FMO DATABASE

FMODB ID: 6YY4Z

Calculation Name: 4WVR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WVR

Chain ID: A

ChEMBL ID:

UniProt ID: Q0E9H6

Base Structure: X-ray

Registration Date: 2023-09-21

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-652817.774988
FMO2-HF: Nuclear repulsion	616167.23325
FMO2-HF: Total energy	-36650.541737
FMO2-MP2: Total energy	-36757.181737

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:5:SER)

Summations of interaction energy for fragment #1(A:5: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.
-7.89	-10.806	11.918	-4.805	-4.198	-0.043

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.001

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

Sort

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	7	PRO	0	0.055	0.038	3.887	1.078	2.465	-0.011	-0.627	-0.749	0.003
4	A	8	PRO	0	-0.026	-0.020	6.393	0.116	0.116	0.000	0.000	0.000	0.000
5	A	9	SER	0	-0.006	0.005	9.851	0.107	0.107	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.024	-0.023	12.746	0.007	0.007	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.011	0.014	16.216	0.022	0.022	0.000	0.000	0.000	0.000
8	A	12	PRO	0	-0.012	-0.006	19.212	0.020	0.020	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.005	-0.008	21.562	0.005	0.005	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.000	-0.023	25.365	0.005	0.005	0.000	0.000	0.000	0.000
11	A	15	PHE	0	0.012	0.006	28.960	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	16	GLY	0	0.007	0.013	31.913	0.011	0.011	0.000	0.000	0.000	0.000
13	A	17	ASP	-1	-0.952	-0.970	33.600	-0.227	-0.227	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.923	-0.954	35.749	-0.148	-0.148	0.000	0.000	0.000	0.000
15	A	19	PRO	0	-0.108	-0.074	37.848	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.048	0.047	36.277	0.005	0.005	0.000	0.000	0.000	0.000
17	A	21	ASN	0	-0.055	-0.043	39.563	0.012	0.012	0.000	0.000	0.000	0.000
18	A	22	THR	0	0.001	-0.009	41.649	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.016	-0.007	42.143	0.005	0.005	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.864	-0.912	39.683	-0.143	-0.143	0.000	0.000	0.000	0.000
21	A	25	ASN	0	0.008	0.019	35.965	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.048	0.028	34.193	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.003	-0.021	30.568	0.004	0.004	0.000	0.000	0.000	0.000
24	A	28	VAL	0	-0.032	0.010	26.021	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	29	GLN	0	0.015	-0.009	23.042	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	30	CYS	0	-0.046	0.030	19.050	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	31	MET	0	0.012	-0.001	18.214	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	32	VAL	0	0.015	0.007	11.692	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	33	GLN	0	-0.013	-0.007	13.511	0.026	0.026	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.928	0.963	8.970	1.435	1.435	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.082	0.038	6.656	0.253	0.253	0.000	0.000	0.000	0.000
32	A	36	ASP	-1	-0.849	-0.900	1.821	-13.689	-18.444	11.289	-3.742	-2.792	-0.046
33	A	37	VAL	0	0.029	0.028	5.460	0.553	0.553	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.010	-0.022	7.757	0.141	0.141	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.004	-0.007	8.967	-0.086	-0.086	0.000	0.000	0.000	0.000
36	A	40	THR	0	0.005	0.013	11.688	0.098	0.098	0.000	0.000	0.000	0.000
37	A	41	ILE	0	-0.027	-0.026	14.431	-0.107	-0.107	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.834	0.914	17.089	0.318	0.318	0.000	0.000	0.000	0.000
39	A	43	TRP	0	0.078	0.012	20.143	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.046	-0.015	22.995	0.024	0.024	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.046	0.025	25.336	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	46	ASN	0	-0.020	-0.027	28.800	0.008	0.008	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.023	-0.022	26.107	0.007	0.007	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.843	0.933	26.462	0.128	0.128	0.000	0.000	0.000	0.000
