FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: MV85Z

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333926.550225
FMO2-HF: Nuclear repulsion 2251543.154447
FMO2-HF: Total energy -82383.395778
FMO2-MP2: Total energy -82618.280906


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.
-141.398-130.3751.346-5.882-6.4880.056
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 : -0.907 / q_NPA : -0.959
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].
3A5ALA0-0.004-0.0083.6302.9285.243-0.016-1.181-1.1170.005
4A6LEU0-0.067-0.0196.233-2.339-2.3390.0000.0000.0000.000
5A7VAL00.015-0.0119.428-2.552-2.5520.0000.0000.0000.000
6A8GLU-1-0.777-0.8747.61232.77532.7750.0000.0000.0000.000
7A9GLY00.001-0.00110.149-1.700-1.7000.0000.0000.0000.000
8A10GLN0-0.0060.00413.0080.7220.7220.0000.0000.0000.000
9A11VAL00.0560.04614.448-0.790-0.7900.0000.0000.0000.000
10A12LYS10.8960.96116.481-12.618-12.6180.0000.0000.0000.000
11A13LEU00.0600.04013.833-0.069-0.0690.0000.0000.0000.000
12A14ARG11.0261.03518.537-12.663-12.6630.0000.0000.0000.000
13A15ASP-1-0.889-0.94416.49017.57717.5770.0000.0000.0000.000
14A16GLY0-0.055-0.04218.1320.5870.5870.0000.0000.0000.000
15A17LYS10.9020.90120.866-15.273-15.2730.0000.0000.0000.000
16A18LYS10.9761.01824.346-11.100-11.1000.0000.0000.0000.000
17A19TRP0-0.016-0.02921.0950.7190.7190.0000.0000.0000.000
18A20LYS10.8470.93719.020-13.521-13.5210.0000.0000.0000.000
19A21SER0-0.001-0.02118.1360.4200.4200.0000.0000.0000.000
20A22ARG10.9170.96013.584-18.041-18.0410.0000.0000.0000.000
21A23TRP0-0.0100.0018.681-1.826-1.8260.0000.0000.0000.000
22A24LEU00.0020.01310.0021.9561.9560.0000.0000.0000.000
23A25VAL00.0130.0014.031-0.893-0.818-0.001-0.015-0.0600.000
24A26LEU00.0200.0157.3070.9850.9850.0000.0000.0000.000
25A27ARG10.9440.9722.474-87.893-81.9721.062-3.623-3.3600.046
26A28LYS10.9240.9897.548-21.835-21.8350.0000.0000.0000.000
27A29PRO0-0.020-0.0117.3964.2214.2210.0000.0000.0000.000
28A30SER00.0280.0108.4700.3910.3910.0000.0000.0000.000
29A31PRO00.003-0.00911.539-0.238-0.2380.0000.0000.0000.000
30A32VAL0-0.019-0.00613.077-0.975-0.9750.0000.0000.0000.000
31A33ALA00.0210.00614.073-0.493-0.4930.0000.0000.0000.000
32A34ASP-1-0.802-0.87715.20617.22817.2280.0000.0000.0000.000
33A35CYS0-0.048-0.01412.624-0.073-0.0730.0000.0000.0000.000
34A36LEU0-0.030-0.00711.2201.3611.3610.0000.0000.0000.000
35A37LEU0-0.008-0.0064.423-0.458-0.314-0.001-0.013-0.1310.000
36A38MET0-0.039-0.0178.3180.9960.9960.0000.0000.0000.000
37A39LEU00.006-0.0063.234-1.856-0.4650.119-0.693-0.8170.005
