FMO DATABASE

FMODB ID: 3JGRL

Calculation Name: 5IFZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YCV4

Base Structure: X-ray

Registration Date: 2023-09-23

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-886121.12532
FMO2-HF: Nuclear repulsion	843042.78072
FMO2-HF: Total energy	-43078.3446
FMO2-MP2: Total energy	-43203.302659

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:14:MET)

Summations of interaction energy for fragment #1(A:14:MET)

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.
-11.06	-1.696	10.135	-5.718	-13.78	-0.041

Interaction energy analysis for fragmet #1(A:14:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.011

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	16	VAL	0	0.000	0.000	3.750	-1.676	-0.059	-0.014	-0.613	-0.990	0.003
4	A	17	ALA	0	0.011	0.015	6.130	0.522	0.522	0.000	0.000	0.000	0.000
5	A	18	VAL	0	-0.011	-0.008	9.797	-0.098	-0.098	0.000	0.000	0.000	0.000
6	A	19	ALA	0	-0.008	-0.003	12.406	0.114	0.114	0.000	0.000	0.000	0.000
7	A	20	GLY	0	0.027	0.008	15.935	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	21	ASP	-1	-0.841	-0.933	19.360	-0.224	-0.224	0.000	0.000	0.000	0.000
9	A	22	SER	0	0.046	0.005	22.784	0.001	0.001	0.000	0.000	0.000	0.000
10	A	23	ALA	0	-0.106	-0.053	25.556	0.009	0.009	0.000	0.000	0.000	0.000
11	A	24	GLY	0	0.004	-0.003	21.504	0.001	0.001	0.000	0.000	0.000	0.000
12	A	25	GLU	-1	-0.932	-0.953	20.365	-0.206	-0.206	0.000	0.000	0.000	0.000
13	A	26	GLY	0	0.028	0.007	20.256	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	27	LEU	0	-0.012	-0.011	18.304	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.034	0.010	16.275	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	29	LYS	1	0.867	0.930	15.532	0.190	0.190	0.000	0.000	0.000	0.000
17	A	30	VAL	0	-0.011	0.008	16.575	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	31	LEU	0	-0.018	-0.019	13.084	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	32	ALA	0	0.013	0.001	11.753	-0.085	-0.085	0.000	0.000	0.000	0.000
20	A	33	ASP	-1	-0.912	-0.969	11.977	-0.218	-0.218	0.000	0.000	0.000	0.000
21	A	34	HIS	0	-0.121	-0.086	12.398	0.075	0.075	0.000	0.000	0.000	0.000
22	A	35	LEU	0	-0.024	-0.020	8.021	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	36	LYS	1	0.885	0.950	7.994	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	37	ASP	-1	-0.887	-0.935	8.545	0.135	0.135	0.000	0.000	0.000	0.000
25	A	38	ARG	1	0.746	0.874	6.696	1.030	1.030	0.000	0.000	0.000	0.000
26	A	39	PHE	0	-0.028	-0.015	2.260	-1.914	-0.743	0.766	-0.412	-1.525	0.000
27	A	40	GLU	-1	-0.870	-0.932	3.159	3.397	4.481	0.008	-0.340	-0.752	0.000
28	A	41	VAL	0	-0.018	-0.005	5.093	-0.772	-0.787	-0.001	-0.011	0.027	0.000
29	A	42	SER	0	-0.032	-0.011	8.126	0.336	0.336	0.000	0.000	0.000	0.000
30	A	43	GLU	-1	-0.755	-0.831	10.917	-0.415	-0.415	0.000	0.000	0.000	0.000
31	A	44	ILE	0	-0.047	-0.018	13.212	0.066	0.066	0.000	0.000	0.000	0.000
32	A	45	SER	0	-0.042	-0.066	16.439	0.035	0.035	0.000	0.000	0.000	0.000
33	A	57	ASN	0	0.013	-0.010	23.541	0.012	0.012	0.000	0.000	0.000	0.000
34	A	58	LEU	0	0.016	0.019	17.923	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	59	SER	0	0.037	0.000	18.065	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	60	ASP	-1	-0.850	-0.915	17.665	-0.310	-0.310	0.000	0.000	0.000	0.000
