FMO DATABASE

FMODB ID: 5J35Z

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497094.476816
FMO2-HF: Nuclear repulsion	466154.280433
FMO2-HF: Total energy	-30940.196383
FMO2-MP2: Total energy	-31030.954471

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.
-31.938	-33.652	20.658	-10.04	-8.903	-0.068

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 : -0.006 / q_NPA : -0.028

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	0.037	0.008	2.658	-1.991	0.339	0.262	-1.080	-1.511	0.004
4	A	31	GLU	-1	-0.841	-0.893	1.650	-35.030	-39.656	20.379	-8.931	-6.822	-0.072
5	A	32	ARG	1	0.787	0.862	3.402	1.735	2.224	0.018	-0.026	-0.481	0.000
6	A	33	SER	0	-0.013	0.002	5.261	0.572	0.665	-0.001	-0.003	-0.089	0.000
7	A	34	ALA	0	0.072	0.051	6.574	0.352	0.352	0.000	0.000	0.000	0.000
8	A	35	ARG	1	0.880	0.928	6.324	1.878	1.878	0.000	0.000	0.000	0.000
9	A	36	PHE	0	0.023	0.009	9.243	0.344	0.344	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.897	-0.945	10.617	-0.899	-0.899	0.000	0.000	0.000	0.000
11	A	38	ARG	1	0.950	0.978	8.990	1.909	1.909	0.000	0.000	0.000	0.000
12	A	39	ASP	-1	-0.876	-0.944	12.393	-0.892	-0.892	0.000	0.000	0.000	0.000
13	A	40	ALA	0	-0.034	-0.022	15.112	0.106	0.106	0.000	0.000	0.000	0.000
14	A	41	LEU	0	-0.026	-0.018	16.245	0.076	0.076	0.000	0.000	0.000	0.000
15	A	42	GLU	-1	-0.939	-0.934	18.246	-0.424	-0.424	0.000	0.000	0.000	0.000
16	A	43	PHE	0	-0.019	-0.042	18.797	0.058	0.058	0.000	0.000	0.000	0.000
17	A	44	LEU	0	0.031	0.024	21.897	0.040	0.040	0.000	0.000	0.000	0.000
18	A	45	ASP	-1	-0.813	-0.912	23.520	-0.206	-0.206	0.000	0.000	0.000	0.000
19	A	46	GLN	0	-0.031	0.003	25.526	0.025	0.025	0.000	0.000	0.000	0.000
20	A	47	MET	0	-0.080	-0.071	22.750	0.034	0.034	0.000	0.000	0.000	0.000
21	A	48	TYR	0	0.046	0.029	26.792	0.019	0.019	0.000	0.000	0.000	0.000
22	A	49	SER	0	0.025	0.012	29.090	0.021	0.021	0.000	0.000	0.000	0.000
23	A	50	ALA	0	-0.087	-0.044	29.664	0.015	0.015	0.000	0.000	0.000	0.000
24	A	51	ALA	0	0.033	0.009	29.975	0.014	0.014	0.000	0.000	0.000	0.000
25	A	52	LEU	0	0.023	0.014	31.963	0.012	0.012	0.000	0.000	0.000	0.000
26	A	53	ARG	1	0.868	0.932	34.668	0.129	0.129	0.000	0.000	0.000	0.000
27	A	54	MET	0	-0.065	-0.026	31.481	0.006	0.006	0.000	0.000	0.000	0.000
28	A	55	THR	0	-0.001	0.001	34.275	0.007	0.007	0.000	0.000	0.000	0.000
29	A	56	ARG	1	0.859	0.949	37.204	0.094	0.094	0.000	0.000	0.000	0.000
30	A	57	ASN	0	0.043	-0.015	37.775	0.003	0.003	0.000	0.000	0.000	0.000
31	A	58	PRO	0	0.045	0.037	35.497	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	59	ALA	0	0.053	0.038	34.256	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.759	-0.880	33.867	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	61	ALA	0	-0.126	-0.044	32.818	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	62	GLU	-1	-0.881	-0.950	29.078	-0.194	-0.194	0.000	0.000	0.000	0.000
