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: VQ8L1

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200270.454368
FMO2-HF: Nuclear repulsion 2121338.119613
FMO2-HF: Total energy -78932.334755
FMO2-MP2: Total energy -79161.650877


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.
-0.6552.54-0.011-1.487-1.6970.004
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 : 0.037 / q_NPA : 0.018
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].
3A910LEU00.031-0.0033.525-0.9072.227-0.010-1.483-1.6410.004
4A911ASN00.0050.0184.756-0.999-0.938-0.001-0.004-0.0560.000
5A912HIS00.0300.0096.9610.2750.2750.0000.0000.0000.000
6A913LEU00.0660.0329.422-0.014-0.0140.0000.0000.0000.000
7A914ILE00.0290.02112.1070.0720.0720.0000.0000.0000.000
8A915GLN00.001-0.00312.4710.0140.0140.0000.0000.0000.000
9A916GLY00.0420.01813.5620.0280.0280.0000.0000.0000.000
10A917LEU00.0400.01015.1100.0470.0470.0000.0000.0000.000
11A918GLN0-0.029-0.01717.3170.0470.0470.0000.0000.0000.000
12A919LYS10.8340.90217.8210.3140.3140.0000.0000.0000.000
13A920GLU-1-0.792-0.87219.515-0.273-0.2730.0000.0000.0000.000
14A921ALA0-0.004-0.00921.2060.0250.0250.0000.0000.0000.000
15A922LYS10.9190.95220.2180.2690.2690.0000.0000.0000.000
16A923GLU-1-0.784-0.86523.186-0.202-0.2020.0000.0000.0000.000
17A924LYS10.8500.92123.6540.2410.2410.0000.0000.0000.000
18A925PHE00.0140.02027.6540.0140.0140.0000.0000.0000.000
19A926LYS10.9510.96629.6140.1430.1430.0000.0000.0000.000
20A927GLY0-0.0120.00532.2400.0080.0080.0000.0000.0000.000
21A928TRP0-0.016-0.01732.027-0.007-0.0070.0000.0000.0000.000
22A929VAL00.0060.00126.3330.0010.0010.0000.0000.0000.000
23A930THR00.0090.00729.796-0.003-0.0030.0000.0000.0000.000
24A931CYS0-0.054-0.02328.147-0.014-0.0140.0000.0000.0000.000
25A932SER00.0160.01927.8030.0090.0090.0000.0000.0000.000
26A933SER0-0.006-0.04529.619-0.008-0.0080.0000.0000.0000.000
27A934THR00.0310.02331.9060.0020.0020.0000.0000.0000.000
28A935ASP-1-0.865-0.91934.418-0.050-0.0500.0000.0000.0000.000
29A936ASN0-0.0030.00537.879-0.001-0.0010.0000.0000.0000.000
30A937THR00.0600.05836.473-0.001-0.0010.0000.0000.0000.000
31A938ASP-1-0.815-0.88936.081-0.068-0.0680.0000.0000.0000.000
32A939LEU0-0.0180.00330.932-0.001-0.0010.0000.0000.0000.000
33A940ALA0-0.051-0.04131.595-0.002-0.0020.0000.0000.0000.000
34A941PHE0-0.001-0.00125.212-0.002-0.0020.0000.0000.0000.000
35A942LYS10.9450.97631.0650.1070.1070.0000.0000.0000.000
36A943LYS10.8220.91225.5520.1850.1850.0000.0000.0000.000
37A944VAL00.0380.00730.3840.0030.0030.0000.0000.0000.000
38A945GLY0-0.039-0.01231.3570.0030.0030.0000.0000.0000.000
39A946ASP-1-0.795-0.89532.375-0.110-0.1100.0000.0000.0000.000
40A947GLY00.0590.04631.4850.0030.0030.0000.0000.0000.000
41A948ASN0-0.017-0.01331.633-0.005-0.0050.0000.0000.0000.000
42A949PRO0-0.008-0.00327.017-0.003-0.0030.0000.0000.0000.000
43A950LEU0-0.0250.00928.490-0.006-0.0060.0000.0000.0000.000
44A951LYS10.8280.91024.2860.1900.1900.0000.0000.0000.000
45A952LEU00.0110.01631.0680.0060.0060.0000.0000.0000.000
46A953TRP00.001-0.01827.958-0.004-0.0040.0000.0000.0000.000
