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: MNQYZ

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2045570.589479
FMO2-HF: Nuclear repulsion 1973365.568585
FMO2-HF: Total energy -72205.020894
FMO2-MP2: Total energy -72416.935588


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.
-24.192-13.8398.368-8.018-10.702-0.033
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 : 0.028 / q_NPA : 0.017
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].
3A2618PRO00.016-0.0132.287-9.534-5.4771.527-3.019-2.565-0.013
4A2619ILE0-0.019-0.0154.8200.9931.088-0.001-0.004-0.0890.000
5A2620ALA0-0.020-0.0076.593-0.111-0.1110.0000.0000.0000.000
6A2621ALA0-0.009-0.0139.3810.0320.0320.0000.0000.0000.000
7A2622ILE0-0.014-0.00311.4210.0130.0130.0000.0000.0000.000
8A2623PHE00.0240.02114.0890.0350.0350.0000.0000.0000.000
9A2624ASP-1-0.787-0.88215.744-0.008-0.0080.0000.0000.0000.000
10A2625THR0-0.022-0.04317.9030.0240.0240.0000.0000.0000.000
11A2626GLU-1-0.854-0.92420.2260.0320.0320.0000.0000.0000.000
12A2627ASN0-0.053-0.03622.8230.0040.0040.0000.0000.0000.000
13A2628LEU0-0.070-0.02620.9220.0060.0060.0000.0000.0000.000
14A2629GLU-1-0.805-0.87420.264-0.026-0.0260.0000.0000.0000.000
15A2630LYS10.7700.86114.2610.0590.0590.0000.0000.0000.000
16A2631ILE00.0010.02116.740-0.012-0.0120.0000.0000.0000.000
17A2632SER00.001-0.04415.913-0.053-0.0530.0000.0000.0000.000
18A2633ILE0-0.004-0.01911.4360.0350.0350.0000.0000.0000.000
19A2634THR0-0.021-0.04815.8750.0160.0160.0000.0000.0000.000
20A2635GLU-1-0.714-0.81519.369-0.188-0.1880.0000.0000.0000.000
21A2636GLY0-0.024-0.01418.3210.0370.0370.0000.0000.0000.000
22A2637ILE0-0.089-0.05618.3340.0160.0160.0000.0000.0000.000
23A2638GLU-1-0.950-0.96621.053-0.202-0.2020.0000.0000.0000.000
24A2639ARG10.7550.84522.1940.1000.1000.0000.0000.0000.000
25A2640GLY0-0.0090.00723.6440.0220.0220.0000.0000.0000.000
26A2641ILE0-0.039-0.01019.3060.0090.0090.0000.0000.0000.000
27A2642VAL0-0.036-0.02216.0510.0020.0020.0000.0000.0000.000
28A2643ASP-1-0.757-0.82518.855-0.312-0.3120.0000.0000.0000.000
29A2644SER00.1280.03519.217-0.035-0.0350.0000.0000.0000.000
30A2645ILE0-0.048-0.01418.938-0.054-0.0540.0000.0000.0000.000
31A2646THR0-0.046-0.05714.655-0.090-0.0900.0000.0000.0000.000
32A2647GLY00.0770.02014.879-0.104-0.1040.0000.0000.0000.000
33A2648GLN00.026-0.00115.402-0.045-0.0450.0000.0000.0000.000
34A2649ARG10.8710.92513.9200.4300.4300.0000.0000.0000.000
35A2650LEU0-0.018-0.0049.740-0.229-0.2290.0000.0000.0000.000
36A2651LEU00.0630.03011.105-0.257-0.2570.0000.0000.0000.000
37A2652GLU-1-0.794-0.87913.481-0.886-0.8860.0000.0000.0000.000
38A2653ALA00.0030.0048.504-0.117-0.1170.0000.0000.0000.000
39A2654GLN0-0.0270.0119.560-0.372-0.3720.0000.0000.0000.000
40A2655ALA00.0100.00610.791-0.046-0.0460.0000.0000.0000.000
41A2656CYS0-0.091-0.02811.796-0.070-0.0700.0000.0000.0000.000
42A2657THR00.013-0.0437.668-0.104-0.1040.0000.0000.0000.000
43A2658GLY0-0.016-0.0149.668-0.271-0.2710.0000.0000.0000.000
44A2659GLY0-0.022-0.00212.2640.2290.2290.0000.0000.0000.000
45A2660ILE0-0.035-0.02812.635-0.208-0.2080.0000.0000.0000.000
46A2661ILE0-0.014-0.0088.640-0.044-0.0440.0000.0000.0000.000
47A2662HIS00.0550.05313.0140.0690.0690.0000.0000.0000.000
48A2663PRO00.0340.01014.038-0.018-0.0180.0000.0000.0000.000
49A2664THR00.010-0.02014.7930.0660.0660.0000.0000.0000.000
50A2665THR00.0150.00516.7180.0200.0200.0000.0000.0000.000
51A2666GLY00.0400.02012.9560.0230.0230.0000.0000.0000.000
52A2667GLN0-0.020-0.00813.169-0.139-0.1390.0000.0000.0000.000
53A2668LYS10.8600.9529.2192.2642.2640.0000.0000.0000.000
54A2669LEU0-0.034-0.01514.7770.1060.1060.0000.0000.0000.000
55A2670SER0-0.011-0.02517.242-0.091-0.0910.0000.0000.0000.000
56A2671LEU00.007-0.02518.5200.0340.0340.0000.0000.0000.000
57A2672GLN0-0.054-0.02420.8320.0410.0410.0000.0000.0000.000
58A2673ASP-1-0.769-0.86121.453-0.418-0.4180.0000.0000.0000.000
59A2674ALA0-0.028-0.00718.8910.0250.0250.0000.0000.0000.000
60A2675VAL0-0.011-0.01320.6770.0290.0290.0000.0000.0000.000
61A2676SER0-0.062-0.02123.8220.0380.0380.0000.0000.0000.000
62A2677GLN0-0.053-0.03521.1640.0360.0360.0000.0000.0000.000
63A2678GLY00.0130.01823.0750.0150.0150.0000.0000.0000.000
64A2679VAL0-0.044-0.01016.733-0.001-0.0010.0000.0000.0000.000
65A2680ILE0-0.0300.00618.117-0.037-0.0370.0000.0000.0000.000
66A2681ASP-1-0.751-0.85920.883-0.328-0.3280.0000.0000.0000.000
67A2682GLN00.0650.00423.773-0.038-0.0380.0000.0000.0000.000
68A2683ASP-1-0.824-0.88925.817-0.308-0.3080.0000.0000.0000.000
69A2684MET0-0.015-0.01119.416-0.040-0.0400.0000.0000.0000.000
70A2685ALA00.0120.00421.517-0.055-0.0550.0000.0000.0000.000
71A2686THR0-0.085-0.05722.566-0.030-0.0300.0000.0000.0000.000
72A2687ARG10.8480.90722.2160.3610.3610.0000.0000.0000.000
73A2688LEU00.0070.01316.535-0.049-0.0490.0000.0000.0000.000
74A2689LYS10.9030.96719.3660.4010.4010.0000.0000.0000.000
75A2690PRO0-0.012-0.01320.536-0.029-0.0290.0000.0000.0000.000
76A2691ALA00.0400.02915.477-0.042-0.0420.0000.0000.0000.000
77A2692GLN00.0640.02816.106-0.095-0.0950.0000.0000.0000.000
78A2693LYS10.9440.99017.6410.4470.4470.0000.0000.0000.000
79A2694ALA0-0.055-0.00515.2340.0130.0130.0000.0000.0000.000
80A2695PHE0-0.0180.00411.289-0.087-0.0870.0000.0000.0000.000
81A2696ILE0-0.014-0.02015.3570.0440.0440.0000.0000.0000.000
82A2697GLY00.011-0.00818.7260.0690.0690.0000.0000.0000.000
83A2698PHE0-0.053-0.04718.9010.0400.0400.0000.0000.0000.000
84A2706LYS10.8530.93721.6120.5020.5020.0000.0000.0000.000
85A2707MET0-0.0260.00122.299-0.007-0.0070.0000.0000.0000.000
86A2708SER00.036-0.02017.151-0.064-0.0640.0000.0000.0000.000
87A2709ALA00.026-0.00116.2970.0530.0530.0000.0000.0000.000
88A2710ALA00.0100.01417.5970.0550.0550.0000.0000.0000.000
89A2711GLU-1-0.797-0.87619.173-0.444-0.4440.0000.0000.0000.000
90A2712ALA00.0290.02921.4750.0440.0440.0000.0000.0000.000
91A2713VAL0-0.054-0.01920.3570.0370.0370.0000.0000.0000.000
92A2714LYS10.8410.92622.5290.4220.4220.0000.0000.0000.000
93A2715GLU-1-0.936-0.97225.404-0.301-0.3010.0000.0000.0000.000
94A2716LYS10.8540.93226.9170.3110.3110.0000.0000.0000.000
95A2717TRP00.0100.01025.279-0.007-0.0070.0000.0000.0000.000
96A2718LEU0-0.052-0.01419.037-0.016-0.0160.0000.0000.0000.000
97A2719PRO00.0380.01422.7750.0120.0120.0000.0000.0000.000
98A2720TYR00.035-0.00619.179-0.045-0.0450.0000.0000.0000.000
99A2721GLU-1-0.919-0.95619.554-0.425-0.4250.0000.0000.0000.000
100A2722ALA0-0.050-0.02517.781-0.065-0.0650.0000.0000.0000.000
101A2723GLY00.0740.02316.639-0.105-0.1050.0000.0000.0000.000
102A2724GLN0-0.042-0.01415.223-0.029-0.0290.0000.0000.0000.000
103A2725ARG10.8360.89313.1760.6290.6290.0000.0000.0000.000
104A2726PHE00.0180.00111.755-0.231-0.2310.0000.0000.0000.000
105A2727LEU00.0230.01111.307-0.291-0.2910.0000.0000.0000.000
106A2728GLU-1-0.811-0.9029.951-1.043-1.0430.0000.0000.0000.000
107A2729PHE0-0.042-0.0307.649-0.433-0.4330.0000.0000.0000.000
108A2730GLN0-0.012-0.0066.618-1.151-1.1510.0000.0000.0000.000
109A2731TYR00.0040.0036.209-0.724-0.7240.0000.0000.0000.000
110A2732LEU0-0.038-0.0263.827-0.1060.2570.001-0.099-0.2650.000
111A2733THR0-0.076-0.0522.168-9.140-6.3704.178-3.375-3.573-0.032
112A2734GLY00.0050.0093.1151.0450.9720.0280.367-0.3220.000
113A2735GLY0-0.0130.0104.7201.1151.165-0.001-0.007-0.0420.000
114A2736LEU0-0.020-0.0117.783-0.305-0.3050.0000.0000.0000.000
115A2737VAL00.0150.00110.2920.0050.0050.0000.0000.0000.000
116A2738ASP-1-0.806-0.88212.411-0.474-0.4740.0000.0000.0000.000
117A2739PRO00.000-0.01515.9570.0180.0180.0000.0000.0000.000
118A2740GLU-1-0.857-0.91717.870-0.411-0.4110.0000.0000.0000.000
119A2741VAL00.0240.01616.2140.0440.0440.0000.0000.0000.000
120A2742HIS0-0.057-0.00912.7890.0350.0350.0000.0000.0000.000
121A2743GLY0-0.019-0.01712.747-0.177-0.1770.0000.0000.0000.000
122A2744ARG10.8270.9106.2623.5923.5920.0000.0000.0000.000
123A2745ILE0-0.0020.01210.9970.2020.2020.0000.0000.0000.000
124A2746SER00.0410.01711.353-0.131-0.1310.0000.0000.0000.000
125A2747THR00.036-0.00811.290-0.044-0.0440.0000.0000.0000.000
126A2748GLU-1-0.951-0.96813.702-0.134-0.1340.0000.0000.0000.000
127A2749GLU-1-0.734-0.84615.921-0.352-0.3520.0000.0000.0000.000
128A2750ALA0-0.007-0.00214.519-0.006-0.0060.0000.0000.0000.000
129A2751ILE0-0.034-0.02616.6320.0200.0200.0000.0000.0000.000
130A2752ARG10.7910.87319.2680.3140.3140.0000.0000.0000.000
131A2753LYS10.8040.89618.5580.5150.5150.0000.0000.0000.000
132A2754GLY00.0090.02121.264-0.001-0.0010.0000.0000.0000.000
133A2755PHE0-0.060-0.04115.782-0.006-0.0060.0000.0000.0000.000
134A2756ILE0-0.029-0.02114.610-0.028-0.0280.0000.0000.0000.000
135A2757ASP-1-0.742-0.87018.818-0.234-0.2340.0000.0000.0000.000
136A2758GLY00.0710.02519.199-0.021-0.0210.0000.0000.0000.000
137A2759ARG10.9110.94819.3940.1320.1320.0000.0000.0000.000
138A2760ALA0-0.029-0.01817.4200.0030.0030.0000.0000.0000.000
139A2761ALA00.0310.02515.118-0.051-0.0510.0000.0000.0000.000
140A2762GLN0-0.024-0.01014.7100.0180.0180.0000.0000.0000.000
141A2763ARG10.9180.95515.7670.3620.3620.0000.0000.0000.000
142A2764LEU00.0090.00411.164-0.005-0.0050.0000.0000.0000.000
143A2765GLN00.0310.02010.913-0.111-0.1110.0000.0000.0000.000
144A2766ASP-1-0.771-0.81911.7390.1990.1990.0000.0000.0000.000
145A2767THR0-0.039-0.0407.6500.0520.0520.0000.0000.0000.000
146A2768SER0-0.118-0.07010.678-0.025-0.0250.0000.0000.0000.000
147A2769SER0-0.055-0.05713.263-0.033-0.0330.0000.0000.0000.000
148A2770TYR0-0.078-0.0398.641-0.183-0.1830.0000.0000.0000.000
149A2771ALA00.0410.01913.6040.0820.0820.0000.0000.0000.000
150A2772LYS10.8410.91414.182-0.018-0.0180.0000.0000.0000.000
151A2773ILE0-0.015-0.02112.4970.0410.0410.0000.0000.0000.000
152A2774LEU00.0090.02310.690-0.040-0.0400.0000.0000.0000.000
153A2775THR0-0.025-0.01315.2870.0720.0720.0000.0000.0000.000
154A2776CYS0-0.076-0.00113.9940.0070.0070.0000.0000.0000.000
155A2777PRO00.0640.03214.1520.0370.0370.0000.0000.0000.000
156A2778LYS10.9160.96916.437-0.273-0.2730.0000.0000.0000.000
157A2779THR00.022-0.02517.189-0.007-0.0070.0000.0000.0000.000
158A2780LYS10.8590.95418.8030.0770.0770.0000.0000.0000.000
159A2781LEU0-0.0180.00718.623-0.013-0.0130.0000.0000.0000.000
160A2782LYS10.8870.93417.7910.2270.2270.0000.0000.0000.000
161A2783ILE0-0.038-0.02811.7530.0750.0750.0000.0000.0000.000
162A2784SER00.003-0.01611.417-0.110-0.1100.0000.0000.0000.000
163A2785TYR00.0870.0285.219-0.025-0.0250.0000.0000.0000.000
164A2786LYS10.9710.9945.478-1.873-1.8730.0000.0000.0000.000
165A2787ASP-1-0.816-0.8727.6430.6040.6040.0000.0000.0000.000
166A2788ALA0-0.002-0.0068.3060.2590.2590.0000.0000.0000.000
167A2789ILE00.0280.0112.466-1.449-0.0691.407-0.900-1.8870.006
168A2790ASN0-0.046-0.0085.3221.3961.459-0.0010.000-0.0620.000
169A2791ARG10.9170.9527.763-0.267-0.2670.0000.0000.0000.000
170A2792SER0-0.061-0.0125.9900.0290.0290.0000.0000.0000.000
171A2793MET00.0230.0128.3820.3940.3940.0000.0000.0000.000
172A2794VAL0-0.043-0.0147.020-0.040-0.0400.0000.0000.0000.000
173A2795GLU-1-0.774-0.8389.568-0.032-0.0320.0000.0000.0000.000
174A2796ASP-1-0.888-0.96212.6920.5120.5120.0000.0000.0000.000
175A2797ILE00.0080.01312.848-0.086-0.0860.0000.0000.0000.000
176A2798THR0-0.015-0.03513.057-0.043-0.0430.0000.0000.0000.000
177A2799GLY0-0.049-0.01210.174-0.130-0.1300.0000.0000.0000.000
178A2800LEU0-0.053-0.0278.2790.1400.1400.0000.0000.0000.000
179A2801ARG10.8410.9442.568-7.018-5.3701.230-0.981-1.8970.006
180A2802LEU00.0420.0177.136-0.530-0.5300.0000.0000.0000.000
181A2803LEU0-0.008-0.0199.6060.2270.2270.0000.0000.0000.000
182A2804GLU-1-0.785-0.87111.0980.2810.2810.0000.0000.0000.000
183A2805ALA0-0.046-0.03514.600-0.044-0.0440.0000.0000.0000.000
184A2806ALA00.0180.01917.4310.0300.0300.0000.0000.0000.000
185A2807SER00.0410.01621.084-0.036-0.0360.0000.0000.0000.000
186A2808VAL0-0.025-0.01424.250-0.015-0.0150.0000.0000.0000.000
187A2809SER0-0.031-0.03922.5010.0210.0210.0000.0000.0000.000
188A2810SER00.0500.02120.6590.0080.0080.0000.0000.0000.000
189A2811LYS10.8660.93922.153-0.091-0.0910.0000.0000.0000.000