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

tag_button

FMODB ID: 98MR2

Calculation Name: 3CEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CEU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8AA18

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2380993.588569
FMO2-HF: Nuclear repulsion 2300146.820229
FMO2-HF: Total energy -80846.76834
FMO2-MP2: Total energy -81082.54947


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-24.569-14.93818.303-6.446-21.484-0.054
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : 0.011
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].
3A3LEU00.0120.0172.811-2.5730.6750.361-1.852-1.757-0.004
4A4ILE0-0.040-0.0254.9310.4830.602-0.001-0.012-0.1060.000
5A5VAL00.0560.0368.1020.0720.0720.0000.0000.0000.000
6A6VAL0-0.042-0.02410.8800.1210.1210.0000.0000.0000.000
7A7THR00.0640.03913.805-0.032-0.0320.0000.0000.0000.000
8A8THR00.0420.02417.1090.0220.0220.0000.0000.0000.000
9A9PRO0-0.023-0.02619.3940.0120.0120.0000.0000.0000.000
10A10THR00.0700.03321.9990.0230.0230.0000.0000.0000.000
11A11PHE00.0030.01023.575-0.025-0.0250.0000.0000.0000.000
12A12PHE0-0.020-0.00420.7780.0170.0170.0000.0000.0000.000
13A13VAL00.0380.01025.901-0.013-0.0130.0000.0000.0000.000
14A14GLU-1-0.915-0.96925.290-0.302-0.3020.0000.0000.0000.000
15A15GLU-1-0.773-0.85821.273-0.354-0.3540.0000.0000.0000.000
16A16ASP-1-0.822-0.94221.652-0.352-0.3520.0000.0000.0000.000
17A17LYS10.9040.97522.6150.2650.2650.0000.0000.0000.000
18A18ILE00.0210.02018.127-0.042-0.0420.0000.0000.0000.000
19A19ILE00.006-0.00617.498-0.071-0.0710.0000.0000.0000.000
20A20THR0-0.050-0.04617.733-0.063-0.0630.0000.0000.0000.000
21A21ALA00.0210.02119.032-0.043-0.0430.0000.0000.0000.000
22A22LEU00.0020.00313.596-0.073-0.0730.0000.0000.0000.000
23A23PHE0-0.032-0.02814.314-0.135-0.1350.0000.0000.0000.000
24A24GLU-1-0.977-0.99115.488-0.604-0.6040.0000.0000.0000.000
25A25GLU-1-0.868-0.92914.260-0.880-0.8800.0000.0000.0000.000
26A26GLY0-0.071-0.05611.778-0.234-0.2340.0000.0000.0000.000
27A27LEU0-0.0100.0079.827-0.352-0.3520.0000.0000.0000.000
28A28ASP-1-0.917-0.9526.659-3.444-3.4440.0000.0000.0000.000
29A29ILE0-0.033-0.0389.5060.3470.3470.0000.0000.0000.000
30A30LEU00.0310.02311.083-0.093-0.0930.0000.0000.0000.000
31A31HIS0-0.013-0.03412.4460.1060.1060.0000.0000.0000.000
32A32LEU00.009-0.00315.238-0.014-0.0140.0000.0000.0000.000
33A33ARG10.9300.96317.8390.1760.1760.0000.0000.0000.000
34A34LYS10.7450.83920.0620.2640.2640.0000.0000.0000.000
35A35PRO0-0.034-0.02022.2170.0170.0170.0000.0000.0000.000
36A36GLU-1-0.925-0.94225.149-0.058-0.0580.0000.0000.0000.000
37A37THR00.004-0.00727.413-0.010-0.0100.0000.0000.0000.000
38A38PRO00.0010.00729.4590.0030.0030.0000.0000.0000.000
39A39ALA00.0680.03529.679-0.011-0.0110.0000.0000.0000.000
40A40MET00.0420.03429.914-0.016-0.0160.0000.0000.0000.000
41A41TYR0-0.015-0.02228.886-0.008-0.0080.0000.0000.0000.000
42A42SER00.0360.00925.759-0.021-0.0210.0000.0000.0000.000
43A43GLU-1-0.859-0.92526.384-0.148-0.1480.0000.0000.0000.000
44A44ARG10.8790.95128.7190.1620.1620.0000.0000.0000.000
