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: 6N4LZ

Calculation Name: 3WZ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WZ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U4Q9

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2762174.362398
FMO2-HF: Nuclear repulsion 2674925.50993
FMO2-HF: Total energy -87248.852468
FMO2-MP2: Total energy -87503.347289


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-4.6341.8181.448-3.046-4.853-0.009
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.003
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].
3A8ASN0-0.034-0.0103.614-0.5242.193-0.015-1.303-1.3990.001
4A9LEU00.005-0.0036.168-0.460-0.4600.0000.0000.0000.000
5A10VAL0-0.041-0.0039.4210.0760.0760.0000.0000.0000.000
6A11LEU00.022-0.00412.378-0.084-0.0840.0000.0000.0000.000
7A12PRO00.0170.02614.8870.0170.0170.0000.0000.0000.000
8A13GLU-1-0.855-0.90917.0480.1710.1710.0000.0000.0000.000
9A14VAL00.0020.00618.868-0.003-0.0030.0000.0000.0000.000
10A15GLU-1-0.909-0.95621.4250.0490.0490.0000.0000.0000.000
11A16ASN0-0.044-0.03223.809-0.008-0.0080.0000.0000.0000.000
12A17ALA00.0030.01720.820-0.006-0.0060.0000.0000.0000.000
13A18ILE00.0180.00622.897-0.012-0.0120.0000.0000.0000.000
14A19PHE00.008-0.00315.2060.0040.0040.0000.0000.0000.000
15A20ILE00.0210.00520.965-0.014-0.0140.0000.0000.0000.000
16A21GLU-1-0.772-0.86316.417-0.120-0.1200.0000.0000.0000.000
17A22GLY00.0360.00919.363-0.004-0.0040.0000.0000.0000.000
18A23TYR0-0.034-0.03112.516-0.017-0.0170.0000.0000.0000.000
19A24PRO0-0.050-0.01617.0950.0010.0010.0000.0000.0000.000
20A25GLY00.0510.01719.057-0.021-0.0210.0000.0000.0000.000
21A26VAL00.0230.00121.6480.0100.0100.0000.0000.0000.000
22A27GLY00.0870.04125.2350.0030.0030.0000.0000.0000.000
23A28LEU0-0.042-0.02122.8450.0060.0060.0000.0000.0000.000
24A29VAL00.0010.01925.3210.0060.0060.0000.0000.0000.000
25A30GLY00.0430.01623.4990.0060.0060.0000.0000.0000.000
26A31HIS0-0.013-0.01420.5640.0050.0050.0000.0000.0000.000
27A32ILE00.0270.01423.4040.0110.0110.0000.0000.0000.000
28A33ALA00.0110.00926.5590.0070.0070.0000.0000.0000.000
29A34ALA00.0090.00622.7170.0070.0070.0000.0000.0000.000
30A35ASN0-0.025-0.03922.6700.0180.0180.0000.0000.0000.000
31A36PHE0-0.023-0.00225.7330.0070.0070.0000.0000.0000.000
32A37LEU00.0210.00227.0210.0040.0040.0000.0000.0000.000
33A38ALA00.0100.01024.7020.0050.0050.0000.0000.0000.000
34A39LYS10.8450.92026.798-0.008-0.0080.0000.0000.0000.000
35A40GLU-1-0.859-0.93429.6890.0160.0160.0000.0000.0000.000
36A41LEU0-0.085-0.03528.7190.0000.0000.0000.0000.0000.000
37A42ASP-1-0.942-0.96430.9190.0520.0520.0000.0000.0000.000
38A43MET0-0.066-0.01925.4740.0060.0060.0000.0000.0000.000
