FMO DATABASE

FMODB ID: 229RR

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:

Apendix: None

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-560774.896985
FMO2-HF: Nuclear repulsion	528172.330845
FMO2-HF: Total energy	-32602.566139
FMO2-MP2: Total energy	-32697.344179

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.
-1.224	0.238	-0.016	-0.656	-0.789	0.001

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 : -0.034 / q_NPA : -0.025

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	15	GLU	-1	-0.790	-0.858	3.876	-1.721	-0.259	-0.016	-0.656	-0.789	0.001
4	A	16	SER	0	-0.034	-0.062	6.499	0.306	0.306	0.000	0.000	0.000	0.000
5	A	17	SER	0	-0.043	-0.018	9.965	0.047	0.047	0.000	0.000	0.000	0.000
6	A	18	TRP	0	-0.003	-0.016	11.926	0.156	0.156	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.903	0.951	16.307	0.319	0.319	0.000	0.000	0.000	0.000
8	A	20	TYR	0	0.023	0.017	20.077	0.016	0.016	0.000	0.000	0.000	0.000
9	A	21	ILE	0	-0.007	0.006	23.060	0.000	0.000	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.764	-0.862	26.884	-0.155	-0.155	0.000	0.000	0.000	0.000
11	A	23	THR	0	0.012	-0.024	29.423	0.004	0.004	0.000	0.000	0.000	0.000
12	A	24	GLN	0	-0.062	-0.013	32.677	0.014	0.014	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.008	0.014	31.847	0.005	0.005	0.000	0.000	0.000	0.000
14	A	26	GLN	0	-0.053	-0.024	28.959	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	27	ILE	0	0.016	0.001	24.269	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	28	HIS	1	0.786	0.879	23.846	0.210	0.210	0.000	0.000	0.000	0.000
17	A	29	GLY	0	0.081	0.047	20.087	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	30	PRO	0	-0.078	-0.048	15.969	0.046	0.046	0.000	0.000	0.000	0.000
19	A	31	PHE	0	0.001	-0.009	16.306	0.021	0.021	0.000	0.000	0.000	0.000
20	A	32	THR	0	0.018	-0.025	10.693	0.082	0.082	0.000	0.000	0.000	0.000
21	A	33	THR	0	0.011	-0.026	9.477	0.194	0.194	0.000	0.000	0.000	0.000
22	A	34	GLN	0	-0.013	0.004	9.998	0.285	0.285	0.000	0.000	0.000	0.000
23	A	35	MET	0	-0.019	0.014	12.198	0.096	0.096	0.000	0.000	0.000	0.000
24	A	36	MET	0	-0.028	-0.006	15.034	0.089	0.089	0.000	0.000	0.000	0.000
25	A	37	SER	0	-0.032	-0.024	13.887	0.072	0.072	0.000	0.000	0.000	0.000
26	A	38	GLN	0	0.008	-0.006	15.862	0.036	0.036	0.000	0.000	0.000	0.000
27	A	39	TRP	0	-0.013	-0.012	17.965	0.029	0.029	0.000	0.000	0.000	0.000
28	A	40	TYR	0	-0.005	-0.018	18.855	0.030	0.030	0.000	0.000	0.000	0.000
29	A	41	ILE	0	-0.012	-0.010	16.890	0.030	0.030	0.000	0.000	0.000	0.000
30	A	42	GLY	0	-0.039	-0.013	21.045	0.021	0.021	0.000	0.000	0.000	0.000
31	A	43	GLY	0	-0.016	-0.004	23.636	0.014	0.014	0.000	0.000	0.000	0.000
32	A	44	TYR	0	-0.053	-0.029	23.614	0.009	0.009	0.000	0.000	0.000	0.000
33	A	45	PHE	0	-0.038	-0.021	19.348	0.000	0.000	0.000	0.000	0.000	0.000
34	A	46	ALA	0	0.055	0.035	25.064	0.007	0.007	0.000	0.000	0.000	0.000
35	A	47	SER	0	0.046	0.009	26.048	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	48	THR	0	0.004	-0.010	26.999	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	49	LEU	0	-0.028	0.008	23.415	0.004	0.004	0.000	0.000	0.000	0.000
38	A	50	GLN	0	0.011	0.004	25.246	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	51	ILE	0	-0.006	-0.020	19.167	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	52	SER	0	0.001	-0.013	19.806	0.014	0.014	0.000	0.000	0.000	0.000
