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: 1N2KZ

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 OptAll
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 -2205385.084533
FMO2-HF: Nuclear repulsion 2126451.840827
FMO2-HF: Total energy -78933.243706
FMO2-MP2: Total energy -79162.60296


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.
-0.6022.118-0.013-1.291-1.4170.003
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 : 0.046 / q_NPA : 0.021
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].
3A910LEU00.0290.0073.736-0.6042.078-0.012-1.288-1.3820.003
4A911ASN00.0440.0355.096-0.915-0.877-0.001-0.003-0.0350.000
5A912HIS00.0200.0126.9060.1630.1630.0000.0000.0000.000
6A913LEU00.0290.0069.497-0.006-0.0060.0000.0000.0000.000
7A914ILE00.0320.01912.2600.0410.0410.0000.0000.0000.000
8A915GLN0-0.0100.00112.6700.0140.0140.0000.0000.0000.000
9A916GLY00.0610.02913.8420.0250.0250.0000.0000.0000.000
10A917LEU00.0400.01215.5690.0380.0380.0000.0000.0000.000
11A918GLN00.0070.00517.3170.0380.0380.0000.0000.0000.000
12A919LYS10.8500.91718.3140.2570.2570.0000.0000.0000.000
13A920GLU-1-0.830-0.91019.704-0.217-0.2170.0000.0000.0000.000
14A921ALA0-0.005-0.00821.6110.0200.0200.0000.0000.0000.000
15A922LYS10.8980.94220.5260.2020.2020.0000.0000.0000.000
16A923GLU-1-0.785-0.86023.498-0.168-0.1680.0000.0000.0000.000
17A924LYS10.8700.93124.0770.1920.1920.0000.0000.0000.000
18A925PHE00.0200.02027.6100.0110.0110.0000.0000.0000.000
19A926LYS10.9190.95329.5110.1210.1210.0000.0000.0000.000
20A927GLY00.0030.01132.2410.0060.0060.0000.0000.0000.000
21A928TRP0-0.012-0.01532.822-0.005-0.0050.0000.0000.0000.000
22A929VAL0-0.010-0.00626.5460.0010.0010.0000.0000.0000.000
23A930THR00.0270.01129.987-0.002-0.0020.0000.0000.0000.000
24A931CYS0-0.056-0.03328.023-0.012-0.0120.0000.0000.0000.000
25A932SER00.0220.02527.6650.0070.0070.0000.0000.0000.000
26A933SER00.011-0.02229.607-0.009-0.0090.0000.0000.0000.000
27A934THR00.0360.01832.0280.0020.0020.0000.0000.0000.000
28A935ASP-1-0.817-0.89634.660-0.036-0.0360.0000.0000.0000.000
29A936ASN0-0.0010.01838.110-0.001-0.0010.0000.0000.0000.000
30A937THR00.0690.04336.657-0.001-0.0010.0000.0000.0000.000
31A938ASP-1-0.815-0.88936.466-0.049-0.0490.0000.0000.0000.000
32A939LEU0-0.053-0.01931.190-0.002-0.0020.0000.0000.0000.000
33A940ALA0-0.029-0.02631.859-0.001-0.0010.0000.0000.0000.000
34A941PHE00.0170.01425.576-0.001-0.0010.0000.0000.0000.000
35A942LYS10.9050.95531.5490.0880.0880.0000.0000.0000.000
36A943LYS10.8110.90025.9030.1510.1510.0000.0000.0000.000
37A944VAL00.0380.00630.8110.0010.0010.0000.0000.0000.000
38A945GLY0-0.0020.00232.0710.0030.0030.0000.0000.0000.000
39A946ASP-1-0.799-0.89833.072-0.099-0.0990.0000.0000.0000.000
40A947GLY00.0180.02631.6410.0020.0020.0000.0000.0000.000
41A948ASN00.0060.00431.531-0.007-0.0070.0000.0000.0000.000
42A949PRO0-0.016-0.00827.030-0.001-0.0010.0000.0000.0000.000
43A950LEU0-0.0010.01328.749-0.003-0.0030.0000.0000.0000.000
44A951LYS10.7990.90524.2260.1630.1630.0000.0000.0000.000
45A952LEU00.0120.02331.0010.0050.0050.0000.0000.0000.000
