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: MN99Z

Calculation Name: 1XAT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAT

Chain ID: A

ChEMBL ID:

UniProt ID: P26841

Base Structure: X-ray

Registration Date: 2023-09-22

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2211624.038712
FMO2-HF: Nuclear repulsion 2129592.81076
FMO2-HF: Total energy -82031.227952
FMO2-MP2: Total energy -82267.807406


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-37.293-27.95718.09-11.022-16.4040.022
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.013
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].
3A5PHE0-0.038-0.0081.979-15.480-11.9606.461-4.667-5.3140.048
4A6GLU-1-0.773-0.8853.157-4.722-3.2130.603-0.659-1.454-0.007
5A7SER0-0.018-0.0155.539-1.181-1.1810.0000.0000.0000.000
6A8PRO00.0100.0095.8170.8650.8650.0000.0000.0000.000
7A9PHE0-0.052-0.0306.6000.4610.4610.0000.0000.0000.000
8A10ARG10.8900.9498.261-0.475-0.4750.0000.0000.0000.000
9A11GLY00.0650.0427.9050.5430.5430.0000.0000.0000.000
10A12LYS10.7680.8676.616-2.017-2.0170.0000.0000.0000.000
11A13LEU00.0590.01810.7510.0660.0660.0000.0000.0000.000
12A14LEU00.0120.02413.1050.1440.1440.0000.0000.0000.000
13A15SER00.041-0.00214.8060.0360.0360.0000.0000.0000.000
14A16GLU-1-0.969-0.97013.7920.4430.4430.0000.0000.0000.000
15A17GLN0-0.062-0.0519.2780.6580.6580.0000.0000.0000.000
16A18VAL0-0.047-0.00512.8200.0820.0820.0000.0000.0000.000
17A19SER0-0.051-0.03215.019-0.100-0.1000.0000.0000.0000.000
18A20ASN0-0.015-0.00716.708-0.158-0.1580.0000.0000.0000.000
19A21PRO00.0430.01218.7380.0060.0060.0000.0000.0000.000
20A22ASN0-0.080-0.03521.859-0.054-0.0540.0000.0000.0000.000
21A23ILE00.0150.00617.0120.0120.0120.0000.0000.0000.000
22A24ARG10.8740.94620.795-0.377-0.3770.0000.0000.0000.000
23A25VAL00.0240.01317.158-0.001-0.0010.0000.0000.0000.000
24A26GLY00.0410.03520.395-0.043-0.0430.0000.0000.0000.000
25A27ARG10.8240.89720.370-0.195-0.1950.0000.0000.0000.000
26A28TYR00.002-0.02619.403-0.012-0.0120.0000.0000.0000.000
27A29SER0-0.0020.01018.041-0.004-0.0040.0000.0000.0000.000
28A30TYR0-0.052-0.02212.4840.0670.0670.0000.0000.0000.000
29A31TYR00.0140.0197.763-0.258-0.2580.0000.0000.0000.000
30A32SER0-0.003-0.0088.1000.4430.4430.0000.0000.0000.000
31A33GLY00.0510.0196.215-0.951-0.9510.0000.0000.0000.000
32A34TYR00.0140.0202.473-3.299-0.3953.227-2.017-4.1140.006
33A35TYR0-0.026-0.0332.090-10.078-9.9204.119-1.909-2.368-0.033
34A36HIS0-0.0040.0264.742-0.180-0.122-0.001-0.007-0.0490.000
35A37GLY0-0.038-0.0022.311-2.661-2.0503.495-2.192-1.9140.016
