FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 39ZML

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 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 269
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3476491.083341
FMO2-HF: Nuclear repulsion 3371107.828174
FMO2-HF: Total energy -105383.255168
FMO2-MP2: Total energy -105689.351876


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.
191.271198.6381.242-3.53-5.0770.009
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 : -0.946 / q_NPA : -0.983
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].
3A8MET0-0.063-0.0292.645-19.481-14.9940.606-2.282-2.8100.016
4A9TYR0-0.010-0.0042.909-7.806-5.8290.326-0.866-1.437-0.007
5A10GLU-1-0.885-0.9234.74742.28942.292-0.001-0.0130.0110.000
6A11LEU0-0.062-0.0386.129-3.075-3.0750.0000.0000.0000.000
7A12GLU-1-0.901-0.9468.67420.06420.0640.0000.0000.0000.000
8A13TYR0-0.061-0.02012.420-0.056-0.0560.0000.0000.0000.000
9A14PRO0-0.037-0.04214.745-0.724-0.7240.0000.0000.0000.000
10A15SER00.0350.01114.0270.5310.5310.0000.0000.0000.000
11A16PRO0-0.0210.00214.538-1.060-1.0600.0000.0000.0000.000
12A17GLU-1-0.845-0.90417.45514.50914.5090.0000.0000.0000.000
13A18VAL00.0200.00615.704-0.283-0.2830.0000.0000.0000.000
14A19SER0-0.082-0.04819.187-0.523-0.5230.0000.0000.0000.000
15A20GLY00.0720.02022.262-0.264-0.2640.0000.0000.0000.000
16A21GLN0-0.045-0.02325.3670.1600.1600.0000.0000.0000.000
17A22THR0-0.019-0.00127.036-0.326-0.3260.0000.0000.0000.000
18A23ALA0-0.027-0.01226.1760.3770.3770.0000.0000.0000.000
19A24GLY00.0030.00424.291-0.156-0.1560.0000.0000.0000.000
20A25GLY00.0140.00920.405-0.023-0.0230.0000.0000.0000.000
21A26PRO00.0300.02417.633-0.571-0.5710.0000.0000.0000.000
22A27THR00.005-0.00219.2060.2490.2490.0000.0000.0000.000
23A28LEU0-0.042-0.01212.9190.1820.1820.0000.0000.0000.000
24A29ILE00.0270.00517.273-0.344-0.3440.0000.0000.0000.000
25A30VAL0-0.006-0.00814.1380.7060.7060.0000.0000.0000.000
26A31ALA0-0.002-0.02216.585-0.762-0.7620.0000.0000.0000.000
27A32LEU0-0.005-0.00213.1720.3340.3340.0000.0000.0000.000
28A33GLN0-0.078-0.04717.208-0.676-0.6760.0000.0000.0000.000
29A34GLY0-0.023-0.02918.9380.6550.6550.0000.0000.0000.000
30A35TYR0-0.053-0.02020.045-0.225-0.2250.0000.0000.0000.000
31A36ALA0-0.012-0.01021.947-0.483-0.4830.0000.0000.0000.000
32A37ASP-1-0.742-0.87223.07612.01712.0170.0000.0000.0000.000
33A38ALA0-0.025-0.00126.031-0.297-0.2970.0000.0000.0000.000
34A39GLY00.023-0.01029.4090.0790.0790.0000.0000.0000.000
35A40HIS10.8040.88427.392-9.983-9.9830.0000.0000.0000.000
36A41ALA00.0540.04227.3100.1610.1610.0000.0000.0000.000
