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: 6NL9Z

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2276026.026886
FMO2-HF: Nuclear repulsion 2193372.746273
FMO2-HF: Total energy -82653.280612
FMO2-MP2: Total energy -82894.700203


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.
-25.832-25.12214.469-7.614-7.566-0.038
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 : -0.026
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-1-0.812-0.9141.797-14.723-16.62112.274-5.680-4.697-0.052
4A105PHE0-0.006-0.0042.426-4.674-2.7942.185-1.645-2.4200.013
5A106GLN00.0380.0073.883-2.959-2.2310.010-0.289-0.4490.001
6A107ALA00.0260.0415.831-0.345-0.3450.0000.0000.0000.000
7A108ALA0-0.006-0.0047.342-0.233-0.2330.0000.0000.0000.000
8A109LEU0-0.030-0.0167.852-0.335-0.3350.0000.0000.0000.000
9A110SER0-0.014-0.0299.531-0.268-0.2680.0000.0000.0000.000
10A111ARG10.8520.91511.572-0.594-0.5940.0000.0000.0000.000
11A112LYS10.8430.90012.621-0.847-0.8470.0000.0000.0000.000
12A113VAL0-0.0090.00213.412-0.080-0.0800.0000.0000.0000.000
13A114ALA00.0260.02015.672-0.074-0.0740.0000.0000.0000.000
14A115GLU-1-0.770-0.84116.8370.5020.5020.0000.0000.0000.000
15A116LEU00.0170.01618.360-0.046-0.0460.0000.0000.0000.000
16A117VAL00.0060.00319.574-0.038-0.0380.0000.0000.0000.000
17A118HIS0-0.017-0.02221.142-0.057-0.0570.0000.0000.0000.000
18A119PHE0-0.021-0.00723.016-0.025-0.0250.0000.0000.0000.000
19A120LEU00.001-0.01122.876-0.023-0.0230.0000.0000.0000.000
20A121LEU00.0150.01125.087-0.021-0.0210.0000.0000.0000.000
21A122LEU0-0.018-0.00427.059-0.019-0.0190.0000.0000.0000.000
22A123LYS10.7890.88128.859-0.211-0.2110.0000.0000.0000.000
23A124TYR0-0.078-0.06429.971-0.010-0.0100.0000.0000.0000.000
24A125ARG10.8130.90630.790-0.157-0.1570.0000.0000.0000.000
25A126ALA0-0.025-0.00533.530-0.011-0.0110.0000.0000.0000.000
26A127ARG10.8950.94734.903-0.133-0.1330.0000.0000.0000.000
27A128GLU-1-0.882-0.92033.4030.1660.1660.0000.0000.0000.000
28A129PRO0-0.017-0.01733.0660.0100.0100.0000.0000.0000.000
29A130VAL0-0.0070.00827.7460.0030.0030.0000.0000.0000.000
30A131THR00.014-0.02629.7650.0090.0090.0000.0000.0000.000
31A132LYS10.9900.98023.157-0.332-0.3320.0000.0000.0000.000
32A133ALA0-0.0090.00224.9600.0280.0280.0000.0000.0000.000
33A134GLU-1-0.756-0.84325.9490.2280.2280.0000.0000.0000.000
34A135MET0-0.0340.00122.7900.0280.0280.0000.0000.0000.000
35A136LEU0-0.027-0.00619.9700.0390.0390.0000.0000.0000.000
36A137GLY00.002-0.00121.3600.0290.0290.0000.0000.0000.000
37A138SER0-0.063-0.03321.8580.0090.0090.0000.0000.0000.000
38A139VAL0-0.036-0.00916.1810.0360.0360.0000.0000.0000.000
