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: NN5ZQ

Calculation Name: 3ZLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLC

Chain ID: A

ChEMBL ID:

UniProt ID: Q04651

Base Structure: X-ray

Registration Date: 2023-09-24

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2835286.185503
FMO2-HF: Nuclear repulsion 2744126.991886
FMO2-HF: Total energy -91159.193617
FMO2-MP2: Total energy -91426.799858


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:51:ILE)


Summations of interaction energy for fragment #1(A:51:ILE)
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.
-13.372-10.71810.623-5.143-8.135-0.026
Interaction energy analysis for fragmet #1(A:51:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.036
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].
3A53GLN0-0.011-0.0103.786-0.7811.556-0.015-1.005-1.3170.004
4A54GLN0-0.021-0.0065.4230.4240.4240.0000.0000.0000.000
5A55TYR00.0180.0199.1360.0870.0870.0000.0000.0000.000
6A56VAL0-0.043-0.02711.9290.0450.0450.0000.0000.0000.000
7A57VAL00.004-0.01314.5600.0090.0090.0000.0000.0000.000
8A58ASP-1-0.879-0.91617.273-0.230-0.2300.0000.0000.0000.000
9A59SER0-0.080-0.03918.2100.0450.0450.0000.0000.0000.000
10A60GLN0-0.055-0.04518.8140.0060.0060.0000.0000.0000.000
11A61VAL00.0490.04019.9990.0000.0000.0000.0000.0000.000
12A62ARG10.9160.96816.8400.0290.0290.0000.0000.0000.000
13A63ASP-1-0.866-0.93622.842-0.067-0.0670.0000.0000.0000.000
14A64THR0-0.084-0.03525.268-0.004-0.0040.0000.0000.0000.000
15A65VAL0-0.013-0.00420.941-0.004-0.0040.0000.0000.0000.000
16A66GLN00.0300.01822.7600.0030.0030.0000.0000.0000.000
17A67ILE00.0010.00422.657-0.016-0.0160.0000.0000.0000.000
18A68ASN0-0.010-0.00320.6970.0300.0300.0000.0000.0000.000
19A69MET0-0.029-0.00823.998-0.022-0.0220.0000.0000.0000.000
20A70ASP-1-0.802-0.88226.329-0.012-0.0120.0000.0000.0000.000
21A71ILE00.000-0.01227.540-0.013-0.0130.0000.0000.0000.000
22A72TYR00.0310.02930.1860.0080.0080.0000.0000.0000.000
23A73VAL00.028-0.00133.380-0.009-0.0090.0000.0000.0000.000
24A74ASN0-0.070-0.02736.0630.0040.0040.0000.0000.0000.000
25A75THR0-0.007-0.03639.1470.0000.0000.0000.0000.0000.000
26A76LYS10.9610.98540.4980.0220.0220.0000.0000.0000.000
27A77CYS00.0120.04037.8600.0020.0020.0000.0000.0000.000
28A78ASP-1-0.864-0.91941.425-0.020-0.0200.0000.0000.0000.000
29A79TRP0-0.045-0.04043.9700.0000.0000.0000.0000.0000.000
30A80LEU0-0.030-0.00837.932-0.004-0.0040.0000.0000.0000.000
31A81GLN0-0.053-0.02840.4040.0060.0060.0000.0000.0000.000
32A82ILE00.0730.03733.845-0.006-0.0060.0000.0000.0000.000
33A83ASN0-0.054-0.03036.2850.0070.0070.0000.0000.0000.000
34A84VAL00.0700.04831.690-0.007-0.0070.0000.0000.0000.000
35A85ARG10.8720.93433.6420.0990.0990.0000.0000.0000.000
