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: VR1K1

Calculation Name: 4TR4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TR4

Chain ID: A

ChEMBL ID:

UniProt ID: Q91ZI8

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2020592.430988
FMO2-HF: Nuclear repulsion 1946301.992679
FMO2-HF: Total energy -74290.438309
FMO2-MP2: Total energy -74506.100682


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:114:GLY)


Summations of interaction energy for fragment #1(A:114:GLY)
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.
1.0833.461.309-1.52-2.1660.001
Interaction energy analysis for fragmet #1(A:114:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.025
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].
3A116ASP-1-0.767-0.8783.866-1.0040.399-0.009-0.699-0.6950.002
4A117PRO0-0.053-0.0266.7680.1580.1580.0000.0000.0000.000
5A118PHE0-0.045-0.0259.1620.2120.2120.0000.0000.0000.000
6A119THR0-0.016-0.01310.7000.1700.1700.0000.0000.0000.000
7A120GLY0-0.0040.0119.3990.1090.1090.0000.0000.0000.000
8A121GLN0-0.028-0.0328.3810.1800.1800.0000.0000.0000.000
9A122LYS10.7940.8844.5981.6031.683-0.001-0.034-0.0450.000
10A123LEU00.0100.0252.4070.9081.5471.317-0.745-1.211-0.001
11A124ASP-1-0.841-0.9164.811-1.438-1.383-0.001-0.006-0.0480.000
12A125PHE00.005-0.0093.4080.1890.3890.003-0.036-0.1670.000
13A126PHE0-0.033-0.0058.9000.2020.2020.0000.0000.0000.000
14A127LYS10.8750.94212.0590.0870.0870.0000.0000.0000.000
15A128GLN00.0330.01715.1310.0290.0290.0000.0000.0000.000
16A129ALA00.0640.04517.8610.0400.0400.0000.0000.0000.000
17A130HIS0-0.024-0.01019.1340.0250.0250.0000.0000.0000.000
18A131GLU-1-0.796-0.90523.438-0.071-0.0710.0000.0000.0000.000
19A132GLY0-0.024-0.01025.7240.0040.0040.0000.0000.0000.000
20A133GLY00.0090.01622.2040.0140.0140.0000.0000.0000.000
21A134PRO0-0.032-0.01918.9680.0010.0010.0000.0000.0000.000
22A135ALA00.020-0.00421.029-0.023-0.0230.0000.0000.0000.000
23A136PRO0-0.013-0.00118.3960.0030.0030.0000.0000.0000.000
24A137ASN00.0500.03719.6870.0000.0000.0000.0000.0000.000
25A138SER0-0.014-0.03219.199-0.011-0.0110.0000.0000.0000.000
26A139GLU-1-0.827-0.87219.660-0.249-0.2490.0000.0000.0000.000
27A140VAL00.0010.01321.746-0.013-0.0130.0000.0000.0000.000
28A141VAL00.0000.00225.3220.0010.0010.0000.0000.0000.000
29A142ARG10.9260.96327.9150.0970.0970.0000.0000.0000.000
30A143PRO00.0410.00631.487-0.003-0.0030.0000.0000.0000.000
31A144ASP-1-0.861-0.91434.278-0.091-0.0910.0000.0000.0000.000
32A145GLY0-0.003-0.01234.5060.0050.0050.0000.0000.0000.000
33A146PHE0-0.044-0.02229.679-0.002-0.0020.0000.0000.0000.000
34A147GLN00.0460.03028.815-0.010-0.0100.0000.0000.0000.000
35A148SER0-0.044-0.03722.8120.0030.0030.0000.0000.0000.000
36A149GLN00.0420.02925.4950.0170.0170.0000.0000.0000.000
37A150ARG10.8120.88219.2390.1960.1960.0000.0000.0000.000
38A151ILE0-0.0030.00723.9240.0170.0170.0000.0000.0000.000
39A152LEU0-0.001-0.02123.2040.0140.0140.0000.0000.0000.000
