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: 5JYJZ

Calculation Name: 4OPA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OPA

Chain ID: B

ChEMBL ID:

UniProt ID: Q20NS3

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1984338.276691
FMO2-HF: Nuclear repulsion 1905484.784288
FMO2-HF: Total energy -78853.492403
FMO2-MP2: Total energy -79080.784444


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:2:ASP)


Summations of interaction energy for fragment #1(B:2:ASP)
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.
19.34124.0411.533-2.92-3.3110.013
Interaction energy analysis for fragmet #1(B:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.818 / q_NPA : -0.905
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].
3B4ASN00.0370.0203.741-13.109-10.0970.053-1.712-1.3530.011
4B5THR0-0.057-0.0242.148-10.032-8.6141.481-1.175-1.7230.002
5B6VAL00.0590.0234.615-5.646-5.376-0.001-0.033-0.2350.000
6B7SER0-0.021-0.0126.879-5.116-5.1160.0000.0000.0000.000
7B8SER0-0.016-0.0287.644-3.839-3.8390.0000.0000.0000.000
8B9PHE0-0.013-0.0118.782-2.370-2.3700.0000.0000.0000.000
9B10GLN00.0260.0139.825-3.310-3.3100.0000.0000.0000.000
10B11VAL00.0190.01312.601-1.820-1.8200.0000.0000.0000.000
11B12ASP-1-0.800-0.88212.54218.89318.8930.0000.0000.0000.000
12B13CYS0-0.048-0.01914.240-1.387-1.3870.0000.0000.0000.000
13B14PHE00.0010.01316.835-1.288-1.2880.0000.0000.0000.000
14B15LEU00.0220.00517.019-1.071-1.0710.0000.0000.0000.000
15B16TRP0-0.034-0.03019.086-1.007-1.0070.0000.0000.0000.000
16B17HIS00.0550.01920.865-0.892-0.8920.0000.0000.0000.000
17B18VAL0-0.042-0.01922.736-0.674-0.6740.0000.0000.0000.000
18B19ARG10.8160.88820.365-13.688-13.6880.0000.0000.0000.000
19B20LYS10.7680.86424.865-11.009-11.0090.0000.0000.0000.000
20B21ARG10.9710.98424.990-12.117-12.1170.0000.0000.0000.000
21B22PHE0-0.0050.00228.369-0.345-0.3450.0000.0000.0000.000
22B23ALA0-0.014-0.02029.256-0.323-0.3230.0000.0000.0000.000
23B24ASP-1-0.819-0.88230.2329.8919.8910.0000.0000.0000.000
24B25GLN0-0.081-0.03132.754-0.221-0.2210.0000.0000.0000.000
25B26GLU-1-0.951-0.97234.6237.7127.7120.0000.0000.0000.000
26B27LEU0-0.021-0.00233.264-0.175-0.1750.0000.0000.0000.000
27B28GLY0-0.052-0.01131.5270.0640.0640.0000.0000.0000.000
28B29ASP-1-0.784-0.91131.4079.1629.1620.0000.0000.0000.000
29B30ALA00.0420.01231.8780.2470.2470.0000.0000.0000.000
30B31PRO00.0440.01730.0300.2660.2660.0000.0000.0000.000
31B32PHE0-0.056-0.00526.7250.4790.4790.0000.0000.0000.000
32B33LEU00.0550.03127.1820.4570.4570.0000.0000.0000.000
33B34ASP-1-0.870-0.93427.7319.9549.9540.0000.0000.0000.000
34B35ARG10.8680.92524.072-10.141-10.1410.0000.0000.0000.000
35B36LEU00.0060.01423.0600.5450.5450.0000.0000.0000.000
36B37ARG10.8700.92723.447-9.461-9.4610.0000.0000.0000.000
37B38ALA00.0030.00322.3460.2760.2760.0000.0000.0000.000
38B39ASP-1-0.768-0.87719.13114.50614.5060.0000.0000.0000.000
39B40GLN00.0080.02918.7470.6920.6920.0000.0000.0000.000
40B41ALA0-0.021-0.01119.9350.4200.4200.0000.0000.0000.000
41B42SER0-0.0080.00115.9430.8100.8100.0000.0000.0000.000
42B43LEU00.006-0.00314.4061.0151.0150.0000.0000.0000.000
