Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2LN3R

Calculation Name: 2PL2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PL2

Chain ID: A

ChEMBL ID:

UniProt ID: Q72L02

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093875.562381
FMO2-HF: Nuclear repulsion 2018941.292748
FMO2-HF: Total energy -74934.269632
FMO2-MP2: Total energy -75158.034796


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:28:ALA)


Summations of interaction energy for fragment #1(A:28:ALA)
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.
-16.904-10.6671.37-3.553-4.054-0.012
Interaction energy analysis for fragmet #1(A:28:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.008
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].
3A30GLN00.0190.0053.029-4.390-1.2220.121-1.675-1.6130.009
4A31ASN00.014-0.0034.473-2.107-1.865-0.001-0.024-0.2170.000
5A32PRO0-0.0020.0124.383-0.395-0.232-0.001-0.043-0.1200.000
6A33LEU00.0800.0467.002-0.092-0.0920.0000.0000.0000.000
7A34ARG10.9020.9448.614-1.780-1.7800.0000.0000.0000.000
8A35LEU0-0.011-0.0059.946-0.153-0.1530.0000.0000.0000.000
9A36GLY00.0370.02011.329-0.101-0.1010.0000.0000.0000.000
10A37VAL00.0170.00413.177-0.056-0.0560.0000.0000.0000.000
11A38GLN0-0.035-0.01314.016-0.002-0.0020.0000.0000.0000.000
12A39LEU00.0400.00214.833-0.045-0.0450.0000.0000.0000.000
13A40TYR00.0020.00917.340-0.033-0.0330.0000.0000.0000.000
14A41ALA0-0.023-0.00719.247-0.022-0.0220.0000.0000.0000.000
15A42LEU0-0.044-0.01519.330-0.012-0.0120.0000.0000.0000.000
16A43GLY00.0040.01422.262-0.017-0.0170.0000.0000.0000.000
17A44ARG10.8050.89720.267-0.052-0.0520.0000.0000.0000.000
18A45TYR00.1040.03419.6390.0030.0030.0000.0000.0000.000
19A46ASP-1-0.788-0.88519.452-0.032-0.0320.0000.0000.0000.000
20A47ALA0-0.029-0.01517.249-0.027-0.0270.0000.0000.0000.000
21A48ALA00.000-0.00115.665-0.017-0.0170.0000.0000.0000.000
22A49LEU0-0.002-0.00114.925-0.016-0.0160.0000.0000.0000.000
23A50THR00.0200.01414.490-0.045-0.0450.0000.0000.0000.000
24A51LEU0-0.076-0.03310.187-0.126-0.1260.0000.0000.0000.000
25A52PHE00.0370.00410.199-0.104-0.1040.0000.0000.0000.000
26A53GLU-1-0.884-0.93711.650-0.377-0.3770.0000.0000.0000.000
27A54ARG10.8650.9257.4780.4800.4800.0000.0000.0000.000
28A55ALA0-0.0100.0026.766-0.504-0.5040.0000.0000.0000.000
29A56LEU00.0620.0307.362-0.166-0.1660.0000.0000.0000.000
30A57LYS10.8540.9307.6800.9210.9210.0000.0000.0000.000
31A58GLU-1-0.945-0.9712.611-8.493-5.9241.252-1.809-2.012-0.021
32A59ASN0-0.072-0.0475.377-0.0890.006-0.001-0.002-0.0920.000
33A60PRO0-0.033-0.0197.4970.2560.2560.0000.0000.0000.000
34A61GLN0-0.065-0.02211.0050.1170.1170.0000.0000.0000.000
35A62ASP-1-0.774-0.8959.9510.1440.1440.0000.0000.0000.000
36A63PRO00.016-0.00712.039-0.001-0.0010.0000.0000.0000.000
37A64GLU-1-0.851-0.91812.4120.4240.4240.0000.0000.0000.000
38A65ALA00.0300.00110.6850.0180.0180.0000.0000.0000.000
39A66LEU00.0020.00912.8320.0020.0020.0000.0000.0000.000
40A67TYR0-0.0370.00115.7520.0080.0080.0000.0000.0000.000
41A68TRP0-0.039-0.03214.206-0.028-0.0280.0000.0000.0000.000
