FMO DATABASE

FMODB ID: YY212

Calculation Name: 1VQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VQ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0X1

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-555051.240583
FMO2-HF: Nuclear repulsion	520070.534586
FMO2-HF: Total energy	-34980.705997
FMO2-MP2: Total energy	-35084.903833

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:HIS)

Summations of interaction energy for fragment #1(A:-3:HIS)

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.
-3.709	-1.014	0.135	-1.043	-1.787	-0.001

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

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 : -0.016

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	A	-1	HIS	0	-0.023	0.004	2.831	-4.325	-1.742	0.136	-1.029	-1.690	-0.001
4	A	0	HIS	0	0.012	0.003	4.501	0.883	0.995	-0.001	-0.014	-0.097	0.000
5	A	1	LEU	0	0.011	0.013	7.980	-0.355	-0.355	0.000	0.000	0.000	0.000
6	A	2	PRO	0	-0.055	-0.019	10.065	0.162	0.162	0.000	0.000	0.000	0.000
7	A	3	LEU	0	0.033	0.025	13.709	0.019	0.019	0.000	0.000	0.000	0.000
8	A	4	PHE	0	-0.047	-0.023	15.354	-0.048	-0.048	0.000	0.000	0.000	0.000
9	A	5	LYS	1	0.930	0.966	19.638	-0.100	-0.100	0.000	0.000	0.000	0.000
10	A	6	PHE	0	0.029	0.010	20.987	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	7	ALA	0	-0.031	-0.016	25.551	0.025	0.025	0.000	0.000	0.000	0.000
12	A	8	ILE	0	-0.022	-0.014	26.473	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	9	ASP	-1	-0.900	-0.953	30.496	0.022	0.022	0.000	0.000	0.000	0.000
14	A	10	VAL	0	0.024	0.018	33.161	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	11	GLN	0	0.019	0.004	35.708	0.008	0.008	0.000	0.000	0.000	0.000
16	A	12	TYR	0	0.004	0.006	39.462	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	13	ARG	1	0.900	0.932	38.583	0.022	0.022	0.000	0.000	0.000	0.000
18	A	14	SER	0	0.013	-0.003	43.356	0.004	0.004	0.000	0.000	0.000	0.000
19	A	15	ASN	0	-0.026	-0.009	46.397	0.002	0.002	0.000	0.000	0.000	0.000
20	A	16	VAL	0	-0.036	-0.004	44.378	0.002	0.002	0.000	0.000	0.000	0.000
21	A	17	ARG	1	0.903	0.959	47.429	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	18	ASP	-1	-0.775	-0.895	45.886	0.027	0.027	0.000	0.000	0.000	0.000
23	A	19	PRO	0	0.026	-0.004	47.983	0.001	0.001	0.000	0.000	0.000	0.000
24	A	20	ARG	1	0.965	0.982	42.293	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	21	GLY	0	0.073	0.043	47.394	0.002	0.002	0.000	0.000	0.000	0.000
26	A	22	GLU	-1	-0.882	-0.958	47.991	0.014	0.014	0.000	0.000	0.000	0.000
27	A	23	THR	0	-0.082	-0.037	50.917	0.000	0.000	0.000	0.000	0.000	0.000
28	A	24	ILE	0	0.001	-0.006	46.258	0.001	0.001	0.000	0.000	0.000	0.000
29	A	25	GLU	-1	-0.857	-0.929	50.472	0.010	0.010	0.000	0.000	0.000	0.000
30	A	26	ARG	1	0.932	0.975	52.136	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	27	VAL	0	0.006	0.004	52.873	0.000	0.000	0.000	0.000	0.000	0.000
32	A	28	LEU	0	-0.004	-0.011	49.084	0.000	0.000	0.000	0.000	0.000	0.000
33	A	29	ARG	1	0.871	0.944	53.786	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	30	GLU	-1	-0.914	-0.979	56.805	0.018	0.018	0.000	0.000	0.000	0.000
35	A	31	GLU	-1	-0.928	-0.955	56.794	0.029	0.029	0.000	0.000	0.000	0.000
36	A	32	LYS	1	0.840	0.925	53.244	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	33	GLY	0	0.030	0.040	56.971	0.000	0.000	0.000	0.000	0.000	0.000
38	A	34	LEU	0	-0.027	-0.021	52.418	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	35	PRO	0	-0.006	0.002	55.429	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	36	VAL	0	-0.011	-0.010	50.522	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	37	LYS	1	0.904	0.938	51.829	0.000	0.000	0.000	0.000	0.000	0.000