39A140VAL00.0350.01018.205-0.004-0.0040.0000.0000.0000.000
40A141GLY00.0290.01216.7230.0770.0770.0000.0000.0000.000
41A142ASN00.029-0.01013.381-0.052-0.0520.0000.0000.0000.000
42A143TRP00.0140.0107.8950.0390.0390.0000.0000.0000.000
43A144GLN0-0.0040.00513.7500.0130.0130.0000.0000.0000.000
44A145TYR0-0.035-0.00712.476-0.037-0.0370.0000.0000.0000.000
45A146PHE0-0.001-0.0079.1830.0740.0740.0000.0000.0000.000
46A147PHE00.0390.02113.267-0.002-0.0020.0000.0000.0000.000
47A148PRO00.0110.00015.884-0.025-0.0250.0000.0000.0000.000
48A149VAL00.0180.02211.198-0.032-0.0320.0000.0000.0000.000
49A150ILE0-0.011-0.00413.067-0.011-0.0110.0000.0000.0000.000
50A151PHE00.0290.00615.174-0.055-0.0550.0000.0000.0000.000
51A152SER00.006-0.00617.169-0.024-0.0240.0000.0000.0000.000
52A153LYS10.9740.99810.205-1.211-1.2110.0000.0000.0000.000
53A154ALA00.0310.02517.039-0.049-0.0490.0000.0000.0000.000
54A155SER00.0290.00519.479-0.048-0.0480.0000.0000.0000.000
55A156SER0-0.019-0.02019.699-0.036-0.0360.0000.0000.0000.000
56A157SER0-0.030-0.02718.939-0.026-0.0260.0000.0000.0000.000
57A158LEU0-0.031-0.01221.502-0.029-0.0290.0000.0000.0000.000
58A159GLN0-0.040-0.03124.858-0.011-0.0110.0000.0000.0000.000
59A160LEU0-0.006-0.00322.083-0.020-0.0200.0000.0000.0000.000
60A161VAL0-0.0010.00122.029-0.018-0.0180.0000.0000.0000.000
61A162PHE00.009-0.01223.267-0.016-0.0160.0000.0000.0000.000
62A163GLY00.0340.02327.993-0.016-0.0160.0000.0000.0000.000
63A164ILE0-0.044-0.02728.344-0.011-0.0110.0000.0000.0000.000
64A165GLU-1-0.716-0.85028.0050.2090.2090.0000.0000.0000.000
65A166LEU00.0030.00624.875-0.007-0.0070.0000.0000.0000.000
66A167MET0-0.024-0.02128.5090.0000.0000.0000.0000.0000.000
67A168GLU-1-0.805-0.86829.1610.2350.2350.0000.0000.0000.000
68A169VAL0-0.014-0.01931.450-0.009-0.0090.0000.0000.0000.000
69A170ASP-1-0.792-0.89133.9720.1610.1610.0000.0000.0000.000
70A171PRO0-0.0210.00132.6960.0120.0120.0000.0000.0000.000
71A172ILE0-0.067-0.03533.0590.0060.0060.0000.0000.0000.000
72A173GLY0-0.001-0.01633.0220.0080.0080.0000.0000.0000.000
73A174HIS10.7390.86628.805-0.210-0.2100.0000.0000.0000.000
74A175LEU00.0540.02529.9670.0160.0160.0000.0000.0000.000
75A176TYR0-0.069-0.06326.8690.0100.0100.0000.0000.0000.000
76A177ILE00.0240.00931.341-0.007-0.0070.0000.0000.0000.000
77A178PHE00.0220.00127.6280.0130.0130.0000.0000.0000.000
78A179ALA0-0.0160.00132.461-0.012-0.0120.0000.0000.0000.000
79A180THR00.0230.00932.6820.0130.0130.0000.0000.0000.000
80A181CYS0-0.095-0.03230.3450.0020.0020.0000.0000.0000.000
81A182LEU0-0.036-0.03133.046-0.010-0.0100.0000.0000.0000.000
