FMO DATABASE

FMODB ID: K3YN3

Calculation Name: 2VTX-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VTX

Chain ID: J

ChEMBL ID:

UniProt ID: P05221

Base Structure: X-ray

Registration Date: 2023-06-20

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-640586.945687
FMO2-HF: Nuclear repulsion	604256.750596
FMO2-HF: Total energy	-36330.195091
FMO2-MP2: Total energy	-36435.368277

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(J:17:LEU)

Summations of interaction energy for fragment #1(J:17:LEU)

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.
-0.789	2.486	0.211	-1.249	-2.235	0

Interaction energy analysis for fragmet #1(J:17:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.007

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].
3	J	19	TRP	0	0.025	0.011	3.861	-1.861	-0.130	-0.014	-0.792	-0.925
4	J	20	GLY	0	0.021	-0.005	6.139	0.446	0.446	0.000	0.000	0.000
5	J	21	CYS	0	-0.086	-0.010	9.867	-0.026	-0.026	0.000	0.000	0.000
6	J	22	GLU	-1	-0.807	-0.905	13.055	-0.161	-0.161	0.000	0.000	0.000
7	J	23	LEU	0	0.006	0.023	16.357	-0.005	-0.005	0.000	0.000	0.000
8	J	24	ASN	0	-0.029	-0.052	19.571	0.023	0.023	0.000	0.000	0.000
9	J	25	GLU	-1	-0.887	-0.958	22.989	-0.082	-0.082	0.000	0.000	0.000
10	J	26	GLN	0	-0.002	0.011	24.222	0.010	0.010	0.000	0.000	0.000
11	J	27	ASN	0	-0.015	0.001	19.263	0.014	0.014	0.000	0.000	0.000
12	J	28	LYS	1	0.939	0.953	21.342	0.091	0.091	0.000	0.000	0.000
13	J	29	THR	0	0.004	0.006	20.894	0.013	0.013	0.000	0.000	0.000
14	J	30	PHE	0	0.011	0.002	11.844	-0.019	-0.019	0.000	0.000	0.000
15	J	31	GLU	-1	-0.917	-0.962	16.731	-0.224	-0.224	0.000	0.000	0.000
16	J	32	PHE	0	-0.047	-0.027	7.645	-0.100	-0.100	0.000	0.000	0.000
17	J	33	LYS	1	0.952	0.979	7.425	1.147	1.147	0.000	0.000	0.000
18	J	43	HIS	0	-0.053	-0.040	5.254	0.088	0.088	0.000	0.000	0.000
19	J	44	GLN	0	-0.020	-0.005	8.989	-0.028	-0.028	0.000	0.000	0.000
20	J	45	LEU	0	-0.053	-0.037	7.708	-0.006	-0.006	0.000	0.000	0.000
21	J	46	ALA	0	0.038	0.024	8.103	0.046	0.046	0.000	0.000	0.000
22	J	47	LEU	0	-0.003	0.000	9.173	-0.037	-0.037	0.000	0.000	0.000
23	J	48	ARG	1	0.853	0.927	8.428	-0.848	-0.848	0.000	0.000	0.000
24	J	49	THR	0	0.002	0.016	12.354	-0.004	-0.004	0.000	0.000	0.000
25	J	50	VAL	0	0.047	0.031	14.641	-0.052	-0.052	0.000	0.000	0.000
26	J	51	CYS	0	-0.050	-0.028	16.174	0.027	0.027	0.000	0.000	0.000
27	J	52	LEU	0	0.049	0.034	18.928	-0.027	-0.027	0.000	0.000	0.000
28	J	53	GLY	0	0.016	0.008	20.732	0.003	0.003	0.000	0.000	0.000
29	J	54	ASP	-1	-0.816	-0.902	21.504	-0.062	-0.062	0.000	0.000	0.000
30	J	55	LYS	1	0.757	0.858	24.205	0.066	0.066	0.000	0.000	0.000
31	J	56	ALA	0	0.005	0.039	24.389	-0.001	-0.001	0.000	0.000	0.000
32	J	57	LYS	1	0.933	0.965	26.291	0.076	0.076	0.000	0.000	0.000
33	J	58	ASP	-1	-0.765	-0.864	29.256	-0.021	-0.021	0.000	0.000	0.000
34	J	59	GLU	-1	-0.854	-0.902	29.751	-0.057	-0.057	0.000	0.000	0.000
35	J	60	PHE	0	-0.007	-0.015	29.663	-0.001	-0.001	0.000	0.000	0.000
36	J	61	HIS	0	-0.018	0.001	24.513	-0.014	-0.014	0.000	0.000	0.000
37	J	62	ILE	0	-0.014	-0.012	25.523	0.009	0.009	0.000	0.000	0.000
38	J	63	VAL	0	0.001	0.010	19.265	-0.011	-0.011	0.000	0.000	0.000
39	J	64	GLU	-1	-0.781	-0.874	22.568	-0.053	-0.053	0.000	0.000	0.000
40	J	65	ILE	0	0.007	-0.004	17.752	-0.020	-0.020	0.000	0.000	0.000
41	J	66	VAL	0	-0.040	-0.027	20.832	0.018	0.018	0.000	0.000	0.000
42	J	67	ASP	-1	-0.885	-0.938	20.693	-0.088	-0.088	0.000	0.000	0.000
43	J	68	GLN	0	-0.042	-0.017	22.753	0.016	0.016	0.000	0.000	0.000
