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: K2RJ3

Calculation Name: 1R0M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R0M

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RYA6

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 360
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5757823.244241
FMO2-HF: Nuclear repulsion 5620214.912448
FMO2-HF: Total energy -137608.331792
FMO2-MP2: Total energy -138011.881147


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:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-116.597-113.931-0.017-1.171-1.4780.004
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.970 / q_NPA : 0.977
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].
3A8PHE00.0370.0343.712-4.289-2.204-0.023-1.038-1.0240.004
4A9LYS10.9160.9626.56724.49124.4910.0000.0000.0000.000
5A10ILE0-0.0070.0049.4070.2880.2880.0000.0000.0000.000
6A11GLU-1-0.959-0.98412.685-20.527-20.5270.0000.0000.0000.000
7A12ALA0-0.030-0.02214.9501.0151.0150.0000.0000.0000.000
8A13ALA00.0010.00017.690-0.592-0.5920.0000.0000.0000.000
9A14GLU-1-0.780-0.85820.305-12.197-12.1970.0000.0000.0000.000
10A15ILE0-0.027-0.00823.150-0.180-0.1800.0000.0000.0000.000
11A16VAL00.0240.00425.6560.2780.2780.0000.0000.0000.000
12A17VAL0-0.023-0.01128.037-0.048-0.0480.0000.0000.0000.000
13A18ALA00.0560.03131.0720.1810.1810.0000.0000.0000.000
14A19ARG10.8640.94432.6887.4797.4790.0000.0000.0000.000
15A20LEU00.0290.01232.1500.0880.0880.0000.0000.0000.000
16A21PRO00.007-0.00935.7660.1470.1470.0000.0000.0000.000
17A22LEU0-0.0040.01637.537-0.105-0.1050.0000.0000.0000.000
18A23LYS10.8370.91439.6687.4417.4410.0000.0000.0000.000
19A34THR0-0.072-0.05241.774-0.053-0.0530.0000.0000.0000.000
20A35HIS00.0420.02839.042-0.026-0.0260.0000.0000.0000.000
21A36LYS10.9130.96232.0938.8748.8740.0000.0000.0000.000
22A37VAL0-0.009-0.00433.691-0.085-0.0850.0000.0000.0000.000
23A38VAL0-0.009-0.00528.957-0.034-0.0340.0000.0000.0000.000
24A39PRO0-0.0130.00328.420-0.107-0.1070.0000.0000.0000.000
25A40LEU00.0160.00724.516-0.233-0.2330.0000.0000.0000.000
26A41LEU0-0.024-0.00520.1250.1590.1590.0000.0000.0000.000
27A42ILE0-0.014-0.00818.837-0.252-0.2520.0000.0000.0000.000
28A43LEU0-0.024-0.01015.3340.1320.1320.0000.0000.0000.000
29A44HIS0-0.002-0.02414.983-1.040-1.0400.0000.0000.0000.000
30A45GLY00.0530.01011.4710.0570.0570.0000.0000.0000.000
31A46GLU-1-0.842-0.9206.641-35.073-35.0730.0000.0000.0000.000
32A47GLY0-0.035-0.0089.088-0.555-0.5550.0000.0000.0000.000
33A48VAL0-0.061-0.0149.8591.4041.4040.0000.0000.0000.000
34A49GLN00.041-0.00512.7620.1650.1650.0000.0000.0000.000
