FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LZGV9

Calculation Name: 2P90-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P90

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NP93

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 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 269
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3482322.355945
FMO2-HF: Nuclear repulsion 3376938.236472
FMO2-HF: Total energy -105384.119472
FMO2-MP2: Total energy -105690.141494


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:ASP)


Summations of interaction energy for fragment #1(A:6:ASP)
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.
188.143195.51.289-3.929-4.7140.004
Interaction energy analysis for fragmet #1(A:6:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.881 / q_NPA : -0.941
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].
3A8MET0-0.043-0.0213.167-19.168-14.7750.143-2.335-2.2000.013
4A9TYR0-0.038-0.0192.721-8.518-6.5390.887-1.112-1.754-0.011
5A10GLU-1-0.856-0.9025.09341.36641.346-0.001-0.0160.0380.000
6A11LEU0-0.087-0.0545.910-2.571-2.5710.0000.0000.0000.000
7A12GLU-1-0.860-0.9258.84019.81719.8170.0000.0000.0000.000
8A13TYR0-0.049-0.02112.597-0.185-0.1850.0000.0000.0000.000
9A14PRO0-0.050-0.03914.796-0.672-0.6720.0000.0000.0000.000
10A15SER00.0230.00814.1420.3810.3810.0000.0000.0000.000
11A16PRO0-0.0150.00514.904-0.995-0.9950.0000.0000.0000.000
12A17GLU-1-0.831-0.89717.64713.94813.9480.0000.0000.0000.000
13A18VAL00.0070.00215.688-0.206-0.2060.0000.0000.0000.000
14A19SER0-0.065-0.03819.164-0.476-0.4760.0000.0000.0000.000
15A20GLY00.0690.00822.153-0.161-0.1610.0000.0000.0000.000
16A21GLN0-0.034-0.01725.4560.2170.2170.0000.0000.0000.000
17A22THR0-0.0090.00826.283-0.248-0.2480.0000.0000.0000.000
18A23ALA0-0.016-0.00625.7870.3780.3780.0000.0000.0000.000
19A24GLY00.007-0.00324.259-0.277-0.2770.0000.0000.0000.000
20A25GLY00.0240.02419.8960.2580.2580.0000.0000.0000.000
21A26PRO0-0.0060.00316.789-0.575-0.5750.0000.0000.0000.000
22A27THR00.005-0.02118.3360.3350.3350.0000.0000.0000.000
23A28LEU0-0.043-0.01112.6870.1710.1710.0000.0000.0000.000
24A29ILE00.0250.00316.845-0.341-0.3410.0000.0000.0000.000
25A30VAL0-0.019-0.01914.1540.8200.8200.0000.0000.0000.000
26A31ALA0-0.003-0.01216.516-0.654-0.6540.0000.0000.0000.000
27A32LEU0-0.022-0.01213.5710.4010.4010.0000.0000.0000.000
28A33GLN0-0.066-0.05217.581-0.586-0.5860.0000.0000.0000.000
29A34GLY0-0.021-0.03119.3270.6710.6710.0000.0000.0000.000
30A35TYR0-0.042-0.01220.839-0.301-0.3010.0000.0000.0000.000
31A36ALA0-0.019-0.01422.648-0.428-0.4280.0000.0000.0000.000
32A37ASP-1-0.745-0.85723.23411.97111.9710.0000.0000.0000.000
