FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2JRNR

Calculation Name: 1WXR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WXR

Chain ID: A

ChEMBL ID:

UniProt ID: O88093

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 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 1048
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -26938090.638341
FMO2-HF: Nuclear repulsion 26547535.816038
FMO2-HF: Total energy -390554.822303
FMO2-MP2: Total energy -391709.232724


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-1.353-9.67643.91-19.647-15.939-0.066
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.007
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].
3A3VAL00.0440.0243.7970.1562.031-0.014-1.003-0.8580.005
4A4ASN00.006-0.0066.656-0.001-0.0010.0000.0000.0000.000
5A5ASN00.036-0.00110.414-0.070-0.0700.0000.0000.0000.000
6A6GLU-1-0.807-0.88912.730-0.351-0.3510.0000.0000.0000.000
7A7LEU0-0.0040.01012.0390.0910.0910.0000.0000.0000.000
8A8GLY0-0.002-0.00212.794-0.115-0.1150.0000.0000.0000.000
9A9TYR00.0410.0114.8450.4810.4810.0000.0000.0000.000
10A10GLN0-0.007-0.02610.412-0.081-0.0810.0000.0000.0000.000
11A11LEU00.0050.00612.5880.0870.0870.0000.0000.0000.000
12A12PHE00.018-0.0077.3850.0250.0250.0000.0000.0000.000
13A13ARG10.7080.8128.3700.4030.4030.0000.0000.0000.000
14A14ASP-1-0.728-0.85610.473-0.013-0.0130.0000.0000.0000.000
15A15PHE0-0.0130.00610.3860.0660.0660.0000.0000.0000.000
16A16ALA0-0.024-0.0138.7940.0950.0950.0000.0000.0000.000
17A17GLU-1-0.773-0.86510.7850.1500.1500.0000.0000.0000.000
18A18ASN0-0.033-0.01813.8950.0260.0260.0000.0000.0000.000
19A19LYS10.8880.95315.888-0.089-0.0890.0000.0000.0000.000
20A20GLY00.0580.02417.512-0.023-0.0230.0000.0000.0000.000
21A21MET0-0.069-0.04318.5130.0170.0170.0000.0000.0000.000
22A22PHE0-0.001-0.01215.3160.0000.0000.0000.0000.0000.000
23A23ARG10.9100.98017.6230.0220.0220.0000.0000.0000.000
24A24PRO00.0350.00119.728-0.005-0.0050.0000.0000.0000.000
25A25GLY0-0.023-0.01820.992-0.016-0.0160.0000.0000.0000.000
26A26ALA0-0.0340.00420.305-0.012-0.0120.0000.0000.0000.000
27A27THR00.0390.00521.6810.0140.0140.0000.0000.0000.000
28A28ASN0-0.051-0.03522.692-0.006-0.0060.0000.0000.0000.000
29A29ILE00.0290.03717.873-0.011-0.0110.0000.0000.0000.000
30A30ALA0-0.0070.00319.578-0.009-0.0090.0000.0000.0000.000
31A31ILE0-0.015-0.02114.880-0.011-0.0110.0000.0000.0000.000
32A32TYR0-0.024-0.02818.5380.0110.0110.0000.0000.0000.000
33A33ASN00.0280.01217.888-0.053-0.0530.0000.0000.0000.000
34A34LYS10.8660.94413.6170.7950.7950.0000.0000.0000.000
35A35GLN0-0.069-0.03119.4030.0460.0460.0000.0000.0000.000
