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: MN9LZ

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2382200.740523
FMO2-HF: Nuclear repulsion 2301352.467123
FMO2-HF: Total energy -80848.2734
FMO2-MP2: Total energy -81084.019248


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.
-21.439-10.97918.397-7.454-21.403-0.053
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 : -0.017 / q_NPA : 0.020
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].
3A3LEU00.0010.0132.779-2.3460.9910.424-1.913-1.849-0.004
4A4ILE0-0.039-0.0224.8450.2930.419-0.001-0.014-0.1110.000
5A5VAL00.0480.0318.0530.0770.0770.0000.0000.0000.000
6A6VAL0-0.042-0.02310.8590.1050.1050.0000.0000.0000.000
7A7THR00.0540.03413.825-0.033-0.0330.0000.0000.0000.000
8A8THR00.0430.02617.0980.0260.0260.0000.0000.0000.000
9A9PRO0-0.024-0.02919.3830.0110.0110.0000.0000.0000.000
10A10THR00.0680.03222.0230.0200.0200.0000.0000.0000.000
11A11PHE00.0100.01123.550-0.023-0.0230.0000.0000.0000.000
12A12PHE0-0.024-0.00220.6330.0150.0150.0000.0000.0000.000
13A13VAL00.0310.00225.823-0.012-0.0120.0000.0000.0000.000
14A14GLU-1-0.912-0.96125.415-0.277-0.2770.0000.0000.0000.000
15A15GLU-1-0.763-0.85621.009-0.309-0.3090.0000.0000.0000.000
16A16ASP-1-0.787-0.89421.555-0.308-0.3080.0000.0000.0000.000
17A17LYS10.8580.91322.5150.2480.2480.0000.0000.0000.000
18A18ILE00.0160.02317.992-0.039-0.0390.0000.0000.0000.000
19A19ILE00.007-0.00517.605-0.064-0.0640.0000.0000.0000.000
20A20THR0-0.041-0.03317.629-0.057-0.0570.0000.0000.0000.000
21A21ALA00.0050.00718.920-0.038-0.0380.0000.0000.0000.000
22A22LEU00.0140.00913.257-0.066-0.0660.0000.0000.0000.000
23A23PHE0-0.039-0.02914.127-0.120-0.1200.0000.0000.0000.000
24A24GLU-1-0.965-0.98315.376-0.536-0.5360.0000.0000.0000.000
25A25GLU-1-0.831-0.88814.210-0.822-0.8220.0000.0000.0000.000
26A26GLY0-0.026-0.02211.805-0.195-0.1950.0000.0000.0000.000
27A27LEU0-0.040-0.0109.581-0.341-0.3410.0000.0000.0000.000
28A28ASP-1-0.910-0.9676.544-2.970-2.9700.0000.0000.0000.000
29A29ILE0-0.017-0.0279.4310.2930.2930.0000.0000.0000.000
30A30LEU00.0290.02311.019-0.075-0.0750.0000.0000.0000.000
31A31HIS00.0060.00312.4360.0930.0930.0000.0000.0000.000
32A32LEU00.009-0.00115.205-0.013-0.0130.0000.0000.0000.000
33A33ARG10.9410.96517.8680.1320.1320.0000.0000.0000.000
34A34LYS10.7510.85020.1180.2190.2190.0000.0000.0000.000
35A35PRO0-0.036-0.02422.2300.0130.0130.0000.0000.0000.000
36A36GLU-1-0.905-0.93925.221-0.040-0.0400.0000.0000.0000.000
37A37THR00.000-0.00527.590-0.010-0.0100.0000.0000.0000.000
38A38PRO0-0.0050.00129.5040.0030.0030.0000.0000.0000.000
39A39ALA00.0850.04829.642-0.010-0.0100.0000.0000.0000.000
40A40MET00.0300.01929.869-0.014-0.0140.0000.0000.0000.000
41A41TYR0-0.029-0.02928.852-0.007-0.0070.0000.0000.0000.000
42A42SER00.0280.00625.705-0.019-0.0190.0000.0000.0000.000
43A43GLU-1-0.825-0.88226.326-0.121-0.1210.0000.0000.0000.000
44A44ARG10.9090.96628.6530.1390.1390.0000.0000.0000.000
45A45LEU0-0.0020.01121.831-0.008-0.0080.0000.0000.0000.000
46A46LEU00.019-0.01022.248-0.022-0.0220.0000.0000.0000.000
