FMO DATABASE

FMODB ID: 17VJZ

Calculation Name: 1KTK-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KTK

Chain ID: F

ChEMBL ID:

UniProt ID: Q8NKX2

Base Structure: X-ray

Registration Date: 2023-06-26

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1302460.004533
FMO2-HF: Nuclear repulsion	1242266.828421
FMO2-HF: Total energy	-60193.176112
FMO2-MP2: Total energy	-60366.643441

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(F:4:VAL)

Summations of interaction energy for fragment #1(F:4:VAL)

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.
-8	-0.9	13.565	-7.257	-13.41	-0.032

Interaction energy analysis for fragmet #1(F:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.002

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	F	6	GLN	0	0.064	0.019	3.421	-2.711	0.440	-0.003	-1.567	-1.581	0.005
4	F	7	HIS	0	-0.023	-0.030	5.604	-0.134	-0.134	0.000	0.000	0.000	0.000
5	F	8	PRO	0	-0.057	0.009	8.595	-0.027	-0.027	0.000	0.000	0.000	0.000
6	F	9	SER	0	0.064	0.036	9.968	-0.056	-0.056	0.000	0.000	0.000	0.000
7	F	10	ARG	1	0.906	0.975	10.890	0.053	0.053	0.000	0.000	0.000	0.000
8	F	11	VAL	0	0.015	-0.006	14.259	0.035	0.035	0.000	0.000	0.000	0.000
9	F	12	ILE	0	-0.014	-0.009	17.009	-0.014	-0.014	0.000	0.000	0.000	0.000
10	F	13	ALA	0	-0.041	0.007	18.331	0.012	0.012	0.000	0.000	0.000	0.000
11	F	14	LYS	1	0.998	0.984	20.287	-0.009	-0.009	0.000	0.000	0.000	0.000
12	F	15	SER	0	0.071	0.030	23.683	-0.004	-0.004	0.000	0.000	0.000	0.000
13	F	16	GLY	0	0.003	0.007	26.429	0.005	0.005	0.000	0.000	0.000	0.000
14	F	17	THR	0	-0.025	-0.036	20.591	0.010	0.010	0.000	0.000	0.000	0.000
15	F	18	SER	0	0.042	0.019	19.523	-0.012	-0.012	0.000	0.000	0.000	0.000
16	F	19	VAL	0	-0.058	-0.026	14.094	0.013	0.013	0.000	0.000	0.000	0.000
17	F	20	LYS	1	0.950	0.992	14.005	-0.106	-0.106	0.000	0.000	0.000	0.000
18	F	21	ILE	0	0.043	-0.016	8.068	-0.005	-0.005	0.000	0.000	0.000	0.000
19	F	22	GLU	-1	-0.901	-0.967	8.427	0.293	0.293	0.000	0.000	0.000	0.000
20	F	92	CYS	0	0.014	0.052	2.808	0.224	-1.960	7.158	-1.341	-3.633	-0.004
21	F	24	ARG	1	0.873	0.937	3.667	-1.279	-0.862	0.004	-0.128	-0.293	0.000
22	F	25	SER	0	0.044	-0.010	2.333	-1.779	0.065	3.427	-2.552	-2.719	-0.021
23	F	26	LEU	0	-0.016	0.012	3.769	-0.950	-0.802	0.009	-0.050	-0.108	0.000
24	F	27	ASP	-1	-0.903	-0.953	5.183	3.349	3.412	-0.001	-0.003	-0.059	0.000
25	F	27	PHE	0	-0.018	0.002	3.685	-0.557	-0.281	0.003	-0.036	-0.243	0.000
26	F	28	GLN	0	-0.049	-0.025	6.814	-0.002	-0.002	0.000	0.000	0.000	0.000
27	F	29	ALA	0	0.010	0.012	5.977	-0.107	-0.107	0.000	0.000	0.000	0.000
28	F	30	THR	0	-0.020	-0.028	7.227	-0.009	-0.009	0.000	0.000	0.000	0.000
29	F	31	THR	0	-0.047	-0.010	8.903	0.023	0.023	0.000	0.000	0.000	0.000
30	F	32	MET	0	0.028	0.009	3.754	-0.388	-0.091	0.006	-0.042	-0.262	0.000
31	F	33	PHE	0	0.037	0.066	6.883	0.122	0.122	0.000	0.000	0.000	0.000