42A69LEU0-0.0270.00715.0670.0030.0030.0000.0000.0000.000
43A70ALA00.0300.00717.0550.0030.0030.0000.0000.0000.000
44A71ARG10.9260.96720.102-0.091-0.0910.0000.0000.0000.000
45A72THR0-0.050-0.05018.2390.0160.0160.0000.0000.0000.000
46A73GLN00.0220.00820.0380.0070.0070.0000.0000.0000.000
47A74LEU0-0.0250.00622.6400.0000.0000.0000.0000.0000.000
48A75LYS10.8490.92523.760-0.057-0.0570.0000.0000.0000.000
49A76LEU0-0.050-0.01421.3830.0010.0010.0000.0000.0000.000
50A77GLY00.0300.01525.589-0.009-0.0090.0000.0000.0000.000
51A78LEU0-0.044-0.01622.575-0.007-0.0070.0000.0000.0000.000
52A79VAL00.0420.00225.593-0.005-0.0050.0000.0000.0000.000
53A80ASN00.0300.01826.8030.0020.0020.0000.0000.0000.000
54A81PRO00.016-0.00222.638-0.002-0.0020.0000.0000.0000.000
55A82ALA00.0550.03622.662-0.010-0.0100.0000.0000.0000.000
56A83LEU0-0.035-0.01423.8270.0070.0070.0000.0000.0000.000
57A84GLU-1-0.835-0.91623.600-0.091-0.0910.0000.0000.0000.000
58A85ASN00.0250.00219.031-0.024-0.0240.0000.0000.0000.000
59A86GLY00.0230.00921.1660.0070.0070.0000.0000.0000.000
60A87LYS10.8290.90423.5370.0860.0860.0000.0000.0000.000
61A88THR0-0.012-0.00519.611-0.001-0.0010.0000.0000.0000.000
62A89LEU0-0.0660.00017.7100.0010.0010.0000.0000.0000.000
63A90VAL0-0.024-0.01121.2000.0120.0120.0000.0000.0000.000
64A91ALA0-0.0170.00023.9360.0040.0040.0000.0000.0000.000
65A92ARG10.9270.96317.7130.1670.1670.0000.0000.0000.000
66A93THR0-0.0080.00018.7250.0040.0040.0000.0000.0000.000
67A94PRO00.0750.05121.4700.0170.0170.0000.0000.0000.000
68A95ARG10.9550.98423.022-0.038-0.0380.0000.0000.0000.000
69A96TYR00.0230.01417.0290.0050.0050.0000.0000.0000.000
70A97LEU00.0410.00421.840-0.013-0.0130.0000.0000.0000.000
71A98GLY00.0220.01120.765-0.008-0.0080.0000.0000.0000.000
72A99GLY00.0430.01421.846-0.011-0.0110.0000.0000.0000.000
73A100TYR0-0.017-0.03723.282-0.011-0.0110.0000.0000.0000.000
74A101MET0-0.0230.00524.453-0.004-0.0040.0000.0000.0000.000
75A102VAL00.0140.00821.443-0.004-0.0040.0000.0000.0000.000
76A103LEU0-0.010-0.01024.879-0.006-0.0060.0000.0000.0000.000
77A104SER00.0200.00327.349-0.003-0.0030.0000.0000.0000.000
78A105GLU-1-0.945-0.97826.3880.0420.0420.0000.0000.0000.000
79A106ALA00.001-0.00727.347-0.004-0.0040.0000.0000.0000.000
80A107TYR00.007-0.00429.375-0.006-0.0060.0000.0000.0000.000
81A108VAL00.0290.01932.6670.0000.0000.0000.0000.0000.000
82A109ALA0-0.048-0.01831.1480.0000.0000.0000.0000.0000.000
83A110LEU0-0.012-0.01932.046-0.001-0.0010.0000.0000.0000.000
84A111TYR0-0.036-0.01534.8110.0000.0000.0000.0000.0000.000
85A112ARG10.9240.97235.076-0.009-0.0090.0000.0000.0000.000
86A113GLN0-0.081-0.02934.2150.0000.0000.0000.0000.0000.000
87A114ALA0-0.0070.00038.085-0.003-0.0030.0000.0000.0000.000
88A115GLU-1-0.919-0.93440.476-0.029-0.0290.0000.0000.0000.000
89A116ASP-1-0.827-0.91242.805-0.016-0.0160.0000.0000.0000.000
90A117ARG10.9360.94844.1040.0060.0060.0000.0000.0000.000
91A118GLU-1-0.956-0.98345.184-0.013-0.0130.0000.0000.0000.000
92A119ARG10.8730.92837.8470.0330.0330.0000.0000.0000.000
93A120GLY00.0280.00340.402-0.001-0.0010.0000.0000.0000.000