33A38ALA0-0.0180.00426.102-0.319-0.3190.0000.0000.0000.000
34A39GLY00.009-0.01629.5820.0480.0480.0000.0000.0000.000
35A40HIS10.8060.88227.490-10.021-10.0210.0000.0000.0000.000
36A41ALA00.0620.04927.6860.1120.1120.0000.0000.0000.000
37A42VAL00.0300.04321.2140.0320.0320.0000.0000.0000.000
38A43GLU-1-0.703-0.84522.37311.27011.2700.0000.0000.0000.000
39A44SER0-0.044-0.02523.4150.0030.0030.0000.0000.0000.000
40A45SER0-0.048-0.04423.636-0.203-0.2030.0000.0000.0000.000
41A46SER0-0.045-0.03320.0120.1560.1560.0000.0000.0000.000
42A47SER00.0250.00421.915-0.077-0.0770.0000.0000.0000.000
43A48HIS0-0.003-0.00924.301-0.195-0.1950.0000.0000.0000.000
44A49LEU0-0.024-0.02722.873-0.198-0.1980.0000.0000.0000.000
45A50MET0-0.014-0.00518.5590.0340.0340.0000.0000.0000.000
46A51ASP-1-0.937-0.96823.51110.52210.5220.0000.0000.0000.000
47A52ALA0-0.090-0.03727.114-0.364-0.3640.0000.0000.0000.000
48A53LEU0-0.061-0.02625.266-0.304-0.3040.0000.0000.0000.000
49A54ASP-1-0.808-0.85525.12711.52511.5250.0000.0000.0000.000
50A55HIS0-0.007-0.01320.1630.5040.5040.0000.0000.0000.000
51A56ARG10.7300.82518.399-12.592-12.5920.0000.0000.0000.000
52A57LEU00.0420.04712.9030.0250.0250.0000.0000.0000.000
53A58ILE0-0.050-0.03411.625-0.157-0.1570.0000.0000.0000.000
54A59ALA0-0.015-0.0107.3721.6201.6200.0000.0000.0000.000
55A60SER00.0390.0309.134-1.926-1.9260.0000.0000.0000.000
56A61PHE0-0.030-0.0415.7893.1033.1030.0000.0000.0000.000
57A62ASN00.001-0.0017.634-4.620-4.6200.0000.0000.0000.000
58A63ASN00.035-0.0069.4221.2781.2780.0000.0000.0000.000
59A64ASP-1-0.869-0.90112.58619.30719.3070.0000.0000.0000.000
60A65GLU-1-0.877-0.9068.53633.51333.5130.0000.0000.0000.000
61A66LEU0-0.036-0.0347.6750.3490.3490.0000.0000.0000.000
62A67ILE00.0250.02111.977-1.256-1.2560.0000.0000.0000.000
63A68ASP-1-0.885-0.92815.67713.89413.8940.0000.0000.0000.000
64A69TYR00.037-0.02515.931-1.282-1.2820.0000.0000.0000.000
65A70ARG10.8490.92420.825-12.651-12.6510.0000.0000.0000.000
66A71SER0-0.058-0.03221.435-0.718-0.7180.0000.0000.0000.000
67A72ARG10.8440.89317.994-15.324-15.3240.0000.0000.0000.000
68A73ARG10.7910.90522.408-11.448-11.4480.0000.0000.0000.000
69A74PRO00.0750.04620.721-0.439-0.4390.0000.0000.0000.000
70A75VAL00.0000.00323.533-0.295-0.2950.0000.0000.0000.000
71A76VAL0-0.0150.00226.6090.1450.1450.0000.0000.0000.000
72A77VAL0-0.028-0.01328.416-0.321-0.3210.0000.0000.0000.000
73A78ILE0-0.024-0.02231.3150.0790.0790.0000.0000.0000.000
74A79GLU-1-0.855-0.89834.4638.5158.5150.0000.0000.0000.000
75A80HIS0-0.065-0.04937.424-0.126-0.1260.0000.0000.0000.000
76A81ASN0-0.104-0.05439.248-0.067-0.0670.0000.0000.0000.000
77A82GLU-1-0.852-0.90334.3329.2129.2120.0000.0000.0000.000
78A83VAL0-0.037-0.04029.741-0.044-0.0440.0000.0000.0000.000
