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: 7MGYK

Calculation Name: 3BUW-B-Xray372

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 3BUW

Chain ID: B

ChEMBL ID:

UniProt ID: P22681

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 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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4748657.871999
FMO2-HF: Nuclear repulsion 4624563.049919
FMO2-HF: Total energy -124094.82208
FMO2-MP2: Total energy -124456.466057


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(B:47:PRO)


Summations of interaction energy for fragment #1(B:47: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.
-3.2670.6940.941-1.709-3.193-0.004
Interaction energy analysis for fragmet #1(B:47:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.015
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].
3B49GLY00.0390.0333.788-1.842-0.456-0.002-0.763-0.6220.001
4B50THR00.018-0.0046.5660.1440.1440.0000.0000.0000.000
5B51VAL0-0.039-0.0188.1880.1930.1930.0000.0000.0000.000
6B52ASP-1-0.782-0.87510.666-0.387-0.3870.0000.0000.0000.000
7B53LYS10.9100.92813.9130.2740.2740.0000.0000.0000.000
8B54LYS10.9000.92716.8070.4560.4560.0000.0000.0000.000
9B55MET0-0.0190.00510.0960.0780.0780.0000.0000.0000.000
10B56VAL00.0550.03614.8160.0280.0280.0000.0000.0000.000
11B57GLU-1-0.775-0.86816.721-0.199-0.1990.0000.0000.0000.000
12B58LYS10.8300.92317.5420.2380.2380.0000.0000.0000.000
13B59CYS00.0230.00815.9830.0380.0380.0000.0000.0000.000
14B60TRP00.0490.01218.0830.0360.0360.0000.0000.0000.000
15B61LYS10.9740.97521.1560.1720.1720.0000.0000.0000.000
16B62LEU0-0.098-0.03518.2700.0140.0140.0000.0000.0000.000
17B63MET00.0480.02119.5650.0230.0230.0000.0000.0000.000
18B64ASP-1-0.812-0.87422.667-0.076-0.0760.0000.0000.0000.000
19B65LYS10.9350.96924.9750.0800.0800.0000.0000.0000.000
20B66VAL00.014-0.00522.7080.0110.0110.0000.0000.0000.000
21B67VAL00.0480.03025.9600.0100.0100.0000.0000.0000.000
22B68ARG10.8730.91828.3250.0860.0860.0000.0000.0000.000
23B69LEU0-0.089-0.03927.3240.0040.0040.0000.0000.0000.000
24B70CYS0-0.048-0.03628.1220.0080.0080.0000.0000.0000.000
25B71GLN00.0240.01131.0330.0020.0020.0000.0000.0000.000
26B72ASN0-0.0170.00834.0530.0030.0030.0000.0000.0000.000
27B73PRO00.0880.03236.0200.0030.0030.0000.0000.0000.000
28B74LYS10.8790.94238.3410.0180.0180.0000.0000.0000.000
29B75LEU0-0.060-0.00832.5120.0030.0030.0000.0000.0000.000
30B76ALA00.0420.02136.4840.0030.0030.0000.0000.0000.000
31B77LEU0-0.019-0.00331.2180.0020.0020.0000.0000.0000.000
32B78LYS10.9300.95733.207-0.013-0.0130.0000.0000.0000.000
33B79ASN0-0.037-0.03033.6280.0030.0030.0000.0000.0000.000
34B80SER0-0.002-0.02033.3690.0010.0010.0000.0000.0000.000
