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: JL489

Calculation Name: 1R88-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R88

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQN7

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 267
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3427440.976321
FMO2-HF: Nuclear repulsion 3328237.559962
FMO2-HF: Total energy -99203.416359
FMO2-MP2: Total energy -99489.463548


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:33:ALA)


Summations of interaction energy for fragment #1(A:33:ALA)
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.
0.6592.447-0.013-0.837-0.9370
Interaction energy analysis for fragmet #1(A:33:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014
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].
3A35PRO0-0.016-0.0043.8670.6442.207-0.017-0.788-0.7580.000
4A36TYR0-0.049-0.0326.063-0.343-0.3430.0000.0000.0000.000
5A37GLU-1-0.777-0.8539.0830.3090.3090.0000.0000.0000.000
6A38ASN00.0120.0089.879-0.014-0.0140.0000.0000.0000.000
7A39LEU0-0.0100.00813.377-0.049-0.0490.0000.0000.0000.000
8A40MET00.0180.02216.8500.0300.0300.0000.0000.0000.000
9A41VAL0-0.016-0.00819.576-0.019-0.0190.0000.0000.0000.000
10A42PRO00.0250.01622.173-0.001-0.0010.0000.0000.0000.000
11A43SER0-0.037-0.03825.838-0.004-0.0040.0000.0000.0000.000
12A44PRO0-0.009-0.01527.528-0.002-0.0020.0000.0000.0000.000
13A45SER0-0.050-0.05330.639-0.006-0.0060.0000.0000.0000.000
14A46MET0-0.049-0.00925.169-0.004-0.0040.0000.0000.0000.000
15A47GLY0-0.022-0.00630.0100.0040.0040.0000.0000.0000.000
16A48ARG10.8140.91324.994-0.143-0.1430.0000.0000.0000.000
17A49ASP-1-0.865-0.92823.3180.1500.1500.0000.0000.0000.000
18A50ILE0-0.054-0.02920.1600.0040.0040.0000.0000.0000.000
19A51PRO00.0650.02516.8810.0030.0030.0000.0000.0000.000
20A52VAL0-0.073-0.03915.972-0.011-0.0110.0000.0000.0000.000
21A53ALA00.0100.02110.5240.0230.0230.0000.0000.0000.000
22A54PHE00.002-0.01212.511-0.064-0.0640.0000.0000.0000.000
23A55LEU00.004-0.0048.0630.0630.0630.0000.0000.0000.000
24A56ALA00.0260.01611.730-0.046-0.0460.0000.0000.0000.000
25A57GLY0-0.003-0.01213.634-0.035-0.0350.0000.0000.0000.000
26A58GLY0-0.030-0.00715.389-0.025-0.0250.0000.0000.0000.000
27A59PRO00.0400.03419.0910.0180.0180.0000.0000.0000.000
28A60HIS10.8970.96121.180-0.021-0.0210.0000.0000.0000.000
29A61ALA00.0220.01117.778-0.004-0.0040.0000.0000.0000.000
30A62VAL00.0230.01115.224-0.010-0.0100.0000.0000.0000.000
31A63TYR00.016-0.00516.3010.0290.0290.0000.0000.0000.000
32A64LEU0-0.040-0.02312.598-0.014-0.0140.0000.0000.0000.000
33A65LEU0-0.0050.00216.6440.0260.0260.0000.0000.0000.000
34A66ASP-1-0.682-0.82816.7560.2480.2480.0000.0000.0000.000