40A153ASP-1-0.866-0.92225.916-0.100-0.1000.0000.0000.0000.000
41A154TYR0-0.056-0.04528.3860.0100.0100.0000.0000.0000.000
42A155ALA0-0.0110.00129.4000.0040.0040.0000.0000.0000.000
43A156GLN0-0.025-0.02031.2510.0080.0080.0000.0000.0000.000
44A157GLY0-0.016-0.01632.6370.0050.0050.0000.0000.0000.000
45A158THR0-0.031-0.02132.147-0.001-0.0010.0000.0000.0000.000
46A159ARG10.7780.87034.5130.0420.0420.0000.0000.0000.000
47A160PRO0-0.045-0.01333.325-0.004-0.0040.0000.0000.0000.000
48A161LEU00.0060.00729.5490.0010.0010.0000.0000.0000.000
49A162VAL0-0.013-0.01631.541-0.005-0.0050.0000.0000.0000.000
50A163LEU0-0.0180.00227.036-0.003-0.0030.0000.0000.0000.000
51A164ASN00.003-0.00831.178-0.003-0.0030.0000.0000.0000.000
52A165PHE00.0500.02525.558-0.001-0.0010.0000.0000.0000.000
53A166GLY00.0590.00030.4770.0050.0050.0000.0000.0000.000
54A167SER0-0.024-0.02532.408-0.004-0.0040.0000.0000.0000.000
55A168CYS00.050-0.00534.4840.0070.0070.0000.0000.0000.000
56A169THR0-0.058-0.04135.5230.0040.0040.0000.0000.0000.000
57A170CYS0-0.024-0.01233.5130.0000.0000.0000.0000.0000.000
58A171PRO00.0400.01336.5310.0050.0050.0000.0000.0000.000
59A172PRO00.0180.00736.6040.0060.0060.0000.0000.0000.000
60A173PHE00.0020.00534.4470.0050.0050.0000.0000.0000.000
61A174MET0-0.0080.01737.1720.0050.0050.0000.0000.0000.000
62A175ALA0-0.028-0.00640.3780.0060.0060.0000.0000.0000.000
63A176ARG10.7640.86133.5570.1200.1200.0000.0000.0000.000
64A177MET00.0280.04137.3480.0060.0060.0000.0000.0000.000
65A178SER00.0320.00641.3360.0040.0040.0000.0000.0000.000
66A179ALA0-0.021-0.02243.1390.0040.0040.0000.0000.0000.000
67A180PHE00.0250.01236.0050.0030.0030.0000.0000.0000.000
68A181GLN00.0620.00840.1100.0050.0050.0000.0000.0000.000
69A182ARG10.9100.96143.2390.0610.0610.0000.0000.0000.000
70A183LEU0-0.047-0.01840.0870.0040.0040.0000.0000.0000.000
71A184VAL00.0390.01939.6930.0030.0030.0000.0000.0000.000
72A185THR0-0.029-0.02742.1070.0040.0040.0000.0000.0000.000
73A186LYS10.8170.92145.3080.0450.0450.0000.0000.0000.000
74A187TYR00.015-0.01541.7350.0030.0030.0000.0000.0000.000
75A188GLN00.0350.03041.8640.0010.0010.0000.0000.0000.000
76A189ARG10.9090.97942.8200.0250.0250.0000.0000.0000.000
77A190ASP-1-0.844-0.91941.711-0.026-0.0260.0000.0000.0000.000
78A191VAL0-0.021-0.00836.8130.0010.0010.0000.0000.0000.000
79A192ASP-1-0.766-0.82735.412-0.050-0.0500.0000.0000.0000.000
80A193PHE0-0.013-0.02435.350-0.003-0.0030.0000.0000.0000.000
81A194LEU0-0.0090.00829.8050.0020.0020.0000.0000.0000.000
82A195ILE0-0.017-0.01832.845-0.004-0.0040.0000.0000.0000.000
83A196ILE0-0.028-0.01627.056-0.002-0.0020.0000.0000.0000.000
84A197TYR0-0.007-0.02530.5260.0010.0010.0000.0000.0000.000
85A198ILE0-0.043-0.01527.293-0.011-0.0110.0000.0000.0000.000
86A199GLU-1-0.822-0.90526.533-0.257-0.2570.0000.0000.0000.000
87A200GLU-1-0.723-0.78929.259-0.140-0.1400.0000.0000.0000.000
88A201ALA0-0.029-0.00731.643-0.010-0.0100.0000.0000.0000.000
89A202HIS0-0.022-0.01933.081-0.001-0.0010.0000.0000.0000.000
