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: 52QQZ

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1997648.363249
FMO2-HF: Nuclear repulsion 1919535.537447
FMO2-HF: Total energy -78112.825802
FMO2-MP2: Total energy -78338.961302


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.
-15.212-8.05813.42-7.479-13.0910.007
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 : 0.008 / q_NPA : 0.004
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].
3F242LEU00.0110.0013.864-1.6110.574-0.025-1.105-1.0540.003
4F243PHE0-0.004-0.0016.0530.0100.0100.0000.0000.0000.000
5F244PRO00.0310.0189.795-0.028-0.0280.0000.0000.0000.000
6F245PRO00.0150.01712.8370.0310.0310.0000.0000.0000.000
7F246LYS10.9380.96515.982-0.208-0.2080.0000.0000.0000.000
8F247PRO00.0790.03918.769-0.012-0.0120.0000.0000.0000.000
9F248LYS10.9530.96821.193-0.097-0.0970.0000.0000.0000.000
10F249ASP-1-0.864-0.94120.3130.1160.1160.0000.0000.0000.000
11F250THR0-0.070-0.02919.322-0.010-0.0100.0000.0000.0000.000
12F251LEU0-0.0150.00922.175-0.009-0.0090.0000.0000.0000.000
13F252MET0-0.0080.00625.712-0.006-0.0060.0000.0000.0000.000
14F253ILE00.0590.02926.7000.0040.0040.0000.0000.0000.000
15F254SER0-0.045-0.02028.3510.0010.0010.0000.0000.0000.000
16F255ARG10.8410.92722.978-0.100-0.1000.0000.0000.0000.000
17F256THR00.021-0.00220.475-0.009-0.0090.0000.0000.0000.000
18F257PRO0-0.0190.02318.7480.0150.0150.0000.0000.0000.000
19F258GLU-1-0.878-0.97014.8460.1410.1410.0000.0000.0000.000
20F259VAL0-0.0050.0099.9810.0190.0190.0000.0000.0000.000
21F260THR0-0.020-0.0069.1180.0010.0010.0000.0000.0000.000
22F261CYS0-0.073-0.0384.373-0.411-0.1700.005-0.037-0.2080.000
23F262VAL0-0.006-0.0115.082-0.260-0.099-0.001-0.025-0.1360.000
24F263VAL00.0060.0012.320-2.4130.0993.578-2.944-3.145-0.010
25F264VAL0-0.0050.0052.520-3.945-3.2642.860-1.261-2.2790.008
26F265ASP-1-0.911-0.9624.378-2.190-2.010-0.001-0.021-0.1570.000
27F266VAL0-0.027-0.0226.484-0.241-0.2410.0000.0000.0000.000
28F267SER00.0070.0138.864-0.055-0.0550.0000.0000.0000.000
29F268HIS0-0.036-0.03311.2270.0150.0150.0000.0000.0000.000
30F269GLU-1-0.969-0.97714.829-0.122-0.1220.0000.0000.0000.000
31F270ASP-1-0.838-0.94013.417-0.180-0.1800.0000.0000.0000.000
32F271PRO0-0.0220.00712.034-0.033-0.0330.0000.0000.0000.000
33F272GLU-1-1.000-1.00112.386-0.026-0.0260.0000.0000.0000.000
34F273VAL00.0020.0047.282-0.077-0.0770.0000.0000.0000.000
35F274GLN0-0.050-0.0329.8320.0140.0140.0000.0000.0000.000
36F275PHE00.023-0.0025.444-0.140-0.1400.0000.0000.0000.000
37F276LYS10.9240.9748.7780.3010.3010.0000.0000.0000.000
38F277TRP00.0570.0138.806-0.081-0.0810.0000.0000.0000.000
39F278TYR0-0.040-0.03010.475-0.007-0.0070.0000.0000.0000.000
40F279VAL00.0360.00713.1910.0080.0080.0000.0000.0000.000
41F280ASP-1-0.812-0.90415.895-0.044-0.0440.0000.0000.0000.000
42F281GLY0-0.057-0.03115.171-0.002-0.0020.0000.0000.0000.000
43F282VAL0-0.019-0.00816.188-0.013-0.0130.0000.0000.0000.000
44F283GLU-1-0.960-0.97814.777-0.166-0.1660.0000.0000.0000.000
