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: 2NRJR

Calculation Name: 3U0J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U0J

Chain ID: B

ChEMBL ID:

UniProt ID: Q88A91

Base Structure: X-ray

Registration Date: 2023-09-22

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3044188.812182
FMO2-HF: Nuclear repulsion 2948516.614171
FMO2-HF: Total energy -95672.198011
FMO2-MP2: Total energy -95948.880507


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:29:GLU)


Summations of interaction energy for fragment #1(B:29: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.
140.776144.3120.91-1.25-3.1950.006
Interaction energy analysis for fragmet #1(B:29:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.984 / q_NPA : -1.002
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].
3B31HIS0-0.0020.0003.777-0.1771.569-0.020-0.601-1.1250.004
4B32TYR0-0.082-0.0895.790-6.584-6.557-0.001-0.001-0.0250.000
5B33SER00.005-0.0078.3381.1761.1760.0000.0000.0000.000
6B34THR0-0.025-0.0119.856-1.720-1.7200.0000.0000.0000.000
7B35GLY00.000-0.02512.292-1.200-1.2000.0000.0000.0000.000
8B36GLN0-0.025-0.00814.359-1.427-1.4270.0000.0000.0000.000
9B37ASP-1-0.771-0.89010.85427.99027.9900.0000.0000.0000.000
10B38ARG10.8810.94513.816-21.538-21.5380.0000.0000.0000.000
11B39HIS0-0.009-0.00117.128-1.394-1.3940.0000.0000.0000.000
12B40ASP-1-0.883-0.93615.54618.51118.5110.0000.0000.0000.000
13B41PHE0-0.017-0.02117.405-0.944-0.9440.0000.0000.0000.000
14B42TYR0-0.044-0.04319.166-0.692-0.6920.0000.0000.0000.000
15B43ARG10.9300.95122.084-12.965-12.9650.0000.0000.0000.000
16B44PHE0-0.068-0.02620.388-0.551-0.5510.0000.0000.0000.000
17B45ALA00.035-0.00322.400-0.555-0.5550.0000.0000.0000.000
18B46ALA0-0.036-0.01624.295-0.561-0.5610.0000.0000.0000.000
19B47ARG10.8760.93322.768-13.496-13.4960.0000.0000.0000.000
20B48LEU0-0.0470.00223.936-0.214-0.2140.0000.0000.0000.000
21B49HIS00.0010.01228.062-0.486-0.4860.0000.0000.0000.000
22B50VAL00.021-0.00730.6350.2600.2600.0000.0000.0000.000
23B51ASP-1-0.879-0.94632.5758.4358.4350.0000.0000.0000.000
24B52ALA00.0080.00335.040-0.056-0.0560.0000.0000.0000.000
25B53GLN0-0.091-0.03338.379-0.322-0.3220.0000.0000.0000.000
26B54CYS0-0.042-0.01335.409-0.063-0.0630.0000.0000.0000.000
27B55PHE0-0.050-0.02636.796-0.106-0.1060.0000.0000.0000.000
28B56GLY00.0440.01833.9940.2070.2070.0000.0000.0000.000
29B57LEU0-0.038-0.00530.864-0.090-0.0900.0000.0000.0000.000
30B58SER00.0100.00430.4170.4070.4070.0000.0000.0000.000
31B59ILE00.0510.01523.7090.1590.1590.0000.0000.0000.000
32B60ASP-1-0.815-0.87127.51411.13211.1320.0000.0000.0000.000
33B61ASP-1-0.785-0.90129.7859.6459.6450.0000.0000.0000.000
