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: PLNY9

Calculation Name: 1WN2-A-Xray20

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WN2

Chain ID: A

ChEMBL ID:

UniProt ID: O74017

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1173499.286832
FMO2-HF: Nuclear repulsion 1122092.142713
FMO2-HF: Total energy -51407.144119
FMO2-MP2: Total energy -51557.886398


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:3:ACE)


Summations of interaction energy for fragment #1(A:3: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.
0.3521.8250.076-0.671-0.8790
Interaction energy analysis for fragmet #1(A:3:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.009
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].
3A5PHE0-0.0140.0063.1890.2911.7640.076-0.671-0.8790.000
4A6LYS10.9751.0085.5860.4930.4930.0000.0000.0000.000
5A7TYR00.0230.0056.2340.2130.2130.0000.0000.0000.000
6A8LYS10.7860.86711.0310.0950.0950.0000.0000.0000.000
7A9GLN0-0.012-0.01114.7930.0220.0220.0000.0000.0000.000
8A10VAL0-0.0050.00518.035-0.016-0.0160.0000.0000.0000.000
9A11ILE0-0.052-0.02321.0110.0130.0130.0000.0000.0000.000
10A12VAL00.0220.01224.480-0.007-0.0070.0000.0000.0000.000
11A13ALA00.006-0.01027.2180.0060.0060.0000.0000.0000.000
12A14ARG10.8060.89230.6020.0030.0030.0000.0000.0000.000
13A15ALA0-0.0130.00433.987-0.001-0.0010.0000.0000.0000.000
14A16ASP-1-0.712-0.82836.089-0.010-0.0100.0000.0000.0000.000
15A17LEU0-0.016-0.00736.7140.0010.0010.0000.0000.0000.000
16A18LYS10.9500.99240.0540.0150.0150.0000.0000.0000.000
17A19LEU00.0000.02336.4760.0000.0000.0000.0000.0000.000
18A20SER00.0300.00239.581-0.002-0.0020.0000.0000.0000.000
19A21LYS11.0481.01236.5500.0320.0320.0000.0000.0000.000
20A22GLY0-0.007-0.00335.756-0.001-0.0010.0000.0000.0000.000
21A23LYS10.8420.91236.0090.0110.0110.0000.0000.0000.000
22A24LEU00.0450.02832.8310.0020.0020.0000.0000.0000.000
23A25ALA00.005-0.00431.5420.0000.0000.0000.0000.0000.000
24A26ALA00.0020.00330.9670.0000.0000.0000.0000.0000.000
25A27GLN00.0110.00631.6310.0040.0040.0000.0000.0000.000
26A28VAL00.0390.01426.7130.0030.0030.0000.0000.0000.000
27A29ALA0-0.010-0.00227.0280.0000.0000.0000.0000.0000.000
28A30HIS0-0.0040.00327.3030.0030.0030.0000.0000.0000.000
29A31GLY00.0280.01526.6900.0060.0060.0000.0000.0000.000
30A32ALA0-0.004-0.00923.0210.0050.0050.0000.0000.0000.000
31A33VAL00.0200.00622.6490.0050.0050.0000.0000.0000.000
32A34THR00.004-0.01223.9580.0080.0080.0000.0000.0000.000
33A35ALA00.0230.00821.1530.0090.0090.0000.0000.0000.000
34A36ALA00.0040.00819.2660.0110.0110.0000.0000.0000.000
35A37PHE0-0.011-0.01519.5370.0150.0150.0000.0000.0000.000
