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: 6NVKZ

Calculation Name: 3DAL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DAL

Chain ID: A

ChEMBL ID:

UniProt ID: O75626

Base Structure: X-ray

Registration Date: 2023-09-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2124715.300824
FMO2-HF: Nuclear repulsion 2046010.871727
FMO2-HF: Total energy -78704.429097
FMO2-MP2: Total energy -78929.72217


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:-10:SER)


Summations of interaction energy for fragment #1(A:-10: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.
-3.913-0.8261.566-1.79-2.8620.007
Interaction energy analysis for fragmet #1(A:-10:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.009
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-8GLY00.0180.0023.8520.1361.717-0.014-0.814-0.7540.003
4A-7LEU00.016-0.0206.270-0.060-0.0600.0000.0000.0000.000
5A-6VAL00.0280.0184.703-0.415-0.274-0.001-0.020-0.1200.000
6A-5PRO0-0.0120.0062.235-2.288-1.0511.580-0.908-1.9080.004
7A-4ARG10.8790.9634.136-0.989-0.8610.001-0.048-0.0800.000
8A-3GLY00.0870.0597.574-0.203-0.2030.0000.0000.0000.000
9A-2SER0-0.032-0.0329.6880.0430.0430.0000.0000.0000.000
10A-1LYS10.7960.87010.373-0.112-0.1120.0000.0000.0000.000
11A0LYS10.7980.89913.867-0.005-0.0050.0000.0000.0000.000
12A1MET00.0350.01618.364-0.001-0.0010.0000.0000.0000.000
13A2ASP-1-0.801-0.88517.3090.0120.0120.0000.0000.0000.000
14A3MET00.0420.01311.974-0.016-0.0160.0000.0000.0000.000
15A4GLU-1-0.890-0.92811.957-0.003-0.0030.0000.0000.0000.000
16A5ASP-1-0.784-0.88215.159-0.010-0.0100.0000.0000.0000.000
17A7ALA0-0.008-0.00717.655-0.020-0.0200.0000.0000.0000.000
18A8ASP-1-0.886-0.90819.706-0.004-0.0040.0000.0000.0000.000
19A9MET0-0.0090.00822.8050.0010.0010.0000.0000.0000.000
20A10THR0-0.075-0.04725.7790.0020.0020.0000.0000.0000.000
21A11LEU0-0.035-0.02827.3180.0010.0010.0000.0000.0000.000
22A12TRP0-0.051-0.02122.1750.0000.0000.0000.0000.0000.000
23A13THR00.017-0.00928.196-0.001-0.0010.0000.0000.0000.000
24A14GLU-1-0.760-0.86230.372-0.005-0.0050.0000.0000.0000.000
25A15ALA00.0340.02231.165-0.003-0.0030.0000.0000.0000.000
26A16GLU-1-0.734-0.84025.4080.0030.0030.0000.0000.0000.000
27A17PHE0-0.015-0.02827.137-0.006-0.0060.0000.0000.0000.000
28A18GLU-1-0.942-0.96728.766-0.019-0.0190.0000.0000.0000.000
29A19GLU-1-1.005-0.99726.492-0.011-0.0110.0000.0000.0000.000
30A20LYS10.7930.88022.1300.0050.0050.0000.0000.0000.000
31A21CYS0-0.105-0.01724.153-0.008-0.0080.0000.0000.0000.000
32A22THR0-0.035-0.02622.826-0.006-0.0060.0000.0000.0000.000
33A23TYR0-0.034-0.02123.143-0.004-0.0040.0000.0000.0000.000
34A24ILE00.0190.00628.4610.0050.0050.0000.0000.0000.000
35A25VAL0-0.057-0.01932.109-0.003-0.0030.0000.0000.0000.000
36A26ASN0-0.028-0.01634.9580.0030.0030.0000.0000.0000.000
37A27ASP-1-0.763-0.86438.455-0.023-0.0230.0000.0000.0000.000
38A28HIS0-0.082-0.04341.668-0.003-0.0030.0000.0000.0000.000
39A29PRO0-0.0350.00843.1590.0020.0020.0000.0000.0000.000