36A86ASP-1-0.732-0.83131.667-0.089-0.0890.0000.0000.0000.000
37A87GLN0-0.043-0.03031.2040.0000.0000.0000.0000.0000.000
38A88THR0-0.132-0.08533.0830.0060.0060.0000.0000.0000.000
39A89MET0-0.064-0.01734.8980.0090.0090.0000.0000.0000.000
40A90ASP-1-0.908-0.96037.536-0.063-0.0630.0000.0000.0000.000
41A91ARG10.8810.93538.2420.0710.0710.0000.0000.0000.000
42A92LYS10.9861.00333.6670.0470.0470.0000.0000.0000.000
43A93LEU0-0.029-0.02637.246-0.003-0.0030.0000.0000.0000.000
44A94VAL00.0000.00533.4810.0030.0030.0000.0000.0000.000
45A95LEU0-0.076-0.04736.5430.0000.0000.0000.0000.0000.000
46A96GLU-1-0.942-0.98236.4690.0000.0000.0000.0000.0000.000
47A97GLU-1-0.938-0.96231.882-0.018-0.0180.0000.0000.0000.000
48A98LEU0-0.072-0.02630.507-0.002-0.0020.0000.0000.0000.000
49A99GLN0-0.0080.01333.3670.0030.0030.0000.0000.0000.000
50A100LEU0-0.030-0.03034.735-0.006-0.0060.0000.0000.0000.000
51A101GLU-1-0.914-0.95936.8410.0100.0100.0000.0000.0000.000
52A102GLU-1-0.902-0.97138.281-0.024-0.0240.0000.0000.0000.000
53A103MET0-0.049-0.00134.7110.0020.0020.0000.0000.0000.000
54A104PRO0-0.053-0.02139.456-0.003-0.0030.0000.0000.0000.000
55A105PHE0-0.006-0.03035.0510.0000.0000.0000.0000.0000.000
56A106PHE0-0.008-0.01232.9200.0010.0010.0000.0000.0000.000
57A107ILE00.0510.02531.547-0.004-0.0040.0000.0000.0000.000
58A108PRO00.0120.01829.2140.0040.0040.0000.0000.0000.000
59A109TYR0-0.033-0.03229.875-0.009-0.0090.0000.0000.0000.000
60A110ASP-1-0.940-0.96824.609-0.047-0.0470.0000.0000.0000.000
61A111THR0-0.0080.01724.966-0.007-0.0070.0000.0000.0000.000
62A112LYS10.8680.93121.4700.2450.2450.0000.0000.0000.000
63A113VAL00.0880.02426.7000.0040.0040.0000.0000.0000.000
64A114ASN00.007-0.02125.6070.0110.0110.0000.0000.0000.000
65A115ASP-1-0.865-0.93129.519-0.125-0.1250.0000.0000.0000.000
66A116ILE0-0.020-0.00730.1620.0050.0050.0000.0000.0000.000
67A117ASN0-0.107-0.06432.5170.0100.0100.0000.0000.0000.000
68A118GLU-1-0.945-0.94535.722-0.088-0.0880.0000.0000.0000.000
69A129GLY0-0.044-0.04134.5430.0020.0020.0000.0000.0000.000
70A130GLU-1-0.843-0.92333.581-0.080-0.0800.0000.0000.0000.000
71A131ALA00.0210.01433.6850.0020.0020.0000.0000.0000.000
72A132ILE0-0.044-0.02232.9420.0010.0010.0000.0000.0000.000
73A133PRO00.0510.03636.2430.0050.0050.0000.0000.0000.000
74A134ALA00.0050.00239.4630.0020.0020.0000.0000.0000.000
75A135GLU-1-0.904-0.95340.631-0.040-0.0400.0000.0000.0000.000
76A136PHE0-0.034-0.02938.0000.0040.0040.0000.0000.0000.000
77A137ARG10.8550.95232.4610.0550.0550.0000.0000.0000.000
78A138GLU-1-0.920-0.96234.682-0.006-0.0060.0000.0000.0000.000
79A139LYS10.7790.89537.5610.0310.0310.0000.0000.0000.000
80A140LEU00.0160.00837.6570.0020.0020.0000.0000.0000.000
81A141ASP-1-0.846-0.94141.4110.0090.0090.0000.0000.0000.000