35A50GLY0-0.038-0.00814.855-0.253-0.2530.0000.0000.0000.000
36A51VAL0-0.022-0.01815.6380.4900.4900.0000.0000.0000.000
37A52ALA0-0.0070.00419.327-0.053-0.0530.0000.0000.0000.000
38A53GLU-1-0.750-0.85721.341-9.871-9.8710.0000.0000.0000.000
39A54GLY0-0.015-0.01425.061-0.045-0.0450.0000.0000.0000.000
40A55THR0-0.023-0.04527.1720.1410.1410.0000.0000.0000.000
41A56MET0-0.031-0.00127.6660.2360.2360.0000.0000.0000.000
42A57GLU-1-0.883-0.93932.103-7.742-7.7420.0000.0000.0000.000
43A58ALA0-0.012-0.02035.477-0.035-0.0350.0000.0000.0000.000
44A59ARG10.9150.94637.8286.9546.9540.0000.0000.0000.000
45A60PRO00.0110.01937.960-0.076-0.0760.0000.0000.0000.000
46A61MET0-0.043-0.02038.8410.1590.1590.0000.0000.0000.000
47A62TYR00.006-0.02133.004-0.056-0.0560.0000.0000.0000.000
48A63ARG10.8520.89933.2398.3508.3500.0000.0000.0000.000
49A64GLU-1-0.857-0.92433.057-8.493-8.4930.0000.0000.0000.000
50A65GLU-1-0.823-0.89629.567-9.628-9.6280.0000.0000.0000.000
51A66THR00.000-0.01534.0000.0930.0930.0000.0000.0000.000
52A67ILE00.022-0.00132.302-0.195-0.1950.0000.0000.0000.000
53A68ALA0-0.017-0.00632.653-0.196-0.1960.0000.0000.0000.000
54A69GLY00.0190.01433.737-0.104-0.1040.0000.0000.0000.000
55A70ALA00.0280.01228.807-0.221-0.2210.0000.0000.0000.000
56A71LEU00.000-0.01328.366-0.341-0.3410.0000.0000.0000.000
57A72ASP-1-0.955-0.97029.200-9.327-9.3270.0000.0000.0000.000
58A73LEU00.0180.02026.981-0.197-0.1970.0000.0000.0000.000
59A74LEU0-0.026-0.02823.380-0.409-0.4090.0000.0000.0000.000
60A75ARG10.8460.89924.8999.2919.2910.0000.0000.0000.000
61A76GLY00.0020.01126.549-0.150-0.1500.0000.0000.0000.000
62A77THR0-0.058-0.02725.2950.0900.0900.0000.0000.0000.000
63A78PHE0-0.017-0.03121.856-0.359-0.3590.0000.0000.0000.000
64A79LEU00.0200.01020.313-0.665-0.6650.0000.0000.0000.000
65A80PRO00.000-0.00520.049-0.688-0.6880.0000.0000.0000.000
66A81ALA0-0.0250.00620.175-0.334-0.3340.0000.0000.0000.000
67A82ILE0-0.018-0.01615.650-0.716-0.7160.0000.0000.0000.000
68A83LEU0-0.0050.01215.170-1.150-1.1500.0000.0000.0000.000
69A84GLY0-0.041-0.02414.6780.4500.4500.0000.0000.0000.000
70A85GLN0-0.040-0.01112.958-0.781-0.7810.0000.0000.0000.000
71A86THR0-0.031-0.0286.576-1.426-1.4260.0000.0000.0000.000
72A87PHE00.0020.0028.2671.2631.2630.0000.0000.0000.000
73A88ALA00.010-0.0115.413-3.291-3.2910.0000.0000.0000.000
74A89ASN00.0230.0106.007-1.434-1.4340.0000.0000.0000.000
75A90PRO00.0820.0338.5810.6070.6070.0000.0000.0000.000
76A91GLU-1-0.914-0.96411.889-17.356-17.3560.0000.0000.0000.000
77A92ALA00.0040.00410.6950.9320.9320.0000.0000.0000.000
78A93VAL0-0.0010.00911.8640.7000.7000.0000.0000.0000.000
79A94SER0-0.030-0.02814.2001.2441.2440.0000.0000.0000.000
