FMO DATABASE

FMODB ID: 174NZ

Calculation Name: 2Z5B-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z5B

Chain ID: B

ChEMBL ID:

UniProt ID: Q07951

Base Structure: X-ray

Registration Date: 2023-06-21

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1277237.956756
FMO2-HF: Nuclear repulsion	1220407.502645
FMO2-HF: Total energy	-56830.454111
FMO2-MP2: Total energy	-56994.487834

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
0.798	2.405	-0.012	-0.641	-0.955	0

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.021

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].
3	B	3	SER	0	-0.005	0.017	3.869	0.341	1.793	-0.011	-0.618	-0.824
4	B	4	TYR	0	-0.006	-0.005	6.270	-0.061	-0.061	0.000	0.000	0.000
5	B	5	GLU	-1	-0.866	-0.937	9.813	-0.168	-0.168	0.000	0.000	0.000
6	B	6	PHE	0	0.013	-0.003	12.730	0.017	0.017	0.000	0.000	0.000
7	B	7	GLN	0	0.021	0.008	16.560	-0.003	-0.003	0.000	0.000	0.000
8	B	8	THR	0	-0.033	-0.010	19.412	0.005	0.005	0.000	0.000	0.000
9	B	9	HIS	0	-0.014	-0.011	23.031	0.000	0.000	0.000	0.000	0.000
10	B	10	LEU	0	-0.027	-0.011	25.991	0.001	0.001	0.000	0.000	0.000
11	B	11	PRO	0	-0.039	-0.020	27.817	0.000	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.936	0.977	30.930	0.002	0.002	0.000	0.000	0.000
13	B	23	GLU	-1	-0.889	-0.949	32.756	-0.004	-0.004	0.000	0.000	0.000
14	B	24	ASN	0	-0.049	-0.018	30.072	0.001	0.001	0.000	0.000	0.000
15	B	25	LYS	1	0.931	0.962	27.675	0.002	0.002	0.000	0.000	0.000
16	B	26	GLU	-1	-0.790	-0.882	23.157	-0.019	-0.019	0.000	0.000	0.000
17	B	27	LEU	0	-0.036	-0.033	21.070	0.002	0.002	0.000	0.000	0.000
18	B	28	TYR	0	-0.051	-0.030	12.972	-0.002	-0.002	0.000	0.000	0.000
19	B	29	VAL	0	-0.029	-0.026	15.100	0.010	0.010	0.000	0.000	0.000
20	B	30	GLN	0	0.055	0.018	7.214	0.096	0.096	0.000	0.000	0.000
21	B	31	ALA	0	-0.002	-0.004	9.992	0.051	0.051	0.000	0.000	0.000
22	B	32	THR	0	-0.004	0.005	3.991	-0.413	-0.328	0.000	-0.021	-0.064
23	B	33	HIS	0	0.013	0.006	5.820	-0.081	-0.081	0.000	0.000	0.000
24	B	34	PHE	0	0.010	0.000	4.648	0.993	1.063	-0.001	-0.002	-0.067
25	B	35	ASN	0	-0.023	-0.021	8.102	-0.067	-0.067	0.000	0.000	0.000
26	B	36	ASN	0	0.004	0.006	11.086	-0.033	-0.033	0.000	0.000	0.000
27	B	37	THR	0	-0.021	-0.007	11.173	-0.105	-0.105	0.000	0.000	0.000
28	B	38	ILE	0	0.033	0.036	10.247	0.156	0.156	0.000	0.000	0.000
29	B	39	LEU	0	-0.034	-0.006	8.549	-0.067	-0.067	0.000	0.000	0.000
30	B	40	LEU	0	0.010	0.002	10.375	-0.013	-0.013	0.000	0.000	0.000
