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: 2J76R

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2267996.884829
FMO2-HF: Nuclear repulsion 2185343.752859
FMO2-HF: Total energy -82653.13197
FMO2-MP2: Total energy -82894.519297


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.
-19.364-16.37210.272-6.386-6.88-0.036
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 : 0.006 / 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].
3A104GLU-1-0.815-0.9221.917-12.054-11.1377.441-4.197-4.162-0.043
4A105PHE0-0.022-0.0102.114-0.719-0.0072.819-1.561-1.9700.005
5A106GLN00.012-0.0073.717-3.308-1.9450.012-0.628-0.7480.002
6A107ALA00.0250.0375.508-0.288-0.2880.0000.0000.0000.000
7A108ALA0-0.0020.0007.162-0.142-0.1420.0000.0000.0000.000
8A109LEU0-0.024-0.0147.585-0.249-0.2490.0000.0000.0000.000
9A110SER0-0.024-0.0379.259-0.257-0.2570.0000.0000.0000.000
10A111ARG10.8760.93211.312-0.520-0.5200.0000.0000.0000.000
11A112LYS10.8360.89512.444-0.772-0.7720.0000.0000.0000.000
12A113VAL0-0.0020.00713.237-0.070-0.0700.0000.0000.0000.000
13A114ALA00.0180.01715.566-0.071-0.0710.0000.0000.0000.000
14A115GLU-1-0.767-0.84916.7890.4660.4660.0000.0000.0000.000
15A116LEU00.0170.02018.342-0.038-0.0380.0000.0000.0000.000
16A117VAL00.0100.00119.511-0.036-0.0360.0000.0000.0000.000
17A118HIS0-0.023-0.03121.064-0.052-0.0520.0000.0000.0000.000
18A119PHE0-0.0190.00122.864-0.022-0.0220.0000.0000.0000.000
19A120LEU0-0.004-0.01723.001-0.021-0.0210.0000.0000.0000.000
20A121LEU00.0070.00725.017-0.020-0.0200.0000.0000.0000.000
21A122LEU0-0.0100.00127.227-0.017-0.0170.0000.0000.0000.000
22A123LYS10.8360.92228.939-0.197-0.1970.0000.0000.0000.000
23A124TYR0-0.079-0.06330.038-0.009-0.0090.0000.0000.0000.000
24A125ARG10.8560.93030.593-0.141-0.1410.0000.0000.0000.000
25A126ALA0-0.0230.00433.595-0.010-0.0100.0000.0000.0000.000
26A127ARG10.8940.94734.966-0.117-0.1170.0000.0000.0000.000
27A128GLU-1-0.885-0.92733.4680.1530.1530.0000.0000.0000.000
28A129PRO0-0.029-0.02333.1030.0090.0090.0000.0000.0000.000
29A130VAL0-0.0040.00427.8660.0040.0040.0000.0000.0000.000
30A131THR00.022-0.01729.8500.0080.0080.0000.0000.0000.000
31A132LYS10.9880.98123.156-0.314-0.3140.0000.0000.0000.000
32A133ALA0-0.026-0.01425.0580.0280.0280.0000.0000.0000.000
33A134GLU-1-0.758-0.85126.1410.2140.2140.0000.0000.0000.000
34A135MET0-0.0460.00022.8000.0250.0250.0000.0000.0000.000
35A136LEU0-0.031-0.00920.0820.0330.0330.0000.0000.0000.000
36A137GLY00.0070.00221.5130.0260.0260.0000.0000.0000.000
37A138SER0-0.073-0.03422.0860.0060.0060.0000.0000.0000.000