36A38GLU-1-0.819-0.87821.4080.0800.0800.0000.0000.0000.000
37A39ALA00.0080.00115.9420.0180.0180.0000.0000.0000.000
38A40TYR0-0.0330.01016.8760.0270.0270.0000.0000.0000.000
39A41LYS10.9100.94018.405-0.057-0.0570.0000.0000.0000.000
40A42LYS10.9300.97319.009-0.083-0.0830.0000.0000.0000.000
41A43LYS10.7930.87613.508-0.259-0.2590.0000.0000.0000.000
42A44ARG10.9820.99913.893-0.137-0.1370.0000.0000.0000.000
43A45GLU-1-0.914-0.9519.1870.6730.6730.0000.0000.0000.000
44A46TRP00.0180.0029.234-0.082-0.0820.0000.0000.0000.000
45A47PHE0-0.015-0.00311.029-0.066-0.0660.0000.0000.0000.000
46A48GLU-1-0.874-0.95011.6970.0270.0270.0000.0000.0000.000
47A49ALA00.0030.0178.014-0.039-0.0390.0000.0000.0000.000
48A50TRP0-0.015-0.0119.846-0.070-0.0700.0000.0000.0000.000
49A51PHE0-0.062-0.02812.397-0.035-0.0350.0000.0000.0000.000
50A52ARG10.9620.9859.2420.0370.0370.0000.0000.0000.000
51A53GLU-1-0.916-0.9588.144-0.645-0.6450.0000.0000.0000.000
52A54GLY00.018-0.00312.804-0.026-0.0260.0000.0000.0000.000
53A55GLN0-0.016-0.00615.1890.0340.0340.0000.0000.0000.000
54A56LYS10.9420.97915.4740.2470.2470.0000.0000.0000.000
55A57LYS10.8510.92517.1830.0850.0850.0000.0000.0000.000
56A58VAL00.0080.01619.644-0.011-0.0110.0000.0000.0000.000
57A59VAL00.0150.01422.1970.0100.0100.0000.0000.0000.000
58A60VAL00.0370.02424.468-0.004-0.0040.0000.0000.0000.000
59A61LYS10.8750.93327.1460.0410.0410.0000.0000.0000.000
60A62VAL0-0.0010.01229.9570.0000.0000.0000.0000.0000.000
61A63GLU-1-0.833-0.90932.526-0.023-0.0230.0000.0000.0000.000
62A64SER00.0310.03735.3100.0020.0020.0000.0000.0000.000
63A65GLU-1-0.853-0.94334.9470.0040.0040.0000.0000.0000.000
64A66GLU-1-0.753-0.88634.6570.0030.0030.0000.0000.0000.000
65A67GLU-1-0.814-0.91130.986-0.011-0.0110.0000.0000.0000.000
66A68LEU0-0.0070.00529.5450.0010.0010.0000.0000.0000.000
67A69PHE00.0280.00829.7070.0040.0040.0000.0000.0000.000
68A70LYS10.9200.96430.408-0.006-0.0060.0000.0000.0000.000
69A71LEU00.0380.01925.8160.0040.0040.0000.0000.0000.000
70A72LYS10.8170.90025.594-0.036-0.0360.0000.0000.0000.000
71A73ALA00.0310.02525.8700.0070.0070.0000.0000.0000.000
72A74GLU-1-0.785-0.83023.2920.0220.0220.0000.0000.0000.000
73A75ALA00.027-0.00221.6110.0090.0090.0000.0000.0000.000
74A76GLU-1-0.880-0.93321.3910.0600.0600.0000.0000.0000.000
75A77LYS10.9330.98222.891-0.042-0.0420.0000.0000.0000.000
76A78LEU0-0.076-0.02818.5310.0120.0120.0000.0000.0000.000
77A79GLY00.0320.02717.9770.0220.0220.0000.0000.0000.000
78A80LEU00.0050.00815.7700.0230.0230.0000.0000.0000.000
79A81PRO0-0.0140.01216.376-0.008-0.0080.0000.0000.0000.000