42	A	38	LYS	1	0.928	0.965	49.690	0.011	0.011	0.000	0.000	0.000	0.000
43	A	39	LEU	0	0.014	0.023	46.445	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	40	ARG	1	0.892	0.956	41.930	0.004	0.004	0.000	0.000	0.000	0.000
45	A	41	LEU	0	-0.011	0.003	41.706	0.002	0.002	0.000	0.000	0.000	0.000
46	A	42	GLY	0	0.054	0.018	39.401	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	43	LYS	1	0.799	0.905	34.399	-0.043	-0.043	0.000	0.000	0.000	0.000
48	A	44	SER	0	0.044	0.018	32.709	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	45	ILE	0	-0.058	-0.014	27.637	0.013	0.013	0.000	0.000	0.000	0.000
50	A	46	HIS	0	0.022	0.008	27.332	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	47	LEU	0	-0.020	-0.014	22.832	0.020	0.020	0.000	0.000	0.000	0.000
52	A	48	GLU	-1	-0.883	-0.947	19.112	0.204	0.204	0.000	0.000	0.000	0.000
53	A	49	VAL	0	-0.033	-0.018	17.171	0.029	0.029	0.000	0.000	0.000	0.000
54	A	50	GLU	-1	-0.902	-0.947	11.437	0.677	0.677	0.000	0.000	0.000	0.000
55	A	51	ALA	0	-0.040	-0.034	12.923	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	52	GLU	-1	-0.883	-0.946	9.192	-1.352	-1.352	0.000	0.000	0.000	0.000
57	A	53	ASN	0	0.001	0.000	12.242	0.039	0.039	0.000	0.000	0.000	0.000
58	A	54	LYS	1	1.024	1.008	15.813	0.277	0.277	0.000	0.000	0.000	0.000
59	A	55	GLU	-1	-0.866	-0.940	19.259	-0.317	-0.317	0.000	0.000	0.000	0.000
60	A	56	LYS	1	0.970	0.984	12.382	0.541	0.541	0.000	0.000	0.000	0.000
61	A	57	ALA	0	0.010	-0.010	17.904	0.049	0.049	0.000	0.000	0.000	0.000
62	A	58	TYR	0	0.007	0.008	18.926	0.047	0.047	0.000	0.000	0.000	0.000
63	A	59	GLU	-1	-0.867	-0.933	20.672	-0.181	-0.181	0.000	0.000	0.000	0.000
64	A	60	ILE	0	-0.032	-0.011	16.231	0.020	0.020	0.000	0.000	0.000	0.000
65	A	61	VAL	0	0.018	0.021	20.847	0.033	0.033	0.000	0.000	0.000	0.000
66	A	62	LYS	1	0.885	0.937	23.708	0.174	0.174	0.000	0.000	0.000	0.000
67	A	63	LYS	1	0.843	0.934	22.506	0.067	0.067	0.000	0.000	0.000	0.000
68	A	64	ALA	0	0.028	0.003	23.423	0.017	0.017	0.000	0.000	0.000	0.000
69	A	65	CYS	0	-0.064	-0.036	25.161	0.015	0.015	0.000	0.000	0.000	0.000
70	A	66	GLU	-1	-0.951	-0.975	27.897	-0.073	-0.073	0.000	0.000	0.000	0.000
71	A	67	GLU	-1	-0.903	-0.945	25.284	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	68	LEU	0	-0.072	-0.033	27.431	0.017	0.017	0.000	0.000	0.000	0.000
73	A	69	LEU	0	-0.078	-0.037	26.480	0.004	0.004	0.000	0.000	0.000	0.000
74	A	70	VAL	0	-0.025	-0.005	30.510	0.000	0.000	0.000	0.000	0.000	0.000
75	A	71	ASN	0	0.034	0.019	33.340	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	72	PRO	0	0.076	0.038	34.988	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	73	VAL	0	-0.003	0.008	36.989	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	74	VAL	0	-0.041	-0.032	40.260	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	75	GLU	-1	-0.871	-0.930	36.702	0.031	0.031	0.000	0.000	0.000	0.000
80	A	76	GLU	-1	-0.942	-0.970	37.027	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	77	TYR	0	-0.003	-0.034	29.554	0.008	0.008	0.000	0.000	0.000	0.000
82	A	78	GLU	-1	-0.920	-0.931	33.486	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	79	VAL	0	-0.013	-0.012	26.797	0.014	0.014	0.000	0.000	0.000	0.000
84	A	80	ARG	1	0.940	0.974	29.589	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	81	GLU	-1	-0.920	-0.951	25.002	-0.103	-0.103	0.000	0.000	0.000	0.000
86	A	82	LEU	0	-0.061	-0.037	25.785	0.004	0.004	0.000	0.000	0.000	0.000

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