37A42VAL00.0360.04420.9720.0090.0090.0000.0000.0000.000
38A43GLU-1-0.729-0.86622.42611.26411.2640.0000.0000.0000.000
39A44SER0-0.037-0.03923.452-0.026-0.0260.0000.0000.0000.000
40A45SER0-0.050-0.03823.781-0.238-0.2380.0000.0000.0000.000
41A46SER0-0.045-0.02820.3540.1130.1130.0000.0000.0000.000
42A47SER00.0650.02222.3130.0690.0690.0000.0000.0000.000
43A48HIS0-0.020-0.01324.481-0.286-0.2860.0000.0000.0000.000
44A49LEU0-0.027-0.03323.274-0.171-0.1710.0000.0000.0000.000
45A50MET0-0.022-0.01518.8050.0360.0360.0000.0000.0000.000
46A51ASP-1-0.947-0.96824.06810.48810.4880.0000.0000.0000.000
47A52ALA0-0.099-0.03427.578-0.320-0.3200.0000.0000.0000.000
48A53LEU0-0.054-0.02025.543-0.275-0.2750.0000.0000.0000.000
49A54ASP-1-0.826-0.87725.23511.38811.3880.0000.0000.0000.000
50A55HIS0-0.029-0.02620.5740.4340.4340.0000.0000.0000.000
51A56ARG10.7670.85618.858-12.713-12.7130.0000.0000.0000.000
52A57LEU00.0400.03613.4120.0850.0850.0000.0000.0000.000
53A58ILE0-0.033-0.01711.2260.1590.1590.0000.0000.0000.000
54A59ALA00.008-0.0018.0321.8681.8680.0000.0000.0000.000
55A60SER00.0530.0449.866-2.220-2.2200.0000.0000.0000.000
56A61PHE0-0.032-0.0385.4413.1553.1550.0000.0000.0000.000
57A62ASN00.0230.0047.525-4.258-4.2580.0000.0000.0000.000
58A63ASN00.030-0.0169.3811.1641.1640.0000.0000.0000.000
59A64ASP-1-0.878-0.90912.37718.98518.9850.0000.0000.0000.000
60A65GLU-1-0.901-0.9368.04631.80931.8090.0000.0000.0000.000
61A66LEU0-0.013-0.0137.328-0.186-0.1860.0000.0000.0000.000
62A67ILE0-0.0140.01811.329-1.287-1.2870.0000.0000.0000.000
63A68ASP-1-0.885-0.92315.03713.81613.8160.0000.0000.0000.000
64A69TYR00.045-0.02415.697-1.192-1.1920.0000.0000.0000.000
65A70ARG10.8460.92420.271-12.203-12.2030.0000.0000.0000.000
66A71SER0-0.055-0.04520.563-0.632-0.6320.0000.0000.0000.000
67A72ARG10.8520.91317.513-15.100-15.1000.0000.0000.0000.000
68A73ARG10.8190.90922.055-11.482-11.4820.0000.0000.0000.000
69A74PRO00.0570.04020.315-0.438-0.4380.0000.0000.0000.000
70A75VAL00.0330.01423.163-0.216-0.2160.0000.0000.0000.000
71A76VAL0-0.0070.00925.9860.2620.2620.0000.0000.0000.000
72A77VAL0-0.046-0.02428.327-0.344-0.3440.0000.0000.0000.000
73A78ILE0-0.022-0.01431.2620.0750.0750.0000.0000.0000.000
74A79GLU-1-0.925-0.96234.1908.3618.3610.0000.0000.0000.000
75A80HIS0-0.055-0.04137.039-0.105-0.1050.0000.0000.0000.000
76A81ASN0-0.111-0.06438.853-0.045-0.0450.0000.0000.0000.000
77A82GLU-1-0.841-0.89934.1359.0829.0820.0000.0000.0000.000
78A83VAL0-0.035-0.02229.272-0.014-0.0140.0000.0000.0000.000
79A84THR0-0.027-0.01631.3480.2030.2030.0000.0000.0000.000
80A85SER00.0020.00227.5920.4420.4420.0000.0000.0000.000