80A95ASP-1-0.998-0.99015.616-14.208-14.2080.0000.0000.0000.000
81A96ALA00.0330.02716.1220.6420.6420.0000.0000.0000.000
82A97LEU0-0.060-0.02617.9860.7180.7180.0000.0000.0000.000
83A98GLY0-0.041-0.02520.8500.6190.6190.0000.0000.0000.000
84A99SER0-0.027-0.01022.6360.4990.4990.0000.0000.0000.000
85A100TYR0-0.023-0.00124.6040.4050.4050.0000.0000.0000.000
86A101ARG10.9630.97227.0358.7488.7480.0000.0000.0000.000
87A102GLY0-0.0030.00529.5770.1320.1320.0000.0000.0000.000
88A103ASN00.003-0.00928.137-0.216-0.2160.0000.0000.0000.000
89A104ARG10.9200.96425.40510.00410.0040.0000.0000.0000.000
90A105MET00.0270.03025.219-0.379-0.3790.0000.0000.0000.000
91A106ALA00.0330.01125.472-0.313-0.3130.0000.0000.0000.000
92A107ARG10.8880.94920.75311.74911.7490.0000.0000.0000.000
93A108ALA0-0.0040.01021.107-0.620-0.6200.0000.0000.0000.000
94A109MET0-0.0270.01720.738-0.285-0.2850.0000.0000.0000.000
95A110VAL00.0430.01817.590-0.492-0.4920.0000.0000.0000.000
96A111GLU-1-0.767-0.88116.511-15.378-15.3780.0000.0000.0000.000
97A112MET00.008-0.01115.838-0.647-0.6470.0000.0000.0000.000
98A113ALA00.0050.01916.480-0.472-0.4720.0000.0000.0000.000
99A114ALA00.0240.00212.688-0.946-0.9460.0000.0000.0000.000
100A115TRP0-0.051-0.03311.481-1.928-1.9280.0000.0000.0000.000
101A116ASP-1-0.779-0.87412.050-16.791-16.7910.0000.0000.0000.000
102A117LEU0-0.0040.00810.262-0.574-0.5740.0000.0000.0000.000
103A118TRP0-0.0080.0013.484-1.447-1.0880.004-0.090-0.2730.000
104A119ALA00.0290.0127.646-2.067-2.0670.0000.0000.0000.000
105A120ARG10.8250.8989.75315.71115.7110.0000.0000.0000.000
106A121THR0-0.081-0.0335.458-2.031-2.0310.0000.0000.0000.000
107A122LEU0-0.058-0.0283.575-2.871-2.6490.002-0.043-0.1810.000
108A123GLY0-0.0150.0067.0290.9120.9120.0000.0000.0000.000
109A124VAL0-0.050-0.0249.4991.3661.3660.0000.0000.0000.000
110A125PRO00.0240.01611.909-0.055-0.0550.0000.0000.0000.000
111A126LEU00.0330.00513.960-0.526-0.5260.0000.0000.0000.000
112A127GLY00.0290.00515.005-0.136-0.1360.0000.0000.0000.000
113A128THR0-0.028-0.01414.0650.1570.1570.0000.0000.0000.000
114A129LEU0-0.0110.0099.258-0.103-0.1030.0000.0000.0000.000
115A130LEU0-0.066-0.02112.966-0.005-0.0050.0000.0000.0000.000
116A131GLY00.000-0.00215.9230.5680.5680.0000.0000.0000.000
117A132GLY0-0.027-0.00317.6490.6000.6000.0000.0000.0000.000
118A133HIS0-0.056-0.03619.228-0.115-0.1150.0000.0000.0000.000
119A134LYS10.9030.96521.68410.26310.2630.0000.0000.0000.000
120A135GLU-1-0.883-0.94223.390-10.999-10.9990.0000.0000.0000.000
121A136GLN0-0.023-0.02025.3580.0850.0850.0000.0000.0000.000
122A137VAL0-0.0010.00526.036-0.017-0.0170.0000.0000.0000.000
