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: 98192

Calculation Name: 1LM5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LM5

Chain ID: A

ChEMBL ID:

UniProt ID: P15924

Base Structure: X-ray

Registration Date: 2023-09-24

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046410.463462
FMO2-HF: Nuclear repulsion 1974206.458524
FMO2-HF: Total energy -72204.004939
FMO2-MP2: Total energy -72416.035661


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(A:2616:SER)


Summations of interaction energy for fragment #1(A:2616:SER)
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.
-18.711-11.919.528-6.939-9.387-0.045
Interaction energy analysis for fragmet #1(A:2616:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.014
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].
3A2618PRO00.026-0.0062.092-8.972-6.9353.616-3.010-2.642-0.023
4A2619ILE0-0.017-0.0164.5341.1601.267-0.001-0.006-0.0990.000
5A2620ALA0-0.025-0.0126.532-0.142-0.1420.0000.0000.0000.000
6A2621ALA0-0.004-0.0129.294-0.008-0.0080.0000.0000.0000.000
7A2622ILE0-0.017-0.00311.4750.0150.0150.0000.0000.0000.000
8A2623PHE00.0270.02514.1590.0300.0300.0000.0000.0000.000
9A2624ASP-1-0.795-0.88615.9040.0180.0180.0000.0000.0000.000
10A2625THR0-0.031-0.04218.2590.0150.0150.0000.0000.0000.000
11A2626GLU-1-0.833-0.91320.4480.0280.0280.0000.0000.0000.000
12A2627ASN0-0.055-0.03622.9980.0030.0030.0000.0000.0000.000
13A2628LEU0-0.077-0.03021.1550.0090.0090.0000.0000.0000.000
14A2629GLU-1-0.818-0.89020.4480.0450.0450.0000.0000.0000.000
15A2630LYS10.7390.83714.320-0.145-0.1450.0000.0000.0000.000
16A2631ILE00.0040.03016.807-0.013-0.0130.0000.0000.0000.000
17A2632SER0-0.004-0.03015.860-0.030-0.0300.0000.0000.0000.000
18A2633ILE00.013-0.00911.4220.0160.0160.0000.0000.0000.000
19A2634THR0-0.023-0.04315.794-0.003-0.0030.0000.0000.0000.000
20A2635GLU-1-0.737-0.85019.252-0.055-0.0550.0000.0000.0000.000
21A2636GLY00.000-0.00918.3180.0210.0210.0000.0000.0000.000
22A2637ILE0-0.095-0.05618.2460.0010.0010.0000.0000.0000.000
23A2638GLU-1-0.955-0.97220.993-0.108-0.1080.0000.0000.0000.000
24A2639ARG10.7730.86422.2610.0250.0250.0000.0000.0000.000
25A2640GLY0-0.0080.00823.6400.0130.0130.0000.0000.0000.000
26A2641ILE0-0.0220.00019.4450.0000.0000.0000.0000.0000.000
27A2642VAL0-0.038-0.02416.033-0.004-0.0040.0000.0000.0000.000
28A2643ASP-1-0.765-0.83818.859-0.265-0.2650.0000.0000.0000.000
29A2644SER00.1260.03219.136-0.026-0.0260.0000.0000.0000.000
30A2645ILE0-0.058-0.01418.606-0.040-0.0400.0000.0000.0000.000
31A2646THR0-0.047-0.06214.446-0.080-0.0800.0000.0000.0000.000
32A2647GLY00.0800.02714.749-0.081-0.0810.0000.0000.0000.000
33A2648GLN00.017-0.00715.226-0.022-0.0220.0000.0000.0000.000
34A2649ARG10.8660.91713.7400.4010.4010.0000.0000.0000.000
35A2650LEU0-0.0140.0019.846-0.190-0.1900.0000.0000.0000.000
36A2651LEU00.0520.01810.862-0.191-0.1910.0000.0000.0000.000
37A2652GLU-1-0.789-0.86413.171-0.713-0.7130.0000.0000.0000.000
38A2653ALA0-0.008-0.0048.142-0.062-0.0620.0000.0000.0000.000
39A2654GLN0-0.0200.0159.182-0.265-0.2650.0000.0000.0000.000
