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

tag_button

FMODB ID: N1VRQ

Calculation Name: 3ZLC-A-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 230
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2862246.636984
FMO2-HF: Nuclear repulsion 2770574.529819
FMO2-HF: Total energy -91672.107165
FMO2-MP2: Total energy -91941.317249


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:50:ACE )


Summations of interaction energy for fragment #1(A:50:ACE )
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.
0.1951.349-0.005-0.511-0.638-0.001
Interaction energy analysis for fragmet #1(A:50:ACE )
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 : -0.017
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].
3A52ASP -1-0.903-0.9313.841-0.0211.083-0.006-0.455-0.643-0.001
4A53GLN 0-0.009-0.0096.670-0.137-0.1370.0000.0000.0000.000
5A54GLN 0-0.022-0.00810.3630.0910.0910.0000.0000.0000.000
6A55TYR 00.0170.01913.170-0.005-0.0050.0000.0000.0000.000
7A56VAL 0-0.047-0.02916.1540.0100.0100.0000.0000.0000.000
8A57VAL 00.007-0.01218.8660.0080.0080.0000.0000.0000.000
9A58ASP -1-0.870-0.91122.101-0.177-0.1770.0000.0000.0000.000
10A59SER 0-0.085-0.04423.0950.0190.0190.0000.0000.0000.000
11A60GLN 0-0.060-0.04823.8750.0040.0040.0000.0000.0000.000
12A61VAL 00.0500.04125.609-0.009-0.0090.0000.0000.0000.000
13A62ARG 10.9150.96822.5610.1870.1870.0000.0000.0000.000
14A63ASP -1-0.865-0.93528.740-0.090-0.0900.0000.0000.0000.000
15A64THR 0-0.088-0.03531.2760.0040.0040.0000.0000.0000.000
16A65VAL 0-0.012-0.00627.303-0.010-0.0100.0000.0000.0000.000
17A66GLN 00.0320.01929.0880.0110.0110.0000.0000.0000.000
18A67ILE 00.0000.00529.186-0.008-0.0080.0000.0000.0000.000
19A68ASN 0-0.010-0.00227.2250.0140.0140.0000.0000.0000.000
20A69MET 0-0.028-0.00830.500-0.001-0.0010.0000.0000.0000.000
21A70ASP -1-0.802-0.88232.360-0.063-0.0630.0000.0000.0000.000
22A71ILE 00.000-0.01233.610-0.001-0.0010.0000.0000.0000.000
23A72TYR 00.0270.02736.2840.0030.0030.0000.0000.0000.000
24A73VAL 00.0320.00039.2900.0000.0000.0000.0000.0000.000
25A74ASN 0-0.072-0.02842.0770.0020.0020.0000.0000.0000.000
26A75THR 0-0.007-0.03544.9870.0030.0030.0000.0000.0000.000
27A76LYS 10.9640.98646.5790.0280.0280.0000.0000.0000.000
28A162CYS 00.0150.04144.0070.0000.0000.0000.0000.0000.000
29A78ASP -1-0.863-0.91847.673-0.034-0.0340.0000.0000.0000.000
30A79TRP 0-0.047-0.04150.2530.0010.0010.0000.0000.0000.000
31A80LEU 0-0.029-0.00744.2570.0000.0000.0000.0000.0000.000
32A81GLN 0-0.052-0.02846.9660.0000.0000.0000.0000.0000.000
33A82ILE 00.0710.03640.4380.0000.0000.0000.0000.0000.000
34A83ASN 0-0.053-0.03042.9110.0010.0010.0000.0000.0000.000
35A84VAL 00.0690.04838.256-0.002-0.0020.0000.0000.0000.000
36A85ARG 10.8710.93440.1850.0540.0540.0000.0000.0000.000
37A86ASP -1-0.732-0.83237.973-0.069-0.0690.0000.0000.0000.000
38A87GLN 0-0.044-0.03037.3420.0040.0040.0000.0000.0000.000
39A88THR 0-0.130-0.08539.2190.0030.0030.0000.0000.0000.000
