FMO DATABASE

FMODB ID: QK7YY

Calculation Name: 4D2K-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4D2K

Chain ID: A

ChEMBL ID:

UniProt ID: Q7K304

Base Structure: X-ray

Registration Date: 2025-07-11

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-563288.835776
FMO2-HF: Nuclear repulsion	531151.068892
FMO2-HF: Total energy	-32137.766885
FMO2-MP2: Total energy	-32233.283404

3D Structure Molmil

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-6.106	-3.04	0.263	-1.799	-1.53	0.01

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.183 / q_NPA : 0.040

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	9	LYS	0	0.074	0.003	3.859	2.331	3.991	-0.011	-0.956	-0.693	0.002
5	A	9	LYS	1	0.771	1.003	7.710	-1.229	-1.229	0.000	0.000	0.000	0.000
6	A	10	ARG	0	0.017	-0.111	5.384	-0.961	-0.961	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.796	1.041	2.990	-10.168	-8.762	0.274	-0.843	-0.837	0.008
8	A	11	PRO	0	-0.025	-0.116	6.210	-0.068	-0.068	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.039	-0.003	9.445	0.048	0.048	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.019	0.114	9.286	0.006	0.006	0.000	0.000	0.000	0.000
11	A	13	LYS	0	0.085	-0.095	11.791	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.790	1.033	14.886	-0.287	-0.287	0.000	0.000	0.000	0.000
13	A	14	ILE	0	0.107	-0.067	15.608	0.039	0.039	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.107	0.100	16.471	0.013	0.013	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.067	-0.110	17.971	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	15	TRP	0	-0.054	0.090	19.860	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	16	ASP	0	0.130	-0.041	21.666	0.042	0.042	0.000	0.000	0.000	0.000
18	A	16	ASP	-1	-0.811	-0.794	25.814	0.231	0.231	0.000	0.000	0.000	0.000
19	A	17	SER	0	0.037	-0.089	24.784	0.004	0.004	0.000	0.000	0.000	0.000
20	A	17	SER	0	-0.037	0.055	26.732	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	18	TRP	0	0.030	-0.099	26.472	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	18	TRP	0	-0.083	0.093	29.563	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	19	ARG	0	0.025	-0.100	25.075	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	19	ARG	1	0.684	0.955	24.540	-0.232	-0.232	0.000	0.000	0.000	0.000
25	A	20	ASN	0	0.177	-0.031	26.098	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	20	ASN	0	-0.163	0.030	29.164	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	21	VAL	0	0.069	-0.130	26.121	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	21	VAL	0	-0.082	0.104	24.147	0.001	0.001	0.000	0.000	0.000	0.000
29	A	22	ARG	0	0.073	-0.105	22.396	0.030	0.030	0.000	0.000	0.000	0.000
30	A	22	ARG	1	0.766	1.027	22.320	-0.195	-0.195	0.000	0.000	0.000	0.000
31	A	23	LYS	0	-0.049	-0.137	20.209	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	23	LYS	1	0.855	1.050	19.941	-0.261	-0.261	0.000	0.000	0.000	0.000
33	A	24	GLY	0	0.062	-0.078	16.127	0.013	0.013	0.000	0.000	0.000	0.000