37	A	61	ARG	1	0.917	0.971	17.700	0.206	0.206	0.000	0.000	0.000	0.000
38	A	62	VAL	0	0.001	-0.003	12.804	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	63	ALA	0	0.031	0.007	13.484	-0.077	-0.077	0.000	0.000	0.000	0.000
40	A	64	SER	0	-0.034	-0.030	13.981	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	65	ALA	0	0.005	0.015	12.778	0.008	0.008	0.000	0.000	0.000	0.000
42	A	66	VAL	0	-0.037	-0.019	8.659	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	67	LEU	0	-0.060	-0.027	9.850	-0.061	-0.061	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.908	-0.926	12.205	-0.290	-0.290	0.000	0.000	0.000	0.000
45	A	69	GLY	0	0.006	0.005	8.395	0.105	0.105	0.000	0.000	0.000	0.000
46	A	70	THR	0	-0.106	-0.062	8.168	0.112	0.112	0.000	0.000	0.000	0.000
47	A	71	TYR	0	-0.070	-0.054	6.830	0.194	0.194	0.000	0.000	0.000	0.000
48	A	72	ASP	-1	-0.812	-0.898	2.637	-8.210	-4.509	1.783	-2.392	-3.091	-0.026
49	A	73	ARG	1	0.796	0.872	4.640	2.831	3.084	-0.001	-0.013	-0.238	0.000
50	A	74	ALA	0	0.001	0.003	6.779	0.122	0.122	0.000	0.000	0.000	0.000
51	A	75	ILE	0	0.011	0.011	9.669	0.038	0.038	0.000	0.000	0.000	0.000
52	A	76	LEU	0	-0.035	-0.015	12.310	0.094	0.094	0.000	0.000	0.000	0.000
53	A	77	VAL	0	0.022	0.012	15.840	0.014	0.014	0.000	0.000	0.000	0.000
54	A	78	CYS	0	0.002	0.032	18.765	0.029	0.029	0.000	0.000	0.000	0.000
55	A	79	GLY	0	0.002	0.003	22.422	0.001	0.001	0.000	0.000	0.000	0.000
56	A	80	THR	0	0.031	-0.008	25.299	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	81	GLY	0	0.108	0.035	21.304	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	82	ILE	0	0.024	0.000	21.617	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	83	GLY	0	0.000	0.002	23.822	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	84	VAL	0	0.032	0.004	19.143	0.004	0.004	0.000	0.000	0.000	0.000
61	A	85	CYS	0	-0.020	0.010	19.435	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	86	ILE	0	-0.022	-0.021	20.491	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	87	ALA	0	-0.024	-0.019	21.825	0.004	0.004	0.000	0.000	0.000	0.000
64	A	88	ALA	0	0.065	0.026	16.929	0.003	0.003	0.000	0.000	0.000	0.000
65	A	89	ASN	0	-0.015	-0.007	18.646	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	90	LYS	1	0.859	0.942	20.180	0.249	0.249	0.000	0.000	0.000	0.000
67	A	91	VAL	0	0.037	0.039	17.530	0.033	0.033	0.000	0.000	0.000	0.000
68	A	92	PRO	0	-0.019	-0.021	18.862	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	93	GLY	0	0.033	0.018	16.660	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	94	ILE	0	-0.038	-0.006	13.090	-0.086	-0.086	0.000	0.000	0.000	0.000
71	A	95	ARG	1	0.839	0.921	12.049	0.744	0.744	0.000	0.000	0.000	0.000
72	A	96	ALA	0	-0.010	-0.013	14.375	-0.098	-0.098	0.000	0.000	0.000	0.000
73	A	97	ALA	0	0.022	0.008	15.706	0.070	0.070	0.000	0.000	0.000	0.000
74	A	98	LEU	0	-0.022	0.005	16.776	-0.037	-0.037	0.000	0.000	0.000	0.000
75	A	99	THR	0	-0.015	-0.012	15.784	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	100	HIS	0	0.048	0.010	18.547	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	101	ASP	-1	-0.787	-0.854	19.888	-0.340	-0.340	0.000	0.000	0.000	0.000
