FMO DATABASE

FMODB ID: 8N2MY

Calculation Name: 3RFI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RFI

Chain ID: A

ChEMBL ID:

UniProt ID: Q6B9W9

Base Structure: X-ray

Registration Date: 2023-09-26

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-460520.987421
FMO2-HF: Nuclear repulsion	426963.810958
FMO2-HF: Total energy	-33557.176462
FMO2-MP2: Total energy	-33647.355136

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:0:ALA)

Summations of interaction energy for fragment #1(A:0: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.
-5.95	-1.842	0.904	-1.826	-3.187	-0.005

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.005

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	2	VAL	0	0.065	0.024	3.858	-2.329	-0.796	-0.007	-0.732	-0.795	0.001
4	A	3	SER	0	-0.018	0.002	3.385	-1.073	-0.488	0.033	-0.158	-0.460	-0.001
5	A	4	MET	0	-0.009	-0.009	2.385	0.158	0.734	0.633	-0.235	-0.974	-0.002
6	A	5	GLU	-1	-0.889	-0.938	5.938	0.221	0.221	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.064	-0.011	7.966	0.133	0.133	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.982	0.972	6.455	1.358	1.358	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.005	0.011	9.854	0.105	0.105	0.000	0.000	0.000	0.000
10	A	9	ILE	0	-0.012	0.004	11.975	0.067	0.067	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.010	-0.009	13.359	0.039	0.039	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.069	-0.041	13.381	0.047	0.047	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.024	-0.015	15.069	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.027	-0.013	15.962	0.041	0.041	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.036	0.035	18.037	0.023	0.023	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.890	-0.958	19.015	-0.101	-0.101	0.000	0.000	0.000	0.000
17	A	16	MET	0	0.024	0.022	22.158	0.012	0.012	0.000	0.000	0.000	0.000
18	A	17	ILE	0	-0.025	-0.024	18.151	0.016	0.016	0.000	0.000	0.000	0.000
19	A	18	TRP	0	-0.007	-0.009	22.165	0.013	0.013	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.861	-0.943	23.609	-0.062	-0.062	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.058	-0.030	24.390	0.010	0.010	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.055	-0.003	22.741	0.008	0.008	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.003	-0.012	26.068	0.007	0.007	0.000	0.000	0.000	0.000
24	A	23	SER	0	-0.036	-0.036	28.954	0.005	0.005	0.000	0.000	0.000	0.000
25	A	24	GLY	0	-0.036	-0.001	29.510	0.004	0.004	0.000	0.000	0.000	0.000
26	A	25	VAL	0	-0.081	-0.028	30.463	0.005	0.005	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.943	0.976	32.202	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.041	0.010	35.758	0.002	0.002	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.782	-0.892	38.214	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.077	-0.029	35.593	0.004	0.004	0.000	0.000	0.000	0.000
31	A	30	VAL	0	0.014	0.009	34.040	0.002	0.002	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.026	-0.014	36.641	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.017	0.001	40.141	0.001	0.001	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.072	-0.038	33.435	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.046	-0.012	38.600	0.001	0.001	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.016	0.003	40.173	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.058	-0.039	42.851	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	37	CYS	0	-0.066	0.020	43.162	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	PHE	0	0.016	-0.008	44.461	0.002	0.002	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.016	0.023	41.797	0.000	0.000	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.884	-0.957	49.189	0.001	0.001	0.000	0.000	0.000	0.000
42	A	65	ALA	0	-0.023	-0.004	49.916	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	66	PRO	0	0.038	-0.002	49.910	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	67	LEU	0	0.015	-0.004	47.056	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	69	THR	0	0.058	0.018	45.069	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	70	ALA	0	-0.014	-0.007	45.667	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	72	GLU	-1	-0.814	-0.946	41.067	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	73	MET	0	-0.068	-0.030	40.892	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	74	ALA	0	0.001	0.002	40.332	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	75	VAL	0	0.023	0.013	35.475	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	76	VAL	0	0.027	0.021	36.413	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	77	TRP	0	-0.031	-0.033	37.314	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	78	MET	0	-0.044	-0.013	33.924	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	79	GLN	0	0.004	-0.012	32.563	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	80	ASN	0	0.020	0.026	32.745	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	81	GLN	0	-0.014	-0.011	31.562	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	82	LEU	0	0.010	0.000	28.268	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	83	LYS	1	0.907	0.943	28.751	0.033	0.033	0.000	0.000	0.000	0.000
59	A	84	GLN	0	-0.109	-0.041	30.631	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	85	GLU	-1	-0.824	-0.922	27.419	-0.102	-0.102	0.000	0.000	0.000	0.000
61	A	86	GLY	0	0.042	0.026	27.278	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	87	THR	0	-0.074	-0.038	26.748	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	88	LYS	1	0.988	1.011	23.935	0.090	0.090	0.000	0.000	0.000	0.000
64	A	89	GLU	-1	-0.890	-0.947	22.933	-0.133	-0.133	0.000	0.000	0.000	0.000
65	A	90	LYS	1	0.920	0.965	21.890	0.085	0.085	0.000	0.000	0.000	0.000
66	A	91	VAL	0	-0.065	-0.026	20.645	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.019	-0.004	18.580	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	93	GLU	-1	-0.863	-0.922	17.095	-0.319	-0.319	0.000	0.000	0.000	0.000
69	A	94	TYR	0	-0.049	-0.026	16.703	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	95	VAL	0	-0.007	-0.017	13.925	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	96	ASN	0	0.038	0.014	12.730	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	97	GLN	0	0.001	0.000	11.844	-0.119	-0.119	0.000	0.000	0.000	0.000
73	A	98	LEU	0	-0.074	-0.038	11.922	-0.041	-0.041	0.000	0.000	0.000	0.000
74	A	100	GLU	-1	-0.966	-0.991	7.081	-0.909	-0.909	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.890	0.950	7.982	0.262	0.262	0.000	0.000	0.000	0.000
76	A	102	ILE	0	-0.059	-0.006	4.357	0.167	0.225	-0.001	-0.005	-0.052	0.000
77	A	103	PRO	0	-0.023	-0.007	2.952	-3.457	-2.101	0.246	-0.696	-0.906	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)