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: K91M3

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 OptHSide
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 -2303392.978296
FMO2-HF: Nuclear repulsion 2222849.70955
FMO2-HF: Total energy -80543.268746
FMO2-MP2: Total energy -80781.876112


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.
-255.542-255.90742.235-20.666-21.207-0.248
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 : 0.802 / q_NPA : 0.883
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].
3B5ARG10.8300.9062.01617.24519.1537.247-3.875-5.280-0.040
4B6CYS00.0270.0164.6962.4072.488-0.001-0.010-0.0700.000
5B7TYR0-0.051-0.0287.0652.0752.0750.0000.0000.0000.000
6B8LEU00.0100.01010.6430.4360.4360.0000.0000.0000.000
7B9ILE0-0.041-0.01213.8490.4470.4470.0000.0000.0000.000
8B10GLY0-0.002-0.00316.5150.6750.6750.0000.0000.0000.000
9B11GLU-1-0.926-0.97418.137-14.306-14.3060.0000.0000.0000.000
10B12THR00.008-0.00519.8690.3000.3000.0000.0000.0000.000
11B13ALA0-0.0050.00316.6990.0810.0810.0000.0000.0000.000
12B14VAL0-0.0110.00310.282-0.261-0.2610.0000.0000.0000.000
13B15VAL00.003-0.00411.5060.4040.4040.0000.0000.0000.000
14B16LEU0-0.0070.0165.263-1.996-1.9960.0000.0000.0000.000
15B17GLU-1-0.847-0.9276.911-28.091-28.0910.0000.0000.0000.000
16B18LEU0-0.018-0.0253.874-6.732-6.3820.001-0.114-0.2380.000
17B19GLU-1-0.866-0.9131.901-49.788-49.0649.726-5.327-5.123-0.051
18B20PRO00.011-0.0044.3681.9342.029-0.001-0.024-0.0710.000
19B21PRO0-0.034-0.0176.3931.5181.5180.0000.0000.0000.000
20B22VAL00.0400.0307.451-1.279-1.2790.0000.0000.0000.000
21B23THR0-0.014-0.0097.9290.6240.6240.0000.0000.0000.000
22B24LEU00.0600.03710.597-0.710-0.7100.0000.0000.0000.000
23B25ALA0-0.014-0.00910.9980.0430.0430.0000.0000.0000.000
24B26SER00.001-0.0107.428-1.666-1.6660.0000.0000.0000.000
25B27GLN00.016-0.0119.491-1.942-1.9420.0000.0000.0000.000
26B28LYS10.8220.90412.46316.75416.7540.0000.0000.0000.000
27B29ARG10.8440.9199.69626.25626.2560.0000.0000.0000.000
28B30ILE00.0030.0139.9350.0660.0660.0000.0000.0000.000
29B31TRP0-0.013-0.01313.0490.6330.6330.0000.0000.0000.000
30B32ARG10.7580.91914.53017.21917.2190.0000.0000.0000.000
31B33LEU00.0060.0019.7410.4240.4240.0000.0000.0000.000
32B34ALA00.010-0.00513.8380.3830.3830.0000.0000.0000.000
33B35GLN0-0.062-0.03716.7120.5030.5030.0000.0000.0000.000
34B36ARG10.9040.94912.78121.06521.0650.0000.0000.0000.000
35B37LEU0-0.041-0.03113.1300.3200.3200.0000.0000.0000.000
36B38VAL00.0280.00817.0410.3380.3380.0000.0000.0000.000
37B39ASP-1-0.908-0.92520.499-13.017-13.0170.0000.0000.0000.000
38B40MET0-0.078-0.01616.3350.3100.3100.0000.0000.0000.000