45A45LEU0-0.0010.01622.118-0.007-0.0070.0000.0000.0000.000
46A46LEU00.026-0.01722.537-0.025-0.0250.0000.0000.0000.000
47A47THR0-0.053-0.04325.146-0.007-0.0070.0000.0000.0000.000
48A48LEU0-0.072-0.02126.7900.0040.0040.0000.0000.0000.000
49A49ILE0-0.0570.01621.012-0.019-0.0190.0000.0000.0000.000
50A50PRO00.0270.00122.6030.0180.0180.0000.0000.0000.000
51A51GLU-1-0.836-0.92422.799-0.255-0.2550.0000.0000.0000.000
52A52LYS10.8900.95620.7230.4440.4440.0000.0000.0000.000
53A53TYR0-0.007-0.01517.652-0.041-0.0410.0000.0000.0000.000
54A54HIS10.8730.92418.5660.2590.2590.0000.0000.0000.000
55A55ARG10.9450.99516.9720.3690.3690.0000.0000.0000.000
56A56ARG10.8950.94610.9310.9610.9610.0000.0000.0000.000
57A57ILE00.0230.02014.583-0.078-0.0780.0000.0000.0000.000
58A58VAL00.0030.01614.4480.0550.0550.0000.0000.0000.000
59A59THR0-0.003-0.00317.387-0.031-0.0310.0000.0000.0000.000
60A60HIS0-0.0070.00416.6070.0200.0200.0000.0000.0000.000
61A61GLU-1-0.783-0.89421.263-0.099-0.0990.0000.0000.0000.000
62A62HIS0-0.030-0.02124.881-0.004-0.0040.0000.0000.0000.000
63A63PHE00.0500.01122.415-0.013-0.0130.0000.0000.0000.000
64A64TYR00.0340.02126.001-0.003-0.0030.0000.0000.0000.000
65A65LEU00.006-0.00325.606-0.006-0.0060.0000.0000.0000.000
66A66LYS10.8470.94621.5100.0800.0800.0000.0000.0000.000
67A67GLU-1-0.880-0.95224.525-0.097-0.0970.0000.0000.0000.000
68A68GLU-1-0.969-0.95027.130-0.115-0.1150.0000.0000.0000.000
69A69PHE0-0.005-0.02625.433-0.012-0.0120.0000.0000.0000.000
70A70ASN0-0.025-0.00422.867-0.014-0.0140.0000.0000.0000.000
71A71LEU0-0.050-0.01320.740-0.031-0.0310.0000.0000.0000.000
72A72MET0-0.053-0.02013.245-0.019-0.0190.0000.0000.0000.000
73A73GLY0-0.013-0.02618.3780.0410.0410.0000.0000.0000.000
74A74ILE0-0.0220.00219.344-0.033-0.0330.0000.0000.0000.000
75A75HIS10.8010.89614.351-0.044-0.0440.0000.0000.0000.000
76A76LEU00.0290.02218.487-0.019-0.0190.0000.0000.0000.000
77A77ASN0-0.094-0.07819.9960.0170.0170.0000.0000.0000.000
78A78ALA00.008-0.01022.242-0.004-0.0040.0000.0000.0000.000
79A79ARG10.9410.98422.1810.0420.0420.0000.0000.0000.000
80A80ASN0-0.0090.00624.633-0.010-0.0100.0000.0000.0000.000
81A81PRO00.0130.00724.4610.0040.0040.0000.0000.0000.000
82A82SER0-0.006-0.01225.5630.0140.0140.0000.0000.0000.000
83A83GLU-1-0.892-0.93823.9020.0500.0500.0000.0000.0000.000
84A84PRO0-0.047-0.02525.7590.0010.0010.0000.0000.0000.000
85A85HIS00.014-0.01828.8830.0070.0070.0000.0000.0000.000
86A86ASP-1-0.919-0.94530.4220.0300.0300.0000.0000.0000.000
87A87TYR0-0.061-0.04620.604-0.026-0.0260.0000.0000.0000.000
88A88ALA00.0520.03025.0580.0150.0150.0000.0000.0000.000
89A89GLY0-0.037-0.03021.553-0.024-0.0240.0000.0000.0000.000
90A90HIS0-0.0080.01712.8420.0020.0020.0000.0000.0000.000
91A91VAL00.0970.07117.795-0.029-0.0290.0000.0000.0000.000
92A92SER0-0.0050.00914.1140.0330.0330.0000.0000.0000.000
93A93CYS00.0160.01015.472-0.030-0.0300.0000.0000.0000.000
94A94SER00.008-0.01014.9560.0530.0530.0000.0000.0000.000
95A95CYS0-0.0340.00715.278-0.021-0.0210.0000.0000.0000.000
96A96HIS0-0.041-0.02915.6360.0100.0100.0000.0000.0000.000
97A97SER00.1050.04517.138-0.014-0.0140.0000.0000.0000.000
