FMO DATABASE

FMODB ID: VKMY1

Calculation Name: 5DTC-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

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	OptAll
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	-617601.033589
FMO2-HF: Nuclear repulsion	583131.195163
FMO2-HF: Total energy	-34469.838426
FMO2-MP2: Total energy	-34572.111175

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.
-3.292	-0.626	2.756	-2.821	-2.604	-0.008

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 : 0.167 / q_NPA : 0.030

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	-0.055	0.054	4.390	0.944	1.158	-0.001	-0.085	-0.128	0.000
5	A	7	GLN	0	-0.010	-0.126	2.949	-1.502	0.037	0.031	-0.746	-0.824	0.002
6	A	7	GLN	0	-0.010	0.106	4.152	-0.232	-0.127	-0.001	-0.011	-0.094	0.000
7	A	8	VAL	0	0.081	-0.050	3.832	-0.795	-0.436	0.007	-0.147	-0.219	-0.001
8	A	8	VAL	0	-0.063	0.091	6.191	-0.055	-0.055	0.000	0.000	0.000	0.000
9	A	9	LYS	0	0.110	-0.083	6.540	0.148	0.148	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.850	1.057	8.415	-0.165	-0.165	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.024	-0.099	9.812	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	10	ILE	0	-0.056	0.082	11.128	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	11	ARG	0	0.087	-0.077	13.050	0.052	0.052	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.895	1.053	16.880	0.054	0.054	0.000	0.000	0.000	0.000
15	A	12	PHE	0	0.035	-0.106	16.825	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	12	PHE	0	-0.073	0.079	16.738	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	13	PHE	0	0.133	-0.046	19.726	0.016	0.016	0.000	0.000	0.000	0.000
18	A	13	PHE	0	-0.072	0.088	20.490	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	14	THR	0	0.026	-0.098	23.072	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	14	THR	0	-0.018	0.074	25.608	0.002	0.002	0.000	0.000	0.000	0.000
21	A	15	ARG	0	0.057	-0.082	26.071	0.004	0.004	0.000	0.000	0.000	0.000
22	A	15	ARG	1	0.859	1.053	27.583	0.058	0.058	0.000	0.000	0.000	0.000
23	A	16	GLU	0	0.084	-0.125	29.171	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	16	GLU	-1	-0.827	-0.726	29.135	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	17	LYS	0	0.050	-0.067	31.130	0.003	0.003	0.000	0.000	0.000	0.000
26	A	17	LYS	1	0.869	1.029	35.131	0.022	0.022	0.000	0.000	0.000	0.000
27	A	18	ASP	0	0.090	-0.087	33.589	0.002	0.002	0.000	0.000	0.000	0.000
28	A	18	ASP	-1	-0.973	-0.849	33.273	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	19	GLU	0	0.173	-0.100	32.358	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	19	GLU	-1	-1.041	-0.848	33.595	0.012	0.012	0.000	0.000	0.000	0.000
31	A	20	LEU	0	0.022	-0.118	31.914	0.004	0.004	0.000	0.000	0.000	0.000
32	A	20	LEU	0	-0.060	0.106	33.551	0.000	0.000	0.000	0.000	0.000	0.000
33	A	21	LEU	0	0.041	-0.080	29.328	0.006	0.006	0.000	0.000	0.000	0.000
34	A	21	LEU	0	-0.094	0.066	28.984	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	22	HIS	0	0.085	-0.091	27.652	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	22	HIS	0	-0.111	0.082	28.875	0.002	0.002	0.000	0.000	0.000	0.000
37	A	23	VAL	0	0.058	-0.087	23.691	0.007	0.007	0.000	0.000	0.000	0.000
38	A	23	VAL	0	-0.078	0.096	22.095	0.001	0.001	0.000	0.000	0.000	0.000