38A139VAL0-0.024-0.00316.3440.0300.0300.0000.0000.0000.000
39A140VAL00.0390.01417.825-0.011-0.0110.0000.0000.0000.000
40A141GLY00.0220.00016.4690.0780.0780.0000.0000.0000.000
41A142ASN00.039-0.00213.379-0.071-0.0710.0000.0000.0000.000
42A143TRP00.0120.0087.6310.0560.0560.0000.0000.0000.000
43A144GLN0-0.0080.00713.6850.0150.0150.0000.0000.0000.000
44A145TYR0-0.028-0.00312.790-0.041-0.0410.0000.0000.0000.000
45A146PHE0-0.014-0.0179.2040.0610.0610.0000.0000.0000.000
46A147PHE00.0430.01613.492-0.003-0.0030.0000.0000.0000.000
47A148PRO00.0200.01216.060-0.032-0.0320.0000.0000.0000.000
48A149VAL00.0300.01811.636-0.039-0.0390.0000.0000.0000.000
49A150ILE0-0.003-0.00412.834-0.023-0.0230.0000.0000.0000.000
50A151PHE00.0120.00815.412-0.057-0.0570.0000.0000.0000.000
51A152SER00.0220.00517.553-0.025-0.0250.0000.0000.0000.000
52A153LYS10.9780.99510.419-1.109-1.1090.0000.0000.0000.000
53A154ALA00.0250.02117.261-0.047-0.0470.0000.0000.0000.000
54A155SER00.015-0.00419.506-0.046-0.0460.0000.0000.0000.000
55A156SER0-0.027-0.02319.610-0.037-0.0370.0000.0000.0000.000
56A157SER0-0.031-0.02418.996-0.027-0.0270.0000.0000.0000.000
57A158LEU0-0.027-0.00621.486-0.028-0.0280.0000.0000.0000.000
58A159GLN0-0.034-0.02224.821-0.015-0.0150.0000.0000.0000.000
59A160LEU0-0.016-0.01021.434-0.019-0.0190.0000.0000.0000.000
60A161VAL0-0.007-0.00321.938-0.017-0.0170.0000.0000.0000.000
61A162PHE00.011-0.01723.132-0.014-0.0140.0000.0000.0000.000
62A163GLY00.0310.02827.848-0.012-0.0120.0000.0000.0000.000
63A164ILE0-0.067-0.03528.297-0.008-0.0080.0000.0000.0000.000
64A165GLU-1-0.769-0.89028.1830.1800.1800.0000.0000.0000.000
65A166LEU0-0.0110.00025.380-0.004-0.0040.0000.0000.0000.000
66A167MET0-0.020-0.01828.9960.0020.0020.0000.0000.0000.000
67A168GLU-1-0.790-0.86329.7310.2120.2120.0000.0000.0000.000
68A169VAL0-0.009-0.01131.968-0.009-0.0090.0000.0000.0000.000
69A170ASP-1-0.834-0.91234.3450.1440.1440.0000.0000.0000.000
70A171PRO0-0.0070.00032.7980.0110.0110.0000.0000.0000.000
71A172ILE0-0.059-0.03132.7920.0090.0090.0000.0000.0000.000
72A173GLY00.001-0.00233.3250.0080.0080.0000.0000.0000.000
73A174HIS10.7270.85728.876-0.198-0.1980.0000.0000.0000.000
74A175LEU00.0630.03030.2290.0140.0140.0000.0000.0000.000
75A176TYR0-0.059-0.06427.3960.0070.0070.0000.0000.0000.000
76A177ILE00.0120.00431.448-0.005-0.0050.0000.0000.0000.000
77A178PHE00.031-0.00127.8620.0110.0110.0000.0000.0000.000
78A179ALA0-0.018-0.00332.553-0.011-0.0110.0000.0000.0000.000
79A180THR00.0420.03732.7910.0120.0120.0000.0000.0000.000
80A181CYS0-0.065-0.02430.3510.0000.0000.0000.0000.0000.000
81A182LEU0-0.069-0.04433.133-0.008-0.0080.0000.0000.0000.000
