FMO DATABASE

FMODB ID: GNM51

Calculation Name: 1JRH-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JRH

Chain ID: I

ChEMBL ID:

UniProt ID: P01869

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-683203.396211
FMO2-HF: Nuclear repulsion	644956.897447
FMO2-HF: Total energy	-38246.498765
FMO2-MP2: Total energy	-38357.049493

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(I:11:SER)

Summations of interaction energy for fragment #1(I:11: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.
-16.688	-13.416	0.128	-1.567	-1.831	0.014

Interaction energy analysis for fragmet #1(I:11:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.037

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	I	13	PRO	0	0.032	0.018	3.882	-1.378	-0.274	-0.010	-0.398	-0.695	0.001
4	I	14	THR	0	0.010	0.000	6.179	0.588	0.588	0.000	0.000	0.000	0.000
5	I	15	PRO	0	-0.042	-0.015	8.262	-0.006	-0.006	0.000	0.000	0.000	0.000
6	I	16	THR	0	-0.028	-0.018	12.030	-0.055	-0.055	0.000	0.000	0.000	0.000
7	I	17	ASN	0	0.026	-0.002	14.480	0.051	0.051	0.000	0.000	0.000	0.000
8	I	18	VAL	0	-0.005	0.011	15.932	0.051	0.051	0.000	0.000	0.000	0.000
9	I	19	THR	0	-0.001	0.002	18.699	0.010	0.010	0.000	0.000	0.000	0.000
10	I	20	ILE	0	-0.032	-0.020	22.516	0.017	0.017	0.000	0.000	0.000	0.000
11	I	21	GLU	-1	-0.875	-0.921	25.327	-0.175	-0.175	0.000	0.000	0.000	0.000
12	I	22	SER	0	0.010	-0.011	28.740	0.014	0.014	0.000	0.000	0.000	0.000
13	I	23	TYR	0	0.014	0.026	32.059	0.003	0.003	0.000	0.000	0.000	0.000
14	I	24	ASN	0	-0.007	-0.004	35.156	0.009	0.009	0.000	0.000	0.000	0.000
15	I	25	MET	0	0.006	-0.009	35.731	-0.009	-0.009	0.000	0.000	0.000	0.000
16	I	26	ASN	0	0.005	0.013	31.712	0.017	0.017	0.000	0.000	0.000	0.000
17	I	27	PRO	0	0.026	0.020	28.835	-0.009	-0.009	0.000	0.000	0.000	0.000
18	I	28	ILE	0	-0.039	-0.019	25.819	0.016	0.016	0.000	0.000	0.000	0.000
19	I	29	VAL	0	0.001	0.006	20.581	-0.019	-0.019	0.000	0.000	0.000	0.000
20	I	30	TYR	0	-0.007	-0.025	21.816	0.023	0.023	0.000	0.000	0.000	0.000
21	I	31	TRP	0	-0.046	-0.017	15.662	-0.018	-0.018	0.000	0.000	0.000	0.000
22	I	32	GLU	-1	-0.863	-0.927	16.880	-0.395	-0.395	0.000	0.000	0.000	0.000
23	I	33	TYR	0	-0.066	-0.062	8.363	-0.047	-0.047	0.000	0.000	0.000	0.000
24	I	34	GLN	0	-0.013	0.006	9.493	-0.273	-0.273	0.000	0.000	0.000	0.000
25	I	35	ILE	0	0.048	0.018	13.850	0.079	0.079	0.000	0.000	0.000	0.000
26	I	36	MET	0	-0.024	-0.015	7.529	-0.138	-0.138	0.000	0.000	0.000	0.000