78	A	102	THR	0	0.071	0.021	17.034	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	103	TYR	0	0.028	0.032	17.384	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	104	SER	0	-0.043	-0.086	18.491	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	105	ALA	0	-0.011	-0.006	14.402	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	106	GLU	-1	-0.906	-0.946	13.798	-0.615	-0.615	0.000	0.000	0.000	0.000
83	A	107	ARG	1	0.902	0.958	14.617	0.343	0.343	0.000	0.000	0.000	0.000
84	A	108	ALA	0	0.024	0.017	14.458	0.006	0.006	0.000	0.000	0.000	0.000
85	A	109	ALA	0	-0.013	0.001	10.586	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	110	LEU	0	0.013	0.005	12.211	0.034	0.034	0.000	0.000	0.000	0.000
87	A	111	SER	0	-0.092	-0.040	14.151	0.084	0.084	0.000	0.000	0.000	0.000
88	A	112	ASN	0	-0.069	-0.045	16.027	0.031	0.031	0.000	0.000	0.000	0.000
89	A	113	ASN	0	0.019	0.023	11.697	-0.024	-0.024	0.000	0.000	0.000	0.000
90	A	114	ALA	0	-0.022	-0.008	12.084	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	115	GLN	0	0.054	0.023	9.298	-0.115	-0.115	0.000	0.000	0.000	0.000
92	A	116	ILE	0	-0.005	-0.003	9.517	-0.159	-0.159	0.000	0.000	0.000	0.000
93	A	117	ILE	0	0.017	0.027	11.749	0.100	0.100	0.000	0.000	0.000	0.000
94	A	118	THR	0	-0.048	-0.040	13.964	0.007	0.007	0.000	0.000	0.000	0.000
95	A	119	MET	0	0.026	0.006	14.462	0.033	0.033	0.000	0.000	0.000	0.000
96	A	120	GLY	0	-0.012	-0.018	19.194	0.015	0.015	0.000	0.000	0.000	0.000
97	A	121	ALA	0	0.024	0.009	22.048	0.006	0.006	0.000	0.000	0.000	0.000
98	A	122	ARG	1	0.885	0.943	23.236	0.203	0.203	0.000	0.000	0.000	0.000
99	A	123	VAL	0	-0.062	-0.017	24.856	0.016	0.016	0.000	0.000	0.000	0.000
100	A	124	ILE	0	0.005	0.015	19.548	0.008	0.008	0.000	0.000	0.000	0.000
101	A	125	GLY	0	0.033	0.015	23.797	0.006	0.006	0.000	0.000	0.000	0.000
102	A	126	ALA	0	0.025	-0.002	20.565	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	127	GLU	-1	-0.820	-0.907	19.260	-0.311	-0.311	0.000	0.000	0.000	0.000
104	A	128	VAL	0	0.022	0.017	19.248	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	129	ALA	0	0.033	0.020	17.556	-0.042	-0.042	0.000	0.000	0.000	0.000
106	A	130	LYS	1	0.884	0.932	14.859	0.245	0.245	0.000	0.000	0.000	0.000
107	A	131	THR	0	-0.035	-0.019	14.096	-0.066	-0.066	0.000	0.000	0.000	0.000
108	A	132	ILE	0	-0.028	-0.010	14.865	-0.047	-0.047	0.000	0.000	0.000	0.000
109	A	133	ALA	0	-0.002	-0.002	10.986	-0.072	-0.072	0.000	0.000	0.000	0.000
110	A	134	ASP	-1	-0.764	-0.860	10.190	-0.982	-0.982	0.000	0.000	0.000	0.000
111	A	135	ALA	0	-0.017	-0.008	10.596	-0.095	-0.095	0.000	0.000	0.000	0.000
112	A	136	PHE	0	-0.027	-0.021	8.706	-0.047	-0.047	0.000	0.000	0.000	0.000
113	A	137	LEU	0	-0.018	-0.024	5.296	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	138	ALA	0	-0.020	-0.007	6.348	-0.359	-0.359	0.000	0.000	0.000	0.000
115	A	139	GLN	0	0.006	0.006	8.531	0.093	0.093	0.000	0.000	0.000	0.000
116	A	140	THR	0	-0.044	0.018	5.519	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	141	PHE	0	-0.039	-0.023	2.642	-4.551	-3.178	7.595	-1.918	-7.050	-0.018
118	A	142	ASP	-1	-0.934	-0.953	4.663	0.297	0.477	-0.001	-0.019	-0.161	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:MET)