34	A	25	VAL	0	-0.002	-0.026	14.246	-0.091	-0.091	0.000	0.000	0.000	0.000
35	A	25	VAL	0	-0.045	0.112	12.709	0.013	0.013	0.000	0.000	0.000	0.000
36	A	26	VAL	0	0.129	-0.088	10.498	0.082	0.082	0.000	0.000	0.000	0.000
37	A	26	VAL	0	-0.099	0.108	9.550	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	27	VAL	0	0.014	-0.150	9.391	-0.213	-0.213	0.000	0.000	0.000	0.000
39	A	27	VAL	0	-0.059	0.130	9.299	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	28	GLY	0	0.046	-0.099	6.925	0.434	0.434	0.000	0.000	0.000	0.000
41	A	29	THR	0	-0.071	-0.005	7.190	1.225	1.225	0.000	0.000	0.000	0.000
42	A	29	THR	0	-0.021	0.036	8.994	-0.073	-0.073	0.000	0.000	0.000	0.000
43	A	30	PHE	0	0.140	-0.065	9.804	-0.102	-0.102	0.000	0.000	0.000	0.000
44	A	30	PHE	0	-0.005	0.130	12.262	0.034	0.034	0.000	0.000	0.000	0.000
45	A	31	GLU	0	0.033	-0.125	12.512	-0.159	-0.159	0.000	0.000	0.000	0.000
46	A	31	GLU	-1	-0.824	-0.769	13.238	1.491	1.491	0.000	0.000	0.000	0.000
47	A	32	GLU	0	0.136	-0.081	13.091	-0.203	-0.203	0.000	0.000	0.000	0.000
48	A	32	GLU	-1	-0.859	-0.760	11.658	1.240	1.240	0.000	0.000	0.000	0.000
49	A	33	LEU	0	0.056	-0.110	13.015	-0.180	-0.180	0.000	0.000	0.000	0.000
50	A	33	LEU	0	-0.065	0.109	12.298	0.034	0.034	0.000	0.000	0.000	0.000
51	A	34	LEU	0	0.089	-0.120	14.118	-0.114	-0.114	0.000	0.000	0.000	0.000
52	A	34	LEU	0	-0.084	0.122	16.860	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	35	VAL	0	0.097	-0.078	17.048	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	35	VAL	0	-0.133	0.075	17.241	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	36	ARG	0	-0.005	-0.128	16.189	-0.095	-0.095	0.000	0.000	0.000	0.000
56	A	36	ARG	1	0.815	1.010	14.776	-0.685	-0.685	0.000	0.000	0.000	0.000
57	A	37	GLY	0	0.033	-0.086	17.201	-0.064	-0.064	0.000	0.000	0.000	0.000
58	A	38	LYS	0	0.113	0.007	18.615	-0.057	-0.057	0.000	0.000	0.000	0.000
59	A	38	LYS	1	0.721	1.007	21.622	-0.472	-0.472	0.000	0.000	0.000	0.000
60	A	39	ASP	0	0.077	-0.059	20.962	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	39	ASP	-1	-0.895	-0.833	19.557	0.440	0.440	0.000	0.000	0.000	0.000
62	A	40	LYS	0	0.064	-0.104	20.460	-0.050	-0.050	0.000	0.000	0.000	0.000
63	A	40	LYS	1	0.737	0.988	18.380	-0.409	-0.409	0.000	0.000	0.000	0.000
64	A	41	LEU	0	0.004	-0.114	21.772	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	41	LEU	0	-0.064	0.113	21.246	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	42	GLY	0	0.022	-0.096	24.251	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	43	VAL	0	0.022	-0.048	25.469	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	43	VAL	0	-0.068	0.132	24.723	0.002	0.002	0.000	0.000	0.000	0.000
69	A	44	PRO	0	0.024	-0.090	25.872	0.016	0.016	0.000	0.000	0.000	0.000
70	A	45	ALA	0	0.182	0.026	24.330	0.018	0.018	0.000	0.000	0.000	0.000
71	A	45	ALA	0	-0.075	0.112	24.186	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	46	SER	0	0.003	-0.080	24.403	0.047	0.047	0.000	0.000	0.000	0.000
