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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: 2JRYR

Calculation Name: 3ML4-A-Xray372

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 3ML4

Chain ID: A

ChEMBL ID:

UniProt ID: Q18PE0

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2340608.027821
FMO2-HF: Nuclear repulsion 2258223.12597
FMO2-HF: Total energy -82384.901852
FMO2-MP2: Total energy -82619.873429


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:3:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
-182.93-189.41332.68-13.782-12.4150.139
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.826 / q_NPA : -0.884
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].
3A5ALA0-0.003-0.0053.8717.0088.588-0.012-0.849-0.7180.003
4A6LEU0-0.048-0.0096.571-3.213-3.2130.0000.0000.0000.000
5A7VAL00.0200.0029.560-3.160-3.1600.0000.0000.0000.000
6A8GLU-1-0.765-0.8636.78135.57235.5720.0000.0000.0000.000
7A9GLY0-0.002-0.0029.786-1.934-1.9340.0000.0000.0000.000
8A10GLN00.0110.03112.6970.6410.6410.0000.0000.0000.000
9A11VAL00.0340.02414.308-0.805-0.8050.0000.0000.0000.000
10A12LYS10.7880.87916.519-13.777-13.7770.0000.0000.0000.000
11A13LEU00.0470.02513.7620.0500.0500.0000.0000.0000.000
12A14ARG10.8940.92618.452-12.862-12.8620.0000.0000.0000.000
13A15ASP-1-0.860-0.92216.31418.03018.0300.0000.0000.0000.000
14A16GLY0-0.045-0.03918.3780.4000.4000.0000.0000.0000.000
15A17LYS10.8590.92620.700-15.239-15.2390.0000.0000.0000.000
16A18LYS11.0611.03424.235-11.172-11.1720.0000.0000.0000.000
17A19TRP0-0.031-0.01721.0880.7240.7240.0000.0000.0000.000
18A20LYS10.8640.94019.220-13.280-13.2800.0000.0000.0000.000
19A21SER00.006-0.01318.3960.3560.3560.0000.0000.0000.000
20A22ARG10.8640.92413.789-18.271-18.2710.0000.0000.0000.000
21A23TRP00.0170.0128.745-1.623-1.6230.0000.0000.0000.000
22A24LEU0-0.0140.0109.8582.1372.1370.0000.0000.0000.000
23A25VAL00.012-0.0073.969-1.290-1.1810.000-0.016-0.0940.000
24A26LEU00.0250.0257.4280.8430.8430.0000.0000.0000.000
25A27ARG10.8500.8921.718-127.925-139.19229.565-10.632-7.6660.123
26A28LYS10.8970.9717.130-22.541-22.5410.0000.0000.0000.000
27A29PRO0-0.046-0.0157.1426.1286.1280.0000.0000.0000.000
28A30SER00.0230.0008.1990.3110.3110.0000.0000.0000.000
29A31PRO0-0.011-0.00911.097-0.194-0.1940.0000.0000.0000.000
30A32VAL0-0.010-0.00812.920-1.246-1.2460.0000.0000.0000.000
31A33ALA00.0330.02313.765-0.766-0.7660.0000.0000.0000.000
32A34ASP-1-0.817-0.87914.54419.02219.0220.0000.0000.0000.000
33A35CYS0-0.028-0.00712.250-0.607-0.6070.0000.0000.0000.000
34A36LEU0-0.037-0.02810.1021.7701.7700.0000.0000.0000.000