40A30TRP00.0850.00144.320-0.001-0.0010.0000.0000.0000.000
41A31ASP-1-1.017-0.99248.362-0.014-0.0140.0000.0000.0000.000
42A40VAL00.0580.03652.8750.0000.0000.0000.0000.0000.000
43A41GLN0-0.021-0.01649.917-0.001-0.0010.0000.0000.0000.000
44A42ALA0-0.0090.01348.815-0.001-0.0010.0000.0000.0000.000
45A43GLU-1-0.902-0.97147.775-0.016-0.0160.0000.0000.0000.000
46A44ALA0-0.018-0.01747.620-0.001-0.0010.0000.0000.0000.000
47A45SER0-0.024-0.01845.330-0.001-0.0010.0000.0000.0000.000
48A46LEU0-0.0090.01141.958-0.001-0.0010.0000.0000.0000.000
49A47PRO0-0.011-0.00438.607-0.001-0.0010.0000.0000.0000.000
50A48ARG11.0120.99337.9380.0390.0390.0000.0000.0000.000
51A49ASN0-0.014-0.00733.6600.0020.0020.0000.0000.0000.000
52A50LEU0-0.028-0.00336.497-0.001-0.0010.0000.0000.0000.000
53A51LEU0-0.001-0.00439.4020.0000.0000.0000.0000.0000.000
54A52PHE00.0340.03042.4590.0000.0000.0000.0000.0000.000
55A53LYS10.7960.89743.9680.0110.0110.0000.0000.0000.000
56A54TYR00.0460.02145.9810.0000.0000.0000.0000.0000.000
57A55ALA0-0.0120.00249.7720.0000.0000.0000.0000.0000.000
58A56THR0-0.002-0.02552.293-0.001-0.0010.0000.0000.0000.000
59A57ASN0-0.084-0.04453.6450.0000.0000.0000.0000.0000.000
60A58SER00.0190.02054.7540.0000.0000.0000.0000.0000.000
61A59GLU-1-0.880-0.93553.998-0.014-0.0140.0000.0000.0000.000
62A60GLU-1-0.992-0.99253.217-0.008-0.0080.0000.0000.0000.000
63A61VAL00.0260.01847.6840.0000.0000.0000.0000.0000.000
64A62ILE0-0.063-0.04447.8660.0010.0010.0000.0000.0000.000
65A63GLY00.0380.01944.6020.0010.0010.0000.0000.0000.000
66A64VAL0-0.0120.00740.263-0.001-0.0010.0000.0000.0000.000
67A65MET0-0.0010.02639.2530.0010.0010.0000.0000.0000.000
68A66SER00.003-0.00734.6800.0000.0000.0000.0000.0000.000
69A67LYS10.8630.93936.9030.0380.0380.0000.0000.0000.000
70A68GLU-1-0.915-0.97533.424-0.046-0.0460.0000.0000.0000.000
71A69TYR0-0.030-0.02424.0250.0040.0040.0000.0000.0000.000
72A70ILE00.0270.01530.397-0.003-0.0030.0000.0000.0000.000
73A71PRO00.0170.01325.1080.0010.0010.0000.0000.0000.000
74A72LYS10.8510.93721.8360.0490.0490.0000.0000.0000.000
75A73GLY00.0550.03425.109-0.007-0.0070.0000.0000.0000.000
76A74THR0-0.032-0.02726.340-0.005-0.0050.0000.0000.0000.000
77A75ARG10.9540.99229.5060.0320.0320.0000.0000.0000.000
78A76PHE00.0200.00032.475-0.002-0.0020.0000.0000.0000.000
79A77GLY00.0580.03736.1000.0020.0020.0000.0000.0000.000
80A78PRO0-0.063-0.04438.882-0.002-0.0020.0000.0000.0000.000
81A79LEU00.015-0.01840.8380.0000.0000.0000.0000.0000.000
82A80ILE0-0.040-0.01643.4200.0000.0000.0000.0000.0000.000
83A81GLY00.029-0.00346.9250.0000.0000.0000.0000.0000.000
84A82GLU-1-0.874-0.91950.102-0.007-0.0070.0000.0000.0000.000
85A83ILE0-0.001-0.00249.0290.0000.0000.0000.0000.0000.000
86A84TYR0-0.028-0.01052.9180.0000.0000.0000.0000.0000.000
87A85THR00.0540.01953.6680.0000.0000.0000.0000.0000.000
88A86ASN00.014-0.03654.6290.0000.0000.0000.0000.0000.000
89A87ASP-1-0.908-0.94457.5540.0010.0010.0000.0000.0000.000
