FMO DATABASE

FMODB ID: LNZ29

Calculation Name: 3KCN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KCN

Chain ID: A

ChEMBL ID:

UniProt ID: Q7UJS6

Base Structure: X-ray

Registration Date: 2023-09-21

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1215254.553443
FMO2-HF: Nuclear repulsion	1160589.921229
FMO2-HF: Total energy	-54664.632214
FMO2-MP2: Total energy	-54817.981407

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-10.272	-2.21	4.697	-4.205	-8.554	-0.03

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.002

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	7	GLU	-1	-0.834	-0.926	2.561	-9.082	-4.408	1.667	-2.339	-4.001	-0.017
4	A	8	ARG	1	0.871	0.965	4.764	0.249	0.390	-0.001	-0.015	-0.125	0.000
5	A	9	ILE	0	-0.030	-0.010	8.099	0.126	0.126	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.032	-0.015	10.368	0.032	0.032	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.023	-0.012	14.112	0.015	0.015	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.021	-0.019	16.821	0.017	0.017	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.848	-0.948	20.171	-0.116	-0.116	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.862	-0.929	23.323	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.772	-0.854	26.224	-0.116	-0.116	0.000	0.000	0.000	0.000
12	A	16	TYR	0	-0.020	-0.052	24.975	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.072	-0.055	24.955	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.024	0.002	21.268	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.007	0.009	20.008	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.039	-0.039	20.014	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	21	THR	0	-0.066	-0.045	21.189	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.019	0.010	17.180	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.927	0.963	16.439	0.261	0.261	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.875	0.949	16.674	0.165	0.165	0.000	0.000	0.000	0.000
21	A	25	ASN	0	-0.019	-0.012	15.772	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	26	LEU	0	0.018	0.001	11.776	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.026	-0.032	11.822	-0.094	-0.094	0.000	0.000	0.000	0.000
24	A	28	PHE	0	-0.088	-0.028	12.527	0.005	0.005	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.783	-0.889	8.449	-0.718	-0.718	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.028	0.013	5.483	-0.176	-0.176	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.865	-0.938	8.333	-0.542	-0.542	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.031	-0.013	10.287	0.104	0.104	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.016	0.001	12.900	0.074	0.074	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.037	-0.028	15.367	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	35	CYS	0	-0.057	-0.021	18.536	0.015	0.015	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.807	-0.874	21.377	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.033	0.010	24.197	0.010	0.010	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.072	0.016	23.575	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	39	PRO	0	0.004	-0.018	23.880	0.008	0.008	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.855	-0.915	23.098	-0.061	-0.061	0.000	0.000	0.000	0.000
37	A	41	ALA	0	0.038	0.012	19.729	0.004	0.004	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.030	-0.008	19.974	0.013	0.013	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.004	-0.004	21.635	0.019	0.019	0.000	0.000	0.000	0.000
40	A	44	CYS	0	-0.048	-0.030	17.772	0.006	0.006	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.011	0.019	16.165	0.005	0.005	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.918	0.961	17.712	-0.107	-0.107	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.875	0.945	19.939	0.038	0.038	0.000	0.000	0.000	0.000
44	A	48	SER	0	-0.024	-0.021	15.582	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.891	-0.938	11.282	0.382	0.382	0.000	0.000	0.000	0.000
46	A	50	PRO	0	-0.016	-0.009	10.197	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	51	PHE	0	0.045	0.028	9.794	0.006	0.006	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.019	-0.015	5.136	0.231	0.231	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.019	0.000	7.724	0.105	0.105	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.003	0.003	10.151	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	55	MET	0	-0.042	-0.007	13.822	0.012	0.012	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.018	0.009	16.130	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.737	-0.851	19.854	-0.091	-0.091	0.000	0.000	0.000	0.000
54	A	58	MET	0	-0.010	-0.007	23.108	0.013	0.013	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.765	0.857	25.516	0.068	0.068	0.000	0.000	0.000	0.000
56	A	60	MET	0	0.023	0.011	23.684	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	61	PRO	0	0.017	0.012	28.649	0.008	0.008	0.000	0.000	0.000	0.000
58	A	62	GLY	0	-0.037	-0.005	30.858	0.001	0.001	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.061	-0.029	26.016	0.008	0.008	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.866	-0.929	27.508	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.011	-0.010	23.787	0.007	0.007	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.027	0.000	22.954	0.007	0.007	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.802	-0.886	24.121	0.019	0.019	0.000	0.000	0.000	0.000