35B81PRO0-0.046-0.00629.5790.0000.0000.0000.0000.0000.000
36B82PRO0-0.032-0.01225.9210.0050.0050.0000.0000.0000.000
37B83TYR00.037-0.00127.9110.0000.0000.0000.0000.0000.000
38B84ILE00.016-0.00823.841-0.006-0.0060.0000.0000.0000.000
39B85LEU0-0.012-0.01126.630-0.009-0.0090.0000.0000.0000.000
40B86ASP-1-0.805-0.88928.980-0.039-0.0390.0000.0000.0000.000
41B87LEU0-0.029-0.01923.639-0.007-0.0070.0000.0000.0000.000
42B88LEU00.0000.01721.842-0.012-0.0120.0000.0000.0000.000
43B89PRO00.0290.00923.652-0.015-0.0150.0000.0000.0000.000
44B90ASP-1-0.783-0.86725.126-0.076-0.0760.0000.0000.0000.000
45B91THR0-0.015-0.02718.722-0.008-0.0080.0000.0000.0000.000
46B92TYR0-0.034-0.01520.589-0.019-0.0190.0000.0000.0000.000
47B93GLN00.0420.01822.357-0.022-0.0220.0000.0000.0000.000
48B94HIS00.0130.01518.8330.0010.0010.0000.0000.0000.000
49B95LEU00.0170.00115.667-0.016-0.0160.0000.0000.0000.000
50B96ARG10.8880.94619.2050.1080.1080.0000.0000.0000.000
51B97THR0-0.034-0.01922.139-0.002-0.0020.0000.0000.0000.000
52B98ILE0-0.021-0.00315.6680.0000.0000.0000.0000.0000.000
53B99LEU0-0.043-0.03616.933-0.013-0.0130.0000.0000.0000.000
54B100SER00.0030.01619.4990.0000.0000.0000.0000.0000.000
55B101ARG10.9090.94820.5330.1300.1300.0000.0000.0000.000
56B102TYR0-0.054-0.06015.9620.0050.0050.0000.0000.0000.000
57B103GLU-1-0.864-0.91819.243-0.230-0.2300.0000.0000.0000.000
58B104GLY00.0020.01921.9690.0060.0060.0000.0000.0000.000
59B105LYS10.8690.95118.5300.1900.1900.0000.0000.0000.000
60B106MET00.000-0.01815.255-0.019-0.0190.0000.0000.0000.000
61B107GLU-1-0.936-0.95214.043-0.488-0.4880.0000.0000.0000.000
62B108THR00.0630.02212.271-0.071-0.0710.0000.0000.0000.000
63B109LEU0-0.062-0.02411.691-0.029-0.0290.0000.0000.0000.000
64B110GLY00.0060.00010.548-0.043-0.0430.0000.0000.0000.000
65B111GLU-1-0.843-0.9407.680-1.005-1.0050.0000.0000.0000.000
66B112ASN0-0.0180.0096.580-0.200-0.2000.0000.0000.0000.000
67B113GLU-1-0.820-0.8993.346-0.675-0.0980.032-0.130-0.4790.000
68B114TYR0-0.030-0.0474.9460.0140.077-0.001-0.002-0.0600.000
69B115PHE00.0580.0107.3930.0440.0440.0000.0000.0000.000
70B116ARG10.8470.9242.5032.0943.1590.895-0.572-1.388-0.004
71B117VAL0-0.0220.0003.778-0.1810.0190.003-0.043-0.1600.000
72B118PHE0-0.016-0.0036.2390.0830.0830.0000.0000.0000.000
73B119MET00.0280.0069.8950.0880.0880.0000.0000.0000.000
74B120GLU-1-0.901-0.9486.668-0.911-0.9110.0000.0000.0000.000
75B121ASN00.0040.0049.7680.1460.1460.0000.0000.0000.000
76B122LEU00.0380.01211.4430.0440.0440.0000.0000.0000.000
77B123MET0-0.0240.00013.3320.0660.0660.0000.0000.0000.000
78B124LYS10.8770.93712.174-0.051-0.0510.0000.0000.0000.000
79B125LYS10.8270.89813.878-0.063-0.0630.0000.0000.0000.000