35A37LEU0-0.0100.0063.970-1.448-1.1910.003-0.065-0.1950.000
36A38MET0-0.003-0.0017.1631.9321.9320.0000.0000.0000.000
37A39LEU00.012-0.0012.598-3.725-2.3911.208-0.938-1.6040.012
38A40VAL0-0.001-0.0057.211-2.458-2.4580.0000.0000.0000.000
39A41TYR00.0390.0122.979-0.0740.6600.127-0.214-0.647-0.001
40A42LYS10.8220.8869.672-23.189-23.1890.0000.0000.0000.000
41A43ASP-1-0.772-0.88512.13116.77116.7710.0000.0000.0000.000
42A44LYS10.8550.9359.227-22.900-22.9000.0000.0000.0000.000
43A45CYS0-0.023-0.01710.8660.9740.9740.0000.0000.0000.000
44A46GLU-1-0.766-0.8749.94321.24321.2430.0000.0000.0000.000
45A47ARG10.7620.8702.040-47.268-46.4981.789-1.068-1.4910.002
46A48SER0-0.011-0.0206.3432.1422.1420.0000.0000.0000.000
47A49LYS10.8390.9318.443-20.309-20.3090.0000.0000.0000.000
48A50GLY00.0150.0205.461-0.508-0.5080.0000.0000.0000.000
49A51LEU0-0.083-0.0296.4700.8840.8840.0000.0000.0000.000
50A52ARG10.8900.9266.237-30.282-30.2820.0000.0000.0000.000
51A53GLU-1-0.797-0.8586.11234.53534.5350.0000.0000.0000.000
52A54ARG10.8680.9267.849-19.007-19.0070.0000.0000.0000.000
53A55SER00.002-0.01110.781-2.118-2.1180.0000.0000.0000.000
54A56SER0-0.036-0.0458.0600.9690.9690.0000.0000.0000.000
55A57LEU00.0070.0129.729-2.476-2.4760.0000.0000.0000.000
56A58THR0-0.020-0.0239.6683.7583.7580.0000.0000.0000.000
57A59LEU0-0.0160.00411.757-1.930-1.9300.0000.0000.0000.000
58A60GLU-1-0.855-0.95013.89222.90322.9030.0000.0000.0000.000
59A61ASP-1-0.753-0.85215.98615.30915.3090.0000.0000.0000.000
60A62ILE0-0.009-0.01314.479-0.752-0.7520.0000.0000.0000.000
61A63CYS0-0.059-0.01819.135-0.503-0.5030.0000.0000.0000.000
62A64GLY00.0570.02621.597-0.615-0.6150.0000.0000.0000.000
63A65LEU0-0.045-0.01717.4610.9170.9170.0000.0000.0000.000
64A66GLU-1-0.748-0.85621.78711.00111.0010.0000.0000.0000.000
65A67PRO0-0.039-0.01623.1220.2380.2380.0000.0000.0000.000
66A68ALA00.013-0.04024.483-0.439-0.4390.0000.0000.0000.000
67A69LEU00.0440.03825.351-0.519-0.5190.0000.0000.0000.000
68A70PRO00.0010.01227.4410.3090.3090.0000.0000.0000.000
69A71TYR00.0440.00124.5020.1200.1200.0000.0000.0000.000
70A72GLU-1-0.843-0.90627.27910.98010.9800.0000.0000.0000.000
71A73GLY00.0030.01128.6090.1700.1700.0000.0000.0000.000
72A74LEU0-0.038-0.01023.518-0.070-0.0700.0000.0000.0000.000
73A75ALA00.0510.01727.634-0.003-0.0030.0000.0000.0000.000
74A76HIS0-0.010-0.00324.711-0.288-0.2880.0000.0000.0000.000
75A77THR0-0.065-0.05422.8310.6480.6480.0000.0000.0000.000
76A78LEU00.014-0.00118.397-0.340-0.3400.0000.0000.0000.000
77A79ALA00.0150.01720.3630.6180.6180.0000.0000.0000.000
78A80ILE0-0.006-0.00414.8570.0280.0280.0000.0000.0000.000