40A89MET 0-0.062-0.01741.3220.0030.0030.0000.0000.0000.000
41A90ASP -1-0.907-0.96043.858-0.042-0.0420.0000.0000.0000.000
42A91ARG 10.8790.93444.7700.0420.0420.0000.0000.0000.000
43A92LYS 10.9891.00440.0470.0630.0630.0000.0000.0000.000
44A93LEU 0-0.029-0.02643.839-0.001-0.0010.0000.0000.0000.000
45A94VAL 0-0.0020.00440.082-0.001-0.0010.0000.0000.0000.000
46A95LEU 0-0.075-0.04643.1390.0020.0020.0000.0000.0000.000
47A96GLU -1-0.943-0.98242.803-0.051-0.0510.0000.0000.0000.000
48A97GLU -1-0.937-0.96138.330-0.062-0.0620.0000.0000.0000.000
49A98LEU 0-0.069-0.02537.049-0.004-0.0040.0000.0000.0000.000
50A99GLN 0-0.0090.01239.6830.0030.0030.0000.0000.0000.000
51A100LEU 0-0.030-0.02941.007-0.001-0.0010.0000.0000.0000.000
52A101GLU -1-0.913-0.96042.642-0.043-0.0430.0000.0000.0000.000
53A102GLU -1-0.903-0.97144.252-0.034-0.0340.0000.0000.0000.000
54A103MET 0-0.0490.00040.258-0.001-0.0010.0000.0000.0000.000
55A104PRO 0-0.063-0.02644.8190.0010.0010.0000.0000.0000.000
56A105PHE 0-0.002-0.02740.717-0.001-0.0010.0000.0000.0000.000
57A106PHE 0-0.007-0.01137.8390.0030.0030.0000.0000.0000.000
58A107ILE 00.0400.02136.637-0.003-0.0030.0000.0000.0000.000
59A108PRO 00.0150.01934.1380.0040.0040.0000.0000.0000.000
60A109TYR 0-0.024-0.02933.8760.0020.0020.0000.0000.0000.000
61A110ASP -1-0.940-0.96728.797-0.047-0.0470.0000.0000.0000.000
62A111THR 0-0.0070.01729.581-0.007-0.0070.0000.0000.0000.000
63A112LYS 10.8670.93026.1960.0800.0800.0000.0000.0000.000
64A113VAL 00.0870.02431.417-0.001-0.0010.0000.0000.0000.000
65A114ASN 00.004-0.02230.6970.0040.0040.0000.0000.0000.000
66A115ASP -1-0.861-0.92834.469-0.039-0.0390.0000.0000.0000.000
67A116ILE 0-0.016-0.00534.4010.0030.0030.0000.0000.0000.000
68A117ASN 0-0.099-0.06137.3750.0020.0020.0000.0000.0000.000
69A118GLU -1-0.871-0.90240.307-0.021-0.0210.0000.0000.0000.000
70A119NME 0-0.091-0.05142.421-0.002-0.0020.0000.0000.0000.000
71A128ACE 0-0.008-0.02139.2080.0000.0000.0000.0000.0000.000
72A129GLY 0-0.033-0.03137.5380.0020.0020.0000.0000.0000.000
73A130GLU -1-0.841-0.91036.979-0.030-0.0300.0000.0000.0000.000
74A131ALA 00.0150.01137.9490.0010.0010.0000.0000.0000.000
75A132ILE 0-0.041-0.02137.6860.0000.0000.0000.0000.0000.000
76A133PRO 00.0480.03440.6770.0020.0020.0000.0000.0000.000
77A134ALA 00.0080.00443.876-0.001-0.0010.0000.0000.0000.000
78A135GLU -1-0.904-0.95244.905-0.021-0.0210.0000.0000.0000.000
79A136PHE 0-0.034-0.02943.023-0.001-0.0010.0000.0000.0000.000
80A137ARG 10.8520.95036.9540.0300.0300.0000.0000.0000.000
81A138GLU -1-0.917-0.96139.337-0.036-0.0360.0000.0000.0000.000
82A139LYS 10.7750.89342.3180.0280.0280.0000.0000.0000.000
83A140LEU 00.0180.00942.106-0.001-0.0010.0000.0000.0000.000
84A141ASP -1-0.848-0.94446.054-0.023-0.0230.0000.0000.0000.000
85A142THR 0-0.097-0.04947.3120.0000.0000.0000.0000.0000.000
86A143ARG 10.8530.91847.3020.0230.0230.0000.0000.0000.000
87A144SER 00.0650.04943.482-0.001-0.0010.0000.0000.0000.000
