FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: JRQL9

Calculation Name: 3U3Z-A-Xray549

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine | phosphoserine

Ligand 3-letter code: PTR | SEP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3U3Z

Chain ID: A

ChEMBL ID:

UniProt ID: P16104

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1973409.670504
FMO2-HF: Nuclear repulsion 1899569.458703
FMO2-HF: Total energy -73840.211801
FMO2-MP2: Total energy -74052.676743


3D Structure Molmil
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:646:PRO)


Summations of interaction energy for fragment #1(A:646:PRO)
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.
23.74127.0731.601-1.713-3.22-0.015
Interaction energy analysis for fragmet #1(A:646:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.920
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].
3A648ARG10.9130.9652.96321.61623.9270.168-1.148-1.331-0.008
4A649THR00.008-0.0134.5374.2724.397-0.001-0.009-0.1160.000
36A681GLU-1-0.865-0.9574.782-40.597-40.464-0.001-0.005-0.1270.000
37A682THR00.0050.0132.431-2.679-1.9201.436-0.549-1.646-0.007
38A683THR0-0.041-0.0145.1240.9410.945-0.001-0.0020.0000.000
5A650LEU00.0040.0126.9051.8011.8010.0000.0000.0000.000
6A651VAL00.0170.01110.655-0.069-0.0690.0000.0000.0000.000
7A652MET00.0370.03612.9441.2741.2740.0000.0000.0000.000
8A653THR00.0090.00416.5530.3030.3030.0000.0000.0000.000
9A654SER0-0.016-0.01519.6250.2190.2190.0000.0000.0000.000
10A655MET00.0030.03019.2720.7090.7090.0000.0000.0000.000
11A656PRO00.0130.01722.658-0.082-0.0820.0000.0000.0000.000
12A657SER00.0410.00823.955-0.409-0.4090.0000.0000.0000.000
13A658GLU-1-0.818-0.90723.839-11.473-11.4730.0000.0000.0000.000
14A659LYS10.8770.94523.24111.10911.1090.0000.0000.0000.000
15A660GLN0-0.033-0.04119.775-0.957-0.9570.0000.0000.0000.000
16A661ASN0-0.0090.00319.714-1.004-1.0040.0000.0000.0000.000
17A662VAL00.0380.02521.101-0.447-0.4470.0000.0000.0000.000
18A663VAL00.001-0.00816.054-0.434-0.4340.0000.0000.0000.000
19A664ILE0-0.009-0.01116.204-0.921-0.9210.0000.0000.0000.000
20A665GLN00.0150.00817.004-0.400-0.4000.0000.0000.0000.000
21A666VAL0-0.0020.00918.347-0.080-0.0800.0000.0000.0000.000
22A667VAL0-0.014-0.01112.080-0.545-0.5450.0000.0000.0000.000
23A668ASP-1-0.910-0.95114.634-18.430-18.4300.0000.0000.0000.000
24A669LYS10.9470.98516.33713.50013.5000.0000.0000.0000.000
25A670LEU0-0.024-0.01216.5270.1640.1640.0000.0000.0000.000
26A671LYS10.8570.93412.47317.67417.6740.0000.0000.0000.000
27A672GLY00.0110.01110.4470.1620.1620.0000.0000.0000.000
28A673PHE0-0.049-0.0288.170-1.576-1.5760.0000.0000.0000.000
29A674SER00.0100.0195.5942.0092.0090.0000.0000.0000.000
30A675ILE00.004-0.0057.620-0.218-0.2180.0000.0000.0000.000
31A676ALA00.0050.0038.124-0.838-0.8380.0000.0000.0000.000
32A677PRO0-0.0110.00110.1601.2391.2390.0000.0000.0000.000
33A678ASP-1-0.829-0.91312.050-17.508-17.5080.0000.0000.0000.000
34A679VAL0-0.052-0.02010.901-1.984-1.9840.0000.0000.0000.000
35A680CYS0-0.031-0.0067.081-0.673-0.6730.0000.0000.0000.000
