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: 72N6K

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 OptH
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 -26931530.075468
FMO2-HF: Nuclear repulsion 26540981.873472
FMO2-HF: Total energy -390548.201996
FMO2-MP2: Total energy -391703.128518


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.
0.674-8.58545.039-19.607-16.171-0.071
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 : 0.048 / q_NPA : 0.016
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].
3A3VAL00.0320.0193.797-0.0802.031-0.015-1.158-0.9380.006
4A4ASN0-0.013-0.0166.660-0.058-0.0580.0000.0000.0000.000
5A5ASN00.0570.00610.418-0.062-0.0620.0000.0000.0000.000
6A6GLU-1-0.807-0.91412.730-0.305-0.3050.0000.0000.0000.000
7A7LEU0-0.0190.00111.7620.0820.0820.0000.0000.0000.000
8A8GLY00.0070.01012.798-0.112-0.1120.0000.0000.0000.000
9A9TYR00.0580.0184.8030.3750.3750.0000.0000.0000.000
10A10GLN00.015-0.01310.420-0.087-0.0870.0000.0000.0000.000
11A11LEU00.0050.00212.5880.0860.0860.0000.0000.0000.000
12A12PHE00.007-0.0107.3680.0290.0290.0000.0000.0000.000
13A13ARG10.7440.8458.3530.4370.4370.0000.0000.0000.000
14A14ASP-1-0.736-0.85510.497-0.015-0.0150.0000.0000.0000.000
15A15PHE0-0.0240.00310.1500.0660.0660.0000.0000.0000.000
16A16ALA0-0.024-0.0168.7850.0920.0920.0000.0000.0000.000
17A17GLU-1-0.789-0.89710.7850.1460.1460.0000.0000.0000.000
18A18ASN0-0.030-0.01013.9330.0200.0200.0000.0000.0000.000
19A19LYS10.8900.94815.890-0.090-0.0900.0000.0000.0000.000
20A20GLY00.0620.02517.513-0.019-0.0190.0000.0000.0000.000
21A21MET0-0.069-0.04118.5580.0180.0180.0000.0000.0000.000
22A22PHE00.007-0.00915.2180.0050.0050.0000.0000.0000.000
23A23ARG10.9601.01517.6240.0130.0130.0000.0000.0000.000
24A24PRO00.027-0.00119.768-0.003-0.0030.0000.0000.0000.000
25A25GLY0-0.017-0.01720.992-0.018-0.0180.0000.0000.0000.000
26A26ALA0-0.0370.00120.291-0.012-0.0120.0000.0000.0000.000
27A27THR00.009-0.01421.6820.0110.0110.0000.0000.0000.000
28A28ASN00.0100.00022.737-0.006-0.0060.0000.0000.0000.000
29A29ILE00.0080.02418.211-0.012-0.0120.0000.0000.0000.000
30A30ALA0-0.011-0.00419.580-0.005-0.0050.0000.0000.0000.000
31A31ILE0-0.022-0.01814.506-0.013-0.0130.0000.0000.0000.000
32A32TYR0-0.005-0.01718.5410.0100.0100.0000.0000.0000.000
33A33ASN0-0.0060.00117.959-0.051-0.0510.0000.0000.0000.000
34A34LYS10.8620.91814.0040.7210.7210.0000.0000.0000.000
35A35GLN0-0.053-0.01919.4070.0450.0450.0000.0000.0000.000
36A36GLY00.0040.01121.9810.0230.0230.0000.0000.0000.000
37A37GLU-1-0.948-0.97222.218-0.174-0.1740.0000.0000.0000.000
38A38PHE0-0.038-0.01921.155-0.021-0.0210.0000.0000.0000.000
