FMO DATABASE

FMODB ID: 228RR

Calculation Name: 1LDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LDD

Chain ID: A

ChEMBL ID:

UniProt ID: Q12440

Base Structure: X-ray

Registration Date: 2023-06-19

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-491023.807117
FMO2-HF: Nuclear repulsion	461362.168683
FMO2-HF: Total energy	-29661.638433
FMO2-MP2: Total energy	-29749.178168

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:773:LYS)

Summations of interaction energy for fragment #1(A:773:LYS)

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.
49.583	55.367	18.686	-10.705	-13.765	-0.051

Interaction energy analysis for fragmet #1(A:773:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.924 / q_NPA : 0.940

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 ES EX CT+mix DI(MP2)

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].
3	A	775	GLU	-1	-0.802	-0.914	3.788	-27.424	-24.213	-0.053	-1.733	-1.425	-0.004
4	A	776	LEU	0	0.021	0.031	6.662	2.106	2.106	0.000	0.000	0.000	0.000
5	A	777	THR	0	-0.039	-0.015	3.701	0.885	1.112	0.002	-0.042	-0.187	0.000
6	A	778	LEU	0	0.016	0.007	4.357	1.073	1.205	-0.001	-0.010	-0.121	0.000
7	A	779	GLN	0	0.007	0.018	6.580	1.474	1.474	0.000	0.000	0.000	0.000
8	A	780	ARG	1	0.907	0.949	9.018	20.515	20.515	0.000	0.000	0.000	0.000
9	A	781	SER	0	-0.057	-0.034	8.480	0.669	0.669	0.000	0.000	0.000	0.000
10	A	782	LEU	0	0.011	0.016	10.310	0.439	0.439	0.000	0.000	0.000	0.000
11	A	783	PRO	0	0.063	0.030	12.617	0.590	0.590	0.000	0.000	0.000	0.000
12	A	784	PHE	0	-0.012	-0.006	12.885	0.557	0.557	0.000	0.000	0.000	0.000
13	A	785	ILE	0	-0.003	0.000	10.038	0.363	0.363	0.000	0.000	0.000	0.000
14	A	786	GLU	-1	-0.820	-0.934	14.418	-12.915	-12.915	0.000	0.000	0.000	0.000
15	A	787	GLY	0	0.045	0.037	17.649	0.590	0.590	0.000	0.000	0.000	0.000
16	A	788	MET	0	-0.076	-0.011	15.059	0.258	0.258	0.000	0.000	0.000	0.000
17	A	789	LEU	0	-0.002	-0.012	17.179	0.377	0.377	0.000	0.000	0.000	0.000
18	A	790	THR	0	-0.043	-0.024	20.046	0.541	0.541	0.000	0.000	0.000	0.000
19	A	791	ASN	0	-0.111	-0.074	21.808	0.708	0.708	0.000	0.000	0.000	0.000
20	A	792	LEU	0	-0.047	-0.026	20.579	0.298	0.298	0.000	0.000	0.000	0.000
21	A	793	GLY	0	0.037	0.049	23.539	0.229	0.229	0.000	0.000	0.000	0.000
22	A	794	ALA	0	-0.001	-0.009	21.907	-0.461	-0.461	0.000	0.000	0.000	0.000
23	A	795	MET	0	-0.013	0.010	17.558	0.043	0.043	0.000	0.000	0.000	0.000
24	A	796	LYS	1	0.925	0.954	18.867	11.570	11.570	0.000	0.000	0.000	0.000
25	A	797	LEU	0	0.093	0.059	12.159	-0.154	-0.154	0.000	0.000	0.000	0.000
26	A	798	HIS	0	0.055	0.008	13.998	-0.191	-0.191	0.000	0.000	0.000	0.000
27	A	799	LYS	1	0.896	0.955	15.015	12.737	12.737	0.000	0.000	0.000	0.000
28	A	800	ILE	0	0.089	0.048	12.106	-0.156	-0.156	0.000	0.000	0.000	0.000
29	A	801	HIS	0	0.019	0.029	6.967	0.568	0.568	0.000	0.000	0.000	0.000
30	A	802	SER	0	-0.088	-0.060	11.310	-0.693	-0.693	0.000	0.000	0.000	0.000
31	A	803	PHE	0	0.057	0.018	13.829	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	804	LEU	0	0.039	0.034	9.218	0.238	0.238	0.000	0.000	0.000	0.000