31	B	41	GLN	0	0.010	0.003	10.717	0.025	0.025	0.000	0.000	0.000
32	B	42	ILE	0	0.013	-0.007	14.427	-0.006	-0.006	0.000	0.000	0.000
33	B	43	ARG	1	0.879	0.922	14.778	0.062	0.062	0.000	0.000	0.000
34	B	44	LEU	0	0.012	0.004	19.530	0.000	0.000	0.000	0.000	0.000
35	B	45	ASN	0	-0.024	-0.027	23.145	0.000	0.000	0.000	0.000	0.000
36	B	46	GLY	0	0.061	0.041	20.058	0.000	0.000	0.000	0.000	0.000
37	B	47	GLU	-1	-0.877	-0.924	20.031	-0.012	-0.012	0.000	0.000	0.000
38	B	48	MET	0	-0.049	-0.039	15.160	-0.002	-0.002	0.000	0.000	0.000
39	B	49	ASP	-1	-0.820	-0.854	20.581	-0.001	-0.001	0.000	0.000	0.000
40	B	50	SER	0	0.012	-0.006	21.894	0.002	0.002	0.000	0.000	0.000
41	B	51	THR	0	-0.051	-0.033	17.616	-0.004	-0.004	0.000	0.000	0.000
42	B	52	TYR	0	-0.020	-0.010	19.353	-0.002	-0.002	0.000	0.000	0.000
43	B	53	GLU	-1	-0.818	-0.886	17.930	0.086	0.086	0.000	0.000	0.000
44	B	54	VAL	0	-0.005	-0.006	18.835	-0.011	-0.011	0.000	0.000	0.000
45	B	55	SER	0	0.031	0.015	19.268	0.016	0.016	0.000	0.000	0.000
46	B	56	SER	0	0.042	0.016	21.535	-0.006	-0.006	0.000	0.000	0.000
47	B	57	LYS	1	0.856	0.915	24.257	-0.045	-0.045	0.000	0.000	0.000
48	B	58	GLY	0	-0.030	0.000	26.637	-0.004	-0.004	0.000	0.000	0.000
49	B	59	LEU	0	0.040	0.035	26.850	0.000	0.000	0.000	0.000	0.000
50	B	80	TYR	0	-0.085	-0.048	49.836	-0.001	-0.001	0.000	0.000	0.000
51	B	81	ASP	-1	-0.975	-0.989	47.487	0.016	0.016	0.000	0.000	0.000
52	B	82	ASP	-1	-0.891	-0.955	44.482	0.018	0.018	0.000	0.000	0.000
53	B	83	GLU	-1	-0.863	-0.926	40.850	0.019	0.019	0.000	0.000	0.000
54	B	84	GLU	-1	-0.955	-0.992	40.279	0.023	0.023	0.000	0.000	0.000
55	B	85	GLU	-1	-0.989	-0.990	40.056	0.025	0.025	0.000	0.000	0.000
56	B	86	GLU	-1	-0.915	-0.954	37.311	0.028	0.028	0.000	0.000	0.000
57	B	87	PHE	0	0.031	0.016	35.893	0.004	0.004	0.000	0.000	0.000
58	B	88	VAL	0	-0.038	-0.029	35.382	0.002	0.002	0.000	0.000	0.000
59	B	89	ARG	1	0.917	0.943	33.261	-0.036	-0.036	0.000	0.000	0.000
60	B	90	ASP	-1	-0.912	-0.950	31.701	0.044	0.044	0.000	0.000	0.000
61	B	91	HIS	1	0.708	0.849	30.651	-0.033	-0.033	0.000	0.000	0.000
62	B	92	LEU	0	0.019	0.039	31.740	-0.001	-0.001	0.000	0.000	0.000
63	B	93	SER	0	-0.054	-0.018	26.988	0.003	0.003	0.000	0.000	0.000
64	B	94	ASP	-1	-0.883	-0.939	28.044	0.039	0.039	0.000	0.000	0.000
65	B	95	TYR	0	-0.081	-0.081	22.142	0.012	0.012	0.000	0.000	0.000
66	B	96	GLN	0	-0.043	-0.007	24.935	-0.010	-0.010	0.000	0.000	0.000
