FMO DATABASE

FMODB ID: ZY39N

Calculation Name: 3ZH6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZH6

Chain ID: A

ChEMBL ID:

UniProt ID: A4NBN9

Base Structure: X-ray

Registration Date: 2023-06-20

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205116.157939
FMO2-HF: Nuclear repulsion	1151079.587832
FMO2-HF: Total energy	-54036.570107
FMO2-MP2: Total energy	-54193.954176

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:26:ASN)

Summations of interaction energy for fragment #1(A:26: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.
12.024	-7.217	-0.442	21.625	-1.941	-0.014

Interaction energy analysis for fragmet #1(A:26:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : 0.019

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	28	MET	0	-0.013	-0.019	2.377	21.042	1.322	-0.443	21.749	-1.586	-0.015
4	A	29	LYS	1	0.890	0.922	4.851	-1.980	-1.821	0.000	-0.021	-0.138	0.000
5	A	30	LEU	0	-0.031	-0.016	7.626	-0.105	-0.105	0.000	0.000	0.000	0.000
6	A	31	ALA	0	0.010	0.013	11.103	-0.120	-0.120	0.000	0.000	0.000	0.000
7	A	32	PRO	0	-0.046	-0.019	14.447	-0.029	-0.029	0.000	0.000	0.000	0.000
8	A	33	PRO	0	-0.016	-0.009	16.706	-0.087	-0.087	0.000	0.000	0.000	0.000
9	A	34	THR	0	0.038	0.016	20.254	0.010	0.010	0.000	0.000	0.000	0.000
10	A	35	ASP	-1	-0.905	-0.935	22.890	0.346	0.346	0.000	0.000	0.000	0.000
11	A	36	VAL	0	-0.070	-0.046	24.747	0.048	0.048	0.000	0.000	0.000	0.000
12	A	37	ARG	1	0.929	0.990	23.467	-0.578	-0.578	0.000	0.000	0.000	0.000
13	A	38	SER	0	0.060	0.011	27.650	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	39	GLY	0	0.074	0.040	30.453	0.018	0.018	0.000	0.000	0.000	0.000
15	A	40	TYR	0	-0.083	-0.062	26.501	0.027	0.027	0.000	0.000	0.000	0.000
16	A	41	ILE	0	0.009	0.004	29.192	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	42	ARG	1	0.841	0.916	23.768	-0.449	-0.449	0.000	0.000	0.000	0.000
18	A	43	MET	0	-0.051	-0.005	26.287	-0.037	-0.037	0.000	0.000	0.000	0.000
19	A	44	VAL	0	0.029	0.004	26.883	0.014	0.014	0.000	0.000	0.000	0.000
20	A	45	LYS	1	0.795	0.891	26.149	-0.300	-0.300	0.000	0.000	0.000	0.000
21	A	46	ASN	0	0.010	0.005	19.545	0.023	0.023	0.000	0.000	0.000	0.000
22	A	47	VAL	0	0.093	0.043	21.352	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	48	ASN	0	-0.005	-0.002	17.349	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	49	TYR	0	-0.018	-0.015	20.837	0.065	0.065	0.000	0.000	0.000	0.000
25	A	50	TYR	0	0.031	0.015	21.682	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	51	ILE	0	-0.008	0.005	25.819	0.033	0.033	0.000	0.000	0.000	0.000
27	A	52	ASP	-1	-0.774	-0.862	27.780	0.456	0.456	0.000	0.000	0.000	0.000
28	A	53	SER	0	0.034	0.010	29.470	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	54	GLU	-1	-0.945	-0.969	32.766	0.324	0.324	0.000	0.000	0.000	0.000
30	A	55	SER	0	-0.075	-0.036	31.039	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	56	ILE	0	-0.063	-0.027	33.155	0.000	0.000	0.000	0.000	0.000	0.000
