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: KG8G3

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1982274.767632
FMO2-HF: Nuclear repulsion 1903423.625775
FMO2-HF: Total energy -78851.141857
FMO2-MP2: Total energy -79078.755113


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.
16.23918.3485.191-2.844-4.4560.013
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 : -0.864 / q_NPA : -0.946
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].
3B4ASN00.0850.0143.599-16.223-12.5990.086-1.943-1.7670.016
4B5THR0-0.088-0.0091.979-7.968-9.9025.106-0.801-2.371-0.003
5B6VAL00.0820.0234.613-6.170-5.751-0.001-0.100-0.3180.000
6B7SER0-0.058-0.0146.663-5.512-5.5120.0000.0000.0000.000
7B8SER0-0.028-0.0257.565-4.227-4.2270.0000.0000.0000.000
8B9PHE0-0.030-0.0158.674-2.541-2.5410.0000.0000.0000.000
9B10GLN00.0490.02410.158-3.504-3.5040.0000.0000.0000.000
10B11VAL00.0490.02812.345-1.861-1.8610.0000.0000.0000.000
11B12ASP-1-0.802-0.85312.68418.81618.8160.0000.0000.0000.000
12B13CYS0-0.067-0.02714.278-1.458-1.4580.0000.0000.0000.000
13B14PHE00.0270.00716.802-1.391-1.3910.0000.0000.0000.000
14B15LEU00.011-0.00617.512-1.151-1.1510.0000.0000.0000.000
15B16TRP0-0.075-0.04419.122-0.962-0.9620.0000.0000.0000.000
16B17HIS00.0380.01720.963-0.764-0.7640.0000.0000.0000.000
17B18VAL0-0.049-0.02322.290-0.736-0.7360.0000.0000.0000.000
18B19ARG10.8670.93520.309-13.951-13.9510.0000.0000.0000.000
19B20LYS10.8340.92925.089-11.227-11.2270.0000.0000.0000.000
20B21ARG10.9690.98825.824-12.037-12.0370.0000.0000.0000.000
21B22PHE0-0.0020.00128.535-0.360-0.3600.0000.0000.0000.000
22B23ALA0-0.018-0.03329.424-0.340-0.3400.0000.0000.0000.000
23B24ASP-1-0.869-0.93131.0359.9219.9210.0000.0000.0000.000
24B25GLN0-0.095-0.03433.010-0.196-0.1960.0000.0000.0000.000
25B26GLU-1-0.961-0.97734.7647.7917.7910.0000.0000.0000.000
26B27LEU0-0.043-0.01633.589-0.181-0.1810.0000.0000.0000.000
27B28GLY0-0.055-0.01631.7990.0000.0000.0000.0000.0000.000
28B29ASP-1-0.836-0.92732.2559.0269.0260.0000.0000.0000.000
29B30ALA00.029-0.00432.2970.2470.2470.0000.0000.0000.000
30B31PRO00.0490.03030.1350.2960.2960.0000.0000.0000.000
31B32PHE00.0180.00626.6860.5400.5400.0000.0000.0000.000
32B33LEU00.0450.02427.3610.4840.4840.0000.0000.0000.000
33B34ASP-1-0.940-0.95827.9849.9609.9600.0000.0000.0000.000
34B35ARG10.9360.95223.425-10.533-10.5330.0000.0000.0000.000
35B36LEU0-0.0180.00123.4380.5590.5590.0000.0000.0000.000
36B37ARG10.9250.95623.751-9.708-9.7080.0000.0000.0000.000
37B38ALA0-0.009-0.00322.9360.3290.3290.0000.0000.0000.000
38B39ASP-1-0.769-0.89719.33814.44314.4430.0000.0000.0000.000
39B40GLN0-0.0210.00618.9590.7480.7480.0000.0000.0000.000
40B41ALA0-0.047-0.02520.1330.5140.5140.0000.0000.0000.000
41B42SER0-0.007-0.00516.4580.8150.8150.0000.0000.0000.000
42B43LEU00.001-0.00514.4531.0991.0990.0000.0000.0000.000
43B44ARG10.9520.96915.779-12.279-12.2790.0000.0000.0000.000
44B45GLY00.0020.02116.3770.3140.3140.0000.0000.0000.000
45B46ARG10.8310.87410.832-20.962-20.9620.0000.0000.0000.000
46B47GLY00.0360.02611.3272.0462.0460.0000.0000.0000.000