39A39VAL00.0160.01616.1950.0000.0000.0000.0000.0000.000
40A40GLY0-0.005-0.00618.8690.0100.0100.0000.0000.0000.000
41A41THR0-0.027-0.02119.495-0.012-0.0120.0000.0000.0000.000
42A42LEU0-0.037-0.01414.6690.0110.0110.0000.0000.0000.000
43A43ASP-1-0.882-0.96318.6450.0260.0260.0000.0000.0000.000
44A44LYS10.9010.96620.479-0.051-0.0510.0000.0000.0000.000
45A45ALA0-0.0260.00420.2440.0070.0070.0000.0000.0000.000
46A46ALA0-0.0030.01521.195-0.013-0.0130.0000.0000.0000.000
47A47MET0-0.073-0.02216.0570.0370.0370.0000.0000.0000.000
48A48PRO00.0240.02115.944-0.014-0.0140.0000.0000.0000.000
49A49ASP-1-0.761-0.85617.8450.2190.2190.0000.0000.0000.000
50A50PHE0-0.006-0.02412.8150.0450.0450.0000.0000.0000.000
51A51SER00.009-0.00816.1700.0460.0460.0000.0000.0000.000
52A52ALA0-0.0160.00318.6590.0020.0020.0000.0000.0000.000
53A53VAL0-0.082-0.04212.0240.0360.0360.0000.0000.0000.000
54A54ASP-1-0.809-0.92113.7880.7600.7600.0000.0000.0000.000
55A55SER00.010-0.01413.8380.0860.0860.0000.0000.0000.000
56A56GLU-1-0.938-0.94813.6430.2810.2810.0000.0000.0000.000
57A57ILE0-0.080-0.04710.0530.0220.0220.0000.0000.0000.000
58A58GLY00.0230.0339.4220.4340.4340.0000.0000.0000.000
59A59VAL0-0.030-0.02010.0880.2850.2850.0000.0000.0000.000
60A60ALA0-0.0310.00911.923-0.091-0.0910.0000.0000.0000.000
61A61THR00.0190.00814.6200.0020.0020.0000.0000.0000.000
62A62LEU0-0.044-0.00816.960-0.029-0.0290.0000.0000.0000.000
63A63ILE0-0.003-0.02820.113-0.003-0.0030.0000.0000.0000.000
64A64ASN00.0290.00122.615-0.032-0.0320.0000.0000.0000.000
65A65PRO00.0380.01325.2360.0180.0180.0000.0000.0000.000
66A66GLN0-0.043-0.01427.124-0.005-0.0050.0000.0000.0000.000
67A67TYR0-0.060-0.07124.7680.0000.0000.0000.0000.0000.000
68A68ILE00.0050.02718.9820.0100.0100.0000.0000.0000.000
69A69ALA0-0.005-0.00418.555-0.026-0.0260.0000.0000.0000.000
70A70SER00.019-0.03814.6920.0830.0830.0000.0000.0000.000
71A71VAL00.0080.00813.547-0.073-0.0730.0000.0000.0000.000
72A72LYS10.8410.92516.228-0.319-0.3190.0000.0000.0000.000
73A73HIS0-0.123-0.07813.0370.0390.0390.0000.0000.0000.000
74A74ASN0-0.0120.01212.360-0.012-0.0120.0000.0000.0000.000
75A75GLY00.003-0.00315.952-0.047-0.0470.0000.0000.0000.000
76A76GLY0-0.050-0.02217.364-0.039-0.0390.0000.0000.0000.000
77A77TYR00.0200.00216.019-0.039-0.0390.0000.0000.0000.000
78A78THR00.0330.01318.104-0.003-0.0030.0000.0000.0000.000
79A79ASN00.0150.02220.057-0.024-0.0240.0000.0000.0000.000
80A80VAL0-0.026-0.01117.1570.0520.0520.0000.0000.0000.000
81A81SER00.016-0.01818.145-0.043-0.0430.0000.0000.0000.000
82A82PHE00.033-0.01318.0780.0570.0570.0000.0000.0000.000
