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: 723LK

Calculation Name: 4V0P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4V0P

Chain ID: A

ChEMBL ID:

UniProt ID: P43357

Base Structure: X-ray

Registration Date: 2023-06-21

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2266491.95145
FMO2-HF: Nuclear repulsion 2183839.475252
FMO2-HF: Total energy -82652.476198
FMO2-MP2: Total energy -82893.755497


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:102:SER)


Summations of interaction energy for fragment #1(A:102: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.
-16.165-9.9364.334-4.72-5.842-0.014
Interaction energy analysis for fragmet #1(A:102:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.006
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].
3A104GLU-1-0.824-0.9222.405-8.510-4.2941.134-2.368-2.981-0.021
4A105PHE0-0.044-0.0172.078-0.474-0.0113.177-1.638-2.0020.004
5A106GLN00.010-0.0083.558-3.926-2.3760.023-0.714-0.8590.003
6A107ALA00.0320.0345.492-0.328-0.3280.0000.0000.0000.000
7A108ALA0-0.002-0.0017.165-0.168-0.1680.0000.0000.0000.000
8A109LEU0-0.023-0.0137.580-0.259-0.2590.0000.0000.0000.000
9A110SER0-0.021-0.0299.252-0.275-0.2750.0000.0000.0000.000
10A111ARG10.9260.97611.308-0.548-0.5480.0000.0000.0000.000
11A112LYS10.8690.92412.441-0.828-0.8280.0000.0000.0000.000
12A113VAL0-0.0020.00813.171-0.074-0.0740.0000.0000.0000.000
13A114ALA00.0060.00815.555-0.070-0.0700.0000.0000.0000.000
14A115GLU-1-0.846-0.92816.3230.4810.4810.0000.0000.0000.000
15A116LEU00.0140.01918.334-0.038-0.0380.0000.0000.0000.000
16A117VAL00.007-0.00119.440-0.037-0.0370.0000.0000.0000.000
17A118HIS0-0.004-0.01621.214-0.050-0.0500.0000.0000.0000.000
18A119PHE0-0.0150.00322.858-0.023-0.0230.0000.0000.0000.000
19A120LEU0-0.005-0.02323.096-0.022-0.0220.0000.0000.0000.000
20A121LEU00.0010.00825.286-0.020-0.0200.0000.0000.0000.000
21A122LEU0-0.0060.00127.587-0.017-0.0170.0000.0000.0000.000
22A123LYS10.9220.97628.819-0.200-0.2000.0000.0000.0000.000
23A124TYR0-0.067-0.04430.025-0.010-0.0100.0000.0000.0000.000
24A125ARG10.8840.93430.494-0.145-0.1450.0000.0000.0000.000
25A126ALA0-0.0100.01633.586-0.009-0.0090.0000.0000.0000.000
26A127ARG10.8960.95034.950-0.114-0.1140.0000.0000.0000.000
27A128GLU-1-0.929-0.96233.4640.1460.1460.0000.0000.0000.000
28A129PRO0-0.033-0.02433.0930.0090.0090.0000.0000.0000.000
29A130VAL00.0260.02127.8140.0050.0050.0000.0000.0000.000
30A131THR00.0350.01629.8420.0070.0070.0000.0000.0000.000
31A132LYS10.9890.98323.366-0.282-0.2820.0000.0000.0000.000
32A133ALA0-0.030-0.01525.0510.0260.0260.0000.0000.0000.000
33A134GLU-1-0.842-0.92626.1380.2080.2080.0000.0000.0000.000
