FMO DATABASE

FMODB ID: 6NGQZ

Calculation Name: 4R24-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R24

Chain ID: B

ChEMBL ID:

UniProt ID: G2RUZ1

Base Structure: X-ray

Registration Date: 2023-06-22

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-608795.249224
FMO2-HF: Nuclear repulsion	573537.471016
FMO2-HF: Total energy	-35257.778207
FMO2-MP2: Total energy	-35360.307694

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(B:6:ALA)

Summations of interaction energy for fragment #1(B:6: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.
-10.558	-5.627	0.949	-2.244	-3.636	0.013

Interaction energy analysis for fragmet #1(B:6: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 : 0.016

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	B	8	TYR	0	-0.002	-0.018	3.138	-2.808	0.128	0.193	-1.433	-1.695	0.008
4	B	9	ARG	1	0.849	0.898	2.664	-4.809	-3.168	0.755	-0.734	-1.663	0.005
5	B	10	ASP	-1	-0.858	-0.931	4.480	-2.379	-2.025	0.001	-0.077	-0.278	0.000
6	B	11	LYS	1	0.934	0.976	6.311	-0.536	-0.536	0.000	0.000	0.000	0.000
7	B	12	LYS	1	0.864	0.932	8.736	-0.016	-0.016	0.000	0.000	0.000	0.000
8	B	13	VAL	0	-0.013	-0.015	10.988	-0.058	-0.058	0.000	0.000	0.000	0.000
9	B	14	MET	0	-0.015	0.018	10.908	-0.078	-0.078	0.000	0.000	0.000	0.000
10	B	15	SER	0	-0.012	-0.006	15.324	-0.039	-0.039	0.000	0.000	0.000	0.000
11	B	16	ILE	0	0.056	0.009	18.587	0.016	0.016	0.000	0.000	0.000	0.000
12	B	17	GLY	0	-0.023	0.000	20.576	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	18	ILE	0	0.084	0.042	15.980	-0.008	-0.008	0.000	0.000	0.000	0.000
14	B	19	VAL	0	0.022	0.013	15.646	0.010	0.010	0.000	0.000	0.000	0.000
15	B	20	LYS	1	0.907	0.962	17.801	-0.173	-0.173	0.000	0.000	0.000	0.000
16	B	21	GLU	-1	-0.983	-0.977	19.902	0.223	0.223	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.027	-0.022	13.725	0.006	0.006	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.025	-0.017	16.592	-0.021	-0.021	0.000	0.000	0.000	0.000
19	B	24	GLY	0	0.031	0.031	18.731	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	25	LEU	0	-0.040	-0.001	19.640	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	26	SER	0	0.016	-0.012	23.199	0.008	0.008	0.000	0.000	0.000	0.000
22	B	27	GLU	-1	-0.834	-0.957	24.206	0.134	0.134	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.910	0.958	25.187	-0.067	-0.067	0.000	0.000	0.000	0.000
24	B	29	GLN	0	0.082	0.034	24.524	0.002	0.002	0.000	0.000	0.000	0.000
25	B	30	ILE	0	0.062	0.054	19.645	-0.009	-0.009	0.000	0.000	0.000	0.000
26	B	31	ARG	1	0.870	0.932	21.761	-0.117	-0.117	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.038	-0.014	24.033	-0.011	-0.011	0.000	0.000	0.000	0.000
28	B	33	TYR	0	0.107	0.034	20.731	-0.016	-0.016	0.000	0.000	0.000	0.000
29	B	34	GLU	-1	-0.796	-0.876	20.644	0.091	0.091	0.000	0.000	0.000	0.000
30	B	35	LYS	1	0.897	0.946	21.798	-0.054	-0.054	0.000	0.000	0.000	0.000
31	B	36	ARG	1	0.855	0.944	24.603	-0.030	-0.030	0.000	0.000	0.000	0.000
32	B	37	SER	0	-0.042	-0.021	22.166	-0.011	-0.011	0.000	0.000	0.000	0.000
33	B	38	LEU	0	0.001	0.001	19.824	-0.011	-0.011	0.000	0.000	0.000	0.000
34	B	39	LEU	0	-0.003	0.011	15.819	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	40	PHE	0	-0.009	-0.015	15.824	-0.004	-0.004	0.000	0.000	0.000	0.000
36	B	41	PRO	0	-0.031	0.013	15.625	0.004	0.004	0.000	0.000	0.000	0.000
37	B	42	ASP	-1	-0.808	-0.890	15.191	0.085	0.085	0.000	0.000	0.000	0.000
38	B	43	ARG	1	0.851	0.899	17.559	-0.078	-0.078	0.000	0.000	0.000	0.000