80B126THR00.0210.00717.1860.0110.0110.0000.0000.0000.000
81B127LYS10.9470.98114.8240.2270.2270.0000.0000.0000.000
82B128GLN00.0180.02316.7190.0280.0280.0000.0000.0000.000
83B129THR00.0310.00520.1060.0110.0110.0000.0000.0000.000
84B130ILE0-0.031-0.02721.8220.0020.0020.0000.0000.0000.000
85B131SER0-0.060-0.04521.8490.0010.0010.0000.0000.0000.000
86B132LEU00.0030.00524.2050.0050.0050.0000.0000.0000.000
87B133PHE00.0530.02326.0370.0030.0030.0000.0000.0000.000
88B134LYS10.8150.90425.3460.0150.0150.0000.0000.0000.000
89B135GLU-1-0.817-0.88925.9970.0010.0010.0000.0000.0000.000
90B136GLY0-0.016-0.01429.4740.0050.0050.0000.0000.0000.000
91B137LYS10.8800.93231.1360.0010.0010.0000.0000.0000.000
92B138GLU-1-0.822-0.92533.9160.0050.0050.0000.0000.0000.000
93B139ARG10.9480.98031.971-0.024-0.0240.0000.0000.0000.000
94B140MET0-0.069-0.00728.6120.0050.0050.0000.0000.0000.000
95B141TYR00.009-0.01133.710-0.003-0.0030.0000.0000.0000.000
96B142GLU-1-0.902-0.93636.9940.0180.0180.0000.0000.0000.000
97B143GLU-1-0.762-0.86635.7770.0180.0180.0000.0000.0000.000
98B144ASN0-0.067-0.04435.8070.0030.0030.0000.0000.0000.000
99B145SER0-0.0040.01033.9640.0060.0060.0000.0000.0000.000
100B146GLN00.0810.01930.1640.0030.0030.0000.0000.0000.000
101B147PRO0-0.021-0.00629.0550.0030.0030.0000.0000.0000.000
102B148ARG10.8310.90728.991-0.009-0.0090.0000.0000.0000.000
103B149ARG10.8200.88527.045-0.052-0.0520.0000.0000.0000.000
104B150ASN0-0.045-0.03625.0630.0120.0120.0000.0000.0000.000
105B151LEU00.0310.01625.1040.0010.0010.0000.0000.0000.000
106B152THR0-0.0140.01126.360-0.005-0.0050.0000.0000.0000.000
107B153LYS10.8740.94920.289-0.115-0.1150.0000.0000.0000.000
108B154LEU0-0.020-0.02319.7460.0050.0050.0000.0000.0000.000
109B155SER0-0.023-0.01221.922-0.010-0.0100.0000.0000.0000.000
110B156LEU0-0.0040.00723.064-0.005-0.0050.0000.0000.0000.000
111B157ILE0-0.051-0.01517.1020.0000.0000.0000.0000.0000.000
112B158PHE00.007-0.01718.632-0.008-0.0080.0000.0000.0000.000
113B159SER00.0200.01820.367-0.012-0.0120.0000.0000.0000.000
114B160HIS0-0.012-0.01118.336-0.011-0.0110.0000.0000.0000.000
115B161MET0-0.016-0.00214.688-0.006-0.0060.0000.0000.0000.000
116B162LEU0-0.0330.00616.776-0.018-0.0180.0000.0000.0000.000
117B163ALA0-0.001-0.00519.394-0.008-0.0080.0000.0000.0000.000
118B164GLU-1-0.773-0.85212.8970.0410.0410.0000.0000.0000.000
119B165LEU0-0.002-0.00414.336-0.013-0.0130.0000.0000.0000.000
120B166LYS10.7800.86316.3750.0550.0550.0000.0000.0000.000
121B167GLY0-0.0010.01318.6490.0010.0010.0000.0000.0000.000
122B168ILE0-0.034-0.01712.4650.0040.0040.0000.0000.0000.000
123B169PHE0-0.009-0.00712.527-0.027-0.0270.0000.0000.0000.000
124B170PRO00.0730.05317.5820.0030.0030.0000.0000.0000.000
125B171SER0-0.017-0.02521.239-0.007-0.0070.0000.0000.0000.000