79A84THR0-0.063-0.04331.0630.3120.3120.0000.0000.0000.000
80A85SER0-0.007-0.00627.3550.3820.3820.0000.0000.0000.000
81A86MET0-0.022-0.02122.549-0.278-0.2780.0000.0000.0000.000
82A87ASP-1-0.864-0.92021.63413.48313.4830.0000.0000.0000.000
83A88GLU-1-0.876-0.93316.94716.58616.5860.0000.0000.0000.000
84A89LEU0-0.047-0.03817.4580.9540.9540.0000.0000.0000.000
85A90ASN0-0.057-0.02514.6361.0611.0610.0000.0000.0000.000
86A91LEU0-0.0040.01510.717-0.506-0.5060.0000.0000.0000.000
87A92GLY00.0550.02711.1601.6591.6590.0000.0000.0000.000
88A93LEU0-0.050-0.0239.742-0.874-0.8740.0000.0000.0000.000
89A94HIS00.0750.02411.8770.2260.2260.0000.0000.0000.000
90A95VAL0-0.026-0.01215.2480.0100.0100.0000.0000.0000.000
91A96VAL00.000-0.01217.582-0.236-0.2360.0000.0000.0000.000
92A97ARG10.7680.88121.042-12.285-12.2850.0000.0000.0000.000
93A98ASP-1-0.742-0.87624.4479.8629.8620.0000.0000.0000.000
94A99ASN0-0.045-0.04227.3310.0390.0390.0000.0000.0000.000
95A100ASP-1-0.906-0.93030.1868.4808.4800.0000.0000.0000.000
96A101ASN0-0.088-0.05126.6810.2820.2820.0000.0000.0000.000
97A102LYS10.8210.90325.269-10.136-10.1360.0000.0000.0000.000
98A103PRO0-0.035-0.01820.7280.0340.0340.0000.0000.0000.000
99A104PHE0-0.023-0.00820.110-0.107-0.1070.0000.0000.0000.000
100A105LEU00.007-0.00113.2880.2790.2790.0000.0000.0000.000
101A106MET0-0.0100.00915.940-0.637-0.6370.0000.0000.0000.000
102A107LEU0-0.0100.01310.3710.6270.6270.0000.0000.0000.000
103A108SER00.009-0.01013.678-0.933-0.9330.0000.0000.0000.000
104A109GLY00.0820.04014.9560.6960.6960.0000.0000.0000.000
105A110PRO0-0.031-0.00314.979-0.764-0.7640.0000.0000.0000.000
106A111GLU-1-0.822-0.92614.73416.18516.1850.0000.0000.0000.000
107A112PRO00.001-0.00311.055-0.510-0.5100.0000.0000.0000.000
108A113ASP-1-0.761-0.84913.87014.75114.7510.0000.0000.0000.000
109A114LEU0-0.072-0.02513.190-0.423-0.4230.0000.0000.0000.000
110A115ARG10.7910.8548.220-31.082-31.0820.0000.0000.0000.000
111A116TRP0-0.0020.0109.8551.6031.6030.0000.0000.0000.000
112A117GLY00.0300.02410.8410.1610.1610.0000.0000.0000.000
113A118ASP-1-0.848-0.9085.99833.18933.1890.0000.0000.0000.000
114A119PHE00.0460.0165.6853.7233.7230.0000.0000.0000.000
115A120SER0-0.002-0.0137.0510.0260.0260.0000.0000.0000.000
116A121ASN0-0.050-0.0515.937-1.859-1.8590.0000.0000.0000.000
117A122ALA00.0490.0362.892-1.176-0.5220.260-0.375-0.5390.002
118A123VAL00.0340.0124.185-1.733-1.6630.000-0.006-0.0640.000
119A124VAL0-0.027-0.0197.348-1.686-1.6860.0000.0000.0000.000
120A125ASP-1-0.923-0.9633.96635.25335.5340.000-0.085-0.1950.000
121A126LEU0-0.041-0.0165.500-1.402-1.4020.0000.0000.0000.000
122A127VAL00.005-0.0057.906-1.728-1.7280.0000.0000.0000.000
