FMO DATABASE

FMODB ID: NN8LQ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1199516.043501
FMO2-HF: Nuclear repulsion	1140602.628796
FMO2-HF: Total energy	-58913.414705
FMO2-MP2: Total energy	-59081.448622

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.
-5.224	-2.064	-0.028	-1.707	-1.425	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 : -0.006 / 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	0.024	0.017	3.799	-0.759	2.401	-0.028	-1.707	-1.425	0.007
4	A	4	ARG	1	1.004	0.982	6.482	0.114	0.114	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.024	0.000	8.802	0.171	0.171	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.809	-0.925	7.295	-1.991	-1.991	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.003	0.013	6.612	0.205	0.205	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.029	-0.020	8.488	0.182	0.182	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.012	0.020	11.870	0.114	0.114	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.818	-0.919	7.107	-2.397	-2.397	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.763	0.853	9.653	0.701	0.701	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.040	-0.017	13.217	0.114	0.114	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.019	0.007	14.596	0.067	0.067	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.805	-0.889	12.635	-0.415	-0.415	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.881	0.949	16.324	0.301	0.301	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.091	-0.043	18.726	0.046	0.046	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.015	0.024	19.898	0.029	0.029	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.017	0.012	18.527	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.014	-0.009	16.229	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.092	-0.057	12.727	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.048	0.028	12.686	0.044	0.044	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.032	-0.020	10.235	-0.223	-0.223	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.055	-0.027	11.633	0.240	0.240	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.020	-0.011	12.922	-0.154	-0.154	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.862	-0.926	14.758	-0.817	-0.817	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.101	-0.044	16.022	0.036	0.036	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.887	0.936	12.534	0.969	0.969	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.015	0.008	15.989	0.046	0.046	0.000	0.000	0.000	0.000
29	A	29	CYS	0	0.009	0.018	15.965	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.048	-0.013	18.112	0.056	0.056	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.033	-0.005	17.889	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.009	0.017	23.307	0.018	0.018	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.024	-0.037	25.838	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.836	-0.906	28.707	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.805	-0.889	32.058	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.069	-0.023	34.499	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.038	-0.008	37.441	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.049	-0.021	37.536	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.055	0.024	43.555	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.087	-0.044	47.041	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.018	0.018	49.853	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.045	-0.023	53.108	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.893	-0.948	56.051	-0.057	-0.057	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.053	-0.028	59.355	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.022	-0.012	61.285	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.888	-0.946	63.977	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.883	-0.944	66.384	-0.046	-0.046	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.122	-0.072	62.656	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	49	MET	0	-0.009	0.005	56.086	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.072	-0.033	56.898	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.023	0.015	51.482	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.012	-0.022	51.239	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.068	0.011	47.746	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.043	-0.034	45.025	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.012	0.002	43.768	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.068	0.043	42.420	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.776	0.861	41.424	0.085	0.085	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.016	-0.019	43.886	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.009	0.019	43.836	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.046	-0.036	45.847	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.929	-0.956	45.614	-0.044	-0.044	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.010	-0.006	45.161	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	SER	0	0.022	-0.005	48.654	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.011	-0.015	48.038	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.050	0.032	44.921	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.044	0.022	48.615	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.027	-0.019	51.650	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.877	-0.925	46.782	-0.060	-0.060	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.007	-0.007	47.030	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.027	-0.024	50.954	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.026	-0.008	52.282	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.037	0.020	50.384	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.000	-0.008	52.411	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.044	-0.009	55.134	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.020	0.021	50.360	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.013	-0.016	49.066	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.041	-0.011	55.063	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.991	-0.981	57.242	-0.051	-0.051	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.120	-0.069	54.946	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.014	-0.008	56.460	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.027	0.012	55.833	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.053	-0.005	52.295	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.001	-0.007	54.592	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.002	0.004	49.519	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.070	-0.039	52.845	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.024	0.010	50.653	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.836	-0.899	51.968	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.010	-0.012	52.208	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.023	-0.005	52.786	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.063	-0.041	48.203	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.023	-0.009	48.043	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.006	0.010	47.253	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.008	-0.008	46.120	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.028	-0.009	47.683	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.022	0.029	48.238	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.011	-0.015	51.036	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.062	0.042	54.374	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.917	0.973	56.347	0.049	0.049	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.007	-0.009	57.613	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.023	0.016	59.731	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.046	0.016	61.695	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.888	-0.938	64.015	-0.049	-0.049	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.971	-0.972	65.998	-0.053	-0.053	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.027	0.002	60.900	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.049	-0.068	59.322	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.039	0.016	55.096	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.789	-0.871	54.733	-0.078	-0.078	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.835	0.913	55.309	0.059	0.059	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.020	-0.013	53.359	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.951	-0.972	49.956	-0.100	-0.100	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.057	-0.039	51.149	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.886	-0.951	52.480	-0.071	-0.071	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.006	-0.005	48.229	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.852	-0.921	47.245	-0.105	-0.105	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.004	0.003	48.680	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.015	0.006	48.712	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.021	0.009	43.734	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.889	0.932	45.199	0.095	0.095	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.040	-0.011	46.562	0.002	0.002	0.000	0.000	0.000	0.000
120	A	120	MET	0	-0.061	-0.029	43.374	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.925	-0.945	41.345	-0.121	-0.121	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.054	-0.037	42.830	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.002	0.005	44.415	0.002	0.002	0.000	0.000	0.000	0.000
124	A	124	TYR	0	0.034	-0.003	39.824	0.002	0.002	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.032	0.010	39.152	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.003	-0.008	41.133	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.023	-0.013	41.754	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	HIS	1	0.881	0.921	36.813	0.122	0.122	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.080	-0.014	37.808	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.011	-0.016	39.830	0.003	0.003	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.117	-0.051	36.958	0.005	0.005	0.000	0.000	0.000	0.000
132	A	132	ILE	0	-0.040	-0.016	37.296	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.011	-0.024	35.231	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.019	0.015	38.511	0.006	0.006	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.817	-0.904	37.969	-0.090	-0.090	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.007	0.001	32.964	0.007	0.007	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.890	-0.939	33.784	-0.145	-0.145	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.088	-0.059	35.262	0.001	0.001	0.000	0.000	0.000	0.000
139	A	139	MET	0	-0.014	0.005	30.780	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.815	0.885	28.372	0.233	0.233	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.039	-0.007	22.862	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.887	-0.925	23.327	-0.288	-0.288	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.920	-0.975	17.973	-0.649	-0.649	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.006	0.003	21.396	0.038	0.038	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.019	0.009	21.106	-0.050	-0.050	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.020	0.007	19.985	0.029	0.029	0.000	0.000	0.000	0.000

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