39A684THR00.0620.0288.2432.2042.2040.0000.0000.0000.000
40A685HIS10.7760.87310.80924.09324.0930.0000.0000.0000.000
41A686VAL00.0130.00912.805-0.930-0.9300.0000.0000.0000.000
42A687LEU00.0130.01915.4290.9280.9280.0000.0000.0000.000
43A688SER00.013-0.01218.0870.3010.3010.0000.0000.0000.000
44A689GLY00.0350.00621.4660.3010.3010.0000.0000.0000.000
45A690LYS10.9300.95023.98910.51110.5110.0000.0000.0000.000
46A691PRO00.0280.03225.153-0.285-0.2850.0000.0000.0000.000
47A692LEU0-0.011-0.00825.0570.5150.5150.0000.0000.0000.000
48A693ARG10.8440.90824.24410.55310.5530.0000.0000.0000.000
49A694THR00.013-0.01120.8460.0540.0540.0000.0000.0000.000
50A695LEU00.0510.00419.059-0.154-0.1540.0000.0000.0000.000
51A696ASN00.0120.00415.939-0.766-0.7660.0000.0000.0000.000
52A697VAL00.0000.01217.210-0.693-0.6930.0000.0000.0000.000
53A698LEU0-0.019-0.01019.492-0.203-0.2030.0000.0000.0000.000
54A699LEU00.010-0.00414.7310.0990.0990.0000.0000.0000.000
55A700GLY00.0260.00815.091-0.963-0.9630.0000.0000.0000.000
56A701ILE0-0.021-0.01116.165-0.295-0.2950.0000.0000.0000.000
57A702ALA0-0.020-0.01917.218-0.037-0.0370.0000.0000.0000.000
58A703ARG10.8890.93810.62824.40824.4080.0000.0000.0000.000
59A704GLY00.0440.03513.652-0.932-0.9320.0000.0000.0000.000
60A705CYS0-0.089-0.03811.829-0.638-0.6380.0000.0000.0000.000
61A706TRP00.0480.03014.4551.3911.3910.0000.0000.0000.000
62A707VAL0-0.011-0.00916.476-0.519-0.5190.0000.0000.0000.000
63A708LEU0-0.0020.01117.8590.7440.7440.0000.0000.0000.000
64A709SER0-0.004-0.01120.600-0.199-0.1990.0000.0000.0000.000
65A710TYR00.013-0.01221.439-0.323-0.3230.0000.0000.0000.000
66A711ASP-1-0.849-0.93422.435-11.702-11.7020.0000.0000.0000.000
67A712TRP0-0.013-0.00414.921-0.334-0.3340.0000.0000.0000.000
68A713VAL0-0.008-0.00418.350-0.334-0.3340.0000.0000.0000.000
69A714LEU0-0.0020.00620.8090.0270.0270.0000.0000.0000.000
70A715TRP00.0430.01424.4790.1830.1830.0000.0000.0000.000
71A716SER0-0.003-0.01419.862-0.144-0.1440.0000.0000.0000.000
72A717LEU0-0.074-0.03621.948-0.213-0.2130.0000.0000.0000.000
73A718GLU-1-0.947-0.96623.329-10.345-10.3450.0000.0000.0000.000
74A719LEU0-0.021-0.01424.9710.2580.2580.0000.0000.0000.000
75A720GLY0-0.0180.00823.623-0.131-0.1310.0000.0000.0000.000
76A721HIS0-0.071-0.04920.000-0.628-0.6280.0000.0000.0000.000
77A722TRP0-0.027-0.03414.1540.4200.4200.0000.0000.0000.000
78A723ILE00.0150.02718.404-0.103-0.1030.0000.0000.0000.000
79A724SER00.0110.00519.766-0.804-0.8040.0000.0000.0000.000
80A725GLU-1-0.780-0.88816.463-17.907-17.9070.0000.0000.0000.000
81A726GLU-1-0.843-0.91920.666-12.444-12.4440.0000.0000.0000.000
82A727PRO0-0.021-0.01123.4150.3060.3060.0000.0000.0000.000
83A728PHE00.0150.01122.4320.3450.3450.0000.0000.0000.000
84A729GLU-1-0.746-0.86620.772-14.749-14.7490.0000.0000.0000.000
85A730LEU0-0.056-0.02122.4080.6860.6860.0000.0000.0000.000
86A731SER00.016-0.01624.9720.0440.0440.0000.0000.0000.000
87A732HIS0-0.0040.00126.6970.3120.3120.0000.0000.0000.000
88A733HIS0-0.028-0.00726.9880.0750.0750.0000.0000.0000.000
89A734PHE0-0.046-0.04323.7060.0930.0930.0000.0000.0000.000