126B172GLY00.0130.01420.151-0.003-0.0030.0000.0000.0000.000
127B173LEU0-0.006-0.01918.923-0.025-0.0250.0000.0000.0000.000
128B174PHE0-0.0210.00011.2020.0040.0040.0000.0000.0000.000
129B175GLN00.005-0.01116.2220.0160.0160.0000.0000.0000.000
130B176GLY00.0180.00113.5110.0250.0250.0000.0000.0000.000
131B177ASP-1-0.875-0.91113.967-0.095-0.0950.0000.0000.0000.000
132B178THR00.005-0.01614.7950.0260.0260.0000.0000.0000.000
133B179PHE0-0.028-0.01016.7260.0110.0110.0000.0000.0000.000
134B180ARG10.9300.96018.6060.0200.0200.0000.0000.0000.000
135B181ILE0-0.0180.00317.7440.0000.0000.0000.0000.0000.000
136B182THR0-0.057-0.06321.507-0.006-0.0060.0000.0000.0000.000
137B183LYS10.8240.92624.320-0.065-0.0650.0000.0000.0000.000
138B184ALA00.0770.02924.5240.0070.0070.0000.0000.0000.000
139B185ASP-1-0.825-0.93225.3800.0780.0780.0000.0000.0000.000
140B186ALA00.0310.01421.8230.0090.0090.0000.0000.0000.000
141B187ALA0-0.032-0.02420.8970.0130.0130.0000.0000.0000.000
142B188GLU-1-0.812-0.88620.8270.0700.0700.0000.0000.0000.000
143B189PHE0-0.0170.00816.9210.0010.0010.0000.0000.0000.000
144B190TRP0-0.008-0.01211.7980.0310.0310.0000.0000.0000.000
145B191ARG10.8760.91816.199-0.047-0.0470.0000.0000.0000.000
146B192LYS10.8630.92217.872-0.097-0.0970.0000.0000.0000.000
147B193ALA0-0.0210.01115.3010.0060.0060.0000.0000.0000.000
148B194PHE0-0.007-0.02811.3590.0580.0580.0000.0000.0000.000
149B195GLY00.0070.02112.409-0.028-0.0280.0000.0000.0000.000
150B196GLU-1-0.936-0.97213.892-0.039-0.0390.0000.0000.0000.000
151B197LYS10.7750.8815.490-0.269-0.2690.0000.0000.0000.000
152B198THR00.0070.0069.8740.0230.0230.0000.0000.0000.000
153B199ILE0-0.027-0.0195.7780.0100.0100.0000.0000.0000.000
154B200VAL00.0290.0346.7290.0240.0240.0000.0000.0000.000
155B201PRO00.0310.0014.772-0.157-0.085-0.001-0.003-0.0680.000
156B202TRP00.0060.0017.520-0.154-0.1540.0000.0000.0000.000
157B203LYS10.8050.8878.310-1.357-1.3570.0000.0000.0000.000
158B204SER00.0510.0368.928-0.118-0.1180.0000.0000.0000.000
159B205PHE00.0390.01510.790-0.113-0.1130.0000.0000.0000.000
160B206ARG10.9650.98212.795-0.543-0.5430.0000.0000.0000.000
161B207GLN0-0.060-0.03812.9640.0340.0340.0000.0000.0000.000
162B208ALA00.0600.02914.311-0.044-0.0440.0000.0000.0000.000
163B209LEU0-0.031-0.01816.137-0.042-0.0420.0000.0000.0000.000
164B210HIS0-0.0020.01318.559-0.021-0.0210.0000.0000.0000.000
165B211GLU-1-0.899-0.95519.4200.2180.2180.0000.0000.0000.000
166B212VAL0-0.092-0.04321.395-0.022-0.0220.0000.0000.0000.000
167B213HIS0-0.052-0.03422.601-0.016-0.0160.0000.0000.0000.000
168B214PRO00.0080.01522.9260.0170.0170.0000.0000.0000.000
169B215ILE0-0.039-0.01719.824-0.005-0.0050.0000.0000.0000.000
