Manual

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: 72N9K

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 OptHSide
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 -2336090.862956
FMO2-HF: Nuclear repulsion 2253706.55625
FMO2-HF: Total energy -82384.306706
FMO2-MP2: Total energy -82619.25174


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.
-176.819-179.00827.011-13.024-11.8010.135
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 : -0.834 / q_NPA : -0.895
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].
3A5ALA0-0.005-0.0093.7975.4767.533-0.025-1.037-0.9950.004
4A6LEU0-0.061-0.0216.049-2.837-2.8370.0000.0000.0000.000
5A7VAL00.021-0.0019.136-2.883-2.8830.0000.0000.0000.000
6A8GLU-1-0.754-0.8616.95433.89633.8960.0000.0000.0000.000
7A9GLY00.0060.0029.988-1.733-1.7330.0000.0000.0000.000
8A10GLN0-0.0070.01213.0320.7910.7910.0000.0000.0000.000
9A11VAL00.0560.04214.590-0.757-0.7570.0000.0000.0000.000
10A12LYS10.8180.90416.670-13.004-13.0040.0000.0000.0000.000
11A13LEU00.0670.04214.0720.0110.0110.0000.0000.0000.000
12A14ARG10.9270.96018.766-12.517-12.5170.0000.0000.0000.000
13A15ASP-1-0.860-0.92416.43217.78017.7800.0000.0000.0000.000
14A16GLY0-0.056-0.03418.2530.4820.4820.0000.0000.0000.000
15A17LYS10.8990.89720.796-15.093-15.0930.0000.0000.0000.000
16A18LYS10.9871.03124.421-10.887-10.8870.0000.0000.0000.000
17A19TRP0-0.007-0.01621.1140.7110.7110.0000.0000.0000.000
18A20LYS10.8520.93619.172-13.218-13.2180.0000.0000.0000.000
19A21SER00.005-0.02518.4270.4290.4290.0000.0000.0000.000
20A22ARG10.8730.92813.729-17.886-17.8860.0000.0000.0000.000
21A23TRP00.0000.0019.111-1.282-1.2820.0000.0000.0000.000
22A24LEU0-0.0010.01310.0071.7611.7610.0000.0000.0000.000
23A25VAL00.007-0.0033.800-0.984-0.8670.001-0.023-0.0960.000
24A26LEU00.0230.0237.3011.1571.1570.0000.0000.0000.000
25A27ARG10.8690.9101.762-125.029-132.70825.672-10.309-7.6850.122
26A28LYS10.9500.9997.479-23.089-23.0890.0000.0000.0000.000
27A29PRO0-0.039-0.0097.1125.2045.2040.0000.0000.0000.000
28A30SER00.0320.0068.1630.3760.3760.0000.0000.0000.000
29A31PRO0-0.002-0.01011.281-0.211-0.2110.0000.0000.0000.000
30A32VAL0-0.007-0.00512.969-1.102-1.1020.0000.0000.0000.000
31A33ALA00.0210.01213.668-0.628-0.6280.0000.0000.0000.000
32A34ASP-1-0.817-0.87114.71118.35418.3540.0000.0000.0000.000
33A35CYS0-0.045-0.02112.154-0.237-0.2370.0000.0000.0000.000
34A36LEU0-0.026-0.00510.5871.5881.5880.0000.0000.0000.000
35A37LEU0-0.012-0.0054.384-0.716-0.558-0.001-0.017-0.1400.000
36A38MET0-0.021-0.0137.6541.5701.5700.0000.0000.0000.000
37A39LEU00.001-0.0102.785-3.152-1.5350.521-0.849-1.2890.010
38A40VAL00.001-0.0017.513-2.569-2.5690.0000.0000.0000.000
39A41TYR00.0460.0163.4180.9651.4580.024-0.132-0.385-0.001
40A42LYS10.8090.8759.928-22.401-22.4010.0000.0000.0000.000
41A43ASP-1-0.780-0.89312.27916.59316.5930.0000.0000.0000.000
42A44LYS10.8930.9579.366-22.131-22.1310.0000.0000.0000.000
43A45CYS00.000-0.00110.7971.0721.0720.0000.0000.0000.000
44A46GLU-1-0.819-0.89610.40621.27821.2780.0000.0000.0000.000
45A47ARG10.8020.8972.302-43.450-42.4020.819-0.657-1.2110.000
46A48SER0-0.021-0.0316.3281.9331.9330.0000.0000.0000.000
47A49LYS10.8260.9368.548-20.696-20.6960.0000.0000.0000.000
