FMO DATABASE

FMODB ID: M348Z

Calculation Name: 3FMA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FMA

Chain ID: A

ChEMBL ID:

UniProt ID: Q12186

Base Structure: X-ray

Registration Date: 2023-06-19

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-558620.607251
FMO2-HF: Nuclear repulsion	526018.439814
FMO2-HF: Total energy	-32602.167437
FMO2-MP2: Total energy	-32696.973615

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:13:SER)

Summations of interaction energy for fragment #1(A:13:SER)

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.
-1.647	0.063	-0.022	-0.749	-0.939	0

Interaction energy analysis for fragmet #1(A:13:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.045

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].
3	A	15	GLU	-1	-0.836	-0.909	3.815	-1.981	-0.271	-0.022	-0.749	-0.939
4	A	16	SER	0	-0.053	-0.052	6.212	0.351	0.351	0.000	0.000	0.000
5	A	17	SER	0	-0.049	-0.025	9.903	0.030	0.030	0.000	0.000	0.000
6	A	18	TRP	0	-0.001	-0.023	12.150	0.135	0.135	0.000	0.000	0.000
7	A	19	ARG	1	0.954	0.976	16.164	0.280	0.280	0.000	0.000	0.000
8	A	20	TYR	0	0.001	-0.002	19.827	0.014	0.014	0.000	0.000	0.000
9	A	21	ILE	0	-0.011	0.013	22.923	0.000	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.777	-0.875	26.662	-0.128	-0.128	0.000	0.000	0.000
11	A	23	THR	0	0.040	-0.014	28.933	0.004	0.004	0.000	0.000	0.000
12	A	24	GLN	0	-0.086	-0.027	32.260	0.012	0.012	0.000	0.000	0.000
13	A	25	GLY	0	0.008	0.012	31.343	0.004	0.004	0.000	0.000	0.000
14	A	26	GLN	0	-0.046	-0.022	28.090	-0.013	-0.013	0.000	0.000	0.000
15	A	27	ILE	0	-0.008	0.000	23.666	-0.008	-0.008	0.000	0.000	0.000
16	A	28	HIS	1	0.824	0.904	23.276	0.178	0.178	0.000	0.000	0.000
17	A	29	GLY	0	0.047	0.033	19.453	-0.010	-0.010	0.000	0.000	0.000
18	A	30	PRO	0	-0.057	-0.050	15.497	0.035	0.035	0.000	0.000	0.000
19	A	31	PHE	0	0.007	-0.006	15.690	0.007	0.007	0.000	0.000	0.000
20	A	32	THR	0	0.060	0.032	10.320	0.062	0.062	0.000	0.000	0.000
21	A	33	THR	0	0.026	-0.003	9.636	0.189	0.189	0.000	0.000	0.000
22	A	34	GLN	0	0.022	0.033	10.459	0.250	0.250	0.000	0.000	0.000
23	A	35	MET	0	-0.034	-0.012	12.095	0.083	0.083	0.000	0.000	0.000
24	A	36	MET	0	-0.024	-0.004	14.955	0.077	0.077	0.000	0.000	0.000
25	A	37	SER	0	-0.034	-0.026	14.108	0.066	0.066	0.000	0.000	0.000
26	A	38	GLN	0	0.013	-0.005	16.120	0.016	0.016	0.000	0.000	0.000
27	A	39	TRP	0	-0.010	-0.002	18.142	0.020	0.020	0.000	0.000	0.000
28	A	40	TYR	0	0.021	-0.003	19.104	0.025	0.025	0.000	0.000	0.000
29	A	41	ILE	0	-0.021	-0.009	17.380	0.022	0.022	0.000	0.000	0.000
30	A	42	GLY	0	-0.049	-0.021	21.514	0.016	0.016	0.000	0.000	0.000
31	A	43	GLY	0	-0.022	-0.002	23.937	0.011	0.011	0.000	0.000	0.000
32	A	44	TYR	0	-0.068	-0.037	23.788	0.006	0.006	0.000	0.000	0.000
33	A	45	PHE	0	-0.046	-0.017	19.549	0.002	0.002	0.000	0.000	0.000
34	A	46	ALA	0	0.058	0.035	25.356	0.009	0.009	0.000	0.000	0.000
35	A	47	SER	0	0.056	0.006	26.205	-0.010	-0.010	0.000	0.000	0.000
36	A	48	THR	0	-0.007	-0.005	27.120	-0.005	-0.005	0.000	0.000	0.000