47B48SER0-0.027-0.01513.506-0.142-0.1420.0000.0000.0000.000
48B49THR0-0.059-0.03110.020-0.072-0.0720.0000.0000.0000.000
49B50LEU0-0.051-0.0106.1011.1891.1890.0000.0000.0000.000
50B51GLY00.0090.0269.2651.7781.7780.0000.0000.0000.000
51B52LEU0-0.058-0.0498.6431.1761.1760.0000.0000.0000.000
52B53ASP-1-0.851-0.90512.86516.27816.2780.0000.0000.0000.000
53B54ILE00.0200.00016.0140.5790.5790.0000.0000.0000.000
54B55GLU-1-0.902-0.92917.63614.64414.6440.0000.0000.0000.000
55B56THR00.0320.00516.201-0.214-0.2140.0000.0000.0000.000
56B57ALA00.002-0.00113.8950.5360.5360.0000.0000.0000.000
57B58THR0-0.022-0.03615.3620.1790.1790.0000.0000.0000.000
58B59ARG10.8600.93118.276-14.759-14.7590.0000.0000.0000.000
59B60ALA0-0.018-0.01413.524-0.317-0.3170.0000.0000.0000.000
60B61GLY00.0620.01415.3990.2240.2240.0000.0000.0000.000
61B62LYS10.8530.92916.173-14.332-14.3320.0000.0000.0000.000
62B63GLN00.0210.00815.388-1.372-1.3720.0000.0000.0000.000
63B64ILE0-0.056-0.01512.527-0.143-0.1430.0000.0000.0000.000
64B65VAL00.0190.00416.720-0.282-0.2820.0000.0000.0000.000
65B66GLU-1-0.871-0.94619.61613.23013.2300.0000.0000.0000.000
66B67ARG10.9160.96816.241-18.943-18.9430.0000.0000.0000.000
67B68ILE00.0110.00916.967-0.379-0.3790.0000.0000.0000.000
68B69LEU0-0.023-0.01820.987-0.524-0.5240.0000.0000.0000.000
69B70GLU-1-0.827-0.89723.78311.17111.1710.0000.0000.0000.000
70B71GLU-1-1.001-1.01620.10915.79115.7910.0000.0000.0000.000
71B72GLU-1-0.953-0.94424.40912.42112.4210.0000.0000.0000.000
72B73SER0-0.014-0.02725.942-0.464-0.4640.0000.0000.0000.000
73B74ASP-1-0.893-0.95828.35910.06610.0660.0000.0000.0000.000
74B75GLU-1-0.862-0.95030.7979.7309.7300.0000.0000.0000.000
75B76ALA0-0.077-0.02332.6570.0010.0010.0000.0000.0000.000
76B77LEU0-0.057-0.03227.398-0.037-0.0370.0000.0000.0000.000
77B78LYS10.8390.95728.111-10.279-10.2790.0000.0000.0000.000
78B79MET0-0.112-0.06427.445-0.336-0.3360.0000.0000.0000.000
79B80PRO00.0300.02427.5510.3740.3740.0000.0000.0000.000
80B81ALA0-0.014-0.02425.051-0.121-0.1210.0000.0000.0000.000
81B82SER0-0.064-0.02527.0820.0570.0570.0000.0000.0000.000
82B83ARG10.8150.89629.202-10.963-10.9630.0000.0000.0000.000
83B84TYR00.0220.00131.5920.0510.0510.0000.0000.0000.000
84B85LEU0-0.025-0.00231.272-0.117-0.1170.0000.0000.0000.000
85B86THR0-0.025-0.02835.537-0.087-0.0870.0000.0000.0000.000
86B87ASP-1-0.735-0.80737.4948.7058.7050.0000.0000.0000.000
87B88MET0-0.078-0.02540.229-0.270-0.2700.0000.0000.0000.000
88B89THR0-0.002-0.00443.4350.0120.0120.0000.0000.0000.000
89B90LEU00.027-0.00746.0040.0630.0630.0000.0000.0000.000
90B91GLU-1-0.797-0.88147.6326.2946.2940.0000.0000.0000.000
91B92GLU-1-0.828-0.91146.2527.0027.0020.0000.0000.0000.000
92B93MET0-0.041-0.02642.1450.0790.0790.0000.0000.0000.000
93B94SER0-0.105-0.03045.980-0.025-0.0250.0000.0000.0000.000
94B95ARG10.7860.87749.185-6.418-6.4180.0000.0000.0000.000
95B96ASP-1-0.887-0.92950.3496.2236.2230.0000.0000.0000.000
96B97TRP0-0.043-0.03546.828-0.065-0.0650.0000.0000.0000.000
97B98PHE0-0.027-0.02852.3670.0080.0080.0000.0000.0000.000
98B99MET0-0.0390.00749.0000.0740.0740.0000.0000.0000.000
99B100LEU0-0.015-0.01053.021-0.102-0.1020.0000.0000.0000.000
100B101MET0-0.070-0.03953.929-0.102-0.1020.0000.0000.0000.000
101B102PRO00.010-0.00251.1100.1480.1480.0000.0000.0000.000
102B103LYS10.9580.99545.057-7.159-7.1590.0000.0000.0000.000
103B104GLN0-0.010-0.01445.1390.0800.0800.0000.0000.0000.000
104B105LYS10.9280.96537.607-8.529-8.5290.0000.0000.0000.000
105B106VAL00.0100.01539.5110.0740.0740.0000.0000.0000.000
106B107ALA0-0.060-0.03835.5550.0090.0090.0000.0000.0000.000
107B108GLY00.0360.02134.5880.1750.1750.0000.0000.0000.000
108B109SER00.033-0.02534.4370.0630.0630.0000.0000.0000.000
109B110LEU00.0420.03233.312-0.027-0.0270.0000.0000.0000.000
110B111CYS0-0.077-0.03137.594-0.151-0.1510.0000.0000.0000.000
111B112ILE00.0020.00637.1060.0650.0650.0000.0000.0000.000
112B113ARG10.9220.94541.236-7.214-7.2140.0000.0000.0000.000
113B114MET00.0150.03342.8400.1140.1140.0000.0000.0000.000
114B115ASP-1-0.753-0.86746.5036.0726.0720.0000.0000.0000.000
115B116GLN00.012-0.01849.0710.1110.1110.0000.0000.0000.000
116B117ALA0-0.020-0.00151.091-0.037-0.0370.0000.0000.0000.000
117B118ILE0-0.065-0.02049.750-0.099-0.0990.0000.0000.0000.000
118B119MET00.0410.01050.6250.0590.0590.0000.0000.0000.000
119B120ASP-1-0.940-0.95150.8996.0936.0930.0000.0000.0000.000
120B121LYS10.9150.95950.011-6.129-6.1290.0000.0000.0000.000
121B122ASN0-0.032-0.01547.1010.3090.3090.0000.0000.0000.000
122B123ILE0-0.015-0.01443.595-0.070-0.0700.0000.0000.0000.000
123B124ILE0-0.086-0.02040.3200.1800.1800.0000.0000.0000.000
124B125LEU0-0.0040.00437.582-0.127-0.1270.0000.0000.0000.000
125B126LYS10.8980.94139.044-7.256-7.2560.0000.0000.0000.000
126B127ALA00.022-0.01136.238-0.073-0.0730.0000.0000.0000.000
127B128ASN00.0240.02837.6160.1030.1030.0000.0000.0000.000
128B129PHE0-0.006-0.03430.5050.0190.0190.0000.0000.0000.000
129B130SER00.0520.02331.416-0.169-0.1690.0000.0000.0000.000
130B131VAL0-0.021-0.01226.8940.1760.1760.0000.0000.0000.000
131B132ILE00.0340.00624.181-0.204-0.2040.0000.0000.0000.000
132B133PHE00.0300.01520.3490.6280.6280.0000.0000.0000.000
133B134ASP-1-0.861-0.95221.18814.02814.0280.0000.0000.0000.000
134B135ARG10.9100.97818.595-15.726-15.7260.0000.0000.0000.000
135B136LEU0-0.0080.00824.000-0.299-0.2990.0000.0000.0000.000
136B137GLU-1-0.852-0.91326.40211.43511.4350.0000.0000.0000.000
137B138THR0-0.014-0.00228.095-0.111-0.1110.0000.0000.0000.000
138B139LEU00.0030.00431.659-0.174-0.1740.0000.0000.0000.000
139B140ILE0-0.088-0.01834.295-0.102-0.1020.0000.0000.0000.000
140B141LEU0-0.041-0.03837.885-0.173-0.1730.0000.0000.0000.000
141B142LEU00.0210.02836.4280.1140.1140.0000.0000.0000.000
142B143ARG10.7930.87439.611-7.100-7.1000.0000.0000.0000.000
143B144ALA00.0020.00842.2800.1380.1380.0000.0000.0000.000
144B145PHE0-0.022-0.02443.922-0.172-0.1720.0000.0000.0000.000
145B146THR00.0290.01846.5800.0610.0610.0000.0000.0000.000
146B147GLU-1-0.883-0.95049.3586.4916.4910.0000.0000.0000.000
147B148GLU-1-0.951-0.97650.4646.0266.0260.0000.0000.0000.000
