FMO DATABASE

FMODB ID: 5J9YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-826899.107837
FMO2-HF: Nuclear repulsion	785022.935885
FMO2-HF: Total energy	-41876.171952
FMO2-MP2: Total energy	-41995.965962

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.
-2.03	-0.841	-0.008	-0.575	-0.606	0.001

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 : 0.020 / q_NPA : -0.014

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	0.892	0.952	3.832	-0.963	0.226	-0.008	-0.575	-0.606	0.001
4	A	4	VAL	0	0.024	0.008	6.364	0.675	0.675	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.030	-0.002	8.351	-0.008	-0.008	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.009	-0.028	11.894	0.095	0.095	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.026	0.020	14.913	0.008	0.008	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.038	-0.023	17.898	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.789	0.875	20.553	0.092	0.092	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.008	-0.006	24.341	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.777	-0.857	25.820	-0.091	-0.091	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.046	-0.041	26.699	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.883	0.920	19.041	0.252	0.252	0.000	0.000	0.000	0.000
14	A	14	HIS	0	0.047	0.020	21.489	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.033	-0.006	21.521	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.788	0.870	14.210	0.438	0.438	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.009	-0.008	18.153	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.912	0.965	9.086	0.477	0.477	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.020	-0.014	13.660	0.049	0.049	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.044	0.021	11.330	-0.041	-0.041	0.000	0.000	0.000	0.000
21	A	21	HIS	0	0.048	0.009	9.763	-0.128	-0.128	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.078	-0.041	11.758	0.070	0.070	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.917	-0.939	13.999	0.321	0.321	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.054	-0.040	16.694	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.040	0.033	17.364	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.027	-0.027	20.315	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.011	0.017	22.450	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.067	0.021	25.518	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.804	0.932	28.765	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.017	-0.001	29.228	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.010	0.001	27.692	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.860	-0.934	23.403	-0.042	-0.042	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.000	-0.027	24.910	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.921	0.963	27.085	0.081	0.081	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.002	0.022	29.089	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.017	-0.012	32.233	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.808	-0.882	35.533	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.968	0.961	36.404	0.012	0.012	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.944	0.982	38.108	0.010	0.010	0.000	0.000	0.000	0.000
40	A	40	CYS	0	0.008	0.039	32.012	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.019	0.000	32.796	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.971	0.982	31.697	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.014	0.019	28.947	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.021	-0.012	29.260	0.004	0.004	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.059	0.018	24.795	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.018	0.009	23.304	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.009	-0.004	19.815	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.861	0.922	17.879	-0.126	-0.126	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.047	0.029	13.595	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.787	-0.885	12.356	0.485	0.485	0.000	0.000	0.000	0.000
51	A	51	CYS	0	0.011	0.005	8.487	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.036	-0.002	7.763	-0.134	-0.134	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.869	0.906	10.035	-0.471	-0.471	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.005	0.023	13.147	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.007	-0.009	14.206	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.016	-0.004	16.209	0.019	0.019	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.825	0.917	18.525	-0.182	-0.182	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.042	0.016	21.403	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.827	0.906	24.013	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.036	0.027	27.031	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.042	-0.031	28.221	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.009	0.003	31.115	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.002	-0.006	33.771	0.001	0.001	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.061	-0.032	36.695	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.040	0.023	35.042	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.009	-0.007	28.681	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.010	-0.004	31.092	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.003	-0.011	25.645	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.769	-0.873	28.173	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.025	0.003	30.926	0.005	0.005	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.022	-0.007	31.917	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.020	-0.024	32.155	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.052	-0.014	27.657	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.065	0.030	31.862	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.806	0.877	32.730	-0.045	-0.045	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.807	-0.882	31.580	0.060	0.060	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.006	0.028	31.239	0.015	0.015	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.842	-0.927	24.231	0.138	0.138	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.031	0.030	26.292	0.005	0.005	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.904	0.957	20.947	-0.116	-0.116	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.047	0.046	21.222	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.045	-0.039	19.874	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.023	-0.005	17.221	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.011	0.003	19.923	0.012	0.012	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.015	0.003	23.187	0.013	0.013	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.018	-0.022	24.185	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.016	-0.006	23.993	0.014	0.014	0.000	0.000	0.000	0.000
88	A	88	HIS	0	0.017	0.033	26.659	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.007	0.001	25.351	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.031	-0.035	29.499	0.010	0.010	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.045	-0.027	33.269	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.845	-0.929	34.010	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.017	0.004	33.872	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.070	-0.079	30.246	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.068	0.052	28.242	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.039	-0.036	22.829	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.023	0.023	20.818	0.011	0.011	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.020	-0.016	17.246	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.775	-0.850	15.434	-0.309	-0.309	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.015	-0.026	11.107	0.033	0.033	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.794	-0.858	10.082	-0.639	-0.639	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.932	-0.958	5.797	-1.791	-1.791	0.000	0.000	0.000	0.000

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