FMO DATABASE

FMODB ID: J23G9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-459225.745147
FMO2-HF: Nuclear repulsion	425667.616573
FMO2-HF: Total energy	-33558.128574
FMO2-MP2: Total energy	-33648.188353

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.
-13.195	-10.924	9.126	-5.538	-5.858	-0.008

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 : 0.032 / q_NPA : 0.007

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	0.048	0.014	3.873	-2.330	-0.804	0.001	-0.704	-0.823	0.002
4	A	3	SER	0	-0.030	-0.012	3.057	-0.859	-0.038	0.060	-0.254	-0.627	-0.001
5	A	4	MET	0	-0.017	-0.014	3.207	0.112	0.906	0.045	-0.232	-0.608	0.000
6	A	5	GLU	-1	-0.873	-0.925	6.103	0.317	0.317	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.052	-0.009	7.682	0.115	0.115	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.838	0.876	7.441	1.115	1.115	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.005	0.019	9.946	0.132	0.132	0.000	0.000	0.000	0.000
10	A	9	ILE	0	-0.021	-0.013	12.126	0.078	0.078	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.004	-0.017	13.190	0.045	0.045	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.059	-0.056	13.355	0.050	0.050	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.030	-0.014	15.375	0.001	0.001	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.020	-0.010	16.088	0.046	0.046	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.027	0.030	18.127	0.024	0.024	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.862	-0.929	18.858	-0.121	-0.121	0.000	0.000	0.000	0.000
17	A	16	MET	0	0.029	0.021	22.450	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ILE	0	-0.009	-0.013	17.876	0.018	0.018	0.000	0.000	0.000	0.000
19	A	18	TRP	0	-0.012	-0.014	21.829	0.014	0.014	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.848	-0.936	23.301	-0.075	-0.075	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.041	-0.013	24.379	0.012	0.012	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.040	-0.006	22.467	0.010	0.010	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.024	-0.025	25.802	0.008	0.008	0.000	0.000	0.000	0.000
24	A	23	SER	0	-0.053	-0.039	28.684	0.004	0.004	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.001	0.018	29.213	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	VAL	0	-0.074	-0.033	30.004	0.007	0.007	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.939	0.963	31.411	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.017	0.013	35.162	0.002	0.002	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.754	-0.873	38.019	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.069	-0.022	35.114	0.005	0.005	0.000	0.000	0.000	0.000
31	A	30	VAL	0	0.019	0.008	33.555	0.002	0.002	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.021	-0.008	36.235	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.027	-0.019	39.693	0.001	0.001	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.067	-0.038	32.697	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.046	-0.014	38.012	0.001	0.001	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.017	-0.004	39.620	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.054	-0.026	42.038	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	37	CYS	0	-0.071	0.009	42.776	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	PHE	0	0.041	0.023	44.297	0.002	0.002	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.023	-0.010	40.777	0.000	0.000	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.906	-0.968	48.498	0.001	0.001	0.000	0.000	0.000	0.000
42	A	65	ALA	0	-0.011	0.003	49.610	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	66	PRO	0	0.017	-0.012	49.376	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	67	LEU	0	0.011	-0.007	46.841	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	69	THR	0	0.074	0.022	44.388	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	70	ALA	0	-0.022	-0.010	45.099	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	72	GLU	-1	-0.846	-0.947	40.571	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	73	MET	0	-0.049	-0.027	40.430	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	74	ALA	0	0.012	0.014	39.867	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	75	VAL	0	0.016	0.003	34.924	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	76	VAL	0	0.035	0.023	35.827	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	77	TRP	0	-0.028	-0.024	36.836	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	78	MET	0	-0.032	-0.010	33.400	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	79	GLN	0	-0.003	-0.014	32.056	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	80	ASN	0	-0.003	-0.006	32.330	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	81	GLN	0	-0.004	0.013	30.960	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	82	LEU	0	0.015	-0.001	27.564	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	83	LYS	1	0.920	0.964	28.140	0.039	0.039	0.000	0.000	0.000	0.000
59	A	84	GLN	0	-0.078	-0.022	29.878	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	85	GLU	-1	-0.803	-0.883	27.753	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	86	GLY	0	0.069	0.039	26.709	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	87	THR	0	-0.095	-0.063	26.322	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	88	LYS	1	0.836	0.908	23.478	0.109	0.109	0.000	0.000	0.000	0.000
64	A	89	GLU	-1	-0.883	-0.954	22.434	-0.167	-0.167	0.000	0.000	0.000	0.000
65	A	90	LYS	1	0.921	0.967	21.241	0.114	0.114	0.000	0.000	0.000	0.000
66	A	91	VAL	0	-0.044	-0.019	20.198	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.011	0.006	18.069	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	93	GLU	-1	-0.771	-0.871	16.516	-0.446	-0.446	0.000	0.000	0.000	0.000
69	A	94	TYR	0	-0.054	-0.019	16.018	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	95	VAL	0	0.014	-0.002	13.296	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	96	ASN	0	0.008	0.001	12.173	-0.165	-0.165	0.000	0.000	0.000	0.000
72	A	97	GLN	0	-0.036	-0.023	11.252	-0.136	-0.136	0.000	0.000	0.000	0.000
73	A	98	LEU	0	0.007	0.010	11.472	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	100	GLU	-1	-0.842	-0.893	6.523	-1.241	-1.241	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.774	0.879	8.017	0.528	0.528	0.000	0.000	0.000	0.000
76	A	102	ILE	0	-0.022	0.009	3.762	0.259	0.372	0.000	-0.021	-0.091	0.000
77	A	103	PRO	0	-0.025	-0.015	2.135	-10.476	-11.459	9.020	-4.327	-3.709	-0.009

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