Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V56Z1

Calculation Name: 4ZNC-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZNC

Chain ID: F

ChEMBL ID:

UniProt ID: P01860

Base Structure: X-ray

Registration Date: 2023-06-26

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007079.201167
FMO2-HF: Nuclear repulsion 1928964.253985
FMO2-HF: Total energy -78114.947183
FMO2-MP2: Total energy -78341.155665


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(F:240:VAL)


Summations of interaction energy for fragment #1(F:240:VAL)
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.
-14.783-5.24411.017-7.127-13.426-8.673617379884E-19
Interaction energy analysis for fragmet #1(F:240:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.013
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].
3F242LEU0-0.008-0.0063.878-1.1260.597-0.019-0.811-0.8930.003
4F243PHE00.000-0.0026.566-0.058-0.0580.0000.0000.0000.000
5F244PRO00.0330.02110.112-0.028-0.0280.0000.0000.0000.000
6F245PRO0-0.0120.00813.5070.0390.0390.0000.0000.0000.000
7F246LYS10.8400.89516.322-0.249-0.2490.0000.0000.0000.000
8F247PRO00.0750.03518.716-0.016-0.0160.0000.0000.0000.000
9F248LYS10.8740.92021.637-0.124-0.1240.0000.0000.0000.000
10F249ASP-1-0.784-0.87520.6760.1630.1630.0000.0000.0000.000
11F250THR0-0.079-0.04419.757-0.012-0.0120.0000.0000.0000.000
12F251LEU0-0.0200.01622.528-0.011-0.0110.0000.0000.0000.000
13F252MET0-0.0200.00426.207-0.008-0.0080.0000.0000.0000.000
14F253ILE00.0620.02426.8060.0060.0060.0000.0000.0000.000
15F254SER0-0.032-0.00828.6570.0010.0010.0000.0000.0000.000
16F255ARG10.8040.88422.101-0.142-0.1420.0000.0000.0000.000
17F256THR00.020-0.00320.545-0.011-0.0110.0000.0000.0000.000
18F257PRO0-0.0020.02818.8330.0210.0210.0000.0000.0000.000
19F258GLU-1-0.870-0.94814.8310.2320.2320.0000.0000.0000.000
20F259VAL00.0050.0189.7960.0210.0210.0000.0000.0000.000
21F260THR0-0.007-0.0058.702-0.005-0.0050.0000.0000.0000.000
22F261CYS0-0.062-0.0244.218-0.371-0.0860.010-0.053-0.2410.000
23F262VAL00.0110.0084.755-0.469-0.275-0.001-0.041-0.1510.000
24F263VAL0-0.023-0.0172.423-1.3261.3423.599-2.914-3.352-0.016
25F264VAL00.0020.0012.479-5.196-4.2412.665-1.278-2.3410.010
26F265ASP-1-0.917-0.9704.104-2.618-2.382-0.001-0.051-0.1840.000
27F266VAL0-0.055-0.0306.148-0.267-0.2670.0000.0000.0000.000
28F267SER00.0140.0068.162-0.024-0.0240.0000.0000.0000.000
29F268HIS0-0.046-0.02510.8330.0380.0380.0000.0000.0000.000
30F269GLU-1-0.899-0.95614.279-0.142-0.1420.0000.0000.0000.000
31F270ASP-1-0.805-0.87612.968-0.237-0.2370.0000.0000.0000.000
32F271PRO00.0330.03011.656-0.053-0.0530.0000.0000.0000.000
33F272GLU-1-0.966-0.98111.874-0.058-0.0580.0000.0000.0000.000
34F273VAL0-0.051-0.0206.546-0.099-0.0990.0000.0000.0000.000
35F274GLN0-0.034-0.0159.0940.0860.0860.0000.0000.0000.000
36F275PHE00.019-0.0135.366-0.198-0.1980.0000.0000.0000.000
37F276LYS10.8090.8968.3310.2480.2480.0000.0000.0000.000
38F277TRP00.0490.0098.780-0.058-0.0580.0000.0000.0000.000
39F278TYR0-0.072-0.06710.023-0.025-0.0250.0000.0000.0000.000
40F279VAL00.0230.01012.8850.0160.0160.0000.0000.0000.000
