FMO DATABASE

FMODB ID: VR3M1

Calculation Name: 4AJ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AJ5

Chain ID: A

ChEMBL ID:

UniProt ID: Q96BD8

Base Structure: X-ray

Registration Date: 2023-06-20

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-366438.005951
FMO2-HF: Nuclear repulsion	334335.39249
FMO2-HF: Total energy	-32102.613461
FMO2-MP2: Total energy	-32195.11135

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-5.681	-0.664	1.383	-2.647	-3.75	0.014

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.018

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	5	ASP	-1	-0.837	-0.921	3.808	-1.952	1.012	-0.020	-1.669	-1.275	0.008
4	A	6	LEU	0	-0.026	-0.008	6.613	0.671	0.671	0.000	0.000	0.000	0.000
5	A	7	GLU	-1	-0.915	-0.973	2.654	0.869	1.473	0.266	-0.227	-0.642	-0.002
6	A	8	GLN	0	-0.025	-0.021	2.581	-2.207	-0.822	1.138	-0.742	-1.780	0.008
7	A	9	LEU	0	0.004	0.020	4.889	-0.800	-0.736	-0.001	-0.009	-0.053	0.000
8	A	10	CYS	0	-0.002	-0.004	7.625	-0.208	-0.208	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.001	-0.002	6.182	-0.366	-0.366	0.000	0.000	0.000	0.000
10	A	12	HIS	0	0.008	0.015	8.449	-0.398	-0.398	0.000	0.000	0.000	0.000
11	A	13	VAL	0	0.008	-0.005	10.457	-0.205	-0.205	0.000	0.000	0.000	0.000
12	A	14	ASN	0	-0.005	-0.010	10.940	-0.233	-0.233	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.915	-0.929	12.109	0.664	0.664	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.953	0.968	13.765	-0.462	-0.462	0.000	0.000	0.000	0.000
15	A	17	ILE	0	0.000	-0.005	16.160	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	18	GLY	0	-0.002	-0.017	16.618	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	19	ASN	0	-0.031	-0.044	17.026	-0.077	-0.077	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.047	0.053	19.347	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.978	0.997	19.600	-0.399	-0.399	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.935	0.979	17.690	-0.474	-0.474	0.000	0.000	0.000	0.000
21	A	23	THR	0	-0.009	-0.021	23.514	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.049	-0.013	25.338	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	25	SER	0	0.006	-0.007	26.667	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.008	0.007	27.447	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.902	0.942	29.560	-0.159	-0.159	0.000	0.000	0.000	0.000
26	A	28	ASN	0	0.009	0.010	31.261	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	29	CYS	0	0.015	0.003	31.361	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.023	0.033	33.916	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.079	-0.042	35.688	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.832	-0.931	36.535	0.107	0.107	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.006	0.004	38.369	0.002	0.002	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.027	-0.027	39.327	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	LEU	0	0.020	0.002	33.855	0.002	0.002	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.967	0.995	38.002	-0.100	-0.100	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.014	-0.001	39.507	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.003	0.003	38.516	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.011	0.008	34.708	0.003	0.003	0.000	0.000	0.000	0.000
38	A	40	ASN	0	-0.012	-0.022	38.764	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.943	0.980	42.025	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.012	0.021	37.257	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	GLY	0	-0.014	-0.010	40.678	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.893	-0.961	41.344	0.084	0.084	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.986	-1.014	43.709	0.087	0.087	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.007	-0.016	39.385	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.015	-0.005	43.114	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	48	VAL	0	0.014	0.020	46.003	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	49	ILE	0	-0.044	-0.007	43.103	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	50	ASN	0	0.006	0.003	44.809	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.834	-0.918	46.473	0.066	0.066	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.040	-0.028	49.029	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.001	0.017	44.235	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	54	ASN	0	0.046	0.022	48.905	0.000	0.000	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.786	0.888	51.464	-0.067	-0.067	0.000	0.000	0.000	0.000
54	A	56	LEU	0	-0.002	0.006	49.168	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.945	-0.963	49.614	0.069	0.069	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.021	-0.024	52.505	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.956	-0.984	55.844	0.051	0.051	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.010	0.002	52.081	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	61	GLN	0	0.009	-0.007	55.394	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.042	-0.023	57.084	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.019	-0.014	56.143	0.001	0.001	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.908	-0.930	56.924	0.050	0.050	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.007	0.001	59.063	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.025	-0.018	62.268	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.004	-0.009	60.693	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.061	-0.025	60.606	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.047	0.024	64.227	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.072	-0.031	65.237	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.816	0.897	63.837	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.912	-0.967	66.783	0.034	0.034	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.029	-0.017	70.016	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	74	CYS	0	-0.069	-0.037	68.486	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.815	-0.885	68.757	0.034	0.034	0.000	0.000	0.000	0.000
74	A	76	SER	0	-0.022	-0.021	71.821	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.039	-0.021	74.475	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.911	-0.935	71.677	0.031	0.031	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.983	-0.973	74.866	0.027	0.027	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.987	-0.979	76.518	0.025	0.025	0.000	0.000	0.000	0.000
79	A	81	TYR	0	-0.189	-0.110	75.759	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)