48A50GLY00.0580.0175.9500.0050.0050.0000.0000.0000.000
49A51LEU0-0.110-0.0327.0021.2211.2210.0000.0000.0000.000
50A52ARG10.9030.9446.432-30.491-30.4910.0000.0000.0000.000
51A53GLU-1-0.811-0.8736.03435.42235.4220.0000.0000.0000.000
52A54ARG10.8800.9357.848-19.466-19.4660.0000.0000.0000.000
53A55SER0-0.001-0.01710.681-2.096-2.0960.0000.0000.0000.000
54A56SER0-0.033-0.0367.9761.0761.0760.0000.0000.0000.000
55A57LEU00.0110.0159.908-2.338-2.3380.0000.0000.0000.000
56A58THR00.0090.0099.4613.2233.2230.0000.0000.0000.000
57A59LEU0-0.029-0.00511.790-1.704-1.7040.0000.0000.0000.000
58A60GLU-1-0.882-0.98014.53221.51621.5160.0000.0000.0000.000
59A61ASP-1-0.777-0.86616.34514.95814.9580.0000.0000.0000.000
60A62ILE0-0.029-0.02014.779-0.689-0.6890.0000.0000.0000.000
61A63CYS0-0.015-0.01219.347-0.417-0.4170.0000.0000.0000.000
62A64GLY00.0510.02521.547-0.635-0.6350.0000.0000.0000.000
63A65LEU0-0.043-0.01418.1530.6990.6990.0000.0000.0000.000
64A66GLU-1-0.782-0.91222.40710.70710.7070.0000.0000.0000.000
65A67PRO0-0.022-0.00423.3380.2720.2720.0000.0000.0000.000
66A68ALA0-0.014-0.04324.740-0.426-0.4260.0000.0000.0000.000
67A69LEU00.0440.03726.041-0.501-0.5010.0000.0000.0000.000
68A70PRO00.0140.01627.5100.2960.2960.0000.0000.0000.000
69A71TYR00.0520.01224.8480.1890.1890.0000.0000.0000.000
70A72GLU-1-0.863-0.91827.44710.72710.7270.0000.0000.0000.000
71A73GLY0-0.0070.00428.5550.2410.2410.0000.0000.0000.000
72A74LEU0-0.047-0.01723.819-0.067-0.0670.0000.0000.0000.000
73A75ALA00.0470.02327.890-0.026-0.0260.0000.0000.0000.000
74A76HIS0-0.015-0.01924.833-0.299-0.2990.0000.0000.0000.000
75A77THR0-0.059-0.04622.8250.6320.6320.0000.0000.0000.000
76A78LEU00.0040.00118.100-0.277-0.2770.0000.0000.0000.000
77A79ALA00.0130.00720.9630.4500.4500.0000.0000.0000.000
78A80ILE0-0.020-0.01415.4220.0510.0510.0000.0000.0000.000
79A81ILE00.010-0.00319.620-0.069-0.0690.0000.0000.0000.000
80A82CYS0-0.040-0.01318.7240.6820.6820.0000.0000.0000.000
81A83LEU0-0.007-0.00421.622-0.696-0.6960.0000.0000.0000.000
82A84SER0-0.085-0.05421.372-0.405-0.4050.0000.0000.0000.000
83A85GLN0-0.017-0.02019.442-0.074-0.0740.0000.0000.0000.000
84A86ALA00.0720.04021.8160.3730.3730.0000.0000.0000.000
85A87VAL0-0.018-0.00816.224-0.107-0.1070.0000.0000.0000.000
86A88MET0-0.026-0.00119.6100.0130.0130.0000.0000.0000.000
87A89LEU0-0.056-0.02915.6550.4060.4060.0000.0000.0000.000
88A90GLY00.0400.00219.239-0.686-0.6860.0000.0000.0000.000
89A91PHE00.001-0.00616.8120.6420.6420.0000.0000.0000.000
90A92ASP-1-0.826-0.89821.37812.46212.4620.0000.0000.0000.000
91A93SER00.0070.00423.306-0.396-0.3960.0000.0000.0000.000
92A94HIS00.0810.03423.7830.5630.5630.0000.0000.0000.000
93A95GLU-1-0.848-0.93324.20811.73611.7360.0000.0000.0000.000
94A96ALA0-0.042-0.01519.5800.5120.5120.0000.0000.0000.000
95A97MET0-0.0080.04719.1500.7580.7580.0000.0000.0000.000
96A98CYS00.0240.00920.4900.3800.3800.0000.0000.0000.000
97A99ALA0-0.0110.00918.4820.3360.3360.0000.0000.0000.000
98A100TRP00.008-0.01611.7721.1301.1300.0000.0000.0000.000
99A101ASP-1-0.757-0.87017.13814.48614.4860.0000.0000.0000.000
100A102THR0-0.030-0.03019.759-0.002-0.0020.0000.0000.0000.000
101A103ARG10.8790.93712.287-21.264-21.2640.0000.0000.0000.000
102A104ILE00.012-0.00214.1060.9680.9680.0000.0000.0000.000