82A183GLY0-0.040-0.00636.128-0.007-0.0070.0000.0000.0000.000
83A184LEU0-0.0230.00436.624-0.006-0.0060.0000.0000.0000.000
84A185SER0-0.084-0.06338.6790.0050.0050.0000.0000.0000.000
85A186TYR00.0070.00236.637-0.002-0.0020.0000.0000.0000.000
86A187ASP-1-0.766-0.86234.2640.1280.1280.0000.0000.0000.000
87A188GLY00.0430.02834.8250.0040.0040.0000.0000.0000.000
88A189LEU0-0.041-0.00632.7450.0000.0000.0000.0000.0000.000
89A190LEU00.0260.00536.679-0.007-0.0070.0000.0000.0000.000
90A191GLY00.0320.01839.428-0.002-0.0020.0000.0000.0000.000
91A192ASP-1-0.831-0.92634.8100.1370.1370.0000.0000.0000.000
92A193ASN0-0.032-0.01335.8000.0010.0010.0000.0000.0000.000
93A194GLN0-0.044-0.01430.7610.0130.0130.0000.0000.0000.000
94A195ILE0-0.025-0.00931.0360.0030.0030.0000.0000.0000.000
95A196MET00.0180.00827.3410.0070.0070.0000.0000.0000.000
96A197PRO0-0.012-0.00129.110-0.011-0.0110.0000.0000.0000.000
97A198LYS10.8640.90830.454-0.098-0.0980.0000.0000.0000.000
98A199ALA00.0430.03132.638-0.005-0.0050.0000.0000.0000.000
99A200GLY00.0040.01329.207-0.003-0.0030.0000.0000.0000.000
100A201LEU00.0320.00428.044-0.006-0.0060.0000.0000.0000.000
101A202LEU0-0.0150.01131.312-0.008-0.0080.0000.0000.0000.000
102A203ILE0-0.007-0.01832.435-0.006-0.0060.0000.0000.0000.000
103A204ILE00.0020.00227.623-0.004-0.0040.0000.0000.0000.000
104A205VAL00.0110.00432.087-0.007-0.0070.0000.0000.0000.000
105A206LEU0-0.014-0.00235.324-0.005-0.0050.0000.0000.0000.000
106A207ALA0-0.002-0.02032.983-0.004-0.0040.0000.0000.0000.000
107A208ILE0-0.044-0.01132.125-0.003-0.0030.0000.0000.0000.000
108A209ILE00.0150.01035.238-0.004-0.0040.0000.0000.0000.000
109A210ALA0-0.045-0.02637.394-0.003-0.0030.0000.0000.0000.000
110A211ARG10.8660.94130.345-0.089-0.0890.0000.0000.0000.000
111A212GLU-1-0.929-0.95937.1580.0390.0390.0000.0000.0000.000
112A213GLY00.0230.01340.143-0.004-0.0040.0000.0000.0000.000
113A214ASP-1-0.944-0.95543.0120.0460.0460.0000.0000.0000.000
114A215CYS0-0.124-0.07344.2050.0010.0010.0000.0000.0000.000
115A216ALA00.0430.02640.1370.0000.0000.0000.0000.0000.000
116A217PRO00.0390.02841.2070.0010.0010.0000.0000.0000.000
117A218GLU-1-0.754-0.86140.7530.0320.0320.0000.0000.0000.000
118A219GLU-1-0.900-0.96039.2510.0250.0250.0000.0000.0000.000
119A220LYS10.8230.90633.360-0.042-0.0420.0000.0000.0000.000
120A221ILE0-0.017-0.00935.5310.0060.0060.0000.0000.0000.000
121A222TRP0-0.038-0.05734.7360.0060.0060.0000.0000.0000.000
122A223GLU-1-0.883-0.91932.6130.0280.0280.0000.0000.0000.000
123A224GLU-1-0.840-0.91230.7690.0660.0660.0000.0000.0000.000