39	A	24	GLN	0	0.095	-0.097	23.976	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	24	GLN	0	-0.086	0.083	23.149	0.003	0.003	0.000	0.000	0.000	0.000
41	A	25	ASP	0	0.103	-0.099	21.987	0.003	0.003	0.000	0.000	0.000	0.000
42	A	25	ASP	-1	-0.997	-0.852	22.146	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	26	THR	0	0.017	-0.097	19.728	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	26	THR	0	-0.061	0.080	18.204	0.004	0.004	0.000	0.000	0.000	0.000
45	A	27	PRO	0	-0.059	-0.120	14.439	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	28	MET	0	0.039	0.004	13.618	0.033	0.033	0.000	0.000	0.000	0.000
47	A	28	MET	0	-0.039	0.107	13.716	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	29	TYR	0	0.039	-0.105	9.239	-0.082	-0.082	0.000	0.000	0.000	0.000
49	A	29	TYR	0	-0.034	0.092	7.049	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	30	ALA	0	0.105	-0.089	8.974	0.077	0.077	0.000	0.000	0.000	0.000
51	A	30	ALA	0	-0.029	0.123	10.877	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	31	PRO	0	-0.003	-0.103	7.794	-0.092	-0.092	0.000	0.000	0.000	0.000
53	A	32	ILE	0	0.092	0.006	6.769	0.155	0.155	0.000	0.000	0.000	0.000
54	A	32	ILE	0	-0.054	0.123	4.888	-0.007	0.046	-0.001	-0.012	-0.040	0.000
55	A	33	SER	0	0.056	-0.085	7.926	-0.043	-0.043	0.000	0.000	0.000	0.000
56	A	33	SER	0	-0.052	0.068	10.513	0.023	0.023	0.000	0.000	0.000	0.000
57	A	34	LEU	0	-0.006	-0.134	10.969	0.035	0.035	0.000	0.000	0.000	0.000
58	A	34	LEU	0	-0.027	0.139	12.103	0.003	0.003	0.000	0.000	0.000	0.000
59	A	35	LYS	0	0.121	-0.044	13.412	-0.071	-0.071	0.000	0.000	0.000	0.000
60	A	35	LYS	1	0.859	1.036	15.657	0.268	0.268	0.000	0.000	0.000	0.000
61	A	36	ARG	0	0.139	-0.067	16.523	0.026	0.026	0.000	0.000	0.000	0.000
62	A	36	ARG	1	0.771	1.009	20.673	0.089	0.089	0.000	0.000	0.000	0.000
63	A	37	TYR	0	0.031	-0.097	19.735	0.011	0.011	0.000	0.000	0.000	0.000
64	A	37	TYR	0	-0.038	0.103	21.174	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	38	GLY	0	0.102	-0.059	17.588	0.013	0.013	0.000	0.000	0.000	0.000
66	A	39	LEU	0	0.079	-0.008	17.656	0.034	0.034	0.000	0.000	0.000	0.000
67	A	39	LEU	0	-0.095	0.098	14.335	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	40	SER	0	0.098	-0.063	18.237	0.014	0.014	0.000	0.000	0.000	0.000
69	A	40	SER	0	-0.037	0.074	22.625	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	41	GLU	0	0.016	-0.106	21.289	0.002	0.002	0.000	0.000	0.000	0.000
71	A	41	GLU	-1	-0.992	-0.859	20.257	0.044	0.044	0.000	0.000	0.000	0.000
72	A	42	ILE	0	0.098	-0.054	18.177	0.013	0.013	0.000	0.000	0.000	0.000
73	A	42	ILE	0	-0.095	0.065	15.275	0.002	0.002	0.000	0.000	0.000	0.000
74	A	43	VAL	0	0.102	-0.107	19.614	0.017	0.017	0.000	0.000	0.000	0.000
75	A	43	VAL	0	-0.082	0.108	20.570	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	44	ASN	0	0.107	-0.050	22.224	0.004	0.004	0.000	0.000	0.000	0.000
77	A	44	ASN	0	-0.136	0.023	24.817	0.000	0.000	0.000	0.000	0.000	0.000
78	A	45	HIS	0	0.154	-0.053	22.355	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	45	HIS	0	-0.141	0.064	21.340	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	46	LEU	0	0.015	-0.124	22.381	0.009	0.009	0.000	0.000	0.000	0.000
81	A	46	LEU	0	-0.106	0.065	19.059	0.001	0.001	0.000	0.000	0.000	0.000