82A183GLY0-0.0230.00236.023-0.006-0.0060.0000.0000.0000.000
83A184LEU0-0.0170.00936.413-0.005-0.0050.0000.0000.0000.000
84A185SER0-0.088-0.06038.9300.0050.0050.0000.0000.0000.000
85A186TYR00.0230.00836.928-0.001-0.0010.0000.0000.0000.000
86A187ASP-1-0.768-0.87334.4850.1090.1090.0000.0000.0000.000
87A188GLY00.0230.01934.9140.0040.0040.0000.0000.0000.000
88A189LEU0-0.0310.00532.867-0.001-0.0010.0000.0000.0000.000
89A190LEU00.0330.00936.873-0.006-0.0060.0000.0000.0000.000
90A191GLY00.0090.01038.7800.0000.0000.0000.0000.0000.000
91A192ASP-1-0.878-0.95435.2910.1200.1200.0000.0000.0000.000
92A193ASN0-0.061-0.02435.5010.0030.0030.0000.0000.0000.000
93A194GLN0-0.017-0.00630.5160.0130.0130.0000.0000.0000.000
94A195ILE0-0.030-0.01231.432-0.001-0.0010.0000.0000.0000.000
95A196MET00.0130.00427.1460.0060.0060.0000.0000.0000.000
96A197PRO00.0060.00228.959-0.009-0.0090.0000.0000.0000.000
97A198LYS10.8760.92330.633-0.082-0.0820.0000.0000.0000.000
98A199ALA00.0420.02432.952-0.005-0.0050.0000.0000.0000.000
99A200GLY00.0290.01829.314-0.003-0.0030.0000.0000.0000.000
100A201LEU00.0210.00328.149-0.005-0.0050.0000.0000.0000.000
101A202LEU0-0.0210.00731.253-0.007-0.0070.0000.0000.0000.000
102A203ILE0-0.009-0.01731.917-0.006-0.0060.0000.0000.0000.000
103A204ILE00.0010.00527.268-0.005-0.0050.0000.0000.0000.000
104A205VAL00.0170.00931.622-0.007-0.0070.0000.0000.0000.000
105A206LEU0-0.004-0.00134.805-0.005-0.0050.0000.0000.0000.000
106A207ALA0-0.003-0.01432.509-0.004-0.0040.0000.0000.0000.000
107A208ILE0-0.045-0.02031.655-0.003-0.0030.0000.0000.0000.000
108A209ILE00.0150.01434.860-0.004-0.0040.0000.0000.0000.000
109A210ALA0-0.020-0.00736.940-0.003-0.0030.0000.0000.0000.000
110A211ARG10.8770.93330.062-0.059-0.0590.0000.0000.0000.000
111A212GLU-1-0.930-0.96136.7200.0130.0130.0000.0000.0000.000
112A213GLY0-0.0120.01939.574-0.003-0.0030.0000.0000.0000.000
113A214ASP-1-0.929-0.95942.4930.0300.0300.0000.0000.0000.000
114A215CYS0-0.130-0.07743.5320.0020.0020.0000.0000.0000.000
115A216ALA00.0350.02639.493-0.001-0.0010.0000.0000.0000.000
116A217PRO00.0480.03440.6940.0010.0010.0000.0000.0000.000
117A218GLU-1-0.730-0.84940.2070.0140.0140.0000.0000.0000.000
118A219GLU-1-0.902-0.96638.8770.0060.0060.0000.0000.0000.000
119A220LYS10.8220.90332.932-0.011-0.0110.0000.0000.0000.000
120A221ILE0-0.015-0.00834.9670.0030.0030.0000.0000.0000.000
121A222TRP0-0.033-0.05934.2050.0050.0050.0000.0000.0000.000
122A223GLU-1-0.890-0.92732.403-0.003-0.0030.0000.0000.0000.000
123A224GLU-1-0.874-0.92530.4630.0250.0250.0000.0000.0000.000