39B41PRO00.0320.00022.052-0.012-0.0120.0000.0000.0000.000
40B42ASN0-0.034-0.03518.789-0.289-0.2890.0000.0000.0000.000
41B43VAL00.0170.02517.249-0.324-0.3240.0000.0000.0000.000
42B44VAL0-0.080-0.03020.2970.4990.4990.0000.0000.0000.000
43B45GLU-1-0.877-0.93920.814-12.609-12.6090.0000.0000.0000.000
44B46ALA0-0.001-0.01716.849-0.900-0.9000.0000.0000.0000.000
45B47ILE0-0.0040.00617.7460.4870.4870.0000.0000.0000.000
46B48PRO0-0.0050.00015.454-1.040-1.0400.0000.0000.0000.000
47B49GLY00.0380.01814.3421.2161.2160.0000.0000.0000.000
48B50MET0-0.047-0.01712.4760.4570.4570.0000.0000.0000.000
49B51ASN00.025-0.0026.4470.3450.3450.0000.0000.0000.000
50B52ASN0-0.017-0.0088.256-1.981-1.9810.0000.0000.0000.000
51B53ILE00.0140.01010.7032.0102.0100.0000.0000.0000.000
52B54THR0-0.0020.01112.196-1.550-1.5500.0000.0000.0000.000
53B55VAL0-0.008-0.00312.8601.1311.1310.0000.0000.0000.000
54B56ILE00.0110.00615.563-0.276-0.2760.0000.0000.0000.000
55B57LEU0-0.011-0.01915.5680.0610.0610.0000.0000.0000.000
56B58ARG10.8940.93819.63612.87812.8780.0000.0000.0000.000
57B59ASN0-0.076-0.04921.6930.7060.7060.0000.0000.0000.000
58B60PRO00.0440.02919.492-0.532-0.5320.0000.0000.0000.000
59B61GLU-1-0.834-0.89619.857-13.521-13.5210.0000.0000.0000.000
60B62SER0-0.068-0.05120.993-0.220-0.2200.0000.0000.0000.000
61B63LEU0-0.020-0.02216.925-0.640-0.6400.0000.0000.0000.000
62B64ALA00.0270.03115.585-1.258-1.2580.0000.0000.0000.000
63B65LEU00.012-0.00514.119-1.284-1.2840.0000.0000.0000.000
64B66ASP-1-0.781-0.88212.531-22.225-22.2250.0000.0000.0000.000
65B67ALA00.0140.01211.752-1.957-1.9570.0000.0000.0000.000
66B68ILE0-0.027-0.0177.857-2.346-2.3460.0000.0000.0000.000
67B69GLU-1-0.963-0.9847.193-28.480-28.4800.0000.0000.0000.000
68B70ARG10.7240.8618.62118.45218.4520.0000.0000.0000.000
69B71LEU00.0160.0048.280-0.669-0.6690.0000.0000.0000.000
70B72GLN00.0570.0211.875-24.466-26.6618.486-3.134-3.157-0.041
71B73ARG10.9420.9864.07722.26922.415-0.001-0.041-0.1030.000
72B74TRP00.003-0.0156.5260.6240.6240.0000.0000.0000.000
73B75TRP0-0.010-0.0013.1437.1247.7150.055-0.139-0.5070.001
74B76GLU-1-0.845-0.9341.941-118.330-120.39516.723-8.002-6.658-0.117
75B77GLU-1-0.923-0.9345.461-20.941-20.9410.0000.0000.0000.000
76B78SER0-0.029-0.0157.8792.6632.6630.0000.0000.0000.000
77B79GLU-1-0.699-0.84210.117-19.110-19.1100.0000.0000.0000.000
78B80ALA0-0.076-0.10213.8361.0231.0230.0000.0000.0000.000
79B81LEU0-0.0130.01314.2630.6380.6380.0000.0000.0000.000
80B82GLU-1-0.843-0.92917.176-15.146-15.1460.0000.0000.0000.000
81B83PRO00.0240.03918.6530.3770.3770.0000.0000.0000.000
82B84GLU-1-0.793-0.87120.859-13.667-13.6670.0000.0000.0000.000
