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: 76MKK

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 OptAll
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 -2384200.230221
FMO2-HF: Nuclear repulsion 2303351.271258
FMO2-HF: Total energy -80848.958963
FMO2-MP2: Total energy -81084.610559


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.
-23.672-13.82622.297-9.039-23.106-0.064
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 : -0.022 / q_NPA : 0.023
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].
3A3LEU0-0.0090.0042.716-2.0731.3600.564-2.010-1.988-0.005
4A4ILE0-0.032-0.0095.0590.1600.272-0.001-0.011-0.0990.000
5A5VAL00.0250.0148.2390.0170.0170.0000.0000.0000.000
6A6VAL0-0.016-0.00610.8780.0950.0950.0000.0000.0000.000
7A7THR00.0460.03513.734-0.038-0.0380.0000.0000.0000.000
8A8THR00.0440.01416.9890.0220.0220.0000.0000.0000.000
9A9PRO0-0.040-0.03219.1840.0150.0150.0000.0000.0000.000
10A10THR00.0680.04321.6450.0230.0230.0000.0000.0000.000
11A11PHE0-0.0060.00123.316-0.024-0.0240.0000.0000.0000.000
12A12PHE0-0.0050.00320.5460.0140.0140.0000.0000.0000.000
13A13VAL00.012-0.00625.880-0.007-0.0070.0000.0000.0000.000
14A14GLU-1-0.896-0.95824.954-0.286-0.2860.0000.0000.0000.000
15A15GLU-1-0.777-0.85720.624-0.314-0.3140.0000.0000.0000.000
16A16ASP-1-0.767-0.89321.147-0.308-0.3080.0000.0000.0000.000
17A17LYS10.8620.92522.4730.2480.2480.0000.0000.0000.000
18A18ILE00.0150.02117.617-0.034-0.0340.0000.0000.0000.000
19A19ILE00.003-0.00517.474-0.062-0.0620.0000.0000.0000.000
20A20THR0-0.037-0.03317.938-0.048-0.0480.0000.0000.0000.000
21A21ALA00.0180.01319.315-0.030-0.0300.0000.0000.0000.000
22A22LEU00.0160.00513.141-0.064-0.0640.0000.0000.0000.000
23A23PHE0-0.019-0.02314.132-0.118-0.1180.0000.0000.0000.000
24A24GLU-1-0.906-0.94115.966-0.472-0.4720.0000.0000.0000.000
25A25GLU-1-0.826-0.87914.023-0.808-0.8080.0000.0000.0000.000
26A26GLY0-0.021-0.00912.246-0.178-0.1780.0000.0000.0000.000
27A27LEU0-0.060-0.0389.984-0.336-0.3360.0000.0000.0000.000
28A28ASP-1-0.798-0.8866.768-2.201-2.2010.0000.0000.0000.000
29A29ILE0-0.016-0.0119.5800.2570.2570.0000.0000.0000.000
30A30LEU00.0200.02711.172-0.061-0.0610.0000.0000.0000.000
31A31HIS00.007-0.00612.8550.0840.0840.0000.0000.0000.000
32A32LEU00.0180.01515.407-0.006-0.0060.0000.0000.0000.000
33A33ARG10.9440.96317.3330.1550.1550.0000.0000.0000.000
34A34LYS10.7370.84619.9140.2280.2280.0000.0000.0000.000
35A35PRO00.007-0.01022.2680.0130.0130.0000.0000.0000.000
36A36GLU-1-0.900-0.94625.355-0.053-0.0530.0000.0000.0000.000
37A37THR0-0.0330.00127.280-0.005-0.0050.0000.0000.0000.000
38A38PRO0-0.008-0.01329.2190.0010.0010.0000.0000.0000.000
39A39ALA00.0650.03429.404-0.011-0.0110.0000.0000.0000.000
40A40MET00.0550.03129.746-0.013-0.0130.0000.0000.0000.000
41A41TYR0-0.041-0.02428.441-0.007-0.0070.0000.0000.0000.000
42A42SER00.0360.01325.759-0.019-0.0190.0000.0000.0000.000
43A43GLU-1-0.825-0.88126.667-0.121-0.1210.0000.0000.0000.000
44A44ARG10.9200.97429.1470.1440.1440.0000.0000.0000.000
45A45LEU00.0080.00721.804-0.008-0.0080.0000.0000.0000.000
