Manual

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: 221VR

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1936767.544658
FMO2-HF: Nuclear repulsion 1863560.744592
FMO2-HF: Total energy -73206.800065
FMO2-MP2: Total energy -73411.755594


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.
-36.442-37.63234.485-16.156-17.142-0.029
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 : -0.046 / q_NPA : -0.039
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-6LEU0-0.029-0.0023.4570.5863.563-0.039-1.557-1.382-0.006
4A-5VAL0-0.0020.0125.580-0.293-0.2930.0000.0000.0000.000
5A-4PRO00.0480.0297.8420.3140.3140.0000.0000.0000.000
6A-3ARG10.9170.9416.9903.7603.7600.0000.0000.0000.000
7A-2GLY00.0760.00411.4060.3030.3030.0000.0000.0000.000
8A-1SER0-0.080-0.04313.0870.1300.1300.0000.0000.0000.000
9A0HIS00.0230.01814.4120.1250.1250.0000.0000.0000.000
10A1MET0-0.058-0.03216.3800.1030.1030.0000.0000.0000.000
11A2ARG10.9040.96116.1340.8720.8720.0000.0000.0000.000
12A3ILE0-0.018-0.02211.7880.0280.0280.0000.0000.0000.000
13A4LYS11.0091.01415.9070.4110.4110.0000.0000.0000.000
14A5PRO00.0040.00617.4290.0080.0080.0000.0000.0000.000
15A6ASP-1-0.910-0.94918.725-0.298-0.2980.0000.0000.0000.000
16A7ASP-1-0.897-0.96720.041-0.121-0.1210.0000.0000.0000.000
17A8ASN0-0.071-0.02720.1460.0660.0660.0000.0000.0000.000
18A9TRP0-0.0480.00314.832-0.031-0.0310.0000.0000.0000.000
19A10ARG10.9570.97415.233-0.131-0.1310.0000.0000.0000.000
20A11TRP00.002-0.00511.0300.0140.0140.0000.0000.0000.000
21A12TYR0-0.052-0.04110.253-0.089-0.0890.0000.0000.0000.000
22A13TYR00.023-0.06510.8940.0830.0830.0000.0000.0000.000
23A14ASP-1-0.836-0.9149.0690.9940.9940.0000.0000.0000.000
24A15GLU-1-0.924-0.99410.7451.1521.1520.0000.0000.0000.000
25A16GLU-1-0.985-0.96710.2440.7480.7480.0000.0000.0000.000
26A17HIS0-0.088-0.0596.0500.0970.0970.0000.0000.0000.000
27A18ASP-1-0.802-0.8427.3573.0403.0400.0000.0000.0000.000
28A19ARG10.7990.9012.269-18.470-18.6794.047-1.450-2.3880.018
29A20MET00.0210.0427.391-0.687-0.6870.0000.0000.0000.000
30A21MET0-0.046-0.0236.1790.8380.8380.0000.0000.0000.000
31A22LEU0-0.013-0.0028.402-0.110-0.1100.0000.0000.0000.000
32A23ASP-1-0.891-0.9399.995-0.421-0.4210.0000.0000.0000.000
33A24LEU0-0.027-0.03310.283-0.041-0.0410.0000.0000.0000.000
34A25ALA00.0150.02413.852-0.015-0.0150.0000.0000.0000.000
35A26ASN0-0.008-0.00714.897-0.008-0.0080.0000.0000.0000.000
36A27GLY0-0.002-0.00415.207-0.025-0.0250.0000.0000.0000.000
37A28MET0-0.121-0.04510.777-0.043-0.0430.0000.0000.0000.000
38A29LEU00.0630.0388.4090.1680.1680.0000.0000.0000.000
39A30PHE00.016-0.0085.188-0.628-0.6280.0000.0000.0000.000
40A31ARG10.8830.9701.5966.484-3.48922.192-6.203-6.0170.010