34B62LEU0-0.078-0.03525.9080.0720.0720.0000.0000.0000.000
35B63MET0-0.077-0.02322.2670.3170.3170.0000.0000.0000.000
36B64ASP-1-0.912-0.93426.69010.10110.1010.0000.0000.0000.000
37B65LYS11.0091.00728.686-10.726-10.7260.0000.0000.0000.000
38B66PHE0-0.058-0.04324.4710.0270.0270.0000.0000.0000.000
39B67SER0-0.073-0.03425.2180.4730.4730.0000.0000.0000.000
40B68ASP-1-0.820-0.88826.9909.6729.6720.0000.0000.0000.000
41B69LYS10.8770.92529.266-8.954-8.9540.0000.0000.0000.000
42B70HIS0-0.061-0.04330.317-0.166-0.1660.0000.0000.0000.000
43B71PHE00.0520.03623.867-0.052-0.0520.0000.0000.0000.000
44B72ARG10.8150.88421.762-13.728-13.7280.0000.0000.0000.000
45B73ALA0-0.065-0.02626.6820.0480.0480.0000.0000.0000.000
46B74GLU-1-0.963-0.97729.9019.4619.4610.0000.0000.0000.000
47B75HIS10.8570.93825.563-11.238-11.2380.0000.0000.0000.000
48B76PRO00.0420.01324.8570.5200.5200.0000.0000.0000.000
49B77GLU-1-0.826-0.91221.01413.10113.1010.0000.0000.0000.000
50B78TYR00.004-0.01520.0140.9320.9320.0000.0000.0000.000
51B79ARG10.8840.95021.316-13.001-13.0010.0000.0000.0000.000
52B80ASP-1-0.950-0.97717.25015.84015.8400.0000.0000.0000.000
53B81VAL0-0.0010.01516.7321.2821.2820.0000.0000.0000.000
54B82TYR0-0.012-0.01215.356-0.787-0.7870.0000.0000.0000.000
55B83PRO00.0500.01419.1470.1100.1100.0000.0000.0000.000
56B84GLU-1-0.822-0.93718.57515.52915.5290.0000.0000.0000.000
57B85GLU-1-0.740-0.83414.05121.90021.9000.0000.0000.0000.000
58B86CYS0-0.023-0.00218.134-0.107-0.1070.0000.0000.0000.000
59B87SER00.016-0.00821.347-0.583-0.5830.0000.0000.0000.000
60B88ALA00.0240.01617.963-0.402-0.4020.0000.0000.0000.000
61B89ILE0-0.007-0.00818.256-0.204-0.2040.0000.0000.0000.000
62B90TYR00.0150.01020.432-0.537-0.5370.0000.0000.0000.000
63B91MET0-0.037-0.02722.714-0.155-0.1550.0000.0000.0000.000
64B92HIS0-0.021-0.00319.071-0.183-0.1830.0000.0000.0000.000
65B93THR0-0.055-0.02522.167-0.267-0.2670.0000.0000.0000.000
66B94ALA00.0240.03924.659-0.471-0.4710.0000.0000.0000.000
67B95GLN0-0.011-0.01027.1910.2830.2830.0000.0000.0000.000
68B96ASP-1-0.822-0.90729.8309.7289.7280.0000.0000.0000.000
69B97TYR00.010-0.00826.649-0.039-0.0390.0000.0000.0000.000
70B98SER0-0.017-0.00327.5490.1130.1130.0000.0000.0000.000
71B99SER0-0.015-0.01925.379-0.278-0.2780.0000.0000.0000.000
72B100HIS0-0.092-0.06727.340-0.382-0.3820.0000.0000.0000.000
73B101LEU00.0470.03530.818-0.035-0.0350.0000.0000.0000.000
74B102VAL0-0.035-0.03234.387-0.044-0.0440.0000.0000.0000.000
75B103ARG10.8590.91936.850-7.687-7.6870.0000.0000.0000.000
76B104GLY0-0.0100.00339.6490.0380.0380.0000.0000.0000.000
77B105GLU-1-0.842-0.92237.4688.0228.0220.0000.0000.0000.000