36A36GLY0-0.0020.00921.9720.0260.0260.0000.0000.0000.000
37A37GLU-1-0.954-0.97522.190-0.199-0.1990.0000.0000.0000.000
38A38PHE0-0.040-0.02021.152-0.024-0.0240.0000.0000.0000.000
39A39VAL00.0220.01616.222-0.001-0.0010.0000.0000.0000.000
40A40GLY0-0.004-0.00118.8650.0070.0070.0000.0000.0000.000
41A41THR0-0.019-0.01419.492-0.011-0.0110.0000.0000.0000.000
42A42LEU0-0.037-0.01414.5040.0070.0070.0000.0000.0000.000
43A43ASP-1-0.798-0.90518.6430.0040.0040.0000.0000.0000.000
44A44LYS10.7940.89220.519-0.003-0.0030.0000.0000.0000.000
45A45ALA0-0.0150.00720.2680.0090.0090.0000.0000.0000.000
46A46ALA00.0110.01721.194-0.014-0.0140.0000.0000.0000.000
47A47MET0-0.063-0.01015.7760.0370.0370.0000.0000.0000.000
48A48PRO00.0210.01515.935-0.011-0.0110.0000.0000.0000.000
49A49ASP-1-0.759-0.84017.8450.2110.2110.0000.0000.0000.000
50A50PHE00.004-0.01712.9880.0470.0470.0000.0000.0000.000
51A51SER00.004-0.02216.1720.0510.0510.0000.0000.0000.000
52A52ALA0-0.0130.00518.5670.0040.0040.0000.0000.0000.000
53A53VAL0-0.072-0.03712.0120.0370.0370.0000.0000.0000.000
54A54ASP-1-0.788-0.89913.9330.8410.8410.0000.0000.0000.000
55A55SER0-0.009-0.04513.7980.0820.0820.0000.0000.0000.000
56A56GLU-1-0.882-0.91113.6150.3180.3180.0000.0000.0000.000
57A57ILE0-0.072-0.04110.0310.0360.0360.0000.0000.0000.000
58A58GLY00.0110.0459.4220.4730.4730.0000.0000.0000.000
59A59VAL0-0.033-0.02610.0720.2880.2880.0000.0000.0000.000
60A60ALA0-0.0270.00711.923-0.097-0.0970.0000.0000.0000.000
61A61THR00.0170.00714.646-0.001-0.0010.0000.0000.0000.000
62A62LEU0-0.042-0.00916.963-0.030-0.0300.0000.0000.0000.000
63A63ILE0-0.004-0.02820.200-0.005-0.0050.0000.0000.0000.000
64A64ASN00.0410.01222.617-0.031-0.0310.0000.0000.0000.000
65A65PRO00.0400.01325.2390.0190.0190.0000.0000.0000.000
66A66GLN0-0.037-0.01627.127-0.007-0.0070.0000.0000.0000.000
67A67TYR0-0.057-0.05624.7710.0000.0000.0000.0000.0000.000
68A68ILE00.0100.02819.0310.0090.0090.0000.0000.0000.000
69A69ALA0-0.020-0.00518.442-0.026-0.0260.0000.0000.0000.000
70A70SER00.023-0.03414.5500.0830.0830.0000.0000.0000.000
71A71VAL00.0090.00913.644-0.075-0.0750.0000.0000.0000.000
72A72LYS10.8450.92616.232-0.333-0.3330.0000.0000.0000.000
73A73HIS0-0.125-0.07612.7620.0440.0440.0000.0000.0000.000
74A74ASN0-0.029-0.00412.4580.0250.0250.0000.0000.0000.000
75A75GLY00.011-0.00216.036-0.051-0.0510.0000.0000.0000.000
76A76GLY0-0.050-0.02117.437-0.042-0.0420.0000.0000.0000.000
77A77TYR00.017-0.00316.057-0.040-0.0400.0000.0000.0000.000
78A78THR00.0550.01618.178-0.004-0.0040.0000.0000.0000.000
79A79ASN0-0.0180.01120.072-0.023-0.0230.0000.0000.0000.000
80A80VAL0-0.014-0.00317.3070.0590.0590.0000.0000.0000.000
