FMO DATABASE

FMODB ID: Z6NGN

Calculation Name: 4B6H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B6H

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NPI6

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1177974.431673
FMO2-HF: Nuclear repulsion	1124757.038374
FMO2-HF: Total energy	-53217.393299
FMO2-MP2: Total energy	-53371.280835

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:0:LEU)

Summations of interaction energy for fragment #1(A:0: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.
-4.565	-0.126	2.037	-1.96	-4.515	-0.001

Interaction energy analysis for fragmet #1(A:0:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.010

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	2	GLU	-1	-0.793	-0.876	2.551	-5.999	-3.261	0.312	-1.026	-2.023	0.002
4	A	3	ALA	0	-0.004	0.014	2.494	-0.465	0.265	1.556	-0.737	-1.549	-0.003
5	A	4	LEU	0	0.021	-0.001	2.964	-0.105	0.866	0.169	-0.197	-0.943	0.000
6	A	5	SER	0	-0.024	0.011	5.760	0.394	0.394	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.888	0.895	4.870	1.311	1.311	0.000	0.000	0.000	0.000
8	A	7	ALA	0	0.040	0.026	7.898	0.132	0.132	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.015	0.005	9.664	0.119	0.119	0.000	0.000	0.000	0.000
10	A	9	GLN	0	-0.010	0.011	11.565	0.067	0.067	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.940	-0.974	11.363	-0.473	-0.473	0.000	0.000	0.000	0.000
12	A	11	MET	0	-0.058	-0.041	11.438	0.053	0.053	0.000	0.000	0.000	0.000
13	A	12	SER	0	-0.002	-0.008	15.073	0.047	0.047	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.012	0.007	17.357	0.029	0.029	0.000	0.000	0.000	0.000
15	A	14	ALA	0	-0.016	-0.013	18.819	0.021	0.021	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.002	-0.005	19.643	0.016	0.016	0.000	0.000	0.000	0.000
17	A	16	LEU	0	0.000	-0.010	21.247	0.016	0.016	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.862	0.937	22.832	0.144	0.144	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.067	-0.022	23.972	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	HIS	0	-0.029	-0.009	26.303	0.004	0.004	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.764	-0.880	27.739	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	21	PRO	0	0.029	0.014	28.129	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	22	TYR	0	-0.030	0.005	29.388	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.005	0.042	24.390	0.001	0.001	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.004	-0.004	25.552	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	25	SER	0	-0.036	-0.023	21.712	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	26	ILE	0	0.028	0.017	17.786	0.011	0.011	0.000	0.000	0.000	0.000
28	A	27	ALA	0	-0.091	-0.055	19.993	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.766	-0.857	19.019	0.009	0.009	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.042	-0.021	14.249	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	30	THR	0	0.012	0.016	17.755	0.012	0.012	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.028	-0.014	15.879	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.080	-0.055	16.773	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.014	0.011	19.119	0.008	0.008	0.000	0.000	0.000	0.000
35	A	34	ALA	0	0.010	-0.003	22.667	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.018	0.007	25.382	0.002	0.002	0.000	0.000	0.000	0.000
37	A	36	TYR	0	-0.026	0.001	28.593	0.000	0.000	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.082	0.039	32.162	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.035	-0.023	35.498	0.002	0.002	0.000	0.000	0.000	0.000
40	A	39	CYS	0	0.004	0.019	38.848	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	40	PRO	0	0.046	0.013	41.747	0.001	0.001	0.000	0.000	0.000	0.000
42	A	41	LYS	1	0.919	0.961	45.056	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	42	ALA	0	-0.030	-0.038	43.978	0.000	0.000	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.036	-0.005	44.754	0.001	0.001	0.000	0.000	0.000	0.000
45	A	44	GLN	0	0.007	0.002	40.249	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	TRP	0	0.000	0.002	35.426	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.958	-0.970	36.273	0.011	0.011	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.904	0.955	30.763	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	48	THR	0	0.050	0.005	29.787	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	49	ASP	-1	-0.916	-0.959	28.689	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.012	0.015	25.460	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.850	-0.919	21.539	0.059	0.059	0.000	0.000	0.000	0.000
53	A	52	GLY	0	-0.031	-0.014	19.318	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	53	THR	0	-0.019	0.019	16.190	0.006	0.006	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.014	0.020	18.839	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.011	-0.014	16.402	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	56	VAL	0	0.064	0.025	21.438	0.004	0.004	0.000	0.000	0.000	0.000
58	A	57	TYR	0	-0.023	-0.016	22.611	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	58	ARG	1	0.975	0.984	22.010	0.081	0.081	0.000	0.000	0.000	0.000
60	A	59	ARG	1	0.775	0.852	27.055	0.046	0.046	0.000	0.000	0.000	0.000
61	A	60	SER	0	-0.042	-0.041	29.831	0.002	0.002	0.000	0.000	0.000	0.000
62	A	61	ALA	0	-0.006	-0.026	31.903	0.001	0.001	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.081	-0.002	34.199	0.000	0.000	0.000	0.000	0.000	0.000