83B85SER0-0.051-0.05022.4170.2060.2060.0000.0000.0000.000
84B86ARG10.7890.87623.68612.92012.9200.0000.0000.0000.000
85B87PHE00.0090.00526.510-0.316-0.3160.0000.0000.0000.000
86B88ILE0-0.0100.00229.0750.3300.3300.0000.0000.0000.000
87B89GLU-1-0.781-0.87230.882-9.160-9.1600.0000.0000.0000.000
88B90ILE0-0.035-0.02130.2500.1970.1970.0000.0000.0000.000
89B91PRO0-0.020-0.00934.2930.0220.0220.0000.0000.0000.000
90B92VAL0-0.0130.00234.0960.0470.0470.0000.0000.0000.000
91B93VAL0-0.007-0.01337.4690.1450.1450.0000.0000.0000.000
92B94TYR00.008-0.03033.3530.1040.1040.0000.0000.0000.000
93B95GLY00.0110.01039.7600.2010.2010.0000.0000.0000.000
94B96GLY0-0.016-0.00641.9280.0140.0140.0000.0000.0000.000
95B97ALA0-0.008-0.01344.268-0.022-0.0220.0000.0000.0000.000
96B98GLY00.0330.00741.072-0.078-0.0780.0000.0000.0000.000
97B99GLY00.0040.00738.894-0.202-0.2020.0000.0000.0000.000
98B100PRO0-0.012-0.00539.7080.0940.0940.0000.0000.0000.000
99B101ASP-1-0.793-0.87636.935-7.629-7.6290.0000.0000.0000.000
100B102LEU0-0.0120.00537.415-0.137-0.1370.0000.0000.0000.000
101B103ALA00.0240.01138.863-0.043-0.0430.0000.0000.0000.000
102B104VAL0-0.022-0.01537.8370.0420.0420.0000.0000.0000.000
103B105VAL0-0.005-0.00833.538-0.090-0.0900.0000.0000.0000.000
104B106ALA0-0.010-0.00735.633-0.113-0.1130.0000.0000.0000.000
105B107ALA0-0.036-0.01138.1210.0410.0410.0000.0000.0000.000
106B108HIS0-0.082-0.04734.2370.1750.1750.0000.0000.0000.000
107B109CYS0-0.0120.01531.767-0.058-0.0580.0000.0000.0000.000
108B110GLY00.0080.02334.520-0.037-0.0370.0000.0000.0000.000
109B111LEU0-0.018-0.01434.4430.0430.0430.0000.0000.0000.000
110B112SER00.0200.00438.376-0.027-0.0270.0000.0000.0000.000
111B113GLU-1-0.844-0.94439.177-7.023-7.0230.0000.0000.0000.000
112B114LYS10.9050.94639.2796.4516.4510.0000.0000.0000.000
113B115GLN00.0080.00737.510-0.150-0.1500.0000.0000.0000.000
114B116VAL0-0.014-0.00434.853-0.201-0.2010.0000.0000.0000.000
115B117VAL0-0.024-0.01434.378-0.197-0.1970.0000.0000.0000.000
116B118GLU-1-0.886-0.92335.756-7.440-7.4400.0000.0000.0000.000
117B119LEU00.0050.01330.108-0.140-0.1400.0000.0000.0000.000
118B120HIS00.0230.02329.135-0.028-0.0280.0000.0000.0000.000
119B121SER00.009-0.00930.542-0.222-0.2220.0000.0000.0000.000
120B122SER0-0.082-0.05231.629-0.040-0.0400.0000.0000.0000.000
121B123VAL0-0.045-0.00525.133-0.122-0.1220.0000.0000.0000.000
122B124GLU-1-0.937-0.95725.752-10.473-10.4730.0000.0000.0000.000
123B125TYR0-0.056-0.04723.727-0.462-0.4620.0000.0000.0000.000
124B126VAL00.0630.03619.1920.0710.0710.0000.0000.0000.000
125B127VAL0-0.020-0.01021.297-0.130-0.1300.0000.0000.0000.000
