FMO DATABASE

FMODB ID: 3QM8L

Calculation Name: 3LAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9L9I0

Base Structure: X-ray

Registration Date: 2023-03-14

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-448157.934072
FMO2-HF: Nuclear repulsion	416993.053195
FMO2-HF: Total energy	-31164.880877
FMO2-MP2: Total energy	-31255.728955

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:44:LEU)

Summations of interaction energy for fragment #1(A:44: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.
-5.698	-1.793	0.641	-1.961	-2.587	-0.004

Interaction energy analysis for fragmet #1(A:44:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.015

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	A	46	THR	0	0.076	0.025	3.817	-2.213	-0.309	-0.017	-1.025	-0.862	0.005
4	A	47	GLU	-1	-0.893	-0.950	6.680	-1.497	-1.497	0.000	0.000	0.000	0.000
5	A	48	GLN	0	0.022	0.020	2.655	-3.578	-2.175	0.651	-0.848	-1.207	-0.009
6	A	49	GLN	0	0.033	0.016	3.445	0.443	0.937	0.008	-0.081	-0.422	0.000
7	A	50	ALA	0	-0.028	0.003	5.427	0.639	0.639	0.000	0.000	0.000	0.000
8	A	51	THR	0	-0.057	-0.048	8.011	0.356	0.356	0.000	0.000	0.000	0.000
9	A	52	ALA	0	0.023	-0.001	6.010	0.241	0.241	0.000	0.000	0.000	0.000
10	A	53	GLN	0	0.018	0.022	8.001	0.251	0.251	0.000	0.000	0.000	0.000
11	A	54	LYS	1	0.943	0.968	10.570	0.473	0.473	0.000	0.000	0.000	0.000
12	A	55	ILE	0	-0.009	0.006	10.045	0.054	0.054	0.000	0.000	0.000	0.000
13	A	56	TYR	0	-0.018	-0.019	12.042	0.070	0.070	0.000	0.000	0.000	0.000
14	A	57	ASP	-1	-0.911	-0.959	13.735	-0.057	-0.057	0.000	0.000	0.000	0.000
15	A	58	ASP	-1	-0.908	-0.943	15.943	-0.048	-0.048	0.000	0.000	0.000	0.000
16	A	59	TYR	0	0.021	-0.002	16.497	0.028	0.028	0.000	0.000	0.000	0.000
17	A	60	TYR	0	-0.002	-0.014	17.892	0.011	0.011	0.000	0.000	0.000	0.000
18	A	61	THR	0	0.000	-0.004	19.736	0.002	0.002	0.000	0.000	0.000	0.000
19	A	62	GLN	0	-0.107	-0.048	21.389	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	63	THR	0	-0.009	-0.005	21.474	0.005	0.005	0.000	0.000	0.000	0.000
21	A	64	SER	0	-0.002	0.013	23.613	0.007	0.007	0.000	0.000	0.000	0.000
22	A	65	ALA	0	0.013	0.006	25.378	0.004	0.004	0.000	0.000	0.000	0.000
23	A	66	LEU	0	0.028	0.016	26.667	0.004	0.004	0.000	0.000	0.000	0.000
24	A	67	ARG	1	0.970	0.992	23.633	-0.124	-0.124	0.000	0.000	0.000	0.000
25	A	68	GLN	0	0.041	0.013	27.522	0.002	0.002	0.000	0.000	0.000	0.000
26	A	69	GLN	0	-0.016	-0.012	30.251	0.002	0.002	0.000	0.000	0.000	0.000
27	A	70	LEU	0	0.024	0.016	28.503	0.003	0.003	0.000	0.000	0.000	0.000
28	A	71	ILE	0	-0.052	-0.030	28.051	0.004	0.004	0.000	0.000	0.000	0.000
29	A	72	SER	0	-0.015	-0.002	32.042	0.000	0.000	0.000	0.000	0.000	0.000
30	A	73	LYS	1	0.882	0.926	35.123	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	74	ARG	1	0.939	0.975	29.913	-0.092	-0.092	0.000	0.000	0.000	0.000
32	A	75	TYR	0	-0.007	-0.011	33.831	0.002	0.002	0.000	0.000	0.000	0.000
33	A	76	GLU	-1	-0.896	-0.935	37.926	0.036	0.036	0.000	0.000	0.000	0.000
34	A	77	TYR	0	0.024	-0.002	38.352	0.000	0.000	0.000	0.000	0.000	0.000
35	A	78	ASN	0	-0.008	-0.017	37.051	0.000	0.000	0.000	0.000	0.000	0.000