39	B	44	THR	0	0.002	0.000	20.396	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	45	ASN	0	0.061	0.012	21.928	-0.010	-0.010	0.000	0.000	0.000	0.000
41	B	46	THR	0	-0.012	0.004	25.078	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	47	GLY	0	0.027	0.024	25.466	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	48	ILE	0	-0.050	-0.021	21.759	0.002	0.002	0.000	0.000	0.000	0.000
44	B	49	ARG	1	0.869	0.920	19.649	-0.109	-0.109	0.000	0.000	0.000	0.000
45	B	50	LYS	1	0.897	0.943	15.826	-0.263	-0.263	0.000	0.000	0.000	0.000
46	B	51	TYR	0	0.048	0.007	13.969	-0.050	-0.050	0.000	0.000	0.000	0.000
47	B	52	SER	0	0.021	0.016	8.383	0.031	0.031	0.000	0.000	0.000	0.000
48	B	53	PHE	0	0.032	0.004	7.116	-0.089	-0.089	0.000	0.000	0.000	0.000
49	B	54	SER	0	0.017	0.014	6.599	-0.109	-0.109	0.000	0.000	0.000	0.000
50	B	55	ASP	-1	-0.829	-0.904	8.371	0.107	0.107	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.011	-0.014	11.667	-0.069	-0.069	0.000	0.000	0.000	0.000
52	B	57	GLU	-1	-0.793	-0.883	8.438	0.421	0.421	0.000	0.000	0.000	0.000
53	B	58	ARG	1	0.796	0.885	12.119	-0.035	-0.035	0.000	0.000	0.000	0.000
54	B	59	LEU	0	-0.068	-0.057	13.802	-0.031	-0.031	0.000	0.000	0.000	0.000
55	B	60	MET	0	-0.007	0.007	13.531	-0.012	-0.012	0.000	0.000	0.000	0.000
56	B	61	ASP	-1	-0.851	-0.905	14.351	0.027	0.027	0.000	0.000	0.000	0.000
57	B	62	ILE	0	-0.124	-0.067	17.507	-0.017	-0.017	0.000	0.000	0.000	0.000
58	B	63	ALA	0	-0.025	-0.028	19.845	-0.010	-0.010	0.000	0.000	0.000	0.000
59	B	64	ASP	-1	-0.812	-0.895	19.625	0.067	0.067	0.000	0.000	0.000	0.000
60	B	65	ARG	1	0.760	0.849	21.111	-0.007	-0.007	0.000	0.000	0.000	0.000
61	B	66	ILE	0	-0.071	-0.049	23.575	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	67	GLU	-1	-0.920	-0.942	24.547	0.057	0.057	0.000	0.000	0.000	0.000
63	B	68	GLU	-1	-0.977	-0.953	24.781	0.003	0.003	0.000	0.000	0.000	0.000
64	B	69	GLY	0	-0.008	0.001	28.072	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	70	VAL	0	-0.014	0.008	25.541	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	71	GLN	0	0.022	0.015	27.366	0.005	0.005	0.000	0.000	0.000	0.000
67	B	72	THR	0	0.078	0.011	25.228	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	73	SER	0	-0.028	-0.035	25.136	-0.003	-0.003	0.000	0.000	0.000	0.000
69	B	74	GLU	-1	-0.904	-0.942	26.423	-0.017	-0.017	0.000	0.000	0.000	0.000
70	B	75	ILE	0	0.040	0.025	21.041	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	76	ARG	1	0.942	0.973	21.582	0.022	0.022	0.000	0.000	0.000	0.000
72	B	77	THR	0	-0.053	-0.024	21.976	-0.011	-0.011	0.000	0.000	0.000	0.000
73	B	78	GLU	-1	-0.871	-0.936	20.924	-0.032	-0.032	0.000	0.000	0.000	0.000
74	B	79	LEU	0	-0.004	-0.023	16.382	-0.017	-0.017	0.000	0.000	0.000	0.000
75	B	80	ALA	0	-0.016	0.007	17.476	-0.019	-0.019	0.000	0.000	0.000	0.000
76	B	81	LYS	1	0.993	0.998	19.056	0.054	0.054	0.000	0.000	0.000	0.000
77	B	82	LYS	1	0.969	0.992	15.027	0.036	0.036	0.000	0.000	0.000	0.000
78	B	83	ASP	-1	-0.800	-0.884	14.136	-0.140	-0.140	0.000	0.000	0.000	0.000
79	B	84	GLU	-1	-1.013	-1.012	14.975	-0.140	-0.140	0.000	0.000	0.000	0.000
80	B	85	ALA	0	0.015	-0.002	16.108	-0.018	-0.018	0.000	0.000	0.000	0.000
81	B	86	ARG	1	0.837	0.918	6.290	0.738	0.738	0.000	0.000	0.000	0.000
82	B	87	LYS	1	0.930	0.955	12.259	0.117	0.117	0.000	0.000	0.000	0.000
83	B	88	MET	0	-0.031	-0.003	13.907	0.008	0.008	0.000	0.000	0.000	0.000
84	B	89	LYS	1	0.889	0.948	12.108	0.280	0.280	0.000	0.000	0.000	0.000
85	B	90	GLU	-1	-0.884	-0.919	10.304	-0.485	-0.485	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:ALA)