FMO DATABASE

FMODB ID: YN3R2

Calculation Name: 5DTC-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12024

Base Structure: X-ray

Registration Date: 2025-07-10

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	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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-616459.641844
FMO2-HF: Nuclear repulsion	581989.963024
FMO2-HF: Total energy	-34469.678821
FMO2-MP2: Total energy	-34571.952719

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:5:LYS)

Summations of interaction energy for fragment #1(A:5: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.
-3.031	0.058	1.037	-1.942	-2.184	-0.007

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.162 / q_NPA : 0.027

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	6	SER	0	-0.060	0.054	4.474	0.890	1.138	-0.001	-0.105	-0.142	0.000
5	A	7	GLN	0	0.010	-0.113	3.044	-1.870	-0.111	-0.012	-0.804	-0.943	0.001
6	A	7	GLN	0	-0.012	0.098	4.476	-0.269	-0.184	-0.001	-0.005	-0.079	0.000
7	A	8	VAL	0	0.072	-0.067	4.542	-0.538	-0.419	-0.002	-0.016	-0.101	0.000
8	A	8	VAL	0	-0.048	0.104	6.528	-0.045	-0.045	0.000	0.000	0.000	0.000
9	A	9	LYS	0	0.108	-0.090	7.258	0.114	0.114	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.883	1.072	8.924	-0.121	-0.121	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.006	-0.083	10.270	-0.072	-0.072	0.000	0.000	0.000	0.000
12	A	10	ILE	0	-0.068	0.086	11.556	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	11	ARG	0	0.109	-0.072	13.527	0.047	0.047	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.874	1.055	17.070	0.044	0.044	0.000	0.000	0.000	0.000
15	A	12	PHE	0	0.064	-0.096	17.182	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	12	PHE	0	-0.074	0.073	16.980	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	13	PHE	0	0.102	-0.055	20.015	0.013	0.013	0.000	0.000	0.000	0.000
18	A	13	PHE	0	-0.056	0.095	20.906	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	14	THR	0	0.031	-0.102	23.435	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	14	THR	0	-0.032	0.075	25.890	0.001	0.001	0.000	0.000	0.000	0.000
21	A	15	ARG	0	0.066	-0.079	26.357	0.005	0.005	0.000	0.000	0.000	0.000
22	A	15	ARG	1	0.861	1.054	27.728	0.046	0.046	0.000	0.000	0.000	0.000
23	A	16	GLU	0	0.079	-0.125	29.368	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	16	GLU	-1	-0.830	-0.730	29.587	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	17	LYS	0	0.075	-0.053	31.389	0.003	0.003	0.000	0.000	0.000	0.000
26	A	17	LYS	1	0.859	1.027	35.418	0.017	0.017	0.000	0.000	0.000	0.000
27	A	18	ASP	0	0.082	-0.091	34.151	0.002	0.002	0.000	0.000	0.000	0.000
28	A	18	ASP	-1	-0.977	-0.851	33.634	0.002	0.002	0.000	0.000	0.000	0.000
29	A	19	GLU	0	0.185	-0.098	32.620	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	19	GLU	-1	-1.038	-0.844	33.774	0.015	0.015	0.000	0.000	0.000	0.000
31	A	20	LEU	0	0.023	-0.119	32.074	0.004	0.004	0.000	0.000	0.000	0.000
32	A	20	LEU	0	-0.056	0.107	33.608	0.000	0.000	0.000	0.000	0.000	0.000
33	A	21	LEU	0	0.032	-0.080	29.634	0.005	0.005	0.000	0.000	0.000	0.000
34	A	21	LEU	0	-0.099	0.065	29.459	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	22	HIS	0	0.088	-0.100	27.915	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	22	HIS	0	-0.099	0.087	28.955	0.003	0.003	0.000	0.000	0.000	0.000
