FMO DATABASE

FMODB ID: 7GQNK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-559324.705903
FMO2-HF: Nuclear repulsion	526722.251852
FMO2-HF: Total energy	-32602.454051
FMO2-MP2: Total energy	-32697.247359

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.
-2.35	-0.661	-0.022	-0.76	-0.908	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 : -0.041 / q_NPA : -0.030

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	-0.797	-0.860	3.815	-2.853	-1.164	-0.022	-0.760	-0.908	0.001
4	A	16	SER	0	-0.051	-0.067	6.577	0.499	0.499	0.000	0.000	0.000	0.000
5	A	17	SER	0	-0.051	-0.025	10.062	0.010	0.010	0.000	0.000	0.000	0.000
6	A	18	TRP	0	-0.002	-0.021	12.072	0.159	0.159	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.945	0.978	16.465	0.303	0.303	0.000	0.000	0.000	0.000
8	A	20	TYR	0	0.006	-0.001	20.215	0.011	0.011	0.000	0.000	0.000	0.000
9	A	21	ILE	0	-0.013	0.009	23.156	0.003	0.003	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.773	-0.871	26.914	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	23	THR	0	0.035	-0.012	29.230	0.004	0.004	0.000	0.000	0.000	0.000
12	A	24	GLN	0	-0.079	-0.024	32.647	0.014	0.014	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.005	0.010	31.644	0.006	0.006	0.000	0.000	0.000	0.000
14	A	26	GLN	0	-0.042	-0.016	28.712	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	27	ILE	0	0.001	-0.002	24.076	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	28	HIS	1	0.801	0.888	23.731	0.214	0.214	0.000	0.000	0.000	0.000
17	A	29	GLY	0	0.054	0.039	19.816	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	30	PRO	0	-0.070	-0.051	15.833	0.045	0.045	0.000	0.000	0.000	0.000
19	A	31	PHE	0	-0.002	-0.014	16.054	0.009	0.009	0.000	0.000	0.000	0.000
20	A	32	THR	0	0.008	-0.019	10.601	0.102	0.102	0.000	0.000	0.000	0.000
21	A	33	THR	0	0.023	-0.016	9.584	0.238	0.238	0.000	0.000	0.000	0.000
22	A	34	GLN	0	0.005	0.014	10.541	0.286	0.286	0.000	0.000	0.000	0.000
23	A	35	MET	0	-0.020	0.003	12.402	0.116	0.116	0.000	0.000	0.000	0.000
24	A	36	MET	0	-0.030	-0.009	15.172	0.101	0.101	0.000	0.000	0.000	0.000
25	A	37	SER	0	-0.034	-0.029	13.932	0.082	0.082	0.000	0.000	0.000	0.000
26	A	38	GLN	0	0.011	-0.003	15.936	0.033	0.033	0.000	0.000	0.000	0.000
27	A	39	TRP	0	-0.004	-0.003	18.242	0.032	0.032	0.000	0.000	0.000	0.000
28	A	40	TYR	0	0.010	-0.009	18.831	0.034	0.034	0.000	0.000	0.000	0.000
29	A	41	ILE	0	-0.019	-0.009	17.179	0.034	0.034	0.000	0.000	0.000	0.000
30	A	42	GLY	0	-0.048	-0.019	21.266	0.023	0.023	0.000	0.000	0.000	0.000
31	A	43	GLY	0	-0.024	-0.002	23.751	0.019	0.019	0.000	0.000	0.000	0.000
32	A	44	TYR	0	-0.066	-0.037	24.020	0.011	0.011	0.000	0.000	0.000	0.000
33	A	45	PHE	0	-0.048	-0.020	19.376	0.008	0.008	0.000	0.000	0.000	0.000
34	A	46	ALA	0	0.057	0.040	25.176	0.009	0.009	0.000	0.000	0.000	0.000
35	A	47	SER	0	0.047	0.003	26.038	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	48	THR	0	0.010	-0.001	26.965	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	49	LEU	0	-0.032	0.001	23.551	0.005	0.005	0.000	0.000	0.000	0.000
38	A	50	GLN	0	0.015	0.011	25.075	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	51	ILE	0	-0.001	-0.018	19.320	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	52	SER	0	0.005	-0.014	19.857	0.016	0.016	0.000	0.000	0.000	0.000