43B44ARG10.9040.94515.462-12.029-12.0290.0000.0000.0000.000
44B45GLY00.0220.03415.9130.3370.3370.0000.0000.0000.000
45B46ARG10.8120.8969.375-21.631-21.6310.0000.0000.0000.000
46B47GLY00.0500.02411.5181.5991.5990.0000.0000.0000.000
47B48SER0-0.046-0.04113.2940.4650.4650.0000.0000.0000.000
48B49THR0-0.080-0.04610.413-0.245-0.2450.0000.0000.0000.000
49B50LEU0-0.044-0.0236.3261.4501.4500.0000.0000.0000.000
50B51GLY0-0.0120.0209.4071.7951.7950.0000.0000.0000.000
51B52LEU0-0.049-0.0368.6210.4760.4760.0000.0000.0000.000
52B53ASP-1-0.834-0.91412.95015.16915.1690.0000.0000.0000.000
53B54ILE00.0460.01016.0430.6020.6020.0000.0000.0000.000
54B55GLU-1-0.902-0.92517.57814.22814.2280.0000.0000.0000.000
55B56THR0-0.048-0.03416.0880.5940.5940.0000.0000.0000.000
56B57ALA00.0170.00713.9570.5820.5820.0000.0000.0000.000
57B58THR0-0.007-0.02915.2180.1430.1430.0000.0000.0000.000
58B59ARG10.8190.88618.417-14.254-14.2540.0000.0000.0000.000
59B60ALA0-0.012-0.00314.382-0.327-0.3270.0000.0000.0000.000
60B61GLY00.0410.00115.6670.2370.2370.0000.0000.0000.000
61B62LYS10.7930.88316.502-13.889-13.8890.0000.0000.0000.000
62B63GLN00.0190.01415.773-1.056-1.0560.0000.0000.0000.000
63B64ILE0-0.023-0.00312.769-0.007-0.0070.0000.0000.0000.000
64B65VAL00.001-0.00816.957-0.318-0.3180.0000.0000.0000.000
65B66GLU-1-0.827-0.90719.71212.99612.9960.0000.0000.0000.000
66B67ARG10.8930.94617.078-17.984-17.9840.0000.0000.0000.000
67B68ILE00.0000.00617.574-0.436-0.4360.0000.0000.0000.000
68B69LEU0-0.029-0.01621.304-0.497-0.4970.0000.0000.0000.000
69B70GLU-1-0.782-0.89124.24910.93210.9320.0000.0000.0000.000
70B71GLU-1-0.929-0.98019.87316.09116.0910.0000.0000.0000.000
71B72GLU-1-0.880-0.90424.10312.45712.4570.0000.0000.0000.000
72B73SER0-0.058-0.04325.629-0.538-0.5380.0000.0000.0000.000
73B74ASP-1-0.876-0.94728.0839.4859.4850.0000.0000.0000.000
74B75GLU-1-0.837-0.92530.52710.09110.0910.0000.0000.0000.000
75B76ALA0-0.091-0.03433.155-0.111-0.1110.0000.0000.0000.000
76B77LEU0-0.080-0.04327.4580.0100.0100.0000.0000.0000.000
77B78LYS10.7820.90028.109-10.451-10.4510.0000.0000.0000.000
78B79MET0-0.091-0.04527.997-0.387-0.3870.0000.0000.0000.000
79B80PRO00.0390.02827.9730.3690.3690.0000.0000.0000.000
80B81ALA0-0.037-0.00825.450-0.130-0.1300.0000.0000.0000.000
81B82SER0-0.055-0.03227.428-0.142-0.1420.0000.0000.0000.000
82B83ARG10.7600.86029.382-11.056-11.0560.0000.0000.0000.000
83B84TYR00.0260.00031.9310.0610.0610.0000.0000.0000.000
84B85LEU0-0.018-0.00131.794-0.057-0.0570.0000.0000.0000.000
85B86THR0-0.025-0.03135.965-0.062-0.0620.0000.0000.0000.000
86B87ASP-1-0.706-0.78438.1588.5608.5600.0000.0000.0000.000
87B88MET0-0.096-0.02040.647-0.293-0.2930.0000.0000.0000.000
88B89THR00.009-0.02743.7690.0150.0150.0000.0000.0000.000
89B90LEU00.0330.00046.5530.0340.0340.0000.0000.0000.000
90B91GLU-1-0.788-0.83647.9856.2456.2450.0000.0000.0000.000
91B92GLU-1-0.713-0.81146.7437.0367.0360.0000.0000.0000.000
92B93MET0-0.039-0.01241.9960.0940.0940.0000.0000.0000.000
93B94SER0-0.088-0.05846.324-0.009-0.0090.0000.0000.0000.000
94B95ARG10.7610.85649.545-6.398-6.3980.0000.0000.0000.000
95B96ASP-1-0.886-0.93550.7576.1646.1640.0000.0000.0000.000