41A32SER0-0.005-0.0052.756-3.172-1.0430.623-1.659-1.093-0.016
42A33ARG10.9050.9242.319-5.379-4.3205.236-2.508-3.7870.007
43A34PHE0-0.023-0.0254.235-0.477-0.3480.000-0.011-0.1180.000
44A35ALA00.0580.0277.420-0.145-0.1450.0000.0000.0000.000
45A36ARG11.0621.0399.101-1.550-1.5500.0000.0000.0000.000
46A37LYS10.8730.93711.387-2.053-2.0530.0000.0000.0000.000
47A38MET0-0.123-0.0678.581-0.285-0.2850.0000.0000.0000.000
48A39LEU00.0240.03410.371-0.132-0.1320.0000.0000.0000.000
49A40THR0-0.004-0.01614.292-0.044-0.0440.0000.0000.0000.000
50A41PRO00.011-0.02617.2240.0500.0500.0000.0000.0000.000
51A42ASP-1-0.867-0.91918.9020.3970.3970.0000.0000.0000.000
52A43ALA0-0.053-0.02413.966-0.018-0.0180.0000.0000.0000.000
53A44PHE0-0.082-0.04314.0660.0640.0640.0000.0000.0000.000
54A45SER0-0.028-0.01117.445-0.058-0.0580.0000.0000.0000.000
55A46PRO0-0.033-0.01417.080-0.009-0.0090.0000.0000.0000.000
56A47ALA00.0390.03417.375-0.031-0.0310.0000.0000.0000.000
57A48GLY00.0160.01217.749-0.013-0.0130.0000.0000.0000.000
58A49PHE0-0.0140.01014.8550.0120.0120.0000.0000.0000.000
59A50CYS00.0030.02118.637-0.023-0.0230.0000.0000.0000.000
60A51VAL00.0670.00421.333-0.029-0.0290.0000.0000.0000.000
61A52ASP-1-0.886-0.93822.955-0.020-0.0200.0000.0000.0000.000
62A53ASP-1-0.752-0.88717.6700.0530.0530.0000.0000.0000.000
63A54ALA0-0.001-0.00518.538-0.064-0.0640.0000.0000.0000.000
64A55ALA0-0.017-0.00920.354-0.054-0.0540.0000.0000.0000.000
65A56LEU0-0.003-0.00117.955-0.031-0.0310.0000.0000.0000.000
66A57TYR0-0.018-0.00713.422-0.100-0.1000.0000.0000.0000.000
67A58PHE00.018-0.01617.108-0.079-0.0790.0000.0000.0000.000
68A59SER0-0.0340.00619.860-0.027-0.0270.0000.0000.0000.000
69A60PHE00.024-0.00315.326-0.014-0.0140.0000.0000.0000.000
70A61GLU-1-0.933-0.96915.911-0.772-0.7720.0000.0000.0000.000
71A62GLU-1-1.002-1.01416.867-0.366-0.3660.0000.0000.0000.000
72A63LYS10.9100.97918.3140.2390.2390.0000.0000.0000.000
73A64CYS00.0000.00814.543-0.007-0.0070.0000.0000.0000.000
74A65ARG10.9080.96216.4100.4230.4230.0000.0000.0000.000
75A66ASP-1-0.888-0.94018.401-0.507-0.5070.0000.0000.0000.000
76A67PHE0-0.037-0.01714.1000.0040.0040.0000.0000.0000.000
77A68ASN0-0.008-0.00516.759-0.047-0.0470.0000.0000.0000.000
78A69LEU0-0.033-0.01710.758-0.102-0.1020.0000.0000.0000.000
79A70SER00.009-0.00110.6050.0140.0140.0000.0000.0000.000
80A71LYS11.0030.97012.3060.9080.9080.0000.0000.0000.000
81A72GLU-1-0.833-0.8886.842-4.759-4.7590.0000.0000.0000.000
82A73GLN00.0470.0157.551-0.012-0.0120.0000.0000.0000.000
83A74LYS10.8800.9608.6440.9380.9380.0000.0000.0000.000
84A75ALA00.0200.0229.9680.1740.1740.0000.0000.0000.000
85A76GLU-1-0.851-0.9472.194-23.176-20.5292.427-2.766-2.309-0.042
86A77LEU0-0.034-0.0116.8540.4350.4350.0000.0000.0000.000