98A98VAL00.0660.02615.4550.0380.0380.0000.0000.0000.000
99A99GLU-1-0.946-0.97417.1800.3330.3330.0000.0000.0000.000
100A100GLU-1-0.860-0.95118.8290.2810.2810.0000.0000.0000.000
101A101VAL00.0030.00212.862-0.012-0.0120.0000.0000.0000.000
102A102LYS10.9780.98716.125-0.419-0.4190.0000.0000.0000.000
103A103ASN0-0.067-0.03018.0670.0060.0060.0000.0000.0000.000
104A104ARG10.9580.95418.236-0.325-0.3250.0000.0000.0000.000
105A105LYS10.8840.97312.688-0.910-0.9100.0000.0000.0000.000
106A106HIS0-0.064-0.05415.6270.0130.0130.0000.0000.0000.000
107A107PHE0-0.049-0.00217.640-0.027-0.0270.0000.0000.0000.000
108A108TYR00.0370.02215.768-0.048-0.0480.0000.0000.0000.000
109A109ASP-1-0.825-0.90414.0010.1790.1790.0000.0000.0000.000
110A110TYR0-0.024-0.0639.8490.0480.0480.0000.0000.0000.000
111A111VAL0-0.045-0.00911.205-0.126-0.1260.0000.0000.0000.000
112A112PHE0-0.028-0.00910.5270.1650.1650.0000.0000.0000.000
113A113MET00.0020.01110.4950.0390.0390.0000.0000.0000.000
114A114SER0-0.0210.01110.905-0.009-0.0090.0000.0000.0000.000
115A115PRO00.009-0.01613.2300.0060.0060.0000.0000.0000.000
116A116ILE00.007-0.0078.0650.0250.0250.0000.0000.0000.000
117A117TYR0-0.0390.0066.945-0.034-0.0340.0000.0000.0000.000
118A127SER0-0.042-0.03615.5560.0180.0180.0000.0000.0000.000
119A128THR0-0.002-0.01216.184-0.028-0.0280.0000.0000.0000.000
120A129TYR0-0.0460.01613.5540.0380.0380.0000.0000.0000.000
121A130THR00.0660.03316.188-0.057-0.0570.0000.0000.0000.000
122A131ALA00.0290.00113.1440.0670.0670.0000.0000.0000.000
123A132GLU-1-0.949-0.98114.1500.4830.4830.0000.0000.0000.000
124A133GLU-1-0.850-0.93716.2520.5050.5050.0000.0000.0000.000
125A134LEU0-0.009-0.00710.1220.0430.0430.0000.0000.0000.000
126A135ARG10.9890.99512.956-0.542-0.5420.0000.0000.0000.000
127A136GLU-1-0.918-0.94414.3070.6300.6300.0000.0000.0000.000
128A137ALA0-0.015-0.01814.228-0.002-0.0020.0000.0000.0000.000
129A138GLN00.012-0.00910.240-0.102-0.1020.0000.0000.0000.000
130A139LYS10.8020.89912.824-0.697-0.6970.0000.0000.0000.000
131A140ALA0-0.046-0.01115.412-0.043-0.0430.0000.0000.0000.000
132A141LYS10.9120.94613.418-1.183-1.1830.0000.0000.0000.000
133A142ILE0-0.0300.00313.749-0.004-0.0040.0000.0000.0000.000
134A143ILE0-0.0070.0217.522-0.105-0.1050.0000.0000.0000.000
135A144ASP-1-0.776-0.9078.6171.3621.3620.0000.0000.0000.000
136A145SER00.008-0.0195.8970.2020.2020.0000.0000.0000.000
137A146LYS10.8430.9666.955-0.783-0.7830.0000.0000.0000.000
138A147VAL0-0.0280.0007.634-0.316-0.3160.0000.0000.0000.000
139A148MET0-0.047-0.0146.0780.5930.5930.0000.0000.0000.000
140A149ALA00.0330.0265.243-0.572-0.5720.0000.0000.0000.000
141A150LEU00.041-0.0017.131-0.342-0.3420.0000.0000.0000.000
142A151GLY00.016-0.0089.4020.0580.0580.0000.0000.0000.000
143A152GLY00.0340.00710.4350.0500.0500.0000.0000.0000.000
144A153ILE0-0.0310.0024.783-0.0280.047-0.001-0.001-0.0720.000
145A154ASN00.0220.0037.369-0.032-0.0320.0000.0000.0000.000
146A155GLU-1-0.859-0.9597.078-1.009-1.0090.0000.0000.0000.000
147A156ASP-1-0.930-0.9529.034-0.498-0.4980.0000.0000.0000.000
148A157ASN0-0.029-0.0036.994-0.129-0.1290.0000.0000.0000.000
