FMO DATABASE

FMODB ID: YZMV2

Calculation Name: 4ODB-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ODB

Chain ID: D

ChEMBL ID:

UniProt ID: Q9Y624

Base Structure: X-ray

Registration Date: 2023-06-26

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-761235.771817
FMO2-HF: Nuclear repulsion	720941.628859
FMO2-HF: Total energy	-40294.142957
FMO2-MP2: Total energy	-40410.45479

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(D:28:SER)

Summations of interaction energy for fragment #1(D:28: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.
-1.395	1.203	0.135	-1.339	-1.395	-0.003

Interaction energy analysis for fragmet #1(D:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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

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	D	30	THR	0	-0.027	-0.014	3.871	0.767	2.257	-0.016	-0.839	-0.636	0.002
4	D	31	VAL	0	0.033	0.007	6.672	-0.056	-0.056	0.000	0.000	0.000	0.000
5	D	32	HIS	0	-0.041	-0.011	10.060	0.172	0.172	0.000	0.000	0.000	0.000
6	D	33	SER	0	0.030	-0.020	12.878	0.004	0.004	0.000	0.000	0.000	0.000
7	D	34	SER	0	-0.021	-0.009	16.665	-0.007	-0.007	0.000	0.000	0.000	0.000
8	D	35	GLU	-1	-0.944	-0.968	19.343	-0.150	-0.150	0.000	0.000	0.000	0.000
9	D	36	PRO	0	0.005	0.001	18.440	0.009	0.009	0.000	0.000	0.000	0.000
10	D	37	GLU	-1	-0.870	-0.923	20.347	-0.056	-0.056	0.000	0.000	0.000	0.000
11	D	38	VAL	0	0.020	0.023	24.145	-0.005	-0.005	0.000	0.000	0.000	0.000
12	D	39	ARG	1	0.932	0.958	26.761	0.086	0.086	0.000	0.000	0.000	0.000
13	D	40	ILE	0	0.012	0.017	30.534	-0.003	-0.003	0.000	0.000	0.000	0.000
14	D	41	PRO	0	0.024	0.006	32.906	0.006	0.006	0.000	0.000	0.000	0.000
15	D	42	GLU	-1	-0.787	-0.884	35.996	-0.048	-0.048	0.000	0.000	0.000	0.000
16	D	43	ASN	0	-0.029	-0.013	37.561	0.002	0.002	0.000	0.000	0.000	0.000
17	D	44	ASN	0	-0.015	0.013	35.120	0.001	0.001	0.000	0.000	0.000	0.000
18	D	45	PRO	0	0.013	0.003	33.315	0.000	0.000	0.000	0.000	0.000	0.000
19	D	46	VAL	0	-0.002	0.005	27.843	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	47	LYS	1	0.849	0.929	22.652	0.220	0.220	0.000	0.000	0.000	0.000
21	D	48	LEU	0	0.010	0.026	22.760	-0.001	-0.001	0.000	0.000	0.000	0.000
22	D	49	SER	0	0.020	-0.002	20.208	-0.009	-0.009	0.000	0.000	0.000	0.000
23	D	50	CYS	0	-0.117	-0.027	15.663	-0.010	-0.010	0.000	0.000	0.000	0.000
24	D	51	ALA	0	0.015	0.016	14.722	-0.001	-0.001	0.000	0.000	0.000	0.000
25	D	52	TYR	0	0.041	0.007	10.328	0.047	0.047	0.000	0.000	0.000	0.000
26	D	53	SER	0	-0.033	-0.021	8.722	0.034	0.034	0.000	0.000	0.000	0.000
27	D	54	GLY	0	0.049	0.016	4.579	-0.396	-0.407	-0.001	-0.010	0.022	0.000
28	D	55	PHE	0	-0.054	-0.017	4.394	-0.962	-0.885	-0.001	-0.014	-0.062	0.000
