FMO DATABASE

FMODB ID: Q897Y

Calculation Name: 3DLV-B-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLV

Chain ID: B

ChEMBL ID:

UniProt ID: Q8TZT9

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	106
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-807380.097007
FMO2-HF: Nuclear repulsion	766140.874582
FMO2-HF: Total energy	-41239.222425
FMO2-MP2: Total energy	-41362.610401

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:1:ACE )

Summations of interaction energy for fragment #1(B:1:ACE )

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.
-0.596	-2.926	13.582	-6.045	-5.208	-0.039

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.023

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	B	3	ARG	1	0.919	0.963	3.756	1.881	2.772	-0.009	-0.456	-0.426	0.000
4	B	4	PHE	0	-0.031	-0.018	4.373	0.234	0.294	0.000	-0.016	-0.044	0.000
5	B	5	VAL	0	0.033	0.015	8.973	0.035	0.035	0.000	0.000	0.000	0.000
6	B	6	VAL	0	-0.039	-0.027	10.882	0.062	0.062	0.000	0.000	0.000	0.000
7	B	7	TRP	0	0.090	0.036	13.278	-0.010	-0.010	0.000	0.000	0.000	0.000
8	B	8	PRO	0	0.055	0.020	16.802	0.028	0.028	0.000	0.000	0.000	0.000
9	B	9	SER	0	0.060	0.026	18.787	0.020	0.020	0.000	0.000	0.000	0.000
10	B	10	GLU	-1	-0.797	-0.885	13.898	0.000	0.000	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.041	-0.034	14.734	0.041	0.041	0.000	0.000	0.000	0.000
12	B	12	ASP	-1	-0.679	-0.846	17.563	0.044	0.044	0.000	0.000	0.000	0.000
13	B	13	SER	0	-0.086	-0.063	21.344	0.002	0.002	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.892	0.952	23.404	-0.024	-0.024	0.000	0.000	0.000	0.000
15	B	15	LEU	0	0.007	0.042	22.375	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	16	SER	0	0.009	0.008	24.177	0.013	0.013	0.000	0.000	0.000	0.000
17	B	17	ARG	1	0.916	0.936	16.725	-0.151	-0.151	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.950	0.983	21.683	-0.030	-0.030	0.000	0.000	0.000	0.000
19	B	19	TYR	0	-0.053	-0.057	24.059	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.072	0.042	20.164	-0.008	-0.008	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.787	0.908	18.443	-0.093	-0.093	0.000	0.000	0.000	0.000
22	B	22	ILE	0	-0.016	-0.016	12.800	0.015	0.015	0.000	0.000	0.000	0.000
23	B	23	VAL	0	-0.016	-0.016	13.916	0.041	0.041	0.000	0.000	0.000	0.000
24	B	24	PRO	0	-0.031	-0.022	15.600	-0.029	-0.029	0.000	0.000	0.000	0.000
25	B	25	ARG	1	1.026	0.995	18.768	-0.110	-0.110	0.000	0.000	0.000	0.000
26	B	26	SER	0	0.024	0.020	21.998	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	27	ILE	0	-0.025	-0.004	16.170	0.002	0.002	0.000	0.000	0.000	0.000
28	B	28	ALA	0	-0.023	-0.002	19.000	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	29	VAL	0	0.045	0.018	19.700	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	30	GLU	-1	-0.918	-0.944	22.049	0.037	0.037	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.028	0.002	24.685	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	32	PRO	0	-0.053	0.002	19.637	-0.004	-0.004	0.000	0.000	0.000	0.000
33	B	33	ARG	1	0.963	0.978	21.622	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	34	VAL	0	0.085	0.033	19.178	0.004	0.004	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.787	-0.896	19.147	-0.021	-0.021	0.000	0.000	0.000	0.000
36	B	36	GLU	-1	-0.786	-0.857	20.310	0.031	0.031	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.013	-0.006	14.494	0.014	0.014	0.000	0.000	0.000	0.000
38	B	38	VAL	0	0.000	0.009	15.164	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.937	0.973	15.984	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	40	ALA	0	-0.020	-0.012	15.093	0.010	0.010	0.000	0.000	0.000	0.000
41	B	41	ALA	0	-0.031	-0.024	11.654	0.024	0.024	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.871	-0.941	12.214	-0.088	-0.088	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.911	-0.968	14.760	0.079	0.079	0.000	0.000	0.000	0.000
44	B	44	LEU	0	-0.110	-0.060	10.581	0.033	0.033	0.000	0.000	0.000	0.000
45	B	45	LYS	1	0.869	0.948	10.601	0.025	0.025	0.000	0.000	0.000	0.000
46	B	46	PHE	0	-0.031	-0.015	7.301	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	47	LYS	1	0.981	0.999	8.807	0.552	0.552	0.000	0.000	0.000	0.000
48	B	48	VAL	0	0.036	-0.002	10.502	-0.086	-0.086	0.000	0.000	0.000	0.000
49	B	49	ILE	0	-0.112	-0.044	10.890	0.009	0.009	0.000	0.000	0.000	0.000
