FMO DATABASE

FMODB ID: YZ482

Calculation Name: 1NEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NEU

Chain ID: A

ChEMBL ID:

UniProt ID: P06907

Base Structure: X-ray

Registration Date: 2023-09-19

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-991891.913608
FMO2-HF: Nuclear repulsion	944696.167671
FMO2-HF: Total energy	-47195.745936
FMO2-MP2: Total energy	-47335.316488

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:ILE)

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

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.
-18.152	-13.441	13.784	-7.199	-11.296	-0.042

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.002

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	3	VAL	0	0.046	0.015	3.496	-1.061	1.134	0.007	-1.112	-1.091	0.000
4	A	4	TYR	0	-0.044	-0.011	5.923	-0.178	-0.178	0.000	0.000	0.000	0.000
5	A	5	THR	0	0.005	-0.015	9.453	0.109	0.109	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.869	-0.931	13.122	-0.124	-0.124	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.843	0.900	15.869	0.057	0.057	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.812	-0.877	16.893	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.001	0.007	20.318	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.050	-0.045	22.789	0.006	0.006	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.041	0.021	26.557	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.023	-0.010	29.169	0.000	0.000	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.049	0.015	32.921	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.037	-0.006	35.151	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.054	-0.019	32.012	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.023	-0.020	28.295	0.006	0.006	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.008	-0.007	23.678	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.003	0.007	20.974	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.016	-0.001	18.861	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.051	0.032	12.952	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	21	CYS	0	-0.026	-0.006	11.728	0.105	0.105	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.018	0.010	9.848	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.016	-0.014	2.781	-1.806	-1.107	2.085	-0.927	-1.857	0.003
24	A	24	TRP	0	0.009	0.006	2.634	-1.989	-0.196	0.596	-0.556	-1.833	-0.003
25	A	25	SER	0	-0.034	-0.057	2.067	-9.622	-8.948	8.934	-5.193	-4.415	-0.048
26	A	26	SER	0	-0.039	-0.032	3.009	2.166	0.502	0.048	2.121	-0.505	-0.001
27	A	27	GLU	-1	-0.888	-0.903	4.591	-0.782	-0.726	-0.001	-0.005	-0.049	0.000
28	A	28	TRP	0	0.007	0.002	6.106	-0.172	-0.172	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.008	0.001	5.087	0.047	0.047	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.011	0.006	8.515	-0.048	-0.048	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.886	-0.956	10.856	0.156	0.156	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.861	-0.920	13.513	0.451	0.451	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.066	-0.028	8.649	0.108	0.108	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.060	-0.056	11.676	-0.101	-0.101	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.036	0.010	10.356	0.198	0.198	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.048	-0.020	13.807	-0.087	-0.087	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.006	-0.002	15.542	0.057	0.057	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.838	0.896	15.759	-0.477	-0.477	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.009	-0.013	20.305	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.033	-0.015	22.407	0.024	0.024	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.021	0.020	24.739	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.848	-0.935	27.940	0.054	0.054	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.032	-0.005	28.642	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.039	-0.009	28.966	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.890	0.926	25.529	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.899	-0.938	24.923	0.161	0.161	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.007	0.004	20.845	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.017	0.008	22.753	0.024	0.024	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.014	-0.019	21.216	0.020	0.020	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.012	-0.006	22.015	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.029	0.013	18.104	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	52	HIS	0	-0.041	-0.026	17.023	0.015	0.015	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.031	0.019	16.169	-0.046	-0.046	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.067	0.027	16.270	0.077	0.077	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.779	0.890	15.731	-0.488	-0.488	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.044	0.036	18.457	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.072	-0.033	20.170	-0.034	-0.034	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.017	0.002	20.741	0.030	0.030	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.029	-0.016	21.352	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.007	-0.009	22.832	0.016	0.016	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.799	-0.883	25.393	0.129	0.129	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.939	-0.972	27.471	0.087	0.087	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.110	-0.065	30.782	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.019	0.009	29.793	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.024	-0.028	28.753	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.024	0.009	26.287	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.834	0.924	28.854	-0.077	-0.077	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.856	-0.919	30.913	0.064	0.064	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.734	0.851	29.838	-0.073	-0.073	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.009	0.006	23.545	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.009	0.009	24.799	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	72	TRP	0	0.005	0.006	15.509	0.011	0.011	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.055	-0.035	19.705	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.063	0.055	16.548	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.840	-0.922	15.436	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.044	0.016	12.977	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.075	-0.053	12.358	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	78	TRP	0	-0.091	-0.039	12.782	-0.081	-0.081	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.810	0.917	7.776	0.006	0.006	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.788	-0.878	9.755	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.018	-0.011	12.557	0.042	0.042	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.021	-0.035	14.322	0.023	0.023	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.042	-0.016	16.705	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.037	-0.016	20.200	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.005	0.014	23.280	0.013	0.013	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.004	-0.028	26.038	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.020	-0.021	29.666	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.022	0.023	28.115	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.782	-0.880	31.994	0.038	0.038	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.020	-0.015	32.757	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.122	-0.074	33.302	0.003	0.003	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.747	-0.848	28.791	0.068	0.068	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.027	-0.010	28.141	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.032	0.015	26.044	0.007	0.007	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.041	-0.002	19.741	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.044	0.024	19.751	0.020	0.020	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.047	-0.036	15.073	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.827	-0.913	11.806	0.904	0.904	0.000	0.000	0.000	0.000
99	A	100	VAL	0	0.035	0.022	7.907	-0.097	-0.097	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.815	0.913	8.715	-0.339	-0.339	0.000	0.000	0.000	0.000
101	A	102	ASN	0	0.044	0.011	6.150	-0.439	-0.439	0.000	0.000	0.000	0.000
102	A	103	PRO	0	0.068	0.030	9.937	-0.062	-0.062	0.000	0.000	0.000	0.000
103	A	104	PRO	0	-0.052	-0.027	12.423	-0.066	-0.066	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.823	-0.889	13.913	0.545	0.545	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.026	-0.008	12.702	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.026	-0.019	10.787	0.075	0.075	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.047	0.026	8.838	0.148	0.148	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.801	0.906	2.133	-5.230	-4.272	2.115	-1.527	-1.546	0.007
109	A	110	THR	0	0.031	0.011	7.812	-0.150	-0.150	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.064	-0.019	9.898	-0.067	-0.067	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.044	-0.035	12.034	0.004	0.004	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.065	0.061	15.559	-0.036	-0.036	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.053	-0.031	18.126	0.017	0.017	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.020	0.002	21.753	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	116	TYR	0	-0.017	-0.033	23.760	0.009	0.009	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.030	-0.009	27.849	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	118	PHE	0	0.006	0.002	29.005	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.976	-0.993	33.943	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:1:ILE)