81A81SER00.022-0.00518.113-0.043-0.0430.0000.0000.0000.000
82A82PHE00.040-0.00418.0420.0580.0580.0000.0000.0000.000
83A83GLY00.0170.00719.231-0.034-0.0340.0000.0000.0000.000
84A84ASP-1-0.806-0.91018.8430.1740.1740.0000.0000.0000.000
85A85GLY00.0600.03219.190-0.009-0.0090.0000.0000.0000.000
86A86GLU-1-0.867-0.89319.8700.1030.1030.0000.0000.0000.000
87A87ASN0-0.073-0.05922.4100.0120.0120.0000.0000.0000.000
88A88ARG10.8490.92519.492-0.235-0.2350.0000.0000.0000.000
89A89TYR0-0.047-0.02323.057-0.027-0.0270.0000.0000.0000.000
90A90ASN0-0.050-0.05223.0450.0410.0410.0000.0000.0000.000
91A91ILE0-0.032-0.02220.677-0.005-0.0050.0000.0000.0000.000
92A92VAL0-0.064-0.01924.772-0.017-0.0170.0000.0000.0000.000
93A93ASP-1-0.831-0.90627.0150.2070.2070.0000.0000.0000.000
94A94ARG10.8000.89819.139-0.401-0.4010.0000.0000.0000.000
95A95ASN00.0810.03823.855-0.023-0.0230.0000.0000.0000.000
96A96ASN0-0.027-0.04222.9750.0440.0440.0000.0000.0000.000
97A97ALA00.0600.04223.004-0.029-0.0290.0000.0000.0000.000
98A98PRO00.0110.00024.5850.0110.0110.0000.0000.0000.000
99A99SER0-0.055-0.03825.208-0.005-0.0050.0000.0000.0000.000
100A100LEU00.0690.03119.763-0.003-0.0030.0000.0000.0000.000
101A101ASP-1-0.810-0.89515.8670.6140.6140.0000.0000.0000.000
102A102PHE00.0280.00417.5590.0570.0570.0000.0000.0000.000
103A103HIS0-0.0200.00718.904-0.010-0.0100.0000.0000.0000.000
104A104ALA00.0190.01120.4370.0430.0430.0000.0000.0000.000
105A105PRO0-0.056-0.02920.658-0.037-0.0370.0000.0000.0000.000
106A106ARG10.8770.96023.763-0.177-0.1770.0000.0000.0000.000
107A107LEU0-0.018-0.01922.5550.0030.0030.0000.0000.0000.000
108A108ASP-1-0.776-0.88326.6150.1990.1990.0000.0000.0000.000
109A109LYS10.7750.87128.539-0.158-0.1580.0000.0000.0000.000
110A110LEU0-0.045-0.00828.3220.0180.0180.0000.0000.0000.000
111A111VAL00.0160.00623.760-0.009-0.0090.0000.0000.0000.000
112A112THR0-0.066-0.04027.110-0.010-0.0100.0000.0000.0000.000
113A113GLU-1-0.697-0.81324.2090.1890.1890.0000.0000.0000.000
114A114VAL0-0.007-0.00621.102-0.009-0.0090.0000.0000.0000.000
115A115ALA00.0020.01324.176-0.005-0.0050.0000.0000.0000.000
116A116PRO0-0.020-0.01122.6540.0230.0230.0000.0000.0000.000
117A117THR00.0150.00718.538-0.019-0.0190.0000.0000.0000.000
118A118ALA0-0.026-0.01021.677-0.006-0.0060.0000.0000.0000.000
119A119VAL00.0380.02120.9760.0340.0340.0000.0000.0000.000
120A120THR0-0.025-0.02721.124-0.038-0.0380.0000.0000.0000.000
121A121ALA00.0210.00322.843-0.005-0.0050.0000.0000.0000.000
122A122GLN0-0.0040.02025.449-0.012-0.0120.0000.0000.0000.000
123A123GLY00.0930.04924.4130.0180.0180.0000.0000.0000.000