78B106ILE00.0090.02531.7920.0970.0970.0000.0000.0000.000
79B107GLY0-0.024-0.01831.781-0.178-0.1780.0000.0000.0000.000
80B108THR0-0.050-0.03127.422-0.209-0.2090.0000.0000.0000.000
81B109PRO00.0520.02727.3510.2800.2800.0000.0000.0000.000
82B110LEU00.0670.02621.6290.2150.2150.0000.0000.0000.000
83B111TYR0-0.009-0.01621.6680.4690.4690.0000.0000.0000.000
84B112ARG10.8910.95121.887-10.614-10.6140.0000.0000.0000.000
85B113GLU-1-0.869-0.89922.77812.75012.7500.0000.0000.0000.000
86B114VAL00.0280.01217.2750.3610.3610.0000.0000.0000.000
87B115ASN00.0380.00218.6471.2021.2020.0000.0000.0000.000
88B116ASN0-0.030-0.03319.4610.3560.3560.0000.0000.0000.000
89B117TYR00.0070.02115.179-0.367-0.3670.0000.0000.0000.000
90B118LEU00.0160.00013.3840.2240.2240.0000.0000.0000.000
91B119ARG10.7880.89016.527-13.107-13.1070.0000.0000.0000.000
92B120LEU0-0.058-0.02318.954-0.334-0.3340.0000.0000.0000.000
93B121GLN00.0670.05014.2680.4560.4560.0000.0000.0000.000
94B122HIS0-0.079-0.03817.220-0.100-0.1000.0000.0000.0000.000
95B123GLU-1-0.944-0.98015.79016.21516.2150.0000.0000.0000.000
96B124ASN0-0.057-0.01410.5742.5052.5050.0000.0000.0000.000
97B125SER0-0.046-0.0278.583-1.095-1.0950.0000.0000.0000.000
98B126GLY0-0.018-0.01410.662-1.258-1.2580.0000.0000.0000.000
99B127ARG10.9160.9516.474-24.150-24.1500.0000.0000.0000.000
100B128GLU-1-0.798-0.9264.07237.60037.8760.000-0.031-0.2440.000
101B129ALA0-0.012-0.0072.4464.8826.3220.905-1.039-1.3060.002
102B130GLU-1-0.899-0.9583.35633.55533.6020.0260.422-0.4950.000
103B131ILE0-0.0050.0225.645-4.855-4.8550.0000.0000.0000.000
104B132ASP-1-0.927-0.9757.05832.54432.5440.0000.0000.0000.000
105B133ASN0-0.063-0.0078.803-2.829-2.8290.0000.0000.0000.000
106B134HIS00.0270.01810.284-2.863-2.8630.0000.0000.0000.000
107B135ASP-1-0.795-0.90313.69815.12215.1220.0000.0000.0000.000
108B136GLU-1-0.895-0.96416.74316.80716.8070.0000.0000.0000.000
109B137LYS10.8400.92317.721-13.697-13.6970.0000.0000.0000.000
110B138LEU00.020-0.00517.914-0.171-0.1710.0000.0000.0000.000
111B139SER00.0030.01413.1310.4570.4570.0000.0000.0000.000
112B140PRO00.0210.01514.1461.2691.2690.0000.0000.0000.000
113B141HIS0-0.011-0.01615.7930.4800.4800.0000.0000.0000.000
114B142ILE0-0.0130.00111.4950.3500.3500.0000.0000.0000.000
115B143LYS10.8860.9479.426-28.442-28.4420.0000.0000.0000.000
116B144MET0-0.0160.01711.6611.5181.5180.0000.0000.0000.000
117B145LEU00.006-0.00314.2270.0260.0260.0000.0000.0000.000
118B146SER0-0.017-0.0129.043-0.044-0.0440.0000.0000.0000.000
119B147SER0-0.001-0.00510.2811.1001.1000.0000.0000.0000.000
120B148ALA0-0.034-0.01111.266-0.516-0.5160.0000.0000.0000.000
121B149LEU0-0.010-0.01712.685-0.731-0.7310.0000.0000.0000.000