39A44ASP-1-0.829-0.89325.2070.0820.0820.0000.0000.0000.000
40A45LEU0-0.058-0.03718.709-0.003-0.0030.0000.0000.0000.000
41A46ILE0-0.003-0.00519.0480.0120.0120.0000.0000.0000.000
42A47GLY00.016-0.00316.1770.0310.0310.0000.0000.0000.000
43A48TYR0-0.061-0.03212.101-0.066-0.0660.0000.0000.0000.000
44A49VAL0-0.0220.0038.2830.0680.0680.0000.0000.0000.000
45A50ASP-1-0.884-0.9337.7521.2901.2900.0000.0000.0000.000
46A51SER00.010-0.0313.806-0.0070.5940.000-0.363-0.2380.001
47A52LEU00.0060.0014.557-0.223-0.063-0.001-0.008-0.1500.000
48A53PHE0-0.040-0.0202.691-0.991-0.2250.586-0.299-1.0540.000
49A54ILE0-0.030-0.0037.191-0.054-0.0540.0000.0000.0000.000
50A55PRO0-0.0110.0029.7830.0680.0680.0000.0000.0000.000
51A56PRO00.0100.00212.7250.0180.0180.0000.0000.0000.000
52A57MET0-0.008-0.01514.351-0.026-0.0260.0000.0000.0000.000
53A58SER0-0.043-0.01716.3060.0300.0300.0000.0000.0000.000
54A59LEU0-0.0030.01419.026-0.016-0.0160.0000.0000.0000.000
55A60ILE0-0.019-0.00621.4510.0140.0140.0000.0000.0000.000
56A61LEU00.0200.01123.071-0.011-0.0110.0000.0000.0000.000
57A62GLU-1-0.836-0.91126.3300.0640.0640.0000.0000.0000.000
58A63GLY0-0.022-0.01028.9320.0030.0030.0000.0000.0000.000
59A64ARG10.8610.91924.832-0.069-0.0690.0000.0000.0000.000
60A65PRO0-0.012-0.00320.795-0.009-0.0090.0000.0000.0000.000
61A66THR0-0.005-0.00819.5880.0090.0090.0000.0000.0000.000
62A67PRO00.0360.02814.347-0.014-0.0140.0000.0000.0000.000
63A68PRO00.0510.00313.778-0.013-0.0130.0000.0000.0000.000
64A69LEU0-0.0120.00110.634-0.037-0.0370.0000.0000.0000.000
65A70ARG10.7990.87114.1520.0090.0090.0000.0000.0000.000
66A71PHE00.0160.00112.485-0.038-0.0380.0000.0000.0000.000
67A72TYR00.0280.01518.1540.0210.0210.0000.0000.0000.000
68A73GLY00.0400.00921.772-0.007-0.0070.0000.0000.0000.000
69A74LYS10.8580.92223.519-0.057-0.0570.0000.0000.0000.000
70A75ASN0-0.015-0.00227.019-0.003-0.0030.0000.0000.0000.000
71A76ASN00.0510.02825.5750.0080.0080.0000.0000.0000.000
72A77ILE0-0.0200.00724.717-0.006-0.0060.0000.0000.0000.000
73A78ILE00.018-0.00218.2560.0120.0120.0000.0000.0000.000
74A79ILE0-0.017-0.00621.199-0.016-0.0160.0000.0000.0000.000
75A80ALA0-0.030-0.00315.9630.0160.0160.0000.0000.0000.000
76A81ILE0-0.011-0.00317.701-0.021-0.0210.0000.0000.0000.000
77A82ALA0-0.004-0.01315.0540.0060.0060.0000.0000.0000.000
78A83ASP-1-0.772-0.87216.743-0.004-0.0040.0000.0000.0000.000
79A84ILE0-0.037-0.01212.6410.0010.0010.0000.0000.0000.000
80A85PHE00.0020.00515.532-0.017-0.0170.0000.0000.0000.000
81A86LEU00.0110.0069.488-0.004-0.0040.0000.0000.0000.000
82A87PRO00.0610.0269.3570.0030.0030.0000.0000.0000.000
83A88PRO00.0740.02210.357-0.073-0.0730.0000.0000.0000.000
84A89THR0-0.003-0.0136.9220.0110.0110.0000.0000.0000.000
