FMO DATABASE

FMODB ID: 76VZK

Calculation Name: 2IVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IVY

Chain ID: A

ChEMBL ID:

UniProt ID: Q97YC2

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626942.028601
FMO2-HF: Nuclear repulsion	590958.520317
FMO2-HF: Total energy	-35983.508284
FMO2-MP2: Total energy	-36089.820634

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-10.767	-6.337	2.36	-2.561	-4.229	-0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.012

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	A	4	LEU	0	0.077	0.056	3.637	-1.680	0.752	-0.010	-1.259	-1.164	0.005
4	A	5	TYR	0	-0.023	-0.023	4.635	0.569	0.651	-0.001	-0.005	-0.076	0.000
5	A	6	LEU	0	0.006	0.011	8.404	0.063	0.063	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.009	-0.021	10.519	0.080	0.080	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.036	0.029	13.889	0.014	0.014	0.000	0.000	0.000	0.000
8	A	9	TYR	0	-0.004	-0.022	17.668	0.022	0.022	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.813	-0.871	20.300	-0.151	-0.151	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.019	-0.011	21.341	0.013	0.013	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.060	0.024	25.540	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.834	-0.909	28.610	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.786	-0.907	27.837	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.058	-0.022	27.640	0.000	0.000	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.015	-0.017	25.147	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.829	0.921	23.504	0.109	0.109	0.000	0.000	0.000	0.000
17	A	18	ASN	0	0.001	-0.005	22.648	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.978	0.996	22.641	0.002	0.002	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.001	0.006	17.913	0.007	0.007	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.005	0.005	18.099	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.990	-0.998	18.378	-0.059	-0.059	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.076	-0.027	14.580	0.008	0.008	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.040	0.007	12.862	0.018	0.018	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.994	0.997	13.585	0.096	0.096	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.901	0.951	15.077	0.004	0.004	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.790	0.906	10.750	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.002	-0.004	10.346	0.028	0.028	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.062	0.000	8.236	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.864	-0.924	11.131	-0.619	-0.619	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.798	0.895	13.478	0.205	0.205	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.006	-0.020	15.343	0.010	0.010	0.000	0.000	0.000	0.000
32	A	33	GLN	0	0.063	0.037	18.052	0.021	0.021	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.010	-0.007	20.346	0.001	0.001	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.024	-0.008	20.685	0.019	0.019	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.026	0.012	16.149	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.002	-0.013	13.069	0.038	0.038	0.000	0.000	0.000	0.000
37	A	38	MET	0	0.003	0.010	10.907	0.033	0.033	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.076	0.027	7.903	0.199	0.199	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.851	-0.910	2.443	-4.736	-4.506	0.699	-0.335	-0.593	-0.001
40	A	41	LEU	0	-0.079	-0.045	2.956	0.762	1.516	0.177	-0.240	-0.691	-0.002
41	A	42	ASN	0	0.074	0.032	2.538	-1.931	-0.902	1.453	-0.867	-1.615	-0.004
42	A	43	SER	0	0.042	0.012	3.560	-1.168	-1.265	0.042	0.145	-0.090	0.000
43	A	44	SER	0	-0.021	-0.018	6.996	-0.369	-0.369	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.912	0.951	5.087	-0.587	-0.587	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.046	0.035	6.619	-0.219	-0.219	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.960	0.976	8.138	-0.927	-0.927	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.855	-0.916	10.860	0.171	0.171	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.025	0.007	9.506	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.880	-0.948	12.099	0.021	0.021	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.003	-0.012	14.001	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.013	0.008	15.617	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.014	-0.017	14.414	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.898	0.951	17.141	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.026	-0.003	19.955	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.086	-0.038	19.403	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.026	0.014	22.223	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.075	-0.014	24.037	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.943	0.958	26.025	0.024	0.024	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.949	0.982	29.208	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.913	0.962	30.340	0.069	0.069	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.056	-0.040	32.550	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.008	0.000	35.229	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.905	-0.947	35.125	-0.052	-0.052	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.896	-0.934	34.805	-0.073	-0.073	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.910	-0.951	30.657	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.805	0.851	27.708	0.121	0.121	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.026	0.002	21.539	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.015	0.002	21.148	0.008	0.008	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.019	-0.001	16.255	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.020	0.007	16.655	0.023	0.023	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.001	-0.008	10.659	-0.038	-0.038	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.009	-0.008	12.490	0.063	0.063	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.004	0.006	8.570	-0.120	-0.120	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.005	-0.003	9.349	0.256	0.256	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.011	0.000	9.046	-0.415	-0.415	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.829	-0.947	8.923	-1.534	-1.534	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.109	-0.053	11.460	0.232	0.232	0.000	0.000	0.000	0.000
78	A	79	GLN	0	0.075	0.038	13.569	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	80	PHE	0	0.031	0.016	13.267	0.119	0.119	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.894	0.938	13.071	1.020	1.020	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.878	-0.922	17.427	-0.523	-0.523	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.844	0.941	17.557	0.625	0.625	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.031	0.011	20.289	0.028	0.028	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.042	-0.026	21.837	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.006	0.002	24.406	0.015	0.015	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.020	0.006	27.596	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.022	-0.009	29.676	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.003	0.012	33.024	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)