47A954LYS10.9530.97334.5560.0900.0900.0000.0000.0000.000
48A955ALA0-0.0300.00436.115-0.003-0.0030.0000.0000.0000.000
49A956SER0-0.033-0.03037.9550.0010.0010.0000.0000.0000.000
50A957VAL00.0470.02240.357-0.001-0.0010.0000.0000.0000.000
51A958GLU-1-0.910-0.93543.094-0.041-0.0410.0000.0000.0000.000
52A959VAL0-0.007-0.02946.3910.0010.0010.0000.0000.0000.000
53A960GLU-1-0.792-0.87748.962-0.034-0.0340.0000.0000.0000.000
54A961ALA00.0430.02052.3180.0020.0020.0000.0000.0000.000
55A962PRO00.0160.03453.595-0.002-0.0020.0000.0000.0000.000
56A963PRO00.0470.01453.4030.0000.0000.0000.0000.0000.000
57A964SER00.0430.00454.272-0.001-0.0010.0000.0000.0000.000
58A965VAL00.0010.01055.8580.0000.0000.0000.0000.0000.000
59A966VAL00.0460.02449.713-0.001-0.0010.0000.0000.0000.000
60A967LEU0-0.012-0.00551.667-0.002-0.0020.0000.0000.0000.000
61A968ASN00.0260.01653.167-0.001-0.0010.0000.0000.0000.000
62A969ARG10.8200.90250.5460.0360.0360.0000.0000.0000.000
63A970VAL0-0.016-0.00847.785-0.001-0.0010.0000.0000.0000.000
64A971LEU0-0.083-0.03750.350-0.001-0.0010.0000.0000.0000.000
65A972ARG10.8000.84452.8740.0380.0380.0000.0000.0000.000
66A973GLU-1-0.832-0.89153.375-0.032-0.0320.0000.0000.0000.000
67A974ARG10.8260.90642.9510.0550.0550.0000.0000.0000.000
68A975HIS00.0030.00349.121-0.001-0.0010.0000.0000.0000.000
69A976LEU0-0.014-0.01150.9560.0010.0010.0000.0000.0000.000
70A977TRP0-0.113-0.06544.266-0.001-0.0010.0000.0000.0000.000
71A978ASP-1-0.760-0.87143.534-0.057-0.0570.0000.0000.0000.000
72A979GLU-1-0.842-0.90643.754-0.045-0.0450.0000.0000.0000.000
73A980ASP-1-0.887-0.93441.010-0.054-0.0540.0000.0000.0000.000
74A981PHE0-0.083-0.05544.738-0.001-0.0010.0000.0000.0000.000
75A982VAL00.0200.01346.9820.0020.0020.0000.0000.0000.000
76A983GLN00.0050.00349.4600.0010.0010.0000.0000.0000.000
77A984TRP00.0020.00051.032-0.002-0.0020.0000.0000.0000.000
78A985LYS10.8970.96953.1270.0380.0380.0000.0000.0000.000
79A986VAL0-0.021-0.01254.781-0.002-0.0020.0000.0000.0000.000
80A987VAL0-0.055-0.04854.0880.0010.0010.0000.0000.0000.000
81A988GLU-1-0.806-0.89157.301-0.037-0.0370.0000.0000.0000.000
82A989THR0-0.062-0.03658.290-0.001-0.0010.0000.0000.0000.000
83A990LEU0-0.0090.00656.4880.0010.0010.0000.0000.0000.000
84A991ASP-1-0.804-0.89060.035-0.038-0.0380.0000.0000.0000.000
85A992ARG10.9190.97561.2360.0340.0340.0000.0000.0000.000
86A993GLN0-0.047-0.04158.185-0.001-0.0010.0000.0000.0000.000
87A994THR00.007-0.01356.116-0.002-0.0020.0000.0000.0000.000
88A995GLU-1-0.755-0.83955.025-0.038-0.0380.0000.0000.0000.000
89A996ILE00.0560.04052.692-0.002-0.0020.0000.0000.0000.000
90A997TYR0-0.041-0.01450.4350.0020.0020.0000.0000.0000.000
91A998GLN00.0330.00250.142-0.002-0.0020.0000.0000.0000.000
92A999TYR0-0.004-0.01143.9460.0020.0020.0000.0000.0000.000
93A1000VAL00.0200.02645.442-0.002-0.0020.0000.0000.0000.000
94A1001LEU0-0.050-0.01441.3350.0010.0010.0000.0000.0000.000
95A1002ASN00.0550.01842.654-0.002-0.0020.0000.0000.0000.000
96A1003SER0-0.039-0.03637.638-0.003-0.0030.0000.0000.0000.000
97A1004MET0-0.0060.00835.7230.0020.0020.0000.0000.0000.000
