FMO DATABASE

FMODB ID: 85Z6Y

Calculation Name: 3FK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FK9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K704

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1580067.289029
FMO2-HF: Nuclear repulsion	1517448.242117
FMO2-HF: Total energy	-62619.046911
FMO2-MP2: Total energy	-62801.702885

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:1:LEU)

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

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.
-10.284	-2.283	4.534	-4.433	-8.1	-0.023

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.001

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	3	ARG	1	0.960	0.976	2.391	-3.774	-0.157	0.907	-1.852	-2.671	0.000
4	A	4	VAL	0	-0.018	-0.001	4.553	0.271	0.368	-0.001	-0.021	-0.075	0.000
5	A	5	THR	0	-0.004	0.010	8.093	-0.090	-0.090	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.081	0.038	11.158	0.028	0.028	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.033	-0.009	14.618	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.009	0.019	17.957	0.019	0.019	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.017	0.000	20.976	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.046	-0.037	24.065	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.841	-0.925	27.318	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.022	-0.013	30.616	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.924	-0.965	32.118	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.021	-0.011	30.607	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.008	-0.015	24.528	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.026	0.014	24.499	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.048	-0.023	21.928	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.040	0.030	20.108	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.093	-0.042	22.304	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.971	0.992	16.010	-0.172	-0.172	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.027	-0.001	21.590	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.907	0.942	23.579	-0.157	-0.157	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.929	0.977	26.885	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.046	0.040	22.885	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	TRP	0	-0.003	-0.010	17.018	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	26	TRP	0	-0.007	-0.010	21.678	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.021	-0.011	16.865	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.015	0.002	17.582	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.028	0.025	17.434	0.007	0.007	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.029	-0.030	14.791	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.080	0.061	12.656	0.042	0.042	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.869	0.915	7.061	-1.067	-1.067	0.000	0.000	0.000	0.000
33	A	33	MET	0	-0.011	0.001	7.157	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.921	-0.954	8.889	0.115	0.115	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.068	-0.060	10.282	-0.076	-0.076	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.034	-0.020	11.189	0.038	0.038	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.726	-0.788	11.895	-0.092	-0.092	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.043	-0.025	11.723	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.029	-0.015	9.422	0.015	0.015	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.024	-0.005	11.998	0.026	0.026	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.907	-0.959	15.357	-0.114	-0.114	0.000	0.000	0.000	0.000
42	A	42	THR	0	0.003	-0.007	10.722	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.003	0.014	13.811	0.034	0.034	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.923	0.950	15.264	0.110	0.110	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.814	0.896	13.362	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.814	-0.911	13.163	0.106	0.106	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.006	-0.005	16.610	0.017	0.017	0.000	0.000	0.000	0.000
48	A	48	TRP	0	-0.021	-0.007	18.935	0.015	0.015	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.903	-0.956	18.568	0.093	0.093	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.895	-0.943	17.745	0.106	0.106	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.029	-0.043	21.100	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.023	0.001	23.942	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.062	-0.027	24.900	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	THR	0	0.022	0.013	23.720	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.002	-0.009	20.560	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.834	0.907	23.661	0.030	0.030	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.032	-0.038	23.620	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.023	0.021	18.975	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.907	-0.964	19.755	-0.123	-0.123	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.036	-0.020	13.001	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.863	0.919	16.517	0.146	0.146	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.043	0.030	14.921	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.025	-0.003	9.151	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.034	0.007	9.568	0.039	0.039	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.011	0.011	5.850	-0.055	-0.055	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.042	-0.020	6.121	0.255	0.255	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.058	0.023	6.503	-0.101	-0.101	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.009	0.014	8.308	0.115	0.115	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.041	-0.053	10.196	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.831	-0.946	12.778	0.200	0.200	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.935	-0.953	15.417	0.092	0.092	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.050	-0.025	17.436	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.907	0.958	12.405	-0.062	-0.062	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.009	0.000	7.057	0.056	0.056	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.051	-0.012	9.920	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.024	-0.026	5.989	0.394	0.394	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.860	-0.950	2.202	-2.306	-2.360	1.820	-0.416	-1.349	-0.004
78	A	78	TRP	0	-0.087	-0.020	2.271	-4.092	-0.547	1.721	-2.349	-2.917	-0.019
79	A	79	MET	0	0.019	0.014	2.942	-0.540	0.236	0.088	0.206	-1.070	0.000
80	A	80	LEU	0	-0.025	-0.005	5.220	0.165	0.185	-0.001	-0.001	-0.018	0.000
81	A	81	PHE	0	-0.018	-0.022	6.142	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.000	0.003	10.864	0.039	0.039	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.033	-0.015	12.949	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.881	0.947	17.185	0.103	0.103	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.015	-0.009	20.929	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.000	0.002	23.623	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.898	-0.936	27.371	-0.033	-0.033	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.078	-0.051	26.478	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.866	-0.915	27.848	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.034	0.014	28.410	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.963	-0.979	30.516	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.008	-0.001	27.833	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.014	0.015	25.480	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.918	0.948	28.714	-0.047	-0.047	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.079	-0.045	26.135	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	96	SER	0	0.092	0.079	21.753	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.017	-0.030	21.570	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.861	-0.931	17.733	0.232	0.232	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.054	-0.046	20.748	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.806	0.915	23.778	-0.052	-0.052	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.024	0.021	23.199	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.840	-0.944	26.803	0.028	0.028	0.000	0.000	0.000	0.000
103	A	103	TRP	0	0.060	0.037	27.696	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.877	0.962	27.565	-0.015	-0.015	0.000	0.000	0.000	0.000
105	A	105	LYS	1	1.015	0.998	30.043	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.956	0.995	28.243	0.049	0.049	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.946	-0.980	29.487	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.975	-0.990	31.282	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.041	-0.021	24.677	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.054	-0.043	24.873	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.906	-0.945	26.965	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.098	-0.020	25.666	0.009	0.009	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.036	-0.029	24.868	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	114	MET	0	0.008	-0.004	20.319	0.003	0.003	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.069	0.046	16.738	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.018	-0.007	18.694	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.014	-0.009	16.024	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.856	-0.932	15.555	-0.076	-0.076	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.892	0.961	17.772	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	TRP	0	-0.014	-0.010	18.614	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.023	0.026	14.272	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	122	PHE	0	0.035	-0.002	18.552	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.947	0.983	21.599	0.068	0.068	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.021	-0.010	20.516	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.001	-0.015	18.790	0.005	0.005	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.031	-0.007	22.119	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.008	-0.009	25.372	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.006	0.022	23.566	0.002	0.002	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.856	-0.922	24.162	-0.097	-0.097	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.867	0.913	22.927	0.111	0.111	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.001	0.017	16.969	0.003	0.003	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.055	-0.018	16.358	0.008	0.008	0.000	0.000	0.000	0.000
133	A	133	TYR	0	0.018	0.001	13.266	-0.036	-0.036	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.015	-0.013	12.058	0.044	0.044	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.074	-0.027	9.325	-0.073	-0.073	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.002	0.009	10.555	0.084	0.084	0.000	0.000	0.000	0.000
137	A	137	HIS	0	-0.007	0.007	10.898	-0.089	-0.089	0.000	0.000	0.000	0.000
138	A	138	TYR	0	0.021	0.005	12.031	0.034	0.034	0.000	0.000	0.000	0.000
139	A	139	THR	0	0.071	0.040	13.400	0.012	0.012	0.000	0.000	0.000	0.000
140	A	140	PRO	0	0.007	-0.009	13.615	0.015	0.015	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.914	-0.936	14.699	0.236	0.236	0.000	0.000	0.000	0.000
142	A	142	PHE	0	-0.124	-0.072	11.079	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.936	-0.947	16.165	0.022	0.022	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.065	-0.052	15.826	-0.007	-0.007	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.014	0.003	15.615	0.001	0.001	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.043	-0.029	16.615	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	147	TYR	0	0.017	-0.003	15.017	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.934	0.979	11.768	0.345	0.345	0.000	0.000	0.000	0.000
149	A	149	LEU	0	0.003	-0.001	14.825	-0.031	-0.031	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.879	-0.908	16.860	-0.181	-0.181	0.000	0.000	0.000	0.000
151	A	151	PRO	0	0.014	-0.008	17.820	-0.016	-0.016	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.927	-0.970	20.805	-0.125	-0.125	0.000	0.000	0.000	0.000
153	A	153	PRO	0	-0.074	-0.024	21.201	0.013	0.013	0.000	0.000	0.000	0.000

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