37	A	23	VAL	0	0.035	-0.085	24.063	0.006	0.006	0.000	0.000	0.000	0.000
38	A	23	VAL	0	-0.075	0.090	22.331	0.001	0.001	0.000	0.000	0.000	0.000
39	A	24	GLN	0	0.105	-0.075	24.238	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	24	GLN	0	-0.100	0.067	23.408	0.002	0.002	0.000	0.000	0.000	0.000
41	A	25	ASP	0	0.129	-0.099	22.451	0.000	0.000	0.000	0.000	0.000	0.000
42	A	25	ASP	-1	-1.012	-0.846	22.367	0.010	0.010	0.000	0.000	0.000	0.000
43	A	26	THR	0	0.008	-0.110	19.972	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	26	THR	0	-0.058	0.079	18.527	0.004	0.004	0.000	0.000	0.000	0.000
45	A	27	PRO	0	-0.061	-0.115	14.625	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	28	MET	0	0.038	-0.012	13.821	0.031	0.031	0.000	0.000	0.000	0.000
47	A	28	MET	0	-0.022	0.128	14.130	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	29	TYR	0	0.047	-0.100	9.404	-0.089	-0.089	0.000	0.000	0.000	0.000
49	A	29	TYR	0	-0.067	0.082	7.226	0.015	0.015	0.000	0.000	0.000	0.000
50	A	30	ALA	0	0.085	-0.096	9.557	0.080	0.080	0.000	0.000	0.000	0.000
51	A	30	ALA	0	-0.036	0.122	11.218	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	31	PRO	0	0.010	-0.103	7.931	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	32	ILE	0	0.096	-0.006	7.001	0.121	0.121	0.000	0.000	0.000	0.000
54	A	32	ILE	0	-0.059	0.127	4.780	-0.031	0.027	-0.001	-0.015	-0.041	0.000
55	A	33	SER	0	0.056	-0.089	8.235	-0.072	-0.072	0.000	0.000	0.000	0.000
56	A	33	SER	0	-0.046	0.073	10.306	0.029	0.029	0.000	0.000	0.000	0.000
57	A	34	LEU	0	-0.010	-0.133	10.876	0.019	0.019	0.000	0.000	0.000	0.000
58	A	34	LEU	0	-0.034	0.139	12.337	0.003	0.003	0.000	0.000	0.000	0.000
59	A	35	LYS	0	0.120	-0.032	13.590	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	35	LYS	1	0.849	1.012	15.689	0.235	0.235	0.000	0.000	0.000	0.000
61	A	36	ARG	0	0.202	-0.072	16.596	0.022	0.022	0.000	0.000	0.000	0.000
62	A	36	ARG	1	0.771	1.031	20.792	0.080	0.080	0.000	0.000	0.000	0.000
63	A	37	TYR	0	-0.010	-0.099	19.868	0.013	0.013	0.000	0.000	0.000	0.000
64	A	37	TYR	0	-0.045	0.098	20.829	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	38	GLY	0	0.094	-0.075	17.287	0.013	0.013	0.000	0.000	0.000	0.000
66	A	39	LEU	0	0.092	-0.009	17.588	0.033	0.033	0.000	0.000	0.000	0.000
67	A	39	LEU	0	-0.092	0.104	14.549	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	40	SER	0	0.112	-0.066	18.287	0.014	0.014	0.000	0.000	0.000	0.000
69	A	40	SER	0	-0.038	0.076	22.761	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	41	GLU	0	0.014	-0.110	20.956	0.002	0.002	0.000	0.000	0.000	0.000
71	A	41	GLU	-1	-0.988	-0.849	20.056	0.047	0.047	0.000	0.000	0.000	0.000
72	A	42	ILE	0	0.087	-0.064	18.185	0.014	0.014	0.000	0.000	0.000	0.000
73	A	42	ILE	0	-0.104	0.062	15.134	0.002	0.002	0.000	0.000	0.000	0.000
74	A	43	VAL	0	0.104	-0.109	19.598	0.016	0.016	0.000	0.000	0.000	0.000
75	A	43	VAL	0	-0.082	0.110	20.528	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	44	ASN	0	0.111	-0.051	22.163	0.004	0.004	0.000	0.000	0.000	0.000
77	A	44	ASN	0	-0.128	0.036	24.786	0.000	0.000	0.000	0.000	0.000	0.000
78	A	45	HIS	0	0.144	-0.049	22.704	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	45	HIS	0	-0.131	0.066	21.770	0.000	0.000	0.000	0.000	0.000	0.000
80	A	46	LEU	0	0.025	-0.118	22.812	0.007	0.007	0.000	0.000	0.000	0.000
