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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZYQ4N

Calculation Name: 5E1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E1L

Chain ID: A

ChEMBL ID:

UniProt ID: P75862

Base Structure: X-ray

Registration Date: 2023-06-20

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941709.341744
FMO2-HF: Nuclear repulsion 1868500.950956
FMO2-HF: Total energy -73208.390789
FMO2-MP2: Total energy -73413.395078


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:-8:SER)


Summations of interaction energy for fragment #1(A:-8:SER)
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.
-50.955-49.32526.992-13.829-14.791-0.039
Interaction energy analysis for fragmet #1(A:-8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.015
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].
3A-6LEU0-0.0050.0013.824-0.1861.774-0.027-1.029-0.9030.001
4A-5VAL0-0.0350.0016.5470.0190.0190.0000.0000.0000.000
5A-4PRO00.0590.0269.1330.2700.2700.0000.0000.0000.000
6A-3ARG10.9280.9286.8992.7462.7460.0000.0000.0000.000
7A-2GLY00.0590.01911.1420.3090.3090.0000.0000.0000.000
8A-1SER0-0.078-0.04012.9960.2070.2070.0000.0000.0000.000
9A0HIS00.0450.02614.8580.1400.1400.0000.0000.0000.000
10A1MET0-0.034-0.03016.5310.1000.1000.0000.0000.0000.000
11A2ARG10.8740.92316.6060.9790.9790.0000.0000.0000.000
12A3ILE0-0.0260.01011.5540.0310.0310.0000.0000.0000.000
13A4LYS10.8700.90815.8660.7160.7160.0000.0000.0000.000
14A5PRO00.0260.03617.6280.0010.0010.0000.0000.0000.000
15A6ASP-1-0.834-0.91418.839-0.566-0.5660.0000.0000.0000.000
16A7ASP-1-0.866-0.93420.352-0.406-0.4060.0000.0000.0000.000
17A8ASN0-0.077-0.03720.9410.0630.0630.0000.0000.0000.000
18A9TRP0-0.054-0.00214.464-0.099-0.0990.0000.0000.0000.000
19A10ARG10.8530.92014.8330.5530.5530.0000.0000.0000.000
20A11TRP00.011-0.01010.824-0.176-0.1760.0000.0000.0000.000
21A12TYR0-0.074-0.06910.7380.0010.0010.0000.0000.0000.000
22A13TYR00.032-0.02111.189-0.096-0.0960.0000.0000.0000.000
23A14ASP-1-0.825-0.8998.905-0.019-0.0190.0000.0000.0000.000
24A15GLU-1-0.777-0.91610.4260.7280.7280.0000.0000.0000.000
25A16GLU-1-0.996-0.96711.0980.3860.3860.0000.0000.0000.000
26A17HIS0-0.040-0.0445.490-0.122-0.1220.0000.0000.0000.000
27A18ASP-1-0.815-0.8637.3282.6282.6280.0000.0000.0000.000
28A19ARG10.7970.8741.814-21.536-25.80810.654-3.307-3.0740.038
29A20MET00.0120.0437.621-0.450-0.4500.0000.0000.0000.000
30A21MET0-0.056-0.0126.702-0.235-0.2350.0000.0000.0000.000
31A22LEU0-0.0080.0078.6710.1870.1870.0000.0000.0000.000
32A23ASP-1-0.806-0.88710.710-1.043-1.0430.0000.0000.0000.000
33A24LEU0-0.001-0.00910.9060.0090.0090.0000.0000.0000.000
34A25ALA00.0120.00914.8750.0540.0540.0000.0000.0000.000
35A26ASN0-0.027-0.01915.6780.0250.0250.0000.0000.0000.000
36A27GLY00.0250.01016.5810.0170.0170.0000.0000.0000.000