82A142THR0-0.093-0.05042.7590.0030.0030.0000.0000.0000.000
83A143ARG10.8430.91542.737-0.020-0.0200.0000.0000.0000.000
84A144SER00.0680.05338.7580.0000.0000.0000.0000.0000.000
85A145PHE00.0200.02434.9270.0020.0020.0000.0000.0000.000
86A154ALA0-0.030-0.02947.4170.0000.0000.0000.0000.0000.000
87A155HIS00.0010.00145.0280.0000.0000.0000.0000.0000.000
88A156LEU00.0450.02247.4980.0000.0000.0000.0000.0000.000
89A157PRO00.0860.03346.7940.0000.0000.0000.0000.0000.000
90A158GLU-1-0.929-0.95344.389-0.043-0.0430.0000.0000.0000.000
91A159PHE00.0260.00641.745-0.001-0.0010.0000.0000.0000.000
92A160ASN0-0.044-0.00242.0880.0050.0050.0000.0000.0000.000
93A161GLY00.0300.02039.512-0.005-0.0050.0000.0000.0000.000
94A163HIS00.0430.00430.399-0.005-0.0050.0000.0000.0000.000
95A164VAL0-0.017-0.01932.2800.0050.0050.0000.0000.0000.000
96A165PHE0-0.014-0.00529.407-0.005-0.0050.0000.0000.0000.000
97A166GLY00.0330.02128.6610.0070.0070.0000.0000.0000.000
98A167SER0-0.019-0.02524.688-0.006-0.0060.0000.0000.0000.000
99A168ILE0-0.004-0.00527.3100.0060.0060.0000.0000.0000.000
100A169PRO0-0.0220.00827.277-0.010-0.0100.0000.0000.0000.000
101A170VAL0-0.034-0.01526.5940.0010.0010.0000.0000.0000.000
102A171ASN00.002-0.01427.4340.0060.0060.0000.0000.0000.000
103A172ARG10.8690.94818.1080.1880.1880.0000.0000.0000.000
104A173VAL0-0.041-0.03025.715-0.010-0.0100.0000.0000.0000.000
105A174SER0-0.027-0.01927.681-0.003-0.0030.0000.0000.0000.000
106A175GLY00.0610.00828.5710.0150.0150.0000.0000.0000.000
107A176GLU-1-0.864-0.92529.647-0.120-0.1200.0000.0000.0000.000
108A177LEU00.0220.02228.9620.0100.0100.0000.0000.0000.000
109A178GLN0-0.129-0.09231.612-0.001-0.0010.0000.0000.0000.000
110A179ILE00.0790.05232.1070.0080.0080.0000.0000.0000.000
111A180THR0-0.007-0.00736.037-0.002-0.0020.0000.0000.0000.000
112A181ALA00.0620.03039.6720.0040.0040.0000.0000.0000.000
113A182LYS10.8630.94443.1610.0260.0260.0000.0000.0000.000
114A183SER0-0.042-0.03045.2220.0010.0010.0000.0000.0000.000
115A184LEU0-0.023-0.00847.7280.0000.0000.0000.0000.0000.000
116A185GLY00.0370.01750.524-0.001-0.0010.0000.0000.0000.000
117A186TYR00.0280.00253.7700.0010.0010.0000.0000.0000.000
118A187VAL00.0150.02657.0480.0010.0010.0000.0000.0000.000
119A188ALA00.034-0.00958.315-0.001-0.0010.0000.0000.0000.000
120A189SER0-0.0200.01054.370-0.001-0.0010.0000.0000.0000.000
121A190ARG10.8270.91152.5130.0300.0300.0000.0000.0000.000
122A191LYS10.9760.97748.4910.0460.0460.0000.0000.0000.000
123A192ALA00.0480.04146.9580.0020.0020.0000.0000.0000.000
124A193PRO00.0060.00948.950-0.003-0.0030.0000.0000.0000.000
125A194LEU0-0.008-0.02447.5670.0000.0000.0000.0000.0000.000
126A195GLU-1-0.942-0.94947.521-0.036-0.0360.0000.0000.0000.000
127A196GLU-1-0.939-0.98547.371-0.034-0.0340.0000.0000.0000.000