36A38HIS0-0.0060.0053.017-1.189-0.6130.1860.429-1.191-0.008
37A39SER00.0440.0055.6380.4160.4160.0000.0000.0000.000
38A40PHE00.029-0.0317.910-0.349-0.3490.0000.0000.0000.000
39A41ASP-1-0.696-0.84010.9440.7730.7730.0000.0000.0000.000
40A42ASP-1-0.924-0.95010.0261.5151.5150.0000.0000.0000.000
41A43CYS0-0.106-0.04011.6170.0570.0570.0000.0000.0000.000
42A44ALA0-0.0120.00513.460-0.189-0.1890.0000.0000.0000.000
43A45ARG10.9240.96513.999-1.011-1.0110.0000.0000.0000.000
44A46TYR00.001-0.01817.899-0.049-0.0490.0000.0000.0000.000
45A47LEU00.0210.02619.274-0.053-0.0530.0000.0000.0000.000
46A48MET0-0.017-0.00920.1410.0190.0190.0000.0000.0000.000
47A49PRO0-0.0140.00919.596-0.010-0.0100.0000.0000.0000.000
48A50ASP-1-0.896-0.96721.9530.3610.3610.0000.0000.0000.000
49A51ARG10.8080.86825.225-0.278-0.2780.0000.0000.0000.000
50A52ASP-1-0.874-0.91927.1790.2700.2700.0000.0000.0000.000
51A53ASP-1-0.777-0.86929.5600.2530.2530.0000.0000.0000.000
52A54VAL0-0.062-0.01425.278-0.005-0.0050.0000.0000.0000.000
53A55ASP-1-0.809-0.89126.7030.3120.3120.0000.0000.0000.000
54A56LYS10.7590.84524.546-0.306-0.3060.0000.0000.0000.000
55A57LEU0-0.0030.01118.186-0.016-0.0160.0000.0000.0000.000
56A58VAL0-0.042-0.02822.1660.0160.0160.0000.0000.0000.000
57A59ILE0-0.027-0.02117.6300.0030.0030.0000.0000.0000.000
58A60GLY00.0470.03221.716-0.010-0.0100.0000.0000.0000.000
59A61SER00.009-0.00721.7710.0570.0570.0000.0000.0000.000
60A62PHE0-0.021-0.02321.150-0.018-0.0180.0000.0000.0000.000
61A63CYS0-0.0270.02518.936-0.031-0.0310.0000.0000.0000.000
62A64SER0-0.0060.00816.2120.0490.0490.0000.0000.0000.000
63A65ILE0-0.023-0.02513.590-0.077-0.0770.0000.0000.0000.000
64A66GLY00.0190.00612.1410.1880.1880.0000.0000.0000.000
65A67SER00.031-0.0327.2370.3420.3420.0000.0000.0000.000
66A68GLY00.0610.0308.999-0.417-0.4170.0000.0000.0000.000
67A69ALA0-0.0180.01710.677-0.210-0.2100.0000.0000.0000.000
68A70ALA0-0.028-0.01713.3570.1680.1680.0000.0000.0000.000
69A71PHE00.018-0.00515.456-0.124-0.1240.0000.0000.0000.000
70A72ILE0-0.015-0.01419.0250.0250.0250.0000.0000.0000.000
71A73MET00.0330.02320.750-0.042-0.0420.0000.0000.0000.000
72A74ALA00.0090.00723.187-0.016-0.0160.0000.0000.0000.000
73A75GLY00.0800.04025.804-0.025-0.0250.0000.0000.0000.000
74A76ASN0-0.043-0.04027.7180.0230.0230.0000.0000.0000.000
75A77GLN0-0.037-0.01223.368-0.016-0.0160.0000.0000.0000.000
76A78GLY0-0.002-0.00428.692-0.007-0.0070.0000.0000.0000.000
77A79HIS10.7980.91028.510-0.274-0.2740.0000.0000.0000.000
78A80ARG10.8500.91433.048-0.170-0.1700.0000.0000.0000.000
79A81ALA00.008-0.00535.510-0.007-0.0070.0000.0000.0000.000