88A145PHE 00.0120.01039.333-0.002-0.0020.0000.0000.0000.000
89A146NME 00.0070.01440.5430.0010.0010.0000.0000.0000.000
90A153ACE 00.0360.00651.5080.0000.0000.0000.0000.0000.000
91A154ALA 0-0.077-0.04152.3340.0010.0010.0000.0000.0000.000
92A155HIS 00.0150.01050.2550.0000.0000.0000.0000.0000.000
93A156LEU 00.0450.02252.7620.0000.0000.0000.0000.0000.000
94A157PRO 00.0870.03352.280-0.001-0.0010.0000.0000.0000.000
95A158GLU -1-0.930-0.95249.641-0.024-0.0240.0000.0000.0000.000
96A159PHE 00.0240.00546.978-0.001-0.0010.0000.0000.0000.000
97A160ASN 0-0.042-0.00247.670-0.001-0.0010.0000.0000.0000.000
98A161GLY 00.0290.02045.289-0.001-0.0010.0000.0000.0000.000
99A163HIS 00.0430.00336.2760.0020.0020.0000.0000.0000.000
100A164VAL 0-0.015-0.01838.6840.0010.0010.0000.0000.0000.000
101A165PHE 0-0.012-0.00435.545-0.004-0.0040.0000.0000.0000.000
102A166GLY 00.0290.02034.9950.0040.0040.0000.0000.0000.000
103A167SER 0-0.016-0.02431.077-0.003-0.0030.0000.0000.0000.000
104A168ILE 0-0.003-0.00633.8440.0050.0050.0000.0000.0000.000
105A169PRO 0-0.0230.00833.621-0.006-0.0060.0000.0000.0000.000
106A170VAL 0-0.034-0.01533.0670.0070.0070.0000.0000.0000.000
107A171ASN 00.000-0.01533.684-0.007-0.0070.0000.0000.0000.000
108A172ARG 10.8710.95024.3110.1530.1530.0000.0000.0000.000
109A173VAL 0-0.043-0.03231.9080.0000.0000.0000.0000.0000.000
110A174SER 0-0.028-0.01933.915-0.001-0.0010.0000.0000.0000.000
111A175GLY 00.0620.00934.9480.0050.0050.0000.0000.0000.000
112A176GLU -1-0.864-0.92536.149-0.055-0.0550.0000.0000.0000.000
113A177LEU 00.0220.02135.5900.0020.0020.0000.0000.0000.000
114A178GLN 0-0.127-0.09038.2250.0020.0020.0000.0000.0000.000
115A179ILE 00.0790.05238.5480.0010.0010.0000.0000.0000.000
116A180THR 0-0.011-0.00842.5210.0010.0010.0000.0000.0000.000
117A181ALA 00.0630.03046.1180.0000.0000.0000.0000.0000.000
118A182LYS 10.8650.94749.5880.0340.0340.0000.0000.0000.000
119A183SER 0-0.036-0.03151.7490.0020.0020.0000.0000.0000.000
120A184LEU 0-0.015-0.00554.2700.0000.0000.0000.0000.0000.000
121A185GLY 0-0.004-0.00357.1630.0010.0010.0000.0000.0000.000
122A186TYR 00.0420.00859.2720.0000.0000.0000.0000.0000.000
123A187VAL 0-0.012-0.00563.0500.0000.0000.0000.0000.0000.000
124A188ALA 0-0.016-0.01364.2380.0010.0010.0000.0000.0000.000
125A189SER 00.0250.00561.3640.0000.0000.0000.0000.0000.000
126A190ARG 10.8460.93959.0840.0250.0250.0000.0000.0000.000
127A191LYS 10.9990.99954.8410.0250.0250.0000.0000.0000.000
128A192ALA 00.0530.04153.2740.0010.0010.0000.0000.0000.000
129A193PRO 00.0030.00755.2820.0000.0000.0000.0000.0000.000
130A194LEU 0-0.006-0.02353.665-0.001-0.0010.0000.0000.0000.000
131A195GLU -1-0.942-0.94853.514-0.022-0.0220.0000.0000.0000.000
132A196GLU -1-0.939-0.98453.463-0.025-0.0250.0000.0000.0000.000
133A197LEU 0-0.129-0.05249.797-0.001-0.0010.0000.0000.0000.000
134A198LYS 10.8930.93147.1970.0290.0290.0000.0000.0000.000
135A199PHE 0-0.008-0.00643.277-0.001-0.0010.0000.0000.0000.000