73	A	46	SER	0	-0.025	0.070	28.446	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	47	GLU	0	0.066	-0.100	27.071	0.001	0.001	0.000	0.000	0.000	0.000
75	A	47	GLU	-1	-0.830	-0.737	27.004	0.273	0.273	0.000	0.000	0.000	0.000
76	A	48	PRO	0	-0.005	-0.094	25.376	0.038	0.038	0.000	0.000	0.000	0.000
77	A	49	VAL	0	-0.010	-0.007	23.721	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	49	VAL	0	-0.039	0.092	21.635	0.002	0.002	0.000	0.000	0.000	0.000
79	A	50	ARG	0	0.078	-0.098	21.636	0.035	0.035	0.000	0.000	0.000	0.000
80	A	50	ARG	1	0.768	1.020	22.518	-0.346	-0.346	0.000	0.000	0.000	0.000
81	A	51	VAL	0	0.101	-0.081	18.076	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	51	VAL	0	-0.105	0.079	16.293	0.016	0.016	0.000	0.000	0.000	0.000
83	A	52	VAL	0	0.025	-0.117	19.180	0.045	0.045	0.000	0.000	0.000	0.000
84	A	52	VAL	0	-0.030	0.126	21.239	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	53	LEU	0	0.116	-0.111	17.711	0.037	0.037	0.000	0.000	0.000	0.000
86	A	53	LEU	0	-0.076	0.107	15.093	0.012	0.012	0.000	0.000	0.000	0.000
87	A	54	GLU	0	0.082	-0.097	18.589	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	54	GLU	-1	-0.923	-0.810	19.812	0.250	0.250	0.000	0.000	0.000	0.000
89	A	55	CYS	0	0.108	-0.080	20.123	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	55	CYS	0	-0.163	0.081	19.555	0.011	0.011	0.000	0.000	0.000	0.000
91	A	56	ASP	0	-0.019	-0.131	21.725	-0.033	-0.033	0.000	0.000	0.000	0.000
92	A	56	ASP	-1	-0.790	-0.756	20.509	0.356	0.356	0.000	0.000	0.000	0.000
93	A	57	GLY	0	0.039	-0.100	22.126	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	58	THR	0	0.028	-0.019	19.907	0.001	0.001	0.000	0.000	0.000	0.000
95	A	58	THR	0	-0.087	0.049	18.622	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	59	GLN	0	0.086	-0.070	19.168	0.050	0.050	0.000	0.000	0.000	0.000
97	A	59	GLN	0	-0.143	0.044	20.712	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	60	ILE	0	0.064	-0.106	15.635	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	60	ILE	0	-0.128	0.075	13.520	0.044	0.044	0.000	0.000	0.000	0.000
100	A	61	GLU	0	0.021	-0.123	16.820	0.016	0.016	0.000	0.000	0.000	0.000
101	A	61	GLU	-1	-0.901	-0.802	19.163	0.467	0.467	0.000	0.000	0.000	0.000
102	A	62	ASP	0	-0.005	-0.136	15.337	-0.046	-0.046	0.000	0.000	0.000	0.000
103	A	62	ASP	-1	-0.820	-0.786	14.264	0.968	0.968	0.000	0.000	0.000	0.000
104	A	63	GLY	0	0.056	-0.094	11.545	0.132	0.132	0.000	0.000	0.000	0.000
105	A	64	GLU	0	-0.007	-0.025	9.768	0.630	0.630	0.000	0.000	0.000	0.000
106	A	64	GLU	-1	-0.856	-0.776	11.985	1.320	1.320	0.000	0.000	0.000	0.000
107	A	65	TYR	0	0.195	-0.100	9.980	0.213	0.213	0.000	0.000	0.000	0.000
108	A	65	TYR	0	-0.051	0.138	13.601	-0.035	-0.035	0.000	0.000	0.000	0.000
109	A	66	PHE	0	0.104	-0.066	10.365	-0.044	-0.044	0.000	0.000	0.000	0.000
110	A	66	PHE	0	-0.113	0.093	7.296	-0.049	-0.049	0.000	0.000	0.000	0.000
111	A	67	ARG	0	0.052	-0.096	6.243	0.325	0.325	0.000	0.000	0.000	0.000
112	A	67	ARG	1	0.713	0.971	5.564	-2.372	-2.372	0.000	0.000	0.000	0.000