35A67ALA00.0260.02018.705-0.022-0.0220.0000.0000.0000.000
36A68PHE0-0.015-0.03021.0240.0070.0070.0000.0000.0000.000
37A69ASN0-0.022-0.01921.0300.0050.0050.0000.0000.0000.000
38A70ALA0-0.020-0.00419.0810.0160.0160.0000.0000.0000.000
39A71GLY00.0430.03416.207-0.007-0.0070.0000.0000.0000.000
40A72PRO0-0.020-0.02217.2870.0050.0050.0000.0000.0000.000
41A73ASP-1-0.872-0.94116.0840.2950.2950.0000.0000.0000.000
42A74VAL0-0.014-0.02710.3940.0430.0430.0000.0000.0000.000
43A75SER0-0.031-0.01813.765-0.030-0.0300.0000.0000.0000.000
44A76ASN00.004-0.02212.2450.0960.0960.0000.0000.0000.000
45A77TRP0-0.020-0.02912.1610.0160.0160.0000.0000.0000.000
46A78VAL0-0.059-0.0267.077-0.016-0.0160.0000.0000.0000.000
47A79THR0-0.014-0.0067.2160.1230.1230.0000.0000.0000.000
48A80ALA00.0090.0029.140-0.048-0.0480.0000.0000.0000.000
49A81GLY0-0.010-0.00911.411-0.061-0.0610.0000.0000.0000.000
50A82ASN0-0.031-0.0226.2620.0490.0490.0000.0000.0000.000
51A83ALA00.0550.0427.736-0.068-0.0680.0000.0000.0000.000
52A84MET00.0080.0005.141-0.164-0.1640.0000.0000.0000.000
53A85ASN0-0.0080.0013.520-0.295-0.0880.005-0.049-0.1630.000
54A86THR0-0.023-0.0145.374-0.150-0.132-0.0010.000-0.0160.000
55A87LEU0-0.017-0.0319.000-0.040-0.0400.0000.0000.0000.000
56A88ALA00.0250.0247.736-0.002-0.0020.0000.0000.0000.000
57A89GLY0-0.022-0.0149.625-0.026-0.0260.0000.0000.0000.000
58A90LYS10.9100.97612.1540.1470.1470.0000.0000.0000.000
59A91GLY00.0120.01715.0250.0170.0170.0000.0000.0000.000
60A92ILE0-0.014-0.01215.3320.0120.0120.0000.0000.0000.000
61A93SER00.0340.00314.762-0.014-0.0140.0000.0000.0000.000
62A94VAL0-0.024-0.00911.104-0.008-0.0080.0000.0000.0000.000
63A95VAL00.0110.00913.7290.0370.0370.0000.0000.0000.000
64A96ALA00.0180.00612.536-0.024-0.0240.0000.0000.0000.000
65A97PRO0-0.035-0.00714.6450.0460.0460.0000.0000.0000.000
66A98ALA00.0050.00815.938-0.008-0.0080.0000.0000.0000.000
67A99GLY00.0340.00617.601-0.027-0.0270.0000.0000.0000.000
68A100GLY00.0040.00320.634-0.020-0.0200.0000.0000.0000.000
69A101ALA0-0.0360.01522.575-0.013-0.0130.0000.0000.0000.000
70A102TYR0-0.011-0.03523.906-0.006-0.0060.0000.0000.0000.000
71A103SER00.015-0.02125.099-0.009-0.0090.0000.0000.0000.000
72A104MET0-0.019-0.01027.251-0.005-0.0050.0000.0000.0000.000
73A105TYR0-0.0020.00119.461-0.005-0.0050.0000.0000.0000.000
74A106THR00.0010.01426.161-0.006-0.0060.0000.0000.0000.000
75A107ASN00.018-0.00229.8690.0110.0110.0000.0000.0000.000
76A108TRP0-0.063-0.03330.351-0.006-0.0060.0000.0000.0000.000
77A109GLU-1-0.801-0.88834.3680.0510.0510.0000.0000.0000.000
78A110GLN0-0.075-0.03437.290-0.004-0.0040.0000.0000.0000.000
79A111ASP-1-0.762-0.84432.2230.0960.0960.0000.0000.0000.000
80A112GLY00.0330.01933.3560.0030.0030.0000.0000.0000.000
