FMO DATABASE

FMODB ID: 2L5KR

Calculation Name: 1LDD-A-Xray540

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: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-491103.297782
FMO2-HF: Nuclear repulsion	461457.695648
FMO2-HF: Total energy	-29645.602134
FMO2-MP2: Total energy	-29732.842005

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.
-2.966	-8.594	31.051	-15.531	-9.89	-0.006

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 : 0 / q_Mulliken : 0.165 / q_NPA : 0.024

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].
4	A	774	TYR	0	-0.115	0.067	3.588	-0.506	0.315	0.027	-0.373	-0.475	0.000
5	A	775	GLU	0	0.261	-0.097	3.788	-2.003	0.862	-0.049	-1.663	-1.152	-0.005
6	A	775	GLU	-1	-0.953	-0.785	6.988	-0.913	-0.913	0.000	0.000	0.000	0.000
7	A	776	LEU	0	0.074	-0.099	6.538	0.164	0.164	0.000	0.000	0.000	0.000
8	A	776	LEU	0	-0.037	0.116	7.659	0.039	0.039	0.000	0.000	0.000	0.000
9	A	777	THR	0	0.031	-0.081	4.430	-0.471	-0.412	-0.001	-0.013	-0.044	0.000
10	A	777	THR	0	-0.069	0.055	3.561	1.041	1.218	0.004	-0.047	-0.134	0.000
11	A	778	LEU	0	0.090	-0.096	5.162	0.093	0.093	0.000	0.000	0.000	0.000
12	A	778	LEU	0	-0.061	0.121	4.338	-0.092	-0.041	-0.001	-0.007	-0.042	0.000
13	A	779	GLN	0	0.138	-0.080	6.512	0.020	0.020	0.000	0.000	0.000	0.000
14	A	779	GLN	0	-0.110	0.090	9.815	0.032	0.032	0.000	0.000	0.000	0.000
15	A	780	ARG	0	0.049	-0.120	8.913	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	780	ARG	1	0.844	1.067	8.918	-0.739	-0.739	0.000	0.000	0.000	0.000
17	A	781	SER	0	-0.027	-0.080	8.939	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	781	SER	0	-0.024	0.064	8.392	0.012	0.012	0.000	0.000	0.000	0.000
19	A	782	LEU	0	0.111	-0.122	10.264	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	782	LEU	0	-0.103	0.127	12.157	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	783	PRO	0	0.046	-0.077	12.573	-0.024	-0.024	0.000	0.000	0.000	0.000
22	A	784	PHE	0	0.097	0.014	13.789	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	784	PHE	0	-0.091	0.091	12.636	0.019	0.019	0.000	0.000	0.000	0.000
24	A	785	ILE	0	0.099	-0.093	13.526	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	785	ILE	0	-0.066	0.087	10.135	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	786	GLU	0	0.073	-0.125	14.434	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	786	GLU	-1	-0.963	-0.829	16.211	0.052	0.052	0.000	0.000	0.000	0.000
28	A	787	GLY	0	0.024	-0.077	17.646	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	788	MET	0	0.145	0.002	17.456	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	788	MET	0	-0.184	0.099	14.369	0.011	0.011	0.000	0.000	0.000	0.000
31	A	789	LEU	0	0.036	-0.124	18.416	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	789	LEU	0	-0.088	0.104	16.800	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	790	THR	0	0.027	-0.061	20.087	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	790	THR	0	-0.076	0.037	21.357	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	791	ASN	0	0.074	-0.090	22.334	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	791	ASN	0	-0.173	0.036	21.903	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	792	LEU	0	-0.027	-0.131	22.628	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	792	LEU	0	-0.067	0.103	20.791	0.002	0.002	0.000	0.000	0.000	0.000
39	A	793	GLY	0	0.060	-0.048	23.578	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	794	ALA	0	0.174	-0.003	21.976	0.006	0.006	0.000	0.000	0.000	0.000
41	A	794	ALA	0	-0.082	0.122	22.970	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	795	MET	0	-0.010	-0.156	19.266	0.003	0.003	0.000	0.000	0.000	0.000
43	A	795	MET	0	-0.090	0.133	17.655	0.006	0.006	0.000	0.000	0.000	0.000
