FMO DATABASE

FMODB ID: 897QY

Calculation Name: 1K3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K3E

Chain ID: A

ChEMBL ID:

UniProt ID: P58233

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1199788.071616
FMO2-HF: Nuclear repulsion	1140876.046418
FMO2-HF: Total energy	-58912.025198
FMO2-MP2: Total energy	-59080.178841

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:1:MET)

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

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.
-5.929	-2.819	-0.028	-1.685	-1.397	0.007

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.006

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	3	SER	0	0.017	0.009	3.799	-0.740	2.370	-0.028	-1.685	-1.397	0.007
4	A	4	ARG	1	0.988	0.974	6.454	0.155	0.155	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.015	-0.004	8.754	0.171	0.171	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.802	-0.922	7.039	-2.144	-2.144	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.032	0.000	6.829	0.222	0.222	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.036	-0.025	8.472	0.181	0.181	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.013	0.024	11.776	0.120	0.120	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.822	-0.921	7.301	-2.612	-2.612	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.938	0.955	10.146	0.567	0.567	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.070	-0.027	13.206	0.124	0.124	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.015	-0.003	14.605	0.075	0.075	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.909	-0.962	12.751	-0.540	-0.540	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.874	0.943	16.318	0.364	0.364	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.113	-0.040	18.717	0.052	0.052	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.013	0.022	19.888	0.035	0.035	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.017	0.011	18.264	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.017	-0.012	16.236	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.087	-0.052	12.739	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.046	0.027	12.681	0.058	0.058	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.014	-0.009	10.409	-0.212	-0.212	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.075	-0.031	11.588	0.245	0.245	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.041	0.007	12.902	-0.167	-0.167	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.884	-0.947	14.698	-0.821	-0.821	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.092	-0.041	15.966	0.036	0.036	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.885	0.936	12.399	0.959	0.959	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.027	0.007	15.932	0.047	0.047	0.000	0.000	0.000	0.000
29	A	29	CYS	0	0.015	0.022	16.066	-0.095	-0.095	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.050	-0.030	18.166	0.054	0.054	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.022	-0.001	17.922	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.001	0.023	23.348	0.020	0.020	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.025	-0.033	25.654	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.889	-0.947	28.739	-0.222	-0.222	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.898	-0.960	32.088	-0.156	-0.156	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.094	-0.035	34.137	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.092	0.029	37.466	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.017	-0.011	38.017	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.057	0.026	43.576	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.082	-0.041	47.064	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.005	0.010	49.874	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.028	-0.015	53.130	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.900	-0.946	56.070	-0.063	-0.063	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.055	-0.026	59.375	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.033	0.000	61.303	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.866	-0.947	63.999	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.889	-0.949	66.406	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.152	-0.097	62.794	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	49	MET	0	0.008	0.019	56.816	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.079	-0.039	56.937	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.031	0.024	51.618	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.034	-0.030	51.177	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.062	0.014	47.762	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.040	-0.035	45.230	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.013	-0.001	43.770	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.058	0.033	42.397	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.809	0.906	41.266	0.099	0.099	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.030	-0.014	43.876	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.013	0.016	43.843	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.048	-0.033	45.836	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.908	-0.945	45.396	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.005	-0.003	45.449	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	SER	0	0.002	-0.015	48.642	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.018	-0.009	48.388	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.025	0.027	44.649	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.037	0.020	48.602	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.024	-0.015	51.638	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.924	-0.953	46.849	-0.069	-0.069	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.007	-0.002	47.222	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.025	-0.029	50.940	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.030	-0.008	52.311	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.039	0.022	50.401	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.023	0.000	52.396	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.040	-0.007	55.120	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.027	0.016	50.548	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.025	-0.027	49.164	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.047	-0.012	55.048	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-1.005	-0.986	57.548	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.100	-0.050	54.159	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.002	-0.017	56.452	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.020	0.012	55.817	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.037	0.001	52.071	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.028	-0.019	54.579	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.002	0.005	49.663	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.066	-0.040	52.855	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.030	0.018	50.594	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.841	-0.898	51.950	-0.065	-0.065	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.004	-0.022	52.199	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.029	-0.003	52.778	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.050	-0.038	48.141	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.038	-0.011	48.035	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.009	0.014	47.239	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.026	-0.015	45.776	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.022	-0.015	47.672	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.026	0.034	48.014	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.027	-0.018	51.024	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.069	0.042	54.363	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.948	0.975	56.335	0.055	0.055	0.000	0.000	0.000	0.000
99	A	99	PHE	0	-0.008	-0.014	57.644	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.024	0.009	59.760	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.039	0.027	61.749	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.869	-0.924	64.045	-0.054	-0.054	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.970	-0.977	66.034	-0.057	-0.057	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.032	-0.002	60.972	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.018	-0.027	59.403	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.032	0.010	55.138	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.816	-0.907	54.771	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.821	0.901	55.348	0.065	0.065	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.011	-0.012	53.588	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.942	-0.969	50.013	-0.108	-0.108	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.025	-0.016	51.186	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.913	-0.966	52.516	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.010	-0.008	48.244	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.920	-0.969	47.640	-0.113	-0.113	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.026	-0.009	48.716	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.033	-0.002	48.725	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.025	0.012	43.845	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.993	0.994	45.186	0.100	0.100	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.032	-0.003	46.548	0.002	0.002	0.000	0.000	0.000	0.000
120	A	120	MET	0	-0.067	-0.033	43.506	0.001	0.001	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.930	-0.948	41.359	-0.132	-0.132	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.052	-0.033	42.815	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.005	0.007	44.354	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	TYR	0	0.038	0.006	39.785	0.002	0.002	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.021	0.012	39.011	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.003	-0.012	41.117	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.037	-0.016	41.600	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	HIS	1	0.911	0.946	36.669	0.136	0.136	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.066	-0.003	37.792	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	130	GLN	0	0.035	0.015	39.813	0.001	0.001	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.119	-0.052	36.942	0.005	0.005	0.000	0.000	0.000	0.000
132	A	132	ILE	0	-0.033	-0.014	37.282	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.015	-0.024	35.494	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.014	0.012	38.499	0.006	0.006	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.853	-0.945	37.958	-0.109	-0.109	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.022	-0.014	32.798	0.007	0.007	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.907	-0.956	33.473	-0.168	-0.168	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.049	-0.008	34.823	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	139	MET	0	-0.024	-0.005	30.647	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.930	0.963	28.715	0.225	0.225	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.036	-0.008	22.458	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.960	-0.972	23.358	-0.348	-0.348	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.949	-0.990	18.033	-0.667	-0.667	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.033	0.013	21.432	0.040	0.040	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.003	0.004	21.155	-0.050	-0.050	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.027	0.017	20.047	0.034	0.034	0.000	0.000	0.000	0.000

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