32	F	34	TRP	0	0.026	-0.004	7.081	-0.056	-0.056	0.000	0.000	0.000	0.000
33	F	35	TYR	0	0.032	0.008	7.154	0.151	0.151	0.000	0.000	0.000	0.000
34	F	36	ARG	1	0.842	0.919	11.090	0.155	0.155	0.000	0.000	0.000	0.000
35	F	37	GLN	0	-0.072	-0.068	13.818	-0.056	-0.056	0.000	0.000	0.000	0.000
36	F	38	PHE	0	0.139	0.067	16.614	0.023	0.023	0.000	0.000	0.000	0.000
37	F	39	PRO	0	-0.067	-0.038	17.694	-0.029	-0.029	0.000	0.000	0.000	0.000
38	F	40	LYS	1	0.937	0.941	19.130	0.141	0.141	0.000	0.000	0.000	0.000
39	F	41	GLN	0	0.077	0.041	20.146	0.018	0.018	0.000	0.000	0.000	0.000
40	F	42	SER	0	-0.076	-0.035	17.194	-0.006	-0.006	0.000	0.000	0.000	0.000
41	F	43	LEU	0	0.078	0.041	12.880	-0.001	-0.001	0.000	0.000	0.000	0.000
42	F	44	MET	0	0.000	0.034	15.135	0.025	0.025	0.000	0.000	0.000	0.000
43	F	45	LEU	0	-0.041	-0.033	12.830	-0.045	-0.045	0.000	0.000	0.000	0.000
44	F	46	MET	0	-0.021	-0.004	11.928	0.042	0.042	0.000	0.000	0.000	0.000
45	F	47	ALA	0	0.039	0.052	13.520	0.012	0.012	0.000	0.000	0.000	0.000
46	F	48	THR	0	-0.041	-0.042	10.284	-0.048	-0.048	0.000	0.000	0.000	0.000
47	F	49	SER	0	-0.017	0.004	11.240	0.027	0.027	0.000	0.000	0.000	0.000
48	F	50	ALA	0	0.047	0.007	12.983	-0.030	-0.030	0.000	0.000	0.000	0.000
49	F	51	GLU	-1	-0.874	-0.932	14.740	-0.049	-0.049	0.000	0.000	0.000	0.000
50	F	52	GLY	0	-0.006	0.008	13.316	-0.012	-0.012	0.000	0.000	0.000	0.000
51	F	52	SER	0	0.019	-0.021	13.229	-0.010	-0.010	0.000	0.000	0.000	0.000
52	F	53	LYS	1	0.842	0.941	15.494	0.089	0.089	0.000	0.000	0.000	0.000
53	F	54	ALA	0	0.024	0.011	17.843	-0.009	-0.009	0.000	0.000	0.000	0.000
54	F	55	THR	0	0.090	0.027	15.728	-0.007	-0.007	0.000	0.000	0.000	0.000
55	F	56	TYR	0	-0.013	-0.013	15.029	-0.010	-0.010	0.000	0.000	0.000	0.000
56	F	57	GLU	-1	-0.947	-0.984	15.691	-0.126	-0.126	0.000	0.000	0.000	0.000
57	F	58	GLN	0	-0.072	-0.057	16.782	-0.002	-0.002	0.000	0.000	0.000	0.000
58	F	59	GLY	0	-0.052	-0.027	20.859	0.003	0.003	0.000	0.000	0.000	0.000
59	F	60	VAL	0	0.042	0.018	24.251	0.002	0.002	0.000	0.000	0.000	0.000
60	F	61	GLU	-1	-1.055	-1.047	24.866	-0.074	-0.074	0.000	0.000	0.000	0.000
61	F	62	LYS	1	0.946	0.920	19.108	0.118	0.118	0.000	0.000	0.000	0.000
62	F	63	ASP	-1	-0.743	-0.748	20.201	-0.076	-0.076	0.000	0.000	0.000	0.000
63	F	64	LYS	1	0.842	0.872	20.750	0.059	0.059	0.000	0.000	0.000	0.000
64	F	65	PHE	0	-0.006	-0.019	15.981	-0.002	-0.002	0.000	0.000	0.000	0.000
65	F	66	LEU	0	0.041	0.022	15.918	-0.015	-0.015	0.000	0.000	0.000	0.000
66	F	67	ILE	0	0.041	0.029	11.143	-0.009	-0.009	0.000	0.000	0.000	0.000
67	F	68	ASN	0	-0.081	-0.040	12.556	-0.011	-0.011	0.000	0.000	0.000	0.000
68	F	69	HIS	0	0.032	0.018	8.483	0.037	0.037	0.000	0.000	0.000	0.000
69	F	70	ALA	0	-0.016	0.001	10.669	0.000	0.000	0.000	0.000	0.000	0.000
70	F	71	SER	0	-0.019	0.008	11.071	-0.002	-0.002	0.000	0.000	0.000	0.000
71	F	72	LEU	0	0.034	0.021	9.226	-0.014	-0.014	0.000	0.000	0.000	0.000
