FMO DATABASE

FMODB ID: JQYV9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1201018.194404
FMO2-HF: Nuclear repulsion	1142104.141896
FMO2-HF: Total energy	-58914.052508
FMO2-MP2: Total energy	-59082.024231

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.
-4.465	-1.973	-0.015	-1.361	-1.115	0.006

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	0.019	0.006	3.877	-0.099	2.393	-0.015	-1.361	-1.115	0.006
4	A	4	ARG	1	0.993	0.973	6.510	0.134	0.134	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.006	-0.002	8.925	0.151	0.151	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.823	-0.908	7.423	-1.864	-1.864	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.045	0.031	6.492	0.232	0.232	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.041	-0.022	8.473	0.226	0.226	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.025	0.023	11.926	0.121	0.121	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.834	-0.908	6.746	-2.633	-2.633	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.747	0.847	9.620	0.772	0.772	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.028	-0.010	13.161	0.108	0.108	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.027	0.012	14.350	0.066	0.066	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.796	-0.885	12.744	-0.425	-0.425	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.881	0.945	16.399	0.280	0.280	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.068	-0.029	18.746	0.048	0.048	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.012	0.021	20.124	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.018	0.010	18.014	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.006	-0.018	15.318	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.088	-0.052	12.426	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.047	0.031	12.746	0.039	0.039	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.034	-0.016	10.195	-0.181	-0.181	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.070	-0.031	11.974	0.231	0.231	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.022	-0.002	13.017	-0.177	-0.177	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.867	-0.939	15.143	-0.772	-0.772	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.093	-0.039	16.396	0.062	0.062	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.879	0.932	12.982	0.904	0.904	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.002	0.010	16.279	0.036	0.036	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.042	-0.028	16.209	-0.080	-0.080	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.044	-0.012	18.340	0.058	0.058	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.018	-0.016	17.910	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.007	0.028	23.446	0.022	0.022	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.026	-0.045	25.556	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.850	-0.904	28.731	-0.206	-0.206	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.780	-0.860	32.174	-0.131	-0.131	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.056	-0.026	34.535	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.026	-0.024	37.360	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.046	-0.035	37.178	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.043	0.025	43.126	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.084	-0.041	46.516	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.003	0.004	49.244	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.028	-0.022	52.791	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.893	-0.941	55.850	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.051	-0.026	59.266	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.047	-0.033	61.014	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.886	-0.939	63.836	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.855	-0.896	66.251	-0.045	-0.045	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.135	-0.101	62.406	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	49	MET	0	0.034	0.041	55.639	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.074	-0.032	56.653	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.007	0.002	51.515	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.005	-0.017	50.835	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.078	0.009	47.240	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.025	-0.027	44.699	0.004	0.004	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.018	0.002	43.667	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.074	0.047	42.195	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.797	0.870	41.470	0.082	0.082	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.019	-0.011	43.696	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.010	0.019	43.793	0.002	0.002	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.040	-0.034	45.727	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.927	-0.957	45.628	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.004	0.003	44.719	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	SER	0	0.030	-0.008	48.339	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.028	-0.006	47.937	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.063	0.027	44.782	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.017	0.010	48.434	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.033	-0.018	51.642	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.883	-0.929	46.656	-0.056	-0.056	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.014	0.006	47.054	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.037	-0.023	50.930	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.033	-0.019	51.799	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.010	0.002	50.075	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.010	-0.026	52.105	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.057	-0.011	54.888	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.021	0.029	50.203	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.014	-0.006	48.949	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.035	-0.014	54.903	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.977	-0.983	56.835	-0.049	-0.049	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.105	-0.054	55.033	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.015	-0.015	55.941	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.035	0.028	56.468	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.062	-0.032	52.624	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.014	0.017	54.059	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.027	0.022	49.286	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.063	-0.032	52.120	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.005	-0.003	50.310	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.832	-0.898	51.714	-0.051	-0.051	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.020	0.005	51.745	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.057	-0.032	52.723	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.044	-0.033	48.043	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.022	-0.008	47.720	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.007	0.011	47.111	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.009	0.000	46.137	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.043	-0.013	47.414	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.022	0.012	47.968	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.003	-0.002	50.819	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.037	0.020	54.062	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.901	0.953	56.195	0.049	0.049	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.032	0.005	57.648	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	PRO	0	-0.001	-0.002	59.783	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.038	0.006	61.976	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.904	-0.945	64.176	-0.048	-0.048	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.997	-0.994	65.457	-0.053	-0.053	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.011	0.023	60.976	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.072	-0.065	59.401	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.020	-0.003	55.119	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.783	-0.876	54.599	-0.077	-0.077	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.833	0.925	55.057	0.059	0.059	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.015	0.010	53.218	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.958	-0.975	49.635	-0.099	-0.099	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.043	-0.036	50.930	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.893	-0.957	52.378	-0.069	-0.069	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.018	-0.013	48.050	0.000	0.000	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.852	-0.908	46.975	-0.103	-0.103	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.020	-0.011	48.397	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.007	0.027	48.504	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	VAL	0	0.004	-0.004	43.476	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.884	0.926	45.137	0.092	0.092	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.035	-0.017	46.501	0.002	0.002	0.000	0.000	0.000	0.000
120	A	120	MET	0	-0.053	-0.004	43.101	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.911	-0.942	41.328	-0.116	-0.116	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.060	-0.039	42.551	0.003	0.003	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.005	0.009	44.299	0.002	0.002	0.000	0.000	0.000	0.000
124	A	124	TYR	0	-0.025	-0.037	39.663	0.002	0.002	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.022	0.006	39.321	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.007	-0.010	40.961	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.003	-0.001	41.684	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	HIS	1	0.814	0.886	36.745	0.116	0.116	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.029	-0.012	37.756	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.071	-0.029	39.773	0.002	0.002	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.051	-0.021	37.086	0.005	0.005	0.000	0.000	0.000	0.000
132	A	132	ILE	0	-0.065	-0.024	37.445	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	THR	0	-0.028	-0.032	35.242	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.011	0.013	38.475	0.007	0.007	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.809	-0.903	37.915	-0.087	-0.087	0.000	0.000	0.000	0.000
136	A	136	ASN	0	0.012	0.012	32.825	0.006	0.006	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.904	-0.941	33.826	-0.140	-0.140	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.059	-0.035	35.452	0.001	0.001	0.000	0.000	0.000	0.000
139	A	139	MET	0	-0.031	0.004	30.987	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.803	0.903	28.163	0.239	0.239	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.025	-0.016	23.061	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.876	-0.926	23.004	-0.281	-0.281	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.847	-0.931	17.855	-0.630	-0.630	0.000	0.000	0.000	0.000
144	A	144	ILE	0	-0.030	-0.013	21.285	0.037	0.037	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.043	0.011	21.441	-0.038	-0.038	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.032	0.008	19.880	0.039	0.039	0.000	0.000	0.000	0.000

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