79A81ILE00.003-0.00219.108-0.251-0.2510.0000.0000.0000.000
80A82CYS0-0.038-0.02918.4540.5970.5970.0000.0000.0000.000
81A83LEU00.0120.00121.457-0.685-0.6850.0000.0000.0000.000
82A84SER0-0.081-0.05521.654-0.484-0.4840.0000.0000.0000.000
83A85GLN0-0.044-0.02618.9870.1540.1540.0000.0000.0000.000
84A86ALA00.0720.03921.1240.1720.1720.0000.0000.0000.000
85A87VAL0-0.040-0.02015.932-0.080-0.0800.0000.0000.0000.000
86A88MET0-0.0300.00619.2610.1950.1950.0000.0000.0000.000
87A89LEU0-0.025-0.00815.0750.2740.2740.0000.0000.0000.000
88A90GLY00.0550.01318.945-0.769-0.7690.0000.0000.0000.000
89A91PHE0-0.025-0.02116.7490.6030.6030.0000.0000.0000.000
90A92ASP-1-0.786-0.87921.42012.85012.8500.0000.0000.0000.000
91A93SER0-0.018-0.01923.293-0.403-0.4030.0000.0000.0000.000
92A94HIS00.0800.03823.6320.6570.6570.0000.0000.0000.000
93A95GLU-1-0.827-0.92324.14511.94011.9400.0000.0000.0000.000
94A96ALA0-0.042-0.00719.4030.5590.5590.0000.0000.0000.000
95A97MET0-0.0280.05019.3040.7600.7600.0000.0000.0000.000
96A98CYS00.0150.00320.7250.3740.3740.0000.0000.0000.000
97A99ALA0-0.0070.01018.7880.2170.2170.0000.0000.0000.000
98A100TRP00.001-0.01911.7821.3301.3300.0000.0000.0000.000
99A101ASP-1-0.750-0.86517.27014.82314.8230.0000.0000.0000.000
100A102THR0-0.017-0.01419.2420.2620.2620.0000.0000.0000.000
101A103ARG10.8920.94412.461-22.205-22.2050.0000.0000.0000.000
102A104ILE00.013-0.00313.8501.0381.0380.0000.0000.0000.000
103A105ARG10.7650.85015.938-13.609-13.6090.0000.0000.0000.000
104A106TYR00.004-0.00117.7490.1460.1460.0000.0000.0000.000
105A107ALA0-0.048-0.02713.3140.2110.2110.0000.0000.0000.000
106A108LEU0-0.013-0.01014.4271.0121.0120.0000.0000.0000.000
107A109GLY00.0630.03816.560-0.012-0.0120.0000.0000.0000.000
108A110GLU-1-0.802-0.83819.59812.79312.7930.0000.0000.0000.000
109A111VAL00.0120.01619.706-0.261-0.2610.0000.0000.0000.000
110A112HIS0-0.057-0.03022.746-0.022-0.0220.0000.0000.0000.000
111A113ARG10.8310.90925.020-11.964-11.9640.0000.0000.0000.000
112A114PHE00.0460.03227.964-0.104-0.1040.0000.0000.0000.000
113A115HIS0-0.0010.01329.4460.1700.1700.0000.0000.0000.000
114A116VAL0-0.009-0.00633.881-0.286-0.2860.0000.0000.0000.000
115A117THR0-0.012-0.01036.840-0.035-0.0350.0000.0000.0000.000
116A118VAL0-0.0120.00537.296-0.117-0.1170.0000.0000.0000.000
117A119ALA00.0350.01740.131-0.142-0.1420.0000.0000.0000.000
118A120PRO00.017-0.00143.3300.1040.1040.0000.0000.0000.000
119A121GLY00.0030.00145.647-0.074-0.0740.0000.0000.0000.000
120A122THR0-0.024-0.01242.0520.0530.0530.0000.0000.0000.000
121A123LYS10.8190.89040.750-7.815-7.8150.0000.0000.0000.000
122A124LEU0-0.0120.00936.3060.1880.1880.0000.0000.0000.000