72	F	73	THR	0	-0.033	-0.036	7.161	0.062	0.062	0.000	0.000	0.000	0.000
73	F	74	LEU	0	-0.014	-0.005	6.181	0.037	0.037	0.000	0.000	0.000	0.000
74	F	75	SER	0	0.078	0.027	6.648	-0.084	-0.084	0.000	0.000	0.000	0.000
75	F	76	THR	0	-0.078	-0.027	7.844	-0.011	-0.011	0.000	0.000	0.000	0.000
76	F	77	LEU	0	0.068	0.031	10.355	-0.024	-0.024	0.000	0.000	0.000	0.000
77	F	78	THR	0	-0.068	-0.031	12.264	0.022	0.022	0.000	0.000	0.000	0.000
78	F	79	VAL	0	0.017	0.004	15.204	-0.012	-0.012	0.000	0.000	0.000	0.000
79	F	80	THR	0	-0.014	-0.003	17.818	0.013	0.013	0.000	0.000	0.000	0.000
80	F	81	SER	0	-0.066	-0.027	21.469	-0.001	-0.001	0.000	0.000	0.000	0.000
81	F	82	ALA	0	0.029	0.043	23.064	0.004	0.004	0.000	0.000	0.000	0.000
82	F	83	HIS	0	-0.011	-0.032	24.691	0.003	0.003	0.000	0.000	0.000	0.000
83	F	84	PRO	0	-0.040	-0.027	24.564	-0.005	-0.005	0.000	0.000	0.000	0.000
84	F	85	GLU	-1	-0.784	-0.829	19.705	-0.156	-0.156	0.000	0.000	0.000	0.000
85	F	86	ASP	-1	-0.795	-0.874	20.726	-0.071	-0.071	0.000	0.000	0.000	0.000
86	F	87	SER	0	-0.061	-0.029	16.678	-0.009	-0.009	0.000	0.000	0.000	0.000
87	F	88	SER	0	0.026	0.034	15.345	0.002	0.002	0.000	0.000	0.000	0.000
88	F	89	PHE	0	-0.078	-0.035	10.841	0.015	0.015	0.000	0.000	0.000	0.000
89	F	90	TYR	0	0.044	0.044	10.447	-0.024	-0.024	0.000	0.000	0.000	0.000
90	F	91	ILE	0	0.013	-0.029	5.774	0.009	0.009	0.000	0.000	0.000	0.000
91	F	107	TYR	0	-0.005	-0.016	2.367	-0.801	-0.065	1.299	-0.461	-1.574	0.001
92	F	108	PHE	0	-0.002	-0.004	4.058	-0.466	0.103	0.007	-0.102	-0.475	0.000
93	F	109	GLY	0	0.016	0.024	2.609	-3.872	-2.102	1.576	-1.433	-1.912	-0.013
94	F	110	PRO	0	-0.055	-0.034	3.235	0.929	0.942	0.080	0.458	-0.551	0.000
95	F	111	GLY	0	0.066	0.046	6.475	0.050	0.050	0.000	0.000	0.000	0.000
96	F	112	THR	0	-0.023	-0.018	8.883	0.060	0.060	0.000	0.000	0.000	0.000
97	F	113	ARG	1	0.796	0.880	10.491	0.185	0.185	0.000	0.000	0.000	0.000
98	F	114	LEU	0	0.008	0.003	14.251	0.021	0.021	0.000	0.000	0.000	0.000
99	F	115	THR	0	0.032	-0.005	17.030	-0.006	-0.006	0.000	0.000	0.000	0.000
100	F	116	VAL	0	-0.118	-0.033	20.836	0.009	0.009	0.000	0.000	0.000	0.000
101	F	124	PRO	0	0.007	-0.021	26.348	0.001	0.001	0.000	0.000	0.000	0.000
102	F	125	PRO	0	-0.094	-0.050	27.907	-0.005	-0.005	0.000	0.000	0.000	0.000
103	F	126	GLU	-1	-0.869	-0.934	29.647	-0.008	-0.008	0.000	0.000	0.000	0.000
104	F	127	VAL	0	-0.072	0.023	29.113	-0.005	-0.005	0.000	0.000	0.000	0.000
105	F	128	ALA	0	-0.021	-0.001	32.464	0.004	0.004	0.000	0.000	0.000	0.000
106	F	129	VAL	0	-0.006	-0.034	32.359	-0.002	-0.002	0.000	0.000	0.000	0.000
107	F	130	PHE	0	0.008	0.011	34.867	-0.002	-0.002	0.000	0.000	0.000	0.000
108	F	131	GLU	-1	-0.913	-0.950	36.646	-0.008	-0.008	0.000	0.000	0.000	0.000
109	F	132	PRO	0	-0.115	-0.037	35.970	-0.003	-0.003	0.000	0.000	0.000	0.000
110	F	146	VAL	0	0.005	-0.010	33.218	-0.002	-0.002	0.000	0.000	0.000	0.000
111	F	147	CYM	-1	-0.825	-0.790	29.531	-0.046	-0.046	0.000	0.000	0.000	0.000