37A28MET0-0.106-0.02311.8890.0210.0210.0000.0000.0000.000
38A29LEU00.0550.0349.5340.1870.1870.0000.0000.0000.000
39A30PHE00.006-0.0165.193-0.652-0.6520.0000.0000.0000.000
40A31ARG10.8450.9222.5684.3495.9640.737-0.733-1.618-0.003
41A32SER00.005-0.0022.384-6.202-4.8091.919-1.613-1.699-0.022
42A33ARG10.8130.8642.259-8.758-4.8942.372-2.457-3.7790.009
43A34PHE0-0.030-0.0144.4870.7980.896-0.001-0.008-0.0900.000
44A35ALA00.0480.0357.588-0.232-0.2320.0000.0000.0000.000
45A36ARG10.8810.9249.456-1.056-1.0560.0000.0000.0000.000
46A37LYS10.8980.93310.962-2.174-2.1740.0000.0000.0000.000
47A38MET0-0.073-0.0298.981-0.167-0.1670.0000.0000.0000.000
48A39LEU00.0240.03610.406-0.097-0.0970.0000.0000.0000.000
49A40THR0-0.034-0.04414.3200.0160.0160.0000.0000.0000.000
50A41PRO0-0.004-0.02117.0520.0170.0170.0000.0000.0000.000
51A42ASP-1-0.803-0.88818.3510.1340.1340.0000.0000.0000.000
52A43ALA0-0.017-0.01313.685-0.052-0.0520.0000.0000.0000.000
53A44PHE0-0.064-0.03614.148-0.005-0.0050.0000.0000.0000.000
54A45SER0-0.0350.00017.467-0.004-0.0040.0000.0000.0000.000
55A46PRO0-0.025-0.02017.046-0.028-0.0280.0000.0000.0000.000
56A47ALA00.0040.01517.5610.0190.0190.0000.0000.0000.000
57A48GLY00.0110.00518.017-0.060-0.0600.0000.0000.0000.000
58A49PHE0-0.021-0.01414.5160.0050.0050.0000.0000.0000.000
59A50CYS0-0.033-0.01018.5240.0200.0200.0000.0000.0000.000
60A51VAL00.0500.00821.029-0.044-0.0440.0000.0000.0000.000
61A52ASP-1-0.863-0.93522.221-0.259-0.2590.0000.0000.0000.000
62A53ASP-1-0.723-0.84217.047-0.390-0.3900.0000.0000.0000.000
63A54ALA00.0080.00518.136-0.088-0.0880.0000.0000.0000.000
64A55ALA0-0.023-0.01320.239-0.031-0.0310.0000.0000.0000.000
65A56LEU0-0.014-0.01317.918-0.007-0.0070.0000.0000.0000.000
66A57TYR0-0.047-0.04313.488-0.101-0.1010.0000.0000.0000.000
67A58PHE00.0240.00017.110-0.059-0.0590.0000.0000.0000.000
68A59SER0-0.0220.00919.7660.0020.0020.0000.0000.0000.000
69A60PHE00.018-0.00315.1110.0160.0160.0000.0000.0000.000
70A61GLU-1-0.835-0.89415.827-0.926-0.9260.0000.0000.0000.000
71A62GLU-1-0.847-0.89016.795-0.502-0.5020.0000.0000.0000.000
72A63LYS10.8040.89718.4950.3110.3110.0000.0000.0000.000
73A64CYS0-0.033-0.01614.337-0.001-0.0010.0000.0000.0000.000
74A65ARG10.7330.83416.2560.5510.5510.0000.0000.0000.000
75A66ASP-1-0.868-0.93018.416-0.530-0.5300.0000.0000.0000.000
76A67PHE0-0.043-0.01313.7280.0120.0120.0000.0000.0000.000
77A68ASN00.0160.00816.420-0.081-0.0810.0000.0000.0000.000
78A69LEU0-0.032-0.02010.125-0.057-0.0570.0000.0000.0000.000
79A70SER00.007-0.01810.547-0.022-0.0220.0000.0000.0000.000
80A71LYS10.9630.95512.0850.9780.9780.0000.0000.0000.000
81A72GLU-1-0.828-0.8887.752-3.236-3.2360.0000.0000.0000.000
82A73GLN00.0640.0447.150-0.278-0.2780.0000.0000.0000.000
83A74LYS10.8400.9228.4330.7980.7980.0000.0000.0000.000