170B216SER0-0.013-0.03424.0060.0050.0050.0000.0000.0000.000
171B217SER0-0.009-0.00525.387-0.003-0.0030.0000.0000.0000.000
172B218GLY00.0490.01522.0320.0150.0150.0000.0000.0000.000
173B219LEU00.008-0.00222.0030.0170.0170.0000.0000.0000.000
174B220GLU-1-0.810-0.87423.8060.1790.1790.0000.0000.0000.000
175B221ALA00.0470.02119.3550.0050.0050.0000.0000.0000.000
176B222MET0-0.024-0.01617.1640.0350.0350.0000.0000.0000.000
177B223ALA00.0130.01420.178-0.003-0.0030.0000.0000.0000.000
178B224LEU00.0210.02619.597-0.007-0.0070.0000.0000.0000.000
179B225LYS10.8180.89013.812-0.424-0.4240.0000.0000.0000.000
180B226SER0-0.112-0.07217.718-0.018-0.0180.0000.0000.0000.000
181B227THR0-0.046-0.02319.944-0.030-0.0300.0000.0000.0000.000
182B228ILE00.0120.00415.927-0.016-0.0160.0000.0000.0000.000
183B229ASP-1-0.716-0.83113.5550.3500.3500.0000.0000.0000.000
184B230LEU0-0.023-0.00815.476-0.023-0.0230.0000.0000.0000.000
185B231THR0-0.046-0.06012.786-0.021-0.0210.0000.0000.0000.000
186B232CYS0-0.089-0.05414.277-0.034-0.0340.0000.0000.0000.000
187B233ASN0-0.005-0.0039.6840.0530.0530.0000.0000.0000.000
188B234ASP-1-0.750-0.8479.2140.8180.8180.0000.0000.0000.000
189B235TYR0-0.042-0.0223.6930.1730.7710.015-0.196-0.416-0.001
190B236ILE00.0090.0158.812-0.101-0.1010.0000.0000.0000.000
191B237SER00.007-0.02810.4090.0280.0280.0000.0000.0000.000
192B238VAL00.0470.01611.6800.0060.0060.0000.0000.0000.000
193B239PHE00.0180.01914.427-0.011-0.0110.0000.0000.0000.000
194B240GLU-1-0.784-0.87212.8620.2150.2150.0000.0000.0000.000
195B241PHE00.0390.01715.7350.0010.0010.0000.0000.0000.000
196B242ASP-1-0.736-0.80917.4140.0470.0470.0000.0000.0000.000
197B243ILE0-0.0100.00018.930-0.006-0.0060.0000.0000.0000.000
198B244PHE00.0090.00120.012-0.005-0.0050.0000.0000.0000.000
199B245THR0-0.024-0.03620.982-0.011-0.0110.0000.0000.0000.000
200B246ARG10.7840.87823.184-0.053-0.0530.0000.0000.0000.000
201B247LEU0-0.048-0.00223.631-0.007-0.0070.0000.0000.0000.000
202B248PHE00.0100.01124.456-0.005-0.0050.0000.0000.0000.000
203B249GLN00.0060.03527.4000.0010.0010.0000.0000.0000.000
204B250PRO0-0.004-0.00728.683-0.003-0.0030.0000.0000.0000.000
205B251TRP00.0800.01920.6410.0040.0040.0000.0000.0000.000
206B252SER00.007-0.00727.3200.0070.0070.0000.0000.0000.000
207B253SER0-0.035-0.03829.6290.0000.0000.0000.0000.0000.000
208B254LEU0-0.0110.01822.3850.0020.0020.0000.0000.0000.000
209B255LEU00.0540.02522.437-0.003-0.0030.0000.0000.0000.000
210B256ARG10.9981.00326.484-0.089-0.0890.0000.0000.0000.000
211B257ASN0-0.0130.02129.037-0.008-0.0080.0000.0000.0000.000
212B258TRP00.019-0.00824.209-0.003-0.0030.0000.0000.0000.000
213B259ASN00.0390.00127.8150.0020.0020.0000.0000.0000.000
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