41F280ASP-1-0.822-0.90815.681-0.029-0.0290.0000.0000.0000.000
42F281GLY0-0.016-0.00315.259-0.007-0.0070.0000.0000.0000.000
43F282VAL0-0.010-0.00216.277-0.015-0.0150.0000.0000.0000.000
44F283GLU-1-0.785-0.87013.966-0.165-0.1650.0000.0000.0000.000
45F284VAL0-0.047-0.02414.3290.0150.0150.0000.0000.0000.000
46F285HIS00.029-0.00114.739-0.004-0.0040.0000.0000.0000.000
47F286ASN0-0.048-0.01816.804-0.008-0.0080.0000.0000.0000.000
48F287ALA0-0.0130.00912.3060.0190.0190.0000.0000.0000.000
49F288LYS10.9240.95713.563-0.125-0.1250.0000.0000.0000.000
50F289THR00.0370.01210.5550.0360.0360.0000.0000.0000.000
51F290LYS10.9450.98412.017-0.378-0.3780.0000.0000.0000.000
52F291PRO00.0490.03611.8190.1030.1030.0000.0000.0000.000
53F302VAL00.0540.0367.323-0.146-0.1460.0000.0000.0000.000
54F303VAL0-0.071-0.0406.5570.4920.4920.0000.0000.0000.000
55F304SER00.0140.0127.735-0.244-0.2440.0000.0000.0000.000
56F305VAL0-0.016-0.0199.1910.0850.0850.0000.0000.0000.000
57F306LEU00.0200.02111.781-0.049-0.0490.0000.0000.0000.000
58F307THR00.0160.00813.3760.0080.0080.0000.0000.0000.000
59F308VAL0-0.004-0.00515.415-0.020-0.0200.0000.0000.0000.000
60F309LEU00.0060.00518.2730.0060.0060.0000.0000.0000.000
61F310HIS00.0120.00621.400-0.006-0.0060.0000.0000.0000.000
62F311GLN00.0280.00423.1900.0050.0050.0000.0000.0000.000
63F312ASP-1-0.807-0.90520.4520.0160.0160.0000.0000.0000.000
64F313TRP00.0230.01514.404-0.002-0.0020.0000.0000.0000.000
65F314LEU00.0030.00219.870-0.005-0.0050.0000.0000.0000.000
66F315ASN0-0.068-0.04323.064-0.006-0.0060.0000.0000.0000.000
67F316GLY0-0.040-0.01219.631-0.007-0.0070.0000.0000.0000.000
68F317LYS10.8470.93718.167-0.001-0.0010.0000.0000.0000.000
69F318GLU-1-0.835-0.88014.148-0.022-0.0220.0000.0000.0000.000
70F319TYR0-0.029-0.02812.020-0.008-0.0080.0000.0000.0000.000
71F320LYS10.8510.9138.5480.2590.2590.0000.0000.0000.000
72F322LYS10.8740.9265.5550.4090.4090.0000.0000.0000.000
73F323VAL00.0190.0032.354-0.780-0.0521.140-0.376-1.492-0.002
74F324SER0-0.010-0.0194.766-0.349-0.295-0.001-0.004-0.0490.000
75F325ASN00.0220.0097.6190.2270.2270.0000.0000.0000.000
76F326LYS10.8470.9149.3830.2250.2250.0000.0000.0000.000
77F327ALA00.0030.0199.9760.0340.0340.0000.0000.0000.000
78F328LEU00.016-0.0105.069-0.192-0.1920.0000.0000.0000.000
79F329PRO0-0.034-0.0118.2500.1030.1030.0000.0000.0000.000
80F330ALA00.012-0.0028.8520.1210.1210.0000.0000.0000.000
81F331PRO0-0.0090.0096.702-0.195-0.1950.0000.0000.0000.000
82F332ILE0-0.005-0.0012.326-1.061-0.3262.225-0.592-2.3680.001
83F333GLU-1-0.787-0.8713.800-0.744-0.3450.006-0.126-0.279-0.001
84F334LYS10.8700.9342.525-0.5140.9891.395-0.880-2.0190.005
85F335THR00.030-0.0015.243-0.061-0.002-0.001-0.001-0.0570.000
86F336ILE0-0.031-0.0098.7690.0040.0040.0000.0000.0000.000
87F337SER00.007-0.01811.1820.0010.0010.0000.0000.0000.000
88F338LYS10.7870.88314.997-0.037-0.0370.0000.0000.0000.000
89F339THR0-0.035-0.03017.962-0.015-0.0150.0000.0000.0000.000
90F340LYS10.8880.94317.4500.0110.0110.0000.0000.0000.000
91F341GLY00.0280.01421.6750.0010.0010.0000.0000.0000.000
92F342GLN0-0.036-0.02225.370-0.001-0.0010.0000.0000.0000.000