103A105ARG10.7900.88416.197-13.185-13.1850.0000.0000.0000.000
104A106TYR00.0050.00917.590-0.202-0.2020.0000.0000.0000.000
105A107ALA0-0.024-0.01413.9240.1470.1470.0000.0000.0000.000
106A108LEU0-0.058-0.04114.3730.8920.8920.0000.0000.0000.000
107A109GLY00.0170.03917.048-0.485-0.4850.0000.0000.0000.000
108A110GLU-1-0.799-0.86420.13112.62712.6270.0000.0000.0000.000
109A111VAL00.0200.01620.304-0.147-0.1470.0000.0000.0000.000
110A112HIS0-0.060-0.03623.317-0.168-0.1680.0000.0000.0000.000
111A113ARG10.8500.92625.198-11.784-11.7840.0000.0000.0000.000
112A114PHE00.0380.01828.485-0.128-0.1280.0000.0000.0000.000
113A115HIS00.0140.01130.0150.0850.0850.0000.0000.0000.000
114A116VAL0-0.018-0.00434.234-0.263-0.2630.0000.0000.0000.000
115A117THR0-0.013-0.01537.182-0.020-0.0200.0000.0000.0000.000
116A118VAL00.0090.00937.562-0.112-0.1120.0000.0000.0000.000
117A119ALA00.0150.01340.473-0.138-0.1380.0000.0000.0000.000
118A120PRO00.022-0.00243.7300.0920.0920.0000.0000.0000.000
119A121GLY00.0050.00445.787-0.066-0.0660.0000.0000.0000.000
120A122THR0-0.031-0.01142.2110.0200.0200.0000.0000.0000.000
121A123LYS10.8240.89441.077-7.741-7.7410.0000.0000.0000.000
122A124LEU0-0.0350.00236.6840.1170.1170.0000.0000.0000.000
123A125GLU-1-0.815-0.88438.9797.9467.9460.0000.0000.0000.000
124A126SER0-0.037-0.02540.0250.0310.0310.0000.0000.0000.000
125A127GLY00.010-0.00541.1180.0580.0580.0000.0000.0000.000
126A128PRO0-0.019-0.02037.9860.1120.1120.0000.0000.0000.000
127A129ALA00.0150.01234.4090.0860.0860.0000.0000.0000.000
128A130THR0-0.058-0.01329.620-0.084-0.0840.0000.0000.0000.000
129A131LEU00.0330.01331.0400.1450.1450.0000.0000.0000.000
130A132HIS0-0.013-0.01726.0650.4940.4940.0000.0000.0000.000
131A133LEU0-0.0120.00126.336-0.154-0.1540.0000.0000.0000.000
132A134CYS0-0.045-0.02221.5340.6130.6130.0000.0000.0000.000
133A135ASN00.002-0.02619.919-0.336-0.3360.0000.0000.0000.000
134A136ASP-1-0.881-0.92324.08712.50112.5010.0000.0000.0000.000
135A137ILE0-0.078-0.04323.558-0.718-0.7180.0000.0000.0000.000
136A138LEU0-0.0010.00527.2160.1260.1260.0000.0000.0000.000
137A139VAL00.034-0.00126.824-0.139-0.1390.0000.0000.0000.000
138A140LEU0-0.0130.01829.662-0.082-0.0820.0000.0000.0000.000
139A141ALA0-0.0130.00128.4440.0480.0480.0000.0000.0000.000
140A142ARG10.8380.89830.487-8.808-8.8080.0000.0000.0000.000
141A143ASP-1-0.872-0.92631.0209.5109.5100.0000.0000.0000.000
142A144ILE0-0.0210.00828.1570.4100.4100.0000.0000.0000.000
143A145PRO0-0.055-0.05725.777-0.225-0.2250.0000.0000.0000.000
144A146PRO00.0230.00725.599-0.194-0.1940.0000.0000.0000.000
145A147THR0-0.033-0.00327.0020.2900.2900.0000.0000.0000.000
146A148VAL00.0210.01026.680-0.241-0.2410.0000.0000.0000.000
147A149MET0-0.020-0.01329.532-0.199-0.1990.0000.0000.0000.000
148A150GLY00.008-0.00831.970-0.375-0.3750.0000.0000.0000.000
149A151GLN0-0.032-0.01528.2450.4580.4580.0000.0000.0000.000
150A152TRP0-0.040-0.02130.808-0.262-0.2620.0000.0000.0000.000
151A153LYS10.9951.00528.218-10.745-10.7450.0000.0000.0000.000
152A154LEU00.0560.02428.957-0.480-0.4800.0000.0000.0000.000
153A155SER0-0.002-0.00531.432-0.195-0.1950.0000.0000.0000.000
154A156ASP-1-0.985-0.99333.2739.4209.4200.0000.0000.0000.000
155A157LEU0-0.020-0.01034.372-0.287-0.2870.0000.0000.0000.000