34A135MET0-0.0390.00022.8310.0250.0250.0000.0000.0000.000
35A136LEU0-0.033-0.00320.0730.0330.0330.0000.0000.0000.000
36A137GLY0-0.001-0.00221.5120.0270.0270.0000.0000.0000.000
37A138SER0-0.075-0.03822.0870.0080.0080.0000.0000.0000.000
38A139VAL0-0.0190.00116.3990.0330.0330.0000.0000.0000.000
39A140VAL00.0420.01217.769-0.010-0.0100.0000.0000.0000.000
40A141GLY00.016-0.00216.4760.0780.0780.0000.0000.0000.000
41A142ASN00.040-0.00313.329-0.067-0.0670.0000.0000.0000.000
42A143TRP00.0100.0097.5900.0330.0330.0000.0000.0000.000
43A144GLN0-0.0020.01113.6880.0060.0060.0000.0000.0000.000
44A145TYR0-0.0200.00113.102-0.047-0.0470.0000.0000.0000.000
45A146PHE0-0.020-0.0178.9130.0500.0500.0000.0000.0000.000
46A147PHE00.0490.01713.484-0.005-0.0050.0000.0000.0000.000
47A148PRO00.0150.00816.151-0.027-0.0270.0000.0000.0000.000
48A149VAL00.0250.00811.618-0.042-0.0420.0000.0000.0000.000
49A150ILE00.0070.00013.043-0.019-0.0190.0000.0000.0000.000
50A151PHE0-0.0010.00315.398-0.052-0.0520.0000.0000.0000.000
51A152SER0-0.0010.00117.230-0.029-0.0290.0000.0000.0000.000
52A153LYS10.9810.98510.930-0.907-0.9070.0000.0000.0000.000
53A154ALA00.0230.01217.219-0.041-0.0410.0000.0000.0000.000
54A155SER0-0.023-0.01719.489-0.045-0.0450.0000.0000.0000.000
55A156SER00.0320.01119.530-0.033-0.0330.0000.0000.0000.000
56A157SER0-0.019-0.01118.810-0.028-0.0280.0000.0000.0000.000
57A158LEU0-0.035-0.00721.393-0.025-0.0250.0000.0000.0000.000
58A159GLN0-0.036-0.03224.761-0.012-0.0120.0000.0000.0000.000
59A160LEU0-0.023-0.01221.326-0.017-0.0170.0000.0000.0000.000
60A161VAL0-0.008-0.00121.855-0.016-0.0160.0000.0000.0000.000
61A162PHE00.007-0.01823.090-0.013-0.0130.0000.0000.0000.000
62A163GLY00.0290.02527.813-0.011-0.0110.0000.0000.0000.000
63A164ILE0-0.063-0.03328.242-0.008-0.0080.0000.0000.0000.000
64A165GLU-1-0.830-0.92328.1330.1670.1670.0000.0000.0000.000
65A166LEU0-0.0120.00025.327-0.003-0.0030.0000.0000.0000.000
66A167MET0-0.027-0.02328.9780.0010.0010.0000.0000.0000.000
67A168GLU-1-0.858-0.93430.1740.1880.1880.0000.0000.0000.000
68A169VAL0-0.020-0.01531.952-0.009-0.0090.0000.0000.0000.000
69A170ASP-1-0.857-0.93934.3260.1310.1310.0000.0000.0000.000
70A171PRO00.0000.00832.7850.0110.0110.0000.0000.0000.000
71A172ILE0-0.055-0.02632.7790.0080.0080.0000.0000.0000.000
72A173GLY0-0.0030.00633.3150.0080.0080.0000.0000.0000.000
73A174HIS10.7750.89428.876-0.184-0.1840.0000.0000.0000.000
74A175LEU00.0490.02330.2180.0140.0140.0000.0000.0000.000
75A176TYR0-0.006-0.01527.0880.0030.0030.0000.0000.0000.000
76A177ILE00.0180.01031.434-0.004-0.0040.0000.0000.0000.000
77A178PHE00.020-0.00527.9040.0100.0100.0000.0000.0000.000