80A82ASN0-0.031-0.01619.422-0.019-0.0190.0000.0000.0000.000
81A83ALA00.0330.00922.5080.0050.0050.0000.0000.0000.000
82A84LEU00.0130.02425.826-0.006-0.0060.0000.0000.0000.000
83A85ILE0-0.0220.00028.3710.0030.0030.0000.0000.0000.000
84A86ARG11.0121.02231.344-0.018-0.0180.0000.0000.0000.000
85A87ASP-1-0.769-0.87034.6840.0000.0000.0000.0000.0000.000
86A88ALA00.0330.01436.940-0.001-0.0010.0000.0000.0000.000
87A89GLY00.0430.04839.4040.0000.0000.0000.0000.0000.000
88A90LEU00.064-0.01737.324-0.002-0.0020.0000.0000.0000.000
89A91THR00.0990.04340.8280.0000.0000.0000.0000.0000.000
90A92GLU-1-0.659-0.75642.161-0.008-0.0080.0000.0000.0000.000
91A93ILE0-0.0170.00638.901-0.001-0.0010.0000.0000.0000.000
92A94PRO00.0870.04243.1900.0010.0010.0000.0000.0000.000
93A95PRO00.0380.03842.2410.0000.0000.0000.0000.0000.000
94A96GLY0-0.004-0.00439.3510.0010.0010.0000.0000.0000.000
95A97THR0-0.024-0.00238.2650.0010.0010.0000.0000.0000.000
96A98VAL0-0.021-0.00533.355-0.001-0.0010.0000.0000.0000.000
97A99THR0-0.002-0.03233.509-0.002-0.0020.0000.0000.0000.000
98A100VAL00.0180.00128.701-0.004-0.0040.0000.0000.0000.000
99A101LEU0-0.0120.01025.2370.0060.0060.0000.0000.0000.000
100A102ALA0-0.0420.00222.866-0.007-0.0070.0000.0000.0000.000
101A103VAL00.0290.00719.0100.0130.0130.0000.0000.0000.000
102A104GLY00.0180.02516.855-0.017-0.0170.0000.0000.0000.000
103A105PRO0-0.050-0.04013.921-0.001-0.0010.0000.0000.0000.000
104A106ALA00.023-0.00512.4160.0410.0410.0000.0000.0000.000
105A107PRO00.0240.0218.804-0.066-0.0660.0000.0000.0000.000
106A108GLU-1-0.773-0.91610.638-0.285-0.2850.0000.0000.0000.000
107A109GLU-1-0.902-0.9369.7430.0180.0180.0000.0000.0000.000
108A110ILE0-0.009-0.00211.8270.0240.0240.0000.0000.0000.000
109A111VAL0-0.004-0.00214.8580.0030.0030.0000.0000.0000.000
110A112ASP-1-0.738-0.85016.509-0.114-0.1140.0000.0000.0000.000
111A113LYS10.8840.94215.807-0.064-0.0640.0000.0000.0000.000
112A114VAL00.0370.03919.8920.0030.0030.0000.0000.0000.000
113A115THR0-0.017-0.02420.410-0.009-0.0090.0000.0000.0000.000
114A116GLY00.0130.02421.590-0.007-0.0070.0000.0000.0000.000
115A117ASN00.0010.00022.107-0.015-0.0150.0000.0000.0000.000
116A118LEU0-0.067-0.01225.1380.0040.0040.0000.0000.0000.000
117A119LYS10.9180.94726.6920.0250.0250.0000.0000.0000.000
118A120LEU00.0340.01024.6830.0020.0020.0000.0000.0000.000
119A121LEU-1-0.823-0.85528.399-0.048-0.0480.0000.0000.0000.000
120A1001NA+10.3210.81343.1410.0050.0050.0000.0000.0000.000
121A1003HOH0-0.036-0.02031.8140.0000.0000.0000.0000.0000.000
122A1005HOH00.005-0.00224.760-0.004-0.0040.0000.0000.0000.000
123A1006HOH00.000-0.00641.7770.0000.0000.0000.0000.0000.000