40A2655ALA00.0140.01510.4500.0350.0350.0000.0000.0000.000
41A2656CYS0-0.091-0.02611.644-0.028-0.0280.0000.0000.0000.000
42A2657THR0-0.015-0.0527.494-0.041-0.0410.0000.0000.0000.000
43A2658GLY0-0.003-0.0169.644-0.002-0.0020.0000.0000.0000.000
44A2659GLY0-0.024-0.00112.2860.1730.1730.0000.0000.0000.000
45A2660ILE0-0.044-0.02312.302-0.136-0.1360.0000.0000.0000.000
46A2661ILE0-0.017-0.0078.3010.0040.0040.0000.0000.0000.000
47A2662HIS00.0710.06412.7890.0380.0380.0000.0000.0000.000
48A2663PRO00.0360.00813.9660.0170.0170.0000.0000.0000.000
49A2664THR0-0.055-0.03114.7840.0690.0690.0000.0000.0000.000
50A2665THR00.0710.02416.7040.0290.0290.0000.0000.0000.000
51A2666GLY00.0360.01412.8410.0450.0450.0000.0000.0000.000
52A2667GLN0-0.020-0.01012.983-0.055-0.0550.0000.0000.0000.000
53A2668LYS10.9160.9678.4191.1231.1230.0000.0000.0000.000
54A2669LEU0-0.020-0.00914.4900.0660.0660.0000.0000.0000.000
55A2670SER00.0410.03616.908-0.072-0.0720.0000.0000.0000.000
56A2671LEU0-0.005-0.03618.1260.0200.0200.0000.0000.0000.000
57A2672GLN0-0.014-0.00220.5000.0140.0140.0000.0000.0000.000
58A2673ASP-1-0.837-0.92421.276-0.153-0.1530.0000.0000.0000.000
59A2674ALA0-0.054-0.02018.6760.0170.0170.0000.0000.0000.000
60A2675VAL0-0.011-0.01620.4120.0160.0160.0000.0000.0000.000
61A2676SER0-0.064-0.02023.5660.0220.0220.0000.0000.0000.000
62A2677GLN0-0.038-0.02920.8300.0210.0210.0000.0000.0000.000
63A2678GLY00.0140.01822.9090.0130.0130.0000.0000.0000.000
64A2679VAL0-0.044-0.01116.541-0.002-0.0020.0000.0000.0000.000
65A2680ILE0-0.043-0.00317.956-0.035-0.0350.0000.0000.0000.000
66A2681ASP-1-0.779-0.86620.669-0.194-0.1940.0000.0000.0000.000
67A2682GLN00.0770.01123.521-0.021-0.0210.0000.0000.0000.000
68A2683ASP-1-0.878-0.93825.532-0.194-0.1940.0000.0000.0000.000
69A2684MET0-0.022-0.01519.086-0.041-0.0410.0000.0000.0000.000
70A2685ALA00.002-0.00221.222-0.042-0.0420.0000.0000.0000.000
71A2686THR0-0.074-0.04222.244-0.023-0.0230.0000.0000.0000.000
72A2687ARG10.9080.94921.8590.2610.2610.0000.0000.0000.000
73A2688LEU00.0140.01416.403-0.043-0.0430.0000.0000.0000.000
74A2689LYS10.9010.96619.0030.2430.2430.0000.0000.0000.000
75A2690PRO0-0.019-0.01620.136-0.013-0.0130.0000.0000.0000.000
76A2691ALA00.0500.03415.132-0.030-0.0300.0000.0000.0000.000
77A2692GLN00.0830.03715.946-0.064-0.0640.0000.0000.0000.000
78A2693LYS10.9380.98017.4450.3110.3110.0000.0000.0000.000
79A2694ALA0-0.0420.00014.9840.0170.0170.0000.0000.0000.000
80A2695PHE0-0.0290.00011.475-0.055-0.0550.0000.0000.0000.000
81A2696ILE0-0.026-0.02315.1580.0530.0530.0000.0000.0000.000
82A2697GLY00.008-0.01218.5300.0500.0500.0000.0000.0000.000
83A2698PHE0-0.056-0.04418.6910.0270.0270.0000.0000.0000.000
84A2706LYS10.9470.99221.5140.2500.2500.0000.0000.0000.000
85A2707MET0-0.0240.01022.145-0.010-0.0100.0000.0000.0000.000
86A2708SER00.0280.00217.048-0.042-0.0420.0000.0000.0000.000
87A2709ALA00.0270.00016.2410.0270.0270.0000.0000.0000.000
88A2710ALA00.0040.01017.5690.0300.0300.0000.0000.0000.000
89A2711GLU-1-0.795-0.90219.119-0.298-0.2980.0000.0000.0000.000