85A90LEU00.0420.0344.682-0.271-0.201-0.001-0.007-0.0620.000
86A91VAL00.0210.0166.940-0.062-0.0620.0000.0000.0000.000
87A92ASN0-0.039-0.0368.9710.0680.0680.0000.0000.0000.000
88A93GLU-1-0.849-0.9162.830-5.293-3.4010.881-1.056-1.718-0.011
89A94ILE00.0080.0045.4690.1190.1190.0000.0000.0000.000
90A95ALA00.0180.0017.5130.1520.1520.0000.0000.0000.000
91A96LYS10.7910.9024.4031.6361.730-0.001-0.003-0.0890.000
92A97GLU-1-0.820-0.9154.922-0.487-0.335-0.001-0.007-0.1430.000
93A98ILE0-0.0030.0018.2250.1290.1290.0000.0000.0000.000
94A99VAL00.0270.00611.6500.0530.0530.0000.0000.0000.000
95A100ASN0-0.086-0.0438.1920.0210.0210.0000.0000.0000.000
96A101TYR0-0.024-0.03811.7710.0300.0300.0000.0000.0000.000
97A102LEU00.009-0.00513.3620.0090.0090.0000.0000.0000.000
98A103LYS10.8900.94512.8450.1390.1390.0000.0000.0000.000
99A104LYS10.8060.91513.800-0.233-0.2330.0000.0000.0000.000
100A105VAL0-0.041-0.01416.8810.0080.0080.0000.0000.0000.000
101A106ASN0-0.084-0.03819.406-0.013-0.0130.0000.0000.0000.000
102A107ALA0-0.0120.00319.7200.0010.0010.0000.0000.0000.000
103A108GLU-1-0.880-0.93621.682-0.008-0.0080.0000.0000.0000.000
104A109LYS10.8230.91123.9940.0120.0120.0000.0000.0000.000
105A110VAL0-0.0070.00518.3780.0050.0050.0000.0000.0000.000
106A111ILE00.000-0.00621.494-0.009-0.0090.0000.0000.0000.000
107A112SER0-0.017-0.02819.1730.0020.0020.0000.0000.0000.000
108A113LEU0-0.049-0.01721.8370.0050.0050.0000.0000.0000.000
109A114ALA00.0310.00222.921-0.007-0.0070.0000.0000.0000.000
110A115GLY00.0210.01624.5410.0090.0090.0000.0000.0000.000
111A116MET0-0.041-0.02726.606-0.008-0.0080.0000.0000.0000.000
112A117GLY0-0.006-0.00729.0470.0060.0060.0000.0000.0000.000
113A118ILE0-0.046-0.02430.669-0.002-0.0020.0000.0000.0000.000
114A119GLY0-0.013-0.00134.0740.0000.0000.0000.0000.0000.000
115A120PHE0-0.064-0.03835.2470.0020.0020.0000.0000.0000.000
116A121PHE0-0.008-0.00137.833-0.001-0.0010.0000.0000.0000.000
117A122LYS10.8270.90138.4560.0390.0390.0000.0000.0000.000
118A123ASP-1-0.894-0.94941.187-0.025-0.0250.0000.0000.0000.000
119A124THR0-0.048-0.03141.0290.0020.0020.0000.0000.0000.000
120A125PHE0-0.0200.00035.969-0.002-0.0020.0000.0000.0000.000
121A126GLU-1-0.851-0.91436.898-0.030-0.0300.0000.0000.0000.000
122A127VAL0-0.016-0.02231.355-0.003-0.0030.0000.0000.0000.000
123A128TRP0-0.090-0.04931.3710.0020.0020.0000.0000.0000.000
124A129GLY00.0540.02329.5110.0000.0000.0000.0000.0000.000
125A130ILE0-0.076-0.03325.761-0.001-0.0010.0000.0000.0000.000
126A131GLY00.0740.03126.8280.0000.0000.0000.0000.0000.000
127A132GLY0-0.029-0.02524.343-0.006-0.0060.0000.0000.0000.000
128A133SER0-0.053-0.04625.066-0.003-0.0030.0000.0000.0000.000
129A134GLU-1-0.830-0.91928.196-0.048-0.0480.0000.0000.0000.000