45F284VAL0-0.042-0.01314.6480.0180.0180.0000.0000.0000.000
46F285HIS00.0550.00615.317-0.014-0.0140.0000.0000.0000.000
47F286ASN0-0.052-0.01117.039-0.005-0.0050.0000.0000.0000.000
48F287ALA0-0.0030.01412.4280.0160.0160.0000.0000.0000.000
49F288LYS10.9690.97813.666-0.067-0.0670.0000.0000.0000.000
50F289THR0-0.006-0.01511.212-0.002-0.0020.0000.0000.0000.000
51F290LYS10.9680.98212.714-0.257-0.2570.0000.0000.0000.000
52F291PRO00.0450.04112.4340.0700.0700.0000.0000.0000.000
53F302VAL00.003-0.0137.051-0.024-0.0240.0000.0000.0000.000
54F303VAL0-0.034-0.0076.5530.2120.2120.0000.0000.0000.000
55F304SER0-0.0250.0037.933-0.153-0.1530.0000.0000.0000.000
56F305VAL0-0.004-0.0039.5050.0260.0260.0000.0000.0000.000
57F306LEU00.0030.01712.164-0.025-0.0250.0000.0000.0000.000
58F307THR00.0100.00113.6520.0060.0060.0000.0000.0000.000
59F308VAL0-0.020-0.01115.420-0.017-0.0170.0000.0000.0000.000
60F309LEU00.0220.00518.1810.0090.0090.0000.0000.0000.000
61F310HIS00.0060.00621.047-0.006-0.0060.0000.0000.0000.000
62F311GLN00.0430.01522.6900.0040.0040.0000.0000.0000.000
63F312ASP-1-0.877-0.94519.814-0.009-0.0090.0000.0000.0000.000
64F313TRP0-0.019-0.01713.650-0.004-0.0040.0000.0000.0000.000
65F314LEU0-0.007-0.01319.129-0.002-0.0020.0000.0000.0000.000
66F315ASN0-0.037-0.01622.2960.0000.0000.0000.0000.0000.000
67F316GLY0-0.057-0.02319.469-0.005-0.0050.0000.0000.0000.000
68F317LYS10.9090.98118.0700.0210.0210.0000.0000.0000.000
69F318GLU-1-0.979-0.98713.754-0.059-0.0590.0000.0000.0000.000
70F319TYR00.001-0.00711.560-0.007-0.0070.0000.0000.0000.000
71F320LYS10.9450.9858.4680.2220.2220.0000.0000.0000.000
72F322LYS10.9490.9795.3440.3140.3140.0000.0000.0000.000
73F323VAL0-0.005-0.0062.610-0.5040.0460.309-0.161-0.699-0.001
74F324SER0-0.053-0.0365.700-0.124-0.1240.0000.0000.0000.000
75F325ASN00.0680.0247.8760.1640.1640.0000.0000.0000.000
76F326LYS10.9441.0059.7010.1780.1780.0000.0000.0000.000
77F327ALA0-0.0040.0039.8280.0050.0050.0000.0000.0000.000
78F328LEU00.017-0.0075.377-0.100-0.1000.0000.0000.0000.000
79F329PRO0-0.0350.0158.8990.0930.0930.0000.0000.0000.000
80F330ALA00.006-0.0179.4870.1090.1090.0000.0000.0000.000
81F331PRO00.0190.0177.115-0.156-0.1560.0000.0000.0000.000
82F332ILE0-0.024-0.0152.224-1.206-0.4122.225-0.681-2.338-0.001
83F333GLU-1-0.889-0.9694.174-0.527-0.2950.001-0.037-0.1950.000
84F334LYS10.8770.9602.053-1.683-2.1294.470-1.205-2.8200.008
85F335THR00.0180.0055.007-0.131-0.067-0.001-0.002-0.0600.000
86F336ILE0-0.016-0.0068.4480.0240.0240.0000.0000.0000.000
87F337SER0-0.001-0.00910.473-0.006-0.0060.0000.0000.0000.000
88F338LYS10.9070.96814.227-0.014-0.0140.0000.0000.0000.000
89F339THR0-0.007-0.00217.304-0.011-0.0110.0000.0000.0000.000
90F340LYS10.9810.98817.3060.0150.0150.0000.0000.0000.000
91F341GLY00.0330.00721.4270.0040.0040.0000.0000.0000.000
92F342GLN0-0.035-0.01724.977-0.001-0.0010.0000.0000.0000.000
93F343PRO00.0270.01726.3240.0020.0020.0000.0000.0000.000
94F344ARG10.8350.91428.322-0.028-0.0280.0000.0000.0000.000
95F345GLU-1-0.870-0.94630.3510.0320.0320.0000.0000.0000.000