128A197LEU0-0.122-0.04943.5690.0000.0000.0000.0000.0000.000
129A198LYS10.8860.93041.4300.0440.0440.0000.0000.0000.000
130A199PHE0-0.012-0.00737.2210.0030.0030.0000.0000.0000.000
131A200ASN00.0320.02836.150-0.011-0.0110.0000.0000.0000.000
132A201HIS0-0.044-0.00430.417-0.003-0.0030.0000.0000.0000.000
133A202VAL00.0290.01429.008-0.007-0.0070.0000.0000.0000.000
134A203ILE0-0.031-0.01024.8270.0090.0090.0000.0000.0000.000
135A204ASN0-0.013-0.03125.622-0.014-0.0140.0000.0000.0000.000
136A205GLU-1-0.827-0.90621.113-0.049-0.0490.0000.0000.0000.000
137A206PHE0-0.020-0.01721.9630.0050.0050.0000.0000.0000.000
138A207SER0-0.0180.00118.475-0.030-0.0300.0000.0000.0000.000
139A208PHE00.005-0.00218.7640.0150.0150.0000.0000.0000.000
140A209GLY0-0.016-0.01117.953-0.021-0.0210.0000.0000.0000.000
141A210ASP-1-0.862-0.91816.5260.0740.0740.0000.0000.0000.000
142A211PHE00.0410.00915.901-0.022-0.0220.0000.0000.0000.000
143A212TYR0-0.053-0.0369.6260.0250.0250.0000.0000.0000.000
144A213PRO0-0.028-0.03210.132-0.046-0.0460.0000.0000.0000.000
145A214TYR0-0.077-0.0466.2830.2320.2320.0000.0000.0000.000
146A215ILE0-0.0470.0119.392-0.148-0.1480.0000.0000.0000.000
147A216ASP-1-0.915-0.95912.360-0.380-0.3800.0000.0000.0000.000
148A217ASN0-0.076-0.03714.109-0.081-0.0810.0000.0000.0000.000
149A218PRO0-0.025-0.02017.0040.0210.0210.0000.0000.0000.000
150A219LEU0-0.020-0.02419.4240.0140.0140.0000.0000.0000.000
151A220ASP-1-0.761-0.84619.146-0.121-0.1210.0000.0000.0000.000
152A221ASN0-0.023-0.00220.9130.0040.0040.0000.0000.0000.000
153A222THR0-0.106-0.05823.565-0.011-0.0110.0000.0000.0000.000
154A223ALA00.0350.01526.1830.0140.0140.0000.0000.0000.000
155A224GLN00.000-0.00129.938-0.009-0.0090.0000.0000.0000.000
156A225PHE0-0.052-0.04432.6390.0100.0100.0000.0000.0000.000
157A226ASN00.1160.05936.2850.0010.0010.0000.0000.0000.000
158A227GLN0-0.035-0.02839.4940.0060.0060.0000.0000.0000.000
159A228ASP-1-0.879-0.92542.661-0.063-0.0630.0000.0000.0000.000
160A229GLU-1-1.043-1.00841.216-0.076-0.0760.0000.0000.0000.000
161A230PRO00.0560.03941.171-0.004-0.0040.0000.0000.0000.000
162A231LEU0-0.054-0.03841.389-0.001-0.0010.0000.0000.0000.000
163A232THR0-0.044-0.02537.248-0.002-0.0020.0000.0000.0000.000
164A233THR0-0.041-0.00836.6990.0040.0040.0000.0000.0000.000
165A234TYR00.0240.00732.456-0.005-0.0050.0000.0000.0000.000
166A235VAL0-0.033-0.01431.0380.0050.0050.0000.0000.0000.000
167A236TYR00.018-0.00526.395-0.012-0.0120.0000.0000.0000.000
168A237TYR0-0.057-0.02926.6440.0150.0150.0000.0000.0000.000
169A238THR0-0.009-0.01521.996-0.020-0.0200.0000.0000.0000.000
170A239SER0-0.069-0.05619.9440.0330.0330.0000.0000.0000.000
171A240VAL0-0.002-0.00918.327-0.044-0.0440.0000.0000.0000.000
172A241VAL0-0.007-0.00613.3440.0000.0000.0000.0000.0000.000
