000
109A109THR00.0090.0058.6700.0480.0480.0000.0000.0000.000
110A110TYR00.0380.0126.9050.0400.0400.0000.0000.0000.000
111A111GLU-1-0.855-0.9205.346-0.169-0.1690.0000.0000.0000.000
112A112GLN0-0.065-0.0318.5400.1690.1690.0000.0000.0000.000
113A113PHE00.0280.02911.9130.0690.0690.0000.0000.0000.000
114A114GLU-1-0.807-0.8939.921-0.367-0.3670.0000.0000.0000.000
115A115ARG10.8270.8909.1400.3020.3020.0000.0000.0000.000
116A116GLU-1-0.810-0.88513.953-0.266-0.2660.0000.0000.0000.000
117A117THR0-0.037-0.03315.1070.0400.0400.0000.0000.0000.000
118A118LEU0-0.036-0.02313.8770.0310.0310.0000.0000.0000.000
119A119GLY0-0.0100.01017.6570.0260.0260.0000.0000.0000.000
120A120ILE0-0.058-0.02619.8610.0180.0180.0000.0000.0000.000
121A121PHE0-0.079-0.06319.1380.0150.0150.0000.0000.0000.000
122A122GLN0-0.038-0.00421.7570.0160.0160.0000.0000.0000.000
123A123GLU-1-0.838-0.90620.208-0.130-0.1300.0000.0000.0000.000
124A124LYS10.8120.89510.2280.3330.3330.0000.0000.0000.000
125A125VAL0-0.0190.00016.9700.0040.0040.0000.0000.0000.000
126A126VAL0-0.013-0.01215.213-0.028-0.0280.0000.0000.0000.000
127A127ILE0-0.0140.00311.7880.0280.0280.0000.0000.0000.000
128A128PHE0-0.051-0.02713.360-0.038-0.0380.0000.0000.0000.000
129A129THR00.024-0.01110.596-0.086-0.0860.0000.0000.0000.000
130A130CYS0-0.057-0.01613.7750.0440.0440.0000.0000.0000.000
131A131LEU00.0630.05311.3690.0020.0020.0000.0000.0000.000
132A132ASN0-0.051-0.04815.6290.0520.0520.0000.0000.0000.000
133A133GLY00.0500.02518.575-0.019-0.0190.0000.0000.0000.000
134A134HIS0-0.069-0.02619.9170.0230.0230.0000.0000.0000.000
135A135LEU00.012-0.00221.131-0.010-0.0100.0000.0000.0000.000
136A136ASP-1-0.790-0.89523.325-0.086-0.0860.0000.0000.0000.000
137A137ASP-1-0.925-0.95725.237-0.089-0.0890.0000.0000.0000.000
138A138ASN0-0.035-0.03627.7230.0160.0160.0000.0000.0000.000
139A139MET00.0020.00530.1230.0040.0040.0000.0000.0000.000
140A140ASN00.0070.00132.4940.0020.0020.0000.0000.0000.000
141A141ILE00.0270.02826.0710.0080.0080.0000.0000.0000.000
142A142VAL00.0230.00428.8100.0050.0050.0000.0000.0000.000
143A143LEU0-0.027-0.00430.7940.0050.0050.0000.0000.0000.000
144A144GLN00.0480.01031.5140.0030.0030.0000.0000.0000.000
145A145LYS10.9631.00127.0680.0330.0330.0000.0000.0000.000
146A146LYS10.9100.94631.1710.0400.0400.0000.0000.0000.000
147A147ALA00.0340.01034.0990.0030.0030.0000.0000.0000.000
148A148ASN0-0.025-0.02732.5790.0070.0070.0000.0000.0000.000
149A149GLN0-0.0100.01130.7800.0010.0010.0000.0000.0000.000
150A150LEU00.0350.01134.5550.0020.0020.0000.0000.0000.000
151A151LEU0-0.0140.00436.7180.0020.0020.0000.0000.0000.000
152A152ASN0-0.068-0.05834.3700.0060.0060.0000.0000.0000.000
153A153GLU-1-0.985-0.97837.229-0.014-0.0140.0000.0000.0000.000
154A154PHE0-0.024-0.00539.2290.0000.0000.0000.0000.0000.000
155A155GLN0-0.043-0.01940.0540.0040.0040.0000.0000.0000.000
156A156ALA0-0.031-0.02340.108-0.001-0.0010.0000.0000.0000.000
157A157ARG10.9780.97342.265-0.010-0.0100.0000.0000.0000.000
158A158SER0-0.146-0.06144.1700.0010.0010.0000.0000.0000.000
159A159VAL00.0190.01338.6970.0010.0010.0000.0000.0000.000
160A160GLU-1-0.791-0.86841.513-0.001-0.0010.0000.0000.0000.000
161A161HIS00.0120.00538.770-0.003-0.0030.0000.0000.0000.000
