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: YV682

Calculation Name: 2PSO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PSO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3M8

Base Structure: X-ray

Registration Date: 2023-09-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2198516.58504
FMO2-HF: Nuclear repulsion 2119585.547586
FMO2-HF: Total energy -78931.037454
FMO2-MP2: Total energy -79160.394457


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:908:THR)


Summations of interaction energy for fragment #1(A:908:THR)
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.
-0.742.404-0.016-1.462-1.6670.004
Interaction energy analysis for fragmet #1(A:908:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.016
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].
3A910LEU00.032-0.0043.570-0.8202.256-0.015-1.458-1.6040.004
4A911ASN00.0080.0214.811-0.984-0.916-0.001-0.004-0.0630.000
5A912HIS00.0230.0067.1280.2670.2670.0000.0000.0000.000
6A913LEU00.0620.0309.436-0.019-0.0190.0000.0000.0000.000
7A914ILE00.0280.02312.1240.0660.0660.0000.0000.0000.000
8A915GLN00.0120.00612.664-0.005-0.0050.0000.0000.0000.000
9A916GLY00.0100.00213.5670.0240.0240.0000.0000.0000.000
10A917LEU00.0480.01015.0970.0430.0430.0000.0000.0000.000
11A918GLN0-0.037-0.01817.2700.0200.0200.0000.0000.0000.000
12A919LYS10.8090.90517.8390.2900.2900.0000.0000.0000.000
13A920GLU-1-0.855-0.92619.493-0.277-0.2770.0000.0000.0000.000
14A921ALA00.003-0.00921.1900.0230.0230.0000.0000.0000.000
15A922LYS10.9570.96320.7440.2430.2430.0000.0000.0000.000
16A923GLU-1-0.865-0.92623.266-0.191-0.1910.0000.0000.0000.000
17A924LYS10.9320.98623.6500.2270.2270.0000.0000.0000.000
18A925PHE0-0.015-0.00127.6460.0130.0130.0000.0000.0000.000
19A926LYS10.9720.97929.6070.1280.1280.0000.0000.0000.000
20A927GLY0-0.017-0.00232.2280.0070.0070.0000.0000.0000.000
21A928TRP0-0.031-0.02532.026-0.006-0.0060.0000.0000.0000.000
22A929VAL00.0080.00126.3820.0000.0000.0000.0000.0000.000
23A930THR00.0110.00629.806-0.003-0.0030.0000.0000.0000.000
24A931CYS0-0.060-0.02328.247-0.012-0.0120.0000.0000.0000.000
25A932SER00.0270.02227.9200.0080.0080.0000.0000.0000.000
26A933SER00.001-0.02229.651-0.008-0.0080.0000.0000.0000.000
27A934THR0-0.0090.00432.1130.0030.0030.0000.0000.0000.000
28A935ASP-1-0.848-0.93034.463-0.042-0.0420.0000.0000.0000.000
29A936ASN0-0.013-0.00937.924-0.001-0.0010.0000.0000.0000.000
30A937THR00.0330.02836.635-0.001-0.0010.0000.0000.0000.000
31A938ASP-1-0.918-0.94936.097-0.062-0.0620.0000.0000.0000.000
32A939LEU0-0.0200.00131.257-0.001-0.0010.0000.0000.0000.000
33A940ALA0-0.042-0.04131.601-0.002-0.0020.0000.0000.0000.000
34A941PHE0-0.013-0.00725.292-0.003-0.0030.0000.0000.0000.000
35A942LYS10.9690.99331.0360.0940.0940.0000.0000.0000.000
36A943LYS10.8580.94625.5620.1700.1700.0000.0000.0000.000
37A944VAL00.0460.00730.3670.0030.0030.0000.0000.0000.000
38A945GLY0-0.034-0.01131.3270.0020.0020.0000.0000.0000.000
39A946ASP-1-0.879-0.94932.345-0.101-0.1010.0000.0000.0000.000
40A947GLY00.0570.04731.4650.0020.0020.0000.0000.0000.000
41A948ASN0-0.005-0.01231.669-0.005-0.0050.0000.0000.0000.000