136A200ASN 00.0180.02141.942-0.002-0.0020.0000.0000.0000.000
137A201HIS 0-0.0360.00036.380-0.003-0.0030.0000.0000.0000.000
138A202VAL 00.0230.01234.6320.0010.0010.0000.0000.0000.000
139A203ILE 0-0.027-0.00830.8690.0000.0000.0000.0000.0000.000
140A204ASN 0-0.022-0.03331.282-0.001-0.0010.0000.0000.0000.000
141A205GLU -1-0.822-0.90427.342-0.119-0.1190.0000.0000.0000.000
142A206PHE 0-0.022-0.01828.2210.0070.0070.0000.0000.0000.000
143A207SER 0-0.0180.00125.022-0.009-0.0090.0000.0000.0000.000
144A208PHE 00.000-0.00425.4140.0100.0100.0000.0000.0000.000
145A209GLY 0-0.010-0.00924.527-0.016-0.0160.0000.0000.0000.000
146A210ASP -1-0.864-0.91922.660-0.155-0.1550.0000.0000.0000.000
147A211PHE 00.0410.00922.221-0.023-0.0230.0000.0000.0000.000
148A212TYR 0-0.049-0.03516.172-0.032-0.0320.0000.0000.0000.000
149A213PRO 0-0.030-0.03215.2920.0070.0070.0000.0000.0000.000
150A214TYR 0-0.077-0.04611.937-0.032-0.0320.0000.0000.0000.000
151A215ILE 0-0.0490.01115.251-0.005-0.0050.0000.0000.0000.000
152A216ASP -1-0.911-0.95718.152-0.143-0.1430.0000.0000.0000.000
153A217ASN 0-0.075-0.03819.994-0.012-0.0120.0000.0000.0000.000
154A218PRO 0-0.024-0.01923.0740.0120.0120.0000.0000.0000.000
155A219LEU 0-0.025-0.02625.2040.0100.0100.0000.0000.0000.000
156A220ASP -1-0.758-0.84525.137-0.112-0.1120.0000.0000.0000.000
157A221ASN 0-0.024-0.00226.1810.0070.0070.0000.0000.0000.000
158A222THR 0-0.108-0.05729.0400.0060.0060.0000.0000.0000.000
159A223ALA 00.0310.01331.5710.0000.0000.0000.0000.0000.000
160A224GLN 00.0080.00435.3520.0040.0040.0000.0000.0000.000
161A225PHE 0-0.053-0.04538.0760.0000.0000.0000.0000.0000.000
162A226ASN 00.1220.06241.6320.0020.0020.0000.0000.0000.000
163A227GLN 0-0.039-0.03044.7280.0000.0000.0000.0000.0000.000
164A228ASP -1-0.879-0.92447.877-0.021-0.0210.0000.0000.0000.000
165A229GLU -1-1.040-1.00746.634-0.025-0.0250.0000.0000.0000.000
166A230PRO 00.0520.03646.773-0.002-0.0020.0000.0000.0000.000
167A231LEU 0-0.061-0.04047.247-0.002-0.0020.0000.0000.0000.000
168A232THR 0-0.045-0.02542.9990.0000.0000.0000.0000.0000.000
169A233THR 0-0.039-0.00742.787-0.001-0.0010.0000.0000.0000.000
170A234TYR 00.0290.00938.3830.0000.0000.0000.0000.0000.000
171A235VAL 0-0.032-0.01337.299-0.001-0.0010.0000.0000.0000.000
172A236TYR 00.017-0.00532.5170.0000.0000.0000.0000.0000.000
173A237TYR 0-0.056-0.02832.9610.0000.0000.0000.0000.0000.000
174A238THR 0-0.011-0.01528.401-0.004-0.0040.0000.0000.0000.000
175A239SER 0-0.067-0.05626.3180.0060.0060.0000.0000.0000.000
176A240VAL 0-0.001-0.00924.795-0.011-0.0110.0000.0000.0000.000
177A241VAL 0-0.010-0.00719.6320.0030.0030.0000.0000.0000.000
178A242PRO 00.0400.03921.001-0.015-0.0150.0000.0000.0000.000
179A243THR 0-0.003-0.02615.680-0.008-0.0080.0000.0000.0000.000
180A244LEU 00.0230.02714.7530.0140.0140.0000.0000.0000.000
181A245PHE 00.0780.03811.305-0.122-0.1220.0000.0000.0000.000
182A246LYS 10.9230.94310.4100.6250.6250.0000.0000.0000.000