33	A	805	LYS	1	0.871	0.939	8.997	22.271	22.271	0.000	0.000	0.000	0.000
34	A	806	ILE	0	-0.056	-0.020	11.215	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	807	THR	0	-0.038	-0.027	14.081	0.399	0.399	0.000	0.000	0.000	0.000
36	A	808	VAL	0	-0.035	0.000	9.044	0.363	0.363	0.000	0.000	0.000	0.000
37	A	809	PRO	0	0.029	0.027	12.166	-0.313	-0.313	0.000	0.000	0.000	0.000
38	A	810	LYS	1	1.038	0.988	11.060	15.960	15.960	0.000	0.000	0.000	0.000
39	A	811	ASP	-1	-0.899	-0.930	10.507	-18.430	-18.430	0.000	0.000	0.000	0.000
40	A	812	TRP	0	-0.083	-0.050	9.621	-0.933	-0.933	0.000	0.000	0.000	0.000
41	A	813	GLY	0	-0.018	-0.001	6.582	-1.759	-1.759	0.000	0.000	0.000	0.000
42	A	814	TYR	0	0.082	0.002	4.788	0.630	0.703	-0.001	-0.003	-0.069	0.000
43	A	815	ASN	0	-0.014	-0.021	5.121	-2.457	-2.398	-0.001	-0.002	-0.056	0.000
44	A	816	ARG	1	0.940	0.967	2.238	45.844	48.253	1.772	-1.238	-2.942	0.002
45	A	817	ILE	0	-0.021	0.006	1.790	-11.667	-12.920	10.920	-4.453	-5.214	-0.025
46	A	818	THR	0	-0.020	-0.005	3.061	6.789	6.446	0.134	0.548	-0.340	0.000
47	A	819	LEU	0	0.049	0.009	6.013	0.492	0.492	0.000	0.000	0.000	0.000
48	A	820	GLN	0	0.074	0.032	7.504	2.763	2.763	0.000	0.000	0.000	0.000
49	A	821	GLN	0	0.007	0.007	2.114	-3.827	-2.558	5.914	-3.772	-3.411	-0.024
50	A	822	LEU	0	-0.005	0.002	6.147	1.419	1.419	0.000	0.000	0.000	0.000
51	A	823	GLU	-1	-0.933	-0.971	8.087	-17.333	-17.333	0.000	0.000	0.000	0.000
52	A	824	GLY	0	0.015	0.014	9.812	1.240	1.240	0.000	0.000	0.000	0.000
53	A	825	TYR	0	0.024	0.005	8.152	1.048	1.048	0.000	0.000	0.000	0.000
54	A	826	LEU	0	0.010	-0.009	10.256	1.261	1.261	0.000	0.000	0.000	0.000
55	A	827	ASN	0	0.049	0.035	13.044	1.716	1.716	0.000	0.000	0.000	0.000
56	A	828	THR	0	0.035	0.027	12.975	0.647	0.647	0.000	0.000	0.000	0.000
57	A	829	LEU	0	-0.025	-0.018	12.819	0.825	0.825	0.000	0.000	0.000	0.000
58	A	830	ALA	0	-0.088	-0.058	16.002	0.777	0.777	0.000	0.000	0.000	0.000
59	A	831	ASP	-1	-0.945	-0.955	18.107	-13.385	-13.385	0.000	0.000	0.000	0.000
60	A	832	GLU	-1	-0.935	-0.939	16.615	-14.168	-14.168	0.000	0.000	0.000	0.000
61	A	833	GLY	0	0.051	0.011	20.448	0.244	0.244	0.000	0.000	0.000	0.000
62	A	834	ARG	1	0.764	0.892	16.436	14.232	14.232	0.000	0.000	0.000	0.000
63	A	835	LEU	0	-0.040	-0.025	15.430	0.090	0.090	0.000	0.000	0.000	0.000
64	A	836	LYS	1	0.883	0.935	19.849	10.187	10.187	0.000	0.000	0.000	0.000
65	A	837	TYR	0	0.015	-0.009	19.368	0.173	0.173	0.000	0.000	0.000	0.000
66	A	838	ILE	0	0.031	0.027	21.469	0.201	0.201	0.000	0.000	0.000	0.000
67	A	839	ALA	0	0.028	-0.004	23.989	-0.246	-0.246	0.000	0.000	0.000	0.000
68	A	840	ASN	0	-0.012	-0.017	25.398	0.161	0.161	0.000	0.000	0.000	0.000
69	A	841	GLY	0	-0.004	0.009	21.126	-0.165	-0.165	0.000	0.000	0.000	0.000
70	A	842	SER	0	-0.099	-0.043	19.995	-0.347	-0.347	0.000	0.000	0.000	0.000
71	A	843	TYR	0	0.012	-0.013	16.015	-0.049	-0.049	0.000	0.000	0.000	0.000
72	A	844	GLU	-1	-0.800	-0.903	19.585	-10.196	-10.196	0.000	0.000	0.000	0.000
73	A	845	ILE	0	-0.003	0.007	19.913	-0.300	-0.300	0.000	0.000	0.000	0.000
74	A	846	VAL	0	-0.017	0.007	21.595	0.655	0.655	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:773:LYS)