47A47THR0-0.052-0.04325.078-0.007-0.0070.0000.0000.0000.000
48A48LEU0-0.057-0.01726.8490.0010.0010.0000.0000.0000.000
49A49ILE0-0.0370.01420.407-0.019-0.0190.0000.0000.0000.000
50A50PRO00.0440.01922.5900.0180.0180.0000.0000.0000.000
51A51GLU-1-0.846-0.92222.715-0.222-0.2220.0000.0000.0000.000
52A52LYS10.8650.94120.9080.4120.4120.0000.0000.0000.000
53A53TYR0-0.012-0.02318.113-0.031-0.0310.0000.0000.0000.000
54A54HIS10.8500.90918.4960.2270.2270.0000.0000.0000.000
55A55ARG10.9611.00317.3380.3220.3220.0000.0000.0000.000
56A56ARG10.8570.93310.6620.9340.9340.0000.0000.0000.000
57A57ILE00.0120.01314.530-0.064-0.0640.0000.0000.0000.000
58A58VAL00.0070.01914.5450.0470.0470.0000.0000.0000.000
59A59THR00.0000.00217.376-0.027-0.0270.0000.0000.0000.000
60A60HIS0-0.014-0.01816.8860.0210.0210.0000.0000.0000.000
61A61GLU-1-0.739-0.86821.259-0.061-0.0610.0000.0000.0000.000
62A62HIS0-0.027-0.01924.871-0.004-0.0040.0000.0000.0000.000
63A63PHE00.0460.00822.531-0.012-0.0120.0000.0000.0000.000
64A64TYR00.007-0.01325.9950.0000.0000.0000.0000.0000.000
65A65LEU0-0.002-0.00825.556-0.006-0.0060.0000.0000.0000.000
66A66LYS10.7610.89622.0760.0440.0440.0000.0000.0000.000
67A67GLU-1-0.788-0.89324.529-0.070-0.0700.0000.0000.0000.000
68A68GLU-1-0.974-0.96127.165-0.092-0.0920.0000.0000.0000.000
69A69PHE0-0.013-0.02525.419-0.011-0.0110.0000.0000.0000.000
70A70ASN0-0.025-0.00923.609-0.017-0.0170.0000.0000.0000.000
71A71LEU0-0.046-0.01520.667-0.027-0.0270.0000.0000.0000.000
72A72MET0-0.059-0.02013.043-0.019-0.0190.0000.0000.0000.000
73A73GLY00.017-0.00918.4220.0340.0340.0000.0000.0000.000
74A74ILE0-0.035-0.00719.359-0.028-0.0280.0000.0000.0000.000
75A75HIS10.8140.90214.171-0.103-0.1030.0000.0000.0000.000
76A76LEU00.0110.01518.478-0.017-0.0170.0000.0000.0000.000
77A77ASN0-0.089-0.07519.9800.0180.0180.0000.0000.0000.000
78A78ALA00.0270.00322.218-0.005-0.0050.0000.0000.0000.000
79A79ARG10.8530.93622.2490.0240.0240.0000.0000.0000.000
80A80ASN0-0.038-0.01324.690-0.012-0.0120.0000.0000.0000.000
81A81PRO00.0210.01424.4480.0060.0060.0000.0000.0000.000
82A82SER00.0180.00325.5620.0150.0150.0000.0000.0000.000
83A83GLU-1-0.901-0.94923.5960.0700.0700.0000.0000.0000.000
84A84PRO0-0.051-0.02825.8770.0000.0000.0000.0000.0000.000
85A85HIS00.004-0.01428.9040.0050.0050.0000.0000.0000.000
86A86ASP-1-0.917-0.94530.4670.0360.0360.0000.0000.0000.000
87A87TYR0-0.058-0.04120.677-0.022-0.0220.0000.0000.0000.000
88A88ALA00.0520.02025.0750.0140.0140.0000.0000.0000.000
89A89GLY0-0.023-0.02321.587-0.023-0.0230.0000.0000.0000.000
90A90HIS0-0.0080.01512.980-0.006-0.0060.0000.0000.0000.000
91A91VAL00.0840.06517.860-0.026-0.0260.0000.0000.0000.000
92A92SER0-0.013-0.00514.1400.0330.0330.0000.0000.0000.000
93A93CYS0-0.0070.00415.470-0.029-0.0290.0000.0000.0000.000
94A94SER00.0200.00714.9490.0590.0590.0000.0000.0000.000
95A95CYS0-0.0600.00215.258-0.039-0.0390.0000.0000.0000.000
96A96HIS0-0.044-0.04115.6190.0190.0190.0000.0000.0000.000
97A97SER00.0800.03617.157-0.019-0.0190.0000.0000.0000.000
98A98VAL00.0620.02715.5800.0360.0360.0000.0000.0000.000