46A46LEU00.001-0.01522.442-0.023-0.0230.0000.0000.0000.000
47A47THR0-0.048-0.03925.436-0.002-0.0020.0000.0000.0000.000
48A48LEU0-0.063-0.02127.201-0.001-0.0010.0000.0000.0000.000
49A49ILE0-0.0250.01520.550-0.016-0.0160.0000.0000.0000.000
50A50PRO00.0170.00122.4980.0150.0150.0000.0000.0000.000
51A51GLU-1-0.871-0.93922.750-0.218-0.2180.0000.0000.0000.000
52A52LYS10.7630.88121.3370.4050.4050.0000.0000.0000.000
53A53TYR00.003-0.01318.222-0.019-0.0190.0000.0000.0000.000
54A54HIS10.8710.94818.7240.2250.2250.0000.0000.0000.000
55A55ARG10.9920.99918.1700.3050.3050.0000.0000.0000.000
56A56ARG10.8040.89110.5640.9400.9400.0000.0000.0000.000
57A57ILE00.0030.00914.889-0.067-0.0670.0000.0000.0000.000
58A58VAL00.0090.02214.9420.0440.0440.0000.0000.0000.000
59A59THR0-0.024-0.02417.604-0.031-0.0310.0000.0000.0000.000
60A60HIS0-0.001-0.00416.4810.0190.0190.0000.0000.0000.000
61A61GLU-1-0.724-0.83821.121-0.072-0.0720.0000.0000.0000.000
62A62HIS0-0.025-0.02224.784-0.004-0.0040.0000.0000.0000.000
63A63PHE00.0230.00122.858-0.010-0.0100.0000.0000.0000.000
64A64TYR00.017-0.01226.3120.0000.0000.0000.0000.0000.000
65A65LEU0-0.012-0.00925.903-0.006-0.0060.0000.0000.0000.000
66A66LYS10.7530.87922.4870.0490.0490.0000.0000.0000.000
67A67GLU-1-0.785-0.88724.790-0.072-0.0720.0000.0000.0000.000
68A68GLU-1-0.970-0.97727.638-0.095-0.0950.0000.0000.0000.000
69A69PHE00.007-0.00525.723-0.009-0.0090.0000.0000.0000.000
70A70ASN0-0.032-0.01024.133-0.020-0.0200.0000.0000.0000.000
71A71LEU0-0.055-0.02620.799-0.031-0.0310.0000.0000.0000.000
72A72MET0-0.059-0.01913.445-0.012-0.0120.0000.0000.0000.000
73A73GLY00.0220.00518.6100.0340.0340.0000.0000.0000.000
74A74ILE0-0.0230.00419.408-0.026-0.0260.0000.0000.0000.000
75A75HIS10.8070.89514.626-0.090-0.0900.0000.0000.0000.000
76A76LEU00.0360.03118.932-0.016-0.0160.0000.0000.0000.000
77A77ASN0-0.101-0.07720.3500.0170.0170.0000.0000.0000.000
78A78ALA00.021-0.00322.617-0.005-0.0050.0000.0000.0000.000
79A79ARG10.8320.92621.8130.0380.0380.0000.0000.0000.000
80A80ASN0-0.026-0.01125.028-0.013-0.0130.0000.0000.0000.000
81A81PRO00.0270.01724.8010.0060.0060.0000.0000.0000.000
82A82SER00.0190.00225.6290.0170.0170.0000.0000.0000.000
83A83GLU-1-0.908-0.95324.1040.0550.0550.0000.0000.0000.000
84A84PRO0-0.046-0.02526.4570.0020.0020.0000.0000.0000.000
85A85HIS0-0.014-0.02429.3940.0020.0020.0000.0000.0000.000
86A86ASP-1-0.895-0.93730.9890.0260.0260.0000.0000.0000.000
87A87TYR0-0.063-0.04821.170-0.019-0.0190.0000.0000.0000.000
88A88ALA00.0510.02225.4280.0130.0130.0000.0000.0000.000
89A89GLY0-0.015-0.01221.968-0.023-0.0230.0000.0000.0000.000
90A90HIS00.0080.02113.3920.0000.0000.0000.0000.0000.000
91A91VAL00.0700.04318.129-0.021-0.0210.0000.0000.0000.000
92A92SER0-0.020-0.01014.6770.0340.0340.0000.0000.0000.000
93A93CYS0-0.0040.01315.962-0.021-0.0210.0000.0000.0000.000
94A94SER00.0150.00715.3220.0440.0440.0000.0000.0000.000
95A95CYS0-0.0460.00915.379-0.028-0.0280.0000.0000.0000.000
96A96HIS0-0.032-0.04015.5550.0220.0220.0000.0000.0000.000
97A97SER00.0700.03617.655-0.019-0.0190.0000.0000.0000.000
