FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: N6QYQ

Calculation Name: 1LM5-B-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LM5

Chain ID: B

ChEMBL ID:

UniProt ID: P15924

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2155589.635615
FMO2-HF: Nuclear repulsion 2080748.951392
FMO2-HF: Total energy -74840.684223
FMO2-MP2: Total energy -75060.259981


3D Structure Molmil
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:2613:LEU)


Summations of interaction energy for fragment #1(B:2613:LEU)
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.
-46.925-39.56612.239-8.09-11.504-0.074
Interaction energy analysis for fragmet #1(B:2613:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.812 / q_NPA : 0.898
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].
3B2615GLU-1-0.877-0.9283.285-45.571-42.8320.003-1.168-1.574-0.005
4B2616SER0-0.038-0.0452.573-11.424-8.5520.666-1.406-2.132-0.014
5B2617SER00.0430.0314.3092.7522.8450.000-0.026-0.0670.000
174B2786LYS10.8270.9123.66464.84065.6500.001-0.424-0.3860.001
175B2787ASP-1-0.813-0.8844.965-35.929-35.887-0.001-0.002-0.0390.000
177B2789ILE00.0390.0222.1530.9900.0323.050-0.366-1.7250.000
178B2790ASN0-0.055-0.0211.930-33.409-32.1478.488-4.643-5.106-0.056
179B2791ARG10.9110.9673.66030.49230.5750.0130.049-0.1450.000
189B2801ARG10.8350.9303.37936.96237.3780.019-0.104-0.3300.000
6B2618PRO00.0460.0066.600-2.690-2.6900.0000.0000.0000.000
7B2619ILE0-0.027-0.0167.6800.1320.1320.0000.0000.0000.000
8B2620ALA0-0.0100.0079.8241.3661.3660.0000.0000.0000.000
9B2621ALA0-0.007-0.00712.8651.3341.3340.0000.0000.0000.000
10B2622ILE0-0.022-0.01013.285-1.418-1.4180.0000.0000.0000.000
11B2623PHE00.0360.01914.4270.4500.4500.0000.0000.0000.000
12B2624ASP-1-0.752-0.86016.128-13.080-13.0800.0000.0000.0000.000
13B2625THR0-0.043-0.05517.658-0.169-0.1690.0000.0000.0000.000
14B2626GLU-1-0.957-0.97219.553-11.114-11.1140.0000.0000.0000.000
15B2627ASN0-0.048-0.04622.9490.7170.7170.0000.0000.0000.000
16B2628LEU0-0.071-0.02020.3060.1250.1250.0000.0000.0000.000
17B2629GLU-1-0.825-0.88620.380-11.728-11.7280.0000.0000.0000.000
18B2630LYS10.7660.86515.76114.67614.6760.0000.0000.0000.000
19B2631ILE00.0120.01818.3360.5960.5960.0000.0000.0000.000
20B2632SER00.0480.00718.232-0.831-0.8310.0000.0000.0000.000
21B2633ILE00.0150.00114.5430.0990.0990.0000.0000.0000.000
22B2634THR0-0.033-0.05318.4540.0260.0260.0000.0000.0000.000
23B2635GLU-1-0.808-0.88622.210-10.879-10.8790.0000.0000.0000.000
24B2636GLY00.013-0.00319.8790.1730.1730.0000.0000.0000.000
25B2637ILE0-0.109-0.05620.946-0.038-0.0380.0000.0000.0000.000
26B2638GLU-1-0.931-0.95223.090-9.780-9.7800.0000.0000.0000.000
27B2639ARG10.7130.81523.44411.95011.9500.0000.0000.0000.000
28B2640GLY00.0110.01724.8590.0380.0380.0000.0000.0000.000
29B2641ILE0-0.042-0.00419.765-0.382-0.3820.0000.0000.0000.000
30B2642VAL0-0.056-0.04417.238-1.030-1.0300.0000.0000.0000.000
31B2643ASP-1-0.715-0.79819.678-13.870-13.8700.0000.0000.0000.000
32B2644SER00.0990.02220.631-0.387-0.3870.0000.0000.0000.000
33B2645ILE0-0.052-0.01720.635-0.072-0.0720.0000.0000.0000.000
34B2646THR0-0.054-0.06315.508-0.825-0.8250.0000.0000.0000.000
35B2647GLY00.0610.02216.821-0.764-0.7640.0000.0000.0000.000