90A2712ALA00.0400.03021.3960.0310.0310.0000.0000.0000.000
91A2713VAL0-0.052-0.02020.1680.0230.0230.0000.0000.0000.000
92A2714LYS10.8880.95523.1280.3330.3330.0000.0000.0000.000
93A2715GLU-1-0.920-0.97325.364-0.224-0.2240.0000.0000.0000.000
94A2716LYS10.8730.93826.8670.2580.2580.0000.0000.0000.000
95A2717TRP00.0010.00825.1450.0000.0000.0000.0000.0000.000
96A2718LEU0-0.059-0.02118.940-0.008-0.0080.0000.0000.0000.000
97A2719PRO00.0300.00922.7260.0040.0040.0000.0000.0000.000
98A2720TYR00.0470.01419.289-0.038-0.0380.0000.0000.0000.000
99A2721GLU-1-0.920-0.96319.552-0.403-0.4030.0000.0000.0000.000
100A2722ALA0-0.047-0.02417.802-0.065-0.0650.0000.0000.0000.000
101A2723GLY00.0650.01916.664-0.084-0.0840.0000.0000.0000.000
102A2724GLN00.0060.00415.326-0.057-0.0570.0000.0000.0000.000
103A2725ARG10.8060.87913.1870.5300.5300.0000.0000.0000.000
104A2726PHE00.013-0.00111.774-0.206-0.2060.0000.0000.0000.000
105A2727LEU00.0320.01411.247-0.226-0.2260.0000.0000.0000.000
106A2728GLU-1-0.872-0.93910.030-1.148-1.1480.0000.0000.0000.000
107A2729PHE0-0.050-0.0277.681-0.491-0.4910.0000.0000.0000.000
108A2730GLN0-0.013-0.0046.560-1.070-1.0700.0000.0000.0000.000
109A2731TYR0-0.0020.0026.125-0.402-0.4020.0000.0000.0000.000
110A2732LEU0-0.048-0.0343.818-0.411-0.0590.001-0.090-0.2630.000
111A2733THR0-0.074-0.0602.021-8.284-6.4524.602-3.077-3.357-0.031
112A2734GLY00.0140.0132.9673.7263.4170.0360.621-0.3480.000
113A2735GLY0-0.0210.0054.6370.4420.482-0.001-0.007-0.0310.000
114A2736LEU0-0.012-0.0097.715-0.121-0.1210.0000.0000.0000.000
115A2737VAL00.0190.00310.1440.0960.0960.0000.0000.0000.000
116A2738ASP-1-0.831-0.90712.251-0.303-0.3030.0000.0000.0000.000
117A2739PRO0-0.015-0.02415.7940.0340.0340.0000.0000.0000.000
118A2740GLU-1-0.919-0.95717.677-0.192-0.1920.0000.0000.0000.000
119A2741VAL00.0060.02316.3030.0350.0350.0000.0000.0000.000
120A2742HIS0-0.073-0.02113.1250.0630.0630.0000.0000.0000.000
121A2743GLY0-0.023-0.02513.124-0.062-0.0620.0000.0000.0000.000
122A2744ARG10.8180.9096.0851.8471.8470.0000.0000.0000.000
123A2745ILE0-0.0070.00911.0740.1280.1280.0000.0000.0000.000
124A2746SER00.0320.01711.282-0.122-0.1220.0000.0000.0000.000
125A2747THR00.027-0.00811.404-0.014-0.0140.0000.0000.0000.000
126A2748GLU-1-0.926-0.95613.724-0.160-0.1600.0000.0000.0000.000
127A2749GLU-1-0.731-0.85115.819-0.211-0.2110.0000.0000.0000.000
128A2750ALA0-0.010-0.00714.5100.0040.0040.0000.0000.0000.000
129A2751ILE0-0.025-0.02416.5960.0150.0150.0000.0000.0000.000
130A2752ARG10.7900.88119.2740.2250.2250.0000.0000.0000.000
131A2753LYS10.8280.91518.4290.3070.3070.0000.0000.0000.000
132A2754GLY0-0.0040.01321.2020.0050.0050.0000.0000.0000.000
133A2755PHE0-0.079-0.04515.665-0.016-0.0160.0000.0000.0000.000
134A2756ILE0-0.026-0.02314.723-0.040-0.0400.0000.0000.0000.000
135A2757ASP-1-0.790-0.88018.835-0.301-0.3010.0000.0000.0000.000
136A2758GLY00.0750.01319.271-0.033-0.0330.0000.0000.0000.000
137A2759ARG10.9170.95919.5100.2160.2160.0000.0000.0000.000
138A2760ALA0-0.005-0.01517.354-0.019-0.0190.0000.0000.0000.000
139A2761ALA00.0160.02215.215-0.076-0.0760.0000.0000.0000.000