98A1005ALA00.0170.01334.1090.0030.0030.0000.0000.0000.000
99A1006PRO00.0350.01935.9100.0000.0000.0000.0000.0000.000
100A1007HIS0-0.035-0.01531.969-0.002-0.0020.0000.0000.0000.000
101A1008PRO00.0360.02836.8070.0040.0040.0000.0000.0000.000
102A1009SER0-0.0040.00639.199-0.003-0.0030.0000.0000.0000.000
103A1010ARG10.8110.90637.3960.0640.0640.0000.0000.0000.000
104A1011ASP-1-0.770-0.88641.041-0.051-0.0510.0000.0000.0000.000
105A1012PHE0-0.058-0.04740.446-0.005-0.0050.0000.0000.0000.000
106A1013VAL00.0500.01645.7830.0030.0030.0000.0000.0000.000
107A1014VAL0-0.052-0.02146.236-0.003-0.0030.0000.0000.0000.000
108A1015LEU00.0670.06248.9160.0030.0030.0000.0000.0000.000
109A1016ARG10.8270.89049.9170.0430.0430.0000.0000.0000.000
110A1017THR00.0020.00251.6210.0020.0020.0000.0000.0000.000
111A1018TRP00.002-0.00452.417-0.002-0.0020.0000.0000.0000.000
112A1019LYS10.8430.91154.4080.0430.0430.0000.0000.0000.000
113A1020THR00.044-0.00855.258-0.001-0.0010.0000.0000.0000.000
114A1021ASP-1-0.926-0.94957.760-0.036-0.0360.0000.0000.0000.000
115A1022LEU00.0080.01653.1260.0000.0000.0000.0000.0000.000
116A1023PRO00.0220.00055.2750.0010.0010.0000.0000.0000.000
117A1024LYS10.8670.92051.4080.0450.0450.0000.0000.0000.000
118A1025GLY00.0550.02355.362-0.001-0.0010.0000.0000.0000.000
119A1026MET0-0.0300.00249.306-0.001-0.0010.0000.0000.0000.000
120A1027CYS0-0.043-0.00452.5770.0020.0020.0000.0000.0000.000
121A1028THR0-0.006-0.01149.706-0.002-0.0020.0000.0000.0000.000
122A1029LEU0-0.0080.00549.0430.0020.0020.0000.0000.0000.000
123A1030VAL0-0.023-0.00847.554-0.003-0.0030.0000.0000.0000.000
124A1031SER0-0.019-0.02545.9950.0030.0030.0000.0000.0000.000
125A1032LEU00.0200.02744.940-0.003-0.0030.0000.0000.0000.000
126A1033SER0-0.0080.00043.8690.0020.0020.0000.0000.0000.000
127A1034VAL0-0.023-0.01045.861-0.001-0.0010.0000.0000.0000.000
128A1035GLU-1-0.981-0.99047.296-0.057-0.0570.0000.0000.0000.000
129A1036HIS00.018-0.02450.3160.0000.0000.0000.0000.0000.000
130A1037GLU-1-0.893-0.94153.783-0.042-0.0420.0000.0000.0000.000
131A1038GLU-1-0.924-0.95856.164-0.033-0.0330.0000.0000.0000.000
132A1039ALA0-0.053-0.01751.9550.0010.0010.0000.0000.0000.000
133A1040GLN00.0300.00551.435-0.003-0.0030.0000.0000.0000.000
134A1041LEU0-0.043-0.03944.9740.0000.0000.0000.0000.0000.000
135A1042LEU0-0.0240.01248.9740.0010.0010.0000.0000.0000.000
136A1043GLY00.0170.00146.7180.0020.0020.0000.0000.0000.000
137A1044GLY0-0.051-0.00742.5480.0000.0000.0000.0000.0000.000
138A1045VAL0-0.011-0.01637.980-0.001-0.0010.0000.0000.0000.000
139A1046ARG10.8830.94241.2380.0520.0520.0000.0000.0000.000
140A1047ALA0-0.018-0.00439.510-0.004-0.0040.0000.0000.0000.000
141A1048VAL00.020-0.00739.2630.0020.0020.0000.0000.0000.000
142A1049VAL0-0.024-0.01739.463-0.005-0.0050.0000.0000.0000.000
143A1050MET0-0.040-0.00536.4490.0000.0000.0000.0000.0000.000
144A1051ASP-1-0.828-0.90439.547-0.084-0.0840.0000.0000.0000.000
145A1052SER0-0.012-0.02240.636-0.002-0.0020.0000.0000.0000.000
146A1053GLN00.002-0.00441.9300.0050.0050.0000.0000.0000.000
147A1054TYR0-0.050-0.04343.708-0.002-0.0020.0000.0000.0000.000