80A82GLU-1-0.832-0.88537.2270.1600.1600.0000.0000.0000.000
81A83TRP0-0.027-0.00339.204-0.007-0.0070.0000.0000.0000.000
82A84ALA00.007-0.00241.0830.0000.0000.0000.0000.0000.000
83A85SER00.0030.00138.6940.0000.0000.0000.0000.0000.000
84A86THR0-0.0080.00934.3220.0040.0040.0000.0000.0000.000
85A87PHE00.0270.01233.1020.0180.0180.0000.0000.0000.000
86A88PRO00.0290.03330.607-0.008-0.0080.0000.0000.0000.000
87A89PHE00.020-0.01633.8250.0040.0040.0000.0000.0000.000
88A90HIS0-0.032-0.02534.8950.0080.0080.0000.0000.0000.000
89A91PHE00.011-0.00630.6460.0020.0020.0000.0000.0000.000
90A92MET0-0.097-0.02232.3570.0120.0120.0000.0000.0000.000
91A93HIS00.001-0.02432.127-0.018-0.0180.0000.0000.0000.000
92A94GLU-1-0.932-0.95533.6270.1480.1480.0000.0000.0000.000
93A95GLU-1-0.904-0.94935.9490.1130.1130.0000.0000.0000.000
94A96PRO00.0550.02338.5380.0010.0010.0000.0000.0000.000
95A97ALA0-0.026-0.00941.550-0.002-0.0020.0000.0000.0000.000
96A98PHE0-0.074-0.05337.029-0.002-0.0020.0000.0000.0000.000
97A99ALA00.0430.02740.0940.0060.0060.0000.0000.0000.000
98A100GLY0-0.040-0.01841.8210.0020.0020.0000.0000.0000.000
99A101ALA0-0.0310.00239.3140.0000.0000.0000.0000.0000.000
100A102VAL00.0340.02340.6240.0030.0030.0000.0000.0000.000
101A103ASN00.019-0.00333.9780.0110.0110.0000.0000.0000.000
102A104GLY00.0370.01436.567-0.002-0.0020.0000.0000.0000.000
103A105TYR00.000-0.00928.7760.0080.0080.0000.0000.0000.000
104A106GLN0-0.071-0.03332.701-0.024-0.0240.0000.0000.0000.000
105A107PRO00.0050.01731.0580.0130.0130.0000.0000.0000.000
106A108ALA0-0.017-0.02529.314-0.013-0.0130.0000.0000.0000.000
107A109GLY0-0.0340.00030.763-0.010-0.0100.0000.0000.0000.000
108A110ASP-1-0.813-0.91927.3920.3530.3530.0000.0000.0000.000
109A111THR0-0.052-0.00722.954-0.006-0.0060.0000.0000.0000.000
110A112LEU0-0.030-0.01724.6810.0220.0220.0000.0000.0000.000
111A113ILE0-0.005-0.00320.699-0.013-0.0130.0000.0000.0000.000
112A114GLY00.0380.01923.8440.0070.0070.0000.0000.0000.000
113A115HIS00.0680.01723.9190.0610.0610.0000.0000.0000.000
114A116GLU-1-0.781-0.87523.1150.2000.2000.0000.0000.0000.000
115A117VAL0-0.0030.00721.448-0.020-0.0200.0000.0000.0000.000
116A118TRP0-0.054-0.02116.8430.0250.0250.0000.0000.0000.000
117A119ILE00.008-0.00316.486-0.045-0.0450.0000.0000.0000.000
118A120GLY00.0190.01716.0220.0600.0600.0000.0000.0000.000
119A121THR0-0.047-0.04911.3390.0370.0370.0000.0000.0000.000
120A122GLU-1-0.810-0.90711.9070.2950.2950.0000.0000.0000.000
121A123ALA0-0.0430.01114.332-0.068-0.0680.0000.0000.0000.000
122A124MET0-0.036-0.02117.0910.0780.0780.0000.0000.0000.000
123A125PHE00.010-0.00918.262-0.080-0.0800.0000.0000.0000.000