42A949PRO0-0.0050.00027.034-0.003-0.0030.0000.0000.0000.000
43A950LEU0-0.0100.01528.452-0.005-0.0050.0000.0000.0000.000
44A951LYS10.8700.94424.2310.1720.1720.0000.0000.0000.000
45A952LEU00.0080.02131.0520.0050.0050.0000.0000.0000.000
46A953TRP00.002-0.01928.120-0.004-0.0040.0000.0000.0000.000
47A954LYS10.9500.96934.5540.0780.0780.0000.0000.0000.000
48A955ALA0-0.0010.01436.125-0.002-0.0020.0000.0000.0000.000
49A956SER0-0.005-0.01537.9690.0020.0020.0000.0000.0000.000
50A957VAL00.0370.02140.385-0.001-0.0010.0000.0000.0000.000
51A958GLU-1-0.978-0.97643.124-0.036-0.0360.0000.0000.0000.000
52A959VAL00.013-0.01846.4200.0010.0010.0000.0000.0000.000
53A960GLU-1-0.864-0.93548.994-0.028-0.0280.0000.0000.0000.000
54A961ALA00.0290.01352.3540.0010.0010.0000.0000.0000.000
55A962PRO00.0140.03553.622-0.001-0.0010.0000.0000.0000.000
56A963PRO00.0530.01453.4050.0000.0000.0000.0000.0000.000
57A964SER00.042-0.00254.286-0.001-0.0010.0000.0000.0000.000
58A965VAL00.0070.02255.5120.0000.0000.0000.0000.0000.000
59A966VAL00.0410.02149.7690.0000.0000.0000.0000.0000.000
60A967LEU0-0.008-0.00251.678-0.001-0.0010.0000.0000.0000.000
61A968ASN00.0110.01053.174-0.001-0.0010.0000.0000.0000.000
62A969ARG10.8460.91050.6880.0310.0310.0000.0000.0000.000
63A970VAL0-0.0100.00147.949-0.001-0.0010.0000.0000.0000.000
64A971LEU0-0.086-0.03850.354-0.001-0.0010.0000.0000.0000.000
65A972ARG10.7990.85152.8710.0330.0330.0000.0000.0000.000
66A973GLU-1-0.851-0.89053.416-0.028-0.0280.0000.0000.0000.000
67A974ARG10.9140.96743.2720.0480.0480.0000.0000.0000.000
68A975HIS00.0210.01149.128-0.001-0.0010.0000.0000.0000.000
69A976LEU0-0.024-0.01850.9670.0010.0010.0000.0000.0000.000
70A977TRP0-0.108-0.06444.364-0.001-0.0010.0000.0000.0000.000
71A978ASP-1-0.847-0.93844.130-0.048-0.0480.0000.0000.0000.000
72A979GLU-1-0.912-0.94343.702-0.038-0.0380.0000.0000.0000.000
73A980ASP-1-0.903-0.95341.158-0.044-0.0440.0000.0000.0000.000
74A981PHE0-0.090-0.04844.738-0.001-0.0010.0000.0000.0000.000
75A982VAL00.0350.01147.2180.0020.0020.0000.0000.0000.000
76A983GLN00.005-0.00449.4510.0000.0000.0000.0000.0000.000
77A984TRP0-0.027-0.00351.014-0.002-0.0020.0000.0000.0000.000
78A985LYS10.9380.97753.1100.0340.0340.0000.0000.0000.000
79A986VAL0-0.009-0.00254.757-0.002-0.0020.0000.0000.0000.000
80A987VAL0-0.066-0.04854.2930.0010.0010.0000.0000.0000.000
81A988GLU-1-0.813-0.89357.270-0.034-0.0340.0000.0000.0000.000
82A989THR0-0.051-0.03058.261-0.001-0.0010.0000.0000.0000.000
83A990LEU0-0.0040.01256.5800.0000.0000.0000.0000.0000.000
84A991ASP-1-0.837-0.93560.190-0.035-0.0350.0000.0000.0000.000
85A992ARG10.9190.95661.2140.0300.0300.0000.0000.0000.000
86A993GLN0-0.086-0.05258.140-0.001-0.0010.0000.0000.0000.000
87A994THR00.0230.02355.829-0.002-0.0020.0000.0000.0000.000
88A995GLU-1-0.721-0.85354.835-0.034-0.0340.0000.0000.0000.000
89A996ILE00.0580.04452.767-0.002-0.0020.0000.0000.0000.000
90A997TYR0-0.054-0.01850.4900.0010.0010.0000.0000.0000.000
91A998GLN00.0550.01450.119-0.002-0.0020.0000.0000.0000.000
92A999TYR0-0.020-0.02344.0090.0020.0020.0000.0000.0000.000
93A1000VAL00.0120.02345.346-0.002-0.0020.0000.0000.0000.000
94A1001LEU0-0.060-0.02341.0540.0010.0010.0000.0000.0000.000