96B97TRP0-0.069-0.05647.103-0.035-0.0350.0000.0000.0000.000
97B98PHE0-0.014-0.01252.755-0.002-0.0020.0000.0000.0000.000
98B99MET0-0.0410.00449.7950.1000.1000.0000.0000.0000.000
99B100LEU0-0.003-0.00653.519-0.081-0.0810.0000.0000.0000.000
100B101MET0-0.058-0.03554.348-0.103-0.1030.0000.0000.0000.000
101B102PRO0-0.006-0.01151.4910.1410.1410.0000.0000.0000.000
102B103LYS10.8570.93845.528-7.051-7.0510.0000.0000.0000.000
103B104GLN00.021-0.00345.3030.1650.1650.0000.0000.0000.000
104B105LYS10.9250.96938.012-8.452-8.4520.0000.0000.0000.000
105B106VAL00.0240.02439.7170.0890.0890.0000.0000.0000.000
106B107ALA0-0.040-0.03735.7510.0130.0130.0000.0000.0000.000
107B108GLY00.0450.03333.6160.0510.0510.0000.0000.0000.000
108B109SER0-0.017-0.03434.1610.0730.0730.0000.0000.0000.000
109B110LEU00.0050.02033.530-0.089-0.0890.0000.0000.0000.000
110B111CYS0-0.040-0.03037.646-0.162-0.1620.0000.0000.0000.000
111B112ILE00.0050.02137.5570.0050.0050.0000.0000.0000.000
112B113ARG10.8350.87641.558-7.295-7.2950.0000.0000.0000.000
113B114MET00.0040.02642.8110.1140.1140.0000.0000.0000.000
114B115ASP-1-0.742-0.86647.1086.0106.0100.0000.0000.0000.000
115B116GLN0-0.022-0.02249.2300.1920.1920.0000.0000.0000.000
116B117ALA0-0.007-0.00351.764-0.048-0.0480.0000.0000.0000.000
117B118ILE0-0.053-0.01250.517-0.087-0.0870.0000.0000.0000.000
118B119MET00.0520.04150.9840.0880.0880.0000.0000.0000.000
119B120ASP-1-0.875-0.92051.4045.9245.9240.0000.0000.0000.000
120B121LYS10.7800.88450.609-6.138-6.1380.0000.0000.0000.000
121B122ASN0-0.014-0.00547.7370.2270.2270.0000.0000.0000.000
122B123ILE0-0.009-0.02044.175-0.079-0.0790.0000.0000.0000.000
123B124ILE0-0.084-0.02440.9750.1500.1500.0000.0000.0000.000
124B125LEU00.0000.00338.117-0.110-0.1100.0000.0000.0000.000
125B126LYS10.7990.87039.869-7.173-7.1730.0000.0000.0000.000
126B127ALA0-0.005-0.02736.492-0.069-0.0690.0000.0000.0000.000
127B128ASN00.0170.01738.0760.0540.0540.0000.0000.0000.000
128B129PHE0-0.012-0.01731.038-0.013-0.0130.0000.0000.0000.000
129B130SER00.023-0.01631.296-0.162-0.1620.0000.0000.0000.000
130B131VAL0-0.035-0.02027.4550.1970.1970.0000.0000.0000.000
131B132ILE00.0600.02824.185-0.164-0.1640.0000.0000.0000.000
132B133PHE00.0280.01720.3700.5250.5250.0000.0000.0000.000
133B134ASP-1-0.811-0.88621.41913.70513.7050.0000.0000.0000.000
134B135ARG10.8830.93618.951-15.411-15.4110.0000.0000.0000.000
135B136LEU00.0080.01924.716-0.244-0.2440.0000.0000.0000.000
136B137GLU-1-0.827-0.86426.53511.46311.4630.0000.0000.0000.000
137B138THR0-0.019-0.01828.282-0.125-0.1250.0000.0000.0000.000
138B139LEU0-0.018-0.00331.819-0.141-0.1410.0000.0000.0000.000
139B140ILE0-0.041-0.01734.666-0.100-0.1000.0000.0000.0000.000
140B141LEU0-0.028-0.03138.095-0.173-0.1730.0000.0000.0000.000
141B142LEU00.0040.01436.5800.1180.1180.0000.0000.0000.000
142B143ARG10.7860.86539.959-7.056-7.0560.0000.0000.0000.000
143B144ALA00.0030.00742.4950.1460.1460.0000.0000.0000.000
144B145PHE00.003-0.00744.230-0.177-0.1770.0000.0000.0000.000
145B146THR0-0.003-0.03846.9640.1320.1320.0000.0000.0000.000
146B147GLU-1-0.783-0.86649.5706.6786.6780.0000.0000.0000.000