87A78VAL00.0120.0108.6820.4260.4260.0000.0000.0000.000
88A79LEU00.0150.0048.4820.2760.2760.0000.0000.0000.000
89A80ASN00.003-0.0064.3882.1282.179-0.001-0.002-0.0480.000
90A81ALA00.0270.0198.6200.3800.3800.0000.0000.0000.000
91A82LEU0-0.013-0.00412.2220.1280.1280.0000.0000.0000.000
92A83VAL0-0.0100.0058.9430.1480.1480.0000.0000.0000.000
93A84ALA0-0.058-0.04111.4360.1050.1050.0000.0000.0000.000
94A85ILE00.008-0.00112.8010.0120.0120.0000.0000.0000.000
95A86ARG10.8610.93615.205-0.160-0.1600.0000.0000.0000.000
96A87TYR00.0250.00513.1510.0310.0310.0000.0000.0000.000
97A88LEU0-0.0430.01111.4570.1620.1620.0000.0000.0000.000
98A89LYS10.8730.94614.649-1.057-1.0570.0000.0000.0000.000
99A90PRO00.0480.03317.0440.0270.0270.0000.0000.0000.000
100A91GLN0-0.034-0.02615.3920.0740.0740.0000.0000.0000.000
101A92MET0-0.002-0.00918.654-0.070-0.0700.0000.0000.0000.000
102A93PRO0-0.003-0.01420.1190.0290.0290.0000.0000.0000.000
103A94LYS10.9150.96316.547-0.614-0.6140.0000.0000.0000.000
104A95SER00.042-0.01021.963-0.023-0.0230.0000.0000.0000.000
105A96TRP00.0130.01124.584-0.019-0.0190.0000.0000.0000.000
106A97HIS00.0170.01321.324-0.035-0.0350.0000.0000.0000.000
107A98PHE0-0.0150.00518.714-0.007-0.0070.0000.0000.0000.000
108A99VAL00.0840.04324.5160.0110.0110.0000.0000.0000.000
109A100SER0-0.106-0.05627.109-0.003-0.0030.0000.0000.0000.000
110A101HIS00.002-0.02026.402-0.015-0.0150.0000.0000.0000.000
111A102GLY0-0.0150.02031.322-0.008-0.0080.0000.0000.0000.000
112A103GLU-1-0.921-0.96032.7300.0120.0120.0000.0000.0000.000
113A104MET0-0.053-0.03129.5980.0070.0070.0000.0000.0000.000
114A105TRP0-0.0050.00623.208-0.003-0.0030.0000.0000.0000.000
115A106VAL0-0.013-0.02427.8110.0160.0160.0000.0000.0000.000
116A107PRO0-0.0210.01522.880-0.015-0.0150.0000.0000.0000.000
117A108MET00.016-0.01124.3720.0230.0230.0000.0000.0000.000
118A109PRO00.002-0.00320.544-0.021-0.0210.0000.0000.0000.000
119A110GLY0-0.051-0.03518.729-0.019-0.0190.0000.0000.0000.000
120A111ASP-1-0.853-0.92319.673-0.182-0.1820.0000.0000.0000.000
121A112ALA0-0.012-0.00218.690-0.009-0.0090.0000.0000.0000.000
122A113ALA0-0.015-0.01518.8400.0370.0370.0000.0000.0000.000
123A114CYS0-0.041-0.00519.170-0.054-0.0540.0000.0000.0000.000
124A115VAL00.0030.01119.1900.0390.0390.0000.0000.0000.000
125A116TRP00.0460.01821.454-0.023-0.0230.0000.0000.0000.000
126A117LEU0-0.029-0.01319.1210.0420.0420.0000.0000.0000.000
127A118SER0-0.017-0.01623.175-0.011-0.0110.0000.0000.0000.000
128A119ASP-1-0.934-0.97024.4640.0910.0910.0000.0000.0000.000
129A120THR00.0030.00122.435-0.016-0.0160.0000.0000.0000.000
130A121HIS0-0.0110.00125.662-0.021-0.0210.0000.0000.0000.000
131A122GLU-1-0.931-0.96618.177-0.096-0.0960.0000.0000.0000.000
132A123GLN0-0.031-0.02220.8000.0450.0450.0000.0000.0000.000