78A179ALA0-0.019-0.00532.536-0.011-0.0110.0000.0000.0000.000
79A180THR00.0450.04132.7730.0120.0120.0000.0000.0000.000
80A181CYS0-0.053-0.01130.242-0.001-0.0010.0000.0000.0000.000
81A182LEU0-0.059-0.04233.053-0.007-0.0070.0000.0000.0000.000
82A183GLY0-0.0180.00335.944-0.006-0.0060.0000.0000.0000.000
83A184LEU0-0.0260.00536.241-0.004-0.0040.0000.0000.0000.000
84A185SER0-0.085-0.06338.8410.0050.0050.0000.0000.0000.000
85A186TYR00.0280.00436.793-0.002-0.0020.0000.0000.0000.000
86A187ASP-1-0.779-0.89034.4680.1060.1060.0000.0000.0000.000
87A188GLY00.0070.01334.8980.0040.0040.0000.0000.0000.000
88A189LEU0-0.040-0.01132.9220.0010.0010.0000.0000.0000.000
89A190LEU00.0390.01236.860-0.006-0.0060.0000.0000.0000.000
90A191GLY00.0040.00738.7710.0000.0000.0000.0000.0000.000
91A192ASP-1-0.907-0.96135.5950.1210.1210.0000.0000.0000.000
92A193ASN0-0.064-0.02835.4950.0040.0040.0000.0000.0000.000
93A194GLN0-0.024-0.00730.3010.0130.0130.0000.0000.0000.000
94A195ILE0-0.028-0.01031.424-0.001-0.0010.0000.0000.0000.000
95A196MET0-0.003-0.00926.8290.0060.0060.0000.0000.0000.000
96A197PRO0-0.009-0.00128.932-0.008-0.0080.0000.0000.0000.000
97A198LYS10.9190.95530.617-0.079-0.0790.0000.0000.0000.000
98A199ALA00.0380.02232.891-0.005-0.0050.0000.0000.0000.000
99A200GLY00.0340.02129.188-0.004-0.0040.0000.0000.0000.000
100A201LEU00.0220.00528.288-0.005-0.0050.0000.0000.0000.000
101A202LEU0-0.0200.00631.105-0.007-0.0070.0000.0000.0000.000
102A203ILE00.002-0.01231.746-0.006-0.0060.0000.0000.0000.000
103A204ILE00.0050.00627.105-0.005-0.0050.0000.0000.0000.000
104A205VAL00.0170.00831.479-0.007-0.0070.0000.0000.0000.000
105A206LEU0-0.009-0.00534.650-0.005-0.0050.0000.0000.0000.000
106A207ALA0-0.002-0.01432.384-0.004-0.0040.0000.0000.0000.000
107A208ILE0-0.041-0.01431.791-0.004-0.0040.0000.0000.0000.000
108A209ILE00.0110.01234.707-0.004-0.0040.0000.0000.0000.000
109A210ALA0-0.020-0.00536.764-0.003-0.0030.0000.0000.0000.000
110A211ARG10.8710.92729.899-0.051-0.0510.0000.0000.0000.000
111A212GLU-1-0.908-0.94836.5090.0080.0080.0000.0000.0000.000
112A213GLY0-0.0210.01339.381-0.003-0.0030.0000.0000.0000.000
113A214ASP-1-0.936-0.97142.3420.0260.0260.0000.0000.0000.000
114A215CYS0-0.128-0.06843.3570.0020.0020.0000.0000.0000.000
115A216ALA00.0240.02039.348-0.002-0.0020.0000.0000.0000.000
116A217PRO00.0480.03440.4850.0020.0020.0000.0000.0000.000
117A218GLU-1-0.810-0.91640.0250.0140.0140.0000.0000.0000.000
118A219GLU-1-0.907-0.96938.6850.0050.0050.0000.0000.0000.000
119A220LYS10.9460.98833.523-0.006-0.0060.0000.0000.0000.000
120A221ILE0-0.018-0.00534.7820.0030.0030.0000.0000.0000.000
121A222TRP0-0.041-0.03834.0180.0050.0050.0000.0000.0000.000
