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

tag_button

FMODB ID: QY9JY

Calculation Name: 5DUD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUD

Chain ID: B

ChEMBL ID:

UniProt ID: P0AAV4

Base Structure: X-ray

Registration Date: 2023-09-20

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301469.219038
FMO2-HF: Nuclear repulsion 2220926.620857
FMO2-HF: Total energy -80542.598181
FMO2-MP2: Total energy -80781.150064


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:3:ARG)


Summations of interaction energy for fragment #1(B:3:ARG)
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.
-249.98-244.735.071-20.623-19.724-0.239
Interaction energy analysis for fragmet #1(B:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.796 / q_NPA : 0.878
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].
3B5ARG10.9250.9562.04816.97419.7746.385-4.061-5.124-0.050
4B6CYS00.0160.0074.7242.3862.462-0.001-0.009-0.0650.000
5B7TYR0-0.0200.0127.2401.9791.9790.0000.0000.0000.000
6B8LEU00.0140.01110.6690.4100.4100.0000.0000.0000.000
7B9ILE0-0.041-0.01014.0440.3790.3790.0000.0000.0000.000
8B10GLY0-0.008-0.00816.6160.6910.6910.0000.0000.0000.000
9B11GLU-1-0.918-0.97018.375-14.091-14.0910.0000.0000.0000.000
10B12THR00.001-0.00920.0890.3030.3030.0000.0000.0000.000
11B13ALA00.0080.00616.7470.0930.0930.0000.0000.0000.000
12B14VAL0-0.0210.00310.437-0.148-0.1480.0000.0000.0000.000
13B15VAL0-0.003-0.00911.3470.4200.4200.0000.0000.0000.000
14B16LEU0-0.0010.0195.570-1.853-1.8530.0000.0000.0000.000
15B17GLU-1-0.900-0.9737.014-28.867-28.8670.0000.0000.0000.000
16B18LEU0-0.020-0.0293.874-6.314-5.9990.001-0.101-0.2150.000
17B19GLU-1-0.910-0.9411.834-52.133-54.72315.299-6.963-5.745-0.058
18B20PRO00.000-0.0044.1982.3142.4140.000-0.031-0.0690.000
19B21PRO0-0.029-0.0146.2141.7301.7300.0000.0000.0000.000
20B22VAL00.0340.0277.539-1.188-1.1880.0000.0000.0000.000
21B23THR0-0.005-0.0048.1420.5430.5430.0000.0000.0000.000
22B24LEU00.0600.04010.825-0.652-0.6520.0000.0000.0000.000
23B25ALA0-0.013-0.00911.3100.0620.0620.0000.0000.0000.000
24B26SER0-0.007-0.0247.838-1.412-1.4120.0000.0000.0000.000
25B27GLN00.0310.0019.821-1.958-1.9580.0000.0000.0000.000
26B28LYS10.8140.90412.74916.72616.7260.0000.0000.0000.000
27B29ARG10.8380.9169.90925.65625.6560.0000.0000.0000.000
28B30ILE00.0080.01510.0150.1210.1210.0000.0000.0000.000
29B31TRP0-0.017-0.01213.3190.6680.6680.0000.0000.0000.000
30B32ARG10.8030.94714.49717.54317.5430.0000.0000.0000.000
31B33LEU0-0.003-0.01210.0950.4200.4200.0000.0000.0000.000
32B34ALA00.010-0.01014.0940.4210.4210.0000.0000.0000.000
33B35GLN0-0.054-0.03317.0120.5080.5080.0000.0000.0000.000
34B36ARG10.9500.98914.43319.17319.1730.0000.0000.0000.000