45	A	49	PRO	0	-0.023	-0.034	24.960	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	50	ILE	0	0.035	0.035	25.701	0.005	0.005	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.054	-0.019	25.801	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.002	-0.013	27.712	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.031	0.015	29.404	0.013	0.013	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.872	-0.929	29.830	-0.108	-0.108	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.818	-0.897	32.886	-0.117	-0.117	0.000	0.000	0.000	0.000
52	A	56	GLY	0	0.019	0.020	35.327	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.066	-0.025	29.808	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	58	THR	0	0.007	0.014	30.076	0.004	0.004	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.031	-0.031	24.670	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.026	0.014	24.799	0.016	0.016	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.814	0.912	15.341	0.482	0.482	0.000	0.000	0.000	0.000
58	A	62	LEU	0	0.019	0.015	21.540	0.009	0.009	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.043	0.011	17.893	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	64	PRO	0	0.024	-0.003	13.708	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.828	0.914	9.180	1.675	1.675	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.007	0.022	14.950	-0.043	-0.043	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.058	-0.024	18.652	0.041	0.041	0.000	0.000	0.000	0.000
64	A	68	VAL	0	0.015	0.009	21.209	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	69	LEU	0	0.010	0.018	24.884	0.012	0.012	0.000	0.000	0.000	0.000
66	A	70	ASN	0	-0.062	-0.057	27.294	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	ILE	0	0.030	0.021	31.053	0.005	0.005	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.023	0.010	34.327	0.002	0.002	0.000	0.000	0.000	0.000
69	A	73	ALA	0	0.003	0.001	37.006	0.004	0.004	0.000	0.000	0.000	0.000
70	A	74	VAL	0	-0.023	-0.001	36.209	0.000	0.000	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.883	-0.953	38.671	-0.093	-0.093	0.000	0.000	0.000	0.000
72	A	76	GLN	0	0.013	-0.004	39.129	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.894	-0.942	38.787	-0.099	-0.099	0.000	0.000	0.000	0.000
74	A	78	HIS	0	-0.019	-0.019	34.775	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.817	0.910	34.357	0.100	0.100	0.000	0.000	0.000	0.000
76	A	80	GLY	0	0.018	0.019	33.071	0.005	0.005	0.000	0.000	0.000	0.000
77	A	81	VAL	0	-0.029	-0.018	26.586	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	82	PHE	0	0.076	0.046	26.770	0.002	0.002	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.874	0.939	20.430	0.300	0.300	0.000	0.000	0.000	0.000
80	A	85	ILE	0	-0.008	-0.024	15.949	-0.038	-0.038	0.000	0.000	0.000	0.000
81	A	86	ALA	0	0.013	0.006	13.526	0.033	0.033	0.000	0.000	0.000	0.000
82	A	87	GLU	-1	-0.810	-0.911	11.186	-0.411	-0.411	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.041	-0.050	5.671	0.336	0.336	0.000	0.000	0.000	0.000
84	A	89	LYS	1	0.926	0.947	5.449	-0.049	-0.049	0.000	0.000	0.000	0.000
85	A	90	ALA	0	0.002	0.023	2.523	0.483	0.884	0.641	-0.423	-0.620	0.000
86	A	91	GLY	0	0.028	0.015	4.477	-0.130	-0.079	-0.001	-0.013	-0.037	0.000
87	A	92	SER	0	-0.030	-0.018	7.885	-0.043	-0.043	0.000	0.000	0.000	0.000
88	A	93	SER	0	0.003	0.009	11.166	-0.056	-0.056	0.000	0.000	0.000	0.000
89	A	94	PHE	0	0.038	-0.006	13.511	0.094	0.094	0.000	0.000	0.000	0.000
90	A	95	THR	0	-0.016	0.001	17.315	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	96	THR	0	-0.002	-0.013	20.291	0.025	0.025	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.001	0.017	24.033	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	98	GLU	-1	-0.849	-0.921	27.672	-0.173	-0.173	0.000	0.000	0.000	0.000
94	A	99	LEU	0	-0.002	0.021	30.910	0.002	0.002	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.898	0.936	33.563	0.187	0.187	0.000	0.000	0.000	0.000
96	A	101	VAL	0	0.003	0.012	36.850	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.021	-0.015	39.737	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)