82	A	47	LEU	0	0.016	-0.123	23.312	0.004	0.004	0.000	0.000	0.000	0.000
83	A	47	LEU	0	-0.073	0.120	25.740	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	48	GLY	0	-0.028	-0.098	26.381	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	49	SER	0	-0.063	-0.020	27.960	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	49	SER	0	-0.038	0.050	28.214	0.000	0.000	0.000	0.000	0.000	0.000
87	A	50	GLU	0	0.157	-0.050	29.883	0.003	0.003	0.000	0.000	0.000	0.000
88	A	50	GLU	-1	-0.957	-0.809	34.349	0.027	0.027	0.000	0.000	0.000	0.000
89	A	51	LYS	0	0.055	-0.115	32.209	0.003	0.003	0.000	0.000	0.000	0.000
90	A	51	LYS	1	0.750	0.985	33.652	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	52	PRO	0	-0.015	-0.101	27.829	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	53	VAL	0	0.071	-0.018	28.962	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	53	VAL	0	-0.033	0.139	28.563	0.000	0.000	0.000	0.000	0.000	0.000
94	A	54	PRO	0	-0.037	-0.105	27.234	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	55	PHE	0	0.078	-0.010	24.706	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	55	PHE	0	-0.053	0.102	23.918	0.000	0.000	0.000	0.000	0.000	0.000
97	A	56	ASP	0	0.061	-0.095	23.584	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	56	ASP	-1	-0.869	-0.805	24.534	-0.096	-0.096	0.000	0.000	0.000	0.000
99	A	57	PHE	0	0.083	-0.084	19.974	0.014	0.014	0.000	0.000	0.000	0.000
100	A	57	PHE	0	-0.082	0.101	19.175	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	58	LEU	0	0.053	-0.103	20.476	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	58	LEU	0	-0.068	0.097	22.140	0.002	0.002	0.000	0.000	0.000	0.000
103	A	59	ILE	0	0.097	-0.066	17.036	0.021	0.021	0.000	0.000	0.000	0.000
104	A	59	ILE	0	-0.093	0.075	14.334	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	60	GLU	0	0.047	-0.091	18.538	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	60	GLU	-1	-0.908	-0.801	18.462	-0.153	-0.153	0.000	0.000	0.000	0.000
107	A	61	GLY	0	0.065	-0.095	20.926	0.000	0.000	0.000	0.000	0.000	0.000
108	A	62	GLU	0	0.063	-0.030	20.909	0.018	0.018	0.000	0.000	0.000	0.000
109	A	62	GLU	-1	-0.948	-0.790	19.768	-0.265	-0.265	0.000	0.000	0.000	0.000
110	A	63	LEU	0	0.169	-0.089	20.394	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	63	LEU	0	-0.162	0.083	22.928	0.001	0.001	0.000	0.000	0.000	0.000
112	A	64	LEU	0	0.077	-0.111	18.121	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	64	LEU	0	-0.089	0.119	14.882	0.001	0.001	0.000	0.000	0.000	0.000
114	A	65	ARG	0	0.032	-0.109	19.014	0.015	0.015	0.000	0.000	0.000	0.000
115	A	65	ARG	1	0.851	1.041	21.031	0.155	0.155	0.000	0.000	0.000	0.000
116	A	66	THR	0	0.005	-0.054	17.704	0.028	0.028	0.000	0.000	0.000	0.000
117	A	66	THR	0	-0.138	-0.014	16.347	0.004	0.004	0.000	0.000	0.000	0.000
118	A	67	SER	0	0.042	-0.077	13.337	0.059	0.059	0.000	0.000	0.000	0.000
119	A	67	SER	0	-0.047	0.013	12.562	-0.047	-0.047	0.000	0.000	0.000	0.000
120	A	68	LEU	0	0.087	-0.080	10.758	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	68	LEU	0	-0.056	0.109	10.148	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	69	HIS	0	0.154	-0.068	8.765	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	69	HIS	0	-0.077	0.090	8.623	-0.230	-0.230	0.000	0.000	0.000	0.000