122B150ASN0-0.012-0.0127.262-2.509-2.5090.0000.0000.0000.000
123B151ARG10.8750.93010.988-24.831-24.8310.0000.0000.0000.000
124B152LEU0-0.010-0.00213.313-0.942-0.9420.0000.0000.0000.000
125B153MET0-0.051-0.02311.475-1.348-1.3480.0000.0000.0000.000
126B154ASP-1-0.834-0.88010.94726.00826.0080.0000.0000.0000.000
127B155VAL0-0.089-0.02613.773-0.777-0.7770.0000.0000.0000.000
128B156ALA0-0.043-0.03217.422-0.974-0.9740.0000.0000.0000.000
129B157ALA0-0.0310.00115.633-0.321-0.3210.0000.0000.0000.000
130B158PHE0-0.0190.00617.584-0.928-0.9280.0000.0000.0000.000
131B159ARG10.9280.95818.792-12.606-12.6060.0000.0000.0000.000
132B160GLY0-0.002-0.00420.901-0.545-0.5450.0000.0000.0000.000
133B161THR0-0.031-0.01623.3950.3040.3040.0000.0000.0000.000
134B162VAL0-0.0040.01222.842-0.171-0.1710.0000.0000.0000.000
135B163TYR00.001-0.01725.952-0.245-0.2450.0000.0000.0000.000
136B164ARG10.9740.99724.069-11.854-11.8540.0000.0000.0000.000
137B165GLY00.0110.01327.493-0.265-0.2650.0000.0000.0000.000
138B166ILE0-0.056-0.02326.7500.2560.2560.0000.0000.0000.000
139B167ARG10.9680.97730.387-8.400-8.4000.0000.0000.0000.000
140B168GLY0-0.044-0.02832.5800.2030.2030.0000.0000.0000.000
141B169ASP-1-0.880-0.92433.6968.3308.3300.0000.0000.0000.000
142B170LEU00.007-0.01335.2970.0960.0960.0000.0000.0000.000
143B171ASP-1-0.901-0.93732.7919.2109.2100.0000.0000.0000.000
144B172THR00.013-0.01029.5450.3020.3020.0000.0000.0000.000
145B173ILE0-0.023-0.01331.2320.2150.2150.0000.0000.0000.000
146B174ALA00.0170.00332.8610.0950.0950.0000.0000.0000.000
147B175ARG10.9620.99326.603-10.377-10.3770.0000.0000.0000.000
148B176LEU0-0.0150.00526.7110.2770.2770.0000.0000.0000.000
149B177TYR0-0.022-0.04029.4130.1270.1270.0000.0000.0000.000
150B178HIS00.0380.03029.182-0.128-0.1280.0000.0000.0000.000
151B179LEU0-0.038-0.02724.5660.1010.1010.0000.0000.0000.000
152B180PHE0-0.039-0.02727.3570.1300.1300.0000.0000.0000.000
153B181ASP-1-0.908-0.94929.0308.7538.7530.0000.0000.0000.000
154B182THR0-0.140-0.07528.5420.0090.0090.0000.0000.0000.000
155B183GLY0-0.0120.00626.4800.1770.1770.0000.0000.0000.000
156B184GLY0-0.048-0.01323.4580.5000.5000.0000.0000.0000.000
157B185ARG10.8700.92415.215-15.630-15.6300.0000.0000.0000.000
158B186TYR0-0.0060.00621.133-0.049-0.0490.0000.0000.0000.000
159B187VAL00.014-0.00615.6310.4690.4690.0000.0000.0000.000
160B188GLU-1-0.858-0.90917.15013.94513.9450.0000.0000.0000.000
161B189PRO00.018-0.01714.6060.8540.8540.0000.0000.0000.000
162B190ALA0-0.036-0.01014.2541.0441.0440.0000.0000.0000.000
163B191PHE00.0320.01512.7010.2250.2250.0000.0000.0000.000
164B192MET0-0.056-0.01216.492-1.163-1.1630.0000.0000.0000.000