98A98VAL00.0600.02315.5640.0360.0360.0000.0000.0000.000
99A99GLU-1-0.759-0.85317.2740.3620.3620.0000.0000.0000.000
100A100GLU-1-0.787-0.87418.8080.2480.2480.0000.0000.0000.000
101A101VAL00.0200.00113.013-0.014-0.0140.0000.0000.0000.000
102A102LYS10.8180.89616.197-0.349-0.3490.0000.0000.0000.000
103A103ASN0-0.066-0.04618.1130.0000.0000.0000.0000.0000.000
104A104ARG10.8280.87618.658-0.304-0.3040.0000.0000.0000.000
105A105LYS10.8000.88312.441-0.936-0.9360.0000.0000.0000.000
106A106HIS00.015-0.01115.393-0.017-0.0170.0000.0000.0000.000
107A107PHE0-0.064-0.01017.706-0.027-0.0270.0000.0000.0000.000
108A108TYR00.0620.03616.233-0.031-0.0310.0000.0000.0000.000
109A109ASP-1-0.823-0.89614.3870.1490.1490.0000.0000.0000.000
110A110TYR0-0.026-0.03210.2790.0500.0500.0000.0000.0000.000
111A111VAL0-0.002-0.00211.614-0.103-0.1030.0000.0000.0000.000
112A112PHE0-0.025-0.01810.7890.1500.1500.0000.0000.0000.000
113A113MET00.0070.02010.600-0.004-0.0040.0000.0000.0000.000
114A114SER0-0.0170.00610.8090.0010.0010.0000.0000.0000.000
115A115PRO0-0.013-0.00113.0510.0030.0030.0000.0000.0000.000
116A116ILE0-0.002-0.0208.0980.0160.0160.0000.0000.0000.000
117A117TYR0-0.085-0.0876.749-0.038-0.0380.0000.0000.0000.000
118A127SER00.0170.02115.122-0.012-0.0120.0000.0000.0000.000
119A128THR0-0.064-0.05015.775-0.029-0.0290.0000.0000.0000.000
120A129TYR0-0.054-0.01413.7280.0570.0570.0000.0000.0000.000
121A130THR0-0.027-0.01716.151-0.048-0.0480.0000.0000.0000.000
122A131ALA00.031-0.00413.6770.0640.0640.0000.0000.0000.000
123A132GLU-1-0.802-0.88714.6670.5120.5120.0000.0000.0000.000
124A133GLU-1-0.813-0.90316.3820.4540.4540.0000.0000.0000.000
125A134LEU00.0140.01410.0380.0450.0450.0000.0000.0000.000
126A135ARG10.9130.93813.256-0.416-0.4160.0000.0000.0000.000
127A136GLU-1-0.866-0.90314.6060.5910.5910.0000.0000.0000.000
128A137ALA00.006-0.00314.0280.0060.0060.0000.0000.0000.000
129A138GLN0-0.0090.0019.479-0.202-0.2020.0000.0000.0000.000
130A139LYS10.7630.84812.707-0.641-0.6410.0000.0000.0000.000
131A140ALA0-0.015-0.01515.722-0.024-0.0240.0000.0000.0000.000
132A141LYS10.8490.93712.941-1.131-1.1310.0000.0000.0000.000
133A142ILE00.0140.01914.153-0.020-0.0200.0000.0000.0000.000
134A143ILE0-0.034-0.0158.218-0.094-0.0940.0000.0000.0000.000
135A144ASP-1-0.781-0.8888.4571.0891.0890.0000.0000.0000.000
136A145SER00.015-0.0106.2120.2070.2070.0000.0000.0000.000
137A146LYS10.8040.9117.292-0.669-0.6690.0000.0000.0000.000
138A147VAL0-0.025-0.0158.229-0.232-0.2320.0000.0000.0000.000
139A148MET0-0.0310.0066.2080.6230.6230.0000.0000.0000.000
140A149ALA00.0360.0325.105-0.606-0.6060.0000.0000.0000.000
141A150LEU00.020-0.0097.074-0.280-0.2800.0000.0000.0000.000
142A151GLY00.0270.0009.3630.0420.0420.0000.0000.0000.000
143A152GLY00.0390.01310.1670.0270.0270.0000.0000.0000.000
144A153ILE0-0.055-0.0034.9000.0160.0160.0000.0000.0000.000
145A154ASN0-0.041-0.0587.5040.0230.0230.0000.0000.0000.000
146A155GLU-1-0.788-0.8847.061-1.039-1.0390.0000.0000.0000.000
147A156ASP-1-0.883-0.9098.228-0.616-0.6160.0000.0000.0000.000
148A157ASN00.003-0.0026.837-0.147-0.1470.0000.0000.0000.000