96F346PRO0-0.054-0.00830.3750.0000.0000.0000.0000.0000.000
97F347GLN00.0020.01132.746-0.002-0.0020.0000.0000.0000.000
98F348VAL00.007-0.01134.2400.0030.0030.0000.0000.0000.000
99F349TYR0-0.022-0.01536.850-0.003-0.0030.0000.0000.0000.000
100F350THR00.0000.00138.5680.0030.0030.0000.0000.0000.000
101F351LEU0-0.020-0.01940.074-0.003-0.0030.0000.0000.0000.000
102F352PRO0-0.0060.00142.0210.0030.0030.0000.0000.0000.000
103F353PRO00.0430.03143.7970.0000.0000.0000.0000.0000.000
104F354SER00.0130.01044.731-0.003-0.0030.0000.0000.0000.000
105F355ARG10.9990.98146.640-0.027-0.0270.0000.0000.0000.000
106F356GLU-1-0.882-0.94647.4870.0330.0330.0000.0000.0000.000
107F357GLU-1-0.846-0.91541.6040.0530.0530.0000.0000.0000.000
108F358MET0-0.032-0.01446.3360.0020.0020.0000.0000.0000.000
109F359THR0-0.041-0.01648.7430.0000.0000.0000.0000.0000.000
110F360LYS10.9450.97843.195-0.048-0.0480.0000.0000.0000.000
111F361ASN00.002-0.00444.609-0.002-0.0020.0000.0000.0000.000
112F362GLN00.003-0.00539.6870.0020.0020.0000.0000.0000.000
113F363VAL0-0.038-0.00843.060-0.002-0.0020.0000.0000.0000.000
114F364SER0-0.019-0.03039.1180.0050.0050.0000.0000.0000.000
115F365LEU0-0.045-0.00939.420-0.004-0.0040.0000.0000.0000.000
116F366THR00.0070.01737.1220.0050.0050.0000.0000.0000.000
117F367CYS0-0.065-0.03735.145-0.004-0.0040.0000.0000.0000.000
118F368LEU0-0.0250.01134.5780.0040.0040.0000.0000.0000.000
119F369VAL00.0250.00731.013-0.003-0.0030.0000.0000.0000.000
120F370LYS11.0090.99531.978-0.031-0.0310.0000.0000.0000.000
121F371GLY00.0510.03132.318-0.001-0.0010.0000.0000.0000.000
122F372PHE0-0.048-0.01225.735-0.002-0.0020.0000.0000.0000.000
123F373TYR00.001-0.00122.9880.0030.0030.0000.0000.0000.000
124F374PRO00.0520.03421.867-0.003-0.0030.0000.0000.0000.000
125F375SER00.007-0.01020.7680.0000.0000.0000.0000.0000.000
126F376ASP-1-0.908-0.95619.0990.0850.0850.0000.0000.0000.000
127F377ILE0-0.024-0.01221.900-0.008-0.0080.0000.0000.0000.000
128F378ALA0-0.054-0.01824.0490.0120.0120.0000.0000.0000.000
129F379VAL00.009-0.00826.259-0.008-0.0080.0000.0000.0000.000
130F380GLU-1-0.911-0.95528.5530.0950.0950.0000.0000.0000.000
131F381TRP0-0.003-0.01831.327-0.008-0.0080.0000.0000.0000.000
132F382GLU-1-0.851-0.93534.6990.0620.0620.0000.0000.0000.000
133F383SER0-0.042-0.04437.297-0.004-0.0040.0000.0000.0000.000
134F384SER0-0.023-0.01140.9310.0000.0000.0000.0000.0000.000
135F385GLY00.0040.00640.2020.0000.0000.0000.0000.0000.000
136F386GLN0-0.026-0.01938.2590.0030.0030.0000.0000.0000.000
137F387PRO00.0190.01533.410-0.001-0.0010.0000.0000.0000.000
138F388GLU-1-0.797-0.89234.7830.0630.0630.0000.0000.0000.000
139F389ASN0-0.022-0.01433.2530.0100.0100.0000.0000.0000.000
140F390ASN0-0.027-0.01432.8780.0010.0010.0000.0000.0000.000
141F391TYR00.0680.03429.084-0.007-0.0070.0000.0000.0000.000
142F392ASN0-0.065-0.03128.9520.0150.0150.0000.0000.0000.000
143F393THR00.0240.01527.304-0.011-0.0110.0000.0000.0000.000
144F394THR0-0.0040.01526.4900.0080.0080.0000.0000.0000.000