123A125GLU-1-0.824-0.89138.3788.0458.0450.0000.0000.0000.000
124A126SER0-0.047-0.02039.2730.0660.0660.0000.0000.0000.000
125A127GLY00.0310.00640.617-0.039-0.0390.0000.0000.0000.000
126A128PRO0-0.025-0.01737.9510.1260.1260.0000.0000.0000.000
127A129ALA0-0.009-0.00134.2830.0920.0920.0000.0000.0000.000
128A130THR0-0.077-0.04429.040-0.030-0.0300.0000.0000.0000.000
129A131LEU00.0100.00131.0160.0410.0410.0000.0000.0000.000
130A132HIS00.006-0.01025.4960.5870.5870.0000.0000.0000.000
131A133LEU0-0.0140.00226.022-0.288-0.2880.0000.0000.0000.000
132A134CYS0-0.014-0.01721.1210.6990.6990.0000.0000.0000.000
133A135ASN00.004-0.02019.637-0.473-0.4730.0000.0000.0000.000
134A136ASP-1-0.876-0.92123.86712.66512.6650.0000.0000.0000.000
135A137ILE0-0.085-0.04323.350-0.714-0.7140.0000.0000.0000.000
136A138LEU00.0020.00426.9530.1280.1280.0000.0000.0000.000
137A139VAL00.024-0.00626.472-0.143-0.1430.0000.0000.0000.000
138A140LEU0-0.0170.01429.252-0.052-0.0520.0000.0000.0000.000
139A141ALA00.007-0.00728.2060.0900.0900.0000.0000.0000.000
140A142ARG10.7840.84530.231-8.995-8.9950.0000.0000.0000.000
141A143ASP-1-0.814-0.88230.6719.5059.5050.0000.0000.0000.000
142A144ILE0-0.004-0.00328.0150.4150.4150.0000.0000.0000.000
143A145PRO0-0.043-0.05225.183-0.228-0.2280.0000.0000.0000.000
144A146PRO0-0.0050.01125.163-0.176-0.1760.0000.0000.0000.000
145A147THR0-0.041-0.00526.3810.3090.3090.0000.0000.0000.000
146A148VAL00.0070.00226.545-0.209-0.2090.0000.0000.0000.000
147A149MET0-0.013-0.00729.321-0.201-0.2010.0000.0000.0000.000
148A150GLY00.0220.00531.942-0.402-0.4020.0000.0000.0000.000
149A151GLN0-0.039-0.01128.1400.4700.4700.0000.0000.0000.000
150A152TRP0-0.044-0.03030.431-0.275-0.2750.0000.0000.0000.000
151A153LYS10.9821.00128.897-10.535-10.5350.0000.0000.0000.000
152A154LEU00.0520.01428.815-0.497-0.4970.0000.0000.0000.000
153A155SER0-0.006-0.00831.332-0.168-0.1680.0000.0000.0000.000
154A156ASP-1-0.875-0.92233.1299.4859.4850.0000.0000.0000.000
155A157LEU0-0.0100.00534.217-0.286-0.2860.0000.0000.0000.000
156A158ARG10.8210.91037.157-7.432-7.4320.0000.0000.0000.000
157A159ARG10.9340.96240.312-7.314-7.3140.0000.0000.0000.000
158A160TYR0-0.045-0.05237.5090.1970.1970.0000.0000.0000.000
159A161GLY00.0200.02239.779-0.156-0.1560.0000.0000.0000.000
160A162ALA00.0120.02040.7020.0420.0420.0000.0000.0000.000
161A163VAL0-0.030-0.01141.859-0.197-0.1970.0000.0000.0000.000
162A164PRO00.025-0.00244.3910.1170.1170.0000.0000.0000.000
163A165ASN0-0.039-0.01143.986-0.093-0.0930.0000.0000.0000.000
164A166GLY00.0530.02441.5720.0450.0450.0000.0000.0000.000
165A167PHE0-0.017-0.00336.0420.0180.0180.0000.0000.0000.000