124A225LEU0-0.038-0.02429.3130.0070.0070.0000.0000.0000.000
125A226SER0-0.079-0.04129.3130.0030.0030.0000.0000.0000.000
126A227VAL00.0040.01424.590-0.006-0.0060.0000.0000.0000.000
127A228LEU0-0.064-0.02824.6010.0070.0070.0000.0000.0000.000
128A229GLU-1-0.893-0.96419.3790.0620.0620.0000.0000.0000.000
129A230VAL0-0.064-0.02723.7950.0000.0000.0000.0000.0000.000
130A231PHE00.003-0.00925.8040.0020.0020.0000.0000.0000.000
131A232GLU-1-0.893-0.93425.0350.0390.0390.0000.0000.0000.000
132A233GLY00.0130.02226.254-0.008-0.0080.0000.0000.0000.000
133A234ARG10.8320.91427.311-0.040-0.0400.0000.0000.0000.000
134A235GLU-1-0.833-0.92830.9790.0100.0100.0000.0000.0000.000
135A236ASP-1-0.974-0.97033.991-0.010-0.0100.0000.0000.0000.000
136A237SER0-0.048-0.02934.7230.0010.0010.0000.0000.0000.000
137A238ILE0-0.013-0.02037.0840.0000.0000.0000.0000.0000.000
138A239LEU0-0.061-0.02739.3770.0000.0000.0000.0000.0000.000
139A240GLY00.0400.02139.8180.0010.0010.0000.0000.0000.000
140A241ASP-1-0.783-0.89835.1130.0180.0180.0000.0000.0000.000
141A242PRO00.0470.02233.1530.0040.0040.0000.0000.0000.000
142A243LYS10.8080.90232.284-0.007-0.0070.0000.0000.0000.000
143A244LYS10.8750.94934.628-0.008-0.0080.0000.0000.0000.000
144A245LEU00.0040.00638.2130.0020.0020.0000.0000.0000.000
145A246LEU0-0.0360.00233.0830.0040.0040.0000.0000.0000.000
146A247THR0-0.013-0.01636.8610.0020.0020.0000.0000.0000.000
147A248GLN00.0120.00038.8230.0010.0010.0000.0000.0000.000
148A249HIS0-0.033-0.01938.9700.0030.0030.0000.0000.0000.000
149A250PHE00.0430.00934.5620.0010.0010.0000.0000.0000.000
150A251VAL0-0.0040.00440.7700.0000.0000.0000.0000.0000.000
151A252GLN0-0.049-0.02244.1090.0010.0010.0000.0000.0000.000
152A253GLU-1-0.883-0.92241.7620.0620.0620.0000.0000.0000.000
153A254ASN0-0.053-0.03344.6830.0020.0020.0000.0000.0000.000
154A255TYR0-0.034-0.05840.8180.0000.0000.0000.0000.0000.000
155A256LEU0-0.040-0.01638.8830.0000.0000.0000.0000.0000.000
156A257GLU-1-0.906-0.96343.3570.0300.0300.0000.0000.0000.000
157A258TYR0-0.093-0.06344.0310.0000.0000.0000.0000.0000.000
158A259ARG10.8490.90846.634-0.021-0.0210.0000.0000.0000.000
159A260GLN0-0.015-0.00548.4650.0000.0000.0000.0000.0000.000
160A261VAL0-0.012-0.00447.5830.0010.0010.0000.0000.0000.000
161A262PRO00.0190.00950.467-0.002-0.0020.0000.0000.0000.000
162A263GLY0-0.020-0.00754.020-0.001-0.0010.0000.0000.0000.000
163A264SER0-0.058-0.03251.531-0.001-0.0010.0000.0000.0000.000
164A265ASP-1-0.911-0.95353.5120.0000.0000.0000.0000.0000.000
165A266PRO0-0.007-0.01551.517-0.001-0.0010.0000.0000.0000.000
166A267ALA0-0.031-0.00951.9650.0000.0000.0000.0000.0000.000