130A135GLU-1-0.886-0.93130.701-0.030-0.0300.0000.0000.0000.000
131A136GLU-1-0.780-0.84326.860-0.052-0.0520.0000.0000.0000.000
132A137ASN00.003-0.02030.1770.0000.0000.0000.0000.0000.000
133A138LYS10.8970.93932.1310.0430.0430.0000.0000.0000.000
134A139GLU-1-0.774-0.86330.714-0.028-0.0280.0000.0000.0000.000
135A140LEU00.0040.02029.0890.0030.0030.0000.0000.0000.000
136A141GLU-1-0.918-0.96833.607-0.040-0.0400.0000.0000.0000.000
137A142SER0-0.111-0.06536.5590.0030.0030.0000.0000.0000.000
138A143LEU0-0.019-0.00833.7040.0030.0030.0000.0000.0000.000
139A144GLY0-0.035-0.01537.6720.0010.0010.0000.0000.0000.000
140A145VAL0-0.042-0.00932.492-0.001-0.0010.0000.0000.0000.000
141A146LYS10.8480.90835.8930.0350.0350.0000.0000.0000.000
142A147ILE00.0120.00631.813-0.003-0.0030.0000.0000.0000.000
143A148LEU0-0.007-0.00328.3450.0010.0010.0000.0000.0000.000
144A149LYS10.8770.94731.4740.0500.0500.0000.0000.0000.000
145A150TYR00.006-0.00531.172-0.002-0.0020.0000.0000.0000.000
146A151GLY00.0350.02029.3120.0040.0040.0000.0000.0000.000
147A152SER0-0.042-0.01624.292-0.005-0.0050.0000.0000.0000.000
148A153ILE00.0450.02121.4490.0060.0060.0000.0000.0000.000
149A154THR0-0.012-0.00519.770-0.013-0.0130.0000.0000.0000.000
150A155GLY00.0300.01416.3100.0100.0100.0000.0000.0000.000
151A156MET00.0150.00811.043-0.020-0.0200.0000.0000.0000.000
152A157SER00.0140.00215.416-0.001-0.0010.0000.0000.0000.000
153A158GLY00.0250.02118.7940.0090.0090.0000.0000.0000.000
154A159LYS10.7950.90912.0220.4320.4320.0000.0000.0000.000
155A160LEU00.0490.00913.558-0.007-0.0070.0000.0000.0000.000
156A161LEU00.0160.03016.3930.0120.0120.0000.0000.0000.000
157A162TRP00.0130.00117.0090.0150.0150.0000.0000.0000.000
158A163GLU-1-0.847-0.93513.461-0.320-0.3200.0000.0000.0000.000
159A164ALA00.0080.00316.4620.0100.0100.0000.0000.0000.000
160A165SER0-0.0010.01018.1030.0150.0150.0000.0000.0000.000
161A166ARG10.8520.91315.3670.2330.2330.0000.0000.0000.000
162A167ALA0-0.100-0.04317.0660.0040.0040.0000.0000.0000.000
163A168GLY0-0.012-0.00219.1860.0150.0150.0000.0000.0000.000
164A169LEU0-0.037-0.00818.1630.0100.0100.0000.0000.0000.000
165A170LYS10.8060.88422.3520.0270.0270.0000.0000.0000.000
166A171SER00.0050.00320.6660.0040.0040.0000.0000.0000.000
167A172TYR0-0.003-0.05123.2390.0030.0030.0000.0000.0000.000
168A173VAL0-0.032-0.00122.269-0.006-0.0060.0000.0000.0000.000
169A174LEU00.0180.01324.8690.0040.0040.0000.0000.0000.000
170A175LEU0-0.046-0.02925.981-0.005-0.0050.0000.0000.0000.000
171A176GLY00.0460.02428.5330.0050.0050.0000.0000.0000.000
172A177GLU-1-0.797-0.87230.485-0.048-0.0480.0000.0000.0000.000
173A178THR0-0.028-0.04229.5750.0030.0030.0000.0000.0000.000
174A179PHE00.0420.02232.958-0.003-0.0030.0000.0000.0000.000
