FMO DATABASE

FMODB ID: JQLZ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1208814.918624
FMO2-HF: Nuclear repulsion	1154151.681965
FMO2-HF: Total energy	-54663.236659
FMO2-MP2: Total energy	-54816.485506

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.
-8.88	-2.206	1.284	-2.417	-5.54	-0.009

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 : 0.009 / q_NPA : 0.001

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	-0.872	-0.947	2.631	-9.785	-5.179	0.882	-2.014	-3.473	-0.009
4	A	8	ARG	1	0.938	0.989	4.723	0.090	0.238	-0.001	-0.013	-0.134	0.000
5	A	9	ILE	0	-0.015	-0.014	8.209	0.182	0.182	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.029	-0.018	10.409	0.021	0.021	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.045	-0.027	14.126	0.011	0.011	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.024	-0.023	16.783	0.016	0.016	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.845	-0.952	20.153	-0.121	-0.121	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.887	-0.940	23.210	-0.073	-0.073	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.874	-0.917	26.010	-0.124	-0.124	0.000	0.000	0.000	0.000
12	A	16	TYR	0	-0.012	-0.078	24.826	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.030	-0.012	25.006	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.034	0.006	21.897	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.045	0.023	19.885	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.006	-0.012	20.252	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	21	THR	0	-0.109	-0.059	21.176	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.013	-0.005	17.413	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.989	1.009	16.388	0.272	0.272	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.927	0.964	16.418	0.202	0.202	0.000	0.000	0.000	0.000
21	A	25	ASN	0	-0.049	-0.036	16.695	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.027	-0.021	12.334	-0.042	-0.042	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.021	-0.011	11.597	-0.122	-0.122	0.000	0.000	0.000	0.000
24	A	28	PHE	0	-0.096	-0.030	12.404	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.920	-0.955	7.915	-0.990	-0.990	0.000	0.000	0.000	0.000
26	A	30	PHE	0	-0.005	-0.004	5.793	-0.212	-0.212	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.928	-0.961	8.355	-0.772	-0.772	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.012	-0.008	10.443	0.094	0.094	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.036	-0.021	13.077	0.071	0.071	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.050	-0.035	15.705	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	35	CYS	0	-0.047	-0.015	18.769	0.019	0.019	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.806	-0.860	21.491	-0.080	-0.080	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.038	0.020	24.215	0.012	0.012	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.060	0.019	23.830	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	39	PRO	0	0.017	-0.009	24.160	0.008	0.008	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.857	-0.916	23.268	-0.069	-0.069	0.000	0.000	0.000	0.000
37	A	41	ALA	0	0.037	0.003	20.119	0.003	0.003	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.047	-0.035	20.484	0.016	0.016	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.019	-0.005	22.332	0.020	0.020	0.000	0.000	0.000	0.000
40	A	44	CYS	0	-0.087	-0.042	18.252	0.015	0.015	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.045	0.050	16.475	0.007	0.007	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.927	0.973	17.831	-0.103	-0.103	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.908	0.948	19.931	0.036	0.036	0.000	0.000	0.000	0.000
44	A	48	SER	0	-0.056	-0.033	15.364	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.901	-0.944	11.425	0.394	0.394	0.000	0.000	0.000	0.000
46	A	50	PRO	0	-0.032	-0.025	9.847	-0.075	-0.075	0.000	0.000	0.000	0.000
47	A	51	PHE	0	0.055	0.029	10.008	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.007	0.008	5.495	0.257	0.257	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.015	-0.009	7.920	0.109	0.109	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.023	0.019	10.226	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	55	MET	0	-0.043	-0.021	13.892	0.010	0.010	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.003	0.011	16.259	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.772	-0.880	19.978	-0.098	-0.098	0.000	0.000	0.000	0.000
54	A	58	MET	0	0.004	-0.007	23.070	0.014	0.014	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.941	0.975	25.686	0.073	0.073	0.000	0.000	0.000	0.000
56	A	60	MET	0	0.008	0.005	24.024	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	61	PRO	0	0.024	0.018	28.848	0.008	0.008	0.000	0.000	0.000	0.000
58	A	62	GLY	0	-0.024	-0.008	30.874	0.001	0.001	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.072	-0.017	26.170	0.006	0.006	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.858	-0.926	27.799	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.022	-0.004	24.265	0.007	0.007	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.018	-0.005	23.464	0.009	0.009	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.797	-0.904	24.634	0.033	0.033	0.000	0.000	0.000	0.000
64	A	68	VAL	0	-0.049	-0.025	21.472	0.013	0.013	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.017	0.005	19.039	0.014	0.014	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.029	-0.005	20.790	0.022	0.022	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.851	0.912	23.290	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.004	0.007	18.547	0.016	0.016	0.000	0.000	0.000	0.000