95A1002ASN00.0620.02142.637-0.003-0.0030.0000.0000.0000.000
96A1003SER0-0.046-0.05137.592-0.003-0.0030.0000.0000.0000.000
97A1004MET0-0.0020.01135.7090.0020.0020.0000.0000.0000.000
98A1005ALA00.0270.01234.2100.0030.0030.0000.0000.0000.000
99A1006PRO00.0190.01535.8250.0000.0000.0000.0000.0000.000
100A1007HIS0-0.024-0.01231.976-0.002-0.0020.0000.0000.0000.000
101A1008PRO00.0410.02536.9310.0040.0040.0000.0000.0000.000
102A1009SER0-0.0040.02639.174-0.002-0.0020.0000.0000.0000.000
103A1010ARG10.8500.92737.2950.0560.0560.0000.0000.0000.000
104A1011ASP-1-0.778-0.89541.015-0.045-0.0450.0000.0000.0000.000
105A1012PHE0-0.067-0.05340.362-0.004-0.0040.0000.0000.0000.000
106A1013VAL00.0420.01745.7530.0030.0030.0000.0000.0000.000
107A1014VAL0-0.059-0.02346.132-0.003-0.0030.0000.0000.0000.000
108A1015LEU00.0790.06648.8850.0020.0020.0000.0000.0000.000
109A1016ARG10.8600.90849.8900.0390.0390.0000.0000.0000.000
110A1017THR0-0.0080.00851.5990.0020.0020.0000.0000.0000.000
111A1018TRP00.009-0.00452.402-0.002-0.0020.0000.0000.0000.000
112A1019LYS10.8900.94454.3980.0390.0390.0000.0000.0000.000
113A1020THR00.037-0.01055.258-0.001-0.0010.0000.0000.0000.000
114A1021ASP-1-0.950-0.95857.762-0.033-0.0330.0000.0000.0000.000
115A1022LEU00.0300.02553.1600.0000.0000.0000.0000.0000.000
116A1023PRO00.0160.00055.1640.0010.0010.0000.0000.0000.000
117A1024LYS10.9220.94451.7210.0400.0400.0000.0000.0000.000
118A1025GLY00.0550.02555.3750.0000.0000.0000.0000.0000.000
119A1026MET0-0.0230.00350.035-0.001-0.0010.0000.0000.0000.000
120A1027CYS0-0.045-0.00452.5680.0020.0020.0000.0000.0000.000
121A1028THR0-0.006-0.00749.833-0.002-0.0020.0000.0000.0000.000
122A1029LEU0-0.015-0.00149.1040.0020.0020.0000.0000.0000.000
123A1030VAL0-0.0060.00747.537-0.003-0.0030.0000.0000.0000.000
124A1031SER0-0.046-0.04145.8960.0030.0030.0000.0000.0000.000
125A1032LEU00.0340.03444.905-0.003-0.0030.0000.0000.0000.000
126A1033SER0-0.0070.00143.8650.0020.0020.0000.0000.0000.000
127A1034VAL0-0.014-0.00245.823-0.001-0.0010.0000.0000.0000.000
128A1035GLU-1-0.984-0.99647.641-0.052-0.0520.0000.0000.0000.000
129A1036HIS00.012-0.03350.2680.0000.0000.0000.0000.0000.000
130A1037GLU-1-0.904-0.94153.737-0.038-0.0380.0000.0000.0000.000
131A1038GLU-1-0.952-0.97256.154-0.030-0.0300.0000.0000.0000.000
132A1039ALA0-0.061-0.01551.8460.0010.0010.0000.0000.0000.000
133A1040GLN00.006-0.02151.392-0.002-0.0020.0000.0000.0000.000
134A1041LEU0-0.041-0.04245.1050.0000.0000.0000.0000.0000.000
135A1042LEU0-0.0250.00948.9310.0010.0010.0000.0000.0000.000
136A1043GLY00.0180.00346.6870.0010.0010.0000.0000.0000.000
137A1044GLY0-0.0460.00342.5100.0000.0000.0000.0000.0000.000
138A1045VAL0-0.004-0.01037.949-0.001-0.0010.0000.0000.0000.000
139A1046ARG10.8980.95941.2020.0480.0480.0000.0000.0000.000
140A1047ALA0-0.016-0.00339.348-0.004-0.0040.0000.0000.0000.000
141A1048VAL00.014-0.00639.1030.0020.0020.0000.0000.0000.000
142A1049VAL0-0.035-0.02939.428-0.005-0.0050.0000.0000.0000.000
143A1050MET0-0.046-0.01736.1460.0000.0000.0000.0000.0000.000
144A1051ASP-1-0.819-0.90239.507-0.074-0.0740.0000.0000.0000.000
145A1052SER0-0.012-0.01840.614-0.002-0.0020.0000.0000.0000.000