64	A	63	PRO	0	-0.011	-0.009	34.121	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	64	TYR	0	0.008	-0.012	32.208	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	65	HIS	0	0.060	0.034	28.505	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.035	0.026	28.247	0.003	0.003	0.000	0.000	0.000	0.000
68	A	67	PHE	0	-0.020	-0.015	25.888	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.022	-0.026	23.013	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	69	ILE	0	0.022	0.005	22.527	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	VAL	0	-0.029	-0.013	19.295	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	71	ASN	0	-0.001	-0.019	20.411	0.011	0.011	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.906	0.949	16.038	0.041	0.041	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.062	-0.052	18.586	0.007	0.007	0.000	0.000	0.000	0.000
75	A	74	ASN	0	-0.034	-0.019	21.576	0.001	0.001	0.000	0.000	0.000	0.000
76	A	75	MET	0	-0.006	-0.002	23.084	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	76	HIS	0	0.011	0.026	24.647	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	77	ASN	0	0.047	0.010	23.207	0.007	0.007	0.000	0.000	0.000	0.000
79	A	78	LEU	0	0.041	0.034	26.050	0.003	0.003	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.056	-0.023	26.959	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	80	GLU	-1	-0.766	-0.838	29.334	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	81	PRO	0	-0.032	-0.002	30.702	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.002	-0.013	30.004	0.004	0.004	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.012	-0.005	33.157	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	LYS	1	0.930	0.943	36.884	0.022	0.022	0.000	0.000	0.000	0.000
86	A	85	ASP	-1	-0.952	-0.973	39.391	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.079	-0.014	32.577	0.002	0.002	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.829	-0.880	37.271	0.004	0.004	0.000	0.000	0.000	0.000
89	A	88	PHE	0	0.041	-0.011	30.861	0.001	0.001	0.000	0.000	0.000	0.000
90	A	89	GLN	0	-0.021	-0.017	34.875	0.002	0.002	0.000	0.000	0.000	0.000
91	A	90	LEU	0	-0.010	0.003	29.433	0.001	0.001	0.000	0.000	0.000	0.000
92	A	91	HIS	0	-0.023	-0.008	32.489	0.003	0.003	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.803	-0.858	28.508	0.070	0.070	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.062	-0.033	26.589	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	PHE	0	0.027	-0.017	27.586	0.001	0.001	0.000	0.000	0.000	0.000
96	A	95	LEU	0	-0.006	-0.001	28.371	0.000	0.000	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.021	-0.012	30.768	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	97	TYR	0	-0.039	-0.050	31.101	0.000	0.000	0.000	0.000	0.000	0.000
99	A	98	ARG	1	0.823	0.908	35.229	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	99	ASN	0	0.052	-0.012	35.880	0.001	0.001	0.000	0.000	0.000	0.000
101	A	100	ALA	0	0.076	0.035	38.573	0.001	0.001	0.000	0.000	0.000	0.000
102	A	101	SER	0	-0.048	-0.020	39.707	0.001	0.001	0.000	0.000	0.000	0.000
103	A	102	LEU	0	-0.030	-0.019	41.506	0.001	0.001	0.000	0.000	0.000	0.000
104	A	103	SER	0	-0.037	-0.003	38.495	0.002	0.002	0.000	0.000	0.000	0.000
105	A	104	ILE	0	-0.017	-0.014	38.099	0.000	0.000	0.000	0.000	0.000	0.000
106	A	105	TYR	0	0.029	0.013	32.807	0.000	0.000	0.000	0.000	0.000	0.000
107	A	106	SER	0	-0.014	-0.016	32.462	0.002	0.002	0.000	0.000	0.000	0.000
108	A	107	ILE	0	0.019	0.018	26.207	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	108	TRP	0	-0.013	-0.001	22.951	0.005	0.005	0.000	0.000	0.000	0.000
110	A	109	PHE	0	0.061	0.011	22.415	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	110	TYR	0	-0.029	0.001	18.384	0.016	0.016	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.811	-0.897	17.869	0.193	0.193	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.889	0.915	20.721	-0.106	-0.106	0.000	0.000	0.000	0.000
114	A	113	ASN	0	-0.054	-0.046	20.007	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	114	ASP	-1	-0.785	-0.888	18.469	0.081	0.081	0.000	0.000	0.000	0.000
116	A	115	CYS	0	-0.095	-0.016	21.270	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	116	HIS	0	-0.037	-0.038	24.916	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.780	0.856	18.311	-0.056	-0.056	0.000	0.000	0.000	0.000
119	A	118	ILE	0	0.003	0.006	21.284	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	119	ALA	0	0.019	0.009	24.858	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	120	LYS	1	0.783	0.883	27.192	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	121	LEU	0	0.014	0.012	23.648	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	122	MET	0	-0.031	-0.022	26.692	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	123	ALA	0	0.002	-0.003	29.730	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	124	ASP	-1	-0.809	-0.889	29.647	0.001	0.001	0.000	0.000	0.000	0.000
126	A	125	VAL	0	-0.060	-0.032	28.832	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	126	VAL	0	-0.048	-0.026	31.892	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-1.019	-1.002	34.898	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	128	GLU	-1	-0.927	-0.955	33.554	-0.022	-0.022	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.880	-0.926	35.509	-0.030	-0.030	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:LEU)