35B37LEU0-0.033-0.03113.3820.3420.3420.0000.0000.0000.000
36B38VAL00.0240.00917.3800.3370.3370.0000.0000.0000.000
37B39ASP-1-0.909-0.92820.851-12.928-12.9280.0000.0000.0000.000
38B40MET0-0.078-0.01216.5420.2910.2910.0000.0000.0000.000
39B41PRO00.020-0.00722.386-0.010-0.0100.0000.0000.0000.000
40B42ASN0-0.030-0.04818.793-0.320-0.3200.0000.0000.0000.000
41B43VAL00.0080.02017.417-0.329-0.3290.0000.0000.0000.000
42B44VAL0-0.070-0.02120.4180.4810.4810.0000.0000.0000.000
43B45GLU-1-0.881-0.94720.953-12.299-12.2990.0000.0000.0000.000
44B46ALA00.001-0.01217.000-0.866-0.8660.0000.0000.0000.000
45B47ILE0-0.0040.00517.8800.4840.4840.0000.0000.0000.000
46B48PRO0-0.008-0.00215.610-1.040-1.0400.0000.0000.0000.000
47B49GLY00.0430.02114.4791.2021.2020.0000.0000.0000.000
48B50MET0-0.049-0.01712.4040.3980.3980.0000.0000.0000.000
49B51ASN00.019-0.0076.6610.4430.4430.0000.0000.0000.000
50B52ASN00.0100.0078.376-1.704-1.7040.0000.0000.0000.000
51B53ILE00.0100.01110.8151.9751.9750.0000.0000.0000.000
52B54THR0-0.0030.00912.350-1.576-1.5760.0000.0000.0000.000
53B55VAL0-0.011-0.00213.0341.1261.1260.0000.0000.0000.000
54B56ILE00.0090.00715.718-0.274-0.2740.0000.0000.0000.000
55B57LEU0-0.008-0.01915.7200.0850.0850.0000.0000.0000.000
56B58ARG10.9120.95619.80212.65512.6550.0000.0000.0000.000
57B59ASN0-0.069-0.04321.8540.6120.6120.0000.0000.0000.000
58B60PRO00.0440.02519.671-0.531-0.5310.0000.0000.0000.000
59B61GLU-1-0.860-0.92220.045-13.064-13.0640.0000.0000.0000.000
60B62SER0-0.040-0.02521.149-0.079-0.0790.0000.0000.0000.000
61B63LEU0-0.038-0.03017.065-0.604-0.6040.0000.0000.0000.000
62B64ALA00.0350.03415.749-1.219-1.2190.0000.0000.0000.000
63B65LEU00.015-0.00114.321-1.247-1.2470.0000.0000.0000.000
64B66ASP-1-0.789-0.88012.698-21.930-21.9300.0000.0000.0000.000
65B67ALA00.0180.01411.878-1.852-1.8520.0000.0000.0000.000
66B68ILE0-0.028-0.0227.989-2.273-2.2730.0000.0000.0000.000
67B69GLU-1-0.956-0.9777.354-28.042-28.0420.0000.0000.0000.000
68B70ARG10.7320.8618.67118.08618.0860.0000.0000.0000.000
69B71LEU00.0060.0008.282-0.643-0.6430.0000.0000.0000.000
70B72GLN00.0410.0022.324-16.892-15.0881.790-1.613-1.980-0.023
71B73ARG10.9320.9834.35822.32422.417-0.001-0.013-0.0780.000
72B74TRP00.018-0.0106.7330.7160.7160.0000.0000.0000.000
73B75TRP0-0.022-0.0083.4116.2906.7270.015-0.100-0.3520.001
74B76GLU-1-0.847-0.9231.859-116.140-113.89511.583-7.732-6.096-0.109
75B77GLU-1-0.984-0.9825.446-21.422-21.4220.0000.0000.0000.000
76B78SER0-0.033-0.0108.5732.2612.2610.0000.0000.0000.000
77B79GLU-1-0.734-0.85210.364-19.652-19.6520.0000.0000.0000.000
78B80ALA0-0.064-0.08514.0651.0011.0010.0000.0000.0000.000
79B81LEU0-0.0030.00114.3040.2630.2630.0000.0000.0000.000
