FMO DATABASE

FMODB ID: 4J3YN

Calculation Name: 1H3L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H3L

Chain ID: A

ChEMBL ID:

UniProt ID: Q7AKG9

Base Structure: X-ray

Registration Date: 2023-09-21

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497363.005492
FMO2-HF: Nuclear repulsion	466423.804845
FMO2-HF: Total energy	-30939.200647
FMO2-MP2: Total energy	-31030.083086

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:28:SER)

Summations of interaction energy for fragment #1(A: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.
-20.896	-28.718	33.006	-14.602	-10.582	-0.081

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.044

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	30	ALA	0	0.060	0.015	2.435	-1.818	0.395	0.774	-1.262	-1.725	-0.001
4	A	31	GLU	-1	-0.833	-0.885	1.630	-25.248	-36.244	32.196	-13.112	-8.088	-0.080
5	A	32	ARG	1	0.762	0.853	2.981	2.046	2.898	0.037	-0.222	-0.667	0.000
6	A	33	SER	0	-0.023	0.001	5.146	0.710	0.819	-0.001	-0.006	-0.102	0.000
7	A	34	ALA	0	0.078	0.055	6.528	0.421	0.421	0.000	0.000	0.000	0.000
8	A	35	ARG	1	0.909	0.938	5.144	2.301	2.301	0.000	0.000	0.000	0.000
9	A	36	PHE	0	0.017	0.003	9.179	0.391	0.391	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.888	-0.935	10.767	-1.149	-1.149	0.000	0.000	0.000	0.000
11	A	38	ARG	1	0.953	0.976	8.614	2.120	2.120	0.000	0.000	0.000	0.000
12	A	39	ASP	-1	-0.882	-0.943	12.807	-0.814	-0.814	0.000	0.000	0.000	0.000
13	A	40	ALA	0	-0.055	-0.042	15.051	0.122	0.122	0.000	0.000	0.000	0.000
14	A	41	LEU	0	-0.039	-0.016	16.094	0.089	0.089	0.000	0.000	0.000	0.000
15	A	42	GLU	-1	-0.942	-0.929	18.242	-0.433	-0.433	0.000	0.000	0.000	0.000
16	A	43	PHE	0	-0.014	-0.046	18.552	0.072	0.072	0.000	0.000	0.000	0.000
17	A	44	LEU	0	0.032	0.020	21.882	0.043	0.043	0.000	0.000	0.000	0.000
18	A	45	ASP	-1	-0.839	-0.930	23.541	-0.234	-0.234	0.000	0.000	0.000	0.000
19	A	46	GLN	0	-0.025	-0.010	25.562	0.030	0.030	0.000	0.000	0.000	0.000
20	A	47	MET	0	-0.091	-0.075	23.023	0.029	0.029	0.000	0.000	0.000	0.000
21	A	48	TYR	0	0.038	0.030	26.702	0.019	0.019	0.000	0.000	0.000	0.000
22	A	49	SER	0	0.041	0.017	29.050	0.025	0.025	0.000	0.000	0.000	0.000
23	A	50	ALA	0	-0.102	-0.042	29.567	0.018	0.018	0.000	0.000	0.000	0.000
24	A	51	ALA	0	0.060	0.015	30.030	0.015	0.015	0.000	0.000	0.000	0.000
25	A	52	LEU	0	-0.002	0.007	31.855	0.014	0.014	0.000	0.000	0.000	0.000
26	A	53	ARG	1	0.865	0.930	34.574	0.144	0.144	0.000	0.000	0.000	0.000
27	A	54	MET	0	-0.077	-0.027	31.041	0.007	0.007	0.000	0.000	0.000	0.000
28	A	55	THR	0	-0.005	0.010	34.195	0.008	0.008	0.000	0.000	0.000	0.000
29	A	56	ARG	1	0.878	0.952	37.043	0.112	0.112	0.000	0.000	0.000	0.000
30	A	57	ASN	0	0.049	0.005	37.627	0.000	0.000	0.000	0.000	0.000	0.000
31	A	58	PRO	0	0.062	0.040	35.398	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	59	ALA	0	0.070	0.051	34.092	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.814	-0.916	33.640	-0.140	-0.140	0.000	0.000	0.000	0.000
34	A	61	ALA	0	-0.125	-0.051	32.629	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	62	GLU	-1	-0.906	-0.970	28.803	-0.249	-0.249	0.000	0.000	0.000	0.000
