FMO DATABASE

FMODB ID: K3JY3

Calculation Name: 3KIO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KIO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1285356.687047
FMO2-HF: Nuclear repulsion	1227917.588854
FMO2-HF: Total energy	-57439.098193
FMO2-MP2: Total energy	-57608.425064

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(B:10:LEU)

Summations of interaction energy for fragment #1(B:10: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.
-1.885	-0.316	-0.018	-0.809	-0.742	0.002

Interaction energy analysis for fragmet #1(B:10:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.007

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	B	12	ALA	0	-0.009	0.003	3.866	1.160	2.729	-0.018	-0.809	-0.742	0.002
4	B	13	ARG	1	0.960	0.976	6.950	-1.668	-1.668	0.000	0.000	0.000	0.000
5	B	14	GLN	0	0.009	0.004	8.620	-0.108	-0.108	0.000	0.000	0.000	0.000
6	B	15	LEU	0	-0.068	-0.046	12.108	-0.015	-0.015	0.000	0.000	0.000	0.000
7	B	16	VAL	0	0.053	0.046	15.500	-0.023	-0.023	0.000	0.000	0.000	0.000
8	B	17	PHE	0	0.004	-0.020	18.463	0.000	0.000	0.000	0.000	0.000	0.000
9	B	18	LEU	0	0.004	0.024	21.474	-0.017	-0.017	0.000	0.000	0.000	0.000
10	B	19	LEU	0	0.022	-0.002	24.097	0.005	0.005	0.000	0.000	0.000	0.000
11	B	20	PRO	0	0.019	0.002	27.416	-0.010	-0.010	0.000	0.000	0.000	0.000
12	B	21	GLU	-1	-0.906	-0.938	30.532	0.091	0.091	0.000	0.000	0.000	0.000
13	B	22	HIS	0	0.052	0.012	32.338	0.002	0.002	0.000	0.000	0.000	0.000
14	B	23	LEU	0	-0.058	-0.026	28.641	0.003	0.003	0.000	0.000	0.000	0.000
15	B	24	LYS	1	0.862	0.933	27.551	-0.123	-0.123	0.000	0.000	0.000	0.000
16	B	25	ASP	-1	-0.834	-0.891	30.371	0.087	0.087	0.000	0.000	0.000	0.000
17	B	26	ALA	0	-0.015	-0.004	31.314	0.005	0.005	0.000	0.000	0.000	0.000
18	B	27	SER	0	0.006	-0.009	33.016	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	28	LYS	1	0.984	0.964	36.635	-0.059	-0.059	0.000	0.000	0.000	0.000
20	B	29	LYS	1	0.834	0.927	32.565	-0.126	-0.126	0.000	0.000	0.000	0.000
21	B	30	LYS	1	0.900	0.942	32.553	-0.103	-0.103	0.000	0.000	0.000	0.000
22	B	31	LYS	1	0.872	0.928	35.061	-0.101	-0.101	0.000	0.000	0.000	0.000
23	B	32	LYS	1	0.961	0.989	31.367	-0.154	-0.154	0.000	0.000	0.000	0.000
24	B	33	SER	0	0.037	0.006	26.264	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	34	SER	0	0.021	-0.002	29.290	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	35	LEU	0	0.001	0.005	26.479	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	36	LEU	0	0.022	0.010	24.990	0.010	0.010	0.000	0.000	0.000	0.000
28	B	37	PHE	0	0.028	0.012	21.961	-0.012	-0.012	0.000	0.000	0.000	0.000
29	B	38	VAL	0	0.012	0.004	24.515	0.010	0.010	0.000	0.000	0.000	0.000
30	B	39	LYS	1	0.878	0.937	21.803	-0.300	-0.300	0.000	0.000	0.000	0.000
31	B	40	LEU	0	-0.020	-0.005	25.966	-0.007	-0.007	0.000	0.000	0.000	0.000
32	B	41	ALA	0	0.122	0.052	29.611	0.003	0.003	0.000	0.000	0.000	0.000
