FMO DATABASE

FMODB ID: 16JYZ

Calculation Name: 1KHY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KHY

Chain ID: A

ChEMBL ID:

UniProt ID: P63284

Base Structure: X-ray

Registration Date: 2023-09-26

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	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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1105175.135728
FMO2-HF: Nuclear repulsion	1055963.226098
FMO2-HF: Total energy	-49211.90963
FMO2-MP2: Total energy	-49357.278045

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:4:ASP)

Summations of interaction energy for fragment #1(A:4:ASP)

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.
7.788	10.347	5.602	-3.283	-4.878	-0.009

Interaction energy analysis for fragmet #1(A:4:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.975

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

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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	6	LEU	0	-0.002	0.020	2.478	-11.942	-8.315	0.860	-1.560	-2.927	0.009
4	A	7	THR	0	0.035	0.019	4.201	-1.483	-1.433	0.000	-0.041	-0.009	0.000
5	A	8	ASN	0	0.065	0.008	6.132	3.903	3.903	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.913	0.955	7.463	-17.259	-17.259	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.029	0.018	7.071	-0.584	-0.584	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.027	0.008	2.057	4.871	3.610	4.743	-1.676	-1.807	-0.018
9	A	12	LEU	0	0.007	-0.005	6.716	-0.813	-0.813	0.000	0.000	0.000	0.000
10	A	13	ALA	0	0.003	0.011	10.143	-1.373	-1.373	0.000	0.000	0.000	0.000
11	A	14	LEU	0	0.013	0.001	6.449	-1.340	-1.340	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.012	0.004	10.242	-1.052	-1.052	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.880	-0.949	11.542	16.069	16.069	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.016	0.001	12.977	-1.300	-1.300	0.000	0.000	0.000	0.000
15	A	18	GLN	0	-0.028	-0.016	12.226	-0.334	-0.334	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.008	-0.002	14.490	-1.197	-1.197	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.027	-0.004	17.436	-1.155	-1.155	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.037	-0.027	17.279	-0.843	-0.843	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.001	0.007	18.615	-0.762	-0.762	0.000	0.000	0.000	0.000
20	A	23	GLY	0	0.012	0.007	20.353	-0.723	-0.723	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.790	0.892	22.382	-12.990	-12.990	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.825	-0.904	23.619	11.571	11.571	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.037	-0.012	20.880	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	27	GLN	0	0.030	0.016	20.626	0.041	0.041	0.000	0.000	0.000	0.000
25	A	28	PHE	0	-0.029	-0.029	17.114	0.666	0.666	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.009	0.030	12.179	-0.603	-0.603	0.000	0.000	0.000	0.000
27	A	30	GLH	0	-0.041	-0.044	15.301	0.848	0.848	0.000	0.000	0.000	0.000
28	A	31	PRO	0	0.032	0.002	14.948	0.359	0.359	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.013	0.001	16.019	0.013	0.013	0.000	0.000	0.000	0.000
30	A	33	HIS	0	0.068	0.044	16.382	0.352	0.352	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.014	0.012	10.515	0.026	0.026	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.023	-0.001	14.521	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.007	0.004	17.049	-0.657	-0.657	0.000	0.000	0.000	0.000
34	A	37	ALA	0	0.057	0.034	14.940	-0.505	-0.505	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.053	-0.039	12.212	-0.317	-0.317	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.051	-0.021	16.072	-0.623	-0.623	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.044	-0.022	19.317	-1.362	-1.362	0.000	0.000	0.000	0.000
