FMO DATABASE

FMODB ID: 3J95L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1210362.897549
FMO2-HF: Nuclear repulsion	1155698.605374
FMO2-HF: Total energy	-54664.292175
FMO2-MP2: Total energy	-54817.535612

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.
-9.621	-2.493	2.91	-3.202	-6.836	-0.018

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 : -0.004 / q_NPA : -0.005

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	-0.854	-0.931	2.526	-10.213	-5.302	1.708	-2.442	-4.177	-0.016
4	A	8	ARG	1	0.927	0.990	4.631	0.067	0.231	-0.001	-0.020	-0.143	0.000
5	A	9	ILE	0	-0.033	-0.025	8.050	0.168	0.168	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.034	-0.020	10.349	0.023	0.023	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.035	-0.024	14.031	0.007	0.007	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.034	-0.027	16.728	0.017	0.017	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.857	-0.961	20.106	-0.125	-0.125	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.878	-0.935	23.160	-0.070	-0.070	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.790	-0.871	25.956	-0.123	-0.123	0.000	0.000	0.000	0.000
12	A	16	TYR	0	-0.023	-0.054	25.061	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.067	-0.044	24.923	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.016	0.009	21.477	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.035	0.018	19.961	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.058	-0.045	20.167	-0.042	-0.042	0.000	0.000	0.000	0.000
17	A	21	THR	0	-0.090	-0.055	21.232	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.026	0.010	17.290	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.937	0.972	16.296	0.272	0.272	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.915	0.981	16.461	0.188	0.188	0.000	0.000	0.000	0.000
21	A	25	ASN	0	-0.033	-0.021	15.915	-0.063	-0.063	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.013	-0.020	11.884	-0.045	-0.045	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.033	-0.033	11.647	-0.114	-0.114	0.000	0.000	0.000	0.000
24	A	28	PHE	0	-0.097	-0.030	12.149	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.847	-0.914	8.149	-0.877	-0.877	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.025	0.005	5.630	-0.186	-0.186	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.913	-0.955	8.315	-0.641	-0.641	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.004	0.000	10.334	0.083	0.083	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.007	0.005	12.982	0.071	0.071	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.018	-0.018	15.620	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	35	CYS	0	-0.065	-0.030	18.692	0.024	0.024	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.793	-0.875	21.426	-0.076	-0.076	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.035	0.014	24.150	0.011	0.011	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.068	0.019	23.788	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	39	PRO	0	0.010	-0.010	24.129	0.009	0.009	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.856	-0.905	23.174	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	41	ALA	0	0.035	0.004	20.055	0.004	0.004	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.037	-0.033	20.449	0.015	0.015	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.025	-0.008	22.305	0.020	0.020	0.000	0.000	0.000	0.000
40	A	44	CYS	0	-0.050	-0.031	17.708	0.008	0.008	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.032	0.030	16.491	0.010	0.010	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.930	0.980	17.820	-0.116	-0.116	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.890	0.943	20.051	0.030	0.030	0.000	0.000	0.000	0.000
44	A	48	SER	0	-0.051	-0.021	15.348	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.906	-0.949	11.347	0.441	0.441	0.000	0.000	0.000	0.000
46	A	50	PRO	0	-0.018	-0.016	9.931	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	51	PHE	0	0.053	0.034	9.973	0.000	0.000	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.015	-0.011	5.268	0.235	0.235	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.031	-0.014	7.877	0.097	0.097	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.018	0.015	10.220	-0.042	-0.042	0.000	0.000	0.000	0.000
51	A	55	MET	0	-0.034	-0.010	13.875	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.005	0.007	16.230	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.721	-0.838	19.956	-0.102	-0.102	0.000	0.000	0.000	0.000
54	A	58	MET	0	-0.015	-0.014	23.045	0.015	0.015	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.766	0.852	25.671	0.069	0.069	0.000	0.000	0.000	0.000
56	A	60	MET	0	0.007	0.002	23.980	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	61	PRO	0	0.010	0.014	28.803	0.008	0.008	0.000	0.000	0.000	0.000
58	A	62	GLY	0	-0.023	-0.004	30.840	0.001	0.001	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.084	-0.030	26.029	0.006	0.006	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.862	-0.929	27.712	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.021	-0.008	24.258	0.006	0.006	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.020	-0.007	23.463	0.008	0.008	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.776	-0.877	24.571	0.029	0.029	0.000	0.000	0.000	0.000