173A242PRO00.0310.03514.617-0.012-0.0120.0000.0000.0000.000
174A243THR00.001-0.0269.459-0.047-0.0470.0000.0000.0000.000
175A244LEU00.0270.0319.6220.1300.1300.0000.0000.0000.000
176A245PHE00.0770.0375.116-0.186-0.1860.0000.0000.0000.000
177A246LYS10.9260.9466.0640.1300.1300.0000.0000.0000.000
178A247LYS10.8860.9352.325-8.661-8.4201.464-0.363-1.3420.005
179A248LEU0-0.052-0.0176.387-0.012-0.0120.0000.0000.0000.000
180A249GLY00.0490.0469.494-0.028-0.0280.0000.0000.0000.000
181A250ALA0-0.044-0.04111.709-0.084-0.0840.0000.0000.0000.000
182A251GLU-1-0.922-0.97113.9350.3070.3070.0000.0000.0000.000
183A252VAL0-0.036-0.00312.274-0.022-0.0220.0000.0000.0000.000
184A253ASP-1-0.892-0.95314.720-0.126-0.1260.0000.0000.0000.000
185A254THR0-0.0220.00211.4900.0130.0130.0000.0000.0000.000
186A255ASN00.0170.00113.936-0.077-0.0770.0000.0000.0000.000
187A256GLN00.0150.02310.038-0.010-0.0100.0000.0000.0000.000
188A257TYR0-0.021-0.03114.355-0.002-0.0020.0000.0000.0000.000
189A258SER0-0.0110.01116.925-0.014-0.0140.0000.0000.0000.000
190A259VAL00.047-0.00218.6530.0290.0290.0000.0000.0000.000
191A260ASN0-0.082-0.02322.3320.0010.0010.0000.0000.0000.000
192A261ASP-1-0.807-0.90925.463-0.200-0.2000.0000.0000.0000.000
193A262TYR0-0.070-0.04728.5390.0050.0050.0000.0000.0000.000
194A263ARG10.9260.96431.4000.1500.1500.0000.0000.0000.000
195A264TYR0-0.036-0.01135.243-0.001-0.0010.0000.0000.0000.000
196A265LEU00.0780.04138.9520.0040.0040.0000.0000.0000.000
197A266TYR00.0920.03742.1130.0020.0020.0000.0000.0000.000
198A267LYS10.9050.95044.4720.0860.0860.0000.0000.0000.000
199A268ASP-1-0.894-0.94943.130-0.089-0.0890.0000.0000.0000.000
200A269VAL00.005-0.00540.8910.0010.0010.0000.0000.0000.000
201A270ALA0-0.043-0.01543.9400.0020.0020.0000.0000.0000.000
202A271ALA0-0.030-0.00947.2490.0030.0030.0000.0000.0000.000
203A272LYS10.7870.87844.5890.0790.0790.0000.0000.0000.000
204A273GLY00.0500.03942.079-0.001-0.0010.0000.0000.0000.000
205A274ASP-1-0.860-0.93638.542-0.096-0.0960.0000.0000.0000.000
206A275LYS10.8910.94541.6820.0660.0660.0000.0000.0000.000
207A276MET0-0.068-0.02242.1060.0040.0040.0000.0000.0000.000
208A277PRO00.0260.01540.778-0.003-0.0030.0000.0000.0000.000
209A278GLY00.0250.00338.1570.0050.0050.0000.0000.0000.000
210A279ILE0-0.0040.01531.790-0.006-0.0060.0000.0000.0000.000
211A280PHE0-0.066-0.03432.6780.0060.0060.0000.0000.0000.000
212A281PHE00.0720.03926.592-0.010-0.0100.0000.0000.0000.000
213A282LYS10.9050.95228.7300.1390.1390.0000.0000.0000.000
214A283TYR00.0350.03324.482-0.014-0.0140.0000.0000.0000.000
215A284ASN00.009-0.00424.0670.0190.0190.0000.0000.0000.000
216A285PHE00.0290.00920.824-0.017-0.0170.0000.0000.0000.000
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