99A99GLU-1-0.772-0.86117.2600.3740.3740.0000.0000.0000.000
100A100GLU-1-0.806-0.89518.7310.2780.2780.0000.0000.0000.000
101A101VAL00.016-0.00112.976-0.014-0.0140.0000.0000.0000.000
102A102LYS10.8600.91916.139-0.359-0.3590.0000.0000.0000.000
103A103ASN0-0.109-0.05918.0970.0010.0010.0000.0000.0000.000
104A104ARG10.8800.90318.246-0.328-0.3280.0000.0000.0000.000
105A105LYS10.8280.91312.713-0.975-0.9750.0000.0000.0000.000
106A106HIS0-0.035-0.02515.646-0.006-0.0060.0000.0000.0000.000
107A107PHE0-0.056-0.01817.696-0.030-0.0300.0000.0000.0000.000
108A108TYR00.0530.02915.904-0.033-0.0330.0000.0000.0000.000
109A109ASP-1-0.826-0.90013.9810.1940.1940.0000.0000.0000.000
110A110TYR0-0.019-0.0509.8930.0490.0490.0000.0000.0000.000
111A111VAL0-0.031-0.01211.244-0.119-0.1190.0000.0000.0000.000
112A112PHE0-0.020-0.01110.5350.1660.1660.0000.0000.0000.000
113A113MET00.0050.01910.4880.0170.0170.0000.0000.0000.000
114A114SER0-0.0100.01710.9430.0050.0050.0000.0000.0000.000
115A115PRO0-0.017-0.01513.260-0.003-0.0030.0000.0000.0000.000
116A116ILE00.012-0.0178.0560.0180.0180.0000.0000.0000.000
117A117TYR0-0.099-0.0767.026-0.048-0.0480.0000.0000.0000.000
118A127SER00.0340.02915.578-0.002-0.0020.0000.0000.0000.000
119A128THR0-0.049-0.05016.354-0.026-0.0260.0000.0000.0000.000
120A129TYR0-0.0550.00213.7790.0450.0450.0000.0000.0000.000
121A130THR00.0300.01016.338-0.058-0.0580.0000.0000.0000.000
122A131ALA00.0320.00013.3010.0620.0620.0000.0000.0000.000
123A132GLU-1-0.847-0.91314.2970.4850.4850.0000.0000.0000.000
124A133GLU-1-0.845-0.92816.4400.4570.4570.0000.0000.0000.000
125A134LEU0-0.019-0.01210.0850.0440.0440.0000.0000.0000.000
126A135ARG10.9370.95913.279-0.424-0.4240.0000.0000.0000.000
127A136GLU-1-0.902-0.93314.4640.6140.6140.0000.0000.0000.000
128A137ALA0-0.007-0.00814.372-0.003-0.0030.0000.0000.0000.000
129A138GLN0-0.004-0.0059.725-0.163-0.1630.0000.0000.0000.000
130A139LYS10.7910.87712.853-0.606-0.6060.0000.0000.0000.000
131A140ALA0-0.043-0.01415.461-0.039-0.0390.0000.0000.0000.000
132A141LYS10.9130.95313.473-1.075-1.0750.0000.0000.0000.000
133A142ILE00.0020.01313.8080.0110.0110.0000.0000.0000.000
134A143ILE0-0.0090.0077.954-0.084-0.0840.0000.0000.0000.000
135A144ASP-1-0.755-0.8798.6691.2291.2290.0000.0000.0000.000
136A145SER00.001-0.0175.9820.1840.1840.0000.0000.0000.000
137A146LYS10.8440.9397.039-0.714-0.7140.0000.0000.0000.000
138A147VAL0-0.032-0.0077.928-0.270-0.2700.0000.0000.0000.000
139A148MET0-0.050-0.0096.1130.5840.5840.0000.0000.0000.000
140A149ALA00.0300.0275.258-0.603-0.6030.0000.0000.0000.000
141A150LEU00.027-0.0057.103-0.262-0.2620.0000.0000.0000.000
142A151GLY00.018-0.0119.3670.0330.0330.0000.0000.0000.000
143A152GLY00.0370.01510.3900.0410.0410.0000.0000.0000.000
144A153ILE0-0.0290.0064.714-0.0510.033-0.001-0.002-0.0800.000
145A154ASN0-0.032-0.0477.269-0.002-0.0020.0000.0000.0000.000
146A155GLU-1-0.780-0.8896.911-1.019-1.0190.0000.0000.0000.000
147A156ASP-1-0.892-0.9178.854-0.506-0.5060.0000.0000.0000.000
148A157ASN0-0.009-0.0046.962-0.131-0.1310.0000.0000.0000.000
