FMO DATABASE

FMODB ID: N9M7Q

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	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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1580803.798874
FMO2-HF: Nuclear repulsion	1518183.643046
FMO2-HF: Total energy	-62620.155828
FMO2-MP2: Total energy	-62802.810979

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.
-10.837	-3.145	4.265	-4.267	-7.687	-0.028

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 : -0.009 / q_NPA : -0.004

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	0.990	0.987	2.785	-3.678	-0.478	0.509	-1.696	-2.013	-0.003
4	A	4	VAL	0	-0.016	0.001	4.740	0.294	0.367	-0.001	-0.010	-0.061	0.000
5	A	5	THR	0	-0.017	0.002	8.158	-0.114	-0.114	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.085	0.041	11.281	0.029	0.029	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.042	-0.011	14.676	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.007	0.015	18.037	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.014	-0.001	20.998	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.034	-0.028	24.136	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.769	-0.879	27.361	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.045	-0.019	30.687	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.860	-0.913	32.029	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.027	-0.014	30.620	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.006	-0.008	24.323	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.031	0.014	24.426	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.033	-0.015	22.017	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.037	0.024	20.034	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.070	-0.021	22.338	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.989	1.000	15.976	-0.196	-0.196	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.049	0.009	21.715	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.896	0.940	24.194	-0.162	-0.162	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.928	0.974	26.868	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.038	0.035	22.873	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	TRP	0	-0.014	-0.025	16.870	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	26	TRP	0	-0.010	-0.013	21.673	0.016	0.016	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.016	-0.010	16.870	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.009	0.001	17.440	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.018	0.019	17.388	0.008	0.008	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.033	-0.034	14.872	-0.047	-0.047	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.053	0.041	12.733	0.046	0.046	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.826	0.885	7.569	-1.375	-1.375	0.000	0.000	0.000	0.000
33	A	33	MET	0	-0.006	0.001	7.638	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.926	-0.949	9.267	0.282	0.282	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.078	-0.064	10.801	-0.093	-0.093	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.020	-0.015	11.687	0.027	0.027	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.730	-0.794	12.362	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.073	-0.072	12.225	-0.061	-0.061	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.005	-0.032	9.814	0.018	0.018	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.019	-0.004	12.371	0.025	0.025	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.833	-0.892	15.840	-0.081	-0.081	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.011	-0.014	10.993	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.008	0.010	14.172	0.036	0.036	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.880	0.937	15.528	0.080	0.080	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.784	0.870	13.920	-0.088	-0.088	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.808	-0.900	13.355	0.193	0.193	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.014	0.001	16.849	0.013	0.013	0.000	0.000	0.000	0.000
48	A	48	TRP	0	-0.020	0.012	19.122	0.014	0.014	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.898	-0.954	18.845	0.148	0.148	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.859	-0.916	18.416	0.129	0.129	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.029	-0.057	21.232	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.029	-0.002	24.069	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.063	-0.029	25.039	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	54	THR	0	0.021	0.014	23.939	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.018	0.005	20.751	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.857	0.909	23.939	0.019	0.019	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.035	-0.040	23.884	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.009	0.020	19.203	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.855	-0.918	19.919	-0.127	-0.127	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.041	-0.021	12.767	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.789	0.869	16.285	0.144	0.144	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.033	0.026	14.537	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.033	-0.007	8.977	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.044	0.012	9.451	0.033	0.033	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.000	0.000	5.169	-0.070	-0.070	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.069	-0.033	6.327	0.276	0.276	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.047	0.014	6.429	-0.147	-0.147	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.003	0.015	8.492	0.143	0.143	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.062	-0.060	10.162	-0.062	-0.062	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.825	-0.943	12.749	0.152	0.152	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.936	-0.956	15.229	0.044	0.044	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.047	-0.022	17.184	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.885	0.952	11.886	0.031	0.031	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.023	0.006	6.753	0.069	0.069	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.038	-0.013	9.669	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.018	-0.020	6.075	0.387	0.387	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.863	-0.926	2.829	-3.026	-2.143	0.208	-0.206	-0.885	-0.001