27	I	37	PRO	0	-0.014	-0.002	11.341	0.058	0.058	0.000	0.000	0.000	0.000
28	I	38	GLN	0	-0.028	-0.018	11.678	0.174	0.174	0.000	0.000	0.000	0.000
29	I	39	VAL	0	0.016	0.007	13.555	-0.096	-0.096	0.000	0.000	0.000	0.000
30	I	40	PRO	0	0.001	0.009	11.945	0.102	0.102	0.000	0.000	0.000	0.000
31	I	41	VAL	0	-0.066	-0.017	12.528	-0.006	-0.006	0.000	0.000	0.000	0.000
32	I	42	PHE	0	0.001	-0.015	12.625	-0.008	-0.008	0.000	0.000	0.000	0.000
33	I	43	THR	0	-0.012	0.001	14.350	0.080	0.080	0.000	0.000	0.000	0.000
34	I	44	VAL	0	-0.019	-0.004	15.556	-0.077	-0.077	0.000	0.000	0.000	0.000
35	I	45	GLU	-1	-0.715	-0.817	16.238	0.091	0.091	0.000	0.000	0.000	0.000
36	I	46	VAL	0	0.011	-0.002	19.828	-0.051	-0.051	0.000	0.000	0.000	0.000
37	I	47	LYS	1	0.843	0.926	22.902	0.095	0.095	0.000	0.000	0.000	0.000
38	I	48	ASN	0	0.047	0.019	25.315	-0.014	-0.014	0.000	0.000	0.000	0.000
39	I	49	TYR	0	-0.043	-0.031	27.840	0.007	0.007	0.000	0.000	0.000	0.000
40	I	50	GLY	0	0.061	0.030	29.874	-0.008	-0.008	0.000	0.000	0.000	0.000
41	I	51	VAL	0	-0.042	-0.001	33.405	0.004	0.004	0.000	0.000	0.000	0.000
42	I	52	LYS	1	0.844	0.912	33.286	0.035	0.035	0.000	0.000	0.000	0.000
43	I	53	ASN	0	0.011	-0.014	29.793	-0.008	-0.008	0.000	0.000	0.000	0.000
44	I	54	SER	0	-0.004	0.009	26.689	0.002	0.002	0.000	0.000	0.000	0.000
45	I	55	GLU	-1	-0.886	-0.946	24.472	0.062	0.062	0.000	0.000	0.000	0.000
46	I	56	TRP	0	-0.038	-0.013	20.055	-0.023	-0.023	0.000	0.000	0.000	0.000
47	I	57	ILE	0	0.029	0.022	22.565	0.029	0.029	0.000	0.000	0.000	0.000
48	I	58	ASP	-1	-0.896	-0.958	19.127	0.104	0.104	0.000	0.000	0.000	0.000
49	I	59	ALA	0	0.008	0.007	21.730	0.001	0.001	0.000	0.000	0.000	0.000
50	I	60	CYS	0	-0.050	-0.030	20.735	0.033	0.033	0.000	0.000	0.000	0.000
51	I	61	ILE	0	0.024	0.010	18.135	-0.008	-0.008	0.000	0.000	0.000	0.000
52	I	62	ASN	0	-0.056	-0.034	16.386	0.035	0.035	0.000	0.000	0.000	0.000
53	I	63	ILE	0	0.040	0.042	17.379	0.016	0.016	0.000	0.000	0.000	0.000
54	I	64	SER	0	0.021	-0.008	17.317	-0.017	-0.017	0.000	0.000	0.000	0.000
55	I	65	HIS	0	-0.027	-0.004	18.418	-0.030	-0.030	0.000	0.000	0.000	0.000
56	I	66	HIS	0	-0.034	-0.024	16.737	-0.039	-0.039	0.000	0.000	0.000	0.000
57	I	67	TYR	0	0.047	0.011	19.824	-0.025	-0.025	0.000	0.000	0.000	0.000
58	I	69	ASN	0	0.001	0.021	23.602	-0.015	-0.015	0.000	0.000	0.000	0.000
59	I	70	ILE	0	0.053	0.015	24.390	0.010	0.010	0.000	0.000	0.000	0.000
60	I	71	SER	0	0.006	-0.025	27.559	-0.001	-0.001	0.000	0.000	0.000	0.000