90A203PRO00.0080.01732.5700.0080.0080.0000.0000.0000.000
91A204SER00.014-0.01735.6930.0010.0010.0000.0000.0000.000
92A205ASP-1-0.848-0.90935.596-0.155-0.1550.0000.0000.0000.000
93A206GLY00.0070.01434.605-0.008-0.0080.0000.0000.0000.000
94A207TRP0-0.033-0.03232.3050.0120.0120.0000.0000.0000.000
95A208VAL0-0.045-0.00935.7010.0070.0070.0000.0000.0000.000
96A209THR00.003-0.00238.0730.0000.0000.0000.0000.0000.000
97A210THR00.0020.00239.6660.0030.0030.0000.0000.0000.000
98A211ASP-1-0.917-0.95741.875-0.092-0.0920.0000.0000.0000.000
99A212SER0-0.033-0.01840.8300.0050.0050.0000.0000.0000.000
100A213PRO0-0.021-0.01242.9560.0010.0010.0000.0000.0000.000
101A214TYR0-0.027-0.01240.7660.0030.0030.0000.0000.0000.000
102A215VAL00.0410.01540.970-0.006-0.0060.0000.0000.0000.000
103A216ILE0-0.007-0.00736.6210.0020.0020.0000.0000.0000.000
104A217PRO0-0.0170.00536.287-0.005-0.0050.0000.0000.0000.000
105A218GLN0-0.033-0.03828.1810.0060.0060.0000.0000.0000.000
106A219HIS0-0.074-0.03129.864-0.009-0.0090.0000.0000.0000.000
107A220ARG10.8560.91829.2230.1510.1510.0000.0000.0000.000
108A221SER0-0.051-0.05628.748-0.011-0.0110.0000.0000.0000.000
109A222LEU00.0510.00927.0280.0020.0020.0000.0000.0000.000
110A223GLU-1-0.835-0.89530.480-0.148-0.1480.0000.0000.0000.000
111A224ASP-1-0.804-0.88432.663-0.152-0.1520.0000.0000.0000.000
112A225ARG10.8010.87825.7550.2400.2400.0000.0000.0000.000
113A226VAL0-0.028-0.01332.6730.0070.0070.0000.0000.0000.000
114A227SER0-0.039-0.00534.7930.0110.0110.0000.0000.0000.000
115A228ALA00.0070.00135.0970.0070.0070.0000.0000.0000.000
116A229ALA00.0170.00134.4390.0050.0050.0000.0000.0000.000
117A230ARG10.8480.90536.5270.1090.1090.0000.0000.0000.000
118A231VAL0-0.0220.00339.8980.0070.0070.0000.0000.0000.000
119A232LEU00.0110.00637.0100.0040.0040.0000.0000.0000.000
120A233GLN0-0.048-0.02937.9030.0020.0020.0000.0000.0000.000
121A234GLN0-0.030-0.00541.3840.0070.0070.0000.0000.0000.000
122A235GLY0-0.032-0.01243.9350.0050.0050.0000.0000.0000.000
123A236ALA0-0.055-0.04341.751-0.002-0.0020.0000.0000.0000.000
124A237PRO00.0270.01642.664-0.002-0.0020.0000.0000.0000.000
125A238GLY00.0260.00542.7440.0030.0030.0000.0000.0000.000
126A239CYS0-0.0430.00537.7600.0010.0010.0000.0000.0000.000
127A240ALA00.0050.01735.559-0.003-0.0030.0000.0000.0000.000
128A241LEU0-0.005-0.00734.193-0.003-0.0030.0000.0000.0000.000
129A242VAL0-0.022-0.00228.9850.0020.0020.0000.0000.0000.000
130A243LEU00.0120.01329.1650.0000.0000.0000.0000.0000.000
131A244ASP-1-0.720-0.83123.713-0.279-0.2790.0000.0000.0000.000
132A245THR0-0.017-0.02020.9990.0040.0040.0000.0000.0000.000
133A246MET00.0260.01224.146-0.001-0.0010.0000.0000.0000.000
134A247ALA0-0.0160.00418.540-0.013-0.0130.0000.0000.0000.000
135A248ASN00.0210.00819.828-0.013-0.0130.0000.0000.0000.000
136A249SER00.0210.03318.903-0.021-0.0210.0000.0000.0000.000
137A250SER00.018-0.01619.472-0.011-0.0110.0000.0000.0000.000
138A251SER0-0.040-0.04422.1480.0180.0180.0000.0000.0000.000
139A252SER0-0.032-0.01917.9160.0010.0010.0000.0000.0000.000