162A162VAL0-0.0100.01240.3470.0010.0010.0000.0000.0000.000
163A163VAL00.000-0.01035.085-0.001-0.0010.0000.0000.0000.000
164A164GLU-1-0.850-0.91838.367-0.021-0.0210.0000.0000.0000.000
165A165PRO00.002-0.01237.630-0.002-0.0020.0000.0000.0000.000
166A166ASN0-0.0020.00235.973-0.006-0.0060.0000.0000.0000.000
167A167PHE00.0380.00638.0740.0000.0000.0000.0000.0000.000
168A168VAL00.0310.02636.1830.0010.0010.0000.0000.0000.000
169A169SER0-0.0080.00138.950-0.001-0.0010.0000.0000.0000.000
170A170ILE0-0.020-0.02137.7270.0010.0010.0000.0000.0000.000
171A171SER00.0020.00741.850-0.002-0.0020.0000.0000.0000.000
172A172ALA0-0.006-0.02042.8570.0010.0010.0000.0000.0000.000
173A173PHE00.030-0.00544.8720.0000.0000.0000.0000.0000.000
174A174THR00.0380.03244.2920.0010.0010.0000.0000.0000.000
175A175ASP-1-0.911-0.97446.9140.0080.0080.0000.0000.0000.000
176A176GLU-1-0.903-0.94246.1660.0030.0030.0000.0000.0000.000
177A177TRP0-0.046-0.02446.826-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.925-0.94952.6870.0030.0030.0000.0000.0000.000
179A179GLU-1-0.923-0.96353.635-0.002-0.0020.0000.0000.0000.000
180A180TYR0-0.039-0.05453.6020.0000.0000.0000.0000.0000.000
181A181ILE0-0.0170.00453.1160.0000.0000.0000.0000.0000.000
182A182MET00.0060.00053.9470.0010.0010.0000.0000.0000.000
183A183THR00.0080.00354.0720.0000.0000.0000.0000.0000.000
184A184SER00.002-0.01552.8540.0010.0010.0000.0000.0000.000
185A185LYS10.9430.97648.123-0.004-0.0040.0000.0000.0000.000
186A186HIS10.8480.91447.2670.0010.0010.0000.0000.0000.000
187A187LYS10.8640.95350.214-0.005-0.0050.0000.0000.0000.000
188A188MET0-0.054-0.00747.9220.0010.0010.0000.0000.0000.000
189A189ASN00.014-0.00548.9700.0000.0000.0000.0000.0000.000
190A190LEU00.0830.06444.119-0.001-0.0010.0000.0000.0000.000
191A191GLN0-0.007-0.01045.5370.0000.0000.0000.0000.0000.000
192A192ILE00.0250.02439.912-0.001-0.0010.0000.0000.0000.000
193A193ALA0-0.009-0.01942.2270.0010.0010.0000.0000.0000.000
194A194LEU0-0.014-0.00337.372-0.001-0.0010.0000.0000.0000.000
195A195ARG10.8020.89939.9160.0270.0270.0000.0000.0000.000
196A196SER00.0210.01236.989-0.002-0.0020.0000.0000.0000.000
197A197ALA00.0170.00938.5850.0030.0030.0000.0000.0000.000
198A198GLY00.0080.00238.165-0.003-0.0030.0000.0000.0000.000
199A199MET0-0.004-0.01637.276-0.002-0.0020.0000.0000.0000.000
200A200GLY00.0800.04734.8290.0030.0030.0000.0000.0000.000
201A201GLY0-0.030-0.02035.8460.0030.0030.0000.0000.0000.000
202A202LYS10.8810.93038.2340.0510.0510.0000.0000.0000.000
203A203HIS00.0090.01834.3870.0040.0040.0000.0000.0000.000
204A204THR0-0.0130.00539.6760.0020.0020.0000.0000.0000.000
205A205VAL00.0270.00839.9050.0000.0000.0000.0000.0000.000
206A206THR0-0.066-0.03642.4760.0010.0010.0000.0000.0000.000
207A207VAL00.0210.00543.5790.0000.0000.0000.0000.0000.000
208A208GLY0-0.028-0.00146.2100.0000.0000.0000.0000.0000.000
209A209THR00.0460.03648.8600.0000.0000.0000.0000.0000.000
210A210PRO0-0.042-0.02651.4570.0000.0000.0000.0000.0000.000
211A211ILE0-0.005-0.01250.3140.0010.0010.0000.0000.0000.000
212A212VAL00.0080.01548.197-0.001-0.0010.0000.0000.0000.000
213A213THR0-0.023-0.01351.1100.0000.0000.0000.0000.0000.000
214A214THR0-0.0030.00253.987-0.001-0.0010.0000.0000.0000.000