29	D	56	SER	0	-0.024	-0.037	6.967	0.232	0.232	0.000	0.000	0.000	0.000
30	D	57	SER	0	-0.095	-0.073	8.989	0.125	0.125	0.000	0.000	0.000	0.000
31	D	58	PRO	0	-0.012	0.008	10.767	0.049	0.049	0.000	0.000	0.000	0.000
32	D	59	ARG	1	0.834	0.896	11.827	0.135	0.135	0.000	0.000	0.000	0.000
33	D	60	VAL	0	-0.009	-0.009	13.472	0.006	0.006	0.000	0.000	0.000	0.000
34	D	61	GLU	-1	-0.864	-0.924	15.733	0.031	0.031	0.000	0.000	0.000	0.000
35	D	62	TRP	0	0.016	-0.004	17.743	-0.014	-0.014	0.000	0.000	0.000	0.000
36	D	63	LYS	1	0.824	0.901	19.437	-0.006	-0.006	0.000	0.000	0.000	0.000
37	D	64	PHE	0	0.000	0.009	22.663	-0.008	-0.008	0.000	0.000	0.000	0.000
38	D	65	ASP	-1	-0.795	-0.880	22.558	0.000	0.000	0.000	0.000	0.000	0.000
39	D	66	GLN	0	-0.065	-0.048	26.046	-0.003	-0.003	0.000	0.000	0.000	0.000
40	D	67	GLY	0	-0.001	0.001	29.267	0.003	0.003	0.000	0.000	0.000	0.000
41	D	68	ASP	-1	-0.908	-0.952	29.052	0.011	0.011	0.000	0.000	0.000	0.000
42	D	69	THR	0	-0.051	-0.019	30.389	0.004	0.004	0.000	0.000	0.000	0.000
43	D	70	THR	0	-0.013	-0.015	24.246	-0.003	-0.003	0.000	0.000	0.000	0.000
44	D	71	ARG	1	0.856	0.916	26.781	0.034	0.034	0.000	0.000	0.000	0.000
45	D	72	LEU	0	-0.001	-0.004	22.365	-0.006	-0.006	0.000	0.000	0.000	0.000
46	D	73	VAL	0	0.001	0.015	24.190	-0.002	-0.002	0.000	0.000	0.000	0.000
47	D	74	CYS	0	-0.093	-0.056	21.742	-0.012	-0.012	0.000	0.000	0.000	0.000
48	D	75	TYR	0	0.061	0.028	20.577	0.008	0.008	0.000	0.000	0.000	0.000
49	D	76	ASN	0	-0.011	-0.012	18.542	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	77	ASN	0	0.023	0.023	16.834	-0.005	-0.005	0.000	0.000	0.000	0.000
51	D	78	LYS	1	0.952	0.983	20.288	0.059	0.059	0.000	0.000	0.000	0.000
52	D	79	ILE	0	0.021	0.022	24.014	0.003	0.003	0.000	0.000	0.000	0.000
53	D	80	THR	0	-0.005	-0.002	26.044	0.007	0.007	0.000	0.000	0.000	0.000
54	D	81	ALA	0	0.105	0.039	28.420	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	82	SER	0	-0.089	-0.027	30.206	0.003	0.003	0.000	0.000	0.000	0.000
56	D	83	TYR	0	0.041	0.009	28.801	0.002	0.002	0.000	0.000	0.000	0.000
57	D	84	GLU	-1	-0.920	-0.969	30.504	-0.060	-0.060	0.000	0.000	0.000	0.000
58	D	85	ASP	-1	-0.860	-0.923	31.890	-0.060	-0.060	0.000	0.000	0.000	0.000
59	D	86	ARG	1	0.763	0.860	32.920	0.054	0.054	0.000	0.000	0.000	0.000
60	D	87	VAL	0	-0.003	0.019	26.953	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	88	THR	0	-0.040	-0.019	27.837	0.000	0.000	0.000	0.000	0.000	0.000
62	D	89	PHE	0	0.082	0.015	18.290	-0.002	-0.002	0.000	0.000	0.000	0.000
63	D	90	LEU	0	-0.017	-0.003	22.159	0.003	0.003	0.000	0.000	0.000	0.000
64	D	91	PRO	0	0.032	0.012	16.832	0.002	0.002	0.000	0.000	0.000	0.000
65	D	92	THR	0	0.028	0.022	17.372	-0.021	-0.021	0.000	0.000	0.000	0.000