37	A	49	LEU	0	-0.026	0.003	23.527	0.002	0.002	0.000	0.000	0.000
38	A	50	GLN	0	0.012	0.011	25.271	-0.006	-0.006	0.000	0.000	0.000
39	A	51	ILE	0	0.004	-0.014	19.263	-0.012	-0.012	0.000	0.000	0.000
40	A	52	SER	0	0.002	-0.002	19.839	0.009	0.009	0.000	0.000	0.000
41	A	53	ARG	1	0.851	0.910	9.305	0.584	0.584	0.000	0.000	0.000
42	A	54	LEU	0	-0.033	-0.024	14.934	0.056	0.056	0.000	0.000	0.000
43	A	55	GLY	0	0.021	0.017	13.652	-0.081	-0.081	0.000	0.000	0.000
44	A	56	SER	0	-0.107	-0.061	10.898	-0.019	-0.019	0.000	0.000	0.000
45	A	57	THR	0	0.020	0.018	7.071	-0.041	-0.041	0.000	0.000	0.000
46	A	58	PRO	0	0.002	-0.005	9.986	-0.043	-0.043	0.000	0.000	0.000
47	A	59	GLU	-1	-0.747	-0.866	10.280	-0.217	-0.217	0.000	0.000	0.000
48	A	60	THR	0	-0.029	-0.030	12.360	0.030	0.030	0.000	0.000	0.000
49	A	61	LEU	0	-0.055	-0.002	14.780	0.013	0.013	0.000	0.000	0.000
50	A	62	GLY	0	-0.048	-0.022	16.604	0.019	0.019	0.000	0.000	0.000
51	A	63	ILE	0	-0.074	-0.066	15.774	0.006	0.006	0.000	0.000	0.000
52	A	64	ASN	0	-0.001	-0.002	13.746	-0.077	-0.077	0.000	0.000	0.000
53	A	65	ASP	-1	-0.861	-0.927	17.150	-0.203	-0.203	0.000	0.000	0.000
54	A	66	ILE	0	-0.032	0.013	19.599	0.022	0.022	0.000	0.000	0.000
55	A	67	PHE	0	-0.054	-0.039	21.562	-0.025	-0.025	0.000	0.000	0.000
56	A	68	ILE	0	0.023	0.027	20.684	0.017	0.017	0.000	0.000	0.000
57	A	69	THR	0	-0.009	-0.004	24.088	-0.013	-0.013	0.000	0.000	0.000
58	A	70	LEU	0	0.016	0.007	20.761	-0.003	-0.003	0.000	0.000	0.000
59	A	71	GLY	0	-0.001	-0.032	23.015	0.000	0.000	0.000	0.000	0.000
60	A	72	GLU	-1	-0.901	-0.950	25.061	-0.092	-0.092	0.000	0.000	0.000
61	A	73	LEU	0	0.019	0.023	17.259	0.005	0.005	0.000	0.000	0.000
62	A	74	MET	0	-0.043	-0.022	20.510	0.001	0.001	0.000	0.000	0.000
63	A	75	THR	0	-0.092	-0.052	21.991	0.011	0.011	0.000	0.000	0.000
64	A	76	LYS	1	0.942	0.977	20.867	0.103	0.103	0.000	0.000	0.000
65	A	77	LEU	0	-0.016	0.007	15.827	0.004	0.004	0.000	0.000	0.000
66	A	78	GLU	-1	-0.963	-0.960	19.492	-0.024	-0.024	0.000	0.000	0.000
67	A	79	LYS	1	0.903	0.932	19.472	0.031	0.031	0.000	0.000	0.000
68	A	80	TYR	0	-0.018	-0.014	17.596	-0.016	-0.016	0.000	0.000	0.000
69	A	81	ASP	-1	-0.952	-0.960	15.654	-0.008	-0.008	0.000	0.000	0.000
70	A	82	THR	0	0.005	0.003	16.084	0.012	0.012	0.000	0.000	0.000
71	A	83	ASP	-1	-0.755	-0.871	15.228	-0.268	-0.268	0.000	0.000	0.000
72	A	84	PRO	0	0.011	0.009	15.691	-0.008	-0.008	0.000	0.000	0.000
73	A	85	PHE	0	-0.006	0.003	13.902	-0.004	-0.004	0.000	0.000	0.000
74	A	86	THR	0	0.020	-0.012	10.131	-0.114	-0.114	0.000	0.000	0.000
75	A	87	THR	0	-0.052	-0.031	10.493	0.000	0.000	0.000	0.000	0.000
76	A	88	PHE	0	0.007	-0.002	11.798	0.027	0.027	0.000	0.000	0.000
77	A	89	ASP	-1	-0.679	-0.804	7.184	-1.201	-1.201	0.000	0.000	0.000
78	A	90	LYS	1	0.909	0.957	7.549	-0.111	-0.111	0.000	0.000	0.000
79	A	91	LEU	0	-0.066	-0.046	8.704	0.081	0.081	0.000	0.000	0.000
80	A	92	HIS	0	0.048	0.038	10.910	0.063	0.063	0.000	0.000	0.000
81	A	93	VAL	0	-0.049	0.008	5.717	0.094	0.094	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:13:SER)