78	A	78	TRP	0	-0.082	-0.021	2.217	-4.062	-1.095	2.919	-2.617	-3.268	-0.024
79	A	79	MET	0	0.013	0.012	2.351	-0.440	0.109	0.631	0.265	-1.444	0.000
80	A	80	LEU	0	-0.022	-0.004	4.944	0.210	0.230	-0.001	-0.003	-0.016	0.000
81	A	81	PHE	0	-0.023	-0.020	6.241	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.010	-0.004	10.851	0.047	0.047	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.025	-0.013	13.085	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.865	0.932	17.292	0.111	0.111	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.014	-0.009	21.019	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.017	-0.017	23.763	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.865	-0.908	27.516	-0.033	-0.033	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.127	-0.095	26.738	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.863	-0.913	28.079	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.030	0.013	28.638	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.951	-0.975	30.732	0.017	0.017	0.000	0.000	0.000	0.000
92	A	92	MET	0	-0.016	-0.002	27.772	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.017	0.020	25.632	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.916	0.947	28.777	-0.056	-0.056	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.105	-0.058	25.848	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	SER	0	0.099	0.076	21.725	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.032	-0.025	21.157	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.854	-0.925	17.628	0.306	0.306	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.044	-0.047	20.730	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.811	0.920	23.763	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.038	0.028	23.252	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.844	-0.930	26.786	0.030	0.030	0.000	0.000	0.000	0.000
103	A	103	TRP	0	0.068	0.040	27.653	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.819	0.915	27.672	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.885	0.918	30.005	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.859	0.911	28.506	0.041	0.041	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.886	-0.937	29.562	-0.040	-0.040	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.848	-0.912	31.402	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.018	-0.006	24.778	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.030	-0.027	24.904	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.896	-0.938	27.004	-0.024	-0.024	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.088	-0.016	25.739	0.009	0.009	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.018	-0.012	24.920	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	MET	0	0.001	-0.006	20.328	0.004	0.004	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.042	0.039	16.583	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.029	-0.004	18.587	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.023	-0.003	15.910	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.850	-0.934	15.652	-0.087	-0.087	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.846	0.924	17.776	0.023	0.023	0.000	0.000	0.000	0.000
120	A	120	TRP	0	-0.017	-0.013	18.953	0.001	0.001	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.020	0.026	14.304	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	122	PHE	0	0.030	-0.003	18.613	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.947	0.979	21.547	0.089	0.089	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.001	0.005	20.247	0.010	0.010	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.024	-0.031	18.432	0.005	0.005	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.035	-0.009	21.829	0.008	0.008	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.021	-0.011	25.062	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.008	0.011	23.094	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.788	-0.879	23.701	-0.106	-0.106	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.867	0.929	22.648	0.134	0.134	0.000	0.000	0.000	0.000
131	A	131	LEU	0	0.004	0.010	16.778	0.003	0.003	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.060	-0.020	16.689	0.007	0.007	0.000	0.000	0.000	0.000
133	A	133	TYR	0	0.021	0.001	13.149	-0.037	-0.037	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.025	-0.006	12.365	0.048	0.048	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.089	-0.039	9.138	-0.094	-0.094	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.003	0.017	10.701	0.099	0.099	0.000	0.000	0.000	0.000
137	A	137	HIS	0	0.027	0.022	10.993	-0.100	-0.100	0.000	0.000	0.000	0.000
138	A	138	TYR	0	0.037	0.010	11.749	0.047	0.047	0.000	0.000	0.000	0.000
139	A	139	THR	0	0.079	0.051	13.561	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	140	PRO	0	0.025	0.001	13.606	0.015	0.015	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.942	-0.956	14.690	0.208	0.208	0.000	0.000	0.000	0.000
142	A	142	PHE	0	-0.116	-0.066	10.906	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.925	-0.945	16.165	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.080	-0.058	15.626	-0.014	-0.014	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.014	0.010	15.517	0.004	0.004	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.033	-0.025	16.679	-0.012	-0.012	0.000	0.000	0.000	0.000
147	A	147	TYR	0	0.001	-0.015	15.059	-0.020	-0.020	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.888	0.959	11.407	0.453	0.453	0.000	0.000	0.000	0.000
149	A	149	LEU	0	0.000	-0.006	14.980	-0.037	-0.037	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.877	-0.906	17.132	-0.221	-0.221	0.000	0.000	0.000	0.000
151	A	151	PRO	0	0.003	-0.013	18.063	-0.016	-0.016	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.935	-0.969	21.098	-0.161	-0.161	0.000	0.000	0.000	0.000
153	A	153	PRO	0	-0.077	-0.029	21.391	0.017	0.017	0.000	0.000	0.000	0.000

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