80B82GLU-1-0.850-0.92317.406-15.200-15.2000.0000.0000.0000.000
81B83PRO00.0270.03518.6850.3350.3350.0000.0000.0000.000
82B84GLU-1-0.817-0.89320.829-13.768-13.7680.0000.0000.0000.000
83B85SER0-0.042-0.04322.6570.2250.2250.0000.0000.0000.000
84B86ARG10.7650.86424.07212.85812.8580.0000.0000.0000.000
85B87PHE00.0210.01127.117-0.324-0.3240.0000.0000.0000.000
86B88ILE0-0.0010.00829.3120.3230.3230.0000.0000.0000.000
87B89GLU-1-0.803-0.88931.141-9.172-9.1720.0000.0000.0000.000
88B90ILE0-0.026-0.01730.2570.2000.2000.0000.0000.0000.000
89B91PRO0-0.012-0.00634.5160.0240.0240.0000.0000.0000.000
90B92VAL0-0.0160.00134.2610.0450.0450.0000.0000.0000.000
91B93VAL0-0.009-0.01437.6490.1430.1430.0000.0000.0000.000
92B94TYR0-0.023-0.04333.6200.0940.0940.0000.0000.0000.000
93B95GLY00.013-0.00439.9030.1870.1870.0000.0000.0000.000
94B96GLY0-0.023-0.00942.0440.0160.0160.0000.0000.0000.000
95B97ALA0-0.008-0.01344.357-0.022-0.0220.0000.0000.0000.000
96B98GLY00.0250.00441.190-0.077-0.0770.0000.0000.0000.000
97B99GLY00.0030.00738.981-0.202-0.2020.0000.0000.0000.000
98B100PRO0-0.011-0.00339.6870.0960.0960.0000.0000.0000.000
99B101ASP-1-0.800-0.88737.017-7.589-7.5890.0000.0000.0000.000
100B102LEU0-0.0120.00537.665-0.129-0.1290.0000.0000.0000.000
101B103ALA00.0370.02038.941-0.051-0.0510.0000.0000.0000.000
102B104VAL0-0.027-0.01837.7000.0330.0330.0000.0000.0000.000
103B105VAL0-0.007-0.00933.643-0.094-0.0940.0000.0000.0000.000
104B106ALA00.001-0.00235.683-0.125-0.1250.0000.0000.0000.000
105B107ALA0-0.032-0.00938.1850.0370.0370.0000.0000.0000.000
106B108HIS0-0.085-0.05034.2590.1720.1720.0000.0000.0000.000
107B109CYS0-0.0200.00832.952-0.126-0.1260.0000.0000.0000.000
108B110GLY00.0100.02634.563-0.035-0.0350.0000.0000.0000.000
109B111LEU0-0.014-0.01534.5740.0470.0470.0000.0000.0000.000
110B112SER00.0230.00838.458-0.024-0.0240.0000.0000.0000.000
111B113GLU-1-0.847-0.94639.283-6.957-6.9570.0000.0000.0000.000
112B114LYS10.9150.94539.4066.4256.4250.0000.0000.0000.000
113B115GLN00.0170.02237.606-0.164-0.1640.0000.0000.0000.000
114B116VAL0-0.0030.00335.025-0.195-0.1950.0000.0000.0000.000
115B117VAL0-0.034-0.01834.512-0.183-0.1830.0000.0000.0000.000
116B118GLU-1-0.916-0.94335.929-7.462-7.4620.0000.0000.0000.000
117B119LEU00.0120.00430.546-0.134-0.1340.0000.0000.0000.000
118B120HIS00.0050.01829.728-0.076-0.0760.0000.0000.0000.000
119B121SER00.007-0.02130.726-0.207-0.2070.0000.0000.0000.000
120B122SER0-0.075-0.03931.838-0.046-0.0460.0000.0000.0000.000
121B123VAL0-0.046-0.00325.279-0.124-0.1240.0000.0000.0000.000
122B124GLU-1-0.936-0.95326.592-10.394-10.3940.0000.0000.0000.000
123B125TYR0-0.062-0.03923.955-0.464-0.4640.0000.0000.0000.000