124A126MET0-0.013-0.00721.9430.0200.0200.0000.0000.0000.000
125A127PRO00.024-0.01124.7090.0040.0040.0000.0000.0000.000
126A128GLY00.0370.03526.256-0.025-0.0250.0000.0000.0000.000
127A129VAL0-0.0740.00224.921-0.021-0.0210.0000.0000.0000.000
128A130ARG10.8570.88626.910-0.221-0.2210.0000.0000.0000.000
129A131VAL0-0.0140.00423.739-0.022-0.0220.0000.0000.0000.000
130A132GLY00.0470.01926.6850.0100.0100.0000.0000.0000.000
131A133HIS00.0920.03427.1860.0280.0280.0000.0000.0000.000
132A134GLY00.0400.04326.600-0.023-0.0230.0000.0000.0000.000
133A135ALA0-0.039-0.00925.936-0.009-0.0090.0000.0000.0000.000
134A136ILE0-0.014-0.01322.1370.0190.0190.0000.0000.0000.000
135A137ILE0-0.061-0.02720.547-0.025-0.0250.0000.0000.0000.000
136A138GLY00.0560.03020.1030.0200.0200.0000.0000.0000.000
137A139SER00.049-0.00216.4850.0580.0580.0000.0000.0000.000
138A140ARG10.7610.86814.764-0.336-0.3360.0000.0000.0000.000
139A141ALA0-0.066-0.01318.798-0.022-0.0220.0000.0000.0000.000
140A142LEU00.0130.01821.0500.0450.0450.0000.0000.0000.000
141A143VAL00.003-0.00823.054-0.039-0.0390.0000.0000.0000.000
142A144THR00.005-0.00925.1660.0210.0210.0000.0000.0000.000
143A145GLY00.0440.02128.109-0.013-0.0130.0000.0000.0000.000
144A146ASP-1-0.812-0.87728.7390.2620.2620.0000.0000.0000.000
145A147VAL0-0.047-0.02226.717-0.012-0.0120.0000.0000.0000.000
146A148GLU-1-0.830-0.91129.7050.1620.1620.0000.0000.0000.000
147A149PRO00.017-0.01430.1940.0070.0070.0000.0000.0000.000
148A150TYR0-0.039-0.03529.255-0.019-0.0190.0000.0000.0000.000
149A151ALA00.0030.03129.700-0.018-0.0180.0000.0000.0000.000
150A152ILE00.0030.00625.7340.0190.0190.0000.0000.0000.000
151A153VAL00.0270.01224.851-0.018-0.0180.0000.0000.0000.000
152A154GLY00.0430.00624.0910.0140.0140.0000.0000.0000.000
153A155GLY0-0.030-0.01723.980-0.022-0.0220.0000.0000.0000.000
154A156ASN00.0060.03424.0370.0240.0240.0000.0000.0000.000
155A157PRO00.0640.00426.158-0.016-0.0160.0000.0000.0000.000
156A158ALA0-0.045-0.01125.132-0.017-0.0170.0000.0000.0000.000
157A159ARG10.9370.96327.093-0.152-0.1520.0000.0000.0000.000
158A160THR00.003-0.01229.4270.0030.0030.0000.0000.0000.000
159A161ILE0-0.054-0.02227.110-0.013-0.0130.0000.0000.0000.000
160A162ARG10.9720.98129.589-0.118-0.1180.0000.0000.0000.000
161A163LYS10.8990.95031.046-0.128-0.1280.0000.0000.0000.000
162A164ARG10.6980.82926.449-0.213-0.2130.0000.0000.0000.000
163A165PHE0-0.014-0.00730.609-0.009-0.0090.0000.0000.0000.000
164A166SER0-0.017-0.02534.6440.0030.0030.0000.0000.0000.000
165A167ASP-1-0.829-0.93437.5030.1180.1180.0000.0000.0000.000