122A223GLU-1-0.927-0.95932.256-0.008-0.0080.0000.0000.0000.000
123A224GLU-1-0.931-0.97230.0060.0170.0170.0000.0000.0000.000
124A225LEU0-0.042-0.02729.1270.0070.0070.0000.0000.0000.000
125A226SER0-0.121-0.05529.1190.0040.0040.0000.0000.0000.000
126A227VAL00.0530.03224.349-0.004-0.0040.0000.0000.0000.000
127A228LEU0-0.071-0.03224.4000.0080.0080.0000.0000.0000.000
128A229GLU-1-0.894-0.96719.2970.0700.0700.0000.0000.0000.000
129A230VAL0-0.062-0.02323.6040.0020.0020.0000.0000.0000.000
130A231PHE0-0.006-0.00925.7720.0010.0010.0000.0000.0000.000
131A232GLU-1-1.003-1.00425.1710.0640.0640.0000.0000.0000.000
132A233GLY00.0140.02126.228-0.007-0.0070.0000.0000.0000.000
133A234ARG10.9400.97827.635-0.050-0.0500.0000.0000.0000.000
134A235GLU-1-0.894-0.96131.1760.0080.0080.0000.0000.0000.000
135A236ASP-1-0.996-0.97933.921-0.001-0.0010.0000.0000.0000.000
136A237SER0-0.038-0.02734.6930.0010.0010.0000.0000.0000.000
137A238ILE0-0.013-0.01937.0610.0000.0000.0000.0000.0000.000
138A239LEU0-0.061-0.02939.4770.0000.0000.0000.0000.0000.000
139A240GLY00.0390.02139.8000.0010.0010.0000.0000.0000.000
140A241ASP-1-0.765-0.88634.8690.0210.0210.0000.0000.0000.000
141A242PRO00.0500.03133.1050.0030.0030.0000.0000.0000.000
142A243LYS10.8640.92932.413-0.011-0.0110.0000.0000.0000.000
143A244LYS10.9260.96934.436-0.009-0.0090.0000.0000.0000.000
144A245LEU00.0150.01638.1350.0010.0010.0000.0000.0000.000
145A246LEU0-0.0280.00332.9150.0030.0030.0000.0000.0000.000
146A247THR0-0.029-0.02836.6940.0010.0010.0000.0000.0000.000
147A248GLN00.0240.00238.6500.0000.0000.0000.0000.0000.000
148A249HIS0-0.014-0.00338.8880.0030.0030.0000.0000.0000.000
149A250PHE00.0130.00134.5360.0020.0020.0000.0000.0000.000
150A251VAL0-0.0010.00440.6170.0000.0000.0000.0000.0000.000
151A252GLN0-0.053-0.02643.9490.0010.0010.0000.0000.0000.000
152A253GLU-1-0.897-0.93241.6360.0590.0590.0000.0000.0000.000
153A254ASN0-0.037-0.02844.5410.0030.0030.0000.0000.0000.000
154A255TYR0-0.047-0.05040.6750.0000.0000.0000.0000.0000.000
155A256LEU0-0.042-0.01838.8870.0000.0000.0000.0000.0000.000
156A257GLU-1-0.913-0.96343.2050.0280.0280.0000.0000.0000.000
157A258TYR0-0.072-0.04943.4480.0000.0000.0000.0000.0000.000
158A259ARG10.8500.92146.462-0.018-0.0180.0000.0000.0000.000
159A260GLN0-0.015-0.00448.2850.0000.0000.0000.0000.0000.000
160A261VAL0-0.020-0.00947.3990.0010.0010.0000.0000.0000.000
161A262PRO00.008-0.00350.285-0.002-0.0020.0000.0000.0000.000
162A263GLY0-0.017-0.00753.840-0.001-0.0010.0000.0000.0000.000
163A264SER0-0.059-0.02351.370-0.001-0.0010.0000.0000.0000.000
164A265ASP-1-0.912-0.95253.3210.0000.0000.0000.0000.0000.000
165A266PRO0-0.003-0.01351.315-0.001-0.0010.0000.0000.0000.000