36B2648GLN0-0.021-0.03318.2340.0620.0620.0000.0000.0000.000
37B2649ARG10.8420.91616.04914.73614.7360.0000.0000.0000.000
38B2650LEU00.0010.00211.978-1.063-1.0630.0000.0000.0000.000
39B2651LEU00.0460.02614.632-0.496-0.4960.0000.0000.0000.000
40B2652GLU-1-0.819-0.89517.084-14.644-14.6440.0000.0000.0000.000
41B2653ALA00.0220.01611.8270.1150.1150.0000.0000.0000.000
42B2654GLN00.0020.02213.6770.4090.4090.0000.0000.0000.000
43B2655ALA00.0120.00515.3280.3560.3560.0000.0000.0000.000
44B2656CYS0-0.073-0.01915.5100.0080.0080.0000.0000.0000.000
45B2657THR00.003-0.02411.976-0.127-0.1270.0000.0000.0000.000
46B2658GLY0-0.015-0.01215.325-0.191-0.1910.0000.0000.0000.000
47B2659GLY0-0.020-0.01518.1950.5670.5670.0000.0000.0000.000
48B2660ILE0-0.043-0.02117.617-0.758-0.7580.0000.0000.0000.000
49B2661ILE0-0.003-0.00313.1200.2920.2920.0000.0000.0000.000
50B2662HIS00.0550.04417.332-0.351-0.3510.0000.0000.0000.000
51B2663PRO00.0160.00517.121-0.493-0.4930.0000.0000.0000.000
52B2664THR0-0.056-0.04117.700-0.172-0.1720.0000.0000.0000.000
53B2665THR00.035-0.00519.362-0.370-0.3700.0000.0000.0000.000
54B2666GLY00.0390.02016.416-0.183-0.1830.0000.0000.0000.000
55B2667GLN0-0.0300.00616.769-0.344-0.3440.0000.0000.0000.000
56B2668LYS10.8510.91815.83116.04516.0450.0000.0000.0000.000
57B2669LEU0-0.0170.00219.4770.6210.6210.0000.0000.0000.000
58B2670SER00.005-0.01222.176-0.340-0.3400.0000.0000.0000.000
59B2671LEU0-0.014-0.02622.5440.0330.0330.0000.0000.0000.000
60B2672GLN0-0.0160.00525.3730.2750.2750.0000.0000.0000.000
61B2673ASP-1-0.792-0.88426.426-10.083-10.0830.0000.0000.0000.000
62B2674ALA0-0.012-0.00223.4850.0120.0120.0000.0000.0000.000
63B2675VAL0-0.010-0.00425.2870.0270.0270.0000.0000.0000.000
64B2676SER0-0.076-0.05028.2900.2750.2750.0000.0000.0000.000
65B2677GLN0-0.053-0.03125.7320.0780.0780.0000.0000.0000.000
66B2678GLY00.0190.02327.074-0.126-0.1260.0000.0000.0000.000
67B2679VAL0-0.029-0.00621.204-0.274-0.2740.0000.0000.0000.000
68B2680ILE0-0.064-0.01622.169-0.576-0.5760.0000.0000.0000.000
69B2681ASP-1-0.754-0.85924.691-10.373-10.3730.0000.0000.0000.000
70B2682GLN00.0640.00327.599-0.382-0.3820.0000.0000.0000.000
71B2683ASP-1-0.885-0.92529.444-9.438-9.4380.0000.0000.0000.000
72B2684MET0-0.043-0.01322.347-0.336-0.3360.0000.0000.0000.000
73B2685ALA00.018-0.00225.096-0.320-0.3200.0000.0000.0000.000
74B2686THR0-0.093-0.05726.4890.0930.0930.0000.0000.0000.000
75B2687ARG10.9050.95025.00210.90610.9060.0000.0000.0000.000
76B2688LEU00.0210.01320.237-0.301-0.3010.0000.0000.0000.000
77B2689LYS10.9230.98023.3139.6449.6440.0000.0000.0000.000
78B2690PRO0-0.005-0.01523.835-0.054-0.0540.0000.0000.0000.000
79B2691ALA00.0360.03119.207-0.225-0.2250.0000.0000.0000.000
80B2692GLN00.0780.03120.382-0.451-0.4510.0000.0000.0000.000
81B2693LYS10.8480.92022.41910.22610.2260.0000.0000.0000.000
82B2694ALA0-0.035-0.01019.5620.0530.0530.0000.0000.0000.000
83B2695PHE0-0.0080.03218.082-0.449-0.4490.0000.0000.0000.000
84B2696ILE0-0.008-0.02320.7050.2050.2050.0000.0000.0000.000
85B2697GLY00.0310.03824.2040.3730.3730.0000.0000.0000.000
86B2698PHE0-0.027-0.02523.3280.2740.2740.0000.0000.0000.000
87B2699GLU-1-0.791-0.90728.046-9.829-9.8290.0000.0000.0000.000