123A138GLU-1-0.897-0.95129.068-7.925-7.9250.0000.0000.0000.000
124A139VAL0-0.046-0.01131.850-0.079-0.0790.0000.0000.0000.000
125A140GLY00.0100.00034.1850.2350.2350.0000.0000.0000.000
126A141VAL0-0.066-0.02436.904-0.097-0.0970.0000.0000.0000.000
127A142SER00.015-0.01138.3580.0500.0500.0000.0000.0000.000
128A143LEU0-0.058-0.01841.059-0.001-0.0010.0000.0000.0000.000
129A144GLY00.0280.01144.716-0.004-0.0040.0000.0000.0000.000
130A145ILE00.001-0.00546.4440.0570.0570.0000.0000.0000.000
131A146GLN0-0.037-0.01948.8420.0490.0490.0000.0000.0000.000
132A147ALA0-0.014-0.00852.5410.0320.0320.0000.0000.0000.000
133A148ASP-1-0.835-0.91856.094-5.071-5.0710.0000.0000.0000.000
134A149GLU-1-0.821-0.93455.730-5.180-5.1800.0000.0000.0000.000
135A150GLN00.0000.00155.688-0.156-0.1560.0000.0000.0000.000
136A151ALA00.0470.02854.688-0.066-0.0660.0000.0000.0000.000
137A152THR0-0.056-0.04050.608-0.148-0.1480.0000.0000.0000.000
138A153VAL00.0120.00951.204-0.124-0.1240.0000.0000.0000.000
139A154ASP-1-0.940-0.96152.156-5.680-5.6800.0000.0000.0000.000
140A155LEU0-0.015-0.00647.299-0.135-0.1350.0000.0000.0000.000
141A156VAL0-0.015-0.02247.300-0.168-0.1680.0000.0000.0000.000
142A157ARG10.9870.99747.6465.4245.4240.0000.0000.0000.000
143A158ARG10.9450.98946.5436.0076.0070.0000.0000.0000.000
144A159HIS10.8030.88443.4006.5356.5350.0000.0000.0000.000
145A160VAL00.0540.01843.707-0.152-0.1520.0000.0000.0000.000
146A161GLU-1-0.926-0.95245.027-6.170-6.1700.0000.0000.0000.000
147A162GLN0-0.056-0.02542.075-0.134-0.1340.0000.0000.0000.000
148A163GLY00.0880.05441.108-0.163-0.1630.0000.0000.0000.000
149A164TYR0-0.125-0.05837.267-0.235-0.2350.0000.0000.0000.000
150A165ARG10.9180.97435.8777.8837.8830.0000.0000.0000.000
151A166ARG10.8090.90035.3627.7357.7350.0000.0000.0000.000
152A167ILE0-0.0080.00940.176-0.075-0.0750.0000.0000.0000.000
153A168LYS10.8880.94036.9817.6037.6030.0000.0000.0000.000
154A169LEU0-0.006-0.00642.5360.0160.0160.0000.0000.0000.000
155A170LYS10.9640.99144.0976.5136.5130.0000.0000.0000.000
156A171ILE0-0.044-0.00846.0180.1390.1390.0000.0000.0000.000
157A172LYS10.9290.97048.2835.5045.5040.0000.0000.0000.000
158A173PRO00.0930.04650.8700.0920.0920.0000.0000.0000.000
159A174GLY0-0.018-0.00754.0110.0330.0330.0000.0000.0000.000
160A175TRP0-0.081-0.04052.1310.1250.1250.0000.0000.0000.000
161A176ASP-1-0.682-0.82451.803-5.607-5.6070.0000.0000.0000.000
162A177VAL00.012-0.00652.727-0.036-0.0360.0000.0000.0000.000
163A178GLN0-0.034-0.02254.876-0.072-0.0720.0000.0000.0000.000
164A179PRO00.0110.01451.6170.0170.0170.0000.0000.0000.000
165A180VAL00.0160.01349.482-0.056-0.0560.0000.0000.0000.000
166A181ARG10.9400.99151.9905.0495.0490.0000.0000.0000.000
167A182ALA00.0130.01055.2810.0110.0110.0000.0000.0000.000
168A183THR0-0.064-0.04849.107-0.023-0.0230.0000.0000.0000.000
169A184ARG10.7850.88247.0775.9925.9920.0000.0000.0000.000
170A185GLU-1-0.951-0.97252.549-5.047-5.0470.0000.0000.0000.000
171A186ALA0-0.065-0.02353.8330.0370.0370.0000.0000.0000.000
172A187PHE0-0.081-0.04949.616-0.030-0.0300.0000.0000.0000.000
173A188PRO00.0540.01850.596-0.107-0.1070.0000.0000.0000.000
174A189ASP-1-0.869-0.92648.322-5.872-5.8720.0000.0000.0000.000
175A190ILE0-0.087-0.02445.406-0.160-0.1600.0000.0000.0000.000
176A191ARG10.9550.98338.1027.4347.4340.0000.0000.0000.000
177A192LEU00.0160.00943.178-0.074-0.0740.0000.0000.0000.000
178A193THR0-0.021-0.01340.175-0.060-0.0600.0000.0000.0000.000
179A194VAL00.0210.00543.4570.0820.0820.0000.0000.0000.000
180A195ASP-1-0.865-0.93440.919-7.160-7.1600.0000.0000.0000.000
181A196ALA0-0.027-0.01843.1380.1430.1430.0000.0000.0000.000
182A197ASN0-0.020-0.01742.849-0.005-0.0050.0000.0000.0000.000
183A198SER0-0.018-0.00142.7400.0050.0050.0000.0000.0000.000
184A199ALA0-0.074-0.02744.8700.0970.0970.0000.0000.0000.000
185A200TYR0-0.061-0.05148.1820.1220.1220.0000.0000.0000.000
186A201THR0-0.009-0.01349.396-0.037-0.0370.0000.0000.0000.000
187A202LEU00.0410.00449.6430.0530.0530.0000.0000.0000.000
188A203ALA0-0.046-0.01952.5360.0580.0580.0000.0000.0000.000
189A204ASP-1-0.839-0.91352.676-5.431-5.4310.0000.0000.0000.000
190A205ALA0-0.002-0.00252.794-0.023-0.0230.0000.0000.0000.000
191A206GLY00.0010.00053.823-0.008-0.0080.0000.0000.0000.000
192A207ARG10.8540.92155.0225.2685.2680.0000.0000.0000.000
193A208LEU00.0440.01149.101-0.015-0.0150.0000.0000.0000.000
194A209ARG10.9100.96252.0865.3765.3760.0000.0000.0000.000
195A210GLN0-0.051-0.03253.845-0.003-0.0030.0000.0000.0000.000
196A211LEU00.009-0.00149.4550.0250.0250.0000.0000.0000.000
197A212ASP-1-0.780-0.87350.942-5.828-5.8280.0000.0000.0000.000
198A213GLU-1-0.996-0.98951.872-5.203-5.2030.0000.0000.0000.000
199A214TYR00.0330.01351.6230.0250.0250.0000.0000.0000.000
200A215ASP-1-0.903-0.93348.618-5.903-5.9030.0000.0000.0000.000
201A216LEU0-0.042-0.02145.605-0.124-0.1240.0000.0000.0000.000
202A217THR0-0.060-0.04639.946-0.069-0.0690.0000.0000.0000.000
203A218TYR00.014-0.01337.749-0.125-0.1250.0000.0000.0000.000
204A219ILE00.0030.00242.5060.0570.0570.0000.0000.0000.000
205A220GLU-1-0.857-0.92637.363-7.682-7.6820.0000.0000.0000.000
206A221GLN00.0160.00438.653-0.017-0.0170.0000.0000.0000.000
207A222PRO00.0350.00941.5090.0770.0770.0000.0000.0000.000
208A223LEU0-0.0110.00344.5120.1520.1520.0000.0000.0000.000
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