FMO DATABASE

FMODB ID: 7GK5K

Calculation Name: 3K8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8A

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F924

Base Structure: X-ray

Registration Date: 2023-03-14

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-717406.996595
FMO2-HF: Nuclear repulsion	676965.101782
FMO2-HF: Total energy	-40441.894813
FMO2-MP2: Total energy	-40558.229187

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.
-4.338	-1.552	0.605	-1.622	-1.769	-0.007

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 : -0.013

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	PHE	0	0.024	0.012	2.713	-5.540	-2.754	0.605	-1.622	-1.769	-0.007
4	A	4	THR	0	-0.011	-0.016	5.520	0.621	0.621	0.000	0.000	0.000	0.000
5	A	5	ASN	0	-0.021	-0.014	7.423	0.075	0.075	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.026	0.005	9.877	0.140	0.140	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.012	0.004	12.711	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.040	0.012	16.504	0.048	0.048	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.037	-0.013	18.945	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.035	0.018	22.433	0.020	0.020	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.017	-0.018	25.814	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.055	0.024	28.289	0.012	0.012	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.060	-0.024	29.112	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.850	-0.912	31.464	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.924	0.954	32.978	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.028	0.006	32.031	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.068	-0.032	31.432	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.022	0.015	32.966	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.026	0.019	30.088	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.809	0.895	27.619	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.047	0.013	28.679	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.065	-0.016	23.806	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.036	-0.001	26.823	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.015	-0.007	25.225	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.039	0.031	27.337	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.037	-0.026	21.617	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.066	0.041	25.786	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.074	-0.041	24.335	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.040	0.032	25.813	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.793	-0.867	26.449	0.012	0.012	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.032	0.009	27.446	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.007	-0.001	28.484	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.020	-0.001	24.636	0.009	0.009	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.951	0.999	28.731	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.060	-0.052	26.571	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.872	-0.956	29.414	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.050	-0.018	28.010	0.007	0.007	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.060	0.025	30.636	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.050	-0.021	25.324	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.851	-0.936	26.452	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.961	-0.994	26.130	-0.102	-0.102	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.042	-0.023	26.853	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.009	-0.008	28.596	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.035	0.005	31.057	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.025	-0.014	30.926	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.022	-0.007	29.920	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.008	0.007	31.316	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.027	-0.014	27.014	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.027	0.011	30.499	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.051	-0.035	24.232	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.901	-0.936	28.925	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.044	-0.024	22.395	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.003	0.014	25.795	0.014	0.014	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.023	-0.010	23.765	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.810	0.893	22.053	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.023	0.023	21.920	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.008	-0.025	19.421	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.007	0.004	22.557	0.019	0.019	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.921	0.939	23.756	-0.198	-0.198	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.043	0.009	20.111	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.017	-0.011	25.107	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.926	-0.970	26.623	0.092	0.092	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.847	-0.913	26.847	0.166	0.166	0.000	0.000	0.000	0.000
64	A	64	TRP	0	0.037	-0.002	26.858	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.062	-0.030	29.953	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.018	-0.018	31.962	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.774	0.885	31.276	-0.102	-0.102	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.039	-0.032	33.632	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.010	0.011	35.238	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.827	-0.886	32.841	0.072	0.072	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.031	-0.003	31.095	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.011	0.005	27.064	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.004	-0.005	22.286	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.019	-0.006	20.853	0.018	0.018	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.899	-0.946	15.883	0.352	0.352	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.010	-0.021	15.783	0.033	0.033	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.019	0.023	13.080	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.057	0.027	14.916	0.011	0.011	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.018	-0.017	15.830	-0.057	-0.057	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.038	0.020	18.268	0.036	0.036	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.951	0.974	21.481	0.072	0.072	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.003	0.005	22.840	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	ARG	1	1.035	1.008	21.221	0.257	0.257	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.902	0.937	23.431	0.167	0.167	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.042	0.017	25.148	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.051	-0.010	25.172	0.010	0.010	0.000	0.000	0.000	0.000
87	A	87	MET	0	0.073	0.054	25.508	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.022	-0.024	20.787	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.042	-0.015	20.887	0.021	0.021	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.043	0.023	18.522	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.867	0.943	16.429	0.009	0.009	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.045	0.023	17.487	0.031	0.031	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.021	-0.018	14.034	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.031	-0.016	17.318	0.020	0.020	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.029	0.020	19.732	-0.022	-0.022	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.896	0.967	21.256	-0.280	-0.280	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.746	-0.863	25.783	0.097	0.097	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.029	-0.019	27.005	0.010	0.010	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.897	0.928	28.444	-0.120	-0.120	0.000	0.000	0.000	0.000
100	A	100	GLY	0	-0.028	0.013	27.286	0.000	0.000	0.000	0.000	0.000	0.000

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