36	A	79	ALA	0	-0.001	0.024	41.013	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	80	LEU	0	-0.035	-0.022	43.676	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	81	LEU	0	-0.038	-0.019	41.330	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	82	THR	0	-0.071	-0.043	44.194	0.000	0.000	0.000	0.000	0.000	0.000
40	A	83	ALA	0	-0.022	0.002	46.776	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	84	SER	0	0.000	-0.001	49.616	0.000	0.000	0.000	0.000	0.000	0.000
42	A	85	SER	0	-0.015	-0.013	53.093	0.000	0.000	0.000	0.000	0.000	0.000
43	A	86	PRO	0	-0.015	-0.006	49.375	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	87	ASP	-1	-0.791	-0.893	49.542	0.030	0.030	0.000	0.000	0.000	0.000
45	A	88	THR	0	0.045	-0.005	48.148	0.000	0.000	0.000	0.000	0.000	0.000
46	A	89	ALA	0	0.026	0.038	47.480	0.001	0.001	0.000	0.000	0.000	0.000
47	A	90	LYS	1	0.930	0.966	46.581	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	91	ILE	0	0.012	0.020	43.531	0.001	0.001	0.000	0.000	0.000	0.000
49	A	92	ASN	0	-0.005	-0.024	42.906	0.004	0.004	0.000	0.000	0.000	0.000
50	A	93	ALA	0	-0.062	-0.018	42.631	0.001	0.001	0.000	0.000	0.000	0.000
51	A	94	VAL	0	0.047	0.015	39.266	0.001	0.001	0.000	0.000	0.000	0.000
52	A	95	ALA	0	0.001	-0.006	38.658	0.002	0.002	0.000	0.000	0.000	0.000
53	A	96	LYS	1	0.990	0.988	37.706	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	97	GLU	-1	-0.874	-0.928	37.338	0.035	0.035	0.000	0.000	0.000	0.000
55	A	98	MET	0	-0.049	-0.029	33.926	0.002	0.002	0.000	0.000	0.000	0.000
56	A	99	GLU	-1	-0.893	-0.935	32.999	0.060	0.060	0.000	0.000	0.000	0.000
57	A	100	SER	0	-0.002	0.021	32.620	0.000	0.000	0.000	0.000	0.000	0.000
58	A	101	LEU	0	-0.063	-0.043	31.244	0.000	0.000	0.000	0.000	0.000	0.000
59	A	102	GLY	0	0.018	0.006	28.769	0.003	0.003	0.000	0.000	0.000	0.000
60	A	103	GLN	0	0.027	0.016	27.894	0.005	0.005	0.000	0.000	0.000	0.000
61	A	104	LYS	1	0.932	0.959	27.703	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	105	LEU	0	-0.038	-0.016	24.302	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	106	ASP	-1	-0.866	-0.952	23.629	0.127	0.127	0.000	0.000	0.000	0.000
64	A	107	GLU	-1	-0.972	-0.975	23.098	0.034	0.034	0.000	0.000	0.000	0.000
65	A	108	GLN	0	0.003	-0.011	21.364	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	109	ARG	1	0.875	0.952	19.268	-0.164	-0.164	0.000	0.000	0.000	0.000
67	A	110	VAL	0	0.016	0.002	18.296	0.020	0.020	0.000	0.000	0.000	0.000
68	A	111	LYS	1	0.920	0.982	18.325	0.025	0.025	0.000	0.000	0.000	0.000
69	A	112	ARG	1	0.914	0.946	13.766	-0.274	-0.274	0.000	0.000	0.000	0.000
70	A	113	ASP	-1	-0.894	-0.940	13.869	0.282	0.282	0.000	0.000	0.000	0.000
71	A	114	VAL	0	0.013	0.005	14.027	0.019	0.019	0.000	0.000	0.000	0.000
72	A	115	ALA	0	-0.036	-0.007	13.774	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	116	MET	0	0.004	-0.010	8.180	-0.139	-0.139	0.000	0.000	0.000	0.000
74	A	117	ALA	0	0.030	0.016	9.672	0.011	0.011	0.000	0.000	0.000	0.000
75	A	118	GLN	0	-0.063	-0.033	11.786	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	119	ALA	0	-0.047	-0.018	8.446	-0.065	-0.065	0.000	0.000	0.000	0.000
77	A	120	GLY	0	-0.038	-0.010	8.099	-0.272	-0.272	0.000	0.000	0.000	0.000
78	A	121	ILE	0	-0.036	-0.019	4.240	-0.111	-0.007	-0.001	-0.007	-0.096	0.000
79	A	122	PRO	0	-0.017	-0.001	4.898	-0.169	-0.169	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:44:LEU)