FMO DATABASE

FMODB ID: 6YVRZ

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	OptAll
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	-627942.499003
FMO2-HF: Nuclear repulsion	591958.473223
FMO2-HF: Total energy	-35984.02578
FMO2-MP2: Total energy	-36090.351299

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.
-11.518	-6.708	4.091	-3.901	-4.998	-0.017

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 : -0.027 / q_NPA : -0.019

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	0.066	0.053	3.698	-0.763	1.420	-0.004	-1.178	-1.000	0.003
4	A	5	TYR	0	-0.017	-0.019	4.786	0.410	0.479	-0.001	-0.004	-0.064	0.000
5	A	6	LEU	0	0.002	0.007	8.188	0.084	0.084	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.002	-0.018	10.277	0.047	0.047	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.048	0.034	13.819	0.028	0.028	0.000	0.000	0.000	0.000
8	A	9	TYR	0	-0.010	-0.016	17.575	0.022	0.022	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.818	-0.865	20.291	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.002	-0.004	21.429	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.037	0.036	25.704	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.754	-0.846	28.575	0.013	0.013	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.753	-0.880	27.714	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.027	-0.004	27.561	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.012	-0.015	25.070	0.008	0.008	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.820	0.877	23.482	0.041	0.041	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.036	-0.027	22.614	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.910	0.976	22.514	-0.069	-0.069	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.011	0.006	17.857	0.020	0.020	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.009	0.003	18.049	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.903	-0.950	18.508	0.075	0.075	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.047	-0.009	14.373	0.028	0.028	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.033	0.007	12.925	0.042	0.042	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.980	0.995	13.408	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.819	0.892	14.857	-0.098	-0.098	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.812	0.911	11.161	-0.396	-0.396	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.015	0.014	10.344	0.100	0.100	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.049	-0.024	7.743	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.867	-0.927	11.022	-0.294	-0.294	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.808	0.897	13.279	0.052	0.052	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.002	-0.012	14.806	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	GLN	0	0.019	0.011	17.832	0.013	0.013	0.000	0.000	0.000	0.000
33	A	34	TYR	0	0.025	0.018	20.192	0.012	0.012	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.017	-0.005	20.690	0.018	0.018	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.000	0.000	16.062	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.015	-0.003	12.999	0.030	0.030	0.000	0.000	0.000	0.000
37	A	38	MET	0	-0.007	0.012	10.635	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.083	0.032	7.681	0.177	0.177	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.884	-0.931	2.412	-3.327	-3.280	0.842	-0.334	-0.554	0.000
40	A	41	LEU	0	-0.051	-0.023	2.862	0.202	1.160	0.293	-0.380	-0.871	-0.004
41	A	42	ASN	0	0.075	0.037	2.505	-3.439	-1.682	2.917	-2.251	-2.423	-0.016
42	A	43	SER	0	0.079	0.022	3.309	-1.565	-1.769	0.044	0.246	-0.086	0.000
43	A	44	SER	0	-0.034	-0.003	6.531	-0.481	-0.481	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.937	0.945	5.223	-1.169	-1.169	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.027	0.033	6.683	-0.273	-0.273	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.921	0.942	8.485	-1.215	-1.215	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.841	-0.902	11.216	0.458	0.458	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.015	0.000	9.882	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.856	-0.916	12.452	0.094	0.094	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.000	-0.005	14.344	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.015	0.004	16.035	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.004	-0.007	14.549	-0.035	-0.035	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.848	0.908	17.139	-0.136	-0.136	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.008	-0.004	20.223	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.090	-0.046	19.186	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.042	0.014	22.403	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.057	-0.009	24.230	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.803	0.884	26.348	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.953	0.985	29.563	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.789	0.873	31.980	0.023	0.023	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.067	-0.049	33.030	0.004	0.004	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.032	-0.027	35.417	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.838	-0.911	35.328	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.813	-0.889	34.806	-0.039	-0.039	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.859	-0.920	30.792	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.813	0.865	27.671	0.063	0.063	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.040	0.011	21.311	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	PHE	0	0.003	0.013	21.480	0.006	0.006	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.003	-0.016	16.513	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.022	0.002	16.744	0.014	0.014	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.001	0.000	10.862	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.006	-0.002	12.301	0.037	0.037	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.002	0.009	8.303	-0.071	-0.071	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.020	-0.015	9.153	0.210	0.210	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.011	-0.016	9.061	-0.385	-0.385	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.794	-0.919	9.706	-0.711	-0.711	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.064	-0.010	11.306	0.175	0.175	0.000	0.000	0.000	0.000
78	A	79	GLN	0	0.127	0.072	13.771	-0.045	-0.045	0.000	0.000	0.000	0.000
79	A	80	PHE	0	-0.003	0.007	12.694	0.106	0.106	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.806	0.877	13.420	0.885	0.885	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.885	-0.937	17.279	-0.526	-0.526	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.846	0.937	17.051	0.488	0.488	0.000	0.000	0.000	0.000
83	A	84	ILE	0	0.026	0.010	19.767	0.026	0.026	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.042	-0.027	21.529	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.017	0.006	24.219	0.010	0.010	0.000	0.000	0.000	0.000
86	A	87	GLY	0	0.014	0.002	27.345	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.017	-0.006	29.761	0.002	0.002	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.005	0.012	32.925	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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