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: 7617K

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2034871.763759
FMO2-HF: Nuclear repulsion 1962666.049267
FMO2-HF: Total energy -72205.714493
FMO2-MP2: Total energy -72417.383001


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.
-34.969-33.90124.685-12.401-13.351-0.05
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 : 0.003 / q_NPA : -0.004
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].
3A2618PRO00.0300.0031.848-13.461-13.5278.295-4.854-3.375-0.041
4A2619ILE0-0.031-0.0204.5161.1861.287-0.001-0.005-0.0950.000
5A2620ALA00.0060.0196.484-0.087-0.0870.0000.0000.0000.000
6A2621ALA0-0.002-0.0058.9500.0780.0780.0000.0000.0000.000
7A2622ILE0-0.035-0.01610.9550.0120.0120.0000.0000.0000.000
8A2623PHE00.0200.01113.6390.0330.0330.0000.0000.0000.000
9A2624ASP-1-0.781-0.88215.5150.0240.0240.0000.0000.0000.000
10A2625THR0-0.054-0.06617.7090.0270.0270.0000.0000.0000.000
11A2626GLU-1-0.869-0.93920.1480.0600.0600.0000.0000.0000.000
12A2627ASN0-0.050-0.03522.8680.0030.0030.0000.0000.0000.000
13A2628LEU0-0.064-0.01920.8650.0060.0060.0000.0000.0000.000
14A2629GLU-1-0.790-0.86320.183-0.019-0.0190.0000.0000.0000.000
15A2630LYS10.7620.85213.8810.0810.0810.0000.0000.0000.000
16A2631ILE0-0.0020.01716.318-0.018-0.0180.0000.0000.0000.000
17A2632SER00.002-0.04015.558-0.059-0.0590.0000.0000.0000.000
18A2633ILE0-0.016-0.02311.2220.0420.0420.0000.0000.0000.000
19A2634THR0-0.039-0.04015.6850.0140.0140.0000.0000.0000.000
20A2635GLU-1-0.688-0.81419.251-0.168-0.1680.0000.0000.0000.000
21A2636GLY0-0.024-0.01717.9770.0390.0390.0000.0000.0000.000
22A2637ILE0-0.090-0.04518.7060.0210.0210.0000.0000.0000.000
23A2638GLU-1-0.938-0.96621.235-0.202-0.2020.0000.0000.0000.000
24A2639ARG10.7570.84621.5830.1000.1000.0000.0000.0000.000
25A2640GLY0-0.0110.00323.7070.0240.0240.0000.0000.0000.000
26A2641ILE0-0.035-0.00219.0800.0060.0060.0000.0000.0000.000
27A2642VAL0-0.058-0.03416.1580.0120.0120.0000.0000.0000.000
28A2643ASP-1-0.736-0.81018.944-0.279-0.2790.0000.0000.0000.000
29A2644SER00.1110.03119.324-0.036-0.0360.0000.0000.0000.000
30A2645ILE0-0.037-0.01119.411-0.053-0.0530.0000.0000.0000.000
31A2646THR0-0.069-0.07014.883-0.089-0.0890.0000.0000.0000.000
32A2647GLY00.0610.01815.004-0.097-0.0970.0000.0000.0000.000
33A2648GLN00.024-0.00515.477-0.051-0.0510.0000.0000.0000.000
34A2649ARG10.8190.90314.2750.3830.3830.0000.0000.0000.000
35A2650LEU00.0020.0049.752-0.221-0.2210.0000.0000.0000.000
36A2651LEU00.0530.03011.195-0.264-0.2640.0000.0000.0000.000
37A2652GLU-1-0.794-0.88213.590-0.864-0.8640.0000.0000.0000.000
38A2653ALA00.0030.0048.822-0.101-0.1010.0000.0000.0000.000
39A2654GLN0-0.0140.0209.376-0.444-0.4440.0000.0000.0000.000
40A2655ALA00.0130.00510.716-0.072-0.0720.0000.0000.0000.000
41A2656CYS0-0.077-0.02111.726-0.081-0.0810.0000.0000.0000.000
42A2657THR00.015-0.0327.604-0.081-0.0810.0000.0000.0000.000
43A2658GLY0-0.015-0.01310.071-0.254-0.2540.0000.0000.0000.000
44A2659GLY0-0.0100.00612.8750.1900.1900.0000.0000.0000.000
45A2660ILE0-0.024-0.02512.652-0.244-0.2440.0000.0000.0000.000
46A2661ILE0-0.023-0.0178.277-0.071-0.0710.0000.0000.0000.000
47A2662HIS00.0640.04612.5650.0750.0750.0000.0000.0000.000
48A2663PRO00.0190.01213.671-0.013-0.0130.0000.0000.0000.000
49A2664THR0-0.024-0.03314.7510.0790.0790.0000.0000.0000.000
50A2665THR00.0520.02116.6840.0180.0180.0000.0000.0000.000
51A2666GLY00.0320.01612.6600.0120.0120.0000.0000.0000.000
52A2667GLN0-0.0180.00012.947-0.152-0.1520.0000.0000.0000.000
53A2668LYS10.8450.9399.5732.2552.2550.0000.0000.0000.000
54A2669LEU0-0.045-0.00814.6360.1310.1310.0000.0000.0000.000
55A2670SER0-0.026-0.04017.097-0.089-0.0890.0000.0000.0000.000
56A2671LEU0-0.008-0.03318.3830.0400.0400.0000.0000.0000.000
57A2672GLN0-0.056-0.02620.8350.0520.0520.0000.0000.0000.000
58A2673ASP-1-0.771-0.85421.025-0.473-0.4730.0000.0000.0000.000
59A2674ALA0-0.022-0.01018.6120.0230.0230.0000.0000.0000.000
60A2675VAL00.0000.00120.3450.0300.0300.0000.0000.0000.000
61A2676SER0-0.055-0.02023.6360.0400.0400.0000.0000.0000.000
62A2677GLN0-0.046-0.03520.8280.0420.0420.0000.0000.0000.000
63A2678GLY00.0060.01322.6610.0110.0110.0000.0000.0000.000
64A2679VAL0-0.032-0.00516.4830.0030.0030.0000.0000.0000.000
65A2680ILE0-0.043-0.01018.061-0.036-0.0360.0000.0000.0000.000
66A2681ASP-1-0.731-0.85020.758-0.330-0.3300.0000.0000.0000.000
67A2682GLN00.046-0.00323.577-0.047-0.0470.0000.0000.0000.000
68A2683ASP-1-0.830-0.87426.029-0.319-0.3190.0000.0000.0000.000
69A2684MET00.0220.00419.795-0.036-0.0360.0000.0000.0000.000
70A2685ALA0-0.005-0.00821.422-0.053-0.0530.0000.0000.0000.000
71A2686THR0-0.095-0.06022.474-0.021-0.0210.0000.0000.0000.000
72A2687ARG10.8200.88122.3330.3580.3580.0000.0000.0000.000
73A2688LEU00.0140.01416.608-0.042-0.0420.0000.0000.0000.000
74A2689LYS10.9040.96919.4850.4070.4070.0000.0000.0000.000
75A2690PRO0-0.003-0.01120.815-0.029-0.0290.0000.0000.0000.000
76A2691ALA00.0290.02615.676-0.039-0.0390.0000.0000.0000.000
77A2692GLN00.0570.02516.287-0.115-0.1150.0000.0000.0000.000
78A2693LYS10.9300.97717.9730.4420.4420.0000.0000.0000.000
79A2694ALA0-0.043-0.01115.4160.0180.0180.0000.0000.0000.000
80A2695PHE0-0.0310.00511.339-0.102-0.1020.0000.0000.0000.000
81A2696ILE00.006-0.01715.6130.0500.0500.0000.0000.0000.000
82A2697GLY00.0230.02019.0960.0650.0650.0000.0000.0000.000
83A2698PHE0-0.050-0.04919.2940.0460.0460.0000.0000.0000.000
84A2706LYS10.8120.90122.2730.5140.5140.0000.0000.0000.000
85A2707MET0-0.024-0.00322.334-0.023-0.0230.0000.0000.0000.000
86A2708SER00.011-0.02817.482-0.069-0.0690.0000.0000.0000.000
87A2709ALA00.018-0.01416.8360.0530.0530.0000.0000.0000.000
88A2710ALA0-0.0140.00617.7400.0490.0490.0000.0000.0000.000
89A2711GLU-1-0.767-0.84319.574-0.489-0.4890.0000.0000.0000.000
90A2712ALA00.0340.03721.8170.0400.0400.0000.0000.0000.000
91A2713VAL0-0.027-0.01520.6720.0350.0350.0000.0000.0000.000
92A2714LYS10.8020.89922.2240.4480.4480.0000.0000.0000.000
93A2715GLU-1-0.885-0.95526.122-0.313-0.3130.0000.0000.0000.000
94A2716LYS10.8050.90226.9380.3180.3180.0000.0000.0000.000
95A2717TRP00.0090.01625.541-0.011-0.0110.0000.0000.0000.000
96A2718LEU0-0.027-0.00219.237-0.024-0.0240.0000.0000.0000.000
97A2719PRO00.0360.01422.7590.0180.0180.0000.0000.0000.000
98A2720TYR00.032-0.00319.312-0.047-0.0470.0000.0000.0000.000
99A2721GLU-1-0.856-0.93719.623-0.413-0.4130.0000.0000.0000.000
100A2722ALA0-0.070-0.01018.002-0.044-0.0440.0000.0000.0000.000
101A2723GLY00.0760.02716.719-0.100-0.1000.0000.0000.0000.000
102A2724GLN0-0.0160.00115.236-0.038-0.0380.0000.0000.0000.000
103A2725ARG10.8100.87713.2620.5970.5970.0000.0000.0000.000
104A2726PHE00.0340.00211.874-0.211-0.2110.0000.0000.0000.000
105A2727LEU00.0120.01011.413-0.266-0.2660.0000.0000.0000.000
106A2728GLU-1-0.810-0.91310.111-0.907-0.9070.0000.0000.0000.000
107A2729PHE0-0.021-0.0297.611-0.372-0.3720.0000.0000.0000.000
108A2730GLN0-0.0170.0046.719-1.086-1.0860.0000.0000.0000.000
109A2731TYR00.0380.0176.222-0.788-0.7880.0000.0000.0000.000
110A2732LEU0-0.030-0.0203.829-0.1740.3240.001-0.192-0.3070.000
111A2733THR0-0.058-0.0322.052-10.546-9.1846.873-4.237-3.999-0.040
112A2734GLY00.0050.0093.1961.5471.374-0.0020.376-0.2020.000
113A2735GLY00.0050.0224.9510.9210.955-0.001-0.002-0.0300.000
114A2736LEU0-0.007-0.0088.070-0.395-0.3950.0000.0000.0000.000
115A2737VAL00.004-0.00210.5010.0000.0000.0000.0000.0000.000
116A2738ASP-1-0.796-0.89112.577-0.483-0.4830.0000.0000.0000.000
117A2739PRO0-0.005-0.01116.1410.0380.0380.0000.0000.0000.000
118A2740GLU-1-0.838-0.89118.128-0.404-0.4040.0000.0000.0000.000
119A2741VAL00.0100.00016.9380.0440.0440.0000.0000.0000.000
120A2742HIS0-0.030-0.00913.6240.0400.0400.0000.0000.0000.000
121A2743GLY00.0010.00813.011-0.170-0.1700.0000.0000.0000.000
122A2744ARG10.8170.9046.4333.6023.6020.0000.0000.0000.000
123A2745ILE0-0.0050.00411.1860.1990.1990.0000.0000.0000.000
124A2746SER00.0470.02011.623-0.127-0.1270.0000.0000.0000.000
125A2747THR00.015-0.02111.962-0.045-0.0450.0000.0000.0000.000
126A2748GLU-1-0.946-0.96414.341-0.165-0.1650.0000.0000.0000.000
127A2749GLU-1-0.751-0.85016.461-0.368-0.3680.0000.0000.0000.000
128A2750ALA00.0070.00215.1290.0010.0010.0000.0000.0000.000
129A2751ILE0-0.030-0.02217.2340.0200.0200.0000.0000.0000.000
130A2752ARG10.8070.88119.9480.3260.3260.0000.0000.0000.000
131A2753LYS10.8120.90219.1400.5340.5340.0000.0000.0000.000
132A2754GLY00.0070.02021.916-0.002-0.0020.0000.0000.0000.000
133A2755PHE0-0.047-0.03416.248-0.005-0.0050.0000.0000.0000.000
134A2756ILE0-0.041-0.02715.132-0.010-0.0100.0000.0000.0000.000
135A2757ASP-1-0.746-0.87219.273-0.213-0.2130.0000.0000.0000.000
136A2758GLY00.0600.02519.524-0.020-0.0200.0000.0000.0000.000
137A2759ARG10.9130.94519.6140.1200.1200.0000.0000.0000.000
138A2760ALA0-0.030-0.01917.8930.0050.0050.0000.0000.0000.000
139A2761ALA00.0380.02315.247-0.054-0.0540.0000.0000.0000.000
140A2762GLN00.0230.00214.722-0.004-0.0040.0000.0000.0000.000
141A2763ARG10.8640.92915.6640.3360.3360.0000.0000.0000.000
142A2764LEU00.0050.01511.235-0.015-0.0150.0000.0000.0000.000
143A2765GLN00.0290.03410.752-0.093-0.0930.0000.0000.0000.000
144A2766ASP-1-0.770-0.83211.8830.2740.2740.0000.0000.0000.000
145A2767THR0-0.046-0.0407.9670.0520.0520.0000.0000.0000.000
146A2768SER0-0.083-0.05510.892-0.009-0.0090.0000.0000.0000.000
147A2769SER0-0.048-0.05613.477-0.052-0.0520.0000.0000.0000.000
148A2770TYR0-0.060-0.0298.708-0.183-0.1830.0000.0000.0000.000
149A2771ALA00.0450.02313.5860.0890.0890.0000.0000.0000.000
150A2772LYS10.7770.89113.838-0.055-0.0550.0000.0000.0000.000
151A2773ILE00.023-0.01312.6820.0320.0320.0000.0000.0000.000
152A2774LEU00.0030.01510.838-0.015-0.0150.0000.0000.0000.000
153A2775THR0-0.014-0.02715.4280.0690.0690.0000.0000.0000.000
154A2776CYS0-0.052-0.00713.8140.0140.0140.0000.0000.0000.000
155A2777PRO00.0490.03113.9810.0450.0450.0000.0000.0000.000
156A2778LYS10.9010.96016.368-0.370-0.3700.0000.0000.0000.000
157A2779THR00.011-0.01317.310-0.003-0.0030.0000.0000.0000.000
158A2780LYS10.8240.93119.2290.0280.0280.0000.0000.0000.000
159A2781LEU0-0.0090.01018.628-0.020-0.0200.0000.0000.0000.000
160A2782LYS10.8460.91917.9430.2080.2080.0000.0000.0000.000
161A2783ILE0-0.037-0.02611.8980.0770.0770.0000.0000.0000.000
162A2784SER0-0.018-0.02911.288-0.109-0.1090.0000.0000.0000.000
163A2785TYR00.0850.0285.324-0.047-0.0470.0000.0000.0000.000
164A2786LYS10.9530.9865.706-2.012-2.0120.0000.0000.0000.000
165A2787ASP-1-0.833-0.8867.6740.7280.7280.0000.0000.0000.000
166A2788ALA00.0150.0038.2100.2360.2360.0000.0000.0000.000
167A2789ILE0-0.0040.0112.305-1.575-0.2041.381-0.891-1.8610.004
168A2790ASN0-0.041-0.0205.3991.5451.610-0.0010.000-0.0630.000
169A2791ARG10.8980.9608.078-0.436-0.4360.0000.0000.0000.000
170A2792SER00.0170.0026.304-0.083-0.0830.0000.0000.0000.000
171A2793MET00.0100.0177.6020.7160.7160.0000.0000.0000.000
172A2794VAL0-0.031-0.0196.4420.1050.1050.0000.0000.0000.000
173A2795GLU-1-0.776-0.8439.069-0.029-0.0290.0000.0000.0000.000
174A2796ASP-1-0.911-0.96312.1790.5300.5300.0000.0000.0000.000
175A2797ILE00.0180.01213.341-0.107-0.1070.0000.0000.0000.000
176A2798THR0-0.036-0.04512.695-0.045-0.0450.0000.0000.0000.000
177A2799GLY0-0.0090.0049.569-0.166-0.1660.0000.0000.0000.000
178A2800LEU0-0.052-0.0277.602-0.037-0.0370.0000.0000.0000.000
179A2801ARG10.8410.9331.960-12.890-15.0148.140-2.596-3.4190.027
180A2802LEU00.0170.0096.828-0.567-0.5670.0000.0000.0000.000
181A2803LEU0-0.024-0.0249.5610.2600.2600.0000.0000.0000.000
182A2804GLU-1-0.780-0.87210.7590.3710.3710.0000.0000.0000.000
183A2805ALA0-0.028-0.03014.314-0.046-0.0460.0000.0000.0000.000
184A2806ALA00.0280.04917.3470.0340.0340.0000.0000.0000.000
185A2807SER00.0490.03821.134-0.035-0.0350.0000.0000.0000.000
186A2808VAL0-0.001-0.00724.322-0.015-0.0150.0000.0000.0000.000
187A2809SER0-0.028-0.03222.5840.0190.0190.0000.0000.0000.000
188A2810SER00.012-0.00720.7620.0080.0080.0000.0000.0000.000
189A2811LYS10.8930.95122.503-0.140-0.1400.0000.0000.0000.000