FMO DATABASE

FMODB ID: 5JNVZ

Calculation Name: 5IW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IW9

Chain ID: A

ChEMBL ID:

UniProt ID: P09425

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-973296.628902
FMO2-HF: Nuclear repulsion	922539.395653
FMO2-HF: Total energy	-50757.233249
FMO2-MP2: Total energy	-50904.878343

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:3:ASN)

Summations of interaction energy for fragment #1(A:3:ASN)

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.
2.385	4.418	-0.021	-0.839	-1.174	0.003

Interaction energy analysis for fragmet #1(A:3:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.009

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	5	ASN	0	-0.018	0.005	3.826	3.214	5.247	-0.021	-0.839	-1.174	0.003
4	A	6	LYS	1	0.961	0.975	6.413	-0.413	-0.413	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.046	0.025	7.669	0.368	0.368	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.013	-0.009	11.178	-0.161	-0.161	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.030	0.005	13.543	-0.008	-0.008	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.963	-0.968	14.297	-0.333	-0.333	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.080	-0.044	16.733	0.011	0.011	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.866	-0.940	18.952	-0.122	-0.122	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.062	-0.030	21.059	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.877	-0.958	24.756	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	15	MET	0	-0.057	-0.014	20.269	0.027	0.027	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.920	0.978	22.308	0.240	0.240	0.000	0.000	0.000	0.000
15	A	17	MET	0	0.002	0.011	21.772	0.031	0.031	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.858	-0.943	22.685	-0.328	-0.328	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.047	-0.038	17.975	0.005	0.005	0.000	0.000	0.000	0.000
18	A	20	ASN	0	0.002	-0.002	22.823	0.006	0.006	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.971	1.001	26.436	0.180	0.180	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.836	-0.915	29.711	-0.128	-0.128	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.015	0.015	27.165	0.006	0.006	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.028	-0.021	29.776	0.008	0.008	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.949	0.967	31.408	0.120	0.120	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.036	-0.037	33.060	0.007	0.007	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.041	-0.031	30.479	0.006	0.006	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.046	0.027	34.820	0.004	0.004	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.027	0.023	37.058	0.006	0.006	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.954	0.975	34.276	0.187	0.187	0.000	0.000	0.000	0.000
29	A	31	SER	0	-0.069	-0.037	38.046	0.003	0.003	0.000	0.000	0.000	0.000
30	A	32	ILE	0	0.068	0.038	40.006	0.003	0.003	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.943	0.980	42.777	0.103	0.103	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.070	-0.048	41.296	0.007	0.007	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.055	-0.030	43.975	0.004	0.004	0.000	0.000	0.000	0.000
34	A	36	LEU	0	0.053	0.019	45.594	0.004	0.004	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.003	0.013	47.812	0.004	0.004	0.000	0.000	0.000	0.000
36	A	38	GLY	0	0.000	0.015	48.065	0.003	0.003	0.000	0.000	0.000	0.000
37	A	39	ILE	0	-0.003	0.012	48.825	0.003	0.003	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.013	-0.020	51.622	0.004	0.004	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.062	-0.053	51.820	0.003	0.003	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.055	-0.027	52.161	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.938	0.976	54.824	0.074	0.074	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.960	0.999	58.097	0.080	0.080	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.028	0.025	58.707	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.133	-0.076	57.242	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.956	0.983	49.231	0.118	0.118	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.025	-0.004	55.025	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	PHE	0	-0.057	-0.040	51.317	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.818	-0.893	52.953	-0.114	-0.114	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.030	-0.009	54.978	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.903	-0.950	56.637	-0.083	-0.083	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.063	-0.021	49.960	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.002	0.003	54.720	0.002	0.002	0.000	0.000	0.000	0.000
53	A	55	CYS	0	-0.025	-0.007	55.665	0.002	0.002	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.975	-0.982	58.422	-0.069	-0.069	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.016	-0.011	58.667	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	SER	0	0.005	0.000	62.709	0.000	0.000	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.802	-0.919	65.306	-0.062	-0.062	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.039	0.008	67.293	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.074	-0.014	64.576	0.002	0.002	0.000	0.000	0.000	0.000