41	A	53	ARG	1	0.850	0.915	9.327	0.595	0.595	0.000	0.000	0.000	0.000
42	A	54	LEU	0	-0.005	-0.014	14.934	0.065	0.065	0.000	0.000	0.000	0.000
43	A	55	GLY	0	0.020	0.019	13.671	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	56	SER	0	-0.096	-0.056	10.403	0.085	0.085	0.000	0.000	0.000	0.000
45	A	57	THR	0	0.018	0.012	7.189	0.001	0.001	0.000	0.000	0.000	0.000
46	A	58	PRO	0	-0.003	-0.006	9.859	-0.064	-0.064	0.000	0.000	0.000	0.000
47	A	59	GLU	-1	-0.749	-0.873	10.294	-0.267	-0.267	0.000	0.000	0.000	0.000
48	A	60	THR	0	-0.022	-0.023	12.373	0.037	0.037	0.000	0.000	0.000	0.000
49	A	61	LEU	0	-0.059	0.001	14.790	0.015	0.015	0.000	0.000	0.000	0.000
50	A	62	GLY	0	-0.039	-0.015	16.618	0.024	0.024	0.000	0.000	0.000	0.000
51	A	63	ILE	0	-0.075	-0.071	15.791	0.004	0.004	0.000	0.000	0.000	0.000
52	A	64	ASN	0	-0.009	-0.005	13.809	-0.084	-0.084	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.863	-0.924	17.168	-0.206	-0.206	0.000	0.000	0.000	0.000
54	A	66	ILE	0	-0.026	0.016	19.617	0.024	0.024	0.000	0.000	0.000	0.000
55	A	67	PHE	0	-0.050	-0.024	21.579	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	68	ILE	0	0.022	0.025	20.810	0.020	0.020	0.000	0.000	0.000	0.000
57	A	69	THR	0	-0.010	-0.004	23.934	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	70	LEU	0	0.025	0.010	20.566	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	71	GLY	0	0.015	-0.022	22.904	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	72	GLU	-1	-0.870	-0.924	24.993	-0.131	-0.131	0.000	0.000	0.000	0.000
61	A	73	LEU	0	0.021	0.016	17.264	0.006	0.006	0.000	0.000	0.000	0.000
62	A	74	MET	0	-0.026	-0.015	20.492	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	75	THR	0	-0.092	-0.049	21.951	0.013	0.013	0.000	0.000	0.000	0.000
64	A	76	LYS	1	0.878	0.937	20.985	0.151	0.151	0.000	0.000	0.000	0.000
65	A	77	LEU	0	-0.017	0.008	15.821	0.002	0.002	0.000	0.000	0.000	0.000
66	A	78	GLU	-1	-0.960	-0.961	19.557	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	79	LYS	1	0.896	0.929	19.661	0.105	0.105	0.000	0.000	0.000	0.000
68	A	80	TYR	0	-0.010	-0.007	17.611	-0.024	-0.024	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.939	-0.956	15.596	-0.163	-0.163	0.000	0.000	0.000	0.000
70	A	82	THR	0	0.010	0.010	15.780	0.020	0.020	0.000	0.000	0.000	0.000
71	A	83	ASP	-1	-0.762	-0.852	15.031	-0.468	-0.468	0.000	0.000	0.000	0.000
72	A	84	PRO	0	0.015	0.019	15.587	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	85	PHE	0	0.005	0.005	13.713	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	86	THR	0	0.018	-0.035	10.097	-0.153	-0.153	0.000	0.000	0.000	0.000
75	A	87	THR	0	-0.065	-0.043	10.436	-0.037	-0.037	0.000	0.000	0.000	0.000
76	A	88	PHE	0	0.010	-0.003	11.606	0.020	0.020	0.000	0.000	0.000	0.000
77	A	89	ASP	-1	-0.673	-0.776	7.080	-1.465	-1.465	0.000	0.000	0.000	0.000
78	A	90	LYS	1	0.892	0.952	7.635	0.118	0.118	0.000	0.000	0.000	0.000
79	A	91	LEU	0	-0.061	-0.044	8.809	0.103	0.103	0.000	0.000	0.000	0.000
80	A	92	HIS	0	0.040	0.029	11.014	0.094	0.094	0.000	0.000	0.000	0.000
81	A	93	VAL	0	-0.046	0.011	5.794	0.111	0.111	0.000	0.000	0.000	0.000

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