36	A	63	ASP	-1	-0.865	-0.930	28.585	-0.202	-0.202	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.014	-0.007	28.384	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	65	VAL	0	-0.023	-0.001	25.579	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	66	GLN	0	-0.046	-0.014	24.164	-0.053	-0.053	0.000	0.000	0.000	0.000
40	A	67	GLU	-1	-0.829	-0.918	23.421	-0.211	-0.211	0.000	0.000	0.000	0.000
41	A	68	THR	0	-0.063	-0.052	22.921	0.001	0.001	0.000	0.000	0.000	0.000
42	A	69	TYR	0	-0.010	-0.030	18.852	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	70	ALA	0	0.016	0.043	18.691	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	71	LYS	1	0.875	0.923	19.062	0.183	0.183	0.000	0.000	0.000	0.000
45	A	72	ALA	0	-0.034	-0.027	17.821	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	73	TYR	0	-0.017	-0.030	14.555	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	74	ALA	0	-0.008	0.006	14.178	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	75	SER	0	-0.035	-0.034	16.268	0.067	0.067	0.000	0.000	0.000	0.000
49	A	76	PHE	0	-0.008	0.025	7.095	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	77	HIS	0	0.018	0.017	11.707	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.034	-0.050	12.775	0.119	0.119	0.000	0.000	0.000	0.000
52	A	79	PHE	0	-0.068	-0.011	12.293	0.073	0.073	0.000	0.000	0.000	0.000
53	A	80	ARG	1	0.940	0.949	12.314	-0.091	-0.091	0.000	0.000	0.000	0.000
54	A	81	GLU	-1	-0.829	-0.873	9.591	0.219	0.219	0.000	0.000	0.000	0.000
55	A	82	GLY	0	0.023	0.010	12.904	-0.062	-0.062	0.000	0.000	0.000	0.000
56	A	83	THR	0	-0.032	-0.021	15.361	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	84	ASN	0	0.052	0.047	17.125	-0.055	-0.055	0.000	0.000	0.000	0.000
58	A	85	LEU	0	0.063	0.031	15.346	0.026	0.026	0.000	0.000	0.000	0.000
59	A	86	LYS	1	1.010	1.016	18.205	0.259	0.259	0.000	0.000	0.000	0.000
60	A	87	ALA	0	-0.054	-0.024	21.617	0.011	0.011	0.000	0.000	0.000	0.000
61	A	88	TRP	0	0.004	-0.008	16.549	0.015	0.015	0.000	0.000	0.000	0.000
62	A	89	LEU	0	0.073	0.038	18.323	0.008	0.008	0.000	0.000	0.000	0.000
63	A	90	TYR	0	0.010	0.010	21.689	0.013	0.013	0.000	0.000	0.000	0.000
64	A	91	ARG	1	0.978	0.992	23.281	0.125	0.125	0.000	0.000	0.000	0.000
65	A	92	ILE	0	-0.008	0.007	19.640	0.021	0.021	0.000	0.000	0.000	0.000
66	A	93	LEU	0	0.067	0.039	24.314	0.011	0.011	0.000	0.000	0.000	0.000
67	A	94	THR	0	-0.098	-0.043	26.746	0.019	0.019	0.000	0.000	0.000	0.000
68	A	95	ASN	0	0.023	-0.003	26.975	0.002	0.002	0.000	0.000	0.000	0.000
69	A	96	THR	0	0.043	0.030	26.606	0.009	0.009	0.000	0.000	0.000	0.000
70	A	97	PHE	0	-0.031	-0.019	29.210	0.008	0.008	0.000	0.000	0.000	0.000
71	A	98	ILE	0	-0.097	-0.067	32.210	0.008	0.008	0.000	0.000	0.000	0.000
72	A	99	ASN	0	-0.111	-0.091	30.971	0.016	0.016	0.000	0.000	0.000	0.000
73	A	100	SER	0	0.018	0.052	30.391	0.005	0.005	0.000	0.000	0.000	0.000
74	A	101	TYR	0	-0.006	0.009	33.331	0.010	0.010	0.000	0.000	0.000	0.000
75	A	102	ARG	1	0.939	0.982	35.345	0.092	0.092	0.000	0.000	0.000	0.000

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