88B2700GLY0-0.020-0.01231.6130.1810.1810.0000.0000.0000.000
89B2701VAL00.0060.00732.7110.2380.2380.0000.0000.0000.000
90B2702LYS10.7780.86627.59411.04111.0410.0000.0000.0000.000
91B2703GLY00.0200.01733.1980.0820.0820.0000.0000.0000.000
92B2704LYS10.9430.95532.6317.8607.8600.0000.0000.0000.000
93B2705LYS10.9560.98631.2149.4239.4230.0000.0000.0000.000
94B2706LYS0-0.0170.00827.412-0.141-0.1410.0000.0000.0000.000
95B2707MET0-0.0620.00127.186-0.202-0.2020.0000.0000.0000.000
96B2708SER00.0910.02221.807-0.286-0.2860.0000.0000.0000.000
97B2709ALA00.032-0.00420.0700.4050.4050.0000.0000.0000.000
98B2710ALA00.0320.02221.2200.2520.2520.0000.0000.0000.000
99B2711GLU-1-0.774-0.85222.926-11.035-11.0350.0000.0000.0000.000
100B2712ALA00.0320.01225.2420.4240.4240.0000.0000.0000.000
101B2713VAL0-0.0080.00823.0370.2640.2640.0000.0000.0000.000
102B2714LYS10.8330.92326.23610.85610.8560.0000.0000.0000.000
103B2715GLU-1-0.868-0.94128.803-9.451-9.4510.0000.0000.0000.000
104B2716LYS10.8470.92229.84410.18110.1810.0000.0000.0000.000
105B2717TRP00.0150.01729.3180.0350.0350.0000.0000.0000.000
106B2718LEU0-0.059-0.00122.149-0.076-0.0760.0000.0000.0000.000
107B2719PRO00.0440.01525.498-0.046-0.0460.0000.0000.0000.000
108B2720TYR00.0560.01921.032-0.449-0.4490.0000.0000.0000.000
109B2721GLU-1-0.900-0.95721.129-13.928-13.9280.0000.0000.0000.000
110B2722ALA0-0.032-0.01620.174-0.653-0.6530.0000.0000.0000.000
111B2723GLY00.0440.00219.538-0.545-0.5450.0000.0000.0000.000
112B2724GLN0-0.073-0.04516.9680.1120.1120.0000.0000.0000.000
113B2725ARG10.8410.91515.42714.02514.0250.0000.0000.0000.000
114B2726PHE00.025-0.00414.524-0.907-0.9070.0000.0000.0000.000
115B2727LEU0-0.0060.00014.969-0.606-0.6060.0000.0000.0000.000
116B2728GLU-1-0.842-0.92312.133-21.278-21.2780.0000.0000.0000.000
117B2729PHE0-0.013-0.01910.469-2.115-2.1150.0000.0000.0000.000
118B2730GLN0-0.028-0.00110.211-1.576-1.5760.0000.0000.0000.000
119B2731TYR00.0220.0099.558-0.927-0.9270.0000.0000.0000.000
120B2732LEU00.0150.0045.751-1.580-1.5800.0000.0000.0000.000
121B2733THR0-0.050-0.0435.777-2.572-2.5720.0000.0000.0000.000
122B2734GLY00.0000.0068.1911.5731.5730.0000.0000.0000.000
123B2735GLY0-0.0140.0099.7671.6081.6080.0000.0000.0000.000
124B2736LEU0-0.018-0.01012.6470.4030.4030.0000.0000.0000.000
125B2737VAL0-0.004-0.00415.6210.1560.1560.0000.0000.0000.000
126B2738ASP-1-0.792-0.89817.918-12.186-12.1860.0000.0000.0000.000
127B2739PRO0-0.033-0.03521.4630.1770.1770.0000.0000.0000.000
128B2740GLU-1-0.953-0.96623.795-10.575-10.5750.0000.0000.0000.000
129B2741VAL00.006-0.00822.5800.3670.3670.0000.0000.0000.000
130B2742HIS0-0.071-0.01922.109-0.083-0.0830.0000.0000.0000.000
131B2743GLY00.0490.03719.334-0.333-0.3330.0000.0000.0000.000
132B2744ARG10.8020.89511.44822.15822.1580.0000.0000.0000.000
133B2745ILE0-0.0130.00516.9690.5450.5450.0000.0000.0000.000
134B2746SER00.002-0.02215.173-0.734-0.7340.0000.0000.0000.000
135B2747THR0-0.030-0.03513.9400.7060.7060.0000.0000.0000.000
136B2748GLU-1-0.792-0.87616.375-17.730-17.7300.0000.0000.0000.000
137B2749GLU-1-0.856-0.93519.456-11.979-11.9790.0000.0000.0000.000
138B2750ALA00.004-0.00518.9480.6740.6740.0000.0000.0000.000
139B2751ILE0-0.033-0.01720.1060.5700.5700.0000.0000.0000.000