33	B	42	ASN	0	-0.047	-0.012	29.570	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	43	PRO	0	-0.005	-0.010	31.711	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	44	HIS	0	-0.010	-0.002	33.720	0.000	0.000	0.000	0.000	0.000	0.000
36	B	45	SER	0	-0.026	-0.012	35.068	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	46	GLY	0	0.046	0.047	31.084	0.002	0.002	0.000	0.000	0.000	0.000
38	B	47	GLU	-1	-0.843	-0.936	29.397	0.179	0.179	0.000	0.000	0.000	0.000
39	B	48	GLY	0	0.038	0.029	26.195	0.007	0.007	0.000	0.000	0.000	0.000
40	B	49	ALA	0	-0.033	-0.007	24.734	0.024	0.024	0.000	0.000	0.000	0.000
41	B	50	THR	0	-0.019	-0.030	21.744	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	51	TYR	0	0.005	-0.021	24.959	-0.018	-0.018	0.000	0.000	0.000	0.000
43	B	52	LEU	0	0.007	0.011	25.548	0.018	0.018	0.000	0.000	0.000	0.000
44	B	53	ILE	0	-0.006	-0.004	27.488	-0.021	-0.021	0.000	0.000	0.000	0.000
45	B	54	ASP	-1	-0.650	-0.804	29.678	0.145	0.145	0.000	0.000	0.000	0.000
46	B	55	MET	0	-0.035	-0.026	29.274	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	56	CYS	0	-0.072	-0.002	33.729	-0.011	-0.011	0.000	0.000	0.000	0.000
48	B	57	LEU	0	-0.027	-0.032	36.365	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	58	GLN	0	-0.025	-0.006	35.069	-0.009	-0.009	0.000	0.000	0.000	0.000
50	B	59	GLN	0	-0.041	-0.047	33.915	0.007	0.007	0.000	0.000	0.000	0.000
51	B	60	LEU	0	-0.006	0.014	31.490	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	61	PHE	0	0.037	0.023	29.197	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	62	GLU	-1	-0.722	-0.831	28.390	0.156	0.156	0.000	0.000	0.000	0.000
54	B	63	ILE	0	-0.047	-0.020	22.143	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	64	LYS	1	0.841	0.920	24.053	-0.117	-0.117	0.000	0.000	0.000	0.000
56	B	65	VAL	0	-0.020	-0.026	20.184	0.008	0.008	0.000	0.000	0.000	0.000
57	B	66	PHE	0	0.025	0.032	22.296	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	67	LYS	1	0.948	0.951	19.551	-0.190	-0.190	0.000	0.000	0.000	0.000
59	B	68	GLU	-1	-0.853	-0.902	21.435	0.066	0.066	0.000	0.000	0.000	0.000
60	B	69	LYS	1	0.937	0.951	20.712	-0.054	-0.054	0.000	0.000	0.000	0.000
61	B	70	HIS	0	0.031	0.008	19.328	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	71	HIS	0	-0.003	0.020	19.401	-0.016	-0.016	0.000	0.000	0.000	0.000
63	B	72	SER	0	-0.089	-0.052	14.631	0.006	0.006	0.000	0.000	0.000	0.000
64	B	73	TRP	0	-0.008	-0.008	15.053	-0.015	-0.015	0.000	0.000	0.000	0.000
65	B	74	PHE	0	0.042	0.022	14.690	-0.011	-0.011	0.000	0.000	0.000	0.000
66	B	75	ILE	0	-0.020	-0.017	14.077	0.037	0.037	0.000	0.000	0.000	0.000
67	B	76	ASN	0	0.006	0.014	14.930	-0.021	-0.021	0.000	0.000	0.000	0.000
68	B	77	GLN	0	0.027	0.022	14.688	0.013	0.013	0.000	0.000	0.000	0.000
69	B	78	SER	0	-0.035	-0.021	10.676	-0.046	-0.046	0.000	0.000	0.000	0.000
70	B	79	VAL	0	0.056	0.023	10.139	0.043	0.043	0.000	0.000	0.000	0.000