94A121LYS10.8600.91240.3250.0020.0020.0000.0000.0000.000
95A122GLY00.0600.03940.9690.0020.0020.0000.0000.0000.000
96A123TYR00.0540.02536.0590.0000.0000.0000.0000.0000.000
97A124LEU00.0130.00736.3530.0020.0020.0000.0000.0000.000
98A125GLU-1-0.831-0.90037.9800.0020.0020.0000.0000.0000.000
99A126GLN0-0.050-0.03034.7080.0010.0010.0000.0000.0000.000
100A127ALA00.0100.00933.4920.0010.0010.0000.0000.0000.000
101A128LEU0-0.0010.00134.1150.0050.0050.0000.0000.0000.000
102A129SER0-0.031-0.01035.9140.0030.0030.0000.0000.0000.000
103A130VAL00.0070.00829.6770.0020.0020.0000.0000.0000.000
104A131LEU0-0.0020.00330.6520.0060.0060.0000.0000.0000.000
105A132LYS10.8290.90432.593-0.021-0.0210.0000.0000.0000.000
106A133ASP-1-0.904-0.96131.7390.0070.0070.0000.0000.0000.000
107A134ALA00.0170.00028.5260.0040.0040.0000.0000.0000.000
108A135GLU-1-0.811-0.88430.0170.0470.0470.0000.0000.0000.000
109A136ARG10.8650.93032.455-0.020-0.0200.0000.0000.0000.000
110A137VAL0-0.053-0.01326.0850.0020.0020.0000.0000.0000.000
111A138ASN0-0.029-0.02426.6820.0070.0070.0000.0000.0000.000
112A139PRO00.0470.02729.9700.0000.0000.0000.0000.0000.000
113A140ARG10.9450.98131.461-0.106-0.1060.0000.0000.0000.000
114A141TYR00.0440.02423.8640.0130.0130.0000.0000.0000.000
115A142ALA00.0850.04129.785-0.009-0.0090.0000.0000.0000.000
116A143PRO00.0370.01026.551-0.009-0.0090.0000.0000.0000.000
117A144LEU00.0300.02628.757-0.009-0.0090.0000.0000.0000.000
118A145HIS0-0.040-0.00931.107-0.012-0.0120.0000.0000.0000.000
119A146LEU00.0330.02130.888-0.006-0.0060.0000.0000.0000.000
120A147GLN0-0.016-0.02529.452-0.010-0.0100.0000.0000.0000.000
121A148ARG10.8160.90033.222-0.045-0.0450.0000.0000.0000.000
122A149GLY00.005-0.00535.978-0.004-0.0040.0000.0000.0000.000
123A150LEU0-0.019-0.00733.959-0.004-0.0040.0000.0000.0000.000
124A151VAL00.018-0.00835.062-0.004-0.0040.0000.0000.0000.000
125A152TYR00.011-0.00337.957-0.002-0.0020.0000.0000.0000.000
126A153ALA00.0170.02240.788-0.002-0.0020.0000.0000.0000.000
127A154LEU0-0.0350.01037.357-0.002-0.0020.0000.0000.0000.000
128A155LEU00.0030.00241.340-0.003-0.0030.0000.0000.0000.000
129A156GLY0-0.040-0.01543.725-0.001-0.0010.0000.0000.0000.000
130A157GLU-1-0.876-0.94044.5000.0130.0130.0000.0000.0000.000
131A158ARG10.9360.95245.147-0.013-0.0130.0000.0000.0000.000
132A159ASP-1-0.798-0.91045.8840.0210.0210.0000.0000.0000.000
133A160LYS10.8150.88843.338-0.014-0.0140.0000.0000.0000.000
134A161ALA0-0.0020.00541.4240.0030.0030.0000.0000.0000.000
135A162GLU-1-0.701-0.81641.3390.0390.0390.0000.0000.0000.000
136A163ALA0-0.0020.00942.6510.0040.0040.0000.0000.0000.000
137A164SER0-0.0040.00238.1670.0030.0030.0000.0000.0000.000
138A165LEU00.0400.03537.2190.0050.0050.0000.0000.0000.000
139A166LYS10.8860.94338.643-0.036-0.0360.0000.0000.0000.000
140A167GLN0-0.023-0.01636.6900.0040.0040.0000.0000.0000.000
141A168ALA0-0.025-0.03134.5130.0050.0050.0000.0000.0000.000
142A169LEU0-0.048-0.02035.2060.0070.0070.0000.0000.0000.000
143A170ALA0-0.045-0.02137.3030.0040.0040.0000.0000.0000.000
144A171LEU0-0.123-0.04533.1100.0030.0030.0000.0000.0000.000