90A88THR0-0.033-0.01458.0860.0000.0000.0000.0000.0000.000
91A89VAL0-0.0560.00156.3800.0000.0000.0000.0000.0000.000
92A90PRO00.0110.02358.4830.0000.0000.0000.0000.0000.000
93A91LYS10.9620.95461.2270.0020.0020.0000.0000.0000.000
94A92ASN0-0.0010.01561.0690.0010.0010.0000.0000.0000.000
95A93ALA0-0.0030.00559.7170.0000.0000.0000.0000.0000.000
96A94ASN0-0.015-0.01255.6530.0010.0010.0000.0000.0000.000
97A95ARG10.9640.98353.0240.0000.0000.0000.0000.0000.000
98A96LYS10.9270.97650.1810.0060.0060.0000.0000.0000.000
99A97TYR00.0320.02348.6450.0000.0000.0000.0000.0000.000
100A98PHE0-0.0020.00549.2970.0000.0000.0000.0000.0000.000
101A99TRP00.0160.01741.0120.0010.0010.0000.0000.0000.000
102A100ARG10.9070.96045.792-0.002-0.0020.0000.0000.0000.000
103A101ILE00.0380.03643.6810.0000.0000.0000.0000.0000.000
104A102TYR00.017-0.01843.8190.0000.0000.0000.0000.0000.000
105A103SER0-0.002-0.00444.601-0.001-0.0010.0000.0000.0000.000
106A104ARG10.9310.95044.689-0.003-0.0030.0000.0000.0000.000
107A105GLY00.0250.01544.4080.0010.0010.0000.0000.0000.000
108A106GLU-1-0.878-0.91645.3900.0070.0070.0000.0000.0000.000
109A107LEU0-0.076-0.03548.114-0.001-0.0010.0000.0000.0000.000
110A108HIS0-0.081-0.05048.7170.0010.0010.0000.0000.0000.000
111A109HIS00.0250.01247.9350.0010.0010.0000.0000.0000.000
112A110PHE0-0.012-0.01949.2820.0000.0000.0000.0000.0000.000
113A111ILE00.0140.01145.3430.0000.0000.0000.0000.0000.000
114A112ASP-1-0.826-0.94149.151-0.005-0.0050.0000.0000.0000.000
115A113GLY00.0310.00149.344-0.001-0.0010.0000.0000.0000.000
116A114PHE0-0.027-0.00650.3050.0000.0000.0000.0000.0000.000
117A115ASN00.005-0.00453.514-0.001-0.0010.0000.0000.0000.000
118A116GLU-1-0.767-0.85252.236-0.011-0.0110.0000.0000.0000.000
119A117GLU-1-0.862-0.92952.951-0.010-0.0100.0000.0000.0000.000
120A118LYS10.7670.89253.6050.0090.0090.0000.0000.0000.000
121A119SER00.004-0.01649.3040.0000.0000.0000.0000.0000.000
122A120ASN00.0300.00243.1610.0010.0010.0000.0000.0000.000
123A121TRP00.017-0.01738.2650.0010.0010.0000.0000.0000.000
124A122MET0-0.066-0.00139.3450.0000.0000.0000.0000.0000.000
125A123ARG10.7610.88343.3450.0110.0110.0000.0000.0000.000
126A124TYR0-0.063-0.06645.4450.0010.0010.0000.0000.0000.000
127A125VAL0-0.064-0.02039.4390.0000.0000.0000.0000.0000.000
128A126ASN0-0.050-0.03242.6490.0020.0020.0000.0000.0000.000
129A127PRO00.0120.00541.048-0.001-0.0010.0000.0000.0000.000
130A128ALA0-0.041-0.02037.3770.0000.0000.0000.0000.0000.000
131A129HIS00.0420.02639.3330.0020.0020.0000.0000.0000.000
132A130SER0-0.068-0.05837.3330.0020.0020.0000.0000.0000.000
133A131PRO00.0680.01633.049-0.002-0.0020.0000.0000.0000.000
134A132ARG10.8150.89032.389-0.006-0.0060.0000.0000.0000.000
135A133GLU-1-0.800-0.87833.041-0.004-0.0040.0000.0000.0000.000
136A134GLN0-0.0090.01133.090-0.001-0.0010.0000.0000.0000.000
137A135ASN0-0.036-0.03431.475-0.001-0.0010.0000.0000.0000.000
138A136LEU00.0440.02831.645-0.004-0.0040.0000.0000.0000.000
139A137ALA00.0170.01832.0270.0030.0030.0000.0000.0000.000