149A158LEU0-0.020-0.0092.414-0.578-0.2211.838-0.358-1.837-0.002
150A159LEU00.017-0.0012.610-2.951-2.3632.123-1.077-1.635-0.016
151A160GLU-1-0.811-0.8734.8301.2211.320-0.001-0.004-0.0940.000
152A161ILE0-0.024-0.0062.544-0.451-0.0592.532-0.725-2.1990.000
153A162LYS10.8760.9082.624-5.645-3.1684.266-1.848-4.8950.000
154A163ASP-1-0.885-0.9364.0591.1200.5990.0980.716-0.2910.000
155A164PHE0-0.046-0.0247.191-0.279-0.2790.0000.0000.0000.000
156A165GLY0-0.028-0.0145.990-0.378-0.3780.0000.0000.0000.000
157A166PHE0-0.047-0.0304.251-1.113-0.7620.012-0.078-0.2860.000
158A167GLY00.0160.0123.322-0.1091.2920.078-0.568-0.911-0.004
159A168GLY00.003-0.0072.183-3.777-3.3024.877-2.764-2.587-0.009
160A169ALA00.0000.0122.4242.5050.3342.1592.306-2.295-0.001
161A170VAL0-0.021-0.0044.231-1.091-1.0570.006-0.005-0.0360.000
162A171VAL00.0100.0026.2780.0170.0170.0000.0000.0000.000
163A172LEU00.019-0.0049.0280.0620.0620.0000.0000.0000.000
164A173GLY00.0270.01612.764-0.028-0.0280.0000.0000.0000.000
165A174ASP-1-0.761-0.87510.513-0.850-0.8500.0000.0000.0000.000
166A175LEU0-0.042-0.00510.748-0.081-0.0810.0000.0000.0000.000
167A176TRP00.020-0.02613.1490.0270.0270.0000.0000.0000.000
168A177ASN0-0.033-0.00416.3200.0320.0320.0000.0000.0000.000
169A178LYS10.7870.87013.8730.6430.6430.0000.0000.0000.000
170A179PHE00.007-0.00118.232-0.016-0.0160.0000.0000.0000.000
171A180ASP-1-0.896-0.92421.269-0.246-0.2460.0000.0000.0000.000
172A181ALA0-0.010-0.01224.4790.0120.0120.0000.0000.0000.000
173A182CYS0-0.083-0.05826.5140.0150.0150.0000.0000.0000.000
174A183LEU0-0.0300.00627.8790.0160.0160.0000.0000.0000.000
175A184ASP-1-0.842-0.91423.782-0.308-0.3080.0000.0000.0000.000
176A185GLN0-0.070-0.03926.9980.0150.0150.0000.0000.0000.000
177A186ASN0-0.015-0.01824.405-0.022-0.0220.0000.0000.0000.000
178A187TYR00.0780.03220.1770.0070.0070.0000.0000.0000.000
179A188LEU0-0.0100.00119.854-0.048-0.0480.0000.0000.0000.000
180A189ALA00.0920.05118.605-0.062-0.0620.0000.0000.0000.000
181A190VAL00.0000.00315.356-0.069-0.0690.0000.0000.0000.000
182A191ILE0-0.032-0.01114.438-0.115-0.1150.0000.0000.0000.000
183A192GLU-1-0.922-0.97214.622-0.626-0.6260.0000.0000.0000.000
184A193HIS0-0.031-0.02610.866-0.030-0.0300.0000.0000.0000.000
185A194PHE00.0150.0038.866-0.226-0.2260.0000.0000.0000.000
186A195LYS10.8020.8829.9090.4850.4850.0000.0000.0000.000
187A196LYS10.7620.87610.4230.6240.6240.0000.0000.0000.000
188A197LEU00.0180.0026.353-0.214-0.2140.0000.0000.0000.000
189A198LYS10.8540.9085.8532.2722.2720.0000.0000.0000.000
190A199LYS10.9500.9826.3110.2630.2630.0000.0000.0000.000
191A200LEU0-0.026-0.0195.6990.2100.2100.0000.0000.0000.000
192A201ALA0-0.0080.0122.732-0.9860.3410.479-0.509-1.2980.001
193A202ASP-1-0.828-0.9192.195-8.815-7.6143.269-2.096-2.375-0.028
194A203LEU0-0.056-0.0164.5131.2521.366-0.001-0.004-0.1080.000
195A204GLU-1-0.841-0.9125.2754.6314.808-0.001-0.004-0.1720.000
196A205HIS0-0.058-0.0226.7670.3390.3390.0000.0000.0000.000
197A206HIS10.8790.9367.895-2.102-2.1020.0000.0000.0000.000
198A207HIS00.0000.02010.633-0.060-0.0600.0000.0000.0000.000