FMO DATABASE

FMODB ID: 6YG3Z

Calculation Name: 3V4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V4D

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFQ6

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-999691.704992
FMO2-HF: Nuclear repulsion	952758.46127
FMO2-HF: Total energy	-46933.243722
FMO2-MP2: Total energy	-47071.444496

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-1.463	0.438	-0.008	-0.961	-0.932	0.005

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.003

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	4	SER	0	0.009	0.013	3.845	-1.984	-0.083	-0.008	-0.961	-0.932	0.005
4	A	5	VAL	0	-0.048	-0.034	6.395	0.144	0.144	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.003	0.013	9.145	0.000	0.000	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.003	-0.020	12.608	0.011	0.011	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.024	0.023	15.372	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.025	0.005	18.584	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	10	GLY	0	-0.001	-0.009	20.816	0.006	0.006	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.057	-0.035	18.351	0.001	0.001	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.011	-0.001	19.808	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.006	0.003	21.885	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	14	PRO	0	-0.023	-0.009	23.876	0.000	0.000	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.010	0.020	18.861	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.013	0.003	18.429	0.004	0.004	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.034	-0.009	16.872	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.021	-0.016	14.829	0.006	0.006	0.000	0.000	0.000	0.000
18	A	19	VAL	0	0.016	0.009	11.251	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.033	0.014	14.468	0.009	0.009	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.096	0.047	13.933	0.016	0.016	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.109	-0.042	8.493	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.074	0.037	8.307	0.037	0.037	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.018	-0.024	5.737	-0.124	-0.124	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.911	-0.943	6.127	0.533	0.533	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.022	0.009	7.945	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.022	0.008	10.377	-0.070	-0.070	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.002	-0.004	10.555	0.010	0.010	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.009	-0.008	10.243	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.027	-0.022	13.758	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.027	-0.045	16.272	0.007	0.007	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.014	0.013	17.859	0.001	0.001	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.039	-0.018	21.273	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.026	-0.009	23.460	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.020	0.014	26.748	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.040	-0.007	25.231	0.000	0.000	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.790	-0.904	28.262	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.011	0.001	24.761	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.026	-0.023	27.226	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.041	-0.013	24.264	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.050	-0.026	28.343	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.003	-0.004	31.270	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.003	0.004	31.137	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.040	-0.037	33.335	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.049	0.034	37.164	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.888	-0.927	38.178	0.004	0.004	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.858	-0.963	38.466	0.005	0.005	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.017	0.023	36.071	0.000	0.000	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.877	0.946	35.160	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.013	0.006	35.080	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.031	-0.020	32.466	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.006	-0.007	30.762	0.000	0.000	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.965	0.984	30.077	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	HIS	0	0.001	0.005	27.372	0.001	0.001	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.028	0.017	25.615	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.008	0.002	25.357	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.882	-0.933	25.507	0.007	0.007	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.060	-0.027	21.931	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.011	-0.011	20.607	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.941	0.960	20.569	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.953	0.997	21.269	0.015	0.015	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.058	-0.020	15.998	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.016	-0.004	16.771	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.941	-0.958	17.511	0.014	0.014	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.110	-0.067	15.117	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.065	-0.033	13.249	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.011	0.002	14.456	0.023	0.023	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.000	0.011	17.053	0.007	0.007	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.009	-0.017	18.729	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.007	-0.017	21.430	0.005	0.005	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.026	-0.010	23.738	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.810	-0.898	18.973	0.067	0.067	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.074	-0.034	19.923	0.007	0.007	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.002	0.000	18.885	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.036	-0.026	20.512	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.011	-0.001	21.182	0.001	0.001	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.016	-0.006	21.978	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.005	-0.003	24.171	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.014	0.003	23.511	0.001	0.001	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.022	-0.003	29.022	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.072	0.050	32.598	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.792	-0.892	35.332	0.008	0.008	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.015	0.000	34.165	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.813	0.894	39.272	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.041	0.016	37.568	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.022	0.009	34.106	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.010	-0.005	36.898	0.001	0.001	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.049	0.017	38.619	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.027	0.017	32.366	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	ASN	0	0.006	-0.010	33.928	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.902	-0.938	34.976	0.009	0.009	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.013	-0.005	32.645	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.037	0.015	27.252	0.001	0.001	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.019	-0.016	31.072	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.951	-0.969	33.086	0.011	0.011	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.053	-0.021	27.935	0.000	0.000	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.044	-0.016	24.551	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.024	0.007	29.605	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.014	-0.008	30.696	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.904	-0.956	28.872	0.029	0.029	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.813	0.916	28.586	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.026	0.020	24.360	0.001	0.001	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.014	0.017	24.836	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.853	0.907	25.378	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.009	0.001	23.769	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	CYS	0	-0.004	0.000	27.941	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.011	0.011	28.180	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.020	-0.011	31.436	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.056	-0.034	29.775	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.019	0.020	31.973	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.007	-0.001	28.312	0.001	0.001	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.006	-0.002	26.843	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.919	0.957	29.384	0.000	0.000	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.001	-0.013	32.234	0.001	0.001	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.850	-0.920	35.568	0.003	0.003	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.064	-0.011	31.198	0.000	0.000	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.023	-0.017	33.213	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.065	-0.043	29.367	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.874	-0.945	23.889	0.009	0.009	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.047	-0.028	23.540	0.002	0.002	0.000	0.000	0.000	0.000
120	A	121	ALA	0	0.046	0.044	19.441	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.002	-0.015	19.064	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.020	0.001	15.312	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.037	0.013	15.986	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	125	HIS	0	-0.056	-0.021	15.235	0.022	0.022	0.000	0.000	0.000	0.000
125	A	126	ILE	0	0.042	0.030	12.680	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	127	ALA	0	-0.026	-0.014	13.367	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)