126B128TRP00.0060.00812.377-0.796-0.7960.0000.0000.0000.000
127B129PHE00.0310.01216.957-0.801-0.8010.0000.0000.0000.000
128B130LEU00.0220.01719.2890.5960.5960.0000.0000.0000.000
129B131GLY00.0590.01921.948-0.522-0.5220.0000.0000.0000.000
130B132PHE0-0.041-0.00123.4050.5150.5150.0000.0000.0000.000
131B133GLN0-0.0060.00425.7680.6240.6240.0000.0000.0000.000
132B134PRO00.025-0.00327.792-0.322-0.3220.0000.0000.0000.000
133B135GLY00.0570.02727.9670.3110.3110.0000.0000.0000.000
134B136PHE0-0.048-0.01324.3100.2930.2930.0000.0000.0000.000
135B137PRO0-0.008-0.00223.919-0.494-0.4940.0000.0000.0000.000
136B138TYR0-0.018-0.00419.7230.3640.3640.0000.0000.0000.000
137B139LEU0-0.032-0.01420.214-0.562-0.5620.0000.0000.0000.000
138B140GLY00.0050.00418.6330.0930.0930.0000.0000.0000.000
139B141SER0-0.052-0.04218.2600.1360.1360.0000.0000.0000.000
140B142LEU00.0420.05220.4880.3050.3050.0000.0000.0000.000
141B143PRO00.018-0.00423.838-0.169-0.1690.0000.0000.0000.000
142B144GLU-1-0.893-0.95524.094-10.532-10.5320.0000.0000.0000.000
143B145GLN0-0.040-0.00725.5590.0340.0340.0000.0000.0000.000
144B146LEU0-0.007-0.02528.5540.2610.2610.0000.0000.0000.000
145B147HIS0-0.036-0.00622.2850.0110.0110.0000.0000.0000.000
146B148THR00.0380.00327.8400.2880.2880.0000.0000.0000.000
147B149PRO0-0.023-0.01029.701-0.200-0.2000.0000.0000.0000.000
148B150ARG10.8650.94124.09010.84710.8470.0000.0000.0000.000
149B151ARG10.7780.87031.6247.6427.6420.0000.0000.0000.000
150B152ALA00.0300.03634.9450.2080.2080.0000.0000.0000.000
151B153GLU-1-0.747-0.85036.018-7.397-7.3970.0000.0000.0000.000
152B154PRO0-0.0120.00738.0530.0060.0060.0000.0000.0000.000
153B155ARG10.8140.86939.7177.0797.0790.0000.0000.0000.000
154B156LEU0-0.009-0.00340.8520.1640.1640.0000.0000.0000.000
155B157LEU0-0.008-0.00438.546-0.176-0.1760.0000.0000.0000.000
156B158VAL0-0.0170.01134.9040.1770.1770.0000.0000.0000.000
157B159PRO00.0230.00437.892-0.064-0.0640.0000.0000.0000.000
158B160ALA00.0150.03336.718-0.185-0.1850.0000.0000.0000.000
159B161GLY00.0570.02735.1820.1830.1830.0000.0000.0000.000
160B162SER0-0.020-0.03235.4160.1840.1840.0000.0000.0000.000
161B163VAL0-0.020-0.00431.517-0.288-0.2880.0000.0000.0000.000
162B164GLY00.012-0.00531.2500.2960.2960.0000.0000.0000.000
163B165ILE00.0000.00728.540-0.330-0.3300.0000.0000.0000.000
164B166GLY00.0600.00627.4610.2750.2750.0000.0000.0000.000
165B167GLY0-0.0380.00925.499-0.448-0.4480.0000.0000.0000.000
166B168PRO00.0530.01920.9360.1480.1480.0000.0000.0000.000
167B169GLN0-0.047-0.01419.752-0.377-0.3770.0000.0000.0000.000
168B170THR00.0280.01023.4140.5660.5660.0000.0000.0000.000
169B171GLY00.0590.02325.142-0.426-0.4260.0000.0000.0000.000