124B126VAL00.0590.03519.4910.0800.0800.0000.0000.0000.000
125B127VAL0-0.032-0.01721.518-0.124-0.1240.0000.0000.0000.000
126B128TRP00.0100.01112.484-0.713-0.7130.0000.0000.0000.000
127B129PHE00.0340.00516.969-0.760-0.7600.0000.0000.0000.000
128B130LEU00.0180.01119.4640.5830.5830.0000.0000.0000.000
129B131GLY00.0560.02222.073-0.512-0.5120.0000.0000.0000.000
130B132PHE0-0.0410.00323.4960.4730.4730.0000.0000.0000.000
131B133GLN00.0000.01025.8140.6190.6190.0000.0000.0000.000
132B134PRO00.027-0.00127.897-0.331-0.3310.0000.0000.0000.000
133B135GLY00.0610.02928.1310.3050.3050.0000.0000.0000.000
134B136PHE0-0.039-0.01124.3410.2930.2930.0000.0000.0000.000
135B137PRO0-0.009-0.00124.083-0.492-0.4920.0000.0000.0000.000
136B138TYR0-0.015-0.00319.7920.3630.3630.0000.0000.0000.000
137B139LEU0-0.029-0.01320.372-0.548-0.5480.0000.0000.0000.000
138B140GLY00.0100.00618.8060.0820.0820.0000.0000.0000.000
139B141SER0-0.052-0.03818.1910.1900.1900.0000.0000.0000.000
140B142LEU00.0310.04220.6370.2900.2900.0000.0000.0000.000
141B143PRO00.013-0.00823.949-0.178-0.1780.0000.0000.0000.000
142B144GLU-1-0.905-0.96123.849-10.338-10.3380.0000.0000.0000.000
143B145GLN0-0.030-0.00425.6350.0490.0490.0000.0000.0000.000
144B146LEU0-0.018-0.02428.6240.2670.2670.0000.0000.0000.000
145B147HIS0-0.0220.00422.4490.0320.0320.0000.0000.0000.000
146B148THR00.023-0.00527.8790.2860.2860.0000.0000.0000.000
147B149PRO0-0.021-0.01029.701-0.203-0.2030.0000.0000.0000.000
148B150ARG10.8650.93824.13210.81310.8130.0000.0000.0000.000
149B151ARG10.7750.86531.5957.6297.6290.0000.0000.0000.000
150B152ALA00.0170.03234.8130.2090.2090.0000.0000.0000.000
151B153GLU-1-0.744-0.84535.928-7.389-7.3890.0000.0000.0000.000
152B154PRO0-0.0050.00838.0300.0040.0040.0000.0000.0000.000
153B155ARG10.8080.86539.6477.0717.0710.0000.0000.0000.000
154B156LEU0-0.009-0.00440.7280.1600.1600.0000.0000.0000.000
155B157LEU0-0.006-0.00238.578-0.172-0.1720.0000.0000.0000.000
156B158VAL0-0.0220.00935.0260.1750.1750.0000.0000.0000.000
157B159PRO00.0240.00537.939-0.058-0.0580.0000.0000.0000.000
158B160ALA00.0160.03936.820-0.185-0.1850.0000.0000.0000.000
159B161GLY00.0520.02335.3210.1790.1790.0000.0000.0000.000
160B162SER0-0.025-0.04535.5470.1780.1780.0000.0000.0000.000
161B163VAL0-0.018-0.00631.615-0.288-0.2880.0000.0000.0000.000
162B164GLY00.008-0.00831.3530.2940.2940.0000.0000.0000.000
163B165ILE00.0070.01228.872-0.329-0.3290.0000.0000.0000.000
164B166GLY00.0570.00127.5090.2760.2760.0000.0000.0000.000
165B167GLY0-0.0320.01125.514-0.447-0.4470.0000.0000.0000.000
166B168PRO00.0510.01920.9850.1520.1520.0000.0000.0000.000
167B169GLN0-0.044-0.01419.771-0.341-0.3410.0000.0000.0000.000
168B170THR00.0300.00723.4820.5720.5720.0000.0000.0000.000