44	A	796	LYS	0	0.169	-0.072	18.983	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	796	LYS	1	0.841	1.070	19.398	0.022	0.022	0.000	0.000	0.000	0.000
46	A	797	LEU	0	0.172	-0.095	14.975	0.026	0.026	0.000	0.000	0.000	0.000
47	A	797	LEU	0	-0.068	0.141	12.355	0.008	0.008	0.000	0.000	0.000	0.000
48	A	798	HIS	0	0.080	-0.086	14.125	0.011	0.011	0.000	0.000	0.000	0.000
49	A	798	HIS	0	-0.049	0.088	15.837	0.010	0.010	0.000	0.000	0.000	0.000
50	A	799	LYS	0	0.018	-0.124	14.970	0.024	0.024	0.000	0.000	0.000	0.000
51	A	799	LYS	1	0.909	1.081	18.294	-0.042	-0.042	0.000	0.000	0.000	0.000
52	A	800	ILE	0	0.168	-0.077	14.190	0.039	0.039	0.000	0.000	0.000	0.000
53	A	800	ILE	0	-0.059	0.131	12.163	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	801	HIS	0	0.107	-0.070	10.792	0.045	0.045	0.000	0.000	0.000	0.000
55	A	801	HIS	0	-0.092	0.092	6.854	0.009	0.009	0.000	0.000	0.000	0.000
56	A	802	SER	0	0.012	-0.104	11.289	0.074	0.074	0.000	0.000	0.000	0.000
57	A	802	SER	0	-0.093	0.049	14.897	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	803	PHE	0	0.070	-0.090	13.708	0.044	0.044	0.000	0.000	0.000	0.000
59	A	803	PHE	0	0.009	0.117	15.265	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	804	LEU	0	0.058	-0.088	10.599	0.021	0.021	0.000	0.000	0.000	0.000
61	A	804	LEU	0	-0.032	0.098	9.018	0.005	0.005	0.000	0.000	0.000	0.000
62	A	805	LYS	0	0.036	-0.101	10.210	0.103	0.103	0.000	0.000	0.000	0.000
63	A	805	LYS	1	0.856	1.034	9.329	-0.228	-0.228	0.000	0.000	0.000	0.000
64	A	806	ILE	0	0.007	-0.117	11.147	0.077	0.077	0.000	0.000	0.000	0.000
65	A	806	ILE	0	-0.120	0.084	15.129	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	807	THR	0	0.041	-0.092	14.147	0.008	0.008	0.000	0.000	0.000	0.000
67	A	807	THR	0	-0.103	0.064	14.250	0.000	0.000	0.000	0.000	0.000	0.000
68	A	808	VAL	0	0.057	-0.084	10.667	-0.057	-0.057	0.000	0.000	0.000	0.000
69	A	808	VAL	0	-0.067	0.096	9.085	0.015	0.015	0.000	0.000	0.000	0.000
70	A	809	PRO	0	-0.009	-0.076	12.163	0.044	0.044	0.000	0.000	0.000	0.000
71	A	810	LYS	0	0.188	0.012	11.113	0.155	0.155	0.000	0.000	0.000	0.000
72	A	810	LYS	1	0.887	1.065	12.234	-0.483	-0.483	0.000	0.000	0.000	0.000
73	A	811	ASP	0	0.021	-0.127	10.595	0.257	0.257	0.000	0.000	0.000	0.000
74	A	811	ASP	-1	-0.928	-0.798	13.748	0.555	0.555	0.000	0.000	0.000	0.000
75	A	812	TRP	0	-0.035	-0.164	9.746	0.088	0.088	0.000	0.000	0.000	0.000
76	A	812	TRP	0	-0.050	0.127	9.464	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	813	GLY	0	-0.082	-0.123	6.663	0.641	0.641	0.000	0.000	0.000	0.000
78	A	814	TYR	0	0.130	-0.032	4.854	-0.279	-0.279	0.000	0.000	0.000	0.000
79	A	814	TYR	0	0.002	0.150	6.135	-0.109	-0.109	0.000	0.000	0.000	0.000
80	A	815	ASN	0	0.053	-0.098	5.067	-0.415	-0.357	-0.002	-0.001	-0.056	0.000
81	A	815	ASN	0	-0.067	0.082	7.320	0.128	0.128	0.000	0.000	0.000	0.000
82	A	816	ARG	0	0.080	-0.067	3.379	-1.069	-0.954	0.002	0.062	-0.180	0.000
83	A	816	ARG	1	0.820	1.035	2.819	-2.597	-1.667	0.332	-0.582	-0.680	0.004
84	A	817	ILE	0	0.033	-0.112	2.244	-3.461	-1.978	1.869	-1.502	-1.850	-0.004
85	A	817	ILE	0	-0.094	0.129	1.681	2.438	-2.787	10.857	-3.448	-2.184	0.006
86	A	818	THR	0	0.062	-0.083	2.910	1.321	0.531	0.163	0.784	-0.157	0.001
87	A	818	THR	0	-0.101	0.054	4.601	-0.009	0.010	-0.001	-0.019	0.001	0.000
88	A	819	LEU	0	0.135	-0.074	6.021	-0.103	-0.103	0.000	0.000	0.000	0.000
89	A	819	LEU	0	-0.054	0.115	10.359	0.014	0.014	0.000	0.000	0.000	0.000
90	A	820	GLN	0	0.137	-0.083	8.256	0.009	0.009	0.000	0.000	0.000	0.000
91	A	820	GLN	0	-0.038	0.116	7.743	0.074	0.074	0.000	0.000	0.000	0.000
92	A	821	GLN	0	0.042	-0.085	4.685	-0.012	0.037	-0.001	-0.038	-0.009	0.000
93	A	821	GLN	0	-0.043	0.085	1.700	3.358	-2.882	17.852	-8.684	-2.928	-0.008
94	A	822	LEU	0	0.141	-0.088	6.204	-0.097	-0.097	0.000	0.000	0.000	0.000
95	A	822	LEU	0	-0.116	0.100	7.832	0.019	0.019	0.000	0.000	0.000	0.000
96	A	823	GLU	0	0.051	-0.130	8.186	0.029	0.029	0.000	0.000	0.000	0.000
97	A	823	GLU	-1	-1.009	-0.839	11.358	-0.225	-0.225	0.000	0.000	0.000	0.000
98	A	824	GLY	0	-0.019	-0.098	9.877	0.037	0.037	0.000	0.000	0.000	0.000
99	A	825	TYR	0	0.154	0.032	9.075	0.029	0.029	0.000	0.000	0.000	0.000
100	A	825	TYR	0	-0.062	0.084	8.186	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	826	LEU	0	0.046	-0.121	10.276	0.048	0.048	0.000	0.000	0.000	0.000
102	A	826	LEU	0	-0.082	0.090	11.486	0.011	0.011	0.000	0.000	0.000	0.000
103	A	827	ASN	0	0.148	-0.048	13.086	0.041	0.041	0.000	0.000	0.000	0.000
104	A	827	ASN	0	-0.065	0.095	14.488	0.032	0.032	0.000	0.000	0.000	0.000
105	A	828	THR	0	0.077	-0.045	13.774	0.036	0.036	0.000	0.000	0.000	0.000
106	A	828	THR	0	-0.039	0.068	13.116	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	829	LEU	0	0.073	-0.081	14.404	0.018	0.018	0.000	0.000	0.000	0.000
108	A	829	LEU	0	-0.101	0.064	12.861	0.016	0.016	0.000	0.000	0.000	0.000
109	A	830	ALA	0	0.048	-0.093	15.996	0.027	0.027	0.000	0.000	0.000	0.000
110	A	830	ALA	0	-0.111	0.056	18.109	0.000	0.000	0.000	0.000	0.000	0.000
111	A	831	ASP	0	0.041	-0.094	18.121	0.022	0.022	0.000	0.000	0.000	0.000
112	A	831	ASP	-1	-1.047	-0.882	18.129	-0.184	-0.184	0.000	0.000	0.000	0.000
113	A	832	GLU	0	-0.025	-0.072	18.773	0.009	0.009	0.000	0.000	0.000	0.000
114	A	832	GLU	-1	-1.034	-0.896	16.616	-0.143	-0.143	0.000	0.000	0.000	0.000
115	A	833	GLY	0	0.078	-0.109	20.424	0.003	0.003	0.000	0.000	0.000	0.000
116	A	834	ARG	0	0.117	0.004	18.979	0.015	0.015	0.000	0.000	0.000	0.000
117	A	834	ARG	1	0.797	1.057	16.587	0.042	0.042	0.000	0.000	0.000	0.000
118	A	835	LEU	0	-0.010	-0.127	18.497	0.020	0.020	0.000	0.000	0.000	0.000
119	A	835	LEU	0	-0.065	0.086	15.503	0.000	0.000	0.000	0.000	0.000	0.000
120	A	836	LYS	0	0.223	-0.071	19.866	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	836	LYS	1	0.821	1.090	23.632	0.036	0.036	0.000	0.000	0.000	0.000
122	A	837	TYR	0	0.118	-0.076	20.532	0.007	0.007	0.000	0.000	0.000	0.000
123	A	837	TYR	0	-0.115	0.089	19.284	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	838	ILE	0	0.076	-0.083	21.534	0.005	0.005	0.000	0.000	0.000	0.000
125	A	838	ILE	0	-0.099	0.118	23.864	0.000	0.000	0.000	0.000	0.000	0.000
126	A	839	ALA	0	0.174	-0.100	24.082	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	839	ALA	0	-0.068	0.111	27.603	0.001	0.001	0.000	0.000	0.000	0.000
128	A	840	ASN	0	-0.014	-0.127	25.514	0.004	0.004	0.000	0.000	0.000	0.000
129	A	840	ASN	0	-0.113	0.087	26.252	0.000	0.000	0.000	0.000	0.000	0.000
130	A	841	GLY	0	0.027	-0.111	21.111	0.002	0.002	0.000	0.000	0.000	0.000
131	A	842	SER	0	-0.043	-0.001	20.110	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	842	SER	0	-0.051	0.044	21.902	0.005	0.005	0.000	0.000	0.000	0.000
133	A	843	TYR	0	0.110	-0.064	18.191	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	843	TYR	0	-0.115	0.048	16.144	0.005	0.005	0.000	0.000	0.000	0.000
135	A	844	GLU	0	0.128	-0.116	19.657	0.015	0.015	0.000	0.000	0.000	0.000
136	A	844	GLU	-1	-0.997	-0.848	23.394	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	845	ILE	0	0.044	-0.113	20.808	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	845	ILE	0	-0.062	0.109	19.926	0.001	0.001	0.000	0.000	0.000	0.000
139	A	846	VAL	0	-0.100	-0.135	21.617	0.008	0.008	0.000	0.000	0.000	0.000
140	A	846	VAL	0	0.027	0.040	22.556	0.000	0.000	0.000	0.000	0.000	0.000

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