145F395PRO00.006-0.00422.325-0.001-0.0010.0000.0000.0000.000
146F396PRO0-0.0050.00422.731-0.007-0.0070.0000.0000.0000.000
147F397MET0-0.019-0.00624.6220.0050.0050.0000.0000.0000.000
148F398LEU0-0.049-0.01125.446-0.004-0.0040.0000.0000.0000.000
149F399ASP-1-0.833-0.92027.4590.0380.0380.0000.0000.0000.000
150F400SER0-0.088-0.04230.922-0.003-0.0030.0000.0000.0000.000
151F401ASP-1-0.805-0.88632.9140.0260.0260.0000.0000.0000.000
152F402GLY0-0.052-0.03329.158-0.002-0.0020.0000.0000.0000.000
153F403SER0-0.109-0.05628.1870.0010.0010.0000.0000.0000.000
154F404PHE00.013-0.01222.8920.0020.0020.0000.0000.0000.000
155F405PHE0-0.011-0.01028.323-0.002-0.0020.0000.0000.0000.000
156F406LEU0-0.021-0.01326.8510.0050.0050.0000.0000.0000.000
157F407TYR00.0430.00830.121-0.006-0.0060.0000.0000.0000.000
158F408SER0-0.046-0.01630.8980.0060.0060.0000.0000.0000.000
159F409LYS10.9720.97632.600-0.080-0.0800.0000.0000.0000.000
160F410LEU00.0190.00534.0730.0060.0060.0000.0000.0000.000
161F411THR0-0.066-0.03836.180-0.004-0.0040.0000.0000.0000.000
162F412VAL00.0160.01937.9690.0020.0020.0000.0000.0000.000
163F413ASP-1-0.886-0.96041.0750.0530.0530.0000.0000.0000.000
164F414LYS10.8770.95244.245-0.041-0.0410.0000.0000.0000.000
165F415SER0-0.019-0.00747.160-0.001-0.0010.0000.0000.0000.000
166F416ARG10.9300.95440.544-0.057-0.0570.0000.0000.0000.000
167F417TRP00.0560.05444.974-0.001-0.0010.0000.0000.0000.000
168F418GLN00.015-0.02147.304-0.001-0.0010.0000.0000.0000.000
169F419GLN0-0.053-0.02650.594-0.001-0.0010.0000.0000.0000.000
170F420GLY00.0080.02250.438-0.001-0.0010.0000.0000.0000.000
171F421ASN0-0.095-0.05546.3180.0000.0000.0000.0000.0000.000
172F422ILE00.0280.01044.3150.0000.0000.0000.0000.0000.000
173F423PHE0-0.040-0.01640.3370.0020.0020.0000.0000.0000.000
174F424SER0-0.021-0.01539.477-0.002-0.0020.0000.0000.0000.000
175F425CYS00.0320.04334.1790.0030.0030.0000.0000.0000.000
176F426SER00.0210.00433.827-0.004-0.0040.0000.0000.0000.000
177F427VAL0-0.001-0.00730.2150.0050.0050.0000.0000.0000.000
178F428MET00.010-0.00327.980-0.003-0.0030.0000.0000.0000.000
179F429HIS00.024-0.01426.0910.0040.0040.0000.0000.0000.000
180F430GLU-1-0.815-0.91824.1360.0290.0290.0000.0000.0000.000
181F431ALA0-0.037-0.00227.482-0.004-0.0040.0000.0000.0000.000
182F432LEU0-0.0280.00330.464-0.001-0.0010.0000.0000.0000.000
183F433HIS00.0700.03532.597-0.001-0.0010.0000.0000.0000.000
184F434ASN0-0.036-0.02733.9040.0010.0010.0000.0000.0000.000
185F435HIS0-0.040-0.02327.7250.0010.0010.0000.0000.0000.000
186F436TYR0-0.036-0.02530.3920.0050.0050.0000.0000.0000.000
187F437THR00.0020.01032.981-0.004-0.0040.0000.0000.0000.000
188F438GLN0-0.015-0.00935.2570.0010.0010.0000.0000.0000.000
189F439LYS10.8870.96237.706-0.039-0.0390.0000.0000.0000.000
190F440SER00.0530.01239.8500.0030.0030.0000.0000.0000.000
191F441LEU0-0.037-0.01042.025-0.002-0.0020.0000.0000.0000.000
192F442SER00.0450.00544.2890.0020.0020.0000.0000.0000.000
193F443LEU0-0.0360.00847.205-0.001-0.0010.0000.0000.0000.000
194F444SER00.0030.00450.183-0.001-0.0010.0000.0000.0000.000