38A40VAL00.0020.0017.389-2.517-2.5170.0000.0000.0000.000
39A41TYR00.0510.0173.9440.0590.3590.001-0.058-0.2430.000
40A42LYS10.8040.87110.081-24.136-24.1360.0000.0000.0000.000
41A43ASP-1-0.807-0.90812.44316.98516.9850.0000.0000.0000.000
42A44LYS10.9900.99511.334-18.953-18.9530.0000.0000.0000.000
43A45CYS0-0.001-0.00110.8751.2121.2120.0000.0000.0000.000
44A46GLU-1-0.825-0.88510.87522.99022.9900.0000.0000.0000.000
45A47ARG10.8160.9062.603-40.265-39.3880.182-0.299-0.7600.000
46A48SER0-0.024-0.0316.4331.8621.8620.0000.0000.0000.000
47A49LYS10.8360.9388.684-22.647-22.6470.0000.0000.0000.000
48A50GLY00.0530.0136.067-0.226-0.2260.0000.0000.0000.000
49A51LEU0-0.100-0.0277.0811.9871.9870.0000.0000.0000.000
50A52ARG10.9190.9506.163-34.165-34.1650.0000.0000.0000.000
51A53GLU-1-0.846-0.9075.80542.01342.0130.0000.0000.0000.000
52A54ARG10.8630.9288.180-20.793-20.7930.0000.0000.0000.000
53A55SER00.006-0.01411.017-2.206-2.2060.0000.0000.0000.000
54A56SER0-0.029-0.0118.2380.5470.5470.0000.0000.0000.000
55A57LEU00.0390.02310.115-2.339-2.3390.0000.0000.0000.000
56A58THR00.0200.0109.7282.7942.7940.0000.0000.0000.000
57A59LEU0-0.028-0.01012.121-1.543-1.5430.0000.0000.0000.000
58A60GLU-1-0.912-0.99015.00519.83219.8320.0000.0000.0000.000
59A61ASP-1-0.766-0.87116.72714.66714.6670.0000.0000.0000.000
60A62ILE0-0.029-0.01915.379-0.613-0.6130.0000.0000.0000.000
61A63CYS0-0.001-0.01319.915-0.250-0.2500.0000.0000.0000.000
62A64GLY00.0400.02022.206-0.613-0.6130.0000.0000.0000.000
63A65LEU0-0.039-0.01618.5160.6910.6910.0000.0000.0000.000
64A66GLU-1-0.803-0.92122.72410.43310.4330.0000.0000.0000.000
65A67PRO0-0.008-0.00323.6020.2920.2920.0000.0000.0000.000
66A68ALA0-0.011-0.03724.960-0.404-0.4040.0000.0000.0000.000
67A69LEU00.0420.03326.239-0.479-0.4790.0000.0000.0000.000
68A70PRO00.0100.03127.5580.3150.3150.0000.0000.0000.000
69A71TYR00.0620.01325.0660.2380.2380.0000.0000.0000.000
70A72GLU-1-0.946-0.97327.34310.56310.5630.0000.0000.0000.000
71A73GLY0-0.0130.00528.3830.2640.2640.0000.0000.0000.000
72A74LEU0-0.044-0.02123.602-0.051-0.0510.0000.0000.0000.000
73A75ALA00.0460.02327.815-0.035-0.0350.0000.0000.0000.000
74A76HIS0-0.004-0.00824.915-0.308-0.3080.0000.0000.0000.000
75A77THR0-0.065-0.05822.8710.6220.6220.0000.0000.0000.000
76A78LEU00.002-0.00318.396-0.278-0.2780.0000.0000.0000.000
77A79ALA00.0110.00721.0360.4570.4570.0000.0000.0000.000
78A80ILE0-0.028-0.01615.9070.0280.0280.0000.0000.0000.000
79A81ILE0-0.001-0.00920.165-0.025-0.0250.0000.0000.0000.000
80A82CYS0-0.0260.00819.0610.5840.5840.0000.0000.0000.000
81A83LEU0-0.021-0.01622.161-0.632-0.6320.0000.0000.0000.000
