FMO DATABASE

FMODB ID: 4JN6N

Calculation Name: 3KT9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KT9

Chain ID: A

ChEMBL ID:

UniProt ID: Q7Z2E3

Base Structure: X-ray

Registration Date: 2023-09-20

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-824559.090465
FMO2-HF: Nuclear repulsion	782683.010136
FMO2-HF: Total energy	-41876.080329
FMO2-MP2: Total energy	-41995.868128

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.
-2.51	-1.232	-0.011	-0.639	-0.628	0.002

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 : 0.016 / q_NPA : -0.015

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	ARG	1	0.919	0.960	3.753	-1.203	0.075	-0.011	-0.639	-0.628	0.002
4	A	4	VAL	0	0.005	-0.007	6.313	0.703	0.703	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.040	-0.010	8.116	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.014	-0.026	11.561	0.129	0.129	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.017	0.002	14.522	0.008	0.008	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.026	-0.016	17.686	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.819	0.880	20.201	0.077	0.077	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.009	-0.007	23.944	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.783	-0.863	25.070	-0.080	-0.080	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.052	-0.037	26.210	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.911	0.922	18.652	0.248	0.248	0.000	0.000	0.000	0.000
14	A	14	HIS	0	0.027	0.013	21.146	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.042	-0.010	21.446	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.804	0.886	14.026	0.398	0.398	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.002	0.000	17.722	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.956	0.987	8.218	0.341	0.341	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.020	-0.014	13.482	0.048	0.048	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.038	0.014	11.358	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	21	HIS	0	0.065	0.021	9.569	-0.139	-0.139	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.084	-0.047	11.609	0.057	0.057	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.922	-0.939	13.886	0.480	0.480	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.087	-0.051	16.646	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.028	0.018	17.232	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.030	-0.019	20.356	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.029	0.023	22.129	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.063	0.015	25.148	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.799	0.935	28.390	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.002	-0.015	29.666	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.014	-0.003	27.568	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.863	-0.929	22.941	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.002	-0.024	24.921	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.922	0.969	26.624	0.062	0.062	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.009	0.026	28.780	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.004	-0.018	31.763	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.795	-0.875	35.133	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.971	0.957	35.919	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.934	0.976	37.871	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	CYS	0	0.013	0.043	31.700	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.007	0.001	32.570	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.997	0.988	31.408	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.002	0.008	28.746	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.026	-0.010	28.857	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.066	0.032	24.444	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.005	-0.001	23.138	0.012	0.012	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.006	-0.003	19.544	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.892	0.939	17.805	-0.168	-0.168	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.053	0.034	13.439	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.811	-0.894	12.518	0.559	0.559	0.000	0.000	0.000	0.000
51	A	51	CYS	0	0.038	0.006	8.513	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.024	-0.001	7.491	-0.200	-0.200	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.863	0.910	9.862	-0.522	-0.522	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.030	0.008	13.106	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.014	-0.003	14.205	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.016	0.004	16.082	0.031	0.031	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.818	0.910	18.342	-0.224	-0.224	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.059	0.027	21.196	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.885	0.952	23.837	-0.120	-0.120	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.034	0.031	26.681	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.023	-0.017	27.963	0.006	0.006	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.000	0.001	30.732	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.007	-0.003	33.330	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.062	-0.036	36.333	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.031	0.019	34.594	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.010	-0.006	28.317	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.002	0.001	30.781	0.004	0.004	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.002	-0.009	25.326	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.765	-0.876	28.193	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.029	-0.003	30.695	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.022	-0.003	32.059	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.035	-0.033	32.027	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.044	-0.007	27.606	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.053	0.023	31.857	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.823	0.882	32.624	-0.062	-0.062	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.833	-0.901	31.274	0.079	0.079	0.000	0.000	0.000	0.000
77	A	77	GLN	0	-0.039	-0.006	31.184	0.015	0.015	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.848	-0.938	24.314	0.170	0.170	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.038	0.026	26.287	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.900	0.956	20.844	-0.139	-0.139	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.037	0.033	20.855	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.030	-0.032	19.887	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.035	0.002	17.322	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.018	-0.002	20.054	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.010	0.010	23.147	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.022	-0.018	23.957	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.029	-0.009	23.623	0.014	0.014	0.000	0.000	0.000	0.000
88	A	88	HIS	0	0.033	0.028	26.392	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.023	-0.010	25.203	0.014	0.014	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.026	-0.032	29.472	0.009	0.009	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.034	-0.015	33.245	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.866	-0.937	33.633	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.016	0.012	33.554	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.085	-0.087	29.761	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.063	0.049	27.798	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.036	-0.037	22.503	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.025	0.025	20.479	0.009	0.009	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.009	-0.009	16.749	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.797	-0.863	15.373	-0.297	-0.297	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.029	-0.026	10.899	0.033	0.033	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.799	-0.867	10.161	-0.617	-0.617	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.913	-0.949	5.711	-1.894	-1.894	0.000	0.000	0.000	0.000

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