140A2762GLN0-0.018-0.01214.844-0.071-0.0710.0000.0000.0000.000
141A2763ARG10.9670.98315.8280.4290.4290.0000.0000.0000.000
142A2764LEU00.0040.00411.288-0.042-0.0420.0000.0000.0000.000
143A2765GLN00.0230.01310.931-0.171-0.1710.0000.0000.0000.000
144A2766ASP-1-0.793-0.83211.705-0.391-0.3910.0000.0000.0000.000
145A2767THR0-0.049-0.0437.5310.0240.0240.0000.0000.0000.000
146A2768SER0-0.124-0.08110.5890.0440.0440.0000.0000.0000.000
147A2769SER0-0.046-0.03213.1980.0330.0330.0000.0000.0000.000
148A2770TYR0-0.059-0.0448.519-0.152-0.1520.0000.0000.0000.000
149A2771ALA00.0390.02213.5750.0890.0890.0000.0000.0000.000
150A2772LYS10.8780.94014.4370.1870.1870.0000.0000.0000.000
151A2773ILE0-0.029-0.03112.6030.0620.0620.0000.0000.0000.000
152A2774LEU00.0040.02510.627-0.014-0.0140.0000.0000.0000.000
153A2775THR0-0.0150.00015.2440.0390.0390.0000.0000.0000.000
154A2776CYS0-0.065-0.01913.8070.0200.0200.0000.0000.0000.000
155A2777PRO00.0780.04414.3170.0220.0220.0000.0000.0000.000
156A2778LYS10.9671.00316.582-0.193-0.1930.0000.0000.0000.000
157A2779THR00.012-0.01517.377-0.015-0.0150.0000.0000.0000.000
158A2780LYS10.8740.96118.9510.0640.0640.0000.0000.0000.000
159A2781LEU0-0.0210.00418.801-0.014-0.0140.0000.0000.0000.000
160A2782LYS10.9070.95517.8870.2400.2400.0000.0000.0000.000
161A2783ILE0-0.038-0.03011.8310.0460.0460.0000.0000.0000.000
162A2784SER00.0440.02511.276-0.097-0.0970.0000.0000.0000.000
163A2785TYR00.0890.0364.9780.0030.0030.0000.0000.0000.000
164A2786LYS11.0131.0205.0990.3910.3910.0000.0000.0000.000
165A2787ASP-1-0.848-0.9187.6620.2540.2540.0000.0000.0000.000
166A2788ALA0-0.007-0.0138.2530.2400.2400.0000.0000.0000.000
167A2789ILE00.0230.0102.668-1.679-0.1251.081-0.878-1.7570.007
168A2790ASN0-0.056-0.0165.5450.9850.9850.0000.0000.0000.000
169A2791ARG10.8790.9317.892-0.098-0.0980.0000.0000.0000.000
170A2792SER0-0.060-0.0106.2630.1950.1950.0000.0000.0000.000
171A2793MET00.0200.0138.6530.2750.2750.0000.0000.0000.000
172A2794VAL0-0.055-0.0207.2180.0510.0510.0000.0000.0000.000
173A2795GLU-1-0.758-0.8179.7260.1280.1280.0000.0000.0000.000
174A2796ASP-1-0.894-0.97112.8270.5420.5420.0000.0000.0000.000
175A2797ILE00.0010.01612.527-0.051-0.0510.0000.0000.0000.000
176A2798THR00.001-0.03513.2600.0230.0230.0000.0000.0000.000
177A2799GLY0-0.049-0.01610.162-0.047-0.0470.0000.0000.0000.000
178A2800LEU0-0.053-0.0288.4070.2210.2210.0000.0000.0000.000
179A2801ARG10.8550.9473.058-5.487-4.2990.194-0.492-0.8900.002
180A2802LEU00.0350.0097.290-0.468-0.4680.0000.0000.0000.000
181A2803LEU00.002-0.0169.6370.1690.1690.0000.0000.0000.000
182A2804GLU-1-0.824-0.89511.2610.2250.2250.0000.0000.0000.000
183A2805ALA0-0.048-0.03714.805-0.047-0.0470.0000.0000.0000.000
184A2806ALA00.0050.00917.5800.0260.0260.0000.0000.0000.000
185A2807SER00.0340.00521.249-0.030-0.0300.0000.0000.0000.000
186A2808VAL0-0.035-0.01424.377-0.015-0.0150.0000.0000.0000.000
187A2809SER0-0.044-0.04822.6740.0150.0150.0000.0000.0000.000
188A2810SER00.0410.01520.8860.0070.0070.0000.0000.0000.000
189A2811LYS10.8850.94822.5150.0050.0050.0000.0000.0000.000