71	B	80	GLN	0	0.008	0.011	10.097	0.112	0.112	0.000	0.000	0.000	0.000
72	B	81	SER	0	0.011	-0.019	10.114	-0.038	-0.038	0.000	0.000	0.000	0.000
73	B	82	GLY	0	-0.020	-0.005	11.857	-0.015	-0.015	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.062	0.034	13.918	-0.011	-0.011	0.000	0.000	0.000	0.000
75	B	84	LEU	0	-0.104	-0.048	14.901	0.001	0.001	0.000	0.000	0.000	0.000
76	B	85	LEU	0	0.046	0.040	18.073	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	86	HIS	0	-0.004	0.003	17.032	-0.028	-0.028	0.000	0.000	0.000	0.000
78	B	87	PHE	0	0.037	0.010	21.923	-0.012	-0.012	0.000	0.000	0.000	0.000
79	B	88	ALA	0	-0.017	-0.005	25.655	0.005	0.005	0.000	0.000	0.000	0.000
80	B	89	THR	0	0.015	-0.002	27.408	-0.010	-0.010	0.000	0.000	0.000	0.000
81	B	90	PRO	0	-0.030	-0.022	31.062	0.005	0.005	0.000	0.000	0.000	0.000
82	B	91	MET	0	0.005	0.008	32.665	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	92	ASP	-1	-0.823	-0.873	34.296	0.083	0.083	0.000	0.000	0.000	0.000
84	B	93	PRO	0	-0.035	0.013	37.291	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	94	LEU	0	0.058	0.004	38.632	0.003	0.003	0.000	0.000	0.000	0.000
86	B	95	PHE	0	-0.064	-0.031	37.966	0.001	0.001	0.000	0.000	0.000	0.000
87	B	96	LEU	0	0.028	0.018	32.990	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	97	LEU	0	-0.018	-0.012	34.719	0.003	0.003	0.000	0.000	0.000	0.000
89	B	98	LEU	0	0.032	0.034	36.891	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	99	HIS	0	-0.015	-0.022	32.253	0.002	0.002	0.000	0.000	0.000	0.000
91	B	100	TYR	0	-0.046	-0.047	28.890	0.004	0.004	0.000	0.000	0.000	0.000
92	B	101	LEU	0	0.003	0.026	31.492	0.000	0.000	0.000	0.000	0.000	0.000
93	B	102	LEU	0	-0.044	-0.014	28.018	-0.008	-0.008	0.000	0.000	0.000	0.000
94	B	146	GLU	-1	-0.886	-0.948	32.908	0.157	0.157	0.000	0.000	0.000	0.000
95	B	147	VAL	0	0.014	0.015	33.260	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	148	ASN	0	-0.066	-0.062	35.024	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	149	SER	0	0.038	0.018	37.579	-0.007	-0.007	0.000	0.000	0.000	0.000
98	B	150	LYS	1	0.989	0.982	40.436	-0.084	-0.084	0.000	0.000	0.000	0.000
99	B	151	LYS	1	0.936	0.973	40.450	-0.089	-0.089	0.000	0.000	0.000	0.000
100	B	152	TYR	0	0.084	0.045	42.077	-0.002	-0.002	0.000	0.000	0.000	0.000
101	B	153	TYR	0	0.092	0.037	44.755	0.000	0.000	0.000	0.000	0.000	0.000
102	B	154	LYS	1	0.962	0.992	47.846	-0.060	-0.060	0.000	0.000	0.000	0.000
103	B	155	TYR	0	-0.067	-0.051	40.898	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	156	SER	0	0.006	-0.021	44.800	0.003	0.003	0.000	0.000	0.000	0.000
105	B	157	SER	0	-0.035	-0.014	46.969	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	158	GLU	-1	-0.767	-0.864	47.625	0.073	0.073	0.000	0.000	0.000	0.000
107	B	159	LYS	1	0.975	0.982	42.312	-0.081	-0.081	0.000	0.000	0.000	0.000