38	A	41	GLN	0	-0.016	0.006	12.456	-0.279	-0.279	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.892	-0.946	18.040	13.093	13.093	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.058	0.043	18.375	0.621	0.621	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.033	-0.015	16.215	0.746	0.746	0.000	0.000	0.000	0.000
42	A	45	SER	0	-0.040	-0.039	14.963	-0.844	-0.844	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.012	0.002	15.358	-0.586	-0.586	0.000	0.000	0.000	0.000
44	A	47	SER	0	0.041	0.019	18.062	-0.655	-0.655	0.000	0.000	0.000	0.000
45	A	48	PRO	0	0.015	0.014	20.366	-0.542	-0.542	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.021	0.031	17.917	-0.381	-0.381	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.007	-0.015	21.032	-0.404	-0.404	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.029	-0.021	23.441	-0.543	-0.543	0.000	0.000	0.000	0.000
49	A	52	SER	0	-0.037	-0.023	24.737	-0.576	-0.576	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.030	0.001	24.199	-0.261	-0.261	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.018	0.000	26.285	-0.266	-0.266	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.045	-0.016	24.469	-0.160	-0.160	0.000	0.000	0.000	0.000
53	A	56	ASN	0	0.025	0.008	27.158	0.330	0.330	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.084	0.032	24.157	0.132	0.132	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.020	-0.004	25.666	0.257	0.257	0.000	0.000	0.000	0.000
56	A	59	GLN	0	0.006	-0.034	28.138	0.142	0.142	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.046	0.030	22.430	0.078	0.078	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.882	0.936	23.049	-12.429	-12.429	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.007	0.014	24.948	0.020	0.020	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.831	-0.914	27.525	10.275	10.275	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.037	-0.020	20.976	0.125	0.125	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.014	-0.024	24.423	0.364	0.364	0.000	0.000	0.000	0.000
63	A	66	GLN	0	-0.028	0.000	25.899	-0.260	-0.260	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.038	-0.028	24.790	-0.166	-0.166	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.001	-0.003	20.554	0.110	0.110	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.021	-0.007	24.674	0.269	0.269	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.876	0.947	27.683	-10.660	-10.660	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.062	-0.007	21.954	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.015	0.004	24.959	-0.261	-0.261	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.026	-0.014	25.339	0.440	0.440	0.000	0.000	0.000	0.000
71	A	74	VAL	0	-0.062	-0.025	23.729	-0.407	-0.407	0.000	0.000	0.000	0.000
72	A	82	GLN	0	0.026	0.004	13.190	0.884	0.884	0.000	0.000	0.000	0.000
73	A	83	PRO	0	0.011	0.022	9.965	-1.291	-1.291	0.000	0.000	0.000	0.000
74	A	84	SER	0	0.040	0.001	12.936	-0.500	-0.500	0.000	0.000	0.000	0.000
75	A	85	GLN	0	0.076	0.013	13.845	1.917	1.917	0.000	0.000	0.000	0.000
76	A	86	ASP	-1	-0.852	-0.894	14.798	17.163	17.163	0.000	0.000	0.000	0.000
77	A	87	LEU	0	-0.004	-0.006	11.098	0.251	0.251	0.000	0.000	0.000	0.000
78	A	88	VAL	0	0.038	0.026	9.557	1.637	1.637	0.000	0.000	0.000	0.000
79	A	89	ARG	1	0.812	0.882	10.814	-16.089	-16.089	0.000	0.000	0.000	0.000
80	A	90	VAL	0	0.005	-0.003	12.791	0.270	0.270	0.000	0.000	0.000	0.000
81	A	91	LEU	0	0.040	0.012	7.162	-0.325	-0.325	0.000	0.000	0.000	0.000
82	A	92	ASN	0	0.003	0.004	8.347	4.408	4.408	0.000	0.000	0.000	0.000
83	A	93	LEU	0	-0.048	-0.010	9.804	-0.450	-0.450	0.000	0.000	0.000	0.000
