FMO DATABASE

FMODB ID: JL5V9

Calculation Name: 3A0J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A0J

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLW8

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-451994.775518
FMO2-HF: Nuclear repulsion	423626.716192
FMO2-HF: Total energy	-28368.059325
FMO2-MP2: Total energy	-28452.250134

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.
-22.563	-11.342	9.697	-7.859	-13.059	-0.083

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 : -0.044 / q_NPA : -0.006

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

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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	LYS	1	0.929	0.960	3.820	0.420	2.849	-0.011	-1.315	-1.103	0.004
4	A	4	GLY	0	0.002	-0.010	6.341	-0.138	-0.138	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.877	0.945	9.718	0.613	0.613	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.020	-0.007	11.876	-0.063	-0.063	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.815	0.901	13.842	0.684	0.684	0.000	0.000	0.000	0.000
8	A	8	TRP	0	0.037	0.004	16.850	0.065	0.065	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.020	-0.008	14.676	-0.051	-0.051	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.026	0.008	18.308	0.053	0.053	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.056	-0.001	20.140	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.934	-0.952	21.181	-0.128	-0.128	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.881	0.938	22.716	0.232	0.232	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.019	0.021	18.957	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.031	-0.027	16.673	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.004	-0.008	16.062	0.061	0.061	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.040	0.001	14.732	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.012	0.012	8.646	0.096	0.096	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.855	-0.928	12.646	-0.650	-0.650	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.775	0.863	8.263	1.643	1.643	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.884	-0.939	11.923	-0.847	-0.847	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.021	0.015	12.973	-0.087	-0.087	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.830	-0.906	10.849	-1.378	-1.378	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.051	-0.018	13.829	0.102	0.102	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.815	-0.895	13.224	-0.858	-0.858	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.040	-0.020	9.218	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.031	-0.017	12.418	0.100	0.100	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.049	0.010	10.646	-0.141	-0.141	0.000	0.000	0.000	0.000
29	A	29	HIS	0	0.049	0.043	12.700	0.105	0.105	0.000	0.000	0.000	0.000
30	A	30	TYR	0	0.066	0.020	13.005	-0.051	-0.051	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.073	-0.062	13.636	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.028	0.000	9.180	0.042	0.042	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.064	-0.006	8.503	-0.161	-0.161	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.018	-0.021	4.823	0.049	0.049	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.003	-0.004	8.963	0.011	0.011	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.903	0.938	6.751	-0.934	-0.934	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.038	0.033	12.140	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.003	-0.001	12.788	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.959	0.967	13.682	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.002	0.001	15.855	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.001	0.015	10.801	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.076	-0.048	14.920	0.032	0.032	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.830	-0.897	16.108	-0.347	-0.347	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.041	-0.031	16.676	0.051	0.051	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.802	-0.892	12.631	-0.228	-0.228	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.035	-0.003	9.741	-0.123	-0.123	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.025	0.004	7.383	0.156	0.156	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.044	0.017	2.596	-0.477	0.264	0.261	-0.213	-0.789	0.002
49	A	49	PHE	0	-0.060	-0.035	2.951	-0.775	0.491	0.407	-0.388	-1.284	-0.003
50	A	50	ASP	-1	-0.774	-0.879	2.343	-20.086	-14.236	7.208	-5.270	-7.788	-0.083
51	A	51	VAL	0	-0.035	-0.036	3.969	1.060	1.238	0.004	-0.030	-0.153	0.000
52	A	52	GLU	-1	-0.916	-0.948	7.380	-0.637	-0.637	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.025	-0.017	10.064	0.033	0.033	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.049	0.027	13.649	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.935	0.954	15.015	0.295	0.295	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.046	-0.040	15.972	0.077	0.077	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.019	0.023	18.741	0.027	0.027	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.907	0.961	18.170	0.410	0.410	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.075	0.040	16.711	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.009	0.009	11.857	0.023	0.023	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.045	0.029	11.646	0.119	0.119	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.022	0.010	7.718	-0.133	-0.133	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.033	-0.025	5.811	0.446	0.446	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.002	0.001	2.412	-0.744	-0.521	1.799	-0.491	-1.531	-0.002
65	A	65	VAL	0	0.007	0.006	3.474	-1.303	-0.859	0.030	-0.152	-0.322	-0.001
66	A	66	THR	0	-0.008	-0.004	4.764	0.567	0.657	-0.001	0.000	-0.089	0.000
67	A	67	VAL	0	-0.001	-0.003	6.365	-0.094	-0.094	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.040	-0.013	7.605	0.223	0.223	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.852	-0.929	10.081	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.005	-0.005	13.590	-0.088	-0.088	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.035	-0.008	15.588	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.809	0.905	15.194	0.209	0.209	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.969	0.986	21.031	0.098	0.098	0.000	0.000	0.000	0.000

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Highlights

Manual

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