147B148GLU-1-0.892-0.91651.1916.0596.0590.0000.0000.0000.000
148B149GLY00.0000.00550.245-0.064-0.0640.0000.0000.0000.000
149B150ALA00.0060.00451.3210.0000.0000.0000.0000.0000.000
150B151ILE0-0.021-0.00547.2280.1100.1100.0000.0000.0000.000
151B152VAL00.008-0.00147.500-0.128-0.1280.0000.0000.0000.000
152B153GLY00.021-0.00745.1280.0130.0130.0000.0000.0000.000
153B154GLU-1-0.801-0.86743.1217.0687.0680.0000.0000.0000.000
154B155ILE00.0020.00136.9580.0490.0490.0000.0000.0000.000
155B156SER00.0360.01739.976-0.027-0.0270.0000.0000.0000.000
156B157PRO00.0210.01236.9660.0150.0150.0000.0000.0000.000
157B158LEU0-0.027-0.00538.528-0.281-0.2810.0000.0000.0000.000
158B159PRO0-0.010-0.01839.3240.1540.1540.0000.0000.0000.000
159B160SER0-0.030-0.00240.8290.0630.0630.0000.0000.0000.000
160B161LEU0-0.020-0.00337.252-0.035-0.0350.0000.0000.0000.000
161B162PRO00.007-0.00132.5420.0540.0540.0000.0000.0000.000
162B163GLY00.0330.03631.678-0.116-0.1160.0000.0000.0000.000
163B164HIS00.0250.03030.8590.2700.2700.0000.0000.0000.000
164B165THR00.001-0.03325.8020.3110.3110.0000.0000.0000.000
165B166ASP-1-0.834-0.93924.46212.74712.7470.0000.0000.0000.000
166B167GLU-1-0.834-0.90524.04712.81812.8180.0000.0000.0000.000
167B168ASP-1-0.855-0.88327.13210.55610.5560.0000.0000.0000.000
168B169VAL00.014-0.00330.526-0.373-0.3730.0000.0000.0000.000
169B170LYS10.8150.91625.154-12.861-12.8610.0000.0000.0000.000
170B171ASN0-0.053-0.04228.088-0.388-0.3880.0000.0000.0000.000
171B172ALA0-0.042-0.02131.913-0.341-0.3410.0000.0000.0000.000
172B173ILE00.0340.00732.892-0.358-0.3580.0000.0000.0000.000
173B174GLY00.0300.02634.001-0.228-0.2280.0000.0000.0000.000
174B175VAL0-0.073-0.04435.165-0.274-0.2740.0000.0000.0000.000
175B176LEU0-0.024-0.01237.904-0.270-0.2700.0000.0000.0000.000
176B177ILE00.0140.01036.110-0.230-0.2300.0000.0000.0000.000
177B178GLY00.0810.04638.916-0.199-0.1990.0000.0000.0000.000
178B179GLY0-0.062-0.04140.480-0.216-0.2160.0000.0000.0000.000
179B180LEU00.021-0.00843.000-0.238-0.2380.0000.0000.0000.000
180B181GLU-1-0.858-0.93540.5517.9067.9060.0000.0000.0000.000
181B182TRP0-0.102-0.05042.223-0.186-0.1860.0000.0000.0000.000
182B183ASN0-0.068-0.02746.145-0.129-0.1290.0000.0000.0000.000
183B184ASP-1-0.877-0.94448.2716.3346.3340.0000.0000.0000.000
184B185ASN0-0.100-0.05746.681-0.158-0.1580.0000.0000.0000.000
185B186THR00.0190.01244.7240.1600.1600.0000.0000.0000.000
186B187VAL0-0.015-0.00940.628-0.086-0.0860.0000.0000.0000.000
187B188ARG10.8050.88540.342-6.951-6.9510.0000.0000.0000.000
188B189VAL00.0400.01135.036-0.056-0.0560.0000.0000.0000.000
189B190SER00.008-0.01036.9980.0930.0930.0000.0000.0000.000
190B191GLU-1-0.907-0.97033.47210.05510.0550.0000.0000.0000.000
191B192THR00.017-0.00332.9820.3930.3930.0000.0000.0000.000
192B193LEU00.0110.00331.8830.4040.4040.0000.0000.0000.000
193B194GLN0-0.062-0.04431.4180.5100.5100.0000.0000.0000.000
194B195ARG10.8870.95426.912-11.054-11.0540.0000.0000.0000.000
195B196PHE0-0.056-0.03726.5020.5460.5460.0000.0000.0000.000
196B197ALA00.0210.00827.6310.2690.2690.0000.0000.0000.000
197B198TRP0-0.094-0.03625.821-0.347-0.3470.0000.0000.0000.000