84	A	94	CYS	0	-0.029	-0.007	8.934	-1.281	-1.281	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.797	-0.870	6.267	35.677	35.677	0.000	0.000	0.000	0.000
86	A	96	LYS	1	0.900	0.940	8.383	-21.386	-21.386	0.000	0.000	0.000	0.000
87	A	97	LEU	0	-0.026	-0.036	11.882	-1.573	-1.573	0.000	0.000	0.000	0.000
88	A	98	ALA	0	0.062	0.038	9.477	-1.224	-1.224	0.000	0.000	0.000	0.000
89	A	99	GLN	0	0.015	0.021	11.128	-1.799	-1.799	0.000	0.000	0.000	0.000
90	A	100	LYS	1	0.852	0.929	12.498	-18.131	-18.131	0.000	0.000	0.000	0.000
91	A	101	ARG	1	0.860	0.929	15.072	-17.760	-17.760	0.000	0.000	0.000	0.000
92	A	102	GLY	0	-0.006	0.018	14.969	-0.726	-0.726	0.000	0.000	0.000	0.000
93	A	103	ASP	-1	-0.845	-0.913	11.939	18.781	18.781	0.000	0.000	0.000	0.000
94	A	104	ASN	0	-0.057	-0.035	10.922	1.931	1.931	0.000	0.000	0.000	0.000
95	A	105	PHE	0	-0.027	-0.018	6.426	1.700	1.700	0.000	0.000	0.000	0.000
96	A	106	ILE	0	-0.010	-0.007	4.663	-2.789	-2.646	-0.001	-0.006	-0.135	0.000
97	A	107	SER	0	-0.006	-0.037	7.579	2.009	2.009	0.000	0.000	0.000	0.000
98	A	108	SER	0	0.017	-0.013	10.305	0.839	0.839	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.776	-0.874	12.015	19.030	19.030	0.000	0.000	0.000	0.000
100	A	110	LEU	0	0.013	0.019	10.679	-0.695	-0.695	0.000	0.000	0.000	0.000
101	A	111	PHE	0	0.020	0.001	11.492	-0.371	-0.371	0.000	0.000	0.000	0.000
102	A	112	VAL	0	-0.013	-0.002	13.139	-0.714	-0.714	0.000	0.000	0.000	0.000
103	A	113	LEU	0	0.035	0.021	16.458	-0.593	-0.593	0.000	0.000	0.000	0.000
104	A	114	ALA	0	0.032	0.000	13.784	-0.504	-0.504	0.000	0.000	0.000	0.000
105	A	115	ALA	0	-0.022	-0.009	15.762	-0.456	-0.456	0.000	0.000	0.000	0.000
106	A	116	LEU	0	-0.035	-0.010	17.264	-0.729	-0.729	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.891	-0.927	18.750	14.363	14.363	0.000	0.000	0.000	0.000
108	A	118	SER	0	-0.053	-0.031	17.000	0.359	0.359	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.896	0.948	19.404	-12.485	-12.485	0.000	0.000	0.000	0.000
110	A	120	GLY	0	0.074	0.041	21.353	0.593	0.593	0.000	0.000	0.000	0.000
111	A	121	THR	0	0.059	0.013	23.362	-0.076	-0.076	0.000	0.000	0.000	0.000
112	A	122	LEU	0	0.020	0.017	17.630	-0.308	-0.308	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.030	0.024	21.544	-0.279	-0.279	0.000	0.000	0.000	0.000
114	A	124	ASP	-1	-0.871	-0.929	22.652	11.348	11.348	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.017	-0.006	24.219	-0.355	-0.355	0.000	0.000	0.000	0.000
116	A	126	LEU	0	0.006	-0.005	19.698	-0.275	-0.275	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.859	0.925	24.437	-12.352	-12.352	0.000	0.000	0.000	0.000
118	A	128	ALA	0	-0.036	-0.010	27.109	-0.347	-0.347	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.047	-0.023	26.485	-0.311	-0.311	0.000	0.000	0.000	0.000
120	A	130	GLY	0	0.034	0.022	28.638	-0.139	-0.139	0.000	0.000	0.000	0.000
121	A	131	ALA	0	-0.044	-0.015	23.601	0.023	0.023	0.000	0.000	0.000	0.000
122	A	132	THR	0	-0.025	-0.028	25.450	-0.182	-0.182	0.000	0.000	0.000	0.000
123	A	133	THR	0	0.026	-0.020	22.172	0.060	0.060	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.013	0.004	23.495	0.312	0.312	0.000	0.000	0.000	0.000
125	A	135	ASN	0	0.081	0.038	25.703	0.399	0.399	0.000	0.000	0.000	0.000
126	A	136	ILE	0	0.005	0.008	19.690	0.180	0.180	0.000	0.000	0.000	0.000
127	A	137	THR	0	-0.023	-0.032	20.783	0.694	0.694	0.000	0.000	0.000	0.000
128	A	138	GLN	0	0.007	0.017	21.858	0.137	0.137	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.012	0.011	22.340	-0.013	-0.013	0.000	0.000	0.000	0.000
130	A	140	ILE	0	-0.073	-0.040	16.998	0.285	0.285	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-1.012	-0.999	19.816	12.343	12.343	0.000	0.000	0.000	0.000
132	A	142	GLN	0	-0.053	-0.014	21.772	-0.022	-0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASP)