FMO DATABASE

FMODB ID: VK2N1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1104887.266569
FMO2-HF: Nuclear repulsion	1055676.218007
FMO2-HF: Total energy	-49211.048562
FMO2-MP2: Total energy	-49356.515366

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.
8.794	13.084	2.896	-2.612	-4.573	-0.003

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 : -0.908 / q_NPA : -0.964

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	0.005	0.025	2.213	-11.753	-8.736	1.792	-1.683	-3.127	0.009
4	A	7	THR	0	0.030	0.021	4.011	-2.079	-1.995	0.001	-0.042	-0.042	0.000
5	A	8	ASN	0	0.048	-0.001	6.138	4.275	4.275	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.944	0.980	7.419	-17.592	-17.592	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.025	0.017	6.954	-0.504	-0.504	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.038	0.010	2.440	5.778	6.967	1.103	-0.887	-1.404	-0.012
9	A	12	LEU	0	0.003	-0.006	6.833	-0.939	-0.939	0.000	0.000	0.000	0.000
10	A	13	ALA	0	0.007	0.016	10.234	-1.413	-1.413	0.000	0.000	0.000	0.000
11	A	14	LEU	0	0.015	0.001	6.260	-1.369	-1.369	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.012	0.003	9.986	-1.170	-1.170	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.880	-0.954	11.215	16.332	16.332	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.032	0.006	12.645	-1.358	-1.358	0.000	0.000	0.000	0.000
15	A	18	GLN	0	-0.037	-0.021	12.284	-0.387	-0.387	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.016	-0.004	14.266	-1.311	-1.311	0.000	0.000	0.000	0.000
17	A	20	LEU	0	-0.043	-0.007	17.139	-1.217	-1.217	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.034	-0.022	17.139	-0.867	-0.867	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.010	0.002	18.418	-0.771	-0.771	0.000	0.000	0.000	0.000
20	A	23	GLY	0	0.011	0.005	20.190	-0.746	-0.746	0.000	0.000	0.000	0.000
21	A	24	HIS	1	0.805	0.913	22.161	-13.203	-13.203	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.858	-0.922	23.523	11.706	11.706	0.000	0.000	0.000	0.000
23	A	26	ASN	0	-0.040	-0.028	20.701	0.089	0.089	0.000	0.000	0.000	0.000
24	A	27	GLN	0	0.034	0.015	20.577	0.081	0.081	0.000	0.000	0.000	0.000
25	A	28	PHE	0	-0.028	-0.023	17.020	0.688	0.688	0.000	0.000	0.000	0.000
26	A	29	ILE	0	0.015	0.031	12.106	-0.545	-0.545	0.000	0.000	0.000	0.000
27	A	30	GLH	0	-0.057	-0.077	15.170	0.753	0.753	0.000	0.000	0.000	0.000
28	A	31	PRO	0	0.023	-0.001	15.002	0.365	0.365	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.021	0.001	16.076	0.040	0.040	0.000	0.000	0.000	0.000
30	A	33	HIS	0	0.060	0.054	16.043	0.448	0.448	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.012	0.015	10.413	0.065	0.065	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.027	0.001	14.615	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.011	0.006	17.042	-0.596	-0.596	0.000	0.000	0.000	0.000
34	A	37	ALA	0	0.074	0.034	15.040	-0.509	-0.509	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.053	-0.038	12.202	-0.296	-0.296	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.078	-0.037	16.081	-0.678	-0.678	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.065	-0.036	19.373	-1.272	-1.272	0.000	0.000	0.000	0.000
38	A	41	GLN	0	-0.045	-0.007	12.485	-0.228	-0.228	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.918	-0.954	18.117	13.441	13.441	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.052	0.032	18.399	0.598	0.598	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.043	-0.030	16.243	0.740	0.740	0.000	0.000	0.000	0.000