67	B	97	VAL	0	0.019	0.004	23.552	0.007	0.007	0.000	0.000	0.000
68	B	98	VAL	0	-0.019	-0.013	23.062	-0.005	-0.005	0.000	0.000	0.000
69	B	99	THR	0	0.003	-0.010	22.672	0.005	0.005	0.000	0.000	0.000
70	B	100	LYS	1	0.760	0.870	19.808	-0.058	-0.058	0.000	0.000	0.000
71	B	101	LEU	0	0.013	0.009	21.142	-0.004	-0.004	0.000	0.000	0.000
72	B	102	GLY	0	0.066	0.042	23.459	0.002	0.002	0.000	0.000	0.000
73	B	103	ASP	-1	-0.836	-0.905	25.989	0.013	0.013	0.000	0.000	0.000
74	B	104	SER	0	0.022	-0.010	27.552	0.002	0.002	0.000	0.000	0.000
75	B	105	ALA	0	-0.032	-0.010	29.582	0.001	0.001	0.000	0.000	0.000
76	B	106	ASP	-1	-0.830	-0.900	30.043	0.013	0.013	0.000	0.000	0.000
77	B	107	PRO	0	0.025	0.012	30.749	0.002	0.002	0.000	0.000	0.000
78	B	108	LYS	1	0.755	0.849	30.760	-0.010	-0.010	0.000	0.000	0.000
79	B	109	VAL	0	0.005	0.015	25.059	0.001	0.001	0.000	0.000	0.000
80	B	110	PRO	0	0.021	0.013	25.964	0.004	0.004	0.000	0.000	0.000
81	B	111	VAL	0	0.040	0.013	26.691	0.004	0.004	0.000	0.000	0.000
82	B	112	VAL	0	-0.007	0.006	23.169	0.002	0.002	0.000	0.000	0.000
83	B	113	CYS	0	-0.056	-0.029	22.163	0.004	0.004	0.000	0.000	0.000
84	B	114	VAL	0	0.022	0.015	22.300	0.008	0.008	0.000	0.000	0.000
85	B	115	GLN	0	0.028	0.005	24.072	0.006	0.006	0.000	0.000	0.000
86	B	116	ILE	0	0.003	0.006	18.504	0.001	0.001	0.000	0.000	0.000
87	B	117	ALA	0	-0.010	-0.007	19.388	0.010	0.010	0.000	0.000	0.000
88	B	118	GLU	-1	-0.761	-0.855	20.370	0.074	0.074	0.000	0.000	0.000
89	B	119	LEU	0	-0.049	-0.010	20.061	0.000	0.000	0.000	0.000	0.000
90	B	120	TYR	0	0.016	-0.017	12.998	-0.003	-0.003	0.000	0.000	0.000
91	B	121	ARG	1	0.879	0.919	18.308	-0.100	-0.100	0.000	0.000	0.000
92	B	122	ARG	1	0.864	0.935	20.553	-0.049	-0.049	0.000	0.000	0.000
93	B	123	VAL	0	-0.058	-0.020	20.957	-0.009	-0.009	0.000	0.000	0.000
94	B	124	ILE	0	-0.009	0.007	14.997	-0.002	-0.002	0.000	0.000	0.000
95	B	125	LEU	0	-0.080	-0.019	13.740	0.022	0.022	0.000	0.000	0.000
96	B	126	PRO	0	-0.044	-0.017	16.271	-0.001	-0.001	0.000	0.000	0.000
97	B	127	GLU	-1	-0.763	-0.868	15.716	0.004	0.004	0.000	0.000	0.000
98	B	138	GLN	0	0.008	-0.002	16.899	0.014	0.014	0.000	0.000	0.000
99	B	139	PHE	0	0.009	-0.014	17.225	-0.001	-0.001	0.000	0.000	0.000
100	B	140	SER	0	-0.001	-0.001	15.428	-0.032	-0.032	0.000	0.000	0.000
101	B	141	LEU	0	-0.007	0.013	14.152	0.041	0.041	0.000	0.000	0.000
102	B	142	LEU	0	-0.005	0.003	13.418	-0.028	-0.028	0.000	0.000	0.000
103	B	143	ILE	0	0.057	0.023	14.262	-0.003	-0.003	0.000	0.000	0.000