60	A	62	PHE	0	-0.027	-0.024	61.813	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.944	-0.966	67.882	-0.048	-0.048	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.099	-0.051	71.332	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	MET	0	0.001	0.036	66.935	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.001	-0.015	71.239	0.002	0.002	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.010	-0.019	70.810	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	68	LEU	0	0.004	0.004	70.540	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.034	0.023	66.532	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.053	0.024	65.021	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.853	-0.922	64.230	-0.054	-0.054	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.056	-0.035	64.789	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.023	0.005	60.939	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.822	-0.913	60.404	-0.058	-0.058	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.952	0.974	59.922	0.054	0.054	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.038	-0.012	60.394	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	77	ILE	0	0.072	0.023	55.337	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.922	-0.963	55.815	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.085	-0.043	55.680	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.035	0.016	55.095	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.005	-0.018	50.367	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.805	0.886	50.979	0.084	0.084	0.000	0.000	0.000	0.000
81	A	83	ASN	0	-0.038	-0.010	52.018	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.075	-0.059	49.953	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.772	-0.845	44.709	-0.146	-0.146	0.000	0.000	0.000	0.000
84	A	86	PRO	0	0.026	0.009	45.093	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.795	0.869	39.469	0.157	0.157	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.020	0.000	44.282	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.864	-0.941	46.643	-0.090	-0.090	0.000	0.000	0.000	0.000
88	A	90	LYS	1	0.903	0.963	48.340	0.072	0.072	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.008	-0.010	50.409	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.007	0.002	52.958	0.003	0.003	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.016	-0.003	55.073	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.024	0.001	57.240	0.003	0.003	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.020	-0.014	59.209	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.030	-0.015	60.753	0.003	0.003	0.000	0.000	0.000	0.000
95	A	97	PRO	0	-0.004	-0.018	63.625	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.023	0.000	63.251	0.002	0.002	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.014	-0.024	66.469	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.993	-0.981	68.119	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.798	-0.847	64.696	-0.045	-0.045	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.066	-0.027	66.502	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.064	-0.074	62.124	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.005	-0.004	61.781	0.002	0.002	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.021	-0.005	57.892	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.009	0.009	55.657	0.001	0.001	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.941	-0.977	54.930	-0.055	-0.055	0.000	0.000	0.000	0.000
106	A	108	ILE	0	0.011	0.011	51.344	0.000	0.000	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.946	0.962	51.052	0.056	0.056	0.000	0.000	0.000	0.000
108	A	110	PHE	0	0.000	-0.015	44.719	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	111	SER	0	0.067	0.050	46.143	0.001	0.001	0.000	0.000	0.000	0.000
110	A	112	VAL	0	0.001	0.007	40.518	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	113	ILE	0	0.014	0.000	42.215	0.003	0.003	0.000	0.000	0.000	0.000
112	A	114	ASP	-1	-0.939	-0.966	37.947	-0.161	-0.161	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.103	-0.055	37.889	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.004	0.017	41.464	0.005	0.005	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.971	-0.991	42.797	-0.079	-0.079	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.824	-0.889	41.680	-0.076	-0.076	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.110	-0.057	45.047	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.899	-0.952	42.917	-0.089	-0.089	0.000	0.000	0.000	0.000
119	A	121	GLN	0	-0.027	-0.041	46.589	0.006	0.006	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.103	-0.045	47.381	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	123	LYS	1	0.959	0.982	49.922	0.056	0.056	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.016	-0.006	50.907	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	125	GLN	0	-0.005	-0.004	54.361	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.064	-0.024	56.271	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.083	0.026	59.316	0.003	0.003	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.018	0.006	62.070	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASN)