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: GNLZ1

Calculation Name: 1LM5-A-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 193
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2064394.054471
FMO2-HF: Nuclear repulsion 1991848.17624
FMO2-HF: Total energy -72545.878231
FMO2-MP2: Total energy -72758.982306


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:2615:ACE )


Summations of interaction energy for fragment #1(A:2615:ACE )
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.
-0.2172.0250.391-1.36-1.273-0.006
Interaction energy analysis for fragmet #1(A:2615:ACE )
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 : 0.003
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].
3A2617SER 00.0220.0353.8400.7551.640-0.006-0.449-0.4290.000
4A2618PRO 00.035-0.0017.146-0.099-0.0990.0000.0000.0000.000
5A2619ILE 0-0.023-0.0169.354-0.009-0.0090.0000.0000.0000.000
6A2620ALA 0-0.020-0.00912.3670.0620.0620.0000.0000.0000.000
7A2621ALA 00.000-0.00814.8860.0480.0480.0000.0000.0000.000
8A2622ILE 0-0.028-0.01217.566-0.031-0.0310.0000.0000.0000.000
9A2623PHE 00.0250.02520.2620.0060.0060.0000.0000.0000.000
10A2624ASP -1-0.795-0.88722.050-0.107-0.1070.0000.0000.0000.000
11A2625THR 0-0.038-0.04624.1990.0070.0070.0000.0000.0000.000
12A2626GLU -1-0.832-0.91226.456-0.086-0.0860.0000.0000.0000.000
13A2627ASN 0-0.056-0.03629.1290.0100.0100.0000.0000.0000.000
14A2628LEU 0-0.079-0.03027.0790.0000.0000.0000.0000.0000.000
15A2629GLU -1-0.816-0.89026.323-0.098-0.0980.0000.0000.0000.000
16A2630LYS 10.7440.84419.9510.1850.1850.0000.0000.0000.000
17A2631ILE 00.0100.03122.8930.0120.0120.0000.0000.0000.000
18A2632SER 0-0.002-0.03221.561-0.020-0.0200.0000.0000.0000.000
19A2633ILE 00.012-0.01216.7850.0030.0030.0000.0000.0000.000
20A2634THR 0-0.017-0.04121.3360.0070.0070.0000.0000.0000.000
21A2635GLU -1-0.738-0.85124.541-0.098-0.0980.0000.0000.0000.000
22A2636GLY 00.004-0.00624.1060.0030.0030.0000.0000.0000.000
23A2637ILE 0-0.091-0.05123.1530.0060.0060.0000.0000.0000.000
24A2638GLU -1-0.957-0.97426.392-0.062-0.0620.0000.0000.0000.000
25A2639ARG 10.7660.85928.2910.0990.0990.0000.0000.0000.000
26A2640GLY 0-0.0060.01029.2400.0020.0020.0000.0000.0000.000
27A2641ILE 0-0.0210.00025.304-0.001-0.0010.0000.0000.0000.000
28A2642VAL 0-0.047-0.02821.379-0.013-0.0130.0000.0000.0000.000
29A2643ASP -1-0.767-0.84023.827-0.079-0.0790.0000.0000.0000.000
30A2644SER 00.1290.03423.961-0.006-0.0060.0000.0000.0000.000
31A2645ILE 0-0.053-0.01122.1540.0010.0010.0000.0000.0000.000
32A2646THR 0-0.041-0.05719.010-0.003-0.0030.0000.0000.0000.000
33A2647GLY 00.0770.02319.202-0.014-0.0140.0000.0000.0000.000
34A2648GLN 00.010-0.01019.785-0.007-0.0070.0000.0000.0000.000
35A2649ARG 10.8690.91317.0350.0570.0570.0000.0000.0000.000
36A2650LEU 0-0.0160.00114.950-0.010-0.0100.0000.0000.0000.000
37A2651LEU 00.0560.02015.141-0.015-0.0150.0000.0000.0000.000
38A2652GLU -1-0.789-0.86216.554-0.022-0.0220.0000.0000.0000.000
39A2653ALA 00.0050.00211.3710.0260.0260.0000.0000.0000.000
40A2654GLN 0-0.0330.00911.7480.0290.0290.0000.0000.0000.000
41A2655ALA 00.0090.01413.7490.0290.0290.0000.0000.0000.000