104	B	144	SER	0	-0.014	-0.009	15.638	-0.006	-0.006	0.000	0.000	0.000
105	B	145	MET	0	0.029	0.010	17.234	-0.005	-0.005	0.000	0.000	0.000
106	B	146	SER	0	-0.004	0.012	19.921	0.001	0.001	0.000	0.000	0.000
107	B	147	SER	0	-0.025	-0.054	23.164	0.002	0.002	0.000	0.000	0.000
108	B	148	LYS	1	0.787	0.876	26.320	0.004	0.004	0.000	0.000	0.000
109	B	149	ILE	0	-0.028	0.002	22.054	0.000	0.000	0.000	0.000	0.000
110	B	150	TRP	0	0.004	-0.011	23.815	0.000	0.000	0.000	0.000	0.000
111	B	151	ARG	1	0.811	0.878	28.847	-0.014	-0.014	0.000	0.000	0.000
112	B	152	ALA	0	0.042	0.024	30.946	0.001	0.001	0.000	0.000	0.000
113	B	153	THR	0	-0.047	-0.040	32.534	0.000	0.000	0.000	0.000	0.000
114	B	154	LYS	1	0.869	0.934	32.268	-0.008	-0.008	0.000	0.000	0.000
115	B	155	GLU	-1	-0.843	-0.892	35.605	0.012	0.012	0.000	0.000	0.000
116	B	156	GLN	0	0.022	-0.008	35.751	0.000	0.000	0.000	0.000	0.000
117	B	157	SER	0	-0.096	-0.059	38.773	-0.001	-0.001	0.000	0.000	0.000
118	B	158	ALA	0	0.016	0.019	37.935	-0.001	-0.001	0.000	0.000	0.000
119	B	159	ASP	-1	-0.802	-0.883	34.407	0.011	0.011	0.000	0.000	0.000
120	B	160	ASP	-1	-0.813	-0.901	33.697	0.004	0.004	0.000	0.000	0.000
121	B	161	ASN	0	-0.043	-0.041	34.347	0.000	0.000	0.000	0.000	0.000
122	B	162	ASP	-1	-0.819	-0.907	31.957	0.012	0.012	0.000	0.000	0.000
123	B	163	PHE	0	0.043	0.034	30.916	0.000	0.000	0.000	0.000	0.000
124	B	164	GLY	0	0.026	0.010	30.927	0.001	0.001	0.000	0.000	0.000
125	B	165	LYS	1	0.818	0.912	28.142	-0.005	-0.005	0.000	0.000	0.000
126	B	166	LEU	0	0.011	0.001	25.591	-0.001	-0.001	0.000	0.000	0.000
127	B	167	VAL	0	0.012	0.008	25.949	0.001	0.001	0.000	0.000	0.000
128	B	168	PHE	0	-0.020	-0.006	24.974	0.000	0.000	0.000	0.000	0.000
129	B	169	VAL	0	0.037	0.021	21.360	-0.002	-0.002	0.000	0.000	0.000
130	B	170	LEU	0	0.007	-0.002	21.476	0.000	0.000	0.000	0.000	0.000
131	B	171	LYS	1	0.847	0.900	21.717	0.006	0.006	0.000	0.000	0.000
132	B	172	CYS	0	-0.052	-0.024	20.083	-0.003	-0.003	0.000	0.000	0.000
133	B	173	ILE	0	0.010	0.005	16.480	-0.008	-0.008	0.000	0.000	0.000
134	B	174	LYS	1	0.821	0.877	17.194	-0.011	-0.011	0.000	0.000	0.000
135	B	175	ASP	-1	-0.868	-0.915	18.924	-0.011	-0.011	0.000	0.000	0.000
136	B	176	MET	0	-0.102	-0.012	12.937	-0.016	-0.016	0.000	0.000	0.000
137	B	177	TYR	0	-0.045	-0.013	13.668	-0.027	-0.027	0.000	0.000	0.000
138	B	178	ALA	0	0.017	0.024	10.582	0.036	0.036	0.000	0.000	0.000

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