FMO DATABASE

FMODB ID: G52L1

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	OptHSide
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	-634822.464847
FMO2-HF: Nuclear repulsion	600379.194866
FMO2-HF: Total energy	-34443.269981
FMO2-MP2: Total energy	-34546.717863

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.
-12.313	-4.16	2.811	-5.055	-5.908	-0.028

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 : -0.035 / q_NPA : -0.015

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	0.843	0.909	3.829	3.013	4.824	-0.009	-0.810	-0.993	0.004
4	A	4	VAL	0	0.024	0.026	5.328	-0.664	-0.620	-0.001	-0.004	-0.039	0.000
5	A	5	LYS	1	0.838	0.911	8.804	0.262	0.262	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.029	0.014	11.576	-0.005	-0.005	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.846	0.912	14.035	0.061	0.061	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.039	-0.004	15.009	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.009	-0.013	20.137	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.027	0.003	23.810	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.857	0.892	26.174	-0.065	-0.065	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.030	0.014	21.910	0.005	0.005	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.802	0.907	21.963	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.019	-0.012	22.876	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.079	-0.034	22.887	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.017	0.010	18.211	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.045	-0.018	19.279	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.018	-0.008	16.421	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.810	-0.910	19.874	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.853	-0.929	15.968	-0.149	-0.149	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.787	-0.839	11.650	0.182	0.182	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.842	-0.894	8.334	-0.569	-0.569	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.049	-0.032	7.513	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.924	-0.961	2.249	-10.232	-6.951	0.968	-2.136	-2.112	-0.016
25	A	25	LEU	0	-0.033	-0.015	3.520	-1.212	-0.639	0.026	-0.182	-0.417	0.001
26	A	26	PRO	0	0.022	0.002	2.527	0.820	2.432	1.765	-1.652	-1.725	-0.015
27	A	27	GLU	-1	-0.925	-0.974	3.127	-2.296	-1.583	0.062	-0.242	-0.532	-0.002
28	A	28	GLY	0	-0.004	0.001	4.226	0.402	0.521	0.000	-0.029	-0.090	0.000
29	A	29	ALA	0	-0.041	0.003	6.296	0.043	0.043	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.839	0.898	7.943	-0.401	-0.401	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.001	0.000	11.464	0.114	0.114	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.851	0.893	13.765	-0.173	-0.173	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.823	-0.905	10.197	0.604	0.604	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.014	-0.003	10.196	0.087	0.087	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.013	-0.005	11.911	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.818	-0.898	14.358	0.295	0.295	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.764	-0.847	9.428	0.758	0.758	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.035	-0.018	12.710	-0.065	-0.065	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.867	0.917	14.929	-0.295	-0.295	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.805	0.892	11.412	-0.730	-0.730	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.767	0.873	7.995	-0.472	-0.472	0.000	0.000	0.000	0.000
42	A	42	HIS	1	0.804	0.885	15.127	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.909	-0.970	18.750	0.163	0.163	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.930	0.984	21.462	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.019	-0.013	19.974	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.838	0.934	19.977	-0.236	-0.236	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.933	-0.970	22.937	0.147	0.147	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.829	-0.862	23.619	0.072	0.072	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.007	-0.004	24.168	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.033	-0.031	18.728	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.098	0.046	23.313	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.909	-0.940	21.627	0.097	0.097	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.015	-0.017	22.245	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.130	-0.076	23.918	0.004	0.004	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.837	-0.932	27.075	0.060	0.060	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.911	-0.964	28.874	0.022	0.022	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.943	-0.965	31.376	0.039	0.039	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.095	-0.023	26.529	0.007	0.007	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.843	-0.918	26.497	0.071	0.071	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.096	-0.056	21.441	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.023	-0.014	23.378	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.037	0.010	17.221	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.029	-0.018	19.268	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.032	0.015	14.550	0.008	0.008	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.057	-0.052	14.743	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.024	-0.010	18.358	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.827	0.923	18.254	0.134	0.134	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.038	0.020	20.612	0.007	0.007	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.056	-0.024	17.055	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.039	0.023	19.284	0.022	0.022	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.026	-0.048	17.608	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.821	-0.885	15.834	0.216	0.216	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.837	-0.899	15.367	-0.120	-0.120	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.875	-0.940	11.104	-0.051	-0.051	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.027	-0.008	8.679	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.818	0.900	8.708	0.300	0.300	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.839	-0.920	5.845	-2.094	-2.094	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.018	-0.007	7.726	0.135	0.135	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.832	-0.884	10.491	-0.252	-0.252	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.049	-0.041	11.742	0.070	0.070	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.015	0.002	12.732	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.053	-0.013	15.425	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.032	0.007	17.047	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.045	-0.034	19.939	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.005	0.019	23.728	0.007	0.007	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.059	0.046	27.097	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.037	-0.003	27.608	-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:1:SER)