82A84SER0-0.074-0.03921.732-0.409-0.4090.0000.0000.0000.000
83A85GLN0-0.006-0.01719.072-0.534-0.5340.0000.0000.0000.000
84A86ALA00.0710.04422.3430.3260.3260.0000.0000.0000.000
85A87VAL0-0.029-0.01516.685-0.047-0.0470.0000.0000.0000.000
86A88MET0-0.0230.00020.081-0.020-0.0200.0000.0000.0000.000
87A89LEU0-0.058-0.03315.3870.4240.4240.0000.0000.0000.000
88A90GLY00.0270.00119.212-0.690-0.6900.0000.0000.0000.000
89A91PHE0-0.006-0.00916.9490.6750.6750.0000.0000.0000.000
90A92ASP-1-0.876-0.93721.38112.46112.4610.0000.0000.0000.000
91A93SER0-0.011-0.01723.374-0.403-0.4030.0000.0000.0000.000
92A94HIS00.0740.02623.9170.6250.6250.0000.0000.0000.000
93A95GLU-1-0.869-0.94224.37511.54811.5480.0000.0000.0000.000
94A96ALA0-0.034-0.00919.6520.4680.4680.0000.0000.0000.000
95A97MET0-0.0020.04319.3790.7070.7070.0000.0000.0000.000
96A98CYS00.0490.02420.7750.3230.3230.0000.0000.0000.000
97A99ALA0-0.0180.01918.7820.2900.2900.0000.0000.0000.000
98A100TRP0-0.002-0.01811.8911.0461.0460.0000.0000.0000.000
99A101ASP-1-0.761-0.87517.44113.99713.9970.0000.0000.0000.000
100A102THR0-0.025-0.04119.913-0.040-0.0400.0000.0000.0000.000
101A103ARG10.8760.93712.237-20.387-20.3870.0000.0000.0000.000
102A104ILE00.006-0.00414.3140.8570.8570.0000.0000.0000.000
103A105ARG10.8060.90116.233-12.781-12.7810.0000.0000.0000.000
104A106TYR00.0150.01617.112-0.218-0.2180.0000.0000.0000.000
105A107ALA0-0.056-0.03213.6070.1010.1010.0000.0000.0000.000
106A108LEU0-0.035-0.03014.8280.8030.8030.0000.0000.0000.000
107A109GLY0-0.0060.02817.141-0.418-0.4180.0000.0000.0000.000
108A110GLU-1-0.804-0.85820.08511.94211.9420.0000.0000.0000.000
109A111VAL00.0170.01620.413-0.110-0.1100.0000.0000.0000.000
110A112HIS0-0.097-0.07223.449-0.162-0.1620.0000.0000.0000.000
111A113ARG10.8890.94425.055-11.446-11.4460.0000.0000.0000.000
112A114PHE00.0350.01628.634-0.129-0.1290.0000.0000.0000.000
113A115HIS00.0220.01230.8600.1380.1380.0000.0000.0000.000
114A116VAL0-0.022-0.00534.426-0.250-0.2500.0000.0000.0000.000
115A117THR0-0.022-0.01937.482-0.014-0.0140.0000.0000.0000.000
116A118VAL00.0190.01338.166-0.118-0.1180.0000.0000.0000.000
117A119ALA00.0130.01141.047-0.132-0.1320.0000.0000.0000.000
118A120PRO00.019-0.00744.3650.0860.0860.0000.0000.0000.000
119A121GLY00.0110.01146.414-0.066-0.0660.0000.0000.0000.000
120A122THR0-0.051-0.01942.9210.0190.0190.0000.0000.0000.000
121A123LYS10.9300.95741.403-7.443-7.4430.0000.0000.0000.000
122A124LEU0-0.0290.00537.0940.1110.1110.0000.0000.0000.000
123A125GLU-1-0.900-0.93739.1647.8947.8940.0000.0000.0000.000