41	A	53	ARG	1	0.847	0.909	9.477	0.497	0.497	0.000	0.000	0.000	0.000
42	A	54	LEU	0	-0.024	-0.021	15.039	0.053	0.053	0.000	0.000	0.000	0.000
43	A	55	GLY	0	0.043	0.027	13.722	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.115	-0.059	10.614	0.092	0.092	0.000	0.000	0.000	0.000
45	A	57	THR	0	0.016	-0.003	7.438	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	58	PRO	0	0.015	0.000	10.763	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	59	GLU	-1	-0.767	-0.851	10.686	-0.156	-0.156	0.000	0.000	0.000	0.000
48	A	60	THR	0	-0.037	-0.026	12.554	0.039	0.039	0.000	0.000	0.000	0.000
49	A	61	LEU	0	-0.042	-0.004	14.913	0.004	0.004	0.000	0.000	0.000	0.000
50	A	62	GLY	0	-0.046	-0.020	16.876	0.012	0.012	0.000	0.000	0.000	0.000
51	A	63	ILE	0	-0.069	-0.070	15.215	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	64	ASN	0	0.012	0.011	14.160	-0.082	-0.082	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.866	-0.932	17.346	-0.226	-0.226	0.000	0.000	0.000	0.000
54	A	66	ILE	0	-0.038	0.002	19.848	0.014	0.014	0.000	0.000	0.000	0.000
55	A	67	PHE	0	-0.034	-0.016	21.502	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	68	ILE	0	0.014	0.021	20.197	0.020	0.020	0.000	0.000	0.000	0.000
57	A	69	THR	0	-0.008	-0.002	24.159	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	70	LEU	0	0.016	0.012	20.816	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	71	GLY	0	0.014	-0.013	23.089	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	72	GLU	-1	-0.837	-0.904	24.596	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	73	LEU	0	0.016	0.018	17.215	0.009	0.009	0.000	0.000	0.000	0.000
62	A	74	MET	0	-0.024	-0.013	20.568	0.002	0.002	0.000	0.000	0.000	0.000
63	A	75	THR	0	-0.091	-0.053	22.146	0.014	0.014	0.000	0.000	0.000	0.000
64	A	76	LYS	1	0.859	0.917	20.687	0.122	0.122	0.000	0.000	0.000	0.000
65	A	77	LEU	0	-0.009	0.005	15.739	0.005	0.005	0.000	0.000	0.000	0.000
66	A	78	GLU	-1	-0.944	-0.947	19.525	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	79	LYS	1	0.862	0.921	20.414	0.061	0.061	0.000	0.000	0.000	0.000
68	A	80	TYR	0	-0.013	-0.007	18.025	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.912	-0.954	15.647	-0.123	-0.123	0.000	0.000	0.000	0.000
70	A	82	THR	0	-0.012	-0.009	15.402	0.011	0.011	0.000	0.000	0.000	0.000
71	A	83	ASP	-1	-0.760	-0.834	15.186	-0.392	-0.392	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.020	0.019	15.926	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	85	PHE	0	0.004	0.006	13.922	0.003	0.003	0.000	0.000	0.000	0.000
74	A	86	THR	0	0.007	-0.045	10.409	-0.124	-0.124	0.000	0.000	0.000	0.000
75	A	87	THR	0	-0.067	-0.042	11.000	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	88	PHE	0	0.022	0.003	11.268	0.040	0.040	0.000	0.000	0.000	0.000
77	A	89	ASP	-1	-0.681	-0.784	7.478	-1.285	-1.285	0.000	0.000	0.000	0.000
78	A	90	LYS	1	0.877	0.951	7.541	0.071	0.071	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.069	-0.045	9.387	0.130	0.130	0.000	0.000	0.000	0.000
80	A	92	HIS	0	0.049	0.042	10.482	0.090	0.090	0.000	0.000	0.000	0.000
81	A	93	VAL	0	-0.028	0.006	5.847	0.072	0.072	0.000	0.000	0.000	0.000

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