170B172VAL00.003-0.00527.4580.3510.3510.0000.0000.0000.000
171B173TYR00.0370.02229.626-0.364-0.3640.0000.0000.0000.000
172B174PRO0-0.0060.01130.1920.3340.3340.0000.0000.0000.000
173B175LEU00.003-0.00433.1710.2640.2640.0000.0000.0000.000
174B176ALA00.0120.00535.205-0.018-0.0180.0000.0000.0000.000
175B177THR0-0.006-0.02133.1630.0590.0590.0000.0000.0000.000
176B178PRO0-0.010-0.00434.9660.0560.0560.0000.0000.0000.000
177B179GLY00.0220.01332.395-0.285-0.2850.0000.0000.0000.000
178B180GLY00.0230.00331.5150.2250.2250.0000.0000.0000.000
179B181TRP0-0.059-0.03825.1450.0390.0390.0000.0000.0000.000
180B182GLN0-0.0040.00031.5390.4330.4330.0000.0000.0000.000
181B183LEU00.0250.00233.422-0.197-0.1970.0000.0000.0000.000
182B184ILE00.006-0.00132.4120.2400.2400.0000.0000.0000.000
183B185GLY00.042-0.01036.2670.1830.1830.0000.0000.0000.000
184B186HIS0-0.079-0.00236.947-0.043-0.0430.0000.0000.0000.000
185B187THR00.0030.01135.397-0.001-0.0010.0000.0000.0000.000
186B188SER00.000-0.00137.955-0.027-0.0270.0000.0000.0000.000
187B189LEU00.0060.00535.0790.0610.0610.0000.0000.0000.000
188B190SER00.0360.01436.372-0.138-0.1380.0000.0000.0000.000
189B191LEU00.0120.00829.796-0.071-0.0710.0000.0000.0000.000
190B192PHE0-0.012-0.01432.237-0.250-0.2500.0000.0000.0000.000
191B193ASP-1-0.896-0.95133.991-7.749-7.7490.0000.0000.0000.000
192B194PRO0-0.041-0.02737.029-0.135-0.1350.0000.0000.0000.000
193B195ALA0-0.024-0.01938.169-0.015-0.0150.0000.0000.0000.000
194B196ARG10.8180.92934.7198.8608.8600.0000.0000.0000.000
195B197ASP-1-0.913-0.96537.821-8.253-8.2530.0000.0000.0000.000
196B198GLU-1-0.785-0.83432.143-10.153-10.1530.0000.0000.0000.000
197B199PRO0-0.019-0.01533.1330.0380.0380.0000.0000.0000.000
198B200ILE0-0.029-0.01828.3180.1190.1190.0000.0000.0000.000
199B201LEU00.0120.01531.292-0.071-0.0710.0000.0000.0000.000
200B202LEU0-0.021-0.01226.491-0.123-0.1230.0000.0000.0000.000
201B203ARG10.8160.88124.71210.73010.7300.0000.0000.0000.000
202B204PRO0-0.068-0.05619.4600.0390.0390.0000.0000.0000.000
203B205GLY00.0570.03120.117-0.276-0.2760.0000.0000.0000.000
204B206ASP-1-0.790-0.86020.893-11.704-11.7040.0000.0000.0000.000
205B207SER0-0.016-0.02723.848-0.305-0.3050.0000.0000.0000.000
206B208VAL0-0.025-0.00725.6270.4420.4420.0000.0000.0000.000
207B209ARG10.9110.93327.5908.7538.7530.0000.0000.0000.000
208B210PHE0-0.0020.00528.6270.1050.1050.0000.0000.0000.000
209B211VAL0-0.004-0.01132.9020.0970.0970.0000.0000.0000.000
210B212PRO0-0.004-0.00636.4420.1400.1400.0000.0000.0000.000
211B213GLN00.0010.00439.0530.1480.1480.0000.0000.0000.000
212B214LYS10.8770.94041.8646.9816.9810.0000.0000.0000.000