166A267ALA0-0.032-0.01151.7570.0000.0000.0000.0000.0000.000
167A268CYS0-0.0040.00646.973-0.001-0.0010.0000.0000.0000.000
168A269TYR00.0180.01345.6360.0010.0010.0000.0000.0000.000
169A270GLU-1-0.765-0.87143.8970.0130.0130.0000.0000.0000.000
170A271PHE0-0.004-0.01340.5540.0020.0020.0000.0000.0000.000
171A272LEU00.0180.00343.089-0.001-0.0010.0000.0000.0000.000
172A273TRP0-0.028-0.02138.3110.0040.0040.0000.0000.0000.000
173A274GLY00.0440.03343.601-0.002-0.0020.0000.0000.0000.000
174A275PRO00.019-0.01345.7970.0020.0020.0000.0000.0000.000
175A276ARG10.8450.92643.314-0.059-0.0590.0000.0000.0000.000
176A277ALA00.0080.00141.5080.0030.0030.0000.0000.0000.000
177A278LEU0-0.029-0.02142.8630.0020.0020.0000.0000.0000.000
178A279VAL0-0.048-0.00245.3520.0000.0000.0000.0000.0000.000
179A280GLU-1-0.755-0.84341.7110.0690.0690.0000.0000.0000.000
180A281THR0-0.013-0.00438.1060.0040.0040.0000.0000.0000.000
181A282SER0-0.016-0.01540.123-0.005-0.0050.0000.0000.0000.000
182A283TYR00.0860.01239.3250.0060.0060.0000.0000.0000.000
183A284VAL0-0.0010.00337.8830.0030.0030.0000.0000.0000.000
184A285LYS10.9250.95836.808-0.060-0.0600.0000.0000.0000.000
185A286VAL00.0570.04534.1610.0070.0070.0000.0000.0000.000
186A287LEU00.0090.00033.1330.0070.0070.0000.0000.0000.000
187A288HIS0-0.034-0.00932.1450.0050.0050.0000.0000.0000.000
188A289HIS00.0200.00429.7470.0050.0050.0000.0000.0000.000
189A290MET0-0.002-0.00427.7920.0120.0120.0000.0000.0000.000
190A291VAL0-0.0020.01427.0970.0070.0070.0000.0000.0000.000
191A292LYS10.9000.95626.446-0.123-0.1230.0000.0000.0000.000
192A293ILE0-0.020-0.01925.1430.0140.0140.0000.0000.0000.000
193A294SER0-0.061-0.01222.6920.0140.0140.0000.0000.0000.000
194A295GLY0-0.011-0.00221.4740.0090.0090.0000.0000.0000.000
195A296GLY0-0.025-0.00822.555-0.007-0.0070.0000.0000.0000.000
196A297PRO0-0.015-0.00824.473-0.001-0.0010.0000.0000.0000.000
197A298HIS00.005-0.00219.508-0.014-0.0140.0000.0000.0000.000
198A299ILE0-0.019-0.01423.253-0.013-0.0130.0000.0000.0000.000
199A300SER00.0020.00622.564-0.001-0.0010.0000.0000.0000.000
200A301TYR0-0.031-0.02123.830-0.001-0.0010.0000.0000.0000.000
201A302PRO00.0500.04225.068-0.011-0.0110.0000.0000.0000.000
202A303PRO00.0420.01724.9560.0020.0020.0000.0000.0000.000
203A304LEU00.0570.01126.7360.0040.0040.0000.0000.0000.000
204A305HIS0-0.044-0.02726.0240.0100.0100.0000.0000.0000.000
205A306GLU-1-0.929-0.96828.393-0.080-0.0800.0000.0000.0000.000
206A307TRP0-0.053-0.02029.7030.0080.0080.0000.0000.0000.000
207A308VAL0-0.0310.00433.2450.0050.0050.0000.0000.0000.000
208A309LEU00.0260.01535.011-0.007-0.0070.0000.0000.0000.000
209A310ARG10.8950.94832.8000.0810.0810.0000.0000.0000.000