FMO DATABASE

FMODB ID: 2JMJR

Calculation Name: 4J4E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4E

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533200.800962
FMO2-HF: Nuclear repulsion	493976.484062
FMO2-HF: Total energy	-39224.3169
FMO2-MP2: Total energy	-39336.216092

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:1:LEU)

Summations of interaction energy for fragment #1(A:1: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.
-13.505	-9.57	3.951	-2.637	-5.248	0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.003

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	3	LYS	1	0.915	0.945	2.463	-10.412	-8.464	2.853	-1.760	-3.041	0.014
4	A	4	PHE	0	0.087	0.039	5.494	0.038	0.038	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.003	-0.001	8.697	0.084	0.084	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.012	-0.005	7.234	0.060	0.060	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.046	0.031	9.468	-0.019	-0.019	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.131	-0.056	11.861	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.056	0.033	14.096	0.047	0.047	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.033	-0.028	17.454	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.018	-0.019	16.206	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.002	0.005	18.480	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.021	0.001	15.631	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.012	0.004	19.618	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.014	0.002	22.180	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.004	-0.007	18.765	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.004	0.007	17.841	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.017	0.011	12.739	0.023	0.023	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.004	-0.003	16.822	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.025	0.015	14.790	0.036	0.036	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.001	0.005	17.565	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.877	-0.939	12.880	-0.175	-0.175	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.885	0.938	14.255	0.168	0.168	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.003	-0.019	13.221	0.011	0.011	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.022	-0.008	15.199	0.016	0.016	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.046	0.045	18.030	0.020	0.020	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.006	-0.004	19.879	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.002	-0.015	16.489	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.018	-0.011	17.835	0.015	0.015	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.026	0.019	18.053	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.071	-0.018	16.217	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.040	-0.009	17.530	0.008	0.008	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.011	-0.003	11.351	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.814	-0.918	15.637	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.025	-0.023	11.685	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.005	-0.001	14.700	0.010	0.010	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.046	-0.004	15.064	0.002	0.002	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.032	-0.015	10.287	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.038	-0.010	11.440	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.862	-0.931	13.687	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.039	-0.040	16.357	0.019	0.019	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.002	-0.005	16.416	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.926	-0.969	19.132	0.040	0.040	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.004	0.016	22.065	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.031	-0.014	17.295	0.013	0.013	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.016	-0.006	15.420	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.921	0.963	12.487	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.024	-0.013	7.805	-0.091	-0.091	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.012	0.027	10.217	0.032	0.032	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.022	-0.010	10.728	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.023	-0.018	12.294	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.040	0.005	14.165	0.031	0.031	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.048	0.014	17.663	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.007	-0.007	18.985	0.005	0.005	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.884	-0.914	18.024	-0.128	-0.128	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.086	-0.080	14.332	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.057	-0.023	16.466	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.822	0.880	19.725	0.017	0.017	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.033	-0.035	23.152	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.020	0.025	24.113	0.003	0.003	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.056	-0.033	26.391	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.009	0.016	28.650	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.021	-0.008	29.723	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.025	0.009	31.617	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.030	-0.022	34.537	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.057	-0.056	32.036	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.845	-0.893	28.180	0.013	0.013	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.032	0.001	24.055	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.006	-0.005	24.926	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.030	-0.009	21.777	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.782	-0.833	21.065	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.907	0.972	14.281	0.107	0.107	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.035	0.022	10.390	0.004	0.004	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.935	0.958	2.971	-1.473	-0.747	0.248	-0.236	-0.737	0.000
75	A	77	ALA	0	0.032	0.019	8.367	0.018	0.018	0.000	0.000	0.000	0.000
76	A	78	GLN	0	-0.011	-0.001	7.296	-0.035	-0.035	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.003	-0.003	5.082	-0.090	-0.090	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.014	0.006	6.715	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.014	-0.010	2.461	-1.351	-0.220	0.851	-0.624	-1.358	-0.003
80	A	82	SER	0	0.003	0.004	5.940	0.120	0.120	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.019	-0.014	4.410	-0.718	-0.588	-0.001	-0.017	-0.112	0.000
82	A	84	LYS	1	0.972	0.975	5.784	0.264	0.264	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.011	0.007	8.144	0.215	0.215	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.002	-0.007	10.915	-0.104	-0.104	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.007	-0.006	14.176	0.018	0.018	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.856	-0.928	17.108	0.097	0.097	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.957	-0.957	14.991	0.325	0.325	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.821	0.893	17.360	-0.228	-0.228	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.035	0.003	19.689	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.063	0.043	22.254	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.018	-0.020	25.726	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.022	-0.025	28.772	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.919	-0.961	31.729	0.033	0.033	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.005	0.010	33.057	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.062	-0.025	30.933	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.002	-0.001	24.895	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.917	0.958	26.316	-0.060	-0.060	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.020	0.019	19.157	0.011	0.011	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.913	-0.950	23.027	0.113	0.113	0.000	0.000	0.000	0.000

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