112	F	148	LEU	0	0.040	-0.006	31.057	-0.003	-0.003	0.000	0.000	0.000	0.000
113	F	149	ALA	0	0.024	-0.002	27.706	0.004	0.004	0.000	0.000	0.000	0.000
114	F	150	THR	0	-0.055	-0.059	29.461	-0.006	-0.006	0.000	0.000	0.000	0.000
115	F	151	GLY	0	0.134	0.072	31.412	0.004	0.004	0.000	0.000	0.000	0.000
116	F	152	PHE	0	-0.078	-0.022	23.029	0.000	0.000	0.000	0.000	0.000	0.000
117	F	186	ASN	0	-0.014	-0.026	36.017	0.000	0.000	0.000	0.000	0.000	0.000
118	F	187	ASP	-1	-0.828	-0.890	33.088	-0.040	-0.040	0.000	0.000	0.000	0.000
119	F	188	SER	0	-0.032	-0.006	30.638	-0.004	-0.004	0.000	0.000	0.000	0.000
120	F	189	ARG	1	0.850	0.908	29.023	0.048	0.048	0.000	0.000	0.000	0.000
121	F	190	TYR	0	-0.041	-0.032	27.981	-0.005	-0.005	0.000	0.000	0.000	0.000
122	F	191	ALA	0	0.035	0.026	29.405	0.006	0.006	0.000	0.000	0.000	0.000
123	F	192	LEU	0	-0.013	-0.011	24.015	-0.010	-0.010	0.000	0.000	0.000	0.000
124	F	193	SER	0	-0.008	-0.001	27.507	0.009	0.009	0.000	0.000	0.000	0.000
125	F	194	SER	0	-0.060	-0.098	26.564	-0.010	-0.010	0.000	0.000	0.000	0.000
126	F	195	ARG	1	0.967	0.972	28.263	0.075	0.075	0.000	0.000	0.000	0.000
127	F	196	LEU	0	0.017	0.022	27.489	-0.005	-0.005	0.000	0.000	0.000	0.000
128	F	204	GLN	0	0.009	-0.007	39.601	-0.002	-0.002	0.000	0.000	0.000	0.000
129	F	205	ASN	0	-0.001	-0.005	34.797	0.002	0.002	0.000	0.000	0.000	0.000
130	F	206	PRO	0	0.055	0.019	37.490	-0.001	-0.001	0.000	0.000	0.000	0.000
131	F	207	ARG	1	0.950	0.973	35.138	-0.023	-0.023	0.000	0.000	0.000	0.000
132	F	208	ASN	0	-0.082	-0.028	32.343	-0.002	-0.002	0.000	0.000	0.000	0.000
133	F	209	HIS	0	-0.008	-0.002	29.092	0.004	0.004	0.000	0.000	0.000	0.000
134	F	210	PHE	0	0.036	0.022	27.546	-0.001	-0.001	0.000	0.000	0.000	0.000
135	F	211	ARG	1	0.965	0.965	23.203	-0.017	-0.017	0.000	0.000	0.000	0.000
136	F	212	CYS	0	-0.021	-0.044	24.072	0.003	0.003	0.000	0.000	0.000	0.000
137	F	213	GLN	0	0.005	0.024	18.854	-0.009	-0.009	0.000	0.000	0.000	0.000
138	F	214	VAL	0	0.024	0.030	20.462	-0.013	-0.013	0.000	0.000	0.000	0.000
139	F	215	GLN	0	-0.089	-0.061	17.744	-0.001	-0.001	0.000	0.000	0.000	0.000
140	F	216	PHE	0	0.094	0.056	21.026	-0.003	-0.003	0.000	0.000	0.000	0.000
141	F	217	TYR	0	0.010	0.001	18.275	-0.002	-0.002	0.000	0.000	0.000	0.000
142	F	233	VAL	0	0.043	-0.012	22.973	-0.004	-0.004	0.000	0.000	0.000	0.000
143	F	234	THR	0	-0.072	-0.036	19.941	0.008	0.008	0.000	0.000	0.000	0.000
144	F	235	GLN	0	0.068	0.017	21.605	-0.016	-0.016	0.000	0.000	0.000	0.000
145	F	236	ILE	0	-0.025	-0.008	20.125	-0.001	-0.001	0.000	0.000	0.000	0.000
146	F	237	VAL	0	0.032	0.019	22.813	0.005	0.005	0.000	0.000	0.000	0.000
147	F	238	SER	0	-0.086	-0.048	24.829	0.000	0.000	0.000	0.000	0.000	0.000
148	F	239	ALA	0	0.058	0.026	27.035	-0.001	-0.001	0.000	0.000	0.000	0.000
149	F	240	GLU	-1	-0.900	-0.940	29.648	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:4:VAL)