123A128GLU-1-0.832-0.90110.14520.37220.3720.0000.0000.0000.000
124A129LYS10.8860.9588.058-27.237-27.2370.0000.0000.0000.000
125A130PHE0-0.024-0.0239.574-0.517-0.5170.0000.0000.0000.000
126A131GLY0-0.0140.00313.434-1.116-1.1160.0000.0000.0000.000
127A132VAL0-0.031-0.01013.719-0.994-0.9940.0000.0000.0000.000
128A133GLU-1-0.807-0.85916.16812.32912.3290.0000.0000.0000.000
129A134ASN0-0.006-0.01418.817-0.232-0.2320.0000.0000.0000.000
130A135THR00.0120.01315.1110.7310.7310.0000.0000.0000.000
131A136ILE00.0000.00417.852-0.452-0.4520.0000.0000.0000.000
132A137CYS0-0.053-0.02217.1980.5040.5040.0000.0000.0000.000
133A138LEU0-0.028-0.00619.291-0.678-0.6780.0000.0000.0000.000
134A139TYR0-0.026-0.03219.5910.3710.3710.0000.0000.0000.000
135A140ALA00.0200.00624.180-0.363-0.3630.0000.0000.0000.000
136A141ALA00.004-0.00227.5970.1350.1350.0000.0000.0000.000
137A142PRO0-0.0220.00330.010-0.255-0.2550.0000.0000.0000.000
138A143MET0-0.014-0.01332.296-0.089-0.0890.0000.0000.0000.000
139A144THR0-0.024-0.01036.082-0.084-0.0840.0000.0000.0000.000
140A145VAL00.0010.00137.457-0.114-0.1140.0000.0000.0000.000
141A146PRO00.0130.00840.5080.0640.0640.0000.0000.0000.000
142A147HIS00.0570.01740.7230.2020.2020.0000.0000.0000.000
143A148THR0-0.082-0.06041.7490.0700.0700.0000.0000.0000.000
144A149ARG10.7120.81442.566-6.482-6.4820.0000.0000.0000.000
145A150PRO00.0160.01440.3370.1360.1360.0000.0000.0000.000
146A151THR00.0310.02434.1800.0220.0220.0000.0000.0000.000
147A152VAL00.0110.01035.0060.0040.0040.0000.0000.0000.000
148A153VAL00.0170.00529.1990.1560.1560.0000.0000.0000.000
149A154THR00.0190.00430.546-0.130-0.1300.0000.0000.0000.000
150A155ALA0-0.002-0.01227.1960.3120.3120.0000.0000.0000.000
151A156HIS0-0.033-0.01322.170-0.687-0.6870.0000.0000.0000.000
152A157GLY00.017-0.00523.4930.4830.4830.0000.0000.0000.000
153A158ASN0-0.084-0.04421.205-0.323-0.3230.0000.0000.0000.000
154A159SER00.0520.03323.166-0.004-0.0040.0000.0000.0000.000
155A160THR0-0.005-0.00625.243-0.105-0.1050.0000.0000.0000.000
156A161ASP-1-0.901-0.95227.6559.1959.1950.0000.0000.0000.000
157A162ARG10.7530.86523.539-11.648-11.6480.0000.0000.0000.000
158A163LEU0-0.0440.00828.674-0.089-0.0890.0000.0000.0000.000
159A164LYS10.8070.88330.673-8.995-8.9950.0000.0000.0000.000
160A165ASP-1-0.881-0.90833.5087.8647.8640.0000.0000.0000.000
161A166GLN00.0150.00630.7940.3350.3350.0000.0000.0000.000
162A167VAL0-0.047-0.02533.941-0.223-0.2230.0000.0000.0000.000
163A168SER0-0.0090.00631.564-0.098-0.0980.0000.0000.0000.000
164A169LEU0-0.032-0.01332.436-0.070-0.0700.0000.0000.0000.000
165A170ASP-1-0.862-0.95031.8278.9268.9260.0000.0000.0000.000
166A171THR0-0.035-0.02433.581-0.017-0.0170.0000.0000.0000.000