46A953TRP00.014-0.00328.291-0.002-0.0020.0000.0000.0000.000
47A954LYS10.8690.92634.6950.0670.0670.0000.0000.0000.000
48A955ALA0-0.0110.01936.286-0.001-0.0010.0000.0000.0000.000
49A956SER0-0.006-0.02838.0250.0000.0000.0000.0000.0000.000
50A957VAL00.0460.02840.375-0.001-0.0010.0000.0000.0000.000
51A958GLU-1-0.849-0.90143.193-0.029-0.0290.0000.0000.0000.000
52A959VAL00.017-0.00746.5200.0000.0000.0000.0000.0000.000
53A960GLU-1-0.800-0.87349.091-0.025-0.0250.0000.0000.0000.000
54A961ALA00.0260.01552.5360.0010.0010.0000.0000.0000.000
55A962PRO00.0440.04553.710-0.001-0.0010.0000.0000.0000.000
56A963PRO00.0420.00753.5220.0000.0000.0000.0000.0000.000
57A964SER00.0490.00654.312-0.001-0.0010.0000.0000.0000.000
58A965VAL0-0.0050.00556.1090.0000.0000.0000.0000.0000.000
59A966VAL00.0110.01049.841-0.001-0.0010.0000.0000.0000.000
60A967LEU0-0.021-0.01251.720-0.001-0.0010.0000.0000.0000.000
61A968ASN0-0.009-0.01253.126-0.001-0.0010.0000.0000.0000.000
62A969ARG10.8140.89350.4440.0280.0280.0000.0000.0000.000
63A970VAL0-0.0020.00447.754-0.001-0.0010.0000.0000.0000.000
64A971LEU0-0.056-0.02850.434-0.001-0.0010.0000.0000.0000.000
65A972ARG10.8010.84953.2000.0320.0320.0000.0000.0000.000
66A973GLU-1-0.800-0.87553.559-0.026-0.0260.0000.0000.0000.000
67A974ARG10.7990.88642.9400.0470.0470.0000.0000.0000.000
68A975HIS00.0180.00549.2130.0000.0000.0000.0000.0000.000
69A976LEU0-0.0190.00251.3900.0010.0010.0000.0000.0000.000
70A977TRP0-0.088-0.05844.281-0.001-0.0010.0000.0000.0000.000
71A978ASP-1-0.774-0.87143.393-0.048-0.0480.0000.0000.0000.000
72A979GLU-1-0.817-0.89943.636-0.037-0.0370.0000.0000.0000.000
73A980ASP-1-0.886-0.92541.057-0.047-0.0470.0000.0000.0000.000
74A981PHE0-0.056-0.03944.576-0.001-0.0010.0000.0000.0000.000
75A982VAL00.0100.01146.9850.0020.0020.0000.0000.0000.000
76A983GLN00.0150.00249.6280.0010.0010.0000.0000.0000.000
77A984TRP0-0.007-0.01750.689-0.002-0.0020.0000.0000.0000.000
78A985LYS10.8800.94853.0890.0340.0340.0000.0000.0000.000
79A986VAL0-0.019-0.00354.795-0.002-0.0020.0000.0000.0000.000
80A987VAL0-0.048-0.03754.2020.0010.0010.0000.0000.0000.000
81A988GLU-1-0.809-0.89857.407-0.033-0.0330.0000.0000.0000.000
82A989THR0-0.053-0.02658.413-0.001-0.0010.0000.0000.0000.000
83A990LEU0-0.0150.00156.9530.0000.0000.0000.0000.0000.000
84A991ASP-1-0.813-0.88560.185-0.032-0.0320.0000.0000.0000.000
85A992ARG10.8760.93861.6100.0290.0290.0000.0000.0000.000
86A993GLN0-0.090-0.05658.3040.0000.0000.0000.0000.0000.000
87A994THR00.004-0.01156.100-0.002-0.0020.0000.0000.0000.000
88A995GLU-1-0.734-0.82555.238-0.033-0.0330.0000.0000.0000.000
89A996ILE00.0360.03152.842-0.002-0.0020.0000.0000.0000.000
90A997TYR0-0.031-0.02250.5660.0020.0020.0000.0000.0000.000
91A998GLN00.0470.01150.328-0.002-0.0020.0000.0000.0000.000
92A999TYR0-0.028-0.01944.2480.0020.0020.0000.0000.0000.000
93A1000VAL00.0140.02145.760-0.002-0.0020.0000.0000.0000.000
94A1001LEU0-0.052-0.01341.5520.0010.0010.0000.0000.0000.000
95A1002ASN00.0590.02642.922-0.002-0.0020.0000.0000.0000.000
96A1003SER0-0.019-0.03037.815-0.004-0.0040.0000.0000.0000.000