81A113SER0-0.059-0.04629.6650.0060.0060.0000.0000.0000.000
82A114LYS10.8480.92228.246-0.089-0.0890.0000.0000.0000.000
83A115GLN0-0.057-0.04329.451-0.009-0.0090.0000.0000.0000.000
84A116TRP00.0840.02922.0570.0010.0010.0000.0000.0000.000
85A117ASP-1-0.834-0.88426.9060.0740.0740.0000.0000.0000.000
86A118THR00.0320.03129.196-0.003-0.0030.0000.0000.0000.000
87A119PHE00.0260.01921.6130.0010.0010.0000.0000.0000.000
88A120LEU0-0.030-0.02422.0050.0040.0040.0000.0000.0000.000
89A121SER0-0.046-0.04525.171-0.004-0.0040.0000.0000.0000.000
90A122ALA00.0160.00628.186-0.007-0.0070.0000.0000.0000.000
91A123GLU-1-0.758-0.83827.1040.1040.1040.0000.0000.0000.000
92A124LEU0-0.0030.00619.8670.0030.0030.0000.0000.0000.000
93A125PRO0-0.031-0.00523.4610.0030.0030.0000.0000.0000.000
94A126ASP-1-0.765-0.85924.7330.0620.0620.0000.0000.0000.000
95A127TRP00.0070.01320.1130.0000.0000.0000.0000.0000.000
96A128LEU00.018-0.00818.8600.0010.0010.0000.0000.0000.000
97A129ALA0-0.026-0.00522.700-0.006-0.0060.0000.0000.0000.000
98A130ALA0-0.034-0.02325.614-0.005-0.0050.0000.0000.0000.000
99A131ASN0-0.086-0.03823.498-0.004-0.0040.0000.0000.0000.000
100A132ARG10.7290.81517.850-0.158-0.1580.0000.0000.0000.000
101A133GLY00.0140.03421.391-0.007-0.0070.0000.0000.0000.000
102A134LEU0-0.068-0.02319.105-0.010-0.0100.0000.0000.0000.000
103A135ALA0-0.007-0.00823.197-0.003-0.0030.0000.0000.0000.000
104A136PRO00.0420.01025.3270.0070.0070.0000.0000.0000.000
105A137GLY00.0400.01726.9340.0060.0060.0000.0000.0000.000
106A138GLY0-0.029-0.01326.626-0.004-0.0040.0000.0000.0000.000
107A139HIS0-0.0330.00522.057-0.008-0.0080.0000.0000.0000.000
108A140ALA00.0110.00020.410-0.007-0.0070.0000.0000.0000.000
109A141ALA0-0.0120.01220.8290.0140.0140.0000.0000.0000.000
110A142VAL00.014-0.00618.032-0.015-0.0150.0000.0000.0000.000
111A143GLY00.0510.02319.1110.0200.0200.0000.0000.0000.000
112A144ALA00.0070.01519.379-0.015-0.0150.0000.0000.0000.000
113A145ALA00.0240.01121.1530.0070.0070.0000.0000.0000.000
114A146GLN00.003-0.00622.630-0.019-0.0190.0000.0000.0000.000
115A147GLY00.0420.02321.758-0.004-0.0040.0000.0000.0000.000
116A148GLY0-0.055-0.00622.835-0.004-0.0040.0000.0000.0000.000
117A149TYR0-0.070-0.06324.242-0.008-0.0080.0000.0000.0000.000
118A150GLY00.0320.01225.219-0.004-0.0040.0000.0000.0000.000
119A151ALA0-0.006-0.00622.819-0.004-0.0040.0000.0000.0000.000
120A152MET0-0.0030.00824.872-0.008-0.0080.0000.0000.0000.000
121A153ALA0-0.013-0.01028.230-0.006-0.0060.0000.0000.0000.000
122A154LEU0-0.010-0.00624.955-0.003-0.0030.0000.0000.0000.000
123A155ALA00.0230.00327.528-0.003-0.0030.0000.0000.0000.000
124A156ALA0-0.058-0.02229.337-0.005-0.0050.0000.0000.0000.000
125A157PHE0-0.046-0.02832.290-0.004-0.0040.0000.0000.0000.000