140B2752ARG10.8690.94422.96011.65111.6510.0000.0000.0000.000
141B2753LYS10.7900.89223.60312.63912.6390.0000.0000.0000.000
142B2754GLY0-0.029-0.00325.4930.3780.3780.0000.0000.0000.000
143B2755PHE0-0.062-0.02821.0710.2020.2020.0000.0000.0000.000
144B2756ILE0-0.025-0.01618.385-0.058-0.0580.0000.0000.0000.000
145B2757ASP-1-0.795-0.90222.558-12.949-12.9490.0000.0000.0000.000
146B2758GLY00.0590.01721.395-0.687-0.6870.0000.0000.0000.000
147B2759ARG10.9350.96620.62512.31512.3150.0000.0000.0000.000
148B2760ALA0-0.022-0.00520.077-0.543-0.5430.0000.0000.0000.000
149B2761ALA00.0440.02817.374-0.974-0.9740.0000.0000.0000.000
150B2762GLN0-0.023-0.02115.688-0.822-0.8220.0000.0000.0000.000
151B2763ARG10.8700.92315.60014.28014.2800.0000.0000.0000.000
152B2764LEU00.0020.00513.723-0.978-0.9780.0000.0000.0000.000
153B2765GLN00.0350.04311.712-2.243-2.2430.0000.0000.0000.000
154B2766ASP-1-0.830-0.88310.526-27.140-27.1400.0000.0000.0000.000
155B2767THR00.009-0.0176.880-0.368-0.3680.0000.0000.0000.000
156B2768SER0-0.031-0.0149.254-1.633-1.6330.0000.0000.0000.000
157B2769SER0-0.108-0.0769.9341.3491.3490.0000.0000.0000.000
158B2770TYR0-0.046-0.02110.2721.1391.1390.0000.0000.0000.000
159B2771ALA00.0380.01813.065-0.048-0.0480.0000.0000.0000.000
160B2772LYS10.8330.90511.42724.40624.4060.0000.0000.0000.000
161B2773ILE0-0.016-0.02613.4771.1531.1530.0000.0000.0000.000
162B2774LEU00.0030.01411.3391.0841.0840.0000.0000.0000.000
163B2775THR0-0.030-0.02315.393-0.124-0.1240.0000.0000.0000.000
164B2776CYS0-0.059-0.00912.120-0.412-0.4120.0000.0000.0000.000
165B2777PRO00.0450.01713.2730.7860.7860.0000.0000.0000.000
166B2778LYS10.9531.00114.54919.18219.1820.0000.0000.0000.000
167B2779THR00.001-0.03314.8260.6430.6430.0000.0000.0000.000
168B2780LYS10.8660.94017.39914.68414.6840.0000.0000.0000.000
169B2781LEU00.0230.02416.1290.3720.3720.0000.0000.0000.000
170B2782LYS10.8610.92816.32115.30315.3030.0000.0000.0000.000
171B2783ILE0-0.014-0.01110.169-0.712-0.7120.0000.0000.0000.000
172B2784SER00.0300.0129.8350.4950.4950.0000.0000.0000.000
173B2785TYR00.0730.0207.792-1.294-1.2940.0000.0000.0000.000
176B2788ALA0-0.019-0.0176.688-1.365-1.3650.0000.0000.0000.000
180B2792SER0-0.036-0.0074.8643.6843.6840.0000.0000.0000.000
181B2793MET00.0200.0225.985-2.910-2.9100.0000.0000.0000.000
182B2794VAL0-0.049-0.0365.661-0.565-0.5650.0000.0000.0000.000
183B2795GLU-1-0.764-0.8358.419-15.330-15.3300.0000.0000.0000.000
184B2796ASP-1-0.868-0.93912.092-16.286-16.2860.0000.0000.0000.000
185B2797ILE0-0.047-0.02313.713-0.002-0.0020.0000.0000.0000.000
186B2798THR0-0.041-0.05014.253-0.187-0.1870.0000.0000.0000.000
187B2799GLY00.0150.01810.525-0.124-0.1240.0000.0000.0000.000
188B2800LEU0-0.058-0.0289.746-1.753-1.7530.0000.0000.0000.000
190B2802LEU00.0370.0129.0221.2321.2320.0000.0000.0000.000
191B2803LEU0-0.032-0.0199.264-1.960-1.9600.0000.0000.0000.000
192B2804GLU-1-0.845-0.91511.286-18.180-18.1800.0000.0000.0000.000
193B2805ALA0-0.041-0.03213.846-0.420-0.4200.0000.0000.0000.000
194B2806ALA00.0240.02117.0050.2450.2450.0000.0000.0000.000
195B2807SER00.0510.02620.419-0.260-0.2600.0000.0000.0000.000
196B2808VAL-1-0.984-0.98122.599-11.407-11.4070.0000.0000.0000.000