FMO DATABASE

FMODB ID: M3RGZ

Calculation Name: 1JNP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JNP

Chain ID: A

ChEMBL ID:

UniProt ID: P56280

Base Structure: X-ray

Registration Date: 2023-03-13

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-883925.486696
FMO2-HF: Nuclear repulsion	840656.56091
FMO2-HF: Total energy	-43268.925786
FMO2-MP2: Total energy	-43395.676993

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:8:ARG)

Summations of interaction energy for fragment #1(A:8:ARG)

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.
-111.773	-104.257	22.22	-12.484	-17.251	-0.129

Interaction energy analysis for fragmet #1(A:8:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.917

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	10	GLU	-1	-0.892	-0.954	3.882	-30.246	-28.168	-0.022	-1.131	-0.925	0.000
4	A	11	THR	0	0.011	0.017	6.767	-0.194	-0.194	0.000	0.000	0.000	0.000
5	A	12	PRO	0	-0.043	-0.016	8.855	1.199	1.199	0.000	0.000	0.000	0.000
6	A	13	ALA	0	-0.014	-0.014	12.429	0.937	0.937	0.000	0.000	0.000	0.000
7	A	14	HIS	1	0.848	0.907	13.195	17.805	17.805	0.000	0.000	0.000	0.000
8	A	15	PRO	0	0.045	0.040	14.903	0.771	0.771	0.000	0.000	0.000	0.000
9	A	16	ASN	0	-0.023	-0.002	18.089	0.395	0.395	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.855	0.923	21.644	11.341	11.341	0.000	0.000	0.000	0.000
11	A	18	LEU	0	0.024	0.025	17.798	-0.365	-0.365	0.000	0.000	0.000	0.000
12	A	19	TRP	0	0.017	-0.004	21.851	0.340	0.340	0.000	0.000	0.000	0.000
13	A	20	ILE	0	-0.028	-0.009	23.977	-0.372	-0.372	0.000	0.000	0.000	0.000
14	A	21	TRP	0	-0.071	-0.044	24.894	0.321	0.321	0.000	0.000	0.000	0.000
15	A	22	GLU	-1	-0.843	-0.952	25.961	-11.115	-11.115	0.000	0.000	0.000	0.000
16	A	23	LYS	1	0.828	0.895	26.329	9.810	9.810	0.000	0.000	0.000	0.000
17	A	24	HIS	0	0.013	0.016	21.280	0.106	0.106	0.000	0.000	0.000	0.000
18	A	25	VAL	0	0.006	0.007	21.685	-0.740	-0.740	0.000	0.000	0.000	0.000
19	A	26	TYR	0	0.035	-0.010	20.265	0.463	0.463	0.000	0.000	0.000	0.000
20	A	27	LEU	0	0.001	-0.002	20.661	-0.437	-0.437	0.000	0.000	0.000	0.000
21	A	28	ASP	-1	-0.752	-0.863	17.590	-14.766	-14.766	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.850	-0.935	21.184	-12.648	-12.648	0.000	0.000	0.000	0.000
23	A	30	PHE	0	-0.053	-0.014	16.855	0.473	0.473	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.834	0.922	20.277	12.439	12.439	0.000	0.000	0.000	0.000
25	A	32	ARG	1	0.757	0.859	14.825	16.892	16.892	0.000	0.000	0.000	0.000
26	A	33	SER	0	-0.001	-0.002	17.877	0.394	0.394	0.000	0.000	0.000	0.000
27	A	34	TRP	0	-0.030	-0.039	12.037	-1.429	-1.429	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.045	0.015	16.639	1.035	1.035	0.000	0.000	0.000	0.000