183A247LYS 10.8870.9386.1521.3831.3830.0000.0000.0000.000
184A248LEU 0-0.052-0.01711.4180.0640.0640.0000.0000.0000.000
185A249GLY 00.0490.04515.0830.0470.0470.0000.0000.0000.000
186A250ALA 0-0.047-0.04316.933-0.009-0.0090.0000.0000.0000.000
187A251GLU -1-0.921-0.97119.216-0.219-0.2190.0000.0000.0000.000
188A252VAL 0-0.035-0.00218.3050.0170.0170.0000.0000.0000.000
189A253ASP -1-0.891-0.95320.632-0.187-0.1870.0000.0000.0000.000
190A254THR 0-0.0230.00217.6020.0000.0000.0000.0000.0000.000
191A255ASN 00.0190.00220.2140.0000.0000.0000.0000.0000.000
192A256GLN 00.0120.02216.420-0.029-0.0290.0000.0000.0000.000
193A257TYR 0-0.019-0.03120.9010.0120.0120.0000.0000.0000.000
194A258SER 0-0.0140.00923.1190.0030.0030.0000.0000.0000.000
195A259VAL 00.047-0.00224.8270.0020.0020.0000.0000.0000.000
196A260ASN 0-0.080-0.02228.4120.0070.0070.0000.0000.0000.000
197A261ASP -1-0.805-0.90831.373-0.068-0.0680.0000.0000.0000.000
198A262TYR 0-0.072-0.04934.3750.0050.0050.0000.0000.0000.000
199A263ARG 10.9300.96736.7670.0400.0400.0000.0000.0000.000
200A264TYR 0-0.041-0.01341.1330.0020.0020.0000.0000.0000.000
201A265LEU 00.0820.04144.8040.0000.0000.0000.0000.0000.000
202A266TYR 00.0980.04147.8370.0000.0000.0000.0000.0000.000
203A267LYS 10.9190.95850.3330.0250.0250.0000.0000.0000.000
204A268ASP -1-0.874-0.93549.037-0.026-0.0260.0000.0000.0000.000
205A269VAL 00.0530.01946.9830.0000.0000.0000.0000.0000.000
206A270ALA 0-0.047-0.01550.0510.0000.0000.0000.0000.0000.000
207A271ALA 0-0.090-0.04353.2520.0010.0010.0000.0000.0000.000
208A272LYS 10.7850.88450.5330.0270.0270.0000.0000.0000.000
209A273GLY 00.0380.01548.386-0.001-0.0010.0000.0000.0000.000
210A274ASP -1-0.884-0.93844.836-0.040-0.0400.0000.0000.0000.000
211A275LYS 10.8980.94848.0480.0300.0300.0000.0000.0000.000
212A276MET 0-0.070-0.02448.5390.0010.0010.0000.0000.0000.000
213A277PRO 00.0300.01546.978-0.001-0.0010.0000.0000.0000.000
214A278GLY 00.0200.00244.4170.0000.0000.0000.0000.0000.000
215A279ILE 00.0010.01638.0870.0000.0000.0000.0000.0000.000
216A280PHE 0-0.069-0.03539.048-0.001-0.0010.0000.0000.0000.000
217A281PHE 00.0730.03932.972-0.001-0.0010.0000.0000.0000.000
218A282LYS 10.9050.95335.1140.0550.0550.0000.0000.0000.000
219A283TYR 00.0380.03530.973-0.004-0.0040.0000.0000.0000.000
220A284ASN 00.006-0.00530.5730.0030.0030.0000.0000.0000.000
221A285PHE 00.0230.00727.136-0.007-0.0070.0000.0000.0000.000
222A286GLU -1-0.870-0.91723.697-0.138-0.1380.0000.0000.0000.000
223A287PRO 0-0.0140.00025.577-0.007-0.0070.0000.0000.0000.000
224A288LEU 0-0.070-0.04020.3400.0000.0000.0000.0000.0000.000
225A289SER 00.0840.03318.8220.0030.0030.0000.0000.0000.000
226A290ILE 0-0.0180.00113.700-0.001-0.0010.0000.0000.0000.000
227A291VAL 0-0.031-0.01212.008-0.025-0.0250.0000.0000.0000.000
228A292VAL 00.0450.0218.476-0.085-0.0850.0000.0000.0000.000
229A293SER 0-0.015-0.0207.9650.1840.1840.0000.0000.0000.000
230A294NME 00.0330.0244.153-0.495-0.4450.001-0.0560.0050.000