83A83GLY00.0170.00219.259-0.035-0.0350.0000.0000.0000.000
84A84ASP-1-0.809-0.91618.8800.1520.1520.0000.0000.0000.000
85A85GLY00.0500.02719.223-0.011-0.0110.0000.0000.0000.000
86A86GLU-1-0.908-0.92019.8990.0880.0880.0000.0000.0000.000
87A87ASN0-0.083-0.05922.5690.0130.0130.0000.0000.0000.000
88A88ARG10.9410.98220.487-0.177-0.1770.0000.0000.0000.000
89A89TYR0-0.076-0.04823.088-0.025-0.0250.0000.0000.0000.000
90A90ASN0-0.033-0.02923.0450.0390.0390.0000.0000.0000.000
91A91ILE0-0.054-0.03621.132-0.003-0.0030.0000.0000.0000.000
92A92VAL0-0.059-0.02624.772-0.017-0.0170.0000.0000.0000.000
93A93ASP-1-0.820-0.89727.0240.1970.1970.0000.0000.0000.000
94A94ARG10.7860.88219.173-0.365-0.3650.0000.0000.0000.000
95A95ASN00.0690.03723.875-0.026-0.0260.0000.0000.0000.000
96A96ASN0-0.052-0.05722.7440.0460.0460.0000.0000.0000.000
97A97ALA00.0520.03823.028-0.028-0.0280.0000.0000.0000.000
98A98PRO00.010-0.00224.5820.0090.0090.0000.0000.0000.000
99A99SER0-0.037-0.03225.161-0.007-0.0070.0000.0000.0000.000
100A100LEU00.0700.03219.948-0.001-0.0010.0000.0000.0000.000
101A101ASP-1-0.829-0.89815.8530.5870.5870.0000.0000.0000.000
102A102PHE00.0410.00717.5560.0570.0570.0000.0000.0000.000
103A103HIS0-0.0130.00818.887-0.013-0.0130.0000.0000.0000.000
104A104ALA00.0320.01720.4340.0440.0440.0000.0000.0000.000
105A105PRO0-0.027-0.01020.593-0.039-0.0390.0000.0000.0000.000
106A106ARG10.8950.96623.763-0.167-0.1670.0000.0000.0000.000
107A107LEU0-0.014-0.01422.5920.0010.0010.0000.0000.0000.000
108A108ASP-1-0.805-0.91326.6150.1800.1800.0000.0000.0000.000
109A109LYS10.8010.88528.540-0.147-0.1470.0000.0000.0000.000
110A110LEU0-0.045-0.01128.3220.0180.0180.0000.0000.0000.000
111A111VAL00.0290.01223.800-0.010-0.0100.0000.0000.0000.000
112A112THR0-0.072-0.03427.126-0.010-0.0100.0000.0000.0000.000
113A113GLU-1-0.663-0.79424.2460.1780.1780.0000.0000.0000.000
114A114VAL00.0000.00421.056-0.008-0.0080.0000.0000.0000.000
115A115ALA0-0.0070.00424.175-0.005-0.0050.0000.0000.0000.000
116A116PRO0-0.020-0.01422.6620.0230.0230.0000.0000.0000.000
117A117THR00.0120.00518.579-0.017-0.0170.0000.0000.0000.000
118A118ALA0-0.029-0.00921.675-0.008-0.0080.0000.0000.0000.000
119A119VAL00.0300.01921.3080.0350.0350.0000.0000.0000.000
120A120THR0-0.026-0.04421.109-0.037-0.0370.0000.0000.0000.000
121A121ALA00.0400.00722.841-0.007-0.0070.0000.0000.0000.000
122A122GLN00.0110.02125.403-0.013-0.0130.0000.0000.0000.000
123A123GLY00.0620.04624.4190.0180.0180.0000.0000.0000.000
124A124ALA00.0450.02623.6860.0110.0110.0000.0000.0000.000
125A125VAL0-0.017-0.00424.692-0.022-0.0220.0000.0000.0000.000
126A126ALA0-0.002-0.03024.8690.0110.0110.0000.0000.0000.000