146A1053GLN00.0140.01342.1100.0040.0040.0000.0000.0000.000
147A1054TYR0-0.060-0.06843.481-0.002-0.0020.0000.0000.0000.000
148A1055LEU0-0.019-0.01944.6620.0010.0010.0000.0000.0000.000
149A1056ILE00.0040.01446.937-0.001-0.0010.0000.0000.0000.000
150A1057GLU-1-0.911-0.96146.909-0.046-0.0460.0000.0000.0000.000
151A1058PRO0-0.0050.00050.8990.0000.0000.0000.0000.0000.000
152A1059CYS0-0.028-0.01349.702-0.001-0.0010.0000.0000.0000.000
153A1060GLY00.0280.02551.9560.0010.0010.0000.0000.0000.000
154A1061SER0-0.033-0.03054.2590.0000.0000.0000.0000.0000.000
155A1062GLY0-0.001-0.00357.0230.0010.0010.0000.0000.0000.000
156A1063LYS10.9130.98651.7550.0280.0280.0000.0000.0000.000
157A1064SER0-0.005-0.03250.8000.0000.0000.0000.0000.0000.000
158A1065ARG10.9571.00041.2170.0490.0490.0000.0000.0000.000
159A1066LEU0-0.0050.00544.7880.0000.0000.0000.0000.0000.000
160A1067THR0-0.023-0.03141.203-0.002-0.0020.0000.0000.0000.000
161A1068HIS10.8730.93640.9490.0620.0620.0000.0000.0000.000
162A1069ILE0-0.033-0.02338.384-0.004-0.0040.0000.0000.0000.000
163A1070CYS0-0.036-0.00337.9910.0020.0020.0000.0000.0000.000
164A1071ARG10.8570.91032.8180.1000.1000.0000.0000.0000.000
165A1072ILE0-0.0020.00235.9150.0030.0030.0000.0000.0000.000
166A1073ASP-1-0.909-0.94934.795-0.100-0.1000.0000.0000.0000.000
167A1074LEU0-0.019-0.02433.5120.0050.0050.0000.0000.0000.000
168A1075LYS10.9910.99634.3210.0710.0710.0000.0000.0000.000
169A1076GLY00.0080.01332.2710.0040.0040.0000.0000.0000.000
170A1077HIS0-0.0150.00529.330-0.001-0.0010.0000.0000.0000.000
171A1078SER00.010-0.00623.188-0.006-0.0060.0000.0000.0000.000
172A1079PRO00.0880.02223.9700.0060.0060.0000.0000.0000.000
173A1080GLU-1-0.974-0.98119.807-0.240-0.2400.0000.0000.0000.000
174A1081TRP0-0.007-0.00622.7870.0010.0010.0000.0000.0000.000
175A1082TYR00.0260.01625.8390.0010.0010.0000.0000.0000.000
176A1083SER0-0.0230.00021.9950.0040.0040.0000.0000.0000.000
177A1084LYS10.9080.91323.8410.1210.1210.0000.0000.0000.000
178A1085GLY00.0440.02326.2420.0090.0090.0000.0000.0000.000
179A1086PHE00.0530.02628.1040.0080.0080.0000.0000.0000.000
180A1087GLY00.0630.02330.1990.0060.0060.0000.0000.0000.000
181A1088HIS00.0080.00128.311-0.002-0.0020.0000.0000.0000.000
182A1089LEU00.0240.02332.3230.0060.0060.0000.0000.0000.000
183A1090CYS0-0.024-0.01134.7550.0050.0050.0000.0000.0000.000
184A1091ALA0-0.007-0.01435.0610.0040.0040.0000.0000.0000.000
185A1092ALA00.0450.02036.5640.0040.0040.0000.0000.0000.000
186A1093GLU-1-0.879-0.90238.235-0.053-0.0530.0000.0000.0000.000
187A1094VAL0-0.009-0.02140.0810.0030.0030.0000.0000.0000.000
188A1095ALA00.0270.02640.1370.0020.0020.0000.0000.0000.000
189A1096ARG10.9270.98240.1290.0500.0500.0000.0000.0000.000
190A1097ILE00.0060.01044.1610.0020.0020.0000.0000.0000.000
191A1098ARG10.8480.94641.7220.0420.0420.0000.0000.0000.000
192A1099ASN00.039-0.00143.2240.0030.0030.0000.0000.0000.000
193A1100SER0-0.046-0.00547.3530.0020.0020.0000.0000.0000.000
194A1101PHE0-0.020-0.02450.0860.0010.0010.0000.0000.0000.000
195A1102GLN0-0.038-0.01846.907-0.001-0.0010.0000.0000.0000.000
196A1103PRO0-0.013-0.02151.8560.0000.0000.0000.0000.0000.000
197A1104LEU0-0.0050.02748.4930.0010.0010.0000.0000.0000.000