29	A	36	PRO	0	-0.024	-0.007	16.878	-1.245	-1.245	0.000	0.000	0.000	0.000
30	A	37	VAL	0	-0.013	-0.001	13.224	0.523	0.523	0.000	0.000	0.000	0.000
31	A	38	VAL	0	-0.040	-0.024	14.032	0.125	0.125	0.000	0.000	0.000	0.000
32	A	39	ILE	0	0.049	0.017	16.970	-0.279	-0.279	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.850	0.937	17.773	15.167	15.167	0.000	0.000	0.000	0.000
34	A	41	SER	0	0.081	0.019	19.662	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	42	ASN	0	-0.099	-0.059	22.719	-0.723	-0.723	0.000	0.000	0.000	0.000
36	A	43	GLU	-1	-0.878	-0.924	24.780	-10.258	-10.258	0.000	0.000	0.000	0.000
37	A	44	LYS	1	0.807	0.925	20.044	15.515	15.515	0.000	0.000	0.000	0.000
38	A	45	PHE	0	0.033	-0.006	22.354	-0.293	-0.293	0.000	0.000	0.000	0.000
39	A	46	GLN	0	-0.018	-0.007	16.764	0.712	0.712	0.000	0.000	0.000	0.000
40	A	47	VAL	0	0.018	0.013	18.015	0.009	0.009	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.004	0.003	11.283	-0.496	-0.496	0.000	0.000	0.000	0.000
42	A	49	LEU	0	-0.004	0.000	14.782	0.737	0.737	0.000	0.000	0.000	0.000
43	A	50	ARG	1	0.851	0.886	7.833	28.449	28.449	0.000	0.000	0.000	0.000
44	A	51	GLN	0	-0.014	-0.006	11.334	2.541	2.541	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.893	-0.950	12.925	-19.745	-19.745	0.000	0.000	0.000	0.000
46	A	53	ASP	-1	-0.883	-0.933	15.626	-14.277	-14.277	0.000	0.000	0.000	0.000
47	A	54	VAL	0	-0.009	0.003	18.461	0.316	0.316	0.000	0.000	0.000	0.000
48	A	55	THR	0	-0.035	-0.019	22.096	0.376	0.376	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.014	0.011	23.663	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	57	GLY	0	0.007	-0.007	26.333	0.112	0.112	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.928	-0.953	29.138	-9.204	-9.204	0.000	0.000	0.000	0.000
52	A	59	ALA	0	0.012	0.015	29.652	-0.201	-0.201	0.000	0.000	0.000	0.000
53	A	60	MET	0	-0.006	0.026	30.152	0.263	0.263	0.000	0.000	0.000	0.000
54	A	61	SER	0	0.008	-0.007	31.675	-0.085	-0.085	0.000	0.000	0.000	0.000
55	A	62	PRO	0	0.018	-0.013	33.340	-0.077	-0.077	0.000	0.000	0.000	0.000
56	A	63	SER	0	0.005	-0.004	34.360	-0.140	-0.140	0.000	0.000	0.000	0.000
57	A	64	GLN	0	0.001	0.023	34.336	0.238	0.238	0.000	0.000	0.000	0.000
58	A	65	LEU	0	0.000	0.022	28.977	-0.180	-0.180	0.000	0.000	0.000	0.000
59	A	66	VAL	0	-0.009	-0.016	32.254	-0.139	-0.139	0.000	0.000	0.000	0.000
60	A	67	PRO	0	-0.034	-0.002	33.491	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	68	TYR	0	-0.027	-0.042	24.957	-0.301	-0.301	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.902	-0.948	25.384	-11.827	-11.827	0.000	0.000	0.000	0.000
63	A	70	LEU	0	-0.034	0.002	22.059	-0.432	-0.432	0.000	0.000	0.000	0.000
64	A	71	PRO	0	-0.032	0.011	24.603	0.548	0.548	0.000	0.000	0.000	0.000
65	A	72	LEU	0	0.027	0.008	26.492	-0.254	-0.254	0.000	0.000	0.000	0.000