44	J	69	GLU	-1	-0.831	-0.915	24.469	-0.020	-0.020	0.000	0.000	0.000
45	J	70	GLU	-1	-0.868	-0.929	26.777	-0.028	-0.028	0.000	0.000	0.000
46	J	71	GLY	0	-0.063	-0.033	28.581	-0.008	-0.008	0.000	0.000	0.000
47	J	72	ALA	0	-0.047	-0.021	30.252	0.001	0.001	0.000	0.000	0.000
48	J	73	GLU	-1	-0.903	-0.961	26.501	-0.091	-0.091	0.000	0.000	0.000
49	J	74	LYS	1	0.798	0.896	26.009	0.040	0.040	0.000	0.000	0.000
50	J	75	VAL	0	-0.018	-0.008	25.280	-0.007	-0.007	0.000	0.000	0.000
51	J	76	VAL	0	0.024	0.000	23.319	0.011	0.011	0.000	0.000	0.000
52	J	77	PRO	0	-0.055	-0.034	23.258	-0.008	-0.008	0.000	0.000	0.000
53	J	78	ILE	0	0.004	-0.006	18.289	0.011	0.011	0.000	0.000	0.000
54	J	79	ALA	0	0.019	0.019	21.094	0.014	0.014	0.000	0.000	0.000
55	J	80	THR	0	-0.025	-0.012	23.172	-0.014	-0.014	0.000	0.000	0.000
56	J	81	LEU	0	-0.054	-0.015	21.312	0.009	0.009	0.000	0.000	0.000
57	J	82	LYS	1	0.852	0.911	26.010	0.014	0.014	0.000	0.000	0.000
58	J	83	PRO	0	0.034	0.026	26.675	0.009	0.009	0.000	0.000	0.000
59	J	84	SER	0	-0.082	-0.063	27.809	0.007	0.007	0.000	0.000	0.000
60	J	85	ILE	0	-0.083	-0.029	29.857	0.004	0.004	0.000	0.000	0.000
61	J	86	LEU	0	0.023	-0.008	25.169	0.008	0.008	0.000	0.000	0.000
62	J	87	PRO	0	0.055	0.037	23.616	-0.005	-0.005	0.000	0.000	0.000
63	J	88	MET	0	-0.027	-0.022	17.895	-0.015	-0.015	0.000	0.000	0.000
64	J	89	ALA	0	0.013	0.013	19.849	0.010	0.010	0.000	0.000	0.000
65	J	90	THR	0	-0.038	-0.025	16.330	-0.016	-0.016	0.000	0.000	0.000
66	J	91	MET	0	-0.027	-0.009	14.918	-0.022	-0.022	0.000	0.000	0.000
67	J	92	VAL	0	-0.001	-0.015	15.503	0.052	0.052	0.000	0.000	0.000
68	J	93	GLY	0	0.021	0.014	15.562	-0.033	-0.033	0.000	0.000	0.000
69	J	94	ILE	0	-0.011	0.009	15.050	-0.027	-0.027	0.000	0.000	0.000
70	J	95	GLU	-1	-0.958	-1.000	11.340	0.481	0.481	0.000	0.000	0.000
71	J	96	LEU	0	0.008	0.006	12.394	-0.023	-0.023	0.000	0.000	0.000
72	J	97	ASP	-1	-0.791	-0.885	12.136	-0.063	-0.063	0.000	0.000	0.000
73	J	98	PRO	0	-0.104	-0.027	11.332	-0.023	-0.023	0.000	0.000	0.000
74	J	99	PRO	0	-0.008	-0.002	14.232	0.021	0.021	0.000	0.000	0.000
75	J	100	VAL	0	0.048	0.007	14.056	0.029	0.029	0.000	0.000	0.000
76	J	101	THR	0	-0.008	0.005	16.064	-0.046	-0.046	0.000	0.000	0.000
77	J	102	PHE	0	0.027	0.020	13.323	0.030	0.030	0.000	0.000	0.000
78	J	103	ARG	1	0.831	0.901	18.766	0.081	0.081	0.000	0.000	0.000
79	J	104	LEU	0	-0.032	-0.021	22.243	0.013	0.013	0.000	0.000	0.000
80	J	105	LYS	1	0.869	0.946	23.831	0.056	0.056	0.000	0.000	0.000
81	J	106	ALA	0	-0.017	-0.016	26.874	0.007	0.007	0.000	0.000	0.000
82	J	107	GLY	0	0.023	0.015	26.949	-0.003	-0.003	0.000	0.000	0.000
83	J	108	SER	0	-0.066	-0.062	27.259	-0.007	-0.007	0.000	0.000	0.000
84	J	109	GLY	0	0.005	0.020	23.220	-0.012	-0.012	0.000	0.000	0.000
85	J	110	PRO	0	0.013	0.000	20.212	0.011	0.011	0.000	0.000	0.000
86	J	111	LEU	0	-0.007	-0.002	18.463	0.022	0.022	0.000	0.000	0.000
87	J	112	TYR	0	-0.056	-0.051	14.567	-0.018	-0.018	0.000	0.000	0.000
88	J	113	ILE	0	-0.001	0.008	13.242	0.047	0.047	0.000	0.000	0.000
89	J	114	SER	0	-0.020	-0.021	10.154	-0.066	-0.066	0.000	0.000	0.000
90	J	115	GLY	0	0.088	0.013	8.741	0.116	0.116	0.000	0.000	0.000
91	J	116	GLN	0	-0.045	-0.013	4.735	-0.839	-0.627	-0.001	-0.031	-0.179
92	J	117	HIS	0	0.041	0.044	2.590	-0.421	0.754	0.227	-0.417	-0.985
93	J	118	VAL	0	0.008	0.020	4.391	1.637	1.794	-0.001	-0.009	-0.146

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Interactive mode: IFIE and PIEDA for fragment #1(J:17:LEU)