81	A	46	LEU	0	-0.112	0.065	19.556	0.001	0.001	0.000	0.000	0.000	0.000
82	A	47	LEU	0	0.003	-0.128	23.777	0.004	0.004	0.000	0.000	0.000	0.000
83	A	47	LEU	0	-0.084	0.111	25.839	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	48	GLY	0	-0.023	-0.092	26.754	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	49	SER	0	-0.036	-0.002	28.280	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	49	SER	0	-0.060	0.031	28.351	0.000	0.000	0.000	0.000	0.000	0.000
87	A	50	GLU	0	0.147	-0.027	30.187	0.004	0.004	0.000	0.000	0.000	0.000
88	A	50	GLU	-1	-1.024	-0.871	34.632	0.029	0.029	0.000	0.000	0.000	0.000
89	A	51	LYS	0	0.136	-0.086	32.525	0.003	0.003	0.000	0.000	0.000	0.000
90	A	51	LYS	1	0.763	1.013	33.919	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	52	PRO	0	-0.029	-0.112	27.897	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	53	VAL	0	0.070	-0.038	28.692	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	53	VAL	0	-0.052	0.137	28.860	0.000	0.000	0.000	0.000	0.000	0.000
94	A	54	PRO	0	-0.040	-0.104	27.275	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	55	PHE	0	0.089	-0.007	24.826	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	55	PHE	0	-0.050	0.112	24.028	0.000	0.000	0.000	0.000	0.000	0.000
97	A	56	ASP	0	0.072	-0.092	23.620	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	56	ASP	-1	-0.860	-0.799	24.678	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	57	PHE	0	0.080	-0.083	20.023	0.013	0.013	0.000	0.000	0.000	0.000
100	A	57	PHE	0	-0.087	0.095	19.314	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	58	LEU	0	0.065	-0.110	20.908	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	58	LEU	0	-0.065	0.111	22.579	0.002	0.002	0.000	0.000	0.000	0.000
103	A	59	ILE	0	0.091	-0.075	17.387	0.020	0.020	0.000	0.000	0.000	0.000
104	A	59	ILE	0	-0.094	0.084	14.674	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	60	GLU	0	0.099	-0.098	18.887	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	60	GLU	-1	-0.960	-0.817	18.746	-0.124	-0.124	0.000	0.000	0.000	0.000
107	A	61	GLY	0	0.039	-0.109	21.235	0.000	0.000	0.000	0.000	0.000	0.000
108	A	62	GLU	0	0.037	-0.046	21.274	0.015	0.015	0.000	0.000	0.000	0.000
109	A	62	GLU	-1	-0.917	-0.774	19.835	-0.228	-0.228	0.000	0.000	0.000	0.000
110	A	63	LEU	0	0.171	-0.075	20.831	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	63	LEU	0	-0.167	0.077	23.017	0.001	0.001	0.000	0.000	0.000	0.000
112	A	64	LEU	0	0.072	-0.127	18.449	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	64	LEU	0	-0.098	0.122	15.239	0.002	0.002	0.000	0.000	0.000	0.000
114	A	65	ARG	0	0.037	-0.100	19.301	0.018	0.018	0.000	0.000	0.000	0.000
115	A	65	ARG	1	0.865	1.052	20.731	0.144	0.144	0.000	0.000	0.000	0.000
116	A	66	THR	0	-0.033	-0.064	17.421	0.026	0.026	0.000	0.000	0.000	0.000
117	A	66	THR	0	-0.123	-0.014	16.045	0.005	0.005	0.000	0.000	0.000	0.000
118	A	67	SER	0	0.055	-0.064	13.202	0.054	0.054	0.000	0.000	0.000	0.000
119	A	67	SER	0	-0.061	0.025	12.448	-0.050	-0.050	0.000	0.000	0.000	0.000
120	A	68	LEU	0	0.097	-0.098	11.010	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	68	LEU	0	-0.057	0.110	10.410	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	69	HIS	0	0.131	-0.070	8.566	-0.031	-0.031	0.000	0.000	0.000	0.000