81A86MET0-0.018-0.01122.094-0.304-0.3040.0000.0000.0000.000
82A87ASP-1-0.861-0.93321.64413.44713.4470.0000.0000.0000.000
83A88GLU-1-0.900-0.94717.19216.52716.5270.0000.0000.0000.000
84A89LEU0-0.060-0.03917.3040.9290.9290.0000.0000.0000.000
85A90ASN0-0.041-0.01014.4951.2441.2440.0000.0000.0000.000
86A91LEU00.0090.02410.380-0.535-0.5350.0000.0000.0000.000
87A92GLY00.0650.03411.3541.7181.7180.0000.0000.0000.000
88A93LEU0-0.052-0.03110.215-0.848-0.8480.0000.0000.0000.000
89A94HIS00.0600.01412.4530.1740.1740.0000.0000.0000.000
90A95VAL0-0.020-0.01115.911-0.030-0.0300.0000.0000.0000.000
91A96VAL00.002-0.00418.287-0.266-0.2660.0000.0000.0000.000
92A97ARG10.7860.89721.595-12.493-12.4930.0000.0000.0000.000
93A98ASP-1-0.709-0.85025.02310.04210.0420.0000.0000.0000.000
94A99ASN0-0.038-0.03727.7490.0630.0630.0000.0000.0000.000
95A100ASP-1-0.909-0.93230.6808.5948.5940.0000.0000.0000.000
96A101ASN0-0.104-0.06227.5260.2680.2680.0000.0000.0000.000
97A102LYS10.8430.91125.940-10.213-10.2130.0000.0000.0000.000
98A103PRO0-0.043-0.01821.227-0.008-0.0080.0000.0000.0000.000
99A104PHE0-0.027-0.00720.625-0.075-0.0750.0000.0000.0000.000
100A105LEU00.004-0.00413.9040.3060.3060.0000.0000.0000.000
101A106MET0-0.0060.01316.494-0.668-0.6680.0000.0000.0000.000
102A107LEU0-0.0140.00610.5600.7310.7310.0000.0000.0000.000
103A108SER0-0.019-0.01514.082-0.986-0.9860.0000.0000.0000.000
104A109GLY00.1010.05214.9810.7580.7580.0000.0000.0000.000
105A110PRO0-0.038-0.01014.673-0.558-0.5580.0000.0000.0000.000
106A111GLU-1-0.820-0.92914.36215.84815.8480.0000.0000.0000.000
107A112PRO00.0040.00610.681-0.385-0.3850.0000.0000.0000.000
108A113ASP-1-0.746-0.84813.41914.69714.6970.0000.0000.0000.000
109A114LEU0-0.083-0.02612.523-0.428-0.4280.0000.0000.0000.000
110A115ARG10.8180.8788.029-29.500-29.5000.0000.0000.0000.000
111A116TRP00.0050.0019.0621.7791.7790.0000.0000.0000.000
112A117GLY00.0170.01910.1640.1790.1790.0000.0000.0000.000
113A118ASP-1-0.869-0.9315.40233.39633.3960.0000.0000.0000.000
114A119PHE00.0520.0215.1832.7962.888-0.001-0.001-0.0890.000
115A120SER0-0.009-0.0186.6830.0190.0190.0000.0000.0000.000
116A121ASN0-0.016-0.0255.652-2.566-2.5660.0000.0000.0000.000
117A122ALA00.0190.0212.562-0.2020.2190.312-0.270-0.4630.000
118A123VAL00.0390.0154.175-1.080-0.9940.000-0.020-0.0660.000
119A124VAL0-0.016-0.0247.582-1.400-1.4000.0000.0000.0000.000
120A125ASP-1-0.911-0.9493.92138.02338.3240.000-0.078-0.2230.000
121A126LEU0-0.040-0.0166.199-1.554-1.5540.0000.0000.0000.000
122A127VAL00.0190.0058.711-1.833-1.8330.0000.0000.0000.000
123A128GLU-1-0.852-0.91010.71120.74620.7460.0000.0000.0000.000
124A129LYS10.8980.9638.372-29.058-29.0580.0000.0000.0000.000