97A1004MET0-0.0110.00235.9930.0020.0020.0000.0000.0000.000
98A1005ALA00.0020.00734.8120.0020.0020.0000.0000.0000.000
99A1006PRO00.008-0.01136.0110.0000.0000.0000.0000.0000.000
100A1007HIS0-0.0070.01432.165-0.004-0.0040.0000.0000.0000.000
101A1008PRO00.0310.02337.0710.0030.0030.0000.0000.0000.000
102A1009SER00.0140.00839.584-0.002-0.0020.0000.0000.0000.000
103A1010ARG10.7910.87637.7810.0530.0530.0000.0000.0000.000
104A1011ASP-1-0.722-0.84541.425-0.045-0.0450.0000.0000.0000.000
105A1012PHE0-0.038-0.03740.672-0.004-0.0040.0000.0000.0000.000
106A1013VAL00.0410.02145.8700.0030.0030.0000.0000.0000.000
107A1014VAL0-0.019-0.02146.253-0.003-0.0030.0000.0000.0000.000
108A1015LEU00.0330.05148.9320.0020.0020.0000.0000.0000.000
109A1016ARG10.8110.89249.9500.0370.0370.0000.0000.0000.000
110A1017THR0-0.013-0.02851.7460.0020.0020.0000.0000.0000.000
111A1018TRP00.0260.01752.498-0.002-0.0020.0000.0000.0000.000
112A1019LYS10.8330.91054.6620.0360.0360.0000.0000.0000.000
113A1020THR00.050-0.00355.360-0.001-0.0010.0000.0000.0000.000
114A1021ASP-1-0.812-0.88757.971-0.030-0.0300.0000.0000.0000.000
115A1022LEU00.0100.01753.745-0.001-0.0010.0000.0000.0000.000
116A1023PRO00.0350.01155.6770.0010.0010.0000.0000.0000.000
117A1024LYS10.8430.89351.2400.0350.0350.0000.0000.0000.000
118A1025GLY00.0560.03855.8400.0000.0000.0000.0000.0000.000
119A1026MET0-0.048-0.01549.3000.0000.0000.0000.0000.0000.000
120A1027CYS0-0.045-0.00152.7340.0020.0020.0000.0000.0000.000
121A1028THR0-0.034-0.01950.079-0.002-0.0020.0000.0000.0000.000
122A1029LEU00.0150.00849.3160.0020.0020.0000.0000.0000.000
123A1030VAL0-0.0020.00047.715-0.002-0.0020.0000.0000.0000.000
124A1031SER0-0.041-0.03446.3710.0030.0030.0000.0000.0000.000
125A1032LEU00.0130.02445.139-0.003-0.0030.0000.0000.0000.000
126A1033SER0-0.006-0.00743.9650.0020.0020.0000.0000.0000.000
127A1034VAL0-0.038-0.01246.005-0.001-0.0010.0000.0000.0000.000
128A1035GLU-1-0.877-0.93247.663-0.052-0.0520.0000.0000.0000.000
129A1036HIS00.037-0.01050.5760.0000.0000.0000.0000.0000.000
130A1037GLU-1-0.877-0.93154.125-0.038-0.0380.0000.0000.0000.000
131A1038GLU-1-0.885-0.93456.605-0.030-0.0300.0000.0000.0000.000
132A1039ALA0-0.058-0.01052.2570.0000.0000.0000.0000.0000.000
133A1040GLN0-0.006-0.01851.454-0.004-0.0040.0000.0000.0000.000
134A1041LEU0-0.044-0.02545.349-0.001-0.0010.0000.0000.0000.000
135A1042LEU0-0.023-0.01048.5200.0020.0020.0000.0000.0000.000
136A1043GLY0-0.041-0.01846.6360.0020.0020.0000.0000.0000.000
137A1044GLY0-0.043-0.02442.9080.0000.0000.0000.0000.0000.000
138A1045VAL0-0.044-0.01938.043-0.001-0.0010.0000.0000.0000.000
139A1046ARG10.7990.88741.4340.0490.0490.0000.0000.0000.000
140A1047ALA0-0.0160.00639.627-0.004-0.0040.0000.0000.0000.000
141A1048VAL0-0.021-0.02139.5250.0030.0030.0000.0000.0000.000
142A1049VAL0-0.010-0.01239.659-0.005-0.0050.0000.0000.0000.000
143A1050MET0-0.041-0.00637.1340.0000.0000.0000.0000.0000.000
144A1051ASP-1-0.825-0.90439.437-0.073-0.0730.0000.0000.0000.000
145A1052SER00.0200.00340.911-0.002-0.0020.0000.0000.0000.000
146A1053GLN0-0.007-0.01742.1240.0040.0040.0000.0000.0000.000