148A1055LEU0-0.014-0.01744.4830.0020.0020.0000.0000.0000.000
149A1056ILE0-0.0010.00746.928-0.001-0.0010.0000.0000.0000.000
150A1057GLU-1-0.869-0.93747.889-0.049-0.0490.0000.0000.0000.000
151A1058PRO00.0050.01050.8810.0000.0000.0000.0000.0000.000
152A1059CYS0-0.033-0.01149.722-0.001-0.0010.0000.0000.0000.000
153A1060GLY00.0350.02351.9310.0010.0010.0000.0000.0000.000
154A1061SER0-0.023-0.02554.2290.0000.0000.0000.0000.0000.000
155A1062GLY00.0020.00256.9930.0010.0010.0000.0000.0000.000
156A1063LYS10.7800.89350.6990.0350.0350.0000.0000.0000.000
157A1064SER0-0.010-0.03450.7150.0000.0000.0000.0000.0000.000
158A1065ARG10.8680.93541.0780.0570.0570.0000.0000.0000.000
159A1066LEU0-0.020-0.00244.9720.0000.0000.0000.0000.0000.000
160A1067THR0-0.005-0.01641.115-0.003-0.0030.0000.0000.0000.000
161A1068HIS10.8470.93440.9740.0690.0690.0000.0000.0000.000
162A1069ILE0-0.034-0.02238.496-0.005-0.0050.0000.0000.0000.000
163A1070CYS0-0.024-0.00438.1950.0030.0030.0000.0000.0000.000
164A1071ARG10.8140.87633.0340.1080.1080.0000.0000.0000.000
165A1072ILE0-0.0050.00235.9460.0040.0040.0000.0000.0000.000
166A1073ASP-1-0.883-0.94334.746-0.107-0.1070.0000.0000.0000.000
167A1074LEU0-0.014-0.01434.0010.0060.0060.0000.0000.0000.000
168A1075LYS10.9660.98634.3610.0780.0780.0000.0000.0000.000
169A1076GLY00.0140.01432.3210.0040.0040.0000.0000.0000.000
170A1077HIS0-0.030-0.00729.476-0.002-0.0020.0000.0000.0000.000
171A1078SER00.0260.00523.184-0.006-0.0060.0000.0000.0000.000
172A1079PRO00.0850.02324.0560.0060.0060.0000.0000.0000.000
173A1080GLU-1-0.973-0.98519.721-0.262-0.2620.0000.0000.0000.000
174A1081TRP0-0.005-0.00622.8150.0000.0000.0000.0000.0000.000
175A1082TYR00.0340.02025.8560.0010.0010.0000.0000.0000.000
176A1083SER00.0080.00622.2040.0040.0040.0000.0000.0000.000
177A1084LYS10.8930.92324.1670.1360.1360.0000.0000.0000.000
178A1085GLY00.0460.02926.2380.0100.0100.0000.0000.0000.000
179A1086PHE00.0630.03128.1000.0080.0080.0000.0000.0000.000
180A1087GLY00.0550.02230.1970.0070.0070.0000.0000.0000.000
181A1088HIS00.006-0.00428.428-0.003-0.0030.0000.0000.0000.000
182A1089LEU00.0340.02932.3070.0060.0060.0000.0000.0000.000
183A1090CYS0-0.034-0.01934.7320.0050.0050.0000.0000.0000.000
184A1091ALA0-0.010-0.01735.0020.0050.0050.0000.0000.0000.000
185A1092ALA00.0480.02236.4890.0050.0050.0000.0000.0000.000
186A1093GLU-1-0.831-0.89238.213-0.059-0.0590.0000.0000.0000.000
187A1094VAL0-0.001-0.01740.0440.0040.0040.0000.0000.0000.000
188A1095ALA00.0300.02840.0740.0030.0030.0000.0000.0000.000
189A1096ARG10.8090.90341.7510.0570.0570.0000.0000.0000.000
190A1097ILE0-0.0010.00744.1360.0030.0030.0000.0000.0000.000
191A1098ARG10.7980.88241.4160.0500.0500.0000.0000.0000.000
192A1099ASN00.0560.01543.1090.0030.0030.0000.0000.0000.000
193A1100SER0-0.0450.00147.3190.0020.0020.0000.0000.0000.000
194A1101PHE0-0.021-0.02650.0580.0010.0010.0000.0000.0000.000
195A1102GLN0-0.023-0.01246.745-0.001-0.0010.0000.0000.0000.000
196A1103PRO0-0.006-0.02051.8160.0000.0000.0000.0000.0000.000
197A1104LEU0-0.0080.02748.4140.0010.0010.0000.0000.0000.000