166A168GLY0-0.0050.01039.5390.0040.0040.0000.0000.0000.000
167A169ASP-1-0.782-0.88436.7000.0930.0930.0000.0000.0000.000
168A170ILE0-0.028-0.01234.0080.0070.0070.0000.0000.0000.000
169A171GLN0-0.028-0.01536.3580.0020.0020.0000.0000.0000.000
170A172ASN0-0.005-0.00138.9330.0020.0020.0000.0000.0000.000
171A173LEU00.004-0.00932.0780.0020.0020.0000.0000.0000.000
172A174LEU0-0.080-0.05633.2200.0100.0100.0000.0000.0000.000
173A175GLU-1-0.815-0.85935.5040.1060.1060.0000.0000.0000.000
174A176MET0-0.045-0.00435.065-0.001-0.0010.0000.0000.0000.000
175A177ALA00.0290.01532.8750.0020.0020.0000.0000.0000.000
176A178TRP00.0790.02725.2710.0080.0080.0000.0000.0000.000
177A179TRP0-0.026-0.00327.1960.0040.0040.0000.0000.0000.000
178A180ASP-1-0.875-0.94928.3200.2480.2480.0000.0000.0000.000
179A181TRP0-0.074-0.01731.023-0.011-0.0110.0000.0000.0000.000
180A182PRO00.0470.02431.0050.0150.0150.0000.0000.0000.000
181A183LEU00.0370.00127.096-0.004-0.0040.0000.0000.0000.000
182A184ALA00.0360.01630.505-0.005-0.0050.0000.0000.0000.000
183A185ASP-1-0.832-0.92033.5630.0960.0960.0000.0000.0000.000
184A186ILE0-0.042-0.01027.830-0.003-0.0030.0000.0000.0000.000
185A187GLU-1-0.963-0.98230.5000.0820.0820.0000.0000.0000.000
186A188ALA0-0.051-0.02831.372-0.010-0.0100.0000.0000.0000.000
187A189ALA0-0.009-0.01333.601-0.009-0.0090.0000.0000.0000.000
188A190MET00.0410.03626.1990.0040.0040.0000.0000.0000.000
189A191PRO0-0.002-0.01331.3600.0000.0000.0000.0000.0000.000
190A192LEU00.003-0.00633.525-0.005-0.0050.0000.0000.0000.000
191A193LEU0-0.040-0.00229.2020.0030.0030.0000.0000.0000.000
192A194CYS0-0.076-0.02828.7750.0110.0110.0000.0000.0000.000
193A195THR0-0.044-0.02229.972-0.016-0.0160.0000.0000.0000.000
194A196GLY00.0210.00331.9560.0110.0110.0000.0000.0000.000
195A197ASP-1-0.889-0.94833.7550.0610.0610.0000.0000.0000.000
196A198ILE00.0150.01833.1630.0010.0010.0000.0000.0000.000
197A199PRO00.0040.00036.9640.0010.0010.0000.0000.0000.000
198A200ALA00.0160.02339.001-0.001-0.0010.0000.0000.0000.000
199A201LEU0-0.014-0.00933.6810.0000.0000.0000.0000.0000.000
200A202TYR0-0.047-0.08737.878-0.001-0.0010.0000.0000.0000.000
201A203GLN0-0.0020.00240.058-0.001-0.0010.0000.0000.0000.000
202A204HIS0-0.0090.00237.167-0.005-0.0050.0000.0000.0000.000
203A205TRP0-0.030-0.01838.234-0.001-0.0010.0000.0000.0000.000
204A206LYS10.8160.90640.056-0.094-0.0940.0000.0000.0000.000
205A207GLN0-0.026-0.00643.567-0.002-0.0020.0000.0000.0000.000
206A208ARG10.8830.94638.220-0.089-0.0890.0000.0000.0000.000
207A209GLN0-0.052-0.01539.9630.0060.0060.0000.0000.0000.000
208A210ALA0-0.066-0.02143.240-0.001-0.0010.0000.0000.0000.000