145A172GLU-1-0.919-0.96830.0180.1430.1430.0000.0000.0000.000
146A173ASP-1-0.801-0.88633.6710.0750.0750.0000.0000.0000.000
147A174THR00.017-0.00931.2590.0040.0040.0000.0000.0000.000
148A175PRO00.0730.01732.816-0.007-0.0070.0000.0000.0000.000
149A176GLU-1-0.913-0.93529.6450.0900.0900.0000.0000.0000.000
150A177ILE00.0080.00232.388-0.009-0.0090.0000.0000.0000.000
151A178ARG10.7740.87735.657-0.074-0.0740.0000.0000.0000.000
152A179SER00.030-0.00836.471-0.006-0.0060.0000.0000.0000.000
153A180ALA0-0.0100.01736.227-0.005-0.0050.0000.0000.0000.000
154A181LEU0-0.004-0.01438.282-0.005-0.0050.0000.0000.0000.000
155A182ALA0-0.0010.00441.254-0.004-0.0040.0000.0000.0000.000
156A183GLU-1-0.848-0.92539.1880.0310.0310.0000.0000.0000.000
157A184LEU0-0.062-0.02842.023-0.004-0.0040.0000.0000.0000.000
158A185TYR0-0.077-0.06143.709-0.002-0.0020.0000.0000.0000.000
159A186LEU00.0210.02344.469-0.002-0.0020.0000.0000.0000.000
160A187SER0-0.102-0.04645.093-0.003-0.0030.0000.0000.0000.000
161A188MET0-0.088-0.04646.558-0.003-0.0030.0000.0000.0000.000
162A189GLY00.0290.02649.699-0.001-0.0010.0000.0000.0000.000
163A190ARG10.7240.85048.982-0.031-0.0310.0000.0000.0000.000
164A191LEU00.0780.01749.8260.0020.0020.0000.0000.0000.000
165A192ASP-1-0.887-0.93750.0390.0310.0310.0000.0000.0000.000
166A193GLU-1-0.855-0.93048.6670.0360.0360.0000.0000.0000.000
167A194ALA0-0.007-0.00845.9820.0030.0030.0000.0000.0000.000
168A195LEU0-0.012-0.00745.5270.0040.0040.0000.0000.0000.000
169A196ALA0-0.0040.00246.5620.0030.0030.0000.0000.0000.000
170A197GLN00.0230.02442.4640.0070.0070.0000.0000.0000.000
171A198TYR00.010-0.01639.7400.0060.0060.0000.0000.0000.000
172A199ALA00.0090.01542.1530.0040.0040.0000.0000.0000.000
173A200LYS10.8790.95939.803-0.074-0.0740.0000.0000.0000.000
174A201ALA0-0.001-0.00638.1480.0050.0050.0000.0000.0000.000
175A202LEU0-0.039-0.04238.2490.0060.0060.0000.0000.0000.000
176A203GLU-1-0.921-0.94440.1750.0700.0700.0000.0000.0000.000
177A204GLN0-0.112-0.06635.9110.0000.0000.0000.0000.0000.000
178A205ALA0-0.0030.00234.2540.0090.0090.0000.0000.0000.000
179A206PRO00.0940.06236.115-0.004-0.0040.0000.0000.0000.000
180A207LYS10.8470.91135.458-0.103-0.1030.0000.0000.0000.000
181A208ASP-1-0.809-0.89934.0550.0870.0870.0000.0000.0000.000
182A209LEU00.007-0.01835.435-0.006-0.0060.0000.0000.0000.000
183A210ASP-1-0.818-0.85933.9200.0530.0530.0000.0000.0000.000
184A211LEU00.0280.00335.973-0.006-0.0060.0000.0000.0000.000
185A212ARG10.8540.91638.176-0.070-0.0700.0000.0000.0000.000
186A213VAL00.0010.00739.417-0.004-0.0040.0000.0000.0000.000
187A214ARG10.8550.91835.119-0.054-0.0540.0000.0000.0000.000
188A215TYR00.0180.01241.696-0.003-0.0030.0000.0000.0000.000
189A216ALA00.000-0.00444.175-0.003-0.0030.0000.0000.0000.000
190A217SER00.007-0.01544.349-0.003-0.0030.0000.0000.0000.000
191A218ALA0-0.020-0.00145.518-0.002-0.0020.0000.0000.0000.000
192A219LEU00.0240.00447.235-0.002-0.0020.0000.0000.0000.000
193A220LEU0-0.154-0.04748.498-0.002-0.0020.0000.0000.0000.000
194A221LEU0-0.059-0.03051.022-0.003-0.0030.0000.0000.0000.000