140A138ALA0-0.0010.00533.840-0.002-0.0020.0000.0000.0000.000
141A139CYS0-0.010-0.00532.7600.0030.0030.0000.0000.0000.000
142A140GLN00.016-0.00436.508-0.001-0.0010.0000.0000.0000.000
143A141ASN0-0.035-0.01033.5190.0000.0000.0000.0000.0000.000
144A142GLY00.0350.01437.405-0.001-0.0010.0000.0000.0000.000
145A143MET0-0.049-0.04240.1130.0010.0010.0000.0000.0000.000
146A144ASN0-0.0090.01240.3510.0010.0010.0000.0000.0000.000
147A145ILE00.0230.01039.6620.0010.0010.0000.0000.0000.000
148A146TYR0-0.0040.00535.754-0.001-0.0010.0000.0000.0000.000
149A147PHE00.0160.00335.7130.0020.0020.0000.0000.0000.000
150A148TYR00.017-0.01730.050-0.004-0.0040.0000.0000.0000.000
151A149THR0-0.014-0.01228.7980.0030.0030.0000.0000.0000.000
152A150ILE00.0420.01127.421-0.004-0.0040.0000.0000.0000.000
153A151LYS10.8110.89425.9250.0130.0130.0000.0000.0000.000
154A152PRO0-0.0050.00324.5300.0010.0010.0000.0000.0000.000
155A153ILE00.0040.01627.3600.0050.0050.0000.0000.0000.000
156A154PRO0-0.005-0.00529.479-0.003-0.0030.0000.0000.0000.000
157A155ALA00.0290.02831.4760.0030.0030.0000.0000.0000.000
158A156ASN0-0.026-0.01534.5590.0020.0020.0000.0000.0000.000
159A157GLN0-0.043-0.01433.8190.0040.0040.0000.0000.0000.000
160A158GLU-1-0.748-0.87636.781-0.013-0.0130.0000.0000.0000.000
161A159LEU0-0.040-0.01535.832-0.001-0.0010.0000.0000.0000.000
162A160LEU0-0.015-0.00736.3630.0020.0020.0000.0000.0000.000
163A161VAL00.0060.00136.171-0.001-0.0010.0000.0000.0000.000
164A162TRP0-0.026-0.02736.4550.0010.0010.0000.0000.0000.000
165A163TYR00.0020.00336.421-0.002-0.0020.0000.0000.0000.000
166A164CYS0-0.0160.01233.1510.0010.0010.0000.0000.0000.000
167A165ARG10.9760.99430.029-0.017-0.0170.0000.0000.0000.000
168A166ASP-1-0.800-0.91234.1530.0080.0080.0000.0000.0000.000
169A167PHE0-0.059-0.03936.7100.0000.0000.0000.0000.0000.000
170A168ALA00.002-0.01138.2030.0000.0000.0000.0000.0000.000
171A169GLU-1-0.838-0.90037.0230.0170.0170.0000.0000.0000.000
172A170ARG10.7780.86638.399-0.002-0.0020.0000.0000.0000.000
173A171LEU0-0.084-0.03442.5050.0000.0000.0000.0000.0000.000
174A172HIS0-0.067-0.02443.9220.0010.0010.0000.0000.0000.000
175A173TYR0-0.061-0.02842.2090.0000.0000.0000.0000.0000.000
176A174PRO00.0510.03940.2360.0010.0010.0000.0000.0000.000
177A175TYR0-0.042-0.06433.764-0.002-0.0020.0000.0000.0000.000
178A176PRO0-0.006-0.01232.5790.0030.0030.0000.0000.0000.000
179A177GLY00.0050.00131.2460.0000.0000.0000.0000.0000.000
180A178GLU-1-0.903-0.93431.9560.0180.0180.0000.0000.0000.000
181A179LEU0-0.054-0.02331.3510.0020.0020.0000.0000.0000.000
182A180THR00.0540.00435.196-0.001-0.0010.0000.0000.0000.000
183A181MET00.037-0.00637.9530.0010.0010.0000.0000.0000.000
184A182MET00.0140.01938.0010.0010.0010.0000.0000.0000.000
185A183ASN00.0060.01933.0270.0000.0000.0000.0000.0000.000
186A184LEU00.0110.01034.8840.0030.0030.0000.0000.0000.000
187A185THR0-0.045-0.03136.9810.0010.0010.0000.0000.0000.000
188A186GLN0-0.079-0.01733.2470.0010.0010.0000.0000.0000.000