61	I	72	ASP	-1	-0.910	-0.953	29.226	-0.005	-0.005	0.000	0.000	0.000	0.000
62	I	73	HIS	0	-0.055	-0.027	26.447	0.003	0.003	0.000	0.000	0.000	0.000
63	I	74	VAL	0	-0.032	-0.005	29.668	-0.010	-0.010	0.000	0.000	0.000	0.000
64	I	75	GLY	0	0.017	-0.006	32.219	0.009	0.009	0.000	0.000	0.000	0.000
65	I	76	ASP	-1	-0.861	-0.902	34.641	-0.044	-0.044	0.000	0.000	0.000	0.000
66	I	77	PRO	0	0.051	0.021	35.633	-0.003	-0.003	0.000	0.000	0.000	0.000
67	I	78	SER	0	-0.037	-0.023	36.535	-0.007	-0.007	0.000	0.000	0.000	0.000
68	I	79	ASN	0	-0.133	-0.073	32.200	-0.001	-0.001	0.000	0.000	0.000	0.000
69	I	80	SER	0	0.008	0.002	29.039	0.004	0.004	0.000	0.000	0.000	0.000
70	I	81	LEU	0	-0.041	-0.030	26.979	0.013	0.013	0.000	0.000	0.000	0.000
71	I	82	TRP	0	-0.044	-0.024	22.211	-0.030	-0.030	0.000	0.000	0.000	0.000
72	I	83	VAL	0	0.032	0.005	19.591	0.028	0.028	0.000	0.000	0.000	0.000
73	I	84	ARG	1	0.713	0.849	15.440	0.010	0.010	0.000	0.000	0.000	0.000
74	I	85	VAL	0	0.032	0.027	14.511	0.065	0.065	0.000	0.000	0.000	0.000
75	I	86	LYS	1	0.831	0.912	10.216	-0.472	-0.472	0.000	0.000	0.000	0.000
76	I	87	ALA	0	0.058	0.028	9.014	0.080	0.080	0.000	0.000	0.000	0.000
77	I	88	ARG	1	0.843	0.913	8.605	-0.777	-0.777	0.000	0.000	0.000	0.000
78	I	89	VAL	0	0.031	0.014	7.878	-0.202	-0.202	0.000	0.000	0.000	0.000
79	I	90	GLY	0	0.032	0.014	8.864	0.620	0.620	0.000	0.000	0.000	0.000
80	I	91	GLN	0	-0.044	-0.030	9.931	-0.364	-0.364	0.000	0.000	0.000	0.000
81	I	92	LYS	1	0.943	0.986	3.114	-15.369	-13.270	0.139	-1.164	-1.074	0.013
82	I	93	GLU	-1	-0.764	-0.878	5.933	0.057	0.057	0.000	0.000	0.000	0.000
83	I	94	SER	0	-0.015	0.005	4.972	0.372	0.441	-0.001	-0.005	-0.062	0.000
84	I	95	ALA	0	-0.001	0.004	5.990	0.493	0.493	0.000	0.000	0.000	0.000
85	I	96	TYR	0	-0.015	-0.040	7.878	-0.120	-0.120	0.000	0.000	0.000	0.000
86	I	97	ALA	0	0.003	0.012	11.528	-0.070	-0.070	0.000	0.000	0.000	0.000
87	I	98	LYS	1	0.918	0.947	13.170	0.659	0.659	0.000	0.000	0.000	0.000
88	I	99	SER	0	-0.007	-0.012	16.524	-0.044	-0.044	0.000	0.000	0.000	0.000
89	I	100	GLU	-1	-0.945	-0.968	19.788	-0.313	-0.313	0.000	0.000	0.000	0.000
90	I	101	GLU	-1	-0.837	-0.884	22.769	-0.148	-0.148	0.000	0.000	0.000	0.000
91	I	102	PHE	0	0.025	0.008	26.080	-0.004	-0.004	0.000	0.000	0.000	0.000
92	I	103	ALA	0	0.025	0.010	28.484	0.011	0.011	0.000	0.000	0.000	0.000
93	I	104	VAL	0	0.019	0.012	32.137	0.012	0.012	0.000	0.000	0.000	0.000
94	I	105	SER	0	-0.068	-0.024	33.692	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:11:SER)