124A126SER0-0.051-0.02940.6490.1170.1170.0000.0000.0000.000
125A127GLY00.0250.01041.7630.0750.0750.0000.0000.0000.000
126A128PRO0-0.025-0.02638.3280.1010.1010.0000.0000.0000.000
127A129ALA00.0100.01134.9240.0800.0800.0000.0000.0000.000
128A130THR0-0.058-0.01229.749-0.124-0.1240.0000.0000.0000.000
129A131LEU00.0310.01331.5740.1220.1220.0000.0000.0000.000
130A132HIS0-0.008-0.01026.5460.3100.3100.0000.0000.0000.000
131A133LEU00.0010.00526.632-0.149-0.1490.0000.0000.0000.000
132A134CYS0-0.043-0.02321.9990.5350.5350.0000.0000.0000.000
133A135ASN00.018-0.00520.195-0.283-0.2830.0000.0000.0000.000
134A136ASP-1-0.885-0.92324.23012.21212.2120.0000.0000.0000.000
135A137ILE0-0.079-0.04523.895-0.683-0.6830.0000.0000.0000.000
136A138LEU00.0010.00627.7540.1050.1050.0000.0000.0000.000
137A139VAL00.020-0.00727.577-0.116-0.1160.0000.0000.0000.000
138A140LEU0-0.0120.01730.266-0.091-0.0910.0000.0000.0000.000
139A141ALA0-0.0130.00429.0820.0570.0570.0000.0000.0000.000
140A142ARG10.9470.96231.131-8.681-8.6810.0000.0000.0000.000
141A143ASP-1-0.875-0.92731.6269.4699.4690.0000.0000.0000.000
142A144ILE0-0.040-0.00328.2480.3850.3850.0000.0000.0000.000
143A145PRO0-0.057-0.05726.206-0.192-0.1920.0000.0000.0000.000
144A146PRO00.0290.00725.995-0.201-0.2010.0000.0000.0000.000
145A147THR0-0.0220.00327.5910.3020.3020.0000.0000.0000.000
146A148VAL00.0090.00327.244-0.236-0.2360.0000.0000.0000.000
147A149MET0-0.010-0.01030.092-0.179-0.1790.0000.0000.0000.000
148A150GLY00.010-0.01032.521-0.357-0.3570.0000.0000.0000.000
149A151GLN0-0.033-0.01429.0210.4590.4590.0000.0000.0000.000
150A152TRP0-0.035-0.02331.344-0.234-0.2340.0000.0000.0000.000
151A153LYS10.9911.00227.988-10.668-10.6680.0000.0000.0000.000
152A154LEU00.0630.02329.196-0.446-0.4460.0000.0000.0000.000
153A155SER0-0.005-0.00231.894-0.190-0.1900.0000.0000.0000.000
154A156ASP-1-0.971-0.98433.7209.0979.0970.0000.0000.0000.000
155A157LEU0-0.024-0.01734.781-0.270-0.2700.0000.0000.0000.000
156A158ARG10.8190.92137.709-7.271-7.2710.0000.0000.0000.000
157A159ARG10.9370.95741.296-7.044-7.0440.0000.0000.0000.000
158A160TYR0-0.039-0.05837.8140.1490.1490.0000.0000.0000.000
159A161GLY00.0110.01340.744-0.119-0.1190.0000.0000.0000.000
160A162ALA00.0220.02441.1540.0460.0460.0000.0000.0000.000
161A163VAL0-0.029-0.00742.544-0.184-0.1840.0000.0000.0000.000
162A164PRO00.020-0.00745.0350.1120.1120.0000.0000.0000.000
163A165ASN0-0.034-0.00844.613-0.102-0.1020.0000.0000.0000.000
164A166GLY00.0600.02642.4550.0440.0440.0000.0000.0000.000
165A167PHE0-0.028-0.01536.9950.0470.0470.0000.0000.0000.000
166A168ILE0-0.0120.00341.285-0.068-0.0680.0000.0000.0000.000