167A172ARG10.8860.94131.259-9.112-9.1120.0000.0000.0000.000
168A173MET00.0470.03828.933-0.138-0.1380.0000.0000.0000.000
169A174THR0-0.087-0.06828.3200.1450.1450.0000.0000.0000.000
170A175VAL00.0560.04624.966-0.350-0.3500.0000.0000.0000.000
171A176PRO00.0050.00124.7410.1970.1970.0000.0000.0000.000
172A177GLY0-0.0020.01721.1090.0360.0360.0000.0000.0000.000
173A178SER00.0610.01918.682-0.196-0.1960.0000.0000.0000.000
174A179ALA00.0360.01413.0170.3630.3630.0000.0000.0000.000
175A180SER00.025-0.00514.0750.8230.8230.0000.0000.0000.000
176A181LEU00.0140.01416.0070.0940.0940.0000.0000.0000.000
177A182MET0-0.095-0.03813.4790.2810.2810.0000.0000.0000.000
178A183LEU00.0400.01410.7660.3980.3980.0000.0000.0000.000
179A184GLU-1-0.719-0.82713.62113.64713.6470.0000.0000.0000.000
180A185LYS10.8450.91317.033-15.314-15.3140.0000.0000.0000.000
181A186LEU0-0.021-0.0049.918-0.479-0.4790.0000.0000.0000.000
182A187LEU00.0280.01112.9370.1420.1420.0000.0000.0000.000
183A188LYS10.9140.95415.165-13.278-13.2780.0000.0000.0000.000
184A189ASP-1-0.887-0.93316.80713.81613.8160.0000.0000.0000.000
185A190LYS10.8220.9169.507-23.937-23.9370.0000.0000.0000.000
186A191GLY0-0.021-0.00915.7940.1750.1750.0000.0000.0000.000
187A192LYS10.8110.90413.931-17.639-17.6390.0000.0000.0000.000
188A193ASN0-0.075-0.02718.107-0.725-0.7250.0000.0000.0000.000
189A194VAL00.010-0.00417.6070.6380.6380.0000.0000.0000.000
190A195SER0-0.009-0.01820.033-0.785-0.7850.0000.0000.0000.000
191A196GLY00.0130.03020.7130.5970.5970.0000.0000.0000.000
192A197TYR0-0.047-0.05322.426-0.461-0.4610.0000.0000.0000.000
193A198THR00.0260.00024.9640.4070.4070.0000.0000.0000.000
194A199VAL0-0.0170.00927.446-0.377-0.3770.0000.0000.0000.000
195A200HIS0-0.018-0.00930.1000.2050.2050.0000.0000.0000.000
196A201VAL00.001-0.00631.453-0.188-0.1880.0000.0000.0000.000
197A202PRO00.0540.03334.3580.0200.0200.0000.0000.0000.000
198A203HIS00.0240.01536.0590.1720.1720.0000.0000.0000.000
199A204TYR0-0.051-0.03937.0790.1200.1200.0000.0000.0000.000
200A205VAL00.0150.01636.272-0.072-0.0720.0000.0000.0000.000
201A206SER0-0.029-0.03432.8030.2220.2220.0000.0000.0000.000
202A207ALA00.0270.02332.2970.2820.2820.0000.0000.0000.000
203A208SER0-0.0180.00433.1250.1270.1270.0000.0000.0000.000
204A209PRO0-0.004-0.01632.4560.1190.1190.0000.0000.0000.000
205A210TYR00.0290.01332.793-0.336-0.3360.0000.0000.0000.000
206A211PRO00.0440.01232.6730.1240.1240.0000.0000.0000.000
207A212ALA00.0170.01733.2440.1000.1000.0000.0000.0000.000
208A213ALA00.0060.00431.0590.0410.0410.0000.0000.0000.000
209A214THR00.0440.01227.7810.1920.1920.0000.0000.0000.000
210A215LEU0-0.0150.00429.3020.1960.1960.0000.0000.0000.000
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