64	A	68	VAL	0	-0.043	-0.013	21.347	0.012	0.012	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.015	0.005	19.021	0.014	0.014	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.035	-0.011	20.745	0.022	0.022	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.831	0.892	23.259	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.005	0.004	18.547	0.016	0.016	0.000	0.000	0.000	0.000
69	A	73	ARG	1	0.908	0.967	17.653	-0.095	-0.095	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.048	-0.017	19.243	0.027	0.027	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.063	-0.025	19.224	0.015	0.015	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.042	-0.033	13.950	0.056	0.056	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.008	0.003	15.512	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	78	ASN	0	-0.019	-0.023	10.816	-0.089	-0.089	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.055	-0.009	10.868	0.022	0.022	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.016	-0.001	9.395	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.012	-0.014	11.987	-0.085	-0.085	0.000	0.000	0.000	0.000
78	A	82	LEU	0	-0.020	-0.013	12.206	0.008	0.008	0.000	0.000	0.000	0.000
79	A	83	MET	0	0.002	0.008	16.059	0.005	0.005	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.011	0.005	18.847	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	85	THR	0	-0.029	-0.015	21.778	0.013	0.013	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.022	0.002	24.932	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	87	ASN	0	-0.018	-0.031	28.320	0.002	0.002	0.000	0.000	0.000	0.000
84	A	88	GLN	0	-0.006	-0.008	30.611	0.001	0.001	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.659	-0.786	27.712	-0.051	-0.051	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.009	0.016	26.576	0.003	0.003	0.000	0.000	0.000	0.000
87	A	91	THR	0	0.012	-0.007	27.653	0.002	0.002	0.000	0.000	0.000	0.000
88	A	92	THR	0	0.066	0.031	28.105	0.005	0.005	0.000	0.000	0.000	0.000
89	A	93	ALA	0	-0.008	0.002	23.729	0.005	0.005	0.000	0.000	0.000	0.000
90	A	94	MET	0	-0.026	-0.010	23.763	0.006	0.006	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.890	-0.943	25.287	0.018	0.018	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.055	0.032	23.226	0.010	0.010	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.045	-0.027	19.945	0.011	0.011	0.000	0.000	0.000	0.000
94	A	98	ASN	0	-0.105	-0.071	21.623	0.018	0.018	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.908	-0.930	24.333	0.076	0.076	0.000	0.000	0.000	0.000
96	A	100	GLY	0	-0.033	-0.007	20.294	0.015	0.015	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.094	-0.050	19.152	0.013	0.013	0.000	0.000	0.000	0.000
98	A	102	VAL	0	0.006	0.001	18.101	0.000	0.000	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.025	0.015	11.065	0.005	0.005	0.000	0.000	0.000	0.000
100	A	104	ARG	1	0.909	0.942	12.758	0.077	0.077	0.000	0.000	0.000	0.000
101	A	105	PHE	0	0.011	0.016	16.894	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.005	-0.009	16.369	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	107	ASN	0	0.001	-0.005	20.682	0.003	0.003	0.000	0.000	0.000	0.000
104	A	108	LYS	1	0.789	0.903	23.926	0.090	0.090	0.000	0.000	0.000	0.000
105	A	109	PRO	0	0.008	-0.028	25.531	0.009	0.009	0.000	0.000	0.000	0.000
106	A	110	CYS	0	-0.032	0.000	20.283	0.003	0.003	0.000	0.000	0.000	0.000
107	A	111	GLN	0	0.027	0.021	20.553	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	112	MET	0	0.014	0.002	15.158	0.003	0.003	0.000	0.000	0.000	0.000
109	A	113	SER	0	-0.005	-0.014	15.866	-0.047	-0.047	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.837	-0.920	15.110	-0.223	-0.223	0.000	0.000	0.000	0.000
111	A	115	ILE	0	-0.021	-0.013	14.487	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.869	0.935	10.482	0.597	0.597	0.000	0.000	0.000	0.000
113	A	117	ALA	0	0.024	0.022	10.373	-0.090	-0.090	0.000	0.000	0.000	0.000
114	A	118	ALA	0	-0.033	-0.014	11.048	0.003	0.003	0.000	0.000	0.000	0.000
115	A	119	ILE	0	0.036	0.018	8.123	0.054	0.054	0.000	0.000	0.000	0.000
116	A	120	ASN	0	0.013	-0.003	6.170	-0.235	-0.235	0.000	0.000	0.000	0.000
117	A	121	ALA	0	-0.073	-0.028	6.339	0.062	0.062	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.011	-0.013	8.097	0.128	0.128	0.000	0.000	0.000	0.000
119	A	123	ILE	0	-0.005	-0.007	2.350	-0.342	0.151	1.082	-0.243	-1.333	0.000
120	A	124	LYS	1	0.981	1.003	3.937	0.040	0.403	0.006	-0.086	-0.283	0.000
121	A	125	GLN	0	-0.038	-0.012	4.888	0.109	0.161	-0.001	-0.002	-0.048	0.000
122	A	126	TYR	0	0.039	0.019	4.848	0.087	0.087	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.928	-0.956	2.992	1.334	2.439	0.117	-0.406	-0.816	-0.002
124	A	128	LEU	0	-0.003	-0.012	4.962	-0.089	-0.049	-0.001	-0.003	-0.036	0.000
125	A	129	VAL	0	-0.045	-0.009	8.499	-0.017	-0.017	0.000	0.000	0.000	0.000
126	A	130	THR	0	0.045	0.006	6.904	-0.073	-0.073	0.000	0.000	0.000	0.000
127	A	131	SER	0	0.009	0.041	7.701	-0.068	-0.068	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.945	0.968	9.366	-0.548	-0.548	0.000	0.000	0.000	0.000
129	A	133	GLU	-1	-0.848	-0.925	12.192	0.663	0.663	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.944	-0.973	8.287	1.826	1.826	0.000	0.000	0.000	0.000
131	A	135	LEU	0	0.002	-0.002	12.563	-0.107	-0.107	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.021	0.019	14.868	-0.099	-0.099	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.818	0.920	14.607	-0.746	-0.746	0.000	0.000	0.000	0.000
134	A	138	LYS	1	0.925	0.958	14.913	-0.660	-0.660	0.000	0.000	0.000	0.000
135	A	139	THR	0	-0.086	-0.065	17.578	-0.083	-0.083	0.000	0.000	0.000	0.000

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