42A2656CYS 0-0.086-0.02412.7900.0280.0280.0000.0000.0000.000
43A2657THR 0-0.016-0.0508.9550.0470.0470.0000.0000.0000.000
44A2658GLY 0-0.009-0.01910.796-0.001-0.0010.0000.0000.0000.000
45A2659GLY 0-0.031-0.00413.4260.0020.0020.0000.0000.0000.000
46A2660ILE 0-0.038-0.02415.227-0.028-0.0280.0000.0000.0000.000
47A2661ILE 0-0.009-0.00512.291-0.002-0.0020.0000.0000.0000.000
48A2662HIS 00.0540.05816.810-0.012-0.0120.0000.0000.0000.000
49A2663PRO 00.0370.00818.739-0.021-0.0210.0000.0000.0000.000
50A2664THR 0-0.054-0.03119.949-0.013-0.0130.0000.0000.0000.000
51A2665THR 00.0690.02420.749-0.011-0.0110.0000.0000.0000.000
52A2666GLY 00.0300.00916.676-0.008-0.0080.0000.0000.0000.000
53A2667GLN 0-0.013-0.00815.903-0.011-0.0110.0000.0000.0000.000
54A2668LYS 10.9140.96910.0110.1660.1660.0000.0000.0000.000
55A2669LEU 0-0.012-0.00816.7270.0200.0200.0000.0000.0000.000
56A2670SER 00.0470.03619.3440.0020.0020.0000.0000.0000.000
57A2671LEU 0-0.007-0.03720.899-0.006-0.0060.0000.0000.0000.000
58A2672GLN 0-0.014-0.00223.324-0.003-0.0030.0000.0000.0000.000
59A2673ASP -1-0.831-0.92323.750-0.025-0.0250.0000.0000.0000.000
60A2674ALA 0-0.054-0.01822.139-0.007-0.0070.0000.0000.0000.000
61A2675VAL 0-0.020-0.02024.025-0.004-0.0040.0000.0000.0000.000
62A2676SER 0-0.066-0.01827.438-0.002-0.0020.0000.0000.0000.000
63A2677GLN 0-0.038-0.03123.838-0.008-0.0080.0000.0000.0000.000
64A2678GLY 00.0170.02027.328-0.006-0.0060.0000.0000.0000.000
65A2679VAL 0-0.041-0.00921.104-0.007-0.0070.0000.0000.0000.000
66A2680ILE 0-0.042-0.00322.111-0.007-0.0070.0000.0000.0000.000
67A2681ASP -1-0.785-0.86725.175-0.042-0.0420.0000.0000.0000.000
68A2682GLN 00.0720.01127.5160.0010.0010.0000.0000.0000.000
69A2683ASP -1-0.877-0.93929.012-0.022-0.0220.0000.0000.0000.000
70A2684MET 0-0.021-0.01423.5490.0050.0050.0000.0000.0000.000
71A2685ALA 00.002-0.00324.5260.0030.0030.0000.0000.0000.000
72A2686THR 0-0.061-0.03625.0530.0080.0080.0000.0000.0000.000
73A2687ARG 10.9060.94924.8690.0440.0440.0000.0000.0000.000
74A2688LEU 00.0060.01319.4920.0040.0040.0000.0000.0000.000
75A2689LYS 10.9030.96721.0840.0080.0080.0000.0000.0000.000
76A2690PRO 0-0.027-0.01921.4150.0090.0090.0000.0000.0000.000
77A2691ALA 00.0510.03317.0970.0130.0130.0000.0000.0000.000
78A2692GLN 00.0880.03417.0700.0030.0030.0000.0000.0000.000
79A2693LYS 10.9330.97818.511-0.020-0.0200.0000.0000.0000.000
80A2694ALA 0-0.037-0.00115.5500.0160.0160.0000.0000.0000.000
81A2695PHE 0-0.0330.00211.9270.0260.0260.0000.0000.0000.000
82A2696ILE 0-0.029-0.02415.9480.0140.0140.0000.0000.0000.000
83A2697GLY 00.015-0.01019.1850.0030.0030.0000.0000.0000.000
84A2698PHE 0-0.088-0.06019.129-0.020-0.0200.0000.0000.0000.000
85A2699NME 00.0170.01823.4220.0010.0010.0000.0000.0000.000
86A2705ACE 00.0560.01725.276-0.001-0.0010.0000.0000.0000.000
87A2706LYS 10.8340.93021.556-0.106-0.1060.0000.0000.0000.000
88A2707MET 00.0380.04621.9890.0110.0110.0000.0000.0000.000
89A2708SER 00.0260.00116.845-0.003-0.0030.0000.0000.0000.000
90A2709ALA 00.0290.00016.312-0.015-0.0150.0000.0000.0000.000
91A2710ALA 0-0.0030.00817.010-0.015-0.0150.0000.0000.0000.000
92A2711GLU -1-0.797-0.90118.7490.1290.1290.0000.0000.0000.000