66	A	73	MET	0	-0.018	-0.010	26.262	-0.119	-0.119	0.000	0.000	0.000	0.000
67	A	74	TRP	0	0.073	0.024	21.173	0.071	0.071	0.000	0.000	0.000	0.000
68	A	75	GLN	0	-0.046	-0.038	23.581	0.051	0.051	0.000	0.000	0.000	0.000
69	A	76	LEU	0	-0.006	0.015	19.690	0.194	0.194	0.000	0.000	0.000	0.000
70	A	77	TYR	0	-0.005	-0.007	23.208	0.641	0.641	0.000	0.000	0.000	0.000
71	A	78	PRO	0	0.007	-0.013	24.147	-0.423	-0.423	0.000	0.000	0.000	0.000
72	A	79	LYS	1	0.857	0.930	24.253	11.014	11.014	0.000	0.000	0.000	0.000
73	A	80	ASP	-1	-0.762	-0.870	17.525	-16.068	-16.068	0.000	0.000	0.000	0.000
74	A	81	ARG	1	0.865	0.947	19.985	11.362	11.362	0.000	0.000	0.000	0.000
75	A	82	TYR	0	0.049	0.003	17.625	0.313	0.313	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.816	0.909	23.044	9.897	9.897	0.000	0.000	0.000	0.000
77	A	84	SER	0	-0.026	-0.039	26.302	-0.188	-0.188	0.000	0.000	0.000	0.000
78	A	85	ALA	0	-0.018	-0.020	27.502	0.350	0.350	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.767	-0.867	30.160	-10.238	-10.238	0.000	0.000	0.000	0.000
80	A	87	SER	0	-0.059	-0.032	31.417	0.152	0.152	0.000	0.000	0.000	0.000
81	A	88	MET	0	0.011	0.037	29.012	0.026	0.026	0.000	0.000	0.000	0.000
82	A	89	TYR	0	-0.011	-0.031	25.746	-0.042	-0.042	0.000	0.000	0.000	0.000
83	A	90	TRP	0	0.088	0.047	21.330	-0.084	-0.084	0.000	0.000	0.000	0.000
84	A	91	GLN	0	-0.070	-0.041	17.490	0.691	0.691	0.000	0.000	0.000	0.000
85	A	92	ILE	0	0.039	0.023	13.743	-0.316	-0.316	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.054	-0.010	13.834	-0.045	-0.045	0.000	0.000	0.000	0.000
87	A	94	TYR	0	-0.001	-0.013	9.726	-0.950	-0.950	0.000	0.000	0.000	0.000
88	A	95	HIS	0	0.005	-0.011	9.739	1.614	1.614	0.000	0.000	0.000	0.000
89	A	96	ILE	0	-0.004	0.010	3.726	-1.115	-0.871	0.005	-0.056	-0.192	0.000
90	A	97	LYN	0	0.102	0.073	3.480	0.792	1.805	0.004	-0.520	-0.497	-0.002
91	A	98	PHE	0	-0.012	-0.034	1.872	-28.169	-28.121	20.123	-8.571	-11.600	-0.087
92	A	99	ARG	1	0.836	0.890	2.344	9.600	13.653	2.110	-2.176	-3.988	-0.040
93	A	100	ASP	-1	-0.861	-0.908	4.496	-28.192	-28.112	0.000	-0.030	-0.049	0.000
94	A	101	VAL	0	0.044	0.038	6.192	2.484	2.484	0.000	0.000	0.000	0.000
95	A	102	GLU	-1	-0.801	-0.886	5.908	-27.692	-27.692	0.000	0.000	0.000	0.000
96	A	103	ASP	-1	-0.806	-0.857	7.969	-29.903	-29.903	0.000	0.000	0.000	0.000
97	A	104	MET	0	-0.001	-0.004	9.723	-0.948	-0.948	0.000	0.000	0.000	0.000
98	A	105	LEU	0	-0.052	0.002	12.450	1.048	1.048	0.000	0.000	0.000	0.000
99	A	106	LEU	0	0.018	0.011	14.155	0.407	0.407	0.000	0.000	0.000	0.000
100	A	107	GLU	-1	-0.824	-0.927	17.754	-16.351	-16.351	0.000	0.000	0.000	0.000
101	A	108	LEU	0	-0.032	0.003	20.125	0.562	0.562	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:ARG)