FMO DATABASE

FMODB ID: GYQR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1108506.299871
FMO2-HF: Nuclear repulsion	1059294.199673
FMO2-HF: Total energy	-49212.100198
FMO2-MP2: Total energy	-49357.41491

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.
-2.627	2.139	4.883	-3.916	-5.732	-0.006

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 : -0.888 / q_NPA : -0.944

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	6	LEU	0	-0.028	0.002	2.121	-17.667	-13.830	1.938	-2.288	-3.486	0.012
4	A	7	THR	0	0.034	0.009	3.811	-3.372	-3.322	0.000	0.003	-0.053	0.000
5	A	8	ASN	0	0.043	0.001	6.029	2.624	2.624	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.909	0.960	7.408	-18.058	-18.058	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.055	0.034	6.555	-0.805	-0.805	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.005	-0.013	2.254	1.576	2.455	2.945	-1.631	-2.193	-0.018
9	A	12	LEU	0	0.000	-0.003	6.660	-0.989	-0.989	0.000	0.000	0.000	0.000
10	A	13	ALA	0	0.013	0.012	10.176	-1.206	-1.206	0.000	0.000	0.000	0.000
11	A	14	LEU	0	0.005	0.001	6.223	-1.126	-1.126	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.002	0.009	10.055	-1.019	-1.019	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.877	-0.934	11.553	15.634	15.634	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.012	-0.004	12.878	-1.079	-1.079	0.000	0.000	0.000	0.000
15	A	18	GLN	0	0.004	-0.011	12.559	-0.382	-0.382	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.020	-0.014	14.840	-1.192	-1.192	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.027	-0.013	17.524	-1.033	-1.033	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.050	-0.028	17.585	-0.733	-0.733	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.016	0.014	18.899	-0.774	-0.774	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.004	-0.004	20.694	-0.684	-0.684	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.816	0.904	22.768	-12.780	-12.780	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.812	-0.876	24.309	11.342	11.342	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.029	-0.005	20.916	0.124	0.124	0.000	0.000	0.000	0.000
24	A	27	GLN	0	0.023	0.012	20.462	0.275	0.275	0.000	0.000	0.000	0.000
25	A	28	PHE	0	-0.022	-0.016	16.774	0.604	0.604	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.009	0.021	12.422	-0.684	-0.684	0.000	0.000	0.000	0.000
27	A	30	GLH	0	-0.013	-0.024	14.835	1.257	1.257	0.000	0.000	0.000	0.000
28	A	31	PRO	0	0.002	-0.009	15.011	0.292	0.292	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.022	0.005	16.085	0.073	0.073	0.000	0.000	0.000	0.000
30	A	33	HIS	0	0.036	0.028	16.317	0.354	0.354	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.034	0.017	10.425	-0.154	-0.154	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.032	0.003	14.424	-0.058	-0.058	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.010	0.004	17.010	-0.652	-0.652	0.000	0.000	0.000	0.000
34	A	37	ALA	0	0.044	0.035	14.735	-0.515	-0.515	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.047	-0.038	11.878	-0.399	-0.399	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.052	-0.022	15.818	-0.559	-0.559	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.018	-0.016	19.224	-1.281	-1.281	0.000	0.000	0.000	0.000
38	A	41	GLN	0	-0.034	-0.005	12.501	-0.263	-0.263	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.828	-0.907	17.954	12.841	12.841	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.002	0.003	18.020	0.781	0.781	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.027	-0.008	16.218	0.806	0.806	0.000	0.000	0.000	0.000
42	A	45	SER	0	-0.053	-0.057	14.778	-0.859	-0.859	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.014	0.008	15.348	-0.620	-0.620	0.000	0.000	0.000	0.000
44	A	47	SER	0	0.051	0.027	18.114	-0.644	-0.644	0.000	0.000	0.000	0.000
45	A	48	PRO	0	0.008	0.017	20.439	-0.560	-0.560	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.010	0.019	17.749	-0.360	-0.360	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.011	-0.015	20.907	-0.364	-0.364	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.024	-0.021	23.247	-0.553	-0.553	0.000	0.000	0.000	0.000
49	A	52	SER	0	-0.052	-0.046	24.854	-0.601	-0.601	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.017	0.005	24.132	-0.252	-0.252	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.007	0.008	26.216	-0.237	-0.237	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.056	-0.015	24.514	-0.206	-0.206	0.000	0.000	0.000	0.000
53	A	56	ASN	0	0.062	0.024	26.800	0.410	0.410	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.059	0.029	23.698	0.080	0.080	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.009	0.019	25.104	0.323	0.323	0.000	0.000	0.000	0.000
56	A	59	GLN	0	0.000	-0.027	27.859	0.059	0.059	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.042	0.022	22.236	0.109	0.109	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.812	0.880	22.759	-12.436	-12.436	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.002	0.010	24.618	0.005	0.005	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.842	-0.917	27.466	10.365	10.365	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.022	-0.011	20.881	0.123	0.123	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.002	-0.021	23.510	0.323	0.323	0.000	0.000	0.000	0.000
63	A	66	GLN	0	-0.018	-0.002	25.660	-0.331	-0.331	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.033	-0.018	24.638	-0.171	-0.171	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.011	-0.001	20.569	0.112	0.112	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.029	-0.004	24.658	0.186	0.186	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.871	0.937	27.386	-10.654	-10.654	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.051	-0.001	21.484	0.045	0.045	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.010	-0.003	24.630	-0.257	-0.257	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.040	-0.013	24.936	0.474	0.474	0.000	0.000	0.000	0.000
71	A	74	VAL	0	-0.066	-0.050	24.145	-0.421	-0.421	0.000	0.000	0.000	0.000
72	A	82	GLN	0	-0.004	-0.008	13.231	0.590	0.590	0.000	0.000	0.000	0.000
73	A	83	PRO	0	0.007	0.012	9.684	-1.048	-1.048	0.000	0.000	0.000	0.000
74	A	84	SER	0	0.034	-0.002	12.416	-0.712	-0.712	0.000	0.000	0.000	0.000
75	A	85	GLN	0	0.065	0.014	13.310	2.036	2.036	0.000	0.000	0.000	0.000
76	A	86	ASP	-1	-0.820	-0.880	14.359	17.575	17.575	0.000	0.000	0.000	0.000
77	A	87	LEU	0	-0.010	0.001	10.392	0.564	0.564	0.000	0.000	0.000	0.000
78	A	88	VAL	0	0.033	0.018	9.337	2.108	2.108	0.000	0.000	0.000	0.000
79	A	89	ARG	1	0.774	0.867	10.469	-16.039	-16.039	0.000	0.000	0.000	0.000
80	A	90	VAL	0	0.017	0.003	12.706	0.067	0.067	0.000	0.000	0.000	0.000
81	A	91	LEU	0	0.031	0.012	6.701	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	92	ASN	0	0.007	-0.001	8.703	4.900	4.900	0.000	0.000	0.000	0.000
83	A	93	LEU	0	-0.036	-0.005	9.865	-0.487	-0.487	0.000	0.000	0.000	0.000
84	A	94	CYS	0	-0.026	-0.006	9.132	-1.631	-1.631	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.797	-0.865	6.603	41.691	41.691	0.000	0.000	0.000	0.000
86	A	96	LYS	1	0.884	0.931	8.683	-23.863	-23.863	0.000	0.000	0.000	0.000
87	A	97	LEU	0	-0.038	-0.031	12.138	-2.001	-2.001	0.000	0.000	0.000	0.000
88	A	98	ALA	0	0.056	0.033	9.968	-1.389	-1.389	0.000	0.000	0.000	0.000
89	A	99	GLN	0	0.016	0.010	11.384	-2.643	-2.643	0.000	0.000	0.000	0.000
90	A	100	LYS	1	0.867	0.933	12.934	-19.439	-19.439	0.000	0.000	0.000	0.000
91	A	101	ARG	1	0.866	0.937	15.456	-18.929	-18.929	0.000	0.000	0.000	0.000
92	A	102	GLY	0	-0.006	0.015	15.310	-0.949	-0.949	0.000	0.000	0.000	0.000
93	A	103	ASP	-1	-0.847	-0.905	12.368	20.359	20.359	0.000	0.000	0.000	0.000
94	A	104	ASN	0	-0.051	-0.037	10.457	0.973	0.973	0.000	0.000	0.000	0.000
95	A	105	PHE	0	-0.024	-0.015	6.652	1.798	1.798	0.000	0.000	0.000	0.000
96	A	106	ILE	0	0.003	0.009	5.124	-3.559	-3.559	0.000	0.000	0.000	0.000
97	A	107	SER	0	0.021	-0.011	7.618	1.490	1.490	0.000	0.000	0.000	0.000
98	A	108	SER	0	0.004	-0.015	10.404	1.127	1.127	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.774	-0.868	11.708	19.584	19.584	0.000	0.000	0.000	0.000
100	A	110	LEU	0	0.004	0.016	10.784	-0.705	-0.705	0.000	0.000	0.000	0.000
101	A	111	PHE	0	0.020	-0.007	11.436	-0.267	-0.267	0.000	0.000	0.000	0.000
102	A	112	VAL	0	-0.009	-0.004	13.124	-0.796	-0.796	0.000	0.000	0.000	0.000
103	A	113	LEU	0	0.017	0.021	16.540	-0.737	-0.737	0.000	0.000	0.000	0.000
104	A	114	ALA	0	0.034	0.007	13.808	-0.575	-0.575	0.000	0.000	0.000	0.000
105	A	115	ALA	0	-0.006	0.001	15.759	-0.469	-0.469	0.000	0.000	0.000	0.000
106	A	116	LEU	0	-0.030	-0.007	17.359	-0.759	-0.759	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.848	-0.923	18.832	15.443	15.443	0.000	0.000	0.000	0.000
108	A	118	SER	0	-0.049	-0.025	17.013	0.032	0.032	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.888	0.947	19.417	-13.119	-13.119	0.000	0.000	0.000	0.000
110	A	120	GLY	0	0.068	0.043	21.319	0.635	0.635	0.000	0.000	0.000	0.000
111	A	121	THR	0	0.055	0.010	23.577	0.160	0.160	0.000	0.000	0.000	0.000
112	A	122	LEU	0	0.019	0.016	17.810	-0.296	-0.296	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.026	0.024	21.642	-0.230	-0.230	0.000	0.000	0.000	0.000
114	A	124	ASP	-1	-0.874	-0.932	22.711	11.813	11.813	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.014	-0.006	24.639	-0.412	-0.412	0.000	0.000	0.000	0.000
116	A	126	LEU	0	-0.004	-0.007	19.789	-0.261	-0.261	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.846	0.916	24.513	-12.816	-12.816	0.000	0.000	0.000	0.000
118	A	128	ALA	0	-0.035	-0.010	27.378	-0.348	-0.348	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.023	-0.004	26.641	-0.336	-0.336	0.000	0.000	0.000	0.000
120	A	130	GLY	0	0.031	0.021	28.775	-0.081	-0.081	0.000	0.000	0.000	0.000
121	A	131	ALA	0	-0.027	-0.012	23.578	0.100	0.100	0.000	0.000	0.000	0.000
122	A	132	THR	0	-0.044	-0.048	25.577	-0.206	-0.206	0.000	0.000	0.000	0.000
123	A	133	THR	0	0.028	-0.026	22.272	0.087	0.087	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.008	0.021	23.550	0.315	0.315	0.000	0.000	0.000	0.000
125	A	135	ASN	0	0.064	0.029	25.383	0.467	0.467	0.000	0.000	0.000	0.000
126	A	136	ILE	0	0.001	0.003	19.787	0.201	0.201	0.000	0.000	0.000	0.000
127	A	137	THR	0	-0.027	-0.035	20.718	0.768	0.768	0.000	0.000	0.000	0.000
128	A	138	GLN	0	0.006	0.009	21.793	0.128	0.128	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.014	0.012	22.067	-0.086	-0.086	0.000	0.000	0.000	0.000
130	A	140	ILE	0	-0.071	-0.040	16.764	0.296	0.296	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-0.987	-0.995	19.322	13.274	13.274	0.000	0.000	0.000	0.000
132	A	142	GLN	0	-0.048	0.009	21.709	-0.165	-0.165	0.000	0.000	0.000	0.000

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