42	A	45	SER	0	-0.020	-0.024	15.383	-0.871	-0.871	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.026	0.012	15.255	-0.604	-0.604	0.000	0.000	0.000	0.000
44	A	47	SER	0	0.025	0.011	17.928	-0.683	-0.683	0.000	0.000	0.000	0.000
45	A	48	PRO	0	-0.006	0.002	20.232	-0.586	-0.586	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.029	0.033	17.667	-0.395	-0.395	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.003	-0.012	21.005	-0.422	-0.422	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.029	-0.013	23.266	-0.579	-0.579	0.000	0.000	0.000	0.000
49	A	52	SER	0	-0.068	-0.025	24.228	-0.544	-0.544	0.000	0.000	0.000	0.000
50	A	53	ALA	0	0.007	0.013	23.979	-0.276	-0.276	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.031	-0.005	26.049	-0.278	-0.278	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.032	-0.007	24.358	-0.177	-0.177	0.000	0.000	0.000	0.000
53	A	56	ASN	0	0.024	0.001	27.016	0.225	0.225	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.080	0.030	24.119	0.116	0.116	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.038	-0.017	25.626	0.251	0.251	0.000	0.000	0.000	0.000
56	A	59	GLN	0	0.014	-0.003	28.126	0.391	0.391	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.104	0.051	22.459	0.120	0.120	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.942	0.968	23.933	-12.294	-12.294	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.028	0.003	24.968	0.015	0.015	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.862	-0.938	27.188	10.552	10.552	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.044	-0.031	20.769	0.150	0.150	0.000	0.000	0.000	0.000
62	A	65	ASN	0	0.000	-0.012	24.468	0.441	0.441	0.000	0.000	0.000	0.000
63	A	66	GLN	0	-0.046	-0.011	25.998	-0.208	-0.208	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.032	-0.024	24.861	-0.181	-0.181	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.009	-0.008	20.483	0.117	0.117	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.023	-0.013	24.508	0.274	0.274	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.909	0.968	27.484	-10.863	-10.863	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.064	-0.011	21.769	-0.036	-0.036	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.014	0.006	24.822	-0.276	-0.276	0.000	0.000	0.000	0.000
70	A	73	GLN	0	-0.016	-0.009	25.221	0.476	0.476	0.000	0.000	0.000	0.000
71	A	74	VAL	0	-0.037	-0.011	23.639	-0.417	-0.417	0.000	0.000	0.000	0.000
72	A	82	GLN	0	0.036	0.006	13.229	0.625	0.625	0.000	0.000	0.000	0.000
73	A	83	PRO	0	-0.003	0.016	10.037	-1.295	-1.295	0.000	0.000	0.000	0.000
74	A	84	SER	0	0.054	0.019	12.914	-0.592	-0.592	0.000	0.000	0.000	0.000
75	A	85	GLN	0	0.085	0.023	13.195	1.700	1.700	0.000	0.000	0.000	0.000
76	A	86	ASP	-1	-0.877	-0.914	14.276	17.507	17.507	0.000	0.000	0.000	0.000
77	A	87	LEU	0	0.002	-0.006	10.773	0.208	0.208	0.000	0.000	0.000	0.000
78	A	88	VAL	0	0.036	0.027	9.118	1.743	1.743	0.000	0.000	0.000	0.000
79	A	89	ARG	1	0.849	0.927	10.334	-16.528	-16.528	0.000	0.000	0.000	0.000
80	A	90	VAL	0	0.000	-0.008	12.677	0.257	0.257	0.000	0.000	0.000	0.000
81	A	91	LEU	0	0.028	0.001	7.161	-0.343	-0.343	0.000	0.000	0.000	0.000
82	A	92	ASN	0	0.013	0.009	8.439	4.505	4.505	0.000	0.000	0.000	0.000
83	A	93	LEU	0	-0.065	-0.011	9.856	-0.538	-0.538	0.000	0.000	0.000	0.000
84	A	94	CYS	0	-0.021	-0.003	8.763	-1.278	-1.278	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.855	-0.944	6.676	34.009	34.009	0.000	0.000	0.000	0.000
86	A	96	LYS	1	0.939	0.976	8.415	-21.058	-21.058	0.000	0.000	0.000	0.000
87	A	97	LEU	0	-0.040	-0.041	11.883	-1.619	-1.619	0.000	0.000	0.000	0.000
88	A	98	ALA	0	0.071	0.033	9.518	-1.286	-1.286	0.000	0.000	0.000	0.000
89	A	99	GLN	0	-0.022	-0.002	11.175	-1.268	-1.268	0.000	0.000	0.000	0.000
90	A	100	LYS	1	0.828	0.909	12.467	-18.498	-18.498	0.000	0.000	0.000	0.000
91	A	101	ARG	1	0.880	0.956	15.090	-17.779	-17.779	0.000	0.000	0.000	0.000
92	A	102	GLY	0	0.001	0.020	14.948	-0.738	-0.738	0.000	0.000	0.000	0.000
93	A	103	ASP	-1	-0.856	-0.928	11.802	19.124	19.124	0.000	0.000	0.000	0.000
94	A	104	ASN	0	-0.081	-0.047	10.467	2.314	2.314	0.000	0.000	0.000	0.000
95	A	105	PHE	0	-0.017	-0.016	6.230	1.631	1.631	0.000	0.000	0.000	0.000
96	A	106	ILE	0	-0.010	0.006	4.859	-2.330	-2.330	0.000	0.000	0.000	0.000
97	A	107	SER	0	0.000	-0.010	7.291	2.231	2.231	0.000	0.000	0.000	0.000
98	A	108	SER	0	0.023	-0.010	10.026	0.836	0.836	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.824	-0.928	11.837	18.972	18.972	0.000	0.000	0.000	0.000
100	A	110	LEU	0	0.010	0.020	10.363	-0.758	-0.758	0.000	0.000	0.000	0.000
101	A	111	PHE	0	0.024	-0.001	11.429	-0.352	-0.352	0.000	0.000	0.000	0.000
102	A	112	VAL	0	-0.018	-0.001	12.961	-0.741	-0.741	0.000	0.000	0.000	0.000
103	A	113	LEU	0	0.036	0.023	16.138	-0.629	-0.629	0.000	0.000	0.000	0.000
104	A	114	ALA	0	0.041	-0.001	13.574	-0.554	-0.554	0.000	0.000	0.000	0.000
105	A	115	ALA	0	-0.023	-0.001	15.550	-0.479	-0.479	0.000	0.000	0.000	0.000
106	A	116	LEU	0	-0.040	-0.004	17.134	-0.792	-0.792	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.915	-0.961	18.711	14.901	14.901	0.000	0.000	0.000	0.000
108	A	118	SER	0	-0.071	-0.044	16.922	0.384	0.384	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.894	0.939	19.338	-12.662	-12.662	0.000	0.000	0.000	0.000
110	A	120	GLY	0	0.065	0.033	21.295	0.625	0.625	0.000	0.000	0.000	0.000
111	A	121	THR	0	0.077	0.023	23.339	-0.143	-0.143	0.000	0.000	0.000	0.000
112	A	122	LEU	0	0.007	0.016	17.540	-0.295	-0.295	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.023	0.017	21.471	-0.278	-0.278	0.000	0.000	0.000	0.000
114	A	124	ASP	-1	-0.925	-0.964	22.558	11.457	11.457	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.025	-0.014	24.186	-0.355	-0.355	0.000	0.000	0.000	0.000
116	A	126	LEU	0	0.007	-0.006	19.631	-0.275	-0.275	0.000	0.000	0.000	0.000
117	A	127	LYS	1	0.930	0.972	24.324	-12.527	-12.527	0.000	0.000	0.000	0.000
118	A	128	ALA	0	-0.029	-0.003	26.965	-0.358	-0.358	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.043	-0.017	26.359	-0.330	-0.330	0.000	0.000	0.000	0.000
120	A	130	GLY	0	0.030	0.021	28.519	-0.146	-0.146	0.000	0.000	0.000	0.000
121	A	131	ALA	0	-0.020	-0.008	23.423	0.000	0.000	0.000	0.000	0.000	0.000
122	A	132	THR	0	-0.041	-0.033	25.170	-0.146	-0.146	0.000	0.000	0.000	0.000
123	A	133	THR	0	0.051	0.009	22.248	0.096	0.096	0.000	0.000	0.000	0.000
124	A	134	ALA	0	-0.011	0.003	23.193	0.322	0.322	0.000	0.000	0.000	0.000
125	A	135	ASN	0	0.079	0.026	25.392	0.591	0.591	0.000	0.000	0.000	0.000
126	A	136	ILE	0	0.029	0.021	19.364	0.203	0.203	0.000	0.000	0.000	0.000
127	A	137	THR	0	-0.053	-0.048	20.456	0.723	0.723	0.000	0.000	0.000	0.000
128	A	138	GLN	0	0.020	0.017	21.533	0.228	0.228	0.000	0.000	0.000	0.000
129	A	139	ALA	0	-0.011	-0.005	21.922	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	140	ILE	0	-0.079	-0.047	16.502	0.328	0.328	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-0.996	-0.993	19.496	12.387	12.387	0.000	0.000	0.000	0.000
132	A	142	GLN	0	-0.034	-0.003	21.411	-0.121	-0.121	0.000	0.000	0.000	0.000

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