108	B	160	THR	0	0.075	0.051	48.234	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	161	LEU	0	0.088	0.040	49.976	0.002	0.002	0.000	0.000	0.000	0.000
110	B	162	LYS	1	0.862	0.901	51.264	-0.043	-0.043	0.000	0.000	0.000	0.000
111	B	163	TRP	0	0.003	-0.019	42.540	0.001	0.001	0.000	0.000	0.000	0.000
112	B	164	LEU	0	0.010	0.003	46.077	0.002	0.002	0.000	0.000	0.000	0.000
113	B	165	GLU	-1	-0.770	-0.865	47.466	0.046	0.046	0.000	0.000	0.000	0.000
114	B	166	LYS	1	0.956	0.974	49.443	-0.051	-0.051	0.000	0.000	0.000	0.000
115	B	167	LYS	1	0.825	0.902	41.561	-0.082	-0.082	0.000	0.000	0.000	0.000
116	B	168	VAL	0	0.038	0.028	44.488	0.002	0.002	0.000	0.000	0.000	0.000
117	B	169	ASN	0	0.006	0.011	45.954	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	170	GLN	0	-0.037	-0.024	43.436	0.002	0.002	0.000	0.000	0.000	0.000
119	B	171	THR	0	0.000	-0.031	40.952	0.000	0.000	0.000	0.000	0.000	0.000
120	B	172	VAL	0	0.036	0.024	43.452	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	173	VAL	0	-0.046	-0.025	45.997	-0.002	-0.002	0.000	0.000	0.000	0.000
122	B	174	ALA	0	0.026	0.011	41.518	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	175	LEU	0	-0.033	-0.024	39.644	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	176	LYS	1	0.924	0.969	43.325	-0.045	-0.045	0.000	0.000	0.000	0.000
125	B	177	ALA	0	-0.001	0.017	44.266	-0.003	-0.003	0.000	0.000	0.000	0.000
126	B	178	ASN	0	-0.044	-0.029	40.612	0.003	0.003	0.000	0.000	0.000	0.000
127	B	179	ASN	0	0.007	0.009	42.541	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	180	VAL	0	0.006	0.012	39.984	0.001	0.001	0.000	0.000	0.000	0.000
129	B	181	ASN	0	0.002	0.003	41.356	-0.003	-0.003	0.000	0.000	0.000	0.000
130	B	267	LEU	0	-0.038	-0.020	46.180	0.001	0.001	0.000	0.000	0.000	0.000
131	B	268	LYS	1	1.006	1.002	45.130	-0.066	-0.066	0.000	0.000	0.000	0.000
132	B	269	THR	0	0.046	0.020	40.893	0.001	0.001	0.000	0.000	0.000	0.000
133	B	270	GLY	0	0.051	0.026	38.119	-0.001	-0.001	0.000	0.000	0.000	0.000
134	B	271	LYS	1	0.819	0.946	38.757	-0.073	-0.073	0.000	0.000	0.000	0.000
135	B	272	LYS	1	0.940	0.977	37.270	-0.106	-0.106	0.000	0.000	0.000	0.000
136	B	273	ASN	0	-0.083	-0.065	38.285	0.004	0.004	0.000	0.000	0.000	0.000
137	B	274	SER	0	0.005	-0.025	38.377	-0.004	-0.004	0.000	0.000	0.000	0.000
138	B	275	LYN	0	0.004	0.006	31.153	0.000	0.000	0.000	0.000	0.000	0.000
139	B	276	MET	0	-0.049	0.008	36.703	0.003	0.003	0.000	0.000	0.000	0.000
140	B	277	THR	0	-0.028	-0.046	39.144	-0.003	-0.003	0.000	0.000	0.000	0.000
141	B	278	ALA	0	-0.040	-0.020	37.634	-0.003	-0.003	0.000	0.000	0.000	0.000
142	B	279	ALA	0	0.051	0.029	36.453	-0.002	-0.002	0.000	0.000	0.000	0.000
143	B	280	GLN	0	-0.016	0.005	38.463	-0.004	-0.004	0.000	0.000	0.000	0.000
144	B	281	LYS	1	0.808	0.893	42.027	-0.082	-0.082	0.000	0.000	0.000	0.000
145	B	282	ALA	0	0.025	0.042	41.585	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:10:LEU)