123	A	69	HIS	0	-0.078	0.081	8.145	-0.235	-0.235	0.000	0.000	0.000	0.000
124	A	70	ASP	0	0.077	-0.106	9.495	-0.099	-0.099	0.000	0.000	0.000	0.000
125	A	70	ASP	-1	-0.845	-0.763	13.754	-0.474	-0.474	0.000	0.000	0.000	0.000
126	A	71	TYR	0	0.080	-0.065	12.830	0.011	0.011	0.000	0.000	0.000	0.000
127	A	71	TYR	0	-0.076	0.092	12.833	0.006	0.006	0.000	0.000	0.000	0.000
128	A	72	LEU	0	0.023	-0.135	9.161	0.104	0.104	0.000	0.000	0.000	0.000
129	A	72	LEU	0	-0.080	0.106	6.836	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	73	THR	0	0.063	-0.065	10.651	0.014	0.014	0.000	0.000	0.000	0.000
131	A	73	THR	0	-0.065	0.053	10.234	-0.054	-0.054	0.000	0.000	0.000	0.000
132	A	74	LYS	0	0.056	-0.077	11.535	0.033	0.033	0.000	0.000	0.000	0.000
133	A	74	LYS	1	0.835	1.056	15.573	0.302	0.302	0.000	0.000	0.000	0.000
134	A	75	LYS	0	-0.006	-0.146	13.914	0.043	0.043	0.000	0.000	0.000	0.000
135	A	75	LYS	1	0.757	0.996	13.689	0.262	0.262	0.000	0.000	0.000	0.000
136	A	76	GLY	0	0.010	-0.080	12.832	0.043	0.043	0.000	0.000	0.000	0.000
137	A	77	LEU	0	0.026	-0.025	10.684	0.030	0.030	0.000	0.000	0.000	0.000
138	A	77	LEU	0	-0.072	0.104	10.527	0.010	0.010	0.000	0.000	0.000	0.000
139	A	78	SER	0	0.071	-0.059	6.824	-0.177	-0.177	0.000	0.000	0.000	0.000
140	A	78	SER	0	-0.056	0.032	5.936	0.030	0.030	0.000	0.000	0.000	0.000
141	A	79	SER	0	0.026	-0.079	3.887	0.224	0.275	0.006	-0.022	-0.035	0.000
142	A	79	SER	0	-0.044	0.072	2.650	-1.279	-0.524	1.050	-0.973	-0.832	-0.008
143	A	80	GLU	0	0.067	-0.120	5.032	0.131	0.145	-0.002	-0.002	-0.011	0.000
144	A	80	GLU	-1	-0.942	-0.805	5.302	-0.399	-0.399	0.000	0.000	0.000	0.000
145	A	81	ALA	0	0.041	-0.118	6.923	0.114	0.114	0.000	0.000	0.000	0.000
146	A	81	ALA	0	-0.065	0.111	9.408	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	82	SER	0	0.018	-0.092	9.387	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	82	SER	0	-0.050	0.065	11.818	0.031	0.031	0.000	0.000	0.000	0.000
149	A	83	LEU	0	-0.042	-0.129	12.149	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	83	LEU	0	-0.056	0.099	10.715	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	84	ASN	0	0.189	-0.055	13.786	0.033	0.033	0.000	0.000	0.000	0.000
152	A	84	ASN	0	-0.160	0.064	18.132	0.018	0.018	0.000	0.000	0.000	0.000
153	A	85	VAL	0	0.054	-0.115	17.288	-0.020	-0.020	0.000	0.000	0.000	0.000
154	A	85	VAL	0	-0.134	0.071	15.208	-0.005	-0.005	0.000	0.000	0.000	0.000
155	A	86	GLU	0	0.215	-0.087	18.240	0.022	0.022	0.000	0.000	0.000	0.000
156	A	86	GLU	-1	-0.995	-0.841	22.538	-0.075	-0.075	0.000	0.000	0.000	0.000
157	A	87	TYR	0	0.031	-0.093	21.555	-0.016	-0.016	0.000	0.000	0.000	0.000
158	A	87	TYR	0	-0.124	0.052	22.086	0.001	0.001	0.000	0.000	0.000	0.000
159	A	88	THR	0	0.084	-0.074	23.562	0.007	0.007	0.000	0.000	0.000	0.000
160	A	88	THR	0	-0.074	0.071	25.746	0.000	0.000	0.000	0.000	0.000	0.000
161	A	89	ARG	0	0.139	-0.062	26.740	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	89	ARG	1	0.754	0.981	30.586	0.021	0.021	0.000	0.000	0.000	0.000
163	A	90	ALA	0	0.071	-0.106	27.773	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	90	ALA	0	-0.113	0.092	28.099	0.000	0.000	0.000	0.000	0.000	0.000
165	A	91	ILE	0	-0.111	-0.161	28.344	0.008	0.008	0.000	0.000	0.000	0.000
166	A	91	ILE	0	-0.008	0.017	27.543	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)