148B149GLY0-0.0010.00649.989-0.078-0.0780.0000.0000.0000.000
149B150ALA0-0.0060.00150.8420.0250.0250.0000.0000.0000.000
150B151ILE00.0000.00447.0340.1110.1110.0000.0000.0000.000
151B152VAL00.0110.00346.819-0.123-0.1230.0000.0000.0000.000
152B153GLY00.012-0.00944.7210.0210.0210.0000.0000.0000.000
153B154GLU-1-0.841-0.92742.8147.1697.1690.0000.0000.0000.000
154B155ILE00.0210.02336.4540.0340.0340.0000.0000.0000.000
155B156SER00.003-0.01339.706-0.030-0.0300.0000.0000.0000.000
156B157PRO00.0290.03136.783-0.022-0.0220.0000.0000.0000.000
157B158LEU0-0.061-0.02338.230-0.275-0.2750.0000.0000.0000.000
158B159PRO00.009-0.00738.8460.1680.1680.0000.0000.0000.000
159B160SER0-0.036-0.00540.2750.1080.1080.0000.0000.0000.000
160B161LEU0-0.043-0.00737.151-0.007-0.0070.0000.0000.0000.000
161B162PRO00.0230.00932.7870.0490.0490.0000.0000.0000.000
162B163GLY00.0340.04431.466-0.138-0.1380.0000.0000.0000.000
163B164HIS00.0200.01630.8960.1500.1500.0000.0000.0000.000
164B165THR0-0.002-0.00425.8140.2940.2940.0000.0000.0000.000
165B166ASP-1-0.819-0.93223.96913.02213.0220.0000.0000.0000.000
166B167GLU-1-0.873-0.93023.25813.20513.2050.0000.0000.0000.000
167B168ASP-1-0.872-0.93626.69910.45310.4530.0000.0000.0000.000
168B169VAL0-0.019-0.01129.733-0.431-0.4310.0000.0000.0000.000
169B170LYS10.8980.95524.629-13.081-13.0810.0000.0000.0000.000
170B171ASN0-0.011-0.01728.350-0.324-0.3240.0000.0000.0000.000
171B172ALA0-0.032-0.02231.407-0.338-0.3380.0000.0000.0000.000
172B173ILE00.009-0.00232.592-0.371-0.3710.0000.0000.0000.000
173B174GLY00.0280.02533.638-0.255-0.2550.0000.0000.0000.000
174B175VAL0-0.082-0.04834.853-0.284-0.2840.0000.0000.0000.000
175B176LEU0-0.024-0.00437.464-0.286-0.2860.0000.0000.0000.000
176B177ILE00.0190.00535.848-0.218-0.2180.0000.0000.0000.000
177B178GLY00.0670.04638.766-0.159-0.1590.0000.0000.0000.000
178B179GLY0-0.081-0.08140.195-0.223-0.2230.0000.0000.0000.000
179B180LEU00.001-0.01242.280-0.197-0.1970.0000.0000.0000.000
180B181GLU-1-0.850-0.93440.2597.9737.9730.0000.0000.0000.000
181B182TRP0-0.105-0.04141.843-0.174-0.1740.0000.0000.0000.000
182B183ASN0-0.125-0.05045.938-0.114-0.1140.0000.0000.0000.000
183B184ASP-1-0.891-0.95047.6306.4426.4420.0000.0000.0000.000
184B185ASN0-0.084-0.04546.260-0.207-0.2070.0000.0000.0000.000
185B186THR00.0220.01143.9800.1640.1640.0000.0000.0000.000
186B187VAL0-0.006-0.00440.344-0.076-0.0760.0000.0000.0000.000
187B188ARG10.9370.97039.645-7.143-7.1430.0000.0000.0000.000
188B189VAL00.0500.02134.403-0.110-0.1100.0000.0000.0000.000
189B190SER0-0.030-0.03436.6070.0720.0720.0000.0000.0000.000
190B191GLU-1-0.892-0.96033.06610.16310.1630.0000.0000.0000.000
191B192THR00.044-0.00232.7330.3770.3770.0000.0000.0000.000
192B193LEU0-0.016-0.01031.5040.4280.4280.0000.0000.0000.000
193B194GLN0-0.090-0.04531.1170.4660.4660.0000.0000.0000.000
194B195ARG10.9070.97426.409-11.215-11.2150.0000.0000.0000.000
195B196PHE0-0.077-0.04426.2240.4630.4630.0000.0000.0000.000
196B197ALA00.0090.00327.1040.3540.3540.0000.0000.0000.000
197B198TRP0-0.061-0.02125.242-0.039-0.0390.0000.0000.0000.000