140A253ALA0-0.040-0.01017.9260.0010.0010.0000.0000.0000.000
141A254TYR00.018-0.01818.8900.0270.0270.0000.0000.0000.000
142A255GLY00.0140.03421.2330.0230.0230.0000.0000.0000.000
143A256ALA0-0.061-0.04522.6450.0230.0230.0000.0000.0000.000
144A257TYR00.0630.01520.5920.0210.0210.0000.0000.0000.000
145A258PHE00.0260.02026.5530.0110.0110.0000.0000.0000.000
146A259GLU-1-0.727-0.84730.086-0.121-0.1210.0000.0000.0000.000
147A260ARG10.7910.91324.7810.1600.1600.0000.0000.0000.000
148A261LEU0-0.0190.00730.5010.0040.0040.0000.0000.0000.000
149A262TYR00.008-0.02724.459-0.004-0.0040.0000.0000.0000.000
150A263VAL0-0.035-0.00630.3040.0040.0040.0000.0000.0000.000
151A264ILE00.0110.01826.266-0.001-0.0010.0000.0000.0000.000
152A265GLN00.024-0.01429.0460.0020.0020.0000.0000.0000.000
153A266SER00.0240.00629.1080.0000.0000.0000.0000.0000.000
154A267GLY00.0190.02225.4210.0080.0080.0000.0000.0000.000
155A268THR0-0.033-0.00224.135-0.003-0.0030.0000.0000.0000.000
156A269ILE0-0.031-0.01322.852-0.005-0.0050.0000.0000.0000.000
157A270MET0-0.045-0.02426.7630.0080.0080.0000.0000.0000.000
158A271TYR0-0.026-0.04730.0510.0030.0030.0000.0000.0000.000
159A272GLN0-0.050-0.05523.8860.0010.0010.0000.0000.0000.000
160A273GLY00.0200.02329.1120.0040.0040.0000.0000.0000.000
161A274GLY00.0340.03129.821-0.012-0.0120.0000.0000.0000.000
162A275ARG10.7900.89027.2460.1630.1630.0000.0000.0000.000
163A276GLY00.0380.00631.6640.0050.0050.0000.0000.0000.000
164A277PRO0-0.0180.00835.205-0.005-0.0050.0000.0000.0000.000
165A278ASP-1-0.870-0.94637.442-0.107-0.1070.0000.0000.0000.000
166A279GLY00.013-0.00138.6480.0060.0060.0000.0000.0000.000
167A280TYR0-0.0030.00437.8570.0030.0030.0000.0000.0000.000
168A281GLN00.0670.04132.4450.0030.0030.0000.0000.0000.000
169A282VAL0-0.008-0.00536.3390.0030.0030.0000.0000.0000.000
170A283SER0-0.097-0.06139.0850.0060.0060.0000.0000.0000.000
171A284GLU-1-0.785-0.86734.862-0.082-0.0820.0000.0000.0000.000
172A285LEU00.0430.02435.1010.0040.0040.0000.0000.0000.000
173A286ARG10.8890.95737.3440.0610.0610.0000.0000.0000.000
174A287THR00.009-0.00739.8020.0050.0050.0000.0000.0000.000
175A288TRP0-0.011-0.00433.8420.0040.0040.0000.0000.0000.000
176A289LEU0-0.005-0.00937.9230.0040.0040.0000.0000.0000.000
177A290GLU-1-0.853-0.93440.243-0.039-0.0390.0000.0000.0000.000
178A291ARG10.8400.91140.6480.0300.0300.0000.0000.0000.000
179A292TYR00.0720.04137.4900.0040.0040.0000.0000.0000.000
180A293ASP-1-0.791-0.88340.794-0.028-0.0280.0000.0000.0000.000
181A294GLU-1-0.800-0.86443.994-0.021-0.0210.0000.0000.0000.000
182A295GLN0-0.053-0.03539.4210.0000.0000.0000.0000.0000.000
183A296LEU0-0.0150.01241.0350.0030.0030.0000.0000.0000.000
184A297HIS10.6690.82344.8000.0250.0250.0000.0000.0000.000
185A298GLY00.0400.04048.1300.0010.0010.0000.0000.0000.000
186A299THR0-0.034-0.05049.600-0.001-0.0010.0000.0000.0000.000
187A300ARG10.7490.84146.6710.0340.0340.0000.0000.0000.000
188A301PRO0-0.0010.01152.028-0.001-0.0010.0000.0000.0000.000