90A735PRO00.0540.02825.305-0.446-0.4460.0000.0000.0000.000
91A736ALA00.000-0.00323.685-0.087-0.0870.0000.0000.0000.000
92A737ALA0-0.026-0.00221.118-0.474-0.4740.0000.0000.0000.000
93A738PRO00.0530.03420.835-0.614-0.6140.0000.0000.0000.000
94A739LEU0-0.034-0.01222.414-0.154-0.1540.0000.0000.0000.000
95A740CYS0-0.022-0.01818.7160.1440.1440.0000.0000.0000.000
96A741ARG10.7680.88617.34713.90613.9060.0000.0000.0000.000
97A742SER0-0.032-0.01418.023-0.670-0.6700.0000.0000.0000.000
98A743GLU-1-0.800-0.88719.940-13.961-13.9610.0000.0000.0000.000
99A744CYS0-0.079-0.03113.511-0.821-0.8210.0000.0000.0000.000
100A745HIS0-0.007-0.01814.551-1.145-1.1450.0000.0000.0000.000
101A746LEU0-0.026-0.00116.5480.1130.1130.0000.0000.0000.000
102A747SER0-0.076-0.03815.4591.0391.0390.0000.0000.0000.000
103A748ALA0-0.0040.00415.729-0.908-0.9080.0000.0000.0000.000
104A749GLY00.0030.00714.700-0.884-0.8840.0000.0000.0000.000
105A750PRO0-0.026-0.02210.834-0.151-0.1510.0000.0000.0000.000
106A751TYR00.010-0.00512.6901.2091.2090.0000.0000.0000.000
107A752ARG10.8000.90414.15414.40714.4070.0000.0000.0000.000
108A753GLY00.0470.04517.0040.6090.6090.0000.0000.0000.000
109A754THR00.037-0.01320.0540.0770.0770.0000.0000.0000.000
110A755LEU0-0.0520.00323.5630.4840.4840.0000.0000.0000.000
111A756PHE0-0.032-0.03824.1100.5570.5570.0000.0000.0000.000
112A757ALA00.0100.01125.1280.1340.1340.0000.0000.0000.000
113A758ASP-1-0.909-0.94726.667-10.055-10.0550.0000.0000.0000.000
114A759GLN0-0.058-0.01829.1370.5370.5370.0000.0000.0000.000
115A760PRO00.0040.00530.433-0.163-0.1630.0000.0000.0000.000
116A761VAL0-0.032-0.01129.475-0.298-0.2980.0000.0000.0000.000
117A762MET00.0250.01228.0840.2860.2860.0000.0000.0000.000
118A763PHE0-0.013-0.00829.181-0.119-0.1190.0000.0000.0000.000
119A764VAL00.0190.00725.4870.1530.1530.0000.0000.0000.000
120A765SER0-0.010-0.01528.422-0.092-0.0920.0000.0000.0000.000
121A766PRO00.001-0.02127.839-0.312-0.3120.0000.0000.0000.000
122A767ALA0-0.018-0.00828.494-0.169-0.1690.0000.0000.0000.000
123A768SER0-0.048-0.02626.5190.1370.1370.0000.0000.0000.000
124A769SER0-0.040-0.00627.665-0.407-0.4070.0000.0000.0000.000
125A770PRO00.013-0.01523.4430.1860.1860.0000.0000.0000.000
126A771PRO00.0710.02722.5470.0870.0870.0000.0000.0000.000
127A772VAL00.0600.04322.844-0.608-0.6080.0000.0000.0000.000
128A773ALA00.0360.02619.119-0.207-0.2070.0000.0000.0000.000
129A774LYS10.9090.94314.90217.61917.6190.0000.0000.0000.000
130A775LEU0-0.019-0.00319.477-0.278-0.2780.0000.0000.0000.000
131A776CYS0-0.018-0.02120.9900.2530.2530.0000.0000.0000.000
132A777GLU-1-0.860-0.91913.630-20.265-20.2650.0000.0000.0000.000
133A778LEU00.002-0.00218.084-0.235-0.2350.0000.0000.0000.000
134A779VAL00.001-0.00319.9850.0770.0770.0000.0000.0000.000
135A780HIS00.0000.00815.9980.8660.8660.0000.0000.0000.000
136A781LEU0-0.006-0.00113.764-0.105-0.1050.0000.0000.0000.000
137A782CYS0-0.0200.00317.681-0.078-0.0780.0000.0000.0000.000
138A783GLY00.0680.03820.4390.6930.6930.0000.0000.0000.000
139A784GLY0-0.017-0.00522.1130.4960.4960.0000.0000.0000.000
