FMO DATABASE

FMODB ID: 22M8R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-717956.543589
FMO2-HF: Nuclear repulsion	677514.159721
FMO2-HF: Total energy	-40442.383867
FMO2-MP2: Total energy	-40558.731843

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.
-3.193	-0.538	0.804	-1.559	-1.899	-0.008

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 : -0.015 / 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	PHE	0	0.004	-0.007	2.651	-4.409	-1.838	0.805	-1.556	-1.819	-0.008
4	A	4	THR	0	0.005	-0.006	5.219	0.516	0.600	-0.001	-0.003	-0.080	0.000
5	A	5	ASN	0	-0.027	-0.013	7.254	0.104	0.104	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.009	0.000	9.769	0.142	0.142	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.011	-0.005	12.556	-0.056	-0.056	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.007	-0.017	16.357	0.027	0.027	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.038	-0.021	18.533	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.022	0.021	22.071	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.020	-0.010	25.643	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.058	0.025	27.915	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.038	-0.017	28.930	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.881	-0.926	31.304	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.895	0.933	32.647	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.067	0.051	31.932	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.062	-0.037	31.962	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.026	0.003	33.306	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.005	0.018	30.439	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.818	0.897	28.401	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.033	0.014	28.955	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.037	-0.017	24.229	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.024	-0.007	27.278	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.010	0.008	25.355	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.037	0.024	27.367	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.033	-0.017	21.863	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.051	0.031	25.963	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.052	-0.030	24.910	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.039	0.036	26.351	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.782	-0.852	26.653	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.015	-0.007	27.584	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.011	-0.002	28.414	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.021	-0.007	24.342	0.009	0.009	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.901	0.953	28.421	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.046	-0.030	26.209	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.832	-0.931	29.136	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.065	-0.029	27.928	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.041	0.015	30.445	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.036	-0.022	25.158	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.854	-0.929	26.306	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.932	-0.972	25.613	-0.070	-0.070	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.071	-0.046	26.534	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.004	0.018	28.365	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.037	-0.021	30.459	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.030	-0.008	30.626	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.021	-0.008	29.747	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.014	-0.003	30.722	0.003	0.003	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.015	-0.010	26.377	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.035	0.030	29.839	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.045	-0.029	23.847	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.902	-0.943	28.435	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.037	-0.017	22.178	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.001	0.018	25.573	0.013	0.013	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.013	-0.010	23.652	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.805	0.883	22.759	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.039	0.041	22.088	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.013	-0.024	19.995	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.002	-0.001	22.868	0.022	0.022	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.908	0.930	24.221	-0.179	-0.179	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.041	0.014	19.916	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.003	-0.005	25.138	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.896	-0.961	26.926	0.086	0.086	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.850	-0.913	26.725	0.155	0.155	0.000	0.000	0.000	0.000
64	A	64	TRP	0	0.020	-0.005	27.227	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.068	-0.044	30.168	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.024	-0.012	32.406	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.783	0.894	31.219	-0.095	-0.095	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.057	-0.037	33.298	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.037	0.026	35.500	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.848	-0.911	32.407	0.070	0.070	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.018	0.001	30.943	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.020	0.000	27.045	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.008	-0.001	22.270	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.009	-0.007	20.727	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.853	-0.907	16.067	0.324	0.324	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.006	-0.008	16.210	0.029	0.029	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.021	0.012	12.969	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.053	0.025	14.810	0.007	0.007	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.013	-0.012	15.504	-0.059	-0.059	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.056	0.031	18.015	0.033	0.033	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.977	1.000	21.408	0.086	0.086	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.035	-0.028	23.268	0.014	0.014	0.000	0.000	0.000	0.000
83	A	83	ARG	1	1.017	0.996	21.897	0.254	0.254	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.933	0.949	24.077	0.159	0.159	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.007	0.010	25.123	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.035	-0.019	24.728	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	MET	0	0.065	0.052	25.268	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.019	-0.023	20.933	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.016	-0.006	21.116	0.019	0.019	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.018	0.015	18.310	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.877	0.947	16.638	0.039	0.039	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.050	0.020	17.912	0.029	0.029	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.011	-0.016	14.272	-0.049	-0.049	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.039	-0.022	17.472	0.030	0.030	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.019	0.021	19.812	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.894	0.955	21.342	-0.257	-0.257	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.754	-0.855	25.888	0.092	0.092	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.035	-0.022	26.762	0.012	0.012	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.863	0.900	28.509	-0.117	-0.117	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.002	0.035	27.384	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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