50	B	50	ARG	1	0.895	0.927	14.076	0.221	0.221	0.000	0.000	0.000	0.000
51	B	51	VAL	0	0.000	0.005	16.039	-0.010	-0.010	0.000	0.000	0.000	0.000
52	B	52	GLU	-1	-0.848	-0.908	18.608	-0.133	-0.133	0.000	0.000	0.000	0.000
53	B	53	GLU	-1	-0.950	-1.001	21.356	-0.042	-0.042	0.000	0.000	0.000	0.000
54	B	54	ASP	-1	-0.927	-0.947	24.006	-0.061	-0.061	0.000	0.000	0.000	0.000
55	B	55	LYS	1	0.896	0.945	27.259	0.049	0.049	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.074	0.018	30.098	0.000	0.000	0.000	0.000	0.000	0.000
57	B	57	ASN	0	0.014	0.007	33.101	0.005	0.005	0.000	0.000	0.000	0.000
58	B	58	PRO	0	-0.078	-0.015	34.148	0.002	0.002	0.000	0.000	0.000	0.000
59	B	59	ARG	1	0.921	0.893	35.291	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	LEU	0	-0.051	-0.027	37.397	0.000	0.000	0.000	0.000	0.000	0.000
61	B	61	SER	0	-0.042	-0.026	38.328	0.002	0.002	0.000	0.000	0.000	0.000
62	B	62	GLY	0	-0.003	-0.016	37.148	0.000	0.000	0.000	0.000	0.000	0.000
63	B	63	ILE	0	-0.014	-0.007	34.356	0.001	0.001	0.000	0.000	0.000	0.000
64	B	64	ASP	-1	-0.815	-0.897	33.059	-0.024	-0.024	0.000	0.000	0.000	0.000
65	B	65	GLU	-1	-0.762	-0.825	33.344	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	66	GLU	-1	-0.901	-0.933	28.988	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	67	LEU	0	-0.034	-0.007	28.075	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	68	ARG	1	0.889	0.970	29.899	0.014	0.014	0.000	0.000	0.000	0.000
69	B	69	THR	0	-0.050	-0.034	25.490	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	70	PHE	0	0.033	0.024	21.570	0.000	0.000	0.000	0.000	0.000	0.000
71	B	71	GLY	0	0.033	0.002	21.613	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	72	MET	0	-0.078	-0.031	17.112	0.009	0.009	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.031	0.022	13.356	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.032	-0.010	11.766	-0.023	-0.023	0.000	0.000	0.000	0.000
75	B	75	LEU	0	0.007	0.006	8.829	0.039	0.039	0.000	0.000	0.000	0.000
76	B	76	GLU	-1	-0.844	-0.939	6.533	-1.275	-1.275	0.000	0.000	0.000	0.000
77	B	77	SER	0	-0.017	-0.002	4.278	0.440	0.654	0.000	-0.082	-0.132	0.000
78	B	78	PRO	0	0.083	0.037	2.499	-3.773	-3.103	1.954	-1.583	-1.040	-0.018
79	B	79	TYR	0	-0.028	-0.013	2.556	3.123	2.385	4.675	-1.906	-2.032	-0.010
80	B	80	GLY	0	0.063	0.028	2.477	1.784	-1.372	6.944	-2.330	-1.458	-0.011
81	B	81	LYS	1	0.873	0.940	3.318	-0.401	-0.672	0.018	0.328	-0.076	0.000
82	B	82	SER	0	-0.001	-0.005	6.362	-0.069	-0.069	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.986	0.979	6.670	-1.513	-1.513	0.000	0.000	0.000	0.000
84	B	84	SER	0	0.044	0.020	5.185	-0.260	-0.260	0.000	0.000	0.000	0.000
85	B	85	LEU	0	0.027	0.015	7.873	-0.144	-0.144	0.000	0.000	0.000	0.000
86	B	86	LYS	1	0.896	0.954	11.160	-0.507	-0.507	0.000	0.000	0.000	0.000
87	B	87	LEU	0	0.024	0.019	8.569	-0.040	-0.040	0.000	0.000	0.000	0.000
88	B	88	ILE	0	0.042	0.025	10.444	-0.056	-0.056	0.000	0.000	0.000	0.000
89	B	89	ALA	0	-0.007	-0.007	13.465	-0.032	-0.032	0.000	0.000	0.000	0.000
90	B	90	GLN	0	-0.054	-0.039	15.175	0.000	0.000	0.000	0.000	0.000	0.000
91	B	91	LYS	1	0.897	0.972	15.424	-0.154	-0.154	0.000	0.000	0.000	0.000
92	B	92	ILE	0	0.043	0.027	17.384	-0.019	-0.019	0.000	0.000	0.000	0.000
93	B	93	ARG	1	0.850	0.928	19.600	-0.137	-0.137	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.885	-0.948	19.830	0.104	0.104	0.000	0.000	0.000	0.000
95	B	95	PHE	0	-0.028	-0.014	18.521	-0.008	-0.008	0.000	0.000	0.000	0.000
96	B	96	ARG	1	0.745	0.818	23.017	-0.049	-0.049	0.000	0.000	0.000	0.000
97	B	97	ARG	1	0.973	0.986	24.991	-0.092	-0.092	0.000	0.000	0.000	0.000
98	B	98	ARG	1	0.902	0.968	22.570	-0.065	-0.065	0.000	0.000	0.000	0.000
99	B	99	SER	0	-0.051	-0.024	27.050	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	100	ALA	0	-0.005	0.005	29.364	-0.003	-0.003	0.000	0.000	0.000	0.000
101	B	101	GLY	0	0.035	0.026	30.877	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	102	THR	0	-0.025	-0.021	32.347	0.001	0.001	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.064	-0.021	31.805	0.003	0.003	0.000	0.000	0.000	0.000
104	B	104	VAL	0	0.005	-0.021	32.758	0.002	0.002	0.000	0.000	0.000	0.000
105	B	105	PRO	0	-0.006	0.002	34.588	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	106	NME	0	0.018	0.028	36.805	-0.001	-0.001	0.000	0.000	0.000	0.000

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