124	A	70	ASP	0	0.065	-0.080	9.676	-0.103	-0.103	0.000	0.000	0.000	0.000
125	A	70	ASP	-1	-0.847	-0.767	14.159	-0.476	-0.476	0.000	0.000	0.000	0.000
126	A	71	TYR	0	0.090	-0.067	13.152	0.003	0.003	0.000	0.000	0.000	0.000
127	A	71	TYR	0	-0.107	0.067	13.001	0.004	0.004	0.000	0.000	0.000	0.000
128	A	72	LEU	0	0.035	-0.123	9.185	0.116	0.116	0.000	0.000	0.000	0.000
129	A	72	LEU	0	-0.103	0.096	6.655	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	73	THR	0	0.063	-0.069	10.679	0.008	0.008	0.000	0.000	0.000	0.000
131	A	73	THR	0	-0.064	0.048	10.665	-0.047	-0.047	0.000	0.000	0.000	0.000
132	A	74	LYS	0	0.067	-0.077	11.915	0.033	0.033	0.000	0.000	0.000	0.000
133	A	74	LYS	1	0.838	1.055	15.746	0.331	0.331	0.000	0.000	0.000	0.000
134	A	75	LYS	0	-0.017	-0.137	13.951	0.060	0.060	0.000	0.000	0.000	0.000
135	A	75	LYS	1	0.767	1.002	13.571	0.303	0.303	0.000	0.000	0.000	0.000
136	A	76	GLY	0	0.025	-0.088	13.108	0.046	0.046	0.000	0.000	0.000	0.000
137	A	77	LEU	0	0.023	-0.027	10.571	0.009	0.009	0.000	0.000	0.000	0.000
138	A	77	LEU	0	-0.075	0.104	10.198	0.012	0.012	0.000	0.000	0.000	0.000
139	A	78	SER	0	0.081	-0.075	6.749	-0.195	-0.195	0.000	0.000	0.000	0.000
140	A	78	SER	0	-0.063	0.044	5.834	0.069	0.069	0.000	0.000	0.000	0.000
141	A	79	SER	0	0.021	-0.087	3.701	0.347	0.426	0.011	-0.027	-0.064	0.000
142	A	79	SER	0	-0.051	0.067	2.395	-1.158	-0.949	2.713	-1.777	-1.145	-0.009
143	A	80	GLU	0	0.042	-0.114	4.720	0.300	0.329	-0.002	-0.005	-0.023	0.000
144	A	80	GLU	-1	-0.869	-0.777	4.800	-1.402	-1.323	-0.001	-0.011	-0.067	0.000
145	A	81	ALA	0	0.082	-0.089	6.216	0.147	0.147	0.000	0.000	0.000	0.000
146	A	81	ALA	0	-0.056	0.107	8.995	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	82	SER	0	-0.013	-0.102	8.802	0.023	0.023	0.000	0.000	0.000	0.000
148	A	82	SER	0	-0.039	0.066	11.047	0.038	0.038	0.000	0.000	0.000	0.000
149	A	83	LEU	0	0.003	-0.098	11.603	0.011	0.011	0.000	0.000	0.000	0.000
150	A	83	LEU	0	-0.057	0.090	10.352	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	84	ASN	0	0.142	-0.062	13.284	0.038	0.038	0.000	0.000	0.000	0.000
152	A	84	ASN	0	-0.134	0.061	17.501	0.021	0.021	0.000	0.000	0.000	0.000
153	A	85	VAL	0	0.080	-0.107	17.038	-0.019	-0.019	0.000	0.000	0.000	0.000
154	A	85	VAL	0	-0.134	0.074	15.113	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	86	GLU	0	0.214	-0.068	17.956	0.025	0.025	0.000	0.000	0.000	0.000
156	A	86	GLU	-1	-0.988	-0.845	22.271	-0.090	-0.090	0.000	0.000	0.000	0.000
157	A	87	TYR	0	-0.002	-0.117	21.137	-0.017	-0.017	0.000	0.000	0.000	0.000
158	A	87	TYR	0	-0.104	0.056	21.755	0.002	0.002	0.000	0.000	0.000	0.000
159	A	88	THR	0	0.116	-0.061	23.353	0.008	0.008	0.000	0.000	0.000	0.000
160	A	88	THR	0	-0.080	0.067	25.662	0.000	0.000	0.000	0.000	0.000	0.000
161	A	89	ARG	0	0.118	-0.064	26.477	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	89	ARG	1	0.762	0.976	30.284	0.025	0.025	0.000	0.000	0.000	0.000
163	A	90	ALA	0	0.072	-0.106	27.587	-0.007	-0.007	0.000	0.000	0.000	0.000
164	A	90	ALA	0	-0.108	0.097	27.782	0.001	0.001	0.000	0.000	0.000	0.000
165	A	91	ILE	0	-0.109	-0.157	28.273	0.009	0.009	0.000	0.000	0.000	0.000
166	A	91	ILE	0	-0.001	0.019	27.551	-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)