126A158HIS10.8170.89929.789-0.063-0.0630.0000.0000.0000.000
127A159PRO00.0390.03130.0080.0030.0030.0000.0000.0000.000
128A160ASP-1-0.876-0.94030.8660.0480.0480.0000.0000.0000.000
129A161ARG10.7360.83926.812-0.064-0.0640.0000.0000.0000.000
130A162PHE0-0.039-0.02122.7400.0020.0020.0000.0000.0000.000
131A163GLY00.0560.03726.622-0.003-0.0030.0000.0000.0000.000
132A164PHE0-0.035-0.02922.020-0.005-0.0050.0000.0000.0000.000
133A165ALA00.0290.01124.6340.0080.0080.0000.0000.0000.000
134A166GLY00.0000.00322.290-0.008-0.0080.0000.0000.0000.000
135A167SER0-0.015-0.01422.8090.0130.0130.0000.0000.0000.000
136A168MET0-0.0360.00217.313-0.006-0.0060.0000.0000.0000.000
137A169SER00.028-0.00922.9800.0100.0100.0000.0000.0000.000
138A170GLY00.0430.02725.4810.0060.0060.0000.0000.0000.000
139A171PHE0-0.017-0.01327.039-0.006-0.0060.0000.0000.0000.000
140A172LEU00.010-0.01227.9220.0010.0010.0000.0000.0000.000
141A173TYR0-0.025-0.02031.465-0.003-0.0030.0000.0000.0000.000
142A174PRO00.0240.02032.950-0.002-0.0020.0000.0000.0000.000
143A175SER0-0.042-0.05334.920-0.001-0.0010.0000.0000.0000.000
144A176ASN0-0.010-0.02038.200-0.005-0.0050.0000.0000.0000.000
145A177THR0-0.020-0.00640.0480.0020.0020.0000.0000.0000.000
146A178THR0-0.028-0.03339.2540.0000.0000.0000.0000.0000.000
147A179THR0-0.046-0.02934.6900.0010.0010.0000.0000.0000.000
148A180ASN0-0.034-0.02236.2900.0040.0040.0000.0000.0000.000
149A181GLY00.0370.02337.6250.0030.0030.0000.0000.0000.000
150A182ALA0-0.013-0.00335.6380.0020.0020.0000.0000.0000.000
151A183ILE0-0.009-0.01132.1040.0030.0030.0000.0000.0000.000
152A184ALA00.0170.01333.7650.0040.0040.0000.0000.0000.000
153A185ALA0-0.011-0.00435.9050.0020.0020.0000.0000.0000.000
154A186GLY00.0430.01632.5380.0020.0020.0000.0000.0000.000
155A187MET0-0.042-0.03129.9400.0080.0080.0000.0000.0000.000
156A188GLN0-0.048-0.00832.0630.0040.0040.0000.0000.0000.000
157A189GLN0-0.039-0.01832.9790.0010.0010.0000.0000.0000.000
158A190PHE0-0.027-0.02528.2310.0010.0010.0000.0000.0000.000
159A191GLY00.0240.01328.6500.0090.0090.0000.0000.0000.000
160A192GLY0-0.0220.01330.0550.0020.0020.0000.0000.0000.000
161A193VAL0-0.039-0.01231.220-0.003-0.0030.0000.0000.0000.000
162A194ASP-1-0.775-0.88334.1320.0530.0530.0000.0000.0000.000
163A195THR00.0380.01233.8020.0010.0010.0000.0000.0000.000
164A196ASN0-0.081-0.06836.348-0.003-0.0030.0000.0000.0000.000
165A197GLY0-0.007-0.00538.124-0.002-0.0020.0000.0000.0000.000
166A198MET0-0.041-0.00232.5620.0040.0040.0000.0000.0000.000
167A199TRP0-0.020-0.03532.123-0.002-0.0020.0000.0000.0000.000
168A200GLY00.0950.04838.149-0.004-0.0040.0000.0000.0000.000
169A201ALA00.0280.02440.6520.0010.0010.0000.0000.0000.000
170A202PRO00.0070.01240.834-0.002-0.0020.0000.0000.0000.000