125A130PHE0-0.018-0.02210.014-0.665-0.6650.0000.0000.0000.000
126A131GLY0-0.0110.00714.046-1.174-1.1740.0000.0000.0000.000
127A132VAL0-0.032-0.01414.337-1.040-1.0400.0000.0000.0000.000
128A133GLU-1-0.810-0.87116.82112.39212.3920.0000.0000.0000.000
129A134ASN00.0120.01519.321-0.320-0.3200.0000.0000.0000.000
130A135THR00.0300.02615.0800.7090.7090.0000.0000.0000.000
131A136ILE0-0.011-0.00118.017-0.397-0.3970.0000.0000.0000.000
132A137CYS0-0.054-0.01717.2740.6780.6780.0000.0000.0000.000
133A138LEU0-0.013-0.00119.421-0.648-0.6480.0000.0000.0000.000
134A139TYR0-0.041-0.03119.5150.4100.4100.0000.0000.0000.000
135A140ALA00.0310.01724.129-0.368-0.3680.0000.0000.0000.000
136A141ALA00.0110.00227.3500.0980.0980.0000.0000.0000.000
137A142PRO0-0.0140.00329.637-0.246-0.2460.0000.0000.0000.000
138A143MET0-0.015-0.02031.642-0.078-0.0780.0000.0000.0000.000
139A144THR0-0.020-0.00335.589-0.087-0.0870.0000.0000.0000.000
140A145VAL0-0.002-0.00537.189-0.120-0.1200.0000.0000.0000.000
141A146PRO00.0180.01240.1030.0520.0520.0000.0000.0000.000
142A147HIS00.0520.01840.5730.1870.1870.0000.0000.0000.000
143A148THR0-0.069-0.06541.5760.0450.0450.0000.0000.0000.000
144A149ARG10.7060.82442.544-6.449-6.4490.0000.0000.0000.000
145A150PRO00.0170.01340.1260.1330.1330.0000.0000.0000.000
146A151THR00.0190.01534.0070.0150.0150.0000.0000.0000.000
147A152VAL00.0260.02034.6070.0130.0130.0000.0000.0000.000
148A153VAL00.004-0.00329.0810.1400.1400.0000.0000.0000.000
149A154THR00.003-0.00830.488-0.112-0.1120.0000.0000.0000.000
150A155ALA0-0.014-0.02327.3830.3250.3250.0000.0000.0000.000
151A156HIS0-0.014-0.00122.228-0.654-0.6540.0000.0000.0000.000
152A157GLY00.011-0.00523.7940.4630.4630.0000.0000.0000.000
153A158ASN0-0.076-0.04821.607-0.371-0.3710.0000.0000.0000.000
154A159SER0-0.002-0.00222.846-0.214-0.2140.0000.0000.0000.000
155A160THR00.0380.00125.720-0.131-0.1310.0000.0000.0000.000
156A161ASP-1-0.905-0.93828.0199.1139.1130.0000.0000.0000.000
157A162ARG10.7200.83224.161-11.765-11.7650.0000.0000.0000.000
158A163LEU0-0.0370.01228.697-0.072-0.0720.0000.0000.0000.000
159A164LYS10.8570.91030.723-8.858-8.8580.0000.0000.0000.000
160A165ASP-1-0.890-0.92334.1657.9057.9050.0000.0000.0000.000
161A166GLN00.0340.03431.1790.2950.2950.0000.0000.0000.000
162A167VAL0-0.039-0.01933.953-0.171-0.1710.0000.0000.0000.000
163A168SER0-0.012-0.00331.577-0.108-0.1080.0000.0000.0000.000
164A169LEU0-0.052-0.00932.526-0.095-0.0950.0000.0000.0000.000
165A170ASP-1-0.878-0.97031.2759.0149.0140.0000.0000.0000.000
166A171THR0-0.034-0.03533.1470.0370.0370.0000.0000.0000.000
167A172ARG10.9190.97531.063-9.108-9.1080.0000.0000.0000.000