149A158LEU00.0030.0032.294-0.196-0.5182.541-0.329-1.889-0.001
150A159LEU0-0.005-0.0292.839-2.330-1.0620.452-0.749-0.970-0.008
151A160GLU-1-0.882-0.9305.0040.9541.033-0.001-0.003-0.0740.000
152A161ILE0-0.007-0.0032.537-0.6170.3091.368-0.449-1.845-0.001
153A162LYS10.8980.9342.300-2.454-1.5125.570-1.886-4.6260.000
154A163ASP-1-0.920-0.9503.7232.8490.4660.1442.668-0.4280.000
155A164PHE0-0.076-0.0466.643-0.366-0.3660.0000.0000.0000.000
156A165GLY0-0.031-0.0116.196-0.474-0.4740.0000.0000.0000.000
157A166PHE0-0.038-0.0183.939-1.139-0.6210.051-0.125-0.4440.000
158A167GLY00.0050.0033.133-0.2361.9170.326-0.987-1.492-0.008
159A168GLY0-0.032-0.0232.215-3.992-2.8572.550-1.660-2.025-0.005
160A169ALA00.0070.0102.5042.6891.6342.4201.165-2.530-0.003
161A170VAL0-0.020-0.0064.151-1.273-1.2650.0090.018-0.0360.000
162A171VAL00.0210.0096.3860.0800.0800.0000.0000.0000.000
163A172LEU0-0.014-0.0189.0830.0490.0490.0000.0000.0000.000
164A173GLY00.0250.00212.819-0.027-0.0270.0000.0000.0000.000
165A174ASP-1-0.831-0.91310.520-0.891-0.8910.0000.0000.0000.000
166A175LEU0-0.0130.00710.671-0.055-0.0550.0000.0000.0000.000
167A176TRP00.001-0.04213.2760.0330.0330.0000.0000.0000.000
168A177ASN0-0.018-0.00316.4490.0460.0460.0000.0000.0000.000
169A178LYS10.8250.93313.9430.6970.6970.0000.0000.0000.000
170A179PHE0-0.007-0.01318.414-0.006-0.0060.0000.0000.0000.000
171A180ASP-1-0.884-0.91421.261-0.278-0.2780.0000.0000.0000.000
172A181ALA00.016-0.01024.5920.0080.0080.0000.0000.0000.000
173A182CYS0-0.100-0.06427.0620.0150.0150.0000.0000.0000.000
174A183LEU0-0.0200.00827.8410.0160.0160.0000.0000.0000.000
175A184ASP-1-0.840-0.90224.126-0.320-0.3200.0000.0000.0000.000
176A185GLN0-0.062-0.04627.2340.0110.0110.0000.0000.0000.000
177A186ASN0-0.028-0.02324.474-0.027-0.0270.0000.0000.0000.000
178A187TYR00.0980.04420.654-0.007-0.0070.0000.0000.0000.000
179A188LEU00.0010.00320.080-0.056-0.0560.0000.0000.0000.000
180A189ALA00.0600.04218.950-0.065-0.0650.0000.0000.0000.000
181A190VAL00.0030.00615.513-0.069-0.0690.0000.0000.0000.000
182A191ILE0-0.020-0.01114.957-0.117-0.1170.0000.0000.0000.000
183A192GLU-1-0.942-0.99315.070-0.659-0.6590.0000.0000.0000.000
184A193HIS0-0.083-0.05611.198-0.053-0.0530.0000.0000.0000.000
185A194PHE00.0310.0189.479-0.200-0.2000.0000.0000.0000.000
186A195LYS10.8950.95710.0210.4980.4980.0000.0000.0000.000
187A196LYS10.8810.95610.6740.6160.6160.0000.0000.0000.000
188A197LEU00.015-0.0036.478-0.193-0.1930.0000.0000.0000.000
189A198LYS10.8970.9556.0311.4901.4900.0000.0000.0000.000
190A199LYS10.9280.9806.5710.4240.4240.0000.0000.0000.000
191A200LEU0-0.012-0.0115.5840.1900.1900.0000.0000.0000.000
192A201ALA00.0020.0092.906-0.3130.8320.280-0.380-1.0450.000
193A202ASP-1-0.883-0.9522.273-11.531-9.8632.235-1.858-2.045-0.024
194A203LEU0-0.076-0.0334.4761.4141.521-0.001-0.006-0.1000.000
195A204GLU-1-0.945-0.9706.2272.6412.6410.0000.0000.0000.000
196A205HIS0-0.0140.0027.0970.4620.4620.0000.0000.0000.000
197A206HIS10.9140.9398.161-2.044-2.0440.0000.0000.0000.000
198A207HIS0-0.0120.01510.297-0.081-0.0810.0000.0000.0000.000