69	A	73	ARG	1	0.947	0.988	17.759	-0.116	-0.116	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.048	-0.017	19.266	0.027	0.027	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.058	-0.021	19.130	0.014	0.014	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.050	-0.033	13.980	0.054	0.054	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.010	-0.001	15.523	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	78	ASN	0	0.004	-0.005	10.777	-0.097	-0.097	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.061	-0.017	10.901	0.021	0.021	0.000	0.000	0.000	0.000
76	A	80	VAL	0	-0.018	0.002	9.513	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.019	-0.003	12.056	-0.087	-0.087	0.000	0.000	0.000	0.000
78	A	82	LEU	0	-0.030	-0.021	12.625	0.009	0.009	0.000	0.000	0.000	0.000
79	A	83	MET	0	0.005	0.010	16.442	0.003	0.003	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.008	-0.009	18.901	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.014	0.011	21.935	0.012	0.012	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.013	-0.010	25.219	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	87	ASN	0	0.009	-0.013	28.480	0.001	0.001	0.000	0.000	0.000	0.000
84	A	88	GLN	0	-0.034	-0.039	30.825	0.002	0.002	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.819	-0.885	28.385	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.021	0.000	26.947	0.003	0.003	0.000	0.000	0.000	0.000
87	A	91	THR	0	0.009	-0.012	28.050	0.002	0.002	0.000	0.000	0.000	0.000
88	A	92	THR	0	0.070	0.032	28.064	0.006	0.006	0.000	0.000	0.000	0.000
89	A	93	ALA	0	-0.010	0.004	24.087	0.005	0.005	0.000	0.000	0.000	0.000
90	A	94	MET	0	-0.040	-0.021	24.139	0.007	0.007	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.903	-0.957	25.798	0.028	0.028	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.050	0.033	23.606	0.010	0.010	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.047	-0.029	20.290	0.011	0.011	0.000	0.000	0.000	0.000
94	A	98	ASN	0	-0.081	-0.049	21.902	0.020	0.020	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.928	-0.944	24.604	0.086	0.086	0.000	0.000	0.000	0.000
96	A	100	GLY	0	-0.053	-0.011	20.394	0.016	0.016	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.089	-0.060	19.205	0.012	0.012	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.005	-0.003	18.352	0.000	0.000	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.014	0.011	11.737	0.005	0.005	0.000	0.000	0.000	0.000
100	A	104	ARG	1	0.934	0.949	13.068	0.058	0.058	0.000	0.000	0.000	0.000
101	A	105	PHE	0	0.006	0.017	17.285	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	106	LEU	0	0.001	-0.009	16.469	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	107	ASN	0	0.012	0.000	20.851	0.003	0.003	0.000	0.000	0.000	0.000
104	A	108	LYS	1	0.805	0.926	23.987	0.091	0.091	0.000	0.000	0.000	0.000
105	A	109	PRO	0	0.010	-0.027	25.607	0.009	0.009	0.000	0.000	0.000	0.000
106	A	110	CYS	0	-0.009	0.011	20.465	0.003	0.003	0.000	0.000	0.000	0.000
107	A	111	GLN	0	0.031	0.019	20.792	-0.021	-0.021	0.000	0.000	0.000	0.000
108	A	112	MET	0	0.020	0.006	15.514	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	113	SER	0	0.004	-0.012	15.986	-0.051	-0.051	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.864	-0.924	15.199	-0.209	-0.209	0.000	0.000	0.000	0.000
111	A	115	ILE	0	-0.022	-0.012	14.583	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.986	0.999	10.886	0.516	0.516	0.000	0.000	0.000	0.000
113	A	117	ALA	0	0.012	0.008	10.463	-0.077	-0.077	0.000	0.000	0.000	0.000
114	A	118	ALA	0	-0.038	-0.012	11.060	0.011	0.011	0.000	0.000	0.000	0.000
115	A	119	ILE	0	0.038	0.018	8.163	0.063	0.063	0.000	0.000	0.000	0.000
116	A	120	ASN	0	0.042	0.011	6.253	-0.239	-0.239	0.000	0.000	0.000	0.000
117	A	121	ALA	0	-0.093	-0.040	6.606	0.079	0.079	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.015	-0.009	8.416	0.130	0.130	0.000	0.000	0.000	0.000
119	A	123	ILE	0	0.010	-0.002	2.870	-0.533	0.297	0.299	-0.160	-0.970	0.000
120	A	124	LYS	1	0.972	0.997	4.162	0.099	0.382	0.001	-0.045	-0.239	0.000
121	A	125	GLN	0	-0.024	0.000	5.079	0.130	0.180	-0.001	-0.001	-0.048	0.000
122	A	126	TYR	0	0.030	0.011	4.805	0.120	0.120	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.930	-0.968	2.896	1.885	2.602	0.105	-0.181	-0.641	0.000
124	A	128	LEU	0	0.019	0.004	4.950	-0.097	-0.057	-0.001	-0.003	-0.035	0.000
125	A	129	VAL	0	-0.051	-0.011	8.499	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	130	THR	0	-0.022	-0.020	6.726	0.130	0.130	0.000	0.000	0.000	0.000
127	A	131	SER	0	0.063	0.063	7.730	-0.086	-0.086	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.951	0.969	9.288	-0.591	-0.591	0.000	0.000	0.000	0.000
129	A	133	GLU	-1	-0.936	-0.979	12.129	0.667	0.667	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.989	-0.998	8.243	1.891	1.891	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.027	-0.024	12.583	-0.109	-0.109	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.016	-0.021	14.862	-0.094	-0.094	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.897	0.961	14.986	-0.759	-0.759	0.000	0.000	0.000	0.000
134	A	138	LYS	1	0.907	0.948	14.317	-0.754	-0.754	0.000	0.000	0.000	0.000
135	A	139	THR	0	-0.023	0.024	17.517	-0.062	-0.062	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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