127A127GLY0-0.009-0.02123.993-0.014-0.0140.0000.0000.0000.000
128A128ALA00.0070.01924.055-0.009-0.0090.0000.0000.0000.000
129A129TYR0-0.012-0.02019.128-0.004-0.0040.0000.0000.0000.000
130A130LEU0-0.023-0.01920.1970.0040.0040.0000.0000.0000.000
131A131ASP-1-0.849-0.92322.2380.1030.1030.0000.0000.0000.000
132A132LYS10.8910.93220.123-0.092-0.0920.0000.0000.0000.000
133A133GLU-1-0.945-0.95523.6820.0730.0730.0000.0000.0000.000
134A134ARG10.8780.97324.943-0.168-0.1680.0000.0000.0000.000
135A135TYR0-0.038-0.03120.2850.0140.0140.0000.0000.0000.000
136A136PRO0-0.0390.00120.9460.0030.0030.0000.0000.0000.000
137A137VAL0-0.063-0.03916.229-0.018-0.0180.0000.0000.0000.000
138A138PHE00.0420.01113.6740.0210.0210.0000.0000.0000.000
139A139TYR00.003-0.00311.559-0.064-0.0640.0000.0000.0000.000
140A140ARG10.8930.9553.171-4.440-4.1690.035-0.094-0.2110.000
141A141LEU00.0480.0086.753-0.184-0.1840.0000.0000.0000.000
142A142GLY00.0130.0146.0100.0260.0260.0000.0000.0000.000
143A143SER00.0150.0095.111-0.217-0.2170.0000.0000.0000.000
144A144GLY00.0260.0283.557-2.715-2.2490.064-0.199-0.3310.002
145A145THR0-0.062-0.0572.737-4.362-2.7272.538-1.955-2.217-0.013
146A146GLN00.0690.0811.679-7.284-23.51933.315-11.186-5.895-0.041
147A147TYR0-0.030-0.0243.2663.3193.3870.0250.295-0.3870.001
148A148ILE00.0360.0285.638-0.801-0.8010.0000.0000.0000.000
149A149LYS10.8840.9448.4500.8800.8800.0000.0000.0000.000
150A150ASP-1-0.812-0.89510.320-0.548-0.5480.0000.0000.0000.000
151A151SER00.0310.01413.9500.0090.0090.0000.0000.0000.000
152A152ASN0-0.051-0.03716.3760.0390.0390.0000.0000.0000.000
153A153GLY0-0.070-0.04213.3360.0280.0280.0000.0000.0000.000
154A154GLN00.0030.01313.2600.0220.0220.0000.0000.0000.000
155A155LEU0-0.020-0.0238.022-0.098-0.0980.0000.0000.0000.000
156A156THR0-0.0080.00310.4840.2470.2470.0000.0000.0000.000
157A157LYS10.9200.9677.2370.5670.5670.0000.0000.0000.000
158A158MET0-0.006-0.0177.1750.4230.4230.0000.0000.0000.000
159A159GLY0-0.011-0.0117.0480.3780.3780.0000.0000.0000.000
160A160GLY0-0.095-0.0386.243-0.444-0.4440.0000.0000.0000.000
161A161ALA00.0240.0105.729-0.135-0.1350.0000.0000.0000.000
162A162TYR0-0.060-0.0376.709-0.302-0.3020.0000.0000.0000.000
163A163SER0-0.045-0.0067.598-0.203-0.2030.0000.0000.0000.000
164A164TRP0-0.002-0.0195.8200.0880.0880.0000.0000.0000.000
165A165LEU00.0680.0386.4490.3580.3580.0000.0000.0000.000
166A166THR0-0.053-0.0272.9520.4240.8980.020-0.208-0.2870.000
167A167GLY00.0450.0015.6260.9840.9840.0000.0000.0000.000
168A168GLY00.0160.0127.194-0.369-0.3690.0000.0000.0000.000
169A169THR0-0.073-0.0558.8570.1690.1690.0000.0000.0000.000
