FMO DATABASE

FMODB ID: 1NL2Z

Calculation Name: 1VJK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3C7

Base Structure: X-ray

Registration Date: 2023-09-23

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-632749.493555
FMO2-HF: Nuclear repulsion	598306.680123
FMO2-HF: Total energy	-34442.813432
FMO2-MP2: Total energy	-34546.19045

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:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
-6.835	-0.64	2.798	-3.888	-5.104	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.010

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	3	LYS	1	0.929	0.978	3.829	3.303	4.975	-0.013	-0.750	-0.908	0.004
4	A	4	VAL	0	0.025	0.026	5.615	-0.509	-0.467	-0.001	-0.003	-0.039	0.000
5	A	5	LYS	1	0.902	0.956	9.037	0.345	0.345	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.028	0.011	11.731	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.892	0.949	14.215	0.108	0.108	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.043	0.000	14.993	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.023	-0.019	20.278	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.023	-0.001	23.959	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.860	0.904	26.289	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.019	0.010	22.007	0.006	0.006	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.916	0.966	22.031	0.054	0.054	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.036	-0.021	22.969	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.086	-0.028	22.920	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.007	0.009	18.182	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.049	-0.016	19.320	0.005	0.005	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.020	-0.003	16.561	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.898	-0.962	20.006	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.960	-1.003	16.241	-0.188	-0.188	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.801	-0.860	11.934	0.147	0.147	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.925	-0.957	8.702	-0.550	-0.550	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.051	-0.029	7.512	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.965	-0.981	2.208	-5.459	-4.004	0.778	-0.959	-1.273	-0.001
25	A	25	LEU	0	-0.019	-0.006	3.566	-0.848	-0.288	0.030	-0.182	-0.408	0.001
26	A	26	PRO	0	0.026	0.004	2.515	1.194	2.808	1.944	-1.713	-1.845	-0.016
27	A	27	GLU	-1	-0.921	-0.972	3.130	-2.302	-1.571	0.060	-0.251	-0.539	-0.002
28	A	28	GLY	0	-0.010	-0.003	4.208	0.438	0.559	0.000	-0.030	-0.092	0.000
29	A	29	ALA	0	-0.051	0.000	6.289	0.042	0.042	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.920	0.950	7.934	-0.452	-0.452	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.005	0.003	11.453	0.115	0.115	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.848	0.879	13.752	-0.162	-0.162	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.829	-0.904	10.192	0.612	0.612	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.003	0.002	10.133	0.090	0.090	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.022	-0.010	11.866	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.881	-0.952	14.148	0.310	0.310	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.846	-0.913	9.400	0.813	0.813	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.028	-0.014	12.597	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.907	0.963	14.877	-0.272	-0.272	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.892	0.958	12.568	-0.618	-0.618	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.788	0.890	8.059	-0.445	-0.445	0.000	0.000	0.000	0.000
42	A	42	HIS	1	0.801	0.885	15.276	-0.202	-0.202	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.909	-0.964	18.666	0.156	0.156	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.972	0.991	21.326	-0.082	-0.082	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.011	-0.010	19.883	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.859	0.938	19.626	-0.243	-0.243	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.940	-0.977	22.838	0.145	0.145	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.813	-0.868	23.650	0.063	0.063	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.009	-0.017	24.114	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.033	-0.028	18.793	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.087	0.041	23.291	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.908	-0.940	21.607	0.079	0.079	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.018	-0.018	22.234	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.135	-0.069	23.903	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.849	-0.937	27.060	0.046	0.046	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.919	-0.962	28.859	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.948	-0.973	31.413	0.029	0.029	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.092	-0.024	26.535	0.007	0.007	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.824	-0.904	26.494	0.062	0.062	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.086	-0.046	21.257	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.009	-0.008	23.417	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.030	0.009	17.199	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.033	-0.021	19.386	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.044	0.020	14.611	0.004	0.004	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.055	-0.044	14.763	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.027	-0.013	18.481	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.931	0.972	19.639	0.174	0.174	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.051	0.033	20.596	0.003	0.003	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.045	-0.022	17.059	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.046	0.021	19.310	0.021	0.021	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.016	-0.036	17.577	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.849	-0.898	15.819	0.199	0.199	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.939	-0.952	14.863	-0.175	-0.175	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.955	-0.989	11.077	-0.123	-0.123	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.039	-0.021	8.696	-0.070	-0.070	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.845	0.920	8.696	0.361	0.361	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.860	-0.940	5.926	-2.840	-2.840	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.022	-0.007	7.726	0.216	0.216	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.834	-0.891	10.335	-0.341	-0.341	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.051	-0.039	11.991	0.061	0.061	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.016	0.004	12.932	0.012	0.012	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.059	-0.017	15.598	0.015	0.015	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.045	0.013	17.159	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.051	-0.039	20.052	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.002	0.013	23.843	0.008	0.008	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.055	0.048	27.189	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.035	-0.014	27.847	-0.002	-0.002	0.000	0.000	0.000	0.000

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