64	A	68	VAL	0	-0.057	-0.015	21.385	0.010	0.010	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.020	0.006	18.774	0.012	0.012	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.052	-0.025	20.409	0.021	0.021	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.844	0.903	22.722	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.023	0.012	18.324	0.015	0.015	0.000	0.000	0.000	0.000
69	A	73	ARG	1	0.887	0.955	17.496	-0.064	-0.064	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.037	-0.010	19.000	0.024	0.024	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.098	-0.045	19.016	0.011	0.011	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.021	-0.029	13.293	0.057	0.057	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.014	0.011	15.047	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	78	ASN	0	-0.027	-0.020	10.586	-0.096	-0.096	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.040	-0.006	10.527	0.042	0.042	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.032	-0.012	8.801	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.018	-0.009	11.480	-0.087	-0.087	0.000	0.000	0.000	0.000
78	A	82	LEU	0	-0.023	-0.021	12.375	0.004	0.004	0.000	0.000	0.000	0.000
79	A	83	MET	0	-0.011	0.002	15.818	0.010	0.010	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.022	0.022	18.785	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.006	-0.011	21.461	0.013	0.013	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.025	0.000	24.559	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	87	ASN	0	-0.048	-0.037	28.081	0.002	0.002	0.000	0.000	0.000	0.000
84	A	88	GLN	0	-0.008	-0.001	30.699	0.001	0.001	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.689	-0.814	27.844	-0.053	-0.053	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.018	0.018	26.033	0.000	0.000	0.000	0.000	0.000	0.000
87	A	91	THR	0	0.009	-0.002	27.079	0.001	0.001	0.000	0.000	0.000	0.000
88	A	92	THR	0	0.071	0.034	27.517	0.003	0.003	0.000	0.000	0.000	0.000
89	A	93	ALA	0	-0.005	-0.006	23.106	0.004	0.004	0.000	0.000	0.000	0.000
90	A	94	MET	0	-0.029	-0.007	23.270	0.005	0.005	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.901	-0.947	24.751	0.007	0.007	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.055	0.030	22.587	0.009	0.009	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.052	-0.027	19.427	0.008	0.008	0.000	0.000	0.000	0.000
94	A	98	ASN	0	-0.101	-0.063	21.149	0.014	0.014	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.874	-0.921	23.875	0.061	0.061	0.000	0.000	0.000	0.000
96	A	100	GLY	0	-0.033	-0.007	19.454	0.014	0.014	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.097	-0.061	18.715	0.009	0.009	0.000	0.000	0.000	0.000
98	A	102	VAL	0	0.010	0.005	17.415	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.030	0.016	10.571	0.008	0.008	0.000	0.000	0.000	0.000
100	A	104	ARG	1	0.867	0.918	12.856	0.083	0.083	0.000	0.000	0.000	0.000
101	A	105	PHE	0	0.033	0.026	16.536	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.003	-0.003	16.215	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	107	ASN	0	0.003	-0.006	20.514	0.003	0.003	0.000	0.000	0.000	0.000
104	A	108	LYS	1	0.823	0.913	23.943	0.086	0.086	0.000	0.000	0.000	0.000
105	A	109	PRO	0	-0.043	-0.030	25.471	0.009	0.009	0.000	0.000	0.000	0.000
106	A	110	CYS	0	-0.023	-0.001	20.200	0.002	0.002	0.000	0.000	0.000	0.000
107	A	111	GLN	0	0.008	0.004	20.154	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	112	MET	0	0.003	0.003	15.346	0.000	0.000	0.000	0.000	0.000	0.000
109	A	113	SER	0	0.003	-0.008	16.011	-0.041	-0.041	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.822	-0.903	15.071	-0.215	-0.215	0.000	0.000	0.000	0.000
111	A	115	ILE	0	0.012	0.003	14.450	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.785	0.893	10.962	0.549	0.549	0.000	0.000	0.000	0.000
113	A	117	ALA	0	0.014	0.013	10.364	-0.088	-0.088	0.000	0.000	0.000	0.000
114	A	118	ALA	0	-0.025	-0.014	10.815	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	119	ILE	0	0.035	0.019	7.945	0.043	0.043	0.000	0.000	0.000	0.000
116	A	120	ASN	0	-0.019	-0.014	6.215	-0.176	-0.176	0.000	0.000	0.000	0.000
117	A	121	ALA	0	-0.047	-0.024	6.309	0.029	0.029	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.007	-0.006	7.960	0.109	0.109	0.000	0.000	0.000	0.000
119	A	123	ILE	0	0.016	0.009	2.290	-0.337	0.024	1.501	-0.293	-1.568	0.000
120	A	124	LYS	1	0.960	0.983	3.665	-0.038	0.531	0.024	-0.187	-0.407	-0.001
121	A	125	GLN	0	-0.025	-0.010	4.603	0.090	0.157	-0.001	-0.003	-0.063	0.000
122	A	126	TYR	0	0.022	0.010	4.439	-0.019	0.093	-0.001	-0.007	-0.104	0.000
123	A	127	ASP	-1	-0.921	-0.948	2.506	-0.710	1.341	1.508	-1.339	-2.220	-0.012
124	A	128	LEU	0	-0.012	-0.018	4.242	-0.070	0.017	0.000	-0.022	-0.066	0.000
125	A	129	VAL	0	-0.043	-0.009	7.874	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	130	THR	0	0.025	0.003	6.264	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	131	SER	0	-0.015	-0.006	7.293	-0.097	-0.097	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.917	0.956	9.001	-0.511	-0.511	0.000	0.000	0.000	0.000
129	A	133	GLU	-1	-0.830	-0.906	11.551	0.610	0.610	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.878	-0.925	8.414	1.687	1.687	0.000	0.000	0.000	0.000
131	A	135	LEU	0	0.006	0.001	12.261	-0.118	-0.118	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.025	0.000	14.566	-0.093	-0.093	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.809	0.898	14.474	-0.681	-0.681	0.000	0.000	0.000	0.000
134	A	138	LYS	1	0.911	0.955	14.436	-0.593	-0.593	0.000	0.000	0.000	0.000
135	A	139	THR	0	-0.073	-0.036	17.489	-0.081	-0.081	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)