124A124ALA00.0410.02823.6900.0080.0080.0000.0000.0000.000
125A125VAL0-0.032-0.01324.693-0.022-0.0220.0000.0000.0000.000
126A126ALA00.006-0.02424.8720.0090.0090.0000.0000.0000.000
127A127GLY0-0.003-0.01423.993-0.015-0.0150.0000.0000.0000.000
128A128ALA00.0020.01523.950-0.010-0.0100.0000.0000.0000.000
129A129TYR0-0.004-0.02619.077-0.003-0.0030.0000.0000.0000.000
130A130LEU0-0.040-0.02320.1970.0000.0000.0000.0000.0000.000
131A131ASP-1-0.838-0.91922.2380.0880.0880.0000.0000.0000.000
132A132LYS10.8910.92319.646-0.063-0.0630.0000.0000.0000.000
133A133GLU-1-0.942-0.95323.6810.0550.0550.0000.0000.0000.000
134A134ARG10.8720.96024.927-0.151-0.1510.0000.0000.0000.000
135A135TYR0-0.032-0.02920.3180.0160.0160.0000.0000.0000.000
136A136PRO0-0.0350.00220.9460.0010.0010.0000.0000.0000.000
137A137VAL0-0.056-0.03216.297-0.021-0.0210.0000.0000.0000.000
138A138PHE00.0250.00313.7620.0270.0270.0000.0000.0000.000
139A139TYR00.004-0.00211.556-0.076-0.0760.0000.0000.0000.000
140A140ARG10.8390.9182.656-6.442-6.0040.321-0.331-0.4270.000
141A141LEU00.0490.0146.747-0.207-0.2070.0000.0000.0000.000
142A142GLY00.0130.0086.0530.0530.0530.0000.0000.0000.000
143A143SER00.020-0.0025.119-0.131-0.1310.0000.0000.0000.000
144A144GLY00.0080.0283.569-2.447-1.9530.076-0.229-0.3410.002
145A145THR0-0.050-0.0532.765-3.947-2.2952.539-1.976-2.215-0.013
146A146GLN00.0640.0761.651-5.939-21.50532.257-11.055-5.636-0.036
147A147TYR0-0.028-0.0263.3123.2293.3190.0260.298-0.4130.001
148A148ILE00.0460.0365.668-0.882-0.8820.0000.0000.0000.000
149A149LYS10.8420.9138.4501.0391.0390.0000.0000.0000.000
150A150ASP-1-0.822-0.90410.320-0.595-0.5950.0000.0000.0000.000
151A151SER00.0250.01613.9500.0070.0070.0000.0000.0000.000
152A152ASN0-0.054-0.03816.3760.0460.0460.0000.0000.0000.000
153A153GLY0-0.056-0.02813.3260.0330.0330.0000.0000.0000.000
154A154GLN0-0.0150.00013.2550.0360.0360.0000.0000.0000.000
155A155LEU0-0.018-0.0198.023-0.110-0.1100.0000.0000.0000.000
156A156THR0-0.0140.00210.4400.2710.2710.0000.0000.0000.000
157A157LYS10.9150.9607.1350.4250.4250.0000.0000.0000.000
158A158MET0-0.003-0.0097.2390.3930.3930.0000.0000.0000.000
159A159GLY00.0130.0007.1200.3600.3600.0000.0000.0000.000
160A160GLY0-0.083-0.0366.216-0.412-0.4120.0000.0000.0000.000
161A161ALA00.0160.0075.768-0.096-0.0960.0000.0000.0000.000
162A162TYR0-0.047-0.0346.748-0.450-0.4500.0000.0000.0000.000
163A163SER0-0.0340.0007.592-0.251-0.2510.0000.0000.0000.000
164A164TRP00.004-0.0256.0860.0400.0400.0000.0000.0000.000
165A165LEU00.0530.0366.4280.4120.4120.0000.0000.0000.000
166A166THR0-0.046-0.0403.2730.1470.4380.007-0.114-0.1840.000
167A167GLY00.0480.0095.6270.9700.9700.0000.0000.0000.000