167A169PHE00.0470.01536.6940.0970.0970.0000.0000.0000.000
168A170GLU-1-0.884-0.94240.3857.0207.0200.0000.0000.0000.000
169A171GLY00.0280.01039.0190.1570.1570.0000.0000.0000.000
170A172GLY00.006-0.00839.231-0.248-0.2480.0000.0000.0000.000
171A173THR00.038-0.01340.2730.0950.0950.0000.0000.0000.000
172A174ARG10.9170.96736.946-8.376-8.3760.0000.0000.0000.000
173A175CYS00.0070.02936.4510.2160.2160.0000.0000.0000.000
174A176GLY00.0050.00837.4030.1210.1210.0000.0000.0000.000
175A177TYR0-0.014-0.01338.300-0.263-0.2630.0000.0000.0000.000
176A178TRP00.0230.01134.591-0.210-0.2100.0000.0000.0000.000
177A179ALA0-0.0100.01138.6870.0620.0620.0000.0000.0000.000
178A180GLY0-0.016-0.01441.211-0.115-0.1150.0000.0000.0000.000
179A181VAL0-0.0010.01142.1890.1760.1760.0000.0000.0000.000
180A182PHE0-0.0030.00439.803-0.073-0.0730.0000.0000.0000.000
181A183PHE00.014-0.00442.2410.0040.0040.0000.0000.0000.000
182A184LEU0-0.0030.00136.9880.0790.0790.0000.0000.0000.000
183A185SER0-0.0080.00541.233-0.178-0.1780.0000.0000.0000.000
184A186SER00.007-0.02837.6880.1790.1790.0000.0000.0000.000
185A187ALA00.0430.02439.993-0.171-0.1710.0000.0000.0000.000
186A188GLU-1-0.920-0.95634.5219.0459.0450.0000.0000.0000.000
187A189GLY00.0190.01537.1740.1820.1820.0000.0000.0000.000
188A190GLU-1-0.924-0.98439.0767.3837.3830.0000.0000.0000.000
189A191GLN00.0050.00632.657-0.116-0.1160.0000.0000.0000.000
190A192MET0-0.032-0.01134.1010.2560.2560.0000.0000.0000.000
191A193SER0-0.019-0.01735.2570.0930.0930.0000.0000.0000.000
192A194PHE00.0450.02533.5440.0880.0880.0000.0000.0000.000
193A195LEU00.0140.02128.8080.1190.1190.0000.0000.0000.000
194A196PHE00.011-0.01132.2100.2490.2490.0000.0000.0000.000
195A197ASP-1-0.849-0.89234.0678.2448.2440.0000.0000.0000.000
196A198CYS0-0.108-0.04431.625-0.013-0.0130.0000.0000.0000.000
197A199ILE00.0570.02627.9860.0990.0990.0000.0000.0000.000
198A200VAL0-0.051-0.01830.7640.1570.1570.0000.0000.0000.000
199A201ARG10.8670.93533.389-8.482-8.4820.0000.0000.0000.000
200A202GLY0-0.018-0.00129.920-0.068-0.0680.0000.0000.0000.000
201A203ILE0-0.043-0.02329.6570.1990.1990.0000.0000.0000.000
202A204SER0-0.013-0.05025.671-0.014-0.0140.0000.0000.0000.000
203A205PRO0-0.015-0.02228.113-0.165-0.1650.0000.0000.0000.000
204A206THR0-0.044-0.02425.069-0.245-0.2450.0000.0000.0000.000
205A207LYS10.9120.95920.261-14.302-14.3020.0000.0000.0000.000
206A208GLY00.0280.03226.203-0.015-0.0150.0000.0000.0000.000
207A209PRO0-0.012-0.01827.9750.2380.2380.0000.0000.0000.000
208A210PHE0-0.0150.02625.0080.5210.5210.0000.0000.0000.000