165B193SER00.0230.02619.0440.2030.2030.0000.0000.0000.000
166B194THR0-0.047-0.05021.506-0.526-0.5260.0000.0000.0000.000
167B195THR00.0690.02624.0800.0070.0070.0000.0000.0000.000
168B196ARG10.9340.95725.714-11.664-11.6640.0000.0000.0000.000
169B197ILE0-0.0180.01228.254-0.292-0.2920.0000.0000.0000.000
170B198LYS10.9280.95431.843-8.560-8.5600.0000.0000.0000.000
171B199ASP-1-0.850-0.92233.3408.1558.1550.0000.0000.0000.000
172B200SER00.0040.00331.495-0.206-0.2060.0000.0000.0000.000
173B201ALA0-0.036-0.00830.4720.1480.1480.0000.0000.0000.000
174B202GLN00.002-0.00731.734-0.288-0.2880.0000.0000.0000.000
175B203VAL00.009-0.00832.398-0.036-0.0360.0000.0000.0000.000
176B204PHE0-0.026-0.03032.555-0.161-0.1610.0000.0000.0000.000
177B205GLU-1-0.854-0.90337.5007.9027.9020.0000.0000.0000.000
178B206PRO0-0.0240.00640.7600.0740.0740.0000.0000.0000.000
179B207GLY00.0180.00243.048-0.074-0.0740.0000.0000.0000.000
180B208THR0-0.062-0.04038.1460.0290.0290.0000.0000.0000.000
181B209PRO00.0210.00536.580-0.061-0.0610.0000.0000.0000.000
182B210ASN0-0.039-0.00832.307-0.073-0.0730.0000.0000.0000.000
183B211ASN00.0160.00035.0930.0430.0430.0000.0000.0000.000
184B212ILE00.0040.00830.258-0.088-0.0880.0000.0000.0000.000
185B213ALA00.0330.01831.2640.2040.2040.0000.0000.0000.000
186B214PHE00.005-0.00726.2560.0430.0430.0000.0000.0000.000
187B215GLN00.008-0.00428.195-0.178-0.1780.0000.0000.0000.000
188B216ILE00.0110.01421.6170.0420.0420.0000.0000.0000.000
189B217SER0-0.0020.00822.685-0.232-0.2320.0000.0000.0000.000
190B218LEU0-0.010-0.00718.3930.3770.3770.0000.0000.0000.000
191B219LYS10.9180.94216.132-15.359-15.3590.0000.0000.0000.000
192B220ARG10.7910.85810.588-22.763-22.7630.0000.0000.0000.000
193B221GLY00.0530.03315.4560.4680.4680.0000.0000.0000.000
194B222ALA00.0630.02415.663-0.109-0.1090.0000.0000.0000.000
195B223ASP-1-0.782-0.86717.59512.10512.1050.0000.0000.0000.000
196B224ILE00.0380.01619.1450.2370.2370.0000.0000.0000.000
197B225SER0-0.046-0.03421.725-0.436-0.4360.0000.0000.0000.000
198B226GLY0-0.032-0.02324.571-0.387-0.3870.0000.0000.0000.000
199B227SER00.007-0.02022.415-0.182-0.1820.0000.0000.0000.000
200B228SER0-0.044-0.02724.448-0.047-0.0470.0000.0000.0000.000
201B229GLN0-0.011-0.01125.693-0.270-0.2700.0000.0000.0000.000
202B230ALA00.0020.00528.333-0.489-0.4890.0000.0000.0000.000
203B231PRO00.0100.01328.3710.0820.0820.0000.0000.0000.000
204B232SER0-0.015-0.01029.4450.0640.0640.0000.0000.0000.000
205B233GLU-1-0.930-0.95728.87610.18310.1830.0000.0000.0000.000
206B234GLU-1-1.022-1.02328.00410.14110.1410.0000.0000.0000.000
207B235GLU-1-0.854-0.93823.86212.31112.3110.0000.0000.0000.000
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