66	D	93	GLY	0	0.036	0.025	19.616	0.010	0.010	0.000	0.000	0.000	0.000
67	D	94	ILE	0	-0.016	0.006	20.749	0.008	0.008	0.000	0.000	0.000	0.000
68	D	95	THR	0	-0.014	-0.021	23.890	-0.006	-0.006	0.000	0.000	0.000	0.000
69	D	96	PHE	0	0.011	0.008	26.215	0.007	0.007	0.000	0.000	0.000	0.000
70	D	97	LYS	1	0.845	0.892	30.536	0.079	0.079	0.000	0.000	0.000	0.000
71	D	98	SER	0	-0.037	-0.034	34.059	0.003	0.003	0.000	0.000	0.000	0.000
72	D	99	VAL	0	-0.010	0.010	30.852	0.000	0.000	0.000	0.000	0.000	0.000
73	D	100	THR	0	0.010	-0.015	34.302	0.003	0.003	0.000	0.000	0.000	0.000
74	D	101	ARG	1	0.884	0.899	34.639	0.040	0.040	0.000	0.000	0.000	0.000
75	D	102	GLU	-1	-0.881	-0.933	34.808	-0.030	-0.030	0.000	0.000	0.000	0.000
76	D	103	ASP	-1	-0.789	-0.844	31.053	-0.056	-0.056	0.000	0.000	0.000	0.000
77	D	104	THR	0	0.010	0.009	30.040	-0.008	-0.008	0.000	0.000	0.000	0.000
78	D	105	GLY	0	0.025	0.007	28.298	0.008	0.008	0.000	0.000	0.000	0.000
79	D	106	THR	0	-0.051	-0.023	21.785	-0.011	-0.011	0.000	0.000	0.000	0.000
80	D	107	TYR	0	-0.011	-0.020	22.591	0.006	0.006	0.000	0.000	0.000	0.000
81	D	108	THR	0	-0.011	0.000	17.402	-0.014	-0.014	0.000	0.000	0.000	0.000
82	D	110	MET	0	0.009	-0.009	13.158	0.033	0.033	0.000	0.000	0.000	0.000
83	D	111	VAL	0	-0.017	-0.008	10.313	-0.037	-0.037	0.000	0.000	0.000	0.000
84	D	112	SER	0	0.002	-0.017	9.253	0.128	0.128	0.000	0.000	0.000	0.000
85	D	113	GLU	-1	-0.749	-0.837	6.853	-1.023	-1.023	0.000	0.000	0.000	0.000
86	D	114	GLU	-1	-0.820	-0.876	8.994	0.054	0.054	0.000	0.000	0.000	0.000
87	D	115	GLY	0	-0.005	-0.010	11.244	0.025	0.025	0.000	0.000	0.000	0.000
88	D	116	GLY	0	-0.054	-0.013	10.239	0.059	0.059	0.000	0.000	0.000	0.000
89	D	117	ASN	0	0.008	0.000	5.839	-0.134	-0.134	0.000	0.000	0.000	0.000
90	D	118	SER	0	-0.007	-0.016	3.029	-0.738	0.276	0.154	-0.475	-0.694	-0.005
91	D	119	TYR	0	-0.011	0.001	5.184	-0.463	-0.435	-0.001	-0.001	-0.025	0.000
92	D	120	GLY	0	0.019	0.012	7.010	0.500	0.500	0.000	0.000	0.000	0.000
93	D	121	GLU	-1	-0.876	-0.933	9.263	-0.065	-0.065	0.000	0.000	0.000	0.000
94	D	122	VAL	0	0.000	0.001	12.018	-0.029	-0.029	0.000	0.000	0.000	0.000
95	D	123	LYS	1	0.836	0.897	14.714	-0.013	-0.013	0.000	0.000	0.000	0.000
96	D	124	VAL	0	-0.005	0.011	18.394	-0.008	-0.008	0.000	0.000	0.000	0.000
97	D	125	LYS	1	0.864	0.917	20.972	0.077	0.077	0.000	0.000	0.000	0.000
98	D	126	LEU	0	0.003	0.003	24.227	-0.012	-0.012	0.000	0.000	0.000	0.000
99	D	127	ILE	0	-0.006	-0.011	27.409	0.010	0.010	0.000	0.000	0.000	0.000
100	D	128	VAL	0	0.011	0.022	30.895	-0.006	-0.006	0.000	0.000	0.000	0.000
101	D	129	LEU	0	-0.049	-0.015	33.953	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:28:SER)