124A1007HOH0-0.034-0.02822.5700.0000.0000.0000.0000.0000.000
125A1008HOH0-0.038-0.02630.482-0.002-0.0020.0000.0000.0000.000
126A1009HOH0-0.020-0.00312.8810.0250.0250.0000.0000.0000.000
127A1010HOH0-0.018-0.01542.8610.0010.0010.0000.0000.0000.000
128A1011HOH0-0.011-0.01222.5670.0030.0030.0000.0000.0000.000
129A1012HOH00.0190.01016.717-0.006-0.0060.0000.0000.0000.000
130A1013HOH00.0140.01339.596-0.001-0.0010.0000.0000.0000.000
131A1015HOH0-0.034-0.02730.4640.0000.0000.0000.0000.0000.000
132A1016HOH00.0070.01539.4170.0010.0010.0000.0000.0000.000
133A1017HOH00.0380.02336.0730.0000.0000.0000.0000.0000.000
134A1018HOH0-0.021-0.01738.1040.0000.0000.0000.0000.0000.000
135A1019HOH0-0.002-0.00341.0050.0010.0010.0000.0000.0000.000
136A1020HOH00.017-0.02943.3620.0000.0000.0000.0000.0000.000
137A1021HOH0-0.013-0.01233.3040.0000.0000.0000.0000.0000.000
138A1022HOH0-0.040-0.02614.4710.0080.0080.0000.0000.0000.000
139A1023HOH0-0.091-0.07325.328-0.002-0.0020.0000.0000.0000.000
140A1024HOH0-0.017-0.01729.5760.0000.0000.0000.0000.0000.000
141A1026HOH0-0.0020.00718.8350.0080.0080.0000.0000.0000.000
142A1027HOH0-0.024-0.01436.877-0.001-0.0010.0000.0000.0000.000
143A1028HOH00.017-0.00538.042-0.001-0.0010.0000.0000.0000.000
144A1029HOH00.0350.02541.0610.0000.0000.0000.0000.0000.000
145A1031HOH0-0.049-0.03836.217-0.001-0.0010.0000.0000.0000.000
146A1032HOH0-0.042-0.03042.7020.0010.0010.0000.0000.0000.000
147A1034HOH00.014-0.00619.887-0.004-0.0040.0000.0000.0000.000
148A1035HOH00.023-0.00140.274-0.001-0.0010.0000.0000.0000.000
149A1036HOH0-0.013-0.0039.6870.0310.0310.0000.0000.0000.000
150A1037HOH0-0.049-0.04024.9340.0000.0000.0000.0000.0000.000
151A1038HOH0-0.006-0.00733.757-0.001-0.0010.0000.0000.0000.000
152A1040HOH0-0.012-0.01121.4170.0020.0020.0000.0000.0000.000
153A1042HOH0-0.016-0.01021.845-0.005-0.0050.0000.0000.0000.000
154A1044HOH0-0.026-0.02413.928-0.010-0.0100.0000.0000.0000.000
155A1045HOH00.0530.00742.3500.0000.0000.0000.0000.0000.000
156A1046HOH0-0.007-0.01736.7770.0010.0010.0000.0000.0000.000
157A1047HOH00.042-0.01045.1440.0000.0000.0000.0000.0000.000
158A1048HOH00.0390.03515.2110.0010.0010.0000.0000.0000.000
159A1049HOH00.0170.01116.5980.0160.0160.0000.0000.0000.000
160A1050HOH0-0.023-0.02443.8170.0000.0000.0000.0000.0000.000
161A1052HOH0-0.071-0.05012.825-0.017-0.0170.0000.0000.0000.000
162A1056HOH00.058-0.00140.2620.0000.0000.0000.0000.0000.000
163A1057HOH0-0.033-0.02943.5430.0000.0000.0000.0000.0000.000
164A1058HOH0-0.027-0.01727.0190.0010.0010.0000.0000.0000.000
165A1059HOH0-0.026-0.0208.232-0.045-0.0450.0000.0000.0000.000
166A1061HOH0-0.043-0.04134.551-0.001-0.0010.0000.0000.0000.000