168A173MET00.0370.02129.079-0.215-0.2150.0000.0000.0000.000
169A174THR0-0.074-0.04428.1150.1760.1760.0000.0000.0000.000
170A175VAL00.0650.03924.338-0.323-0.3230.0000.0000.0000.000
171A176PRO0-0.0020.00224.3560.2330.2330.0000.0000.0000.000
172A177GLY0-0.0050.01320.6170.0530.0530.0000.0000.0000.000
173A178SER00.0770.03418.393-0.096-0.0960.0000.0000.0000.000
174A179ALA00.0360.01112.7840.3120.3120.0000.0000.0000.000
175A180SER00.023-0.02213.9030.8140.8140.0000.0000.0000.000
176A181LEU00.0090.02015.741-0.004-0.0040.0000.0000.0000.000
177A182MET0-0.083-0.03413.2640.2350.2350.0000.0000.0000.000
178A183LEU00.0240.01110.6530.3220.3220.0000.0000.0000.000
179A184GLU-1-0.726-0.83413.57513.47713.4770.0000.0000.0000.000
180A185LYS10.8460.91617.073-14.920-14.9200.0000.0000.0000.000
181A186LEU0-0.0130.00410.002-0.505-0.5050.0000.0000.0000.000
182A187LEU00.0420.00713.1260.1000.1000.0000.0000.0000.000
183A188LYS10.8980.94715.476-13.303-13.3030.0000.0000.0000.000
184A189ASP-1-0.896-0.94616.79313.76413.7640.0000.0000.0000.000
185A190LYS10.8100.91110.325-23.092-23.0920.0000.0000.0000.000
186A191GLY0-0.057-0.01616.5260.0300.0300.0000.0000.0000.000
187A192LYS10.8280.91414.167-18.135-18.1350.0000.0000.0000.000
188A193ASN0-0.061-0.02318.590-0.775-0.7750.0000.0000.0000.000
189A194VAL0-0.014-0.02217.4960.6700.6700.0000.0000.0000.000
190A195SER0-0.003-0.01420.084-0.681-0.6810.0000.0000.0000.000
191A196GLY00.0200.02620.9770.5910.5910.0000.0000.0000.000
192A197TYR0-0.024-0.03622.764-0.444-0.4440.0000.0000.0000.000
193A198THR00.0240.00325.0890.3780.3780.0000.0000.0000.000
194A199VAL0-0.0080.00827.381-0.375-0.3750.0000.0000.0000.000
195A200HIS0-0.044-0.01430.0230.2190.2190.0000.0000.0000.000
196A201VAL00.009-0.00731.264-0.209-0.2090.0000.0000.0000.000
197A202PRO00.0400.03634.1380.0390.0390.0000.0000.0000.000
198A203HIS00.0540.01835.7280.1640.1640.0000.0000.0000.000
199A204TYR0-0.066-0.05036.7960.1100.1100.0000.0000.0000.000
200A205VAL00.0060.01036.212-0.071-0.0710.0000.0000.0000.000
201A206SER0-0.019-0.02232.5550.2140.2140.0000.0000.0000.000
202A207ALA00.0180.02132.1040.2720.2720.0000.0000.0000.000
203A208SER0-0.015-0.00133.1070.0980.0980.0000.0000.0000.000
204A209PRO0-0.011-0.01132.2580.0720.0720.0000.0000.0000.000
205A210TYR00.0430.01732.584-0.326-0.3260.0000.0000.0000.000
206A211PRO00.0400.01332.8030.1510.1510.0000.0000.0000.000
207A212ALA00.0180.01733.2960.1240.1240.0000.0000.0000.000
208A213ALA00.0030.00630.9860.0340.0340.0000.0000.0000.000
209A214THR00.0380.01227.9170.1700.1700.0000.0000.0000.000
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