175A180GLY00.015-0.01529.925-0.003-0.0030.0000.0000.0000.000
176A181ASP-1-0.967-0.97229.165-0.055-0.0550.0000.0000.0000.000
177A182ARG10.8830.93330.6230.0380.0380.0000.0000.0000.000
178A183PRO0-0.028-0.00728.840-0.003-0.0030.0000.0000.0000.000
179A184ASP-1-0.761-0.85829.822-0.033-0.0330.0000.0000.0000.000
180A185PRO00.0350.01131.400-0.001-0.0010.0000.0000.0000.000
181A186ARG10.9530.97732.5150.0210.0210.0000.0000.0000.000
182A187ALA00.0430.03131.7490.0010.0010.0000.0000.0000.000
183A188ALA0-0.026-0.01429.606-0.001-0.0010.0000.0000.0000.000
184A189ALA00.0130.00130.8200.0020.0020.0000.0000.0000.000
185A190ASN00.0180.00733.9090.0040.0040.0000.0000.0000.000
186A191VAL0-0.0030.00427.8090.0000.0000.0000.0000.0000.000
187A192VAL0-0.011-0.00629.7950.0010.0010.0000.0000.0000.000
188A193GLU-1-0.850-0.90931.654-0.011-0.0110.0000.0000.0000.000
189A194VAL0-0.024-0.01732.1940.0020.0020.0000.0000.0000.000
190A195LEU00.0280.00726.9270.0010.0010.0000.0000.0000.000
191A196ASN0-0.009-0.00231.0300.0050.0050.0000.0000.0000.000
192A197LYS10.8340.90133.7270.0170.0170.0000.0000.0000.000
193A198MET0-0.056-0.01228.1180.0000.0000.0000.0000.0000.000
194A199LEU0-0.023-0.01527.6110.0010.0010.0000.0000.0000.000
195A200GLY0-0.0170.02232.1480.0040.0040.0000.0000.0000.000
196A201LEU0-0.044-0.01430.1620.0040.0040.0000.0000.0000.000
197A202ASN0-0.048-0.03734.888-0.003-0.0030.0000.0000.0000.000
198A203VAL00.0190.00332.4600.0020.0020.0000.0000.0000.000
199A204SER00.0070.01235.843-0.004-0.0040.0000.0000.0000.000
200A205VAL00.0710.01234.5430.0010.0010.0000.0000.0000.000
201A206GLU-1-0.912-0.95436.884-0.006-0.0060.0000.0000.0000.000
202A207PRO0-0.027-0.02736.594-0.001-0.0010.0000.0000.0000.000
203A208LEU0-0.0050.01632.1070.0000.0000.0000.0000.0000.000
204A209LEU0-0.015-0.01635.636-0.002-0.0020.0000.0000.0000.000
205A210LYS10.9040.95838.393-0.004-0.0040.0000.0000.0000.000
206A211GLU-1-0.944-0.96835.8810.0060.0060.0000.0000.0000.000
207A212ALA0-0.018-0.00535.444-0.001-0.0010.0000.0000.0000.000
208A213GLU-1-0.935-0.96835.429-0.011-0.0110.0000.0000.0000.000
209A214MET00.0380.01634.493-0.001-0.0010.0000.0000.0000.000
210A215ILE0-0.004-0.00930.344-0.001-0.0010.0000.0000.0000.000
211A216GLU-1-0.887-0.94131.349-0.030-0.0300.0000.0000.0000.000
212A217GLU-1-0.940-0.96432.254-0.017-0.0170.0000.0000.0000.000
213A218GLN0-0.077-0.04329.119-0.001-0.0010.0000.0000.0000.000
214A219LEU0-0.031-0.02125.8970.0000.0000.0000.0000.0000.000
215A220ARG10.9090.95327.5550.0190.0190.0000.0000.0000.000
216A221ARG10.9540.98525.3860.0060.0060.0000.0000.0000.000
217A222MET00.0100.01020.436-0.003-0.0030.0000.0000.0000.000
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