FMO DATABASE

FMODB ID: R5288

Calculation Name: 1Y96-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y96

Chain ID: B

ChEMBL ID:

UniProt ID: Q8WXD5

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	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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509566.876809
FMO2-HF: Nuclear repulsion	476495.09426
FMO2-HF: Total energy	-33071.782549
FMO2-MP2: Total energy	-33168.813633

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(B:47:ALA)

Summations of interaction energy for fragment #1(B:47: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.
0.042	1.894	-0.008	-0.911	-0.932	0.004

Interaction energy analysis for fragmet #1(B:47:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.020

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	B	49	GLU	-1	-0.741	-0.805	3.869	-1.962	-0.110	-0.008	-0.911	-0.932	0.004
4	B	50	SER	0	0.042	0.018	5.948	0.300	0.300	0.000	0.000	0.000	0.000
5	B	51	LEU	0	0.071	0.013	8.702	-0.010	-0.010	0.000	0.000	0.000	0.000
6	B	52	GLU	-1	-0.900	-0.928	11.829	-0.368	-0.368	0.000	0.000	0.000	0.000
7	B	53	SER	0	-0.037	-0.045	10.417	0.125	0.125	0.000	0.000	0.000	0.000
8	B	54	GLN	0	-0.050	-0.032	8.889	0.182	0.182	0.000	0.000	0.000	0.000
9	B	55	GLU	-1	-0.816	-0.894	12.926	-0.342	-0.342	0.000	0.000	0.000	0.000
10	B	56	GLN	0	0.023	0.020	15.910	0.067	0.067	0.000	0.000	0.000	0.000
11	B	57	ARG	1	0.826	0.877	10.246	1.057	1.057	0.000	0.000	0.000	0.000
12	B	58	ALA	0	-0.002	-0.001	16.460	0.051	0.051	0.000	0.000	0.000	0.000
13	B	59	ARG	1	0.824	0.881	18.540	0.410	0.410	0.000	0.000	0.000	0.000
14	B	60	ALA	0	0.006	0.011	19.519	0.036	0.036	0.000	0.000	0.000	0.000
15	B	61	ALA	0	0.009	0.003	19.910	0.032	0.032	0.000	0.000	0.000	0.000
16	B	62	LEU	0	-0.027	-0.023	21.819	0.032	0.032	0.000	0.000	0.000	0.000
17	B	63	ARG	1	0.866	0.933	24.291	0.201	0.201	0.000	0.000	0.000	0.000
18	B	64	GLU	-1	-0.823	-0.888	24.653	-0.184	-0.184	0.000	0.000	0.000	0.000
19	B	65	ARG	1	0.970	0.979	24.146	0.265	0.265	0.000	0.000	0.000	0.000
20	B	66	TYR	0	-0.001	0.008	27.954	0.014	0.014	0.000	0.000	0.000	0.000
21	B	67	LEU	0	0.043	0.032	28.837	0.014	0.014	0.000	0.000	0.000	0.000
22	B	68	ARG	1	0.846	0.898	28.420	0.187	0.187	0.000	0.000	0.000	0.000
23	B	69	SER	0	-0.089	-0.060	32.070	0.011	0.011	0.000	0.000	0.000	0.000
24	B	70	LEU	0	0.024	0.012	34.061	0.009	0.009	0.000	0.000	0.000	0.000
25	B	71	LEU	0	-0.005	-0.015	33.298	0.008	0.008	0.000	0.000	0.000	0.000
26	B	72	ALA	0	-0.037	-0.015	36.103	0.007	0.007	0.000	0.000	0.000	0.000
27	B	73	MET	0	-0.049	-0.013	37.883	0.007	0.007	0.000	0.000	0.000	0.000
28	B	74	VAL	0	0.016	0.010	39.598	0.006	0.006	0.000	0.000	0.000	0.000
29	B	75	GLY	0	-0.004	0.009	42.095	0.001	0.001	0.000	0.000	0.000	0.000
30	B	76	HIS	1	0.799	0.901	42.246	0.092	0.092	0.000	0.000	0.000	0.000
31	B	77	GLN	0	0.051	0.041	46.143	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	78	VAL	0	-0.047	-0.033	43.460	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	79	SER	0	-0.010	-0.010	46.156	0.005	0.005	0.000	0.000	0.000	0.000
34	B	80	PHE	0	-0.004	-0.010	43.336	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	81	THR	0	-0.051	-0.028	45.139	0.006	0.006	0.000	0.000	0.000	0.000
36	B	82	LEU	0	0.044	0.024	45.540	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	83	HIS	0	0.025	0.018	46.612	0.000	0.000	0.000	0.000	0.000	0.000
38	B	84	GLU	-1	-0.931	-0.981	48.333	-0.058	-0.058	0.000	0.000	0.000	0.000
39	B	85	GLY	0	-0.022	-0.002	50.471	0.002	0.002	0.000	0.000	0.000	0.000