93F343PRO00.0290.01727.0690.0030.0030.0000.0000.0000.000
94F344ARG10.7540.86228.966-0.038-0.0380.0000.0000.0000.000
95F345GLU-1-0.851-0.93130.9910.0450.0450.0000.0000.0000.000
96F346PRO0-0.058-0.02030.470-0.001-0.0010.0000.0000.0000.000
97F347GLN0-0.0130.00633.292-0.002-0.0020.0000.0000.0000.000
98F348VAL0-0.004-0.01534.6370.0030.0030.0000.0000.0000.000
99F349TYR0-0.002-0.00837.237-0.004-0.0040.0000.0000.0000.000
100F350THR0-0.001-0.00439.0630.0030.0030.0000.0000.0000.000
101F351LEU0-0.023-0.01639.582-0.003-0.0030.0000.0000.0000.000
102F352PRO00.0060.00742.0400.0030.0030.0000.0000.0000.000
103F353PRO00.0420.02743.7310.0000.0000.0000.0000.0000.000
104F354SER00.0230.01244.765-0.004-0.0040.0000.0000.0000.000
105F355ARG10.9990.98446.789-0.033-0.0330.0000.0000.0000.000
106F356GLU-1-0.858-0.93247.8440.0380.0380.0000.0000.0000.000
107F357GLU-1-0.849-0.88241.7900.0630.0630.0000.0000.0000.000
108F358MET0-0.0130.01046.5040.0020.0020.0000.0000.0000.000
109F359THR0-0.004-0.00848.7690.0000.0000.0000.0000.0000.000
110F360LYS10.9060.95843.771-0.053-0.0530.0000.0000.0000.000
111F361ASN00.006-0.01344.423-0.003-0.0030.0000.0000.0000.000
112F362GLN0-0.018-0.00139.7310.0020.0020.0000.0000.0000.000
113F363VAL0-0.055-0.02142.891-0.002-0.0020.0000.0000.0000.000
114F364SER00.005-0.04339.3950.0060.0060.0000.0000.0000.000
115F365LEU0-0.0240.01439.615-0.004-0.0040.0000.0000.0000.000
116F366THR0-0.005-0.00937.1500.0060.0060.0000.0000.0000.000
117F367CYS0-0.054-0.02935.277-0.005-0.0050.0000.0000.0000.000
118F368LEU0-0.0110.01734.9000.0040.0040.0000.0000.0000.000
119F369VAL00.0280.00431.632-0.003-0.0030.0000.0000.0000.000
120F370LYS10.8850.91032.731-0.040-0.0400.0000.0000.0000.000
121F371GLY00.0220.03232.968-0.002-0.0020.0000.0000.0000.000
122F372PHE0-0.0070.00926.401-0.004-0.0040.0000.0000.0000.000
123F373TYR00.028-0.00123.3080.0030.0030.0000.0000.0000.000
124F374PRO00.0370.02922.484-0.003-0.0030.0000.0000.0000.000
125F375SER00.004-0.00521.125-0.001-0.0010.0000.0000.0000.000
126F376ASP-1-0.862-0.93319.9690.1060.1060.0000.0000.0000.000
127F377ILE0-0.0120.00422.458-0.008-0.0080.0000.0000.0000.000
128F378ALA0-0.037-0.01823.9860.0160.0160.0000.0000.0000.000
129F379VAL00.008-0.00626.104-0.011-0.0110.0000.0000.0000.000
130F380GLU-1-0.809-0.87428.5020.1240.1240.0000.0000.0000.000
131F381TRP00.040-0.00231.158-0.010-0.0100.0000.0000.0000.000
132F382GLU-1-0.777-0.82934.6700.0790.0790.0000.0000.0000.000
133F383SER0-0.011-0.02437.376-0.004-0.0040.0000.0000.0000.000
134F384SER0-0.028-0.01241.0750.0000.0000.0000.0000.0000.000
135F385GLY00.0140.02140.774-0.001-0.0010.0000.0000.0000.000
136F386GLN0-0.058-0.03338.0810.0040.0040.0000.0000.0000.000
137F387PRO00.0260.01733.230-0.002-0.0020.0000.0000.0000.000
138F388GLU-1-0.784-0.88835.0490.0740.0740.0000.0000.0000.000
139F389ASN0-0.036-0.01933.5110.0130.0130.0000.0000.0000.000
140F390ASN0-0.008-0.01333.2500.0010.0010.0000.0000.0000.000
141F391TYR00.0120.01428.695-0.005-0.0050.0000.0000.0000.000
142F392ASN0-0.038-0.00829.4910.0170.0170.0000.0000.0000.000
143F393THR00.0150.00527.477-0.014-0.0140.0000.0000.0000.000