133A124VAL0-0.033-0.01715.732-0.026-0.0260.0000.0000.0000.000
134A125ASN00.014-0.00615.7360.0860.0860.0000.0000.0000.000
135A126LEU0-0.043-0.03514.742-0.007-0.0070.0000.0000.0000.000
136A127LEU00.0230.02212.847-0.059-0.0590.0000.0000.0000.000
137A128VAL00.0210.00815.4730.0960.0960.0000.0000.0000.000
138A129VAL0-0.038-0.03213.828-0.058-0.0580.0000.0000.0000.000
139A130GLU-1-0.907-0.95817.2560.2880.2880.0000.0000.0000.000
140A131SER0-0.004-0.01620.3090.0240.0240.0000.0000.0000.000
141A132GLY00.0270.02023.3880.0060.0060.0000.0000.0000.000
142A133GLU-1-0.912-0.96125.9520.1080.1080.0000.0000.0000.000
143A134ASN0-0.005-0.02128.012-0.021-0.0210.0000.0000.0000.000
144A135ALA0-0.023-0.01123.1370.0060.0060.0000.0000.0000.000
145A136ALA00.0560.05421.135-0.002-0.0020.0000.0000.0000.000
146A137LEU0-0.045-0.02015.0370.0520.0520.0000.0000.0000.000
147A138CYS0-0.0100.00115.958-0.082-0.0820.0000.0000.0000.000
148A139LEU0-0.0040.0009.5940.1640.1640.0000.0000.0000.000
149A140LEU0-0.0250.0029.573-0.119-0.1190.0000.0000.0000.000
150A141ALA00.0240.01110.119-0.246-0.2460.0000.0000.0000.000
151A142GLN00.0560.03311.305-0.037-0.0370.0000.0000.0000.000
152A143PRO00.012-0.0058.428-0.067-0.0670.0000.0000.0000.000
153A144CYS0-0.043-0.0368.050-0.002-0.0020.0000.0000.0000.000
154A145VAL00.0710.04910.436-0.039-0.0390.0000.0000.0000.000
155A146VAL00.0000.00912.9430.1530.1530.0000.0000.0000.000
156A147ILE00.0570.02215.552-0.053-0.0530.0000.0000.0000.000
157A148ALA0-0.020-0.01517.6970.0820.0820.0000.0000.0000.000
158A149GLY00.0000.00719.1450.0340.0340.0000.0000.0000.000
159A150ARG10.9180.96713.317-0.912-0.9120.0000.0000.0000.000
160A151ALA00.0140.00711.375-0.109-0.1090.0000.0000.0000.000
161A152MET0-0.057-0.0259.8840.2690.2690.0000.0000.0000.000
162A153GLN0-0.026-0.0325.1110.5170.5170.0000.0000.0000.000
163A154LEU0-0.009-0.0025.7090.3640.3640.0000.0000.0000.000
164A155GLY0-0.032-0.0185.286-0.394-0.3940.0000.0000.0000.000
165A156ASP-1-0.816-0.8956.7913.4783.4780.0000.0000.0000.000
166A157ALA00.0190.0068.468-0.419-0.4190.0000.0000.0000.000
167A158ILE0-0.071-0.04011.6520.1350.1350.0000.0000.0000.000
168A159LYS10.9390.99515.138-0.446-0.4460.0000.0000.0000.000
169A160ILE0-0.042-0.02217.8620.0270.0270.0000.0000.0000.000
170A161MET00.0110.00721.236-0.017-0.0170.0000.0000.0000.000
171A162ASN00.0860.01124.989-0.004-0.0040.0000.0000.0000.000
172A163ASP-1-0.833-0.89826.5020.0930.0930.0000.0000.0000.000
173A164ARG10.7860.88824.139-0.134-0.1340.0000.0000.0000.000
174A165LEU0-0.044-0.00920.619-0.017-0.0170.0000.0000.0000.000
175A166LYS10.9360.98024.0210.0320.0320.0000.0000.0000.000
176A167PRO00.0220.02923.604-0.013-0.0130.0000.0000.0000.000
177A168GLN0-0.004-0.02218.581-0.010-0.0100.0000.0000.0000.000