167A268CYS0-0.019-0.00147.249-0.001-0.0010.0000.0000.0000.000
168A269TYR00.0200.00645.9140.0010.0010.0000.0000.0000.000
169A270GLU-1-0.762-0.85344.0780.0160.0160.0000.0000.0000.000
170A271PHE00.002-0.01140.9510.0020.0020.0000.0000.0000.000
171A272LEU00.0150.00443.258-0.001-0.0010.0000.0000.0000.000
172A273TRP0-0.013-0.02038.5150.0040.0040.0000.0000.0000.000
173A274GLY00.0380.03343.742-0.003-0.0030.0000.0000.0000.000
174A275PRO00.023-0.01245.9270.0020.0020.0000.0000.0000.000
175A276ARG10.8230.90043.503-0.062-0.0620.0000.0000.0000.000
176A277ALA00.004-0.00141.6170.0030.0030.0000.0000.0000.000
177A278LEU0-0.035-0.02142.9730.0030.0030.0000.0000.0000.000
178A279VAL0-0.041-0.00145.4650.0000.0000.0000.0000.0000.000
179A280GLU-1-0.748-0.82241.8180.0730.0730.0000.0000.0000.000
180A281THR0-0.028-0.02038.2060.0050.0050.0000.0000.0000.000
181A282SER00.000-0.00340.222-0.005-0.0050.0000.0000.0000.000
182A283TYR00.0720.00739.4250.0060.0060.0000.0000.0000.000
183A284VAL0-0.007-0.00237.9850.0030.0030.0000.0000.0000.000
184A285LYS10.9330.96836.896-0.068-0.0680.0000.0000.0000.000
185A286VAL00.0510.03634.3400.0080.0080.0000.0000.0000.000
186A287LEU00.0070.00033.2330.0080.0080.0000.0000.0000.000
187A288HIS0-0.030-0.00832.2720.0060.0060.0000.0000.0000.000
188A289HIS00.0140.00029.9200.0080.0080.0000.0000.0000.000
189A290MET00.002-0.00127.6490.0130.0130.0000.0000.0000.000
190A291VAL00.0040.01427.1910.0080.0080.0000.0000.0000.000
191A292LYS10.8350.93226.550-0.141-0.1410.0000.0000.0000.000
192A293ILE0-0.024-0.02425.2010.0160.0160.0000.0000.0000.000
193A294SER0-0.055-0.01322.7810.0140.0140.0000.0000.0000.000
194A295GLY0-0.0120.00421.5580.0120.0120.0000.0000.0000.000
195A296GLY0-0.021-0.00522.639-0.005-0.0050.0000.0000.0000.000
196A297PRO0-0.014-0.00924.573-0.001-0.0010.0000.0000.0000.000
197A298HIS0-0.005-0.01119.407-0.009-0.0090.0000.0000.0000.000
198A299ILE0-0.026-0.01823.358-0.015-0.0150.0000.0000.0000.000
199A300SER00.0030.00622.7500.0010.0010.0000.0000.0000.000
200A301TYR0-0.032-0.01923.935-0.003-0.0030.0000.0000.0000.000
201A302PRO00.0490.04125.150-0.009-0.0090.0000.0000.0000.000
202A303PRO00.0400.02524.9740.0030.0030.0000.0000.0000.000
203A304LEU00.0600.01126.8070.0020.0020.0000.0000.0000.000
204A305HIS0-0.051-0.03026.0530.0060.0060.0000.0000.0000.000
205A306GLU-1-0.913-0.96827.870-0.068-0.0680.0000.0000.0000.000
206A307TRP0-0.063-0.03329.6250.0070.0070.0000.0000.0000.000
207A308VAL0-0.0310.00433.4480.0040.0040.0000.0000.0000.000
208A309LEU00.0290.02235.072-0.007-0.0070.0000.0000.0000.000
209A310ARG10.8970.94832.2410.0660.0660.0000.0000.0000.000