113	A	68	THR	0	-0.025	-0.122	5.750	0.550	0.550	0.000	0.000	0.000	0.000
114	A	68	THR	0	-0.034	0.067	9.557	-0.134	-0.134	0.000	0.000	0.000	0.000
115	A	69	LEU	0	0.033	-0.097	8.420	-0.371	-0.371	0.000	0.000	0.000	0.000
116	A	69	LEU	0	-0.083	0.115	9.252	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	70	ALA	0	0.154	-0.073	7.648	0.593	0.593	0.000	0.000	0.000	0.000
118	A	70	ALA	0	-0.042	0.127	10.063	-0.059	-0.059	0.000	0.000	0.000	0.000
119	A	71	ASN	0	0.145	-0.035	7.705	0.185	0.185	0.000	0.000	0.000	0.000
120	A	71	ASN	0	-0.119	0.042	5.675	0.475	0.475	0.000	0.000	0.000	0.000
121	A	72	ASN	0	0.019	-0.046	8.550	-0.153	-0.153	0.000	0.000	0.000	0.000
122	A	72	ASN	0	-0.130	0.023	11.989	0.023	0.023	0.000	0.000	0.000	0.000
123	A	73	THR	0	0.123	-0.099	11.414	-0.166	-0.166	0.000	0.000	0.000	0.000
124	A	73	THR	0	-0.040	0.067	11.159	-0.021	-0.021	0.000	0.000	0.000	0.000
125	A	74	VAL	0	-0.019	-0.113	13.335	0.080	0.080	0.000	0.000	0.000	0.000
126	A	74	VAL	0	-0.032	0.112	17.295	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	75	LEU	0	0.078	-0.074	16.476	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	75	LEU	0	-0.055	0.093	13.140	0.034	0.034	0.000	0.000	0.000	0.000
129	A	76	LEU	0	0.058	-0.123	17.549	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	76	LEU	0	-0.045	0.121	21.381	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	77	LEU	0	0.118	-0.067	20.600	0.047	0.047	0.000	0.000	0.000	0.000
132	A	77	LEU	0	-0.086	0.079	20.536	0.001	0.001	0.000	0.000	0.000	0.000
133	A	78	LEU	0	0.026	-0.115	21.807	-0.038	-0.038	0.000	0.000	0.000	0.000
134	A	78	LEU	0	-0.117	0.101	23.475	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	79	ARG	0	0.178	-0.040	25.029	0.024	0.024	0.000	0.000	0.000	0.000
136	A	79	ARG	1	0.727	0.954	26.474	-0.273	-0.273	0.000	0.000	0.000	0.000
137	A	80	GLN	0	0.009	-0.153	27.328	0.002	0.002	0.000	0.000	0.000	0.000
138	A	80	GLN	0	-0.098	0.090	30.726	-0.014	-0.014	0.000	0.000	0.000	0.000
139	A	81	GLY	0	0.035	-0.094	30.795	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	82	GLU	0	0.052	-0.022	29.105	-0.016	-0.016	0.000	0.000	0.000	0.000
141	A	82	GLU	-1	-0.863	-0.765	27.773	0.282	0.282	0.000	0.000	0.000	0.000
142	A	83	ARG	0	0.036	-0.112	28.114	0.022	0.022	0.000	0.000	0.000	0.000
143	A	83	ARG	1	0.902	1.071	29.663	-0.214	-0.214	0.000	0.000	0.000	0.000
144	A	84	TRP	0	0.155	-0.063	25.812	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	84	TRP	0	-0.058	0.109	23.619	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	85	LEU	0	-0.031	-0.124	26.854	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	85	LEU	0	-0.038	0.109	29.913	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	86	GLU	0	0.122	-0.062	27.519	0.021	0.021	0.000	0.000	0.000	0.000
149	A	86	GLU	-1	-0.943	-0.821	29.532	0.138	0.138	0.000	0.000	0.000	0.000
150	A	87	HIS	0	-0.137	-0.171	27.833	0.006	0.006	0.000	0.000	0.000	0.000
151	A	87	HIS	0	0.042	0.013	30.022	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)