93A2712ALA 00.0430.03021.367-0.013-0.0130.0000.0000.0000.000
94A2713VAL 0-0.055-0.02120.074-0.010-0.0100.0000.0000.0000.000
95A2714LYS 10.8880.95822.574-0.119-0.1190.0000.0000.0000.000
96A2715GLU -1-0.921-0.97224.9690.0680.0680.0000.0000.0000.000
97A2716LYS 10.8720.93626.734-0.050-0.0500.0000.0000.0000.000
98A2717TRP 00.0110.00925.393-0.005-0.0050.0000.0000.0000.000
99A2718LEU 0-0.057-0.02019.400-0.007-0.0070.0000.0000.0000.000
100A2719PRO 00.0290.00923.5180.0050.0050.0000.0000.0000.000
101A2720TYR 00.0520.01419.1770.0070.0070.0000.0000.0000.000
102A2721GLU -1-0.926-0.96519.8860.0120.0120.0000.0000.0000.000
103A2722ALA 0-0.047-0.02518.743-0.005-0.0050.0000.0000.0000.000
104A2723GLY 00.0670.02017.3900.0020.0020.0000.0000.0000.000
105A2724GLN 00.0070.00615.7630.0320.0320.0000.0000.0000.000
106A2725ARG 10.8120.88514.1130.0300.0300.0000.0000.0000.000
107A2726PHE 00.014-0.00212.704-0.007-0.0070.0000.0000.0000.000
108A2727LEU 00.0310.01511.6770.0230.0230.0000.0000.0000.000
109A2728GLU -1-0.881-0.9439.8640.1070.1070.0000.0000.0000.000
110A2729PHE 0-0.046-0.0248.213-0.018-0.0180.0000.0000.0000.000
111A2730GLN 0-0.008-0.0027.462-0.016-0.0160.0000.0000.0000.000
112A2731TYR 0-0.0070.0026.0810.3530.3530.0000.0000.0000.000
113A2732LEU 0-0.051-0.0364.2200.2920.5640.000-0.049-0.2240.000
114A2733THR 0-0.076-0.0593.180-1.852-1.2510.142-0.563-0.180-0.004
115A2734GLY 0-0.015-0.0042.947-0.0530.4810.243-0.355-0.422-0.002
116A2735GLY 0-0.0050.0133.774-0.247-0.2970.0120.056-0.0180.000
117A2736LEU 0-0.008-0.0086.617-0.239-0.2390.0000.0000.0000.000
118A2737VAL 00.0160.00310.0680.0610.0610.0000.0000.0000.000
119A2738ASP -1-0.822-0.90712.0990.1910.1910.0000.0000.0000.000
120A2739PRO 0-0.016-0.02115.421-0.008-0.0080.0000.0000.0000.000
121A2740GLU -1-0.920-0.94817.6960.1030.1030.0000.0000.0000.000
122A2741VAL 00.0080.02515.374-0.011-0.0110.0000.0000.0000.000
123A2742HIS 0-0.061-0.01413.188-0.024-0.0240.0000.0000.0000.000
124A2743GLY 0-0.030-0.02812.2930.0180.0180.0000.0000.0000.000
125A2744ARG 10.8150.9066.586-0.547-0.5470.0000.0000.0000.000
126A2745ILE 0-0.0070.00910.093-0.045-0.0450.0000.0000.0000.000
127A2746SER 00.0240.0159.8540.1340.1340.0000.0000.0000.000
128A2747THR 00.029-0.0089.544-0.059-0.0590.0000.0000.0000.000
129A2748GLU -1-0.920-0.95211.8610.2370.2370.0000.0000.0000.000
130A2749GLU -1-0.725-0.84914.2310.2150.2150.0000.0000.0000.000
131A2750ALA 0-0.012-0.00713.200-0.044-0.0440.0000.0000.0000.000
132A2751ILE 0-0.027-0.02615.194-0.049-0.0490.0000.0000.0000.000
133A2752ARG 10.7900.87917.654-0.247-0.2470.0000.0000.0000.000
134A2753LYS 10.8220.91317.432-0.250-0.2500.0000.0000.0000.000
135A2754GLY 00.0030.01819.876-0.019-0.0190.0000.0000.0000.000
136A2755PHE 0-0.086-0.04814.842-0.012-0.0120.0000.0000.0000.000
137A2756ILE 0-0.032-0.02413.367-0.013-0.0130.0000.0000.0000.000
138A2757ASP -1-0.783-0.87917.6150.1420.1420.0000.0000.0000.000
139A2758GLY 00.0700.01117.6870.0190.0190.0000.0000.0000.000
140A2759ARG 10.9180.95917.737-0.092-0.0920.0000.0000.0000.000
141A2760ALA 00.002-0.01516.191-0.004-0.0040.0000.0000.0000.000
142A2761ALA 00.0140.02413.5910.0130.0130.0000.0000.0000.000
143A2762GLN 0-0.024-0.01313.1110.0200.0200.0000.0000.0000.000
144A2763ARG 10.9670.98414.340-0.117-0.1170.0000.0000.0000.000
145A2764LEU 0-0.0030.00210.154-0.017-0.0170.0000.0000.0000.000
146A2765GLN 00.0240.0149.4750.0280.0280.0000.0000.0000.000
147A2766ASP -1-0.793-0.83210.2800.0240.0240.0000.0000.0000.000
148A2767THR 0-0.052-0.0467.280-0.091-0.0910.0000.0000.0000.000
149A2768SER 0-0.117-0.07910.707-0.059-0.0590.0000.0000.0000.000
150A2769SER 0-0.041-0.03013.912-0.012-0.0120.0000.0000.0000.000
151A2770TYR 0-0.065-0.0469.108-0.006-0.0060.0000.0000.0000.000
152A2771ALA 00.0450.02414.563-0.020-0.0200.0000.0000.0000.000
153A2772LYS 10.8820.94616.3620.0890.0890.0000.0000.0000.000
154A2773ILE 0-0.026-0.03114.9890.0060.0060.0000.0000.0000.000
155A2774LEU 0-0.0050.02014.7170.0040.0040.0000.0000.0000.000
156A2775THR 0-0.0130.00118.9830.0060.0060.0000.0000.0000.000
157A2776CYS 0-0.066-0.01918.660-0.011-0.0110.0000.0000.0000.000
158A2777PRO 00.0750.04219.4980.0150.0150.0000.0000.0000.000
159A2778LYS 10.9540.99821.9030.1750.1750.0000.0000.0000.000
160A2779THR 00.009-0.01521.9730.0140.0140.0000.0000.0000.000
161A2780LYS 10.8800.96123.8150.1160.1160.0000.0000.0000.000
162A2781LEU 0-0.0140.00522.7140.0110.0110.0000.0000.0000.000
163A2782LYS 10.9110.95621.5580.0630.0630.0000.0000.0000.000
164A2783ILE 0-0.038-0.02816.029-0.001-0.0010.0000.0000.0000.000
165A2784SER 00.0280.01913.518-0.002-0.0020.0000.0000.0000.000
166A2785TYR 00.0920.0368.701-0.049-0.0490.0000.0000.0000.000
167A2786LYS 11.0161.0226.6300.5720.5720.0000.0000.0000.000
168A2787ASP -1-0.840-0.91610.182-0.258-0.2580.0000.0000.0000.000
169A2788ALA 0-0.004-0.01212.714-0.022-0.0220.0000.0000.0000.000
170A2789ILE 00.0100.0076.3850.0070.0070.0000.0000.0000.000
171A2790ASN 0-0.047-0.01410.333-0.124-0.1240.0000.0000.0000.000
172A2791ARG 10.8780.93011.8920.2390.2390.0000.0000.0000.000
173A2792SER 0-0.067-0.01211.860-0.008-0.0080.0000.0000.0000.000
174A2793MET 00.0280.01513.994-0.034-0.0340.0000.0000.0000.000
175A2794VAL 0-0.054-0.01912.060-0.034-0.0340.0000.0000.0000.000
176A2795GLU -1-0.763-0.81914.757-0.172-0.1720.0000.0000.0000.000
177A2796ASP -1-0.889-0.96817.212-0.213-0.2130.0000.0000.0000.000
178A2797ILE 0-0.0040.01615.9320.0100.0100.0000.0000.0000.000
179A2798THR 00.009-0.03717.249-0.013-0.0130.0000.0000.0000.000
180A2799GLY 0-0.045-0.01213.827-0.005-0.0050.0000.0000.0000.000
181A2800LEU 0-0.063-0.03212.579-0.114-0.1140.0000.0000.0000.000
182A2801ARG 10.8660.9518.1071.1171.1170.0000.0000.0000.000
183A2802LEU 00.0350.00913.0580.0500.0500.0000.0000.0000.000
184A2803LEU 0-0.003-0.01915.293-0.024-0.0240.0000.0000.0000.000
185A2804GLU -1-0.819-0.89317.267-0.169-0.1690.0000.0000.0000.000
186A2805ALA 0-0.050-0.03720.7350.0000.0000.0000.0000.0000.000
187A2806ALA 00.0090.00823.4330.0020.0020.0000.0000.0000.000
188A2807SER 00.0350.00827.0190.0020.0020.0000.0000.0000.000
189A2808VAL 0-0.035-0.01630.0870.0050.0050.0000.0000.0000.000
190A2809SER 0-0.038-0.04427.665-0.007-0.0070.0000.0000.0000.000
191A2810SER 00.0480.01225.8550.0000.0000.0000.0000.0000.000
192A2811LYS 10.8180.91626.9380.0810.0810.0000.0000.0000.000
193A2812NME 00.0520.03328.8040.0060.0060.0000.0000.0000.000