166A168ILE0-0.0120.00140.411-0.071-0.0710.0000.0000.0000.000
167A169PHE00.0260.00735.6310.1150.1150.0000.0000.0000.000
168A170GLU-1-0.863-0.92439.7077.2407.2400.0000.0000.0000.000
169A171GLY00.0710.04037.8730.1590.1590.0000.0000.0000.000
170A172GLY00.026-0.00338.645-0.268-0.2680.0000.0000.0000.000
171A173THR00.008-0.02439.2890.1650.1650.0000.0000.0000.000
172A174ARG10.8560.91535.710-8.979-8.9790.0000.0000.0000.000
173A175CYS0-0.0300.01835.5280.2600.2600.0000.0000.0000.000
174A176GLY00.0240.01736.6010.0870.0870.0000.0000.0000.000
175A177TYR00.0020.00237.484-0.285-0.2850.0000.0000.0000.000
176A178TRP00.0610.03333.380-0.275-0.2750.0000.0000.0000.000
177A179ALA0-0.0250.00437.6890.0410.0410.0000.0000.0000.000
178A180GLY00.013-0.00140.253-0.167-0.1670.0000.0000.0000.000
179A181VAL0-0.013-0.00841.3410.1700.1700.0000.0000.0000.000
180A182PHE0-0.020-0.00439.116-0.064-0.0640.0000.0000.0000.000
181A183PHE00.0250.00041.2650.0030.0030.0000.0000.0000.000
182A184LEU00.0000.00635.9950.0520.0520.0000.0000.0000.000
183A185SER00.0070.00640.188-0.140-0.1400.0000.0000.0000.000
184A186SER00.003-0.03337.0510.1590.1590.0000.0000.0000.000
185A187ALA00.0290.01739.841-0.119-0.1190.0000.0000.0000.000
186A188GLU-1-0.845-0.93033.5849.6489.6480.0000.0000.0000.000
187A189GLY00.0060.01236.9950.1740.1740.0000.0000.0000.000
188A190GLU-1-0.911-0.97938.6467.7117.7110.0000.0000.0000.000
189A191GLN0-0.035-0.00733.3850.0300.0300.0000.0000.0000.000
190A192MET0-0.020-0.00133.6560.2790.2790.0000.0000.0000.000
191A193SER0-0.015-0.01234.5190.1150.1150.0000.0000.0000.000
192A194PHE00.0240.01533.7330.1190.1190.0000.0000.0000.000
193A195LEU00.0370.02828.1230.1520.1520.0000.0000.0000.000
194A196PHE00.022-0.00531.7170.2300.2300.0000.0000.0000.000
195A197ASP-1-0.786-0.86433.4308.5848.5840.0000.0000.0000.000
196A198CYS0-0.061-0.00731.755-0.136-0.1360.0000.0000.0000.000
197A199ILE00.0400.01727.4570.1250.1250.0000.0000.0000.000
198A200VAL0-0.051-0.03030.2650.1510.1510.0000.0000.0000.000
199A201ARG10.7600.86032.836-8.931-8.9310.0000.0000.0000.000
200A202GLY0-0.0020.01729.561-0.088-0.0880.0000.0000.0000.000
201A203ILE0-0.037-0.01629.6720.1930.1930.0000.0000.0000.000
202A204SER00.003-0.02525.717-0.147-0.1470.0000.0000.0000.000
203A205PRO0-0.017-0.02928.077-0.142-0.1420.0000.0000.0000.000
204A206THR0-0.049-0.03025.547-0.159-0.1590.0000.0000.0000.000
205A207LYS10.7900.88421.099-14.514-14.5140.0000.0000.0000.000
206A208GLY00.0470.04326.1670.0370.0370.0000.0000.0000.000
207A209PRO0-0.017-0.02228.1860.2280.2280.0000.0000.0000.000
208A210PHE0-0.0080.00924.8340.6100.6100.0000.0000.0000.000