FMO DATABASE

FMODB ID: 531YZ

Calculation Name: 3RD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD4

Chain ID: A

ChEMBL ID:

UniProt ID: C0AZM8

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptH
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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500991.538958
FMO2-HF: Nuclear repulsion	469430.236806
FMO2-HF: Total energy	-31561.302153
FMO2-MP2: Total energy	-31652.878308

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
0.207	3.728	0.044	-1.634	-1.932	0.005

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.018

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	4	VAL	0	0.028	0.000	3.663	-1.282	1.172	-0.003	-1.373	-1.079	0.005
4	A	5	LYS	1	0.906	0.956	4.740	0.133	0.211	-0.001	-0.005	-0.072	0.000
5	A	6	LEU	0	0.020	0.013	7.482	0.033	0.033	0.000	0.000	0.000	0.000
6	A	7	TYR	0	-0.041	-0.019	7.192	0.147	0.147	0.000	0.000	0.000	0.000
7	A	8	MET	0	0.031	0.025	13.210	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.004	-0.013	16.443	0.030	0.030	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.869	-0.937	18.492	-0.064	-0.064	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.037	-0.004	20.932	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.020	0.004	21.990	0.007	0.007	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.829	-0.941	23.039	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.856	0.921	23.326	0.066	0.066	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.867	0.954	23.830	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.858	-0.931	24.034	-0.046	-0.046	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.072	-0.025	22.109	0.009	0.009	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.020	0.006	25.053	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.004	0.001	24.482	0.004	0.004	0.000	0.000	0.000	0.000
19	A	20	ASN	0	0.055	0.027	26.587	0.001	0.001	0.000	0.000	0.000	0.000
20	A	33	GLU	-1	-0.898	-0.950	30.226	0.012	0.012	0.000	0.000	0.000	0.000
21	A	34	ILE	0	-0.129	-0.069	25.709	0.004	0.004	0.000	0.000	0.000	0.000
22	A	35	THR	0	-0.044	-0.021	21.709	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	36	HIS	0	-0.008	0.004	23.958	0.007	0.007	0.000	0.000	0.000	0.000
24	A	37	TYR	0	-0.038	-0.025	17.933	0.000	0.000	0.000	0.000	0.000	0.000
25	A	38	TYR	0	0.003	0.004	20.360	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	39	GLN	0	0.040	0.016	19.099	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	40	VAL	0	0.026	0.013	18.097	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	41	THR	0	-0.040	-0.013	18.498	0.006	0.006	0.000	0.000	0.000	0.000
29	A	42	PHE	0	0.032	0.020	16.319	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	43	ARG	1	0.918	0.959	17.514	0.010	0.010	0.000	0.000	0.000	0.000
31	A	44	LEU	0	-0.069	-0.050	14.070	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	45	THR	0	-0.013	-0.009	18.036	0.012	0.012	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.123	-0.120	17.879	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.917	-0.956	20.381	0.034	0.034	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.854	-0.860	16.048	0.047	0.047	0.000	0.000	0.000	0.000
36	A	49	ARG	1	0.940	0.954	18.784	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	50	LYS	1	0.942	0.988	11.584	-0.142	-0.142	0.000	0.000	0.000	0.000
38	A	51	ASP	-1	-0.795	-0.884	17.947	0.014	0.014	0.000	0.000	0.000	0.000
39	A	52	LEU	0	-0.065	-0.048	12.073	0.039	0.039	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.010	0.012	15.540	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.035	-0.017	11.865	0.024	0.024	0.000	0.000	0.000	0.000
42	A	55	ASN	0	-0.005	0.003	14.424	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	56	ILE	0	-0.029	-0.019	14.475	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	57	ASP	-1	-0.810	-0.904	16.493	-0.223	-0.223	0.000	0.000	0.000	0.000
45	A	58	LYS	1	0.961	0.980	18.612	0.093	0.093	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.023	-0.027	21.442	0.012	0.012	0.000	0.000	0.000	0.000
47	A	60	SER	0	0.034	0.005	17.768	0.015	0.015	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.026	-0.014	20.589	0.012	0.012	0.000	0.000	0.000	0.000
49	A	62	GLN	0	-0.041	-0.035	22.188	0.006	0.006	0.000	0.000	0.000	0.000
50	A	63	ASN	0	-0.036	0.003	23.446	0.015	0.015	0.000	0.000	0.000	0.000
51	A	64	ILE	0	-0.037	-0.008	19.252	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	65	GLU	-1	-0.901	-0.996	23.828	-0.065	-0.065	0.000	0.000	0.000	0.000
53	A	66	PRO	0	-0.025	-0.031	25.770	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.918	-0.964	25.999	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	68	MET	0	-0.033	0.037	23.485	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	69	LYS	1	0.923	0.964	22.499	0.074	0.074	0.000	0.000	0.000	0.000
57	A	70	GLY	0	0.059	0.031	20.592	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.817	0.927	15.944	0.273	0.273	0.000	0.000	0.000	0.000
59	A	72	LEU	0	0.009	0.011	12.452	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	73	PHE	0	0.008	-0.004	10.827	-0.041	-0.041	0.000	0.000	0.000	0.000
61	A	74	MET	0	0.024	0.026	7.734	0.045	0.045	0.000	0.000	0.000	0.000
62	A	75	GLN	0	0.047	0.039	3.180	1.100	1.696	0.034	-0.149	-0.481	0.000
63	A	76	GLY	0	-0.037	-0.029	3.705	0.126	0.448	0.011	-0.081	-0.252	0.000
64	A	77	SER	0	0.010	-0.008	4.232	-0.187	-0.116	0.003	-0.026	-0.048	0.000
65	A	78	ARG	1	0.899	0.953	6.531	1.038	1.038	0.000	0.000	0.000	0.000
66	A	79	PHE	0	0.038	0.026	8.232	-0.178	-0.178	0.000	0.000	0.000	0.000
67	A	80	VAL	0	-0.095	-0.052	8.234	-0.079	-0.079	0.000	0.000	0.000	0.000
68	A	81	GLN	0	0.092	0.048	11.143	0.045	0.045	0.000	0.000	0.000	0.000
69	A	82	PHE	0	-0.021	-0.026	14.360	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.925	-0.961	17.158	-0.383	-0.383	0.000	0.000	0.000	0.000
71	A	84	THR	0	0.012	0.001	19.680	0.012	0.012	0.000	0.000	0.000	0.000
72	A	85	ASP	-1	-0.867	-0.933	22.630	-0.185	-0.185	0.000	0.000	0.000	0.000
73	A	86	VAL	0	-0.047	-0.027	24.962	0.014	0.014	0.000	0.000	0.000	0.000
74	A	87	PRO	0	-0.015	-0.015	28.060	0.000	0.000	0.000	0.000	0.000	0.000
75	A	88	ILE	0	-0.035	-0.013	30.351	0.001	0.001	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.940	-0.955	31.101	-0.124	-0.124	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)