124A225LEU0-0.029-0.02129.6760.0090.0090.0000.0000.0000.000
125A226SER0-0.066-0.04129.5720.0030.0030.0000.0000.0000.000
126A227VAL0-0.0160.00324.676-0.004-0.0040.0000.0000.0000.000
127A228LEU0-0.059-0.02324.7710.0130.0130.0000.0000.0000.000
128A229GLU-1-0.898-0.97019.5200.1250.1250.0000.0000.0000.000
129A230VAL0-0.063-0.02323.843-0.001-0.0010.0000.0000.0000.000
130A231PHE00.0130.00025.8840.0000.0000.0000.0000.0000.000
131A232GLU-1-0.880-0.92325.1730.0570.0570.0000.0000.0000.000
132A233GLY00.0240.02726.242-0.011-0.0110.0000.0000.0000.000
133A234ARG10.7970.89427.517-0.061-0.0610.0000.0000.0000.000
134A235GLU-1-0.821-0.91430.8090.0370.0370.0000.0000.0000.000
135A236ASP-1-0.939-0.96333.9400.0070.0070.0000.0000.0000.000
136A237SER0-0.064-0.04034.5600.0000.0000.0000.0000.0000.000
137A238ILE0-0.010-0.01636.9510.0010.0010.0000.0000.0000.000
138A239LEU0-0.065-0.02339.1940.0000.0000.0000.0000.0000.000
139A240GLY00.0160.00340.0040.0010.0010.0000.0000.0000.000
140A241ASP-1-0.779-0.88035.4930.0370.0370.0000.0000.0000.000
141A242PRO00.0190.00933.1570.0040.0040.0000.0000.0000.000
142A243LYS10.8190.88932.571-0.029-0.0290.0000.0000.0000.000
143A244LYS10.8730.94134.713-0.025-0.0250.0000.0000.0000.000
144A245LEU00.0040.01137.8310.0030.0030.0000.0000.0000.000
145A246LEU0-0.0240.00532.8290.0030.0030.0000.0000.0000.000
146A247THR0-0.017-0.02136.9540.0010.0010.0000.0000.0000.000
147A248GLN00.006-0.00438.9590.0010.0010.0000.0000.0000.000
148A249HIS0-0.029-0.01938.4970.0030.0030.0000.0000.0000.000
149A250PHE00.0520.01234.6120.0000.0000.0000.0000.0000.000
150A251VAL00.0020.01640.8820.0000.0000.0000.0000.0000.000
151A252GLN0-0.050-0.02044.2640.0000.0000.0000.0000.0000.000
152A253GLU-1-0.876-0.92541.3340.0770.0770.0000.0000.0000.000
153A254ASN0-0.057-0.03044.4200.0020.0020.0000.0000.0000.000
154A255TYR0-0.039-0.05640.9430.0000.0000.0000.0000.0000.000
155A256LEU0-0.034-0.01339.1900.0010.0010.0000.0000.0000.000
156A257GLU-1-0.907-0.96643.5960.0420.0420.0000.0000.0000.000
157A258TYR0-0.073-0.05744.5760.0010.0010.0000.0000.0000.000
158A259ARG10.8410.90847.069-0.036-0.0360.0000.0000.0000.000
159A260GLN0-0.012-0.00248.8550.0010.0010.0000.0000.0000.000
160A261VAL0-0.0090.00147.9480.0010.0010.0000.0000.0000.000
161A262PRO00.0150.00050.824-0.002-0.0020.0000.0000.0000.000
162A263GLY0-0.022-0.00954.244-0.001-0.0010.0000.0000.0000.000
163A264SER0-0.059-0.02751.788-0.002-0.0020.0000.0000.0000.000
164A265ASP-1-0.882-0.94453.7840.0100.0100.0000.0000.0000.000
165A266PRO0-0.014-0.01551.852-0.001-0.0010.0000.0000.0000.000
166A267ALA0-0.024-0.00252.2940.0010.0010.0000.0000.0000.000