171A203GLN00.009-0.00742.5820.0000.0000.0000.0000.0000.000
172A204LEU0-0.039-0.01244.896-0.002-0.0020.0000.0000.0000.000
173A205GLY00.0040.01044.6250.0000.0000.0000.0000.0000.000
174A206ARG10.8560.89941.225-0.045-0.0450.0000.0000.0000.000
175A207TRP00.0290.01235.8560.0020.0020.0000.0000.0000.000
176A208LYS10.9020.94437.995-0.034-0.0340.0000.0000.0000.000
177A209TRP0-0.020-0.01639.610-0.001-0.0010.0000.0000.0000.000
178A210HIS10.8990.96934.406-0.056-0.0560.0000.0000.0000.000
179A211ASP-1-0.703-0.81234.0730.0470.0470.0000.0000.0000.000
180A212PRO00.0550.01731.102-0.003-0.0030.0000.0000.0000.000
181A213TRP00.0120.01134.147-0.003-0.0030.0000.0000.0000.000
182A214VAL0-0.067-0.04036.470-0.003-0.0030.0000.0000.0000.000
183A215HIS0-0.013-0.00636.691-0.003-0.0030.0000.0000.0000.000
184A216ALA00.0350.02735.6780.0000.0000.0000.0000.0000.000
185A217SER00.006-0.01336.746-0.002-0.0020.0000.0000.0000.000
186A218LEU0-0.0290.00236.188-0.002-0.0020.0000.0000.0000.000
187A219LEU0-0.0010.00330.924-0.001-0.0010.0000.0000.0000.000
188A220ALA0-0.022-0.00634.381-0.002-0.0020.0000.0000.0000.000
189A221GLN0-0.042-0.02236.916-0.002-0.0020.0000.0000.0000.000
190A222ASN0-0.019-0.00834.399-0.003-0.0030.0000.0000.0000.000
191A223ASN0-0.025-0.01334.4150.0000.0000.0000.0000.0000.000
192A224THR00.0200.02529.130-0.002-0.0020.0000.0000.0000.000
193A225ARG10.7730.85226.280-0.007-0.0070.0000.0000.0000.000
194A226VAL0-0.0100.00727.1130.0050.0050.0000.0000.0000.000
195A227TRP00.015-0.00122.393-0.007-0.0070.0000.0000.0000.000
196A228VAL0-0.046-0.02825.6540.0080.0080.0000.0000.0000.000
197A229TRP0-0.030-0.00223.037-0.002-0.0020.0000.0000.0000.000
198A230SER00.017-0.03225.2620.0100.0100.0000.0000.0000.000
199A231PRO0-0.0030.03325.713-0.005-0.0050.0000.0000.0000.000
200A232THR0-0.042-0.03828.4200.0020.0020.0000.0000.0000.000
201A233ASN0-0.062-0.04828.1880.0000.0000.0000.0000.0000.000
202A234PRO00.0280.00730.1060.0030.0030.0000.0000.0000.000
203A235GLY00.0060.01828.7200.0030.0030.0000.0000.0000.000
204A236ALA00.012-0.00825.3050.0010.0010.0000.0000.0000.000
205A237SER0-0.085-0.07321.4500.0040.0040.0000.0000.0000.000
206A238ASP-1-0.791-0.88121.1050.1330.1330.0000.0000.0000.000
207A239PRO0-0.006-0.02023.4870.0010.0010.0000.0000.0000.000
208A240ALA00.0270.02524.358-0.003-0.0030.0000.0000.0000.000
209A241ALA0-0.025-0.00121.3150.0010.0010.0000.0000.0000.000
210A242MET0-0.025-0.01223.1740.0000.0000.0000.0000.0000.000
211A243ILE0-0.047-0.00426.302-0.008-0.0080.0000.0000.0000.000
212A244GLY00.0240.01028.883-0.005-0.0050.0000.0000.0000.000
213A245GLN0-0.043-0.01830.300-0.008-0.0080.0000.0000.0000.000
214A246ALA00.0440.00428.139-0.001-0.0010.0000.0000.0000.000
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