40	B	86	VAL	0	-0.010	0.006	51.711	0.001	0.001	0.000	0.000	0.000	0.000
41	B	87	ARG	1	0.877	0.928	47.216	0.071	0.071	0.000	0.000	0.000	0.000
42	B	88	VAL	0	0.020	0.023	49.754	0.003	0.003	0.000	0.000	0.000	0.000
43	B	89	ALA	0	-0.019	-0.015	49.767	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	90	ALA	0	0.025	0.024	48.603	0.003	0.003	0.000	0.000	0.000	0.000
45	B	91	HIS	0	-0.003	-0.009	48.084	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	92	PHE	0	0.018	0.010	39.149	0.001	0.001	0.000	0.000	0.000	0.000
47	B	93	GLY	0	0.019	0.012	44.193	0.001	0.001	0.000	0.000	0.000	0.000
48	B	94	ALA	0	-0.005	-0.012	40.269	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	95	THR	0	-0.011	-0.009	36.415	0.001	0.001	0.000	0.000	0.000	0.000
50	B	96	ASP	-1	-0.774	-0.863	37.450	-0.106	-0.106	0.000	0.000	0.000	0.000
51	B	97	LEU	0	0.016	-0.009	31.726	-0.006	-0.006	0.000	0.000	0.000	0.000
52	B	98	ASP	-1	-0.885	-0.930	32.647	-0.136	-0.136	0.000	0.000	0.000	0.000
53	B	99	VAL	0	-0.069	-0.027	33.038	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	100	ALA	0	0.039	0.029	35.877	0.002	0.002	0.000	0.000	0.000	0.000
55	B	101	ASN	0	-0.060	-0.047	38.696	0.009	0.009	0.000	0.000	0.000	0.000
56	B	102	PHE	0	0.017	-0.010	38.374	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	103	TYR	0	0.010	0.011	41.437	0.006	0.006	0.000	0.000	0.000	0.000
58	B	104	VAL	0	-0.036	-0.025	44.609	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	105	SER	0	0.046	0.023	47.287	0.003	0.003	0.000	0.000	0.000	0.000
60	B	106	GLN	0	-0.032	-0.029	50.617	0.001	0.001	0.000	0.000	0.000	0.000
61	B	107	LEU	0	-0.006	0.015	50.419	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	108	GLN	0	-0.009	-0.015	53.158	0.004	0.004	0.000	0.000	0.000	0.000
63	B	109	THR	0	-0.005	-0.023	55.493	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	110	PRO	0	-0.002	-0.019	58.165	0.001	0.001	0.000	0.000	0.000	0.000
65	B	111	ILE	0	0.002	0.014	61.408	0.002	0.002	0.000	0.000	0.000	0.000
66	B	112	GLY	0	0.021	0.018	61.400	0.001	0.001	0.000	0.000	0.000	0.000
67	B	113	VAL	0	-0.045	-0.005	56.204	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	114	GLN	0	0.005	0.009	55.461	0.002	0.002	0.000	0.000	0.000	0.000
69	B	115	ALA	0	0.005	-0.003	55.007	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	116	GLU	-1	-0.912	-0.966	50.435	-0.062	-0.062	0.000	0.000	0.000	0.000
71	B	117	ALA	0	-0.042	-0.020	50.260	0.002	0.002	0.000	0.000	0.000	0.000
72	B	118	LEU	0	0.005	0.004	44.932	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	119	LEU	0	-0.033	-0.006	45.545	0.003	0.003	0.000	0.000	0.000	0.000
74	B	120	ARG	1	0.910	0.932	43.588	0.071	0.071	0.000	0.000	0.000	0.000
75	B	121	CYS	0	-0.053	-0.042	38.565	0.002	0.002	0.000	0.000	0.000	0.000
76	B	122	SER	0	-0.033	-0.026	41.349	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	123	ASP	-1	-0.812	-0.872	42.605	-0.074	-0.074	0.000	0.000	0.000	0.000
78	B	124	ILE	0	-0.050	-0.023	42.166	0.003	0.003	0.000	0.000	0.000	0.000
79	B	125	ILE	0	0.002	0.015	41.838	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	126	SER	0	-0.045	-0.029	40.893	-0.004	-0.004	0.000	0.000	0.000	0.000
81	B	127	TYR	0	0.112	0.061	36.375	0.004	0.004	0.000	0.000	0.000	0.000
82	B	128	THR	0	-0.070	-0.037	41.181	-0.004	-0.004	0.000	0.000	0.000	0.000
83	B	129	PHE	0	0.060	0.028	38.846	0.005	0.005	0.000	0.000	0.000	0.000
84	B	130	LYS	1	0.954	0.979	42.926	0.073	0.073	0.000	0.000	0.000	0.000
85	B	131	PRO	0	0.037	0.040	39.186	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:47:ALA)