140A785ARG10.8940.92123.43010.26510.2650.0000.0000.0000.000
141A786VAL00.0270.01124.1630.4820.4820.0000.0000.0000.000
142A787SER0-0.009-0.01125.490-0.294-0.2940.0000.0000.0000.000
143A788GLN00.0230.00124.0740.0690.0690.0000.0000.0000.000
144A789VAL0-0.004-0.01027.9420.3280.3280.0000.0000.0000.000
145A790PRO00.019-0.00131.8160.0130.0130.0000.0000.0000.000
146A791ARG10.9090.95634.2698.7838.7830.0000.0000.0000.000
147A792GLN00.0070.01131.5240.0010.0010.0000.0000.0000.000
148A793ALA00.0040.02932.336-0.111-0.1110.0000.0000.0000.000
149A794SER00.0200.00833.9570.2370.2370.0000.0000.0000.000
150A795ILE0-0.020-0.00132.1040.2000.2000.0000.0000.0000.000
151A796VAL0-0.028-0.01332.649-0.229-0.2290.0000.0000.0000.000
152A797ILE00.0000.00728.4610.1540.1540.0000.0000.0000.000
153A798GLY00.0620.03130.866-0.228-0.2280.0000.0000.0000.000
154A799PRO0-0.019-0.01332.1610.2330.2330.0000.0000.0000.000
155A800TYR0-0.0090.00634.531-0.069-0.0690.0000.0000.0000.000
156A801SER00.0410.01836.8690.1070.1070.0000.0000.0000.000
157A802GLY00.0180.02338.8790.1690.1690.0000.0000.0000.000
158A803LYS10.9480.95640.2956.7926.7920.0000.0000.0000.000
159A804LYS10.8860.96939.6277.5797.5790.0000.0000.0000.000
160A805LYS10.9300.95640.5727.7997.7990.0000.0000.0000.000
161A806ALA00.0740.02742.470-0.114-0.1140.0000.0000.0000.000
162A807THR0-0.016-0.00340.9370.0380.0380.0000.0000.0000.000
163A808VAL0-0.054-0.01936.721-0.186-0.1860.0000.0000.0000.000
164A809LYS10.9600.98836.7038.1188.1180.0000.0000.0000.000
165A810TYR00.0460.01836.156-0.198-0.1980.0000.0000.0000.000
166A811LEU00.0050.01433.5050.1850.1850.0000.0000.0000.000
167A812SER00.0270.01133.492-0.221-0.2210.0000.0000.0000.000
168A813GLU-1-0.741-0.89328.169-9.933-9.9330.0000.0000.0000.000
169A814LYS10.8490.90328.8238.9978.9970.0000.0000.0000.000
170A815TRP00.0200.01730.093-0.212-0.2120.0000.0000.0000.000
171A816VAL00.0200.02425.124-0.119-0.1190.0000.0000.0000.000
172A817LEU00.008-0.00424.511-0.269-0.2690.0000.0000.0000.000
173A818ASP-1-0.736-0.81526.866-10.082-10.0820.0000.0000.0000.000
174A819SER00.032-0.01028.1980.0670.0670.0000.0000.0000.000
175A820ILE0-0.012-0.00821.987-0.097-0.0970.0000.0000.0000.000
176A821THR0-0.048-0.04024.628-0.267-0.2670.0000.0000.0000.000
177A822GLN0-0.025-0.02426.3500.1690.1690.0000.0000.0000.000
178A823HIS10.8280.91722.41413.10913.1090.0000.0000.0000.000
179A824LYS10.9921.00226.7489.4249.4240.0000.0000.0000.000
180A825VAL00.0140.00829.473-0.075-0.0750.0000.0000.0000.000
181A826CYS0-0.051-0.00731.1720.3090.3090.0000.0000.0000.000
182A827ALA00.0600.03233.754-0.037-0.0370.0000.0000.0000.000
183A828PRO0-0.001-0.01235.3590.0280.0280.0000.0000.0000.000
184A829GLU-1-0.859-0.94337.071-7.829-7.8290.0000.0000.0000.000
185A830ASN0-0.029-0.01137.8220.2810.2810.0000.0000.0000.000
186A831TYR0-0.101-0.07033.749-0.066-0.0660.0000.0000.0000.000
187A832LEU0-0.0090.00736.766-0.176-0.1760.0000.0000.0000.000
188A833LEU0-0.047-0.01435.0610.0410.0410.0000.0000.0000.000
189A834SER-1-0.882-0.94738.827-7.531-7.5310.0000.0000.0000.000