169B171GLY00.0610.02425.268-0.421-0.4210.0000.0000.0000.000
170B172VAL00.005-0.00427.5850.3470.3470.0000.0000.0000.000
171B173TYR00.0200.01629.746-0.328-0.3280.0000.0000.0000.000
172B174PRO0-0.0050.01130.3420.3320.3320.0000.0000.0000.000
173B175LEU00.005-0.00333.2440.2550.2550.0000.0000.0000.000
174B176ALA00.0090.00635.285-0.020-0.0200.0000.0000.0000.000
175B177THR0-0.017-0.03333.0960.0710.0710.0000.0000.0000.000
176B178PRO0-0.008-0.00234.9080.0660.0660.0000.0000.0000.000
177B179GLY00.0480.02732.396-0.276-0.2760.0000.0000.0000.000
178B180GLY00.020-0.00131.5150.2210.2210.0000.0000.0000.000
179B181TRP0-0.066-0.03925.3320.0610.0610.0000.0000.0000.000
180B182GLN00.0120.00731.5600.4360.4360.0000.0000.0000.000
181B183LEU00.0220.00833.482-0.189-0.1890.0000.0000.0000.000
182B184ILE00.0070.00332.8580.2380.2380.0000.0000.0000.000
183B185GLY00.041-0.00936.3640.1800.1800.0000.0000.0000.000
184B186HIS0-0.0690.00537.064-0.077-0.0770.0000.0000.0000.000
185B187THR00.0020.01135.711-0.004-0.0040.0000.0000.0000.000
186B188SER00.0090.00238.121-0.026-0.0260.0000.0000.0000.000
187B189LEU00.0030.00434.8610.0650.0650.0000.0000.0000.000
188B190SER00.0310.01036.557-0.140-0.1400.0000.0000.0000.000
189B191LEU00.0130.00930.104-0.068-0.0680.0000.0000.0000.000
190B192PHE0-0.016-0.01332.421-0.248-0.2480.0000.0000.0000.000
191B193ASP-1-0.909-0.96134.157-7.661-7.6610.0000.0000.0000.000
192B194PRO0-0.048-0.02237.210-0.137-0.1370.0000.0000.0000.000
193B195ALA0-0.023-0.01438.331-0.016-0.0160.0000.0000.0000.000
194B196ARG10.8220.92334.9148.8278.8270.0000.0000.0000.000
195B197ASP-1-0.907-0.96238.257-8.176-8.1760.0000.0000.0000.000
196B198GLU-1-0.918-0.93332.148-10.030-10.0300.0000.0000.0000.000
197B199PRO0-0.020-0.01433.1540.0490.0490.0000.0000.0000.000
198B200ILE0-0.040-0.02828.4090.1100.1100.0000.0000.0000.000
199B201LEU00.0100.01531.516-0.066-0.0660.0000.0000.0000.000
200B202LEU0-0.011-0.00826.657-0.142-0.1420.0000.0000.0000.000
201B203ARG10.9961.00125.00710.90910.9090.0000.0000.0000.000
202B204PRO0-0.049-0.04219.7660.0620.0620.0000.0000.0000.000
203B205GLY00.0560.03020.401-0.271-0.2710.0000.0000.0000.000
204B206ASP-1-0.833-0.89121.179-11.678-11.6780.0000.0000.0000.000
205B207SER0-0.004-0.02224.115-0.299-0.2990.0000.0000.0000.000
206B208VAL0-0.023-0.00825.9050.4320.4320.0000.0000.0000.000
207B209ARG10.9260.95327.8318.6728.6720.0000.0000.0000.000
208B210PHE0-0.012-0.00228.8350.1100.1100.0000.0000.0000.000
209B211VAL0-0.004-0.01233.1140.0960.0960.0000.0000.0000.000
210B212PRO0-0.007-0.00736.8150.1320.1320.0000.0000.0000.000
211B213GLN00.0040.00539.2510.1660.1660.0000.0000.0000.000
212B214LYS10.9250.97541.9516.9846.9840.0000.0000.0000.000