149A158LEU00.0090.0092.526-0.686-0.4851.987-0.318-1.870-0.002
150A159LEU0-0.002-0.0242.862-2.329-1.0900.455-0.738-0.956-0.008
151A160GLU-1-0.843-0.8834.9400.8910.967-0.001-0.003-0.0710.000
152A161ILE00.0080.0022.556-0.3210.2041.774-0.510-1.789-0.002
153A162LYS10.8530.9052.443-1.753-0.4034.793-1.731-4.413-0.002
154A163ASP-1-0.876-0.9313.8981.8020.6290.1171.402-0.3450.000
155A164PHE0-0.064-0.0276.864-0.288-0.2880.0000.0000.0000.000
156A165GLY0-0.021-0.0146.243-0.403-0.4030.0000.0000.0000.000
157A166PHE0-0.037-0.0214.119-0.985-0.5420.027-0.100-0.3720.000
158A167GLY00.0050.0073.168-0.2851.6840.256-0.878-1.347-0.007
159A168GLY0-0.038-0.0252.169-3.845-2.8312.750-1.743-2.020-0.004
160A169ALA00.0080.0092.4952.8691.3563.1271.196-2.811-0.003
161A170VAL0-0.033-0.0124.315-1.351-1.4110.0150.092-0.0470.001
162A171VAL00.0220.0086.3440.0210.0210.0000.0000.0000.000
163A172LEU0-0.006-0.0119.0890.0410.0410.0000.0000.0000.000
164A173GLY00.0360.01312.810-0.033-0.0330.0000.0000.0000.000
165A174ASP-1-0.796-0.90110.428-0.818-0.8180.0000.0000.0000.000
166A175LEU0-0.0150.00210.648-0.059-0.0590.0000.0000.0000.000
167A176TRP00.025-0.02413.1610.0230.0230.0000.0000.0000.000
168A177ASN0-0.027-0.01216.3740.0310.0310.0000.0000.0000.000
169A178LYS10.7810.90913.6550.6400.6400.0000.0000.0000.000
170A179PHE0-0.010-0.01318.273-0.006-0.0060.0000.0000.0000.000
171A180ASP-1-0.888-0.91921.126-0.235-0.2350.0000.0000.0000.000
172A181ALA00.006-0.01324.4730.0060.0060.0000.0000.0000.000
173A182CYS0-0.096-0.06526.9450.0140.0140.0000.0000.0000.000
174A183LEU0-0.0170.01227.6480.0150.0150.0000.0000.0000.000
175A184ASP-1-0.842-0.90123.885-0.298-0.2980.0000.0000.0000.000
176A185GLN0-0.073-0.05027.0720.0100.0100.0000.0000.0000.000
177A186ASN0-0.020-0.02024.302-0.023-0.0230.0000.0000.0000.000
178A187TYR00.0980.04120.3620.0080.0080.0000.0000.0000.000
179A188LEU00.0050.00519.894-0.049-0.0490.0000.0000.0000.000
180A189ALA00.0760.04718.738-0.060-0.0600.0000.0000.0000.000
181A190VAL0-0.0010.00415.398-0.065-0.0650.0000.0000.0000.000
182A191ILE0-0.030-0.01614.766-0.108-0.1080.0000.0000.0000.000
183A192GLU-1-0.939-0.98914.850-0.616-0.6160.0000.0000.0000.000
184A193HIS0-0.062-0.04010.906-0.051-0.0510.0000.0000.0000.000
185A194PHE00.0170.0058.963-0.196-0.1960.0000.0000.0000.000
186A195LYS10.8360.9049.7940.4830.4830.0000.0000.0000.000
187A196LYS10.7710.88010.6260.5980.5980.0000.0000.0000.000
188A197LEU00.0180.0006.289-0.194-0.1940.0000.0000.0000.000
189A198LYS10.8460.9095.7762.5302.5300.0000.0000.0000.000
190A199LYS10.9440.9856.5830.4020.4020.0000.0000.0000.000
191A200LEU0-0.017-0.0135.7160.1540.1540.0000.0000.0000.000
192A201ALA00.0180.0152.831-0.6340.5740.359-0.420-1.1470.001
193A202ASP-1-0.848-0.9102.261-10.007-8.4832.317-1.767-2.073-0.023
194A203LEU0-0.042-0.0124.4831.2501.360-0.001-0.007-0.1020.000
195A204GLU-1-0.937-0.9626.1892.7852.7850.0000.0000.0000.000
196A205HIS0-0.0150.0037.0740.4120.4120.0000.0000.0000.000
197A206HIS10.9020.9418.126-1.801-1.8010.0000.0000.0000.000
198A207HIS0-0.0070.01510.266-0.032-0.0320.0000.0000.0000.000