156A158ARG10.8130.91137.205-7.397-7.3970.0000.0000.0000.000
157A159ARG10.9390.96440.772-7.183-7.1830.0000.0000.0000.000
158A160TYR0-0.016-0.04137.5160.1600.1600.0000.0000.0000.000
159A161GLY00.0040.01040.336-0.122-0.1220.0000.0000.0000.000
160A162ALA00.0170.02441.1450.0440.0440.0000.0000.0000.000
161A163VAL0-0.030-0.00942.412-0.191-0.1910.0000.0000.0000.000
162A164PRO00.027-0.00444.9320.1140.1140.0000.0000.0000.000
163A165ASN0-0.046-0.01344.504-0.122-0.1220.0000.0000.0000.000
164A166GLY00.0660.02842.2550.0430.0430.0000.0000.0000.000
165A167PHE0-0.036-0.01736.5730.0540.0540.0000.0000.0000.000
166A168ILE0-0.0080.00540.999-0.072-0.0720.0000.0000.0000.000
167A169PHE00.0500.01335.8380.1030.1030.0000.0000.0000.000
168A170GLU-1-0.879-0.93239.8367.1977.1970.0000.0000.0000.000
169A171GLY00.0340.01338.5120.1670.1670.0000.0000.0000.000
170A172GLY00.019-0.00638.767-0.259-0.2590.0000.0000.0000.000
171A173THR00.038-0.01339.8410.1160.1160.0000.0000.0000.000
172A174ARG10.9350.97736.420-8.659-8.6590.0000.0000.0000.000
173A175CYS00.0000.02336.0450.2300.2300.0000.0000.0000.000
174A176GLY00.0110.01136.9970.1200.1200.0000.0000.0000.000
175A177TYR00.0140.00037.840-0.276-0.2760.0000.0000.0000.000
176A178TRP00.0540.03134.016-0.250-0.2500.0000.0000.0000.000
177A179ALA0-0.0140.01238.2140.0570.0570.0000.0000.0000.000
178A180GLY00.0150.00140.742-0.122-0.1220.0000.0000.0000.000
179A181VAL00.0100.01641.6510.1840.1840.0000.0000.0000.000
180A182PHE0-0.0090.00539.361-0.076-0.0760.0000.0000.0000.000
181A183PHE00.013-0.00641.6680.0090.0090.0000.0000.0000.000
182A184LEU00.0050.00936.5720.0800.0800.0000.0000.0000.000
183A185SER0-0.007-0.00140.808-0.185-0.1850.0000.0000.0000.000
184A186SER00.003-0.02737.5940.2000.2000.0000.0000.0000.000
185A187ALA00.0320.01839.960-0.175-0.1750.0000.0000.0000.000
186A188GLU-1-0.907-0.95334.1739.3999.3990.0000.0000.0000.000
187A189GLY00.0290.02037.1960.1950.1950.0000.0000.0000.000
188A190GLU-1-0.918-0.97939.0367.5637.5630.0000.0000.0000.000
189A191GLN0-0.011-0.00133.174-0.072-0.0720.0000.0000.0000.000
190A192MET0-0.022-0.00633.9810.2680.2680.0000.0000.0000.000
191A193SER0-0.020-0.01835.1660.1000.1000.0000.0000.0000.000
192A194PHE00.0380.02234.0610.0840.0840.0000.0000.0000.000
193A195LEU00.0260.02828.7930.1340.1340.0000.0000.0000.000
194A196PHE00.021-0.00632.1540.2610.2610.0000.0000.0000.000
195A197ASP-1-0.813-0.87333.8858.4568.4560.0000.0000.0000.000
196A198CYS0-0.078-0.03231.870-0.036-0.0360.0000.0000.0000.000
197A199ILE00.0400.01727.8750.1080.1080.0000.0000.0000.000
198A200VAL0-0.043-0.01330.6250.1740.1740.0000.0000.0000.000
199A201ARG10.7780.88033.097-8.782-8.7820.0000.0000.0000.000
200A202GLY0-0.0120.00729.791-0.080-0.0800.0000.0000.0000.000
201A203ILE0-0.049-0.02529.7330.2250.2250.0000.0000.0000.000
202A204SER00.001-0.02425.953-0.059-0.0590.0000.0000.0000.000
203A205PRO0-0.022-0.02828.400-0.152-0.1520.0000.0000.0000.000
204A206THR0-0.065-0.02125.661-0.027-0.0270.0000.0000.0000.000
205A207LYS10.8660.91421.841-14.366-14.3660.0000.0000.0000.000
206A208GLY00.0390.03626.364-0.020-0.0200.0000.0000.0000.000
207A209PRO0-0.014-0.02128.1910.2540.2540.0000.0000.0000.000
208A210PHE00.0000.02325.0400.5640.5640.0000.0000.0000.000