167A1063HOH0-0.018-0.01325.4390.0020.0020.0000.0000.0000.000
168A1064HOH0-0.047-0.03138.6170.0000.0000.0000.0000.0000.000
169A1065HOH0-0.068-0.05139.5700.0000.0000.0000.0000.0000.000
170A1068HOH0-0.040-0.02737.7890.0010.0010.0000.0000.0000.000
171A1069HOH00.0470.03415.517-0.011-0.0110.0000.0000.0000.000
172A1070HOH0-0.072-0.04715.8390.0130.0130.0000.0000.0000.000
173A1071HOH0-0.014-0.01445.5970.0000.0000.0000.0000.0000.000
174A1074HOH00.0000.00031.107-0.002-0.0020.0000.0000.0000.000
175A1080HOH00.0220.01741.844-0.001-0.0010.0000.0000.0000.000
176A1084HOH00.0260.00611.327-0.036-0.0360.0000.0000.0000.000
177A1088HOH0-0.035-0.02642.8470.0000.0000.0000.0000.0000.000
178A1089HOH0-0.008-0.01639.8850.0000.0000.0000.0000.0000.000
179A1091HOH0-0.042-0.03440.1530.0000.0000.0000.0000.0000.000
180A1092HOH0-0.023-0.02118.1070.0060.0060.0000.0000.0000.000
181A1095HOH00.0190.01324.5230.0000.0000.0000.0000.0000.000
182A1096HOH0-0.033-0.02041.7180.0000.0000.0000.0000.0000.000
183A1097HOH0-0.009-0.00139.811-0.001-0.0010.0000.0000.0000.000
184A1098HOH0-0.051-0.03616.1720.0050.0050.0000.0000.0000.000
185A1102HOH0-0.051-0.02741.1570.0010.0010.0000.0000.0000.000
186A1103HOH0-0.011-0.00536.5780.0010.0010.0000.0000.0000.000
187A1112HOH0-0.015-0.01444.3000.0000.0000.0000.0000.0000.000
188A1113HOH0-0.019-0.02215.734-0.001-0.0010.0000.0000.0000.000
189A1117HOH0-0.035-0.02041.0200.0000.0000.0000.0000.0000.000
190A1118HOH00.0160.00542.1170.0000.0000.0000.0000.0000.000
191A1126HOH0-0.059-0.03018.6250.0020.0020.0000.0000.0000.000
192A1129HOH0-0.054-0.05023.713-0.001-0.0010.0000.0000.0000.000
193A1133HOH00.0100.01312.013-0.039-0.0390.0000.0000.0000.000
194A1134HOH0-0.042-0.02846.5870.0000.0000.0000.0000.0000.000
195A1147HOH00.0170.01719.846-0.008-0.0080.0000.0000.0000.000
196A1159HOH0-0.017-0.00626.076-0.003-0.0030.0000.0000.0000.000
197A1160HOH0-0.019-0.02022.8300.0020.0020.0000.0000.0000.000
198A1161HOH0-0.002-0.0149.359-0.043-0.0430.0000.0000.0000.000
199A1163HOH0-0.027-0.02523.3600.0020.0020.0000.0000.0000.000
200A1168HOH00.0340.02711.869-0.034-0.0340.0000.0000.0000.000
201A1169HOH0-0.017-0.01040.3720.0010.0010.0000.0000.0000.000
202A1174HOH00.0510.00644.2570.0000.0000.0000.0000.0000.000
203A1175HOH00.0220.02814.427-0.005-0.0050.0000.0000.0000.000
204A1176HOH00.0320.01745.0750.0000.0000.0000.0000.0000.000
205A1177HOH0-0.013-0.02523.4160.0050.0050.0000.0000.0000.000
206A1185HOH0-0.010-0.02733.7250.0010.0010.0000.0000.0000.000
207A1187HOH0-0.054-0.03427.635-0.003-0.0030.0000.0000.0000.000
208A1188HOH0-0.046-0.03230.880-0.001-0.0010.0000.0000.0000.000