147A1054TYR0-0.046-0.04643.801-0.002-0.0020.0000.0000.0000.000
148A1055LEU0-0.036-0.02944.4440.0010.0010.0000.0000.0000.000
149A1056ILE00.0070.01046.917-0.001-0.0010.0000.0000.0000.000
150A1057GLU-1-0.858-0.92447.964-0.038-0.0380.0000.0000.0000.000
151A1058PRO00.0040.01751.1380.0000.0000.0000.0000.0000.000
152A1059CYS0-0.094-0.04649.588-0.001-0.0010.0000.0000.0000.000
153A1060GLY00.0570.02152.4220.0010.0010.0000.0000.0000.000
154A1061SER0-0.021-0.02054.5850.0000.0000.0000.0000.0000.000
155A1062GLY0-0.0020.00457.1090.0010.0010.0000.0000.0000.000
156A1063LYS10.7790.88550.2460.0250.0250.0000.0000.0000.000
157A1064SER0-0.010-0.03850.7520.0000.0000.0000.0000.0000.000
158A1065ARG10.8570.91941.6210.0410.0410.0000.0000.0000.000
159A1066LEU00.0040.00745.1080.0000.0000.0000.0000.0000.000
160A1067THR0-0.008-0.00441.118-0.002-0.0020.0000.0000.0000.000
161A1068HIS10.8460.92741.1980.0570.0570.0000.0000.0000.000
162A1069ILE0-0.027-0.00638.981-0.003-0.0030.0000.0000.0000.000
163A1070CYS0-0.040-0.01938.3110.0020.0020.0000.0000.0000.000
164A1071ARG10.7930.86333.4100.0930.0930.0000.0000.0000.000
165A1072ILE00.0060.00636.0300.0030.0030.0000.0000.0000.000
166A1073ASP-1-0.861-0.93335.147-0.095-0.0950.0000.0000.0000.000
167A1074LEU0-0.012-0.01234.0620.0050.0050.0000.0000.0000.000
168A1075LYS10.9600.98733.9860.0700.0700.0000.0000.0000.000
169A1076GLY00.0140.00533.3710.0040.0040.0000.0000.0000.000
170A1077HIS0-0.056-0.01630.104-0.003-0.0030.0000.0000.0000.000
171A1078SER00.0280.01123.665-0.006-0.0060.0000.0000.0000.000
172A1079PRO00.0920.02824.3640.0050.0050.0000.0000.0000.000
173A1080GLU-1-0.898-0.94920.074-0.208-0.2080.0000.0000.0000.000
174A1081TRP00.0030.01223.2740.0000.0000.0000.0000.0000.000
175A1082TYR00.0480.00826.2420.0020.0020.0000.0000.0000.000
176A1083SER0-0.059-0.03422.5440.0070.0070.0000.0000.0000.000
177A1084LYS10.8600.91324.8410.1000.1000.0000.0000.0000.000
178A1085GLY00.0460.03626.7580.0090.0090.0000.0000.0000.000
179A1086PHE00.0620.02428.5470.0070.0070.0000.0000.0000.000
180A1087GLY00.0710.03530.4800.0060.0060.0000.0000.0000.000
181A1088HIS00.009-0.00428.841-0.001-0.0010.0000.0000.0000.000
182A1089LEU00.0160.02132.5420.0050.0050.0000.0000.0000.000
183A1090CYS0-0.041-0.01634.9130.0040.0040.0000.0000.0000.000
184A1091ALA0-0.015-0.01734.9880.0040.0040.0000.0000.0000.000
185A1092ALA00.0450.01536.5070.0040.0040.0000.0000.0000.000
186A1093GLU-1-0.804-0.85638.274-0.050-0.0500.0000.0000.0000.000
187A1094VAL0-0.002-0.00939.5610.0030.0030.0000.0000.0000.000
188A1095ALA00.0210.01240.0160.0030.0030.0000.0000.0000.000
189A1096ARG10.7810.87641.1980.0470.0470.0000.0000.0000.000
190A1097ILE00.0070.01744.1140.0020.0020.0000.0000.0000.000
191A1098ARG10.7750.85341.6740.0360.0360.0000.0000.0000.000
192A1099ASN00.0110.00342.8940.0040.0040.0000.0000.0000.000
193A1100SER0-0.036-0.00947.1620.0020.0020.0000.0000.0000.000
194A1101PHE0-0.012-0.01950.0450.0010.0010.0000.0000.0000.000
195A1102GLN0-0.0090.00846.4730.0000.0000.0000.0000.0000.000
196A1103PRO0-0.009-0.01151.6440.0000.0000.0000.0000.0000.000
197A1104LEU0-0.0140.01248.4680.0010.0010.0000.0000.0000.000