144F394THR0-0.0150.00226.9730.0080.0080.0000.0000.0000.000
145F395PRO00.0270.00322.6650.0020.0020.0000.0000.0000.000
146F396PRO0-0.0150.01122.961-0.010-0.0100.0000.0000.0000.000
147F397MET0-0.028-0.01224.7820.0060.0060.0000.0000.0000.000
148F398LEU00.0000.00525.864-0.004-0.0040.0000.0000.0000.000
149F399ASP-1-0.781-0.87028.2020.0440.0440.0000.0000.0000.000
150F400SER0-0.064-0.05531.753-0.004-0.0040.0000.0000.0000.000
151F401ASP-1-0.780-0.85133.4560.0320.0320.0000.0000.0000.000
152F402GLY0-0.023-0.00329.770-0.003-0.0030.0000.0000.0000.000
153F403SER0-0.103-0.06528.7180.0020.0020.0000.0000.0000.000
154F404PHE00.015-0.00523.3560.0030.0030.0000.0000.0000.000
155F405PHE0-0.041-0.03128.863-0.003-0.0030.0000.0000.0000.000
156F406LEU0-0.0060.00327.3980.0060.0060.0000.0000.0000.000
157F407TYR00.0370.00930.423-0.008-0.0080.0000.0000.0000.000
158F408SER0-0.014-0.01230.9660.0080.0080.0000.0000.0000.000
159F409LYS10.8710.91132.767-0.088-0.0880.0000.0000.0000.000
160F410LEU00.0270.03534.4190.0060.0060.0000.0000.0000.000
161F411THR0-0.046-0.01835.930-0.006-0.0060.0000.0000.0000.000
162F412VAL00.0140.00838.1690.0030.0030.0000.0000.0000.000
163F413ASP-1-0.851-0.93141.1620.0630.0630.0000.0000.0000.000
164F414LYS10.8460.91944.483-0.048-0.0480.0000.0000.0000.000
165F415SER00.0010.00447.409-0.001-0.0010.0000.0000.0000.000
166F416ARG10.9090.93740.673-0.068-0.0680.0000.0000.0000.000
167F417TRP00.0510.02745.394-0.001-0.0010.0000.0000.0000.000
168F418GLN0-0.002-0.02547.506-0.001-0.0010.0000.0000.0000.000
169F419GLN0-0.058-0.02750.3240.0000.0000.0000.0000.0000.000
170F420GLY0-0.0050.01350.493-0.001-0.0010.0000.0000.0000.000
171F421ASN0-0.077-0.03645.9590.0000.0000.0000.0000.0000.000
172F422ILE00.0060.00244.6730.0000.0000.0000.0000.0000.000
173F423PHE0-0.024-0.00740.5350.0020.0020.0000.0000.0000.000
174F424SER0-0.054-0.06438.899-0.005-0.0050.0000.0000.0000.000
175F425CYS0-0.0220.01134.0090.0040.0040.0000.0000.0000.000
176F426SER00.010-0.02633.708-0.004-0.0040.0000.0000.0000.000
177F427VAL0-0.006-0.01130.5520.0060.0060.0000.0000.0000.000
178F428MET0-0.030-0.02228.091-0.004-0.0040.0000.0000.0000.000
179F429HIS00.030-0.02126.5560.0050.0050.0000.0000.0000.000
180F430GLU-1-0.791-0.89424.4960.0490.0490.0000.0000.0000.000
181F431ALA0-0.033-0.00228.097-0.005-0.0050.0000.0000.0000.000
182F432LEU0-0.047-0.00131.104-0.002-0.0020.0000.0000.0000.000
183F433HIS00.0730.02533.1720.0000.0000.0000.0000.0000.000
184F434ASN0-0.050-0.03234.3850.0010.0010.0000.0000.0000.000
185F435HIS0-0.015-0.01228.6950.0010.0010.0000.0000.0000.000
186F436TYR0-0.047-0.02830.7340.0060.0060.0000.0000.0000.000
187F437THR00.0130.01433.261-0.006-0.0060.0000.0000.0000.000
188F438GLN0-0.019-0.01735.1930.0030.0030.0000.0000.0000.000
189F439LYS10.8790.96137.654-0.052-0.0520.0000.0000.0000.000
190F440SER00.0630.01639.9320.0040.0040.0000.0000.0000.000
191F441LEU0-0.043-0.01441.775-0.002-0.0020.0000.0000.0000.000
192F442SER00.008-0.00344.2320.0020.0020.0000.0000.0000.000
193F443LEU0-0.0070.02047.208-0.001-0.0010.0000.0000.0000.000
194F444SER00.0210.01150.169-0.001-0.0010.0000.0000.0000.000