36	A	63	ASP	-1	-0.851	-0.920	28.797	-0.142	-0.142	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.027	-0.014	28.658	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	65	VAL	0	-0.020	-0.008	25.711	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	66	GLN	0	-0.082	-0.037	24.483	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	67	GLU	-1	-0.793	-0.897	23.706	-0.132	-0.132	0.000	0.000	0.000	0.000
41	A	68	THR	0	-0.039	-0.028	23.117	0.004	0.004	0.000	0.000	0.000	0.000
42	A	69	TYR	0	-0.005	-0.034	18.932	0.004	0.004	0.000	0.000	0.000	0.000
43	A	70	ALA	0	0.015	0.035	18.969	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	71	LYS	1	0.857	0.907	19.445	0.121	0.121	0.000	0.000	0.000	0.000
45	A	72	ALA	0	-0.042	-0.026	18.002	0.003	0.003	0.000	0.000	0.000	0.000
46	A	73	TYR	0	-0.017	-0.038	14.809	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	74	ALA	0	-0.007	0.004	14.576	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	75	SER	0	-0.037	-0.024	16.672	0.066	0.066	0.000	0.000	0.000	0.000
49	A	76	PHE	0	-0.012	0.018	7.331	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	77	HIS	0	0.027	0.021	11.735	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.047	-0.051	12.790	0.112	0.112	0.000	0.000	0.000	0.000
52	A	79	PHE	0	-0.056	-0.006	12.405	0.043	0.043	0.000	0.000	0.000	0.000
53	A	80	ARG	1	0.926	0.945	12.834	-0.156	-0.156	0.000	0.000	0.000	0.000
54	A	81	GLU	-1	-0.828	-0.880	9.766	0.100	0.100	0.000	0.000	0.000	0.000
55	A	82	GLY	0	0.027	0.016	13.182	-0.069	-0.069	0.000	0.000	0.000	0.000
56	A	83	THR	0	-0.026	-0.022	15.776	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	84	ASN	0	0.032	0.032	17.346	-0.049	-0.049	0.000	0.000	0.000	0.000
58	A	85	LEU	0	0.044	0.023	15.178	0.032	0.032	0.000	0.000	0.000	0.000
59	A	86	LYS	1	0.979	1.001	18.383	0.264	0.264	0.000	0.000	0.000	0.000
60	A	87	ALA	0	-0.049	-0.021	21.772	0.016	0.016	0.000	0.000	0.000	0.000
61	A	88	TRP	0	-0.012	-0.008	16.846	0.014	0.014	0.000	0.000	0.000	0.000
62	A	89	LEU	0	0.077	0.039	18.615	0.013	0.013	0.000	0.000	0.000	0.000
63	A	90	TYR	0	-0.009	-0.018	21.870	0.012	0.012	0.000	0.000	0.000	0.000
64	A	91	ARG	1	0.967	0.992	23.785	0.091	0.091	0.000	0.000	0.000	0.000
65	A	92	ILE	0	-0.013	0.002	20.065	0.019	0.019	0.000	0.000	0.000	0.000
66	A	93	LEU	0	0.069	0.037	24.524	0.011	0.011	0.000	0.000	0.000	0.000
67	A	94	THR	0	-0.059	-0.041	26.924	0.012	0.012	0.000	0.000	0.000	0.000
68	A	95	ASN	0	-0.018	-0.007	27.143	0.005	0.005	0.000	0.000	0.000	0.000
69	A	96	THR	0	0.051	0.031	26.794	0.011	0.011	0.000	0.000	0.000	0.000
70	A	97	PHE	0	-0.037	-0.016	29.498	0.007	0.007	0.000	0.000	0.000	0.000
71	A	98	ILE	0	-0.092	-0.059	32.415	0.007	0.007	0.000	0.000	0.000	0.000
72	A	99	ASN	0	-0.100	-0.073	31.213	0.013	0.013	0.000	0.000	0.000	0.000
73	A	100	SER	0	-0.004	0.036	30.607	0.007	0.007	0.000	0.000	0.000	0.000
74	A	101	TYR	0	-0.017	0.014	33.676	0.005	0.005	0.000	0.000	0.000	0.000
75	A	102	ARG	1	0.957	0.983	35.642	0.064	0.064	0.000	0.000	0.000	0.000

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