84A75ALA00.0340.02410.0590.0930.0930.0000.0000.0000.000
85A76GLU-1-0.792-0.8961.853-24.449-27.61011.340-4.679-3.500-0.062
86A77LEU0-0.032-0.0076.6220.2440.2440.0000.0000.0000.000
87A78VAL00.0320.0198.4510.3430.3430.0000.0000.0000.000
88A79LEU0-0.003-0.0048.5880.2750.2750.0000.0000.0000.000
89A80ASN00.012-0.0114.1611.3351.412-0.001-0.002-0.0740.000
90A81ALA00.0200.0088.5140.4320.4320.0000.0000.0000.000
91A82LEU0-0.0210.00012.0980.1730.1730.0000.0000.0000.000
92A83VAL00.003-0.0018.7420.1540.1540.0000.0000.0000.000
93A84ALA0-0.052-0.03111.4470.2190.2190.0000.0000.0000.000
94A85ILE0-0.019-0.01312.8670.0890.0890.0000.0000.0000.000
95A86ARG10.8090.91314.6940.2680.2680.0000.0000.0000.000
96A87TYR00.0600.02012.8870.0060.0060.0000.0000.0000.000
97A88LEU0-0.0390.01111.2640.1720.1720.0000.0000.0000.000
98A89LYS10.8590.92814.255-0.784-0.7840.0000.0000.0000.000
99A90PRO00.0420.02116.8590.0350.0350.0000.0000.0000.000
100A91GLN0-0.039-0.02415.1950.1170.1170.0000.0000.0000.000
101A92MET00.0050.00618.470-0.068-0.0680.0000.0000.0000.000
102A93PRO00.010-0.00819.7700.0490.0490.0000.0000.0000.000
103A94LYS10.8760.94317.363-0.569-0.5690.0000.0000.0000.000
104A95SER00.0440.00521.788-0.027-0.0270.0000.0000.0000.000
105A96TRP00.0220.01124.281-0.014-0.0140.0000.0000.0000.000
106A97HIS00.0200.00820.304-0.038-0.0380.0000.0000.0000.000
107A98PHE00.0000.01218.1860.0080.0080.0000.0000.0000.000
108A99VAL00.0490.02824.1460.0000.0000.0000.0000.0000.000
109A100SER0-0.072-0.06026.575-0.002-0.0020.0000.0000.0000.000
110A101HIS0-0.002-0.01525.980-0.015-0.0150.0000.0000.0000.000
111A102GLY0-0.0260.01331.137-0.010-0.0100.0000.0000.0000.000
112A103GLU-1-0.854-0.92031.3520.0110.0110.0000.0000.0000.000
113A104MET0-0.043-0.02729.5860.0120.0120.0000.0000.0000.000
114A105TRP00.0380.02822.740-0.007-0.0070.0000.0000.0000.000
115A106VAL0-0.011-0.01327.1990.0140.0140.0000.0000.0000.000
116A107PRO0-0.0100.01822.576-0.016-0.0160.0000.0000.0000.000
117A108MET00.0130.00723.9240.0150.0150.0000.0000.0000.000
118A109PRO00.008-0.00420.107-0.018-0.0180.0000.0000.0000.000
119A110GLY00.0310.00817.716-0.021-0.0210.0000.0000.0000.000
120A111ASP-1-0.849-0.91318.799-0.232-0.2320.0000.0000.0000.000
121A112ALA00.0130.01418.2110.0050.0050.0000.0000.0000.000
122A113ALA00.0080.00918.3770.0410.0410.0000.0000.0000.000
123A114CYS0-0.071-0.02718.850-0.026-0.0260.0000.0000.0000.000
124A115VAL00.0110.02318.9950.0220.0220.0000.0000.0000.000
125A116TRP00.0360.00721.240-0.013-0.0130.0000.0000.0000.000
126A117LEU0-0.021-0.00619.0190.0240.0240.0000.0000.0000.000
127A118SER0-0.058-0.04523.032-0.018-0.0180.0000.0000.0000.000
128A119ASP-1-0.907-0.94224.7170.2530.2530.0000.0000.0000.000
129A120THR00.0340.00222.267-0.023-0.0230.0000.0000.0000.000
130A121HIS0-0.038-0.00625.510-0.033-0.0330.0000.0000.0000.000
131A122GLU-1-0.924-0.96217.7790.1870.1870.0000.0000.0000.000