168A168GLY00.0190.0127.193-0.380-0.3800.0000.0000.0000.000
169A169THR0-0.071-0.0498.8560.1810.1810.0000.0000.0000.000
170A170VAL00.004-0.0018.817-0.015-0.0150.0000.0000.0000.000
171A171GLY00.0410.03611.274-0.018-0.0180.0000.0000.0000.000
172A172SER00.0160.00414.7660.0440.0440.0000.0000.0000.000
173A173LEU0-0.0140.01813.398-0.011-0.0110.0000.0000.0000.000
174A174SER0-0.0290.00717.644-0.022-0.0220.0000.0000.0000.000
175A175SER00.0420.01019.0150.0250.0250.0000.0000.0000.000
176A176TYR0-0.051-0.04816.314-0.032-0.0320.0000.0000.0000.000
177A177GLN0-0.036-0.03721.8410.0260.0260.0000.0000.0000.000
178A178ASN0-0.019-0.01423.963-0.004-0.0040.0000.0000.0000.000
179A179GLY00.0170.00023.667-0.003-0.0030.0000.0000.0000.000
180A180GLU-1-0.872-0.91322.6250.2480.2480.0000.0000.0000.000
181A181MET0-0.055-0.00116.4000.0570.0570.0000.0000.0000.000
182A182ILE0-0.0100.00115.393-0.051-0.0510.0000.0000.0000.000
183A183SER00.0050.00514.1680.0650.0650.0000.0000.0000.000
184A184THR00.038-0.00212.452-0.064-0.0640.0000.0000.0000.000
185A185SER0-0.060-0.01212.2770.0490.0490.0000.0000.0000.000
186A186SER00.0590.0018.070-0.156-0.1560.0000.0000.0000.000
187A187GLY00.0130.0068.018-0.137-0.1370.0000.0000.0000.000
188A188LEU0-0.099-0.0499.048-0.170-0.1700.0000.0000.0000.000
189A189VAL00.011-0.0027.1890.1090.1090.0000.0000.0000.000
190A190PHE00.0480.02810.471-0.056-0.0560.0000.0000.0000.000
191A191ASP-1-0.847-0.89913.905-0.103-0.1030.0000.0000.0000.000
192A192TYR00.045-0.01013.5610.0310.0310.0000.0000.0000.000
193A193LYS10.7900.88816.2350.1620.1620.0000.0000.0000.000
194A194LEU0-0.099-0.04115.8880.0320.0320.0000.0000.0000.000
195A195ASN0-0.024-0.03811.7150.1300.1300.0000.0000.0000.000
196A196GLY00.0330.05312.8300.0260.0260.0000.0000.0000.000
197A197ALA00.038-0.00114.185-0.049-0.0490.0000.0000.0000.000
198A198MET0-0.030-0.00110.506-0.020-0.0200.0000.0000.0000.000
199A199PRO0-0.0200.0199.2980.0140.0140.0000.0000.0000.000
200A200ILE00.0020.0153.217-0.502-0.2190.045-0.106-0.2220.000
201A201TYR0-0.101-0.0454.1640.6240.8440.000-0.069-0.1520.000
202A202GLY0-0.006-0.0072.4110.7030.6774.089-2.232-1.831-0.019
203A203GLU-1-0.771-0.8782.264-5.389-4.7993.816-2.274-2.132-0.002
204A204ALA00.0220.0013.6980.9251.0230.0040.033-0.1350.000
205A205GLY00.0280.0055.3410.1510.1510.0000.0000.0000.000
206A206ASP-1-0.719-0.8572.90614.71515.9530.744-0.589-1.393-0.004
207A207SER0-0.010-0.0016.387-0.546-0.5460.0000.0000.0000.000
208A208GLY0-0.044-0.0039.769-0.032-0.0320.0000.0000.0000.000
209A209SER0-0.048-0.0177.739-0.132-0.1320.0000.0000.0000.000
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