167A268CYS0-0.0210.00047.812-0.001-0.0010.0000.0000.0000.000
168A269TYR00.0160.00446.2950.0010.0010.0000.0000.0000.000
169A270GLU-1-0.768-0.86344.5600.0320.0320.0000.0000.0000.000
170A271PHE0-0.002-0.00641.6010.0010.0010.0000.0000.0000.000
171A272LEU00.0110.00543.898-0.001-0.0010.0000.0000.0000.000
172A273TRP0-0.016-0.02439.0060.0040.0040.0000.0000.0000.000
173A274GLY00.0350.03144.105-0.003-0.0030.0000.0000.0000.000
174A275PRO00.008-0.01645.9850.0030.0030.0000.0000.0000.000
175A276ARG10.8140.89043.258-0.077-0.0770.0000.0000.0000.000
176A277ALA00.0170.00741.8020.0040.0040.0000.0000.0000.000
177A278LEU0-0.033-0.01943.2190.0030.0030.0000.0000.0000.000
178A279VAL0-0.0300.00845.896-0.001-0.0010.0000.0000.0000.000
179A280GLU-1-0.720-0.79841.8180.0900.0900.0000.0000.0000.000
180A281THR0-0.046-0.04438.4760.0050.0050.0000.0000.0000.000
181A282SER00.0410.00840.623-0.003-0.0030.0000.0000.0000.000
182A283TYR00.0490.00939.7780.0080.0080.0000.0000.0000.000
183A284VAL0-0.009-0.00138.3600.0040.0040.0000.0000.0000.000
184A285LYS10.8930.96337.487-0.086-0.0860.0000.0000.0000.000
185A286VAL00.0410.02334.9320.0090.0090.0000.0000.0000.000
186A287LEU00.0040.00633.8060.0100.0100.0000.0000.0000.000
187A288HIS0-0.022-0.00532.7450.0090.0090.0000.0000.0000.000
188A289HIS00.012-0.00330.0590.0100.0100.0000.0000.0000.000
189A290MET00.0080.00628.2160.0140.0140.0000.0000.0000.000
190A291VAL0-0.0010.00927.8470.0120.0120.0000.0000.0000.000
191A292LYS10.7900.90227.203-0.171-0.1710.0000.0000.0000.000
192A293ILE0-0.020-0.02025.5360.0200.0200.0000.0000.0000.000
193A294SER0-0.050-0.01423.4710.0190.0190.0000.0000.0000.000
194A295GLY00.0090.01022.3520.0180.0180.0000.0000.0000.000
195A296GLY0-0.023-0.00223.4270.0010.0010.0000.0000.0000.000
196A297PRO0-0.024-0.02025.386-0.001-0.0010.0000.0000.0000.000
197A298HIS00.016-0.00120.188-0.006-0.0060.0000.0000.0000.000
198A299ILE0-0.043-0.02824.094-0.016-0.0160.0000.0000.0000.000
199A300SER00.0060.00823.5310.0040.0040.0000.0000.0000.000
200A301TYR0-0.043-0.01824.619-0.011-0.0110.0000.0000.0000.000
201A302PRO00.0420.03825.728-0.005-0.0050.0000.0000.0000.000
202A303PRO00.0280.01925.1760.0030.0030.0000.0000.0000.000
203A304LEU00.031-0.00927.127-0.003-0.0030.0000.0000.0000.000
204A305HIS0-0.085-0.05826.196-0.001-0.0010.0000.0000.0000.000
205A306GLU-1-0.859-0.92928.152-0.024-0.0240.0000.0000.0000.000
206A307TRP0-0.054-0.02629.9100.0030.0030.0000.0000.0000.000
207A308VAL0-0.0190.01033.6640.0030.0030.0000.0000.0000.000
208A309LEU00.0580.04035.262-0.006-0.0060.0000.0000.0000.000
209A310ARG10.8590.92631.9120.0320.0320.0000.0000.0000.000