132A123GLN0-0.008-0.00720.5260.0380.0380.0000.0000.0000.000
133A124VAL0-0.029-0.01115.490-0.008-0.0080.0000.0000.0000.000
134A125ASN00.025-0.02615.944-0.009-0.0090.0000.0000.0000.000
135A126LEU0-0.044-0.03214.3720.0160.0160.0000.0000.0000.000
136A127LEU00.0320.02212.335-0.066-0.0660.0000.0000.0000.000
137A128VAL00.0250.01414.9200.0590.0590.0000.0000.0000.000
138A129VAL0-0.043-0.02813.457-0.076-0.0760.0000.0000.0000.000
139A130GLU-1-0.809-0.89916.8930.1070.1070.0000.0000.0000.000
140A131SER0-0.044-0.06420.1060.0270.0270.0000.0000.0000.000
141A132GLY00.0550.03923.138-0.006-0.0060.0000.0000.0000.000
142A133GLU-1-0.917-0.95826.3540.0560.0560.0000.0000.0000.000
143A134ASN0-0.003-0.01128.176-0.004-0.0040.0000.0000.0000.000
144A135ALA0-0.025-0.01323.2490.0190.0190.0000.0000.0000.000
145A136ALA00.0540.03920.956-0.021-0.0210.0000.0000.0000.000
146A137LEU0-0.044-0.01415.1950.0680.0680.0000.0000.0000.000
147A138CYS0-0.0110.00215.605-0.099-0.0990.0000.0000.0000.000
148A139LEU0-0.0080.0039.4370.1430.1430.0000.0000.0000.000
149A140LEU0-0.0280.0019.367-0.103-0.1030.0000.0000.0000.000
150A141ALA00.0230.0119.696-0.289-0.2890.0000.0000.0000.000
151A142GLN00.0550.03110.763-0.047-0.0470.0000.0000.0000.000
152A143PRO0-0.008-0.0138.051-0.078-0.0780.0000.0000.0000.000
153A144CYS0-0.015-0.0197.6350.1490.1490.0000.0000.0000.000
154A145VAL00.0280.03110.191-0.158-0.1580.0000.0000.0000.000
155A146VAL00.0010.00012.8690.2290.2290.0000.0000.0000.000
156A147ILE00.0570.02715.252-0.109-0.1090.0000.0000.0000.000
157A148ALA0-0.003-0.00717.1380.0900.0900.0000.0000.0000.000
158A149GLY00.0100.01118.5300.0250.0250.0000.0000.0000.000
159A150ARG10.9130.96012.774-1.124-1.1240.0000.0000.0000.000
160A151ALA00.0310.01711.285-0.095-0.0950.0000.0000.0000.000
161A152MET0-0.051-0.0219.0490.2810.2810.0000.0000.0000.000
162A153GLN0-0.006-0.0165.4571.1671.1670.0000.0000.0000.000
163A154LEU0-0.0110.0055.1480.1680.1680.0000.0000.0000.000
164A155GLY00.0060.0014.787-0.469-0.413-0.001-0.001-0.0540.000
165A156ASP-1-0.804-0.8636.3614.1684.1680.0000.0000.0000.000
166A157ALA00.0100.0008.346-0.414-0.4140.0000.0000.0000.000
167A158ILE0-0.051-0.03111.7120.1910.1910.0000.0000.0000.000
168A159LYS10.8480.93215.116-0.310-0.3100.0000.0000.0000.000
169A160ILE0-0.052-0.02817.6150.0540.0540.0000.0000.0000.000
170A161MET00.0170.01021.050-0.033-0.0330.0000.0000.0000.000
171A162ASN00.0440.00024.742-0.002-0.0020.0000.0000.0000.000
172A163ASP-1-0.785-0.86226.2620.1260.1260.0000.0000.0000.000
173A164ARG10.7620.87323.688-0.173-0.1730.0000.0000.0000.000
174A165LEU0-0.0300.00220.221-0.008-0.0080.0000.0000.0000.000
175A166LYS10.8090.89423.546-0.006-0.0060.0000.0000.0000.000
176A167PRO00.0200.01423.115-0.008-0.0080.0000.0000.0000.000
177A168GLN0-0.024-0.01818.168-0.004-0.0040.0000.0000.0000.000