170A170VAL00.006-0.0048.5660.0110.0110.0000.0000.0000.000
171A171GLY00.0500.04111.276-0.031-0.0310.0000.0000.0000.000
172A172SER0-0.014-0.01814.7660.0410.0410.0000.0000.0000.000
173A173LEU0-0.0030.01913.477-0.009-0.0090.0000.0000.0000.000
174A174SER0-0.0190.00417.644-0.013-0.0130.0000.0000.0000.000
175A175SER00.0190.00119.0160.0250.0250.0000.0000.0000.000
176A176TYR0-0.007-0.00717.157-0.025-0.0250.0000.0000.0000.000
177A177GLN0-0.020-0.01822.0680.0190.0190.0000.0000.0000.000
178A178ASN00.013-0.00423.9630.0000.0000.0000.0000.0000.000
179A179GLY00.0230.00923.673-0.004-0.0040.0000.0000.0000.000
180A180GLU-1-0.928-0.95222.6240.2570.2570.0000.0000.0000.000
181A181MET0-0.072-0.01216.0910.0420.0420.0000.0000.0000.000
182A182ILE00.0140.01315.336-0.052-0.0520.0000.0000.0000.000
183A183SER0-0.0010.00714.1840.0590.0590.0000.0000.0000.000
184A184THR00.0450.00512.278-0.062-0.0620.0000.0000.0000.000
185A185SER0-0.059-0.01412.2800.0540.0540.0000.0000.0000.000
186A186SER00.0600.0018.105-0.165-0.1650.0000.0000.0000.000
187A187GLY00.0230.0118.027-0.101-0.1010.0000.0000.0000.000
188A188LEU0-0.098-0.0479.053-0.178-0.1780.0000.0000.0000.000
189A189VAL0-0.002-0.0057.1940.0930.0930.0000.0000.0000.000
190A190PHE00.0420.02710.474-0.062-0.0620.0000.0000.0000.000
191A191ASP-1-0.860-0.91613.906-0.057-0.0570.0000.0000.0000.000
192A192TYR00.0680.03113.6390.0310.0310.0000.0000.0000.000
193A193LYS10.8160.91516.2380.1020.1020.0000.0000.0000.000
194A194LEU0-0.116-0.05415.4170.0270.0270.0000.0000.0000.000
195A195ASN0-0.019-0.02911.7180.1170.1170.0000.0000.0000.000
196A196GLY00.0250.05212.8320.0340.0340.0000.0000.0000.000
197A197ALA00.0450.00314.187-0.042-0.0420.0000.0000.0000.000
198A198MET0-0.031-0.00210.464-0.028-0.0280.0000.0000.0000.000
199A199PRO0-0.0130.0239.3010.0400.0400.0000.0000.0000.000
200A200ILE00.0030.0133.193-0.333-0.0550.054-0.103-0.2280.000
201A201TYR0-0.108-0.0474.1810.4830.7050.000-0.067-0.1550.000
202A202GLY00.0080.0052.4141.2961.2054.101-2.191-1.818-0.018
203A203GLU-1-0.744-0.8522.139-4.932-4.4573.714-2.207-1.982-0.002
204A204ALA00.015-0.0053.6970.8450.9340.0030.038-0.1310.000
205A205GLY00.0260.0045.273-0.012-0.0120.0000.0000.0000.000
206A206ASP-1-0.744-0.8732.95715.90216.8801.185-0.572-1.591-0.006
207A207SER00.0080.0126.382-0.498-0.4980.0000.0000.0000.000
208A208GLY0-0.052-0.0099.765-0.047-0.0470.0000.0000.0000.000
209A209SER0-0.054-0.0277.874-0.134-0.1340.0000.0000.0000.000
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211A211LEU0-0.036-0.01310.5070.1270.1270.0000.0000.0000.000
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