32	A	57	TRP	0	0.004	0.010	35.423	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	58	VAL	0	-0.022	-0.020	38.271	0.008	0.008	0.000	0.000	0.000	0.000
34	A	59	ASP	-1	-0.873	-0.942	41.000	0.217	0.217	0.000	0.000	0.000	0.000
35	A	60	ASN	0	-0.010	-0.018	42.679	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	61	GLN	0	-0.059	-0.018	45.855	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	62	GLU	-1	-0.903	-0.951	44.535	0.175	0.175	0.000	0.000	0.000	0.000
38	A	63	PRO	0	0.069	0.031	44.256	0.011	0.011	0.000	0.000	0.000	0.000
39	A	64	GLN	0	-0.029	-0.025	43.247	0.012	0.012	0.000	0.000	0.000	0.000
40	A	65	ILE	0	-0.063	-0.020	38.911	0.014	0.014	0.000	0.000	0.000	0.000
41	A	66	VAL	0	0.020	0.012	36.444	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	67	HIS	0	0.026	0.025	34.612	0.032	0.032	0.000	0.000	0.000	0.000
43	A	68	PHE	0	0.037	0.010	29.259	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	69	ASP	-1	-0.772	-0.880	27.215	0.537	0.537	0.000	0.000	0.000	0.000
45	A	70	ALA	0	-0.074	-0.032	25.190	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	71	VAL	0	-0.007	-0.012	21.863	0.042	0.042	0.000	0.000	0.000	0.000
47	A	72	VAL	0	-0.029	-0.015	17.616	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	73	ASN	0	0.052	0.042	17.372	0.146	0.146	0.000	0.000	0.000	0.000
49	A	74	MET	0	-0.032	-0.017	12.743	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	75	ASP	-1	-0.841	-0.927	11.615	1.336	1.336	0.000	0.000	0.000	0.000
51	A	76	ARG	1	0.860	0.914	6.056	-2.677	-2.677	0.000	0.000	0.000	0.000
52	A	77	GLY	0	0.009	0.021	7.648	-0.417	-0.417	0.000	0.000	0.000	0.000
53	A	78	LEU	0	-0.016	-0.001	7.450	0.973	0.973	0.000	0.000	0.000	0.000
54	A	79	TYR	0	0.024	0.010	4.012	-2.474	-2.154	0.001	-0.103	-0.217	0.001
55	A	80	VAL	0	-0.030	-0.020	9.098	-0.222	-0.222	0.000	0.000	0.000	0.000
56	A	81	TYR	0	-0.057	-0.052	12.176	-0.268	-0.268	0.000	0.000	0.000	0.000
57	A	82	PRO	0	-0.004	-0.006	13.461	0.042	0.042	0.000	0.000	0.000	0.000
58	A	83	GLU	-1	-0.772	-0.848	13.379	0.715	0.715	0.000	0.000	0.000	0.000
59	A	84	PRO	0	0.032	0.018	9.128	0.194	0.194	0.000	0.000	0.000	0.000
60	A	85	LYS	1	0.894	0.928	8.495	-0.460	-0.460	0.000	0.000	0.000	0.000
61	A	86	ARG	1	0.799	0.898	9.673	-0.800	-0.800	0.000	0.000	0.000	0.000
62	A	87	TYR	0	0.021	0.009	8.034	0.123	0.123	0.000	0.000	0.000	0.000
63	A	88	ALA	0	-0.011	-0.004	10.173	-0.320	-0.320	0.000	0.000	0.000	0.000
64	A	89	ARG	1	0.927	0.948	11.918	-1.083	-1.083	0.000	0.000	0.000	0.000
65	A	90	SER	0	-0.023	-0.025	14.089	-0.124	-0.124	0.000	0.000	0.000	0.000
66	A	91	VAL	0	-0.033	-0.016	16.620	0.041	0.041	0.000	0.000	0.000	0.000
67	A	92	ARG	1	0.781	0.875	18.952	-0.633	-0.633	0.000	0.000	0.000	0.000
68	A	93	GLN	0	-0.050	-0.044	21.900	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	94	TYR	0	0.098	0.029	24.676	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	95	LYS	1	0.818	0.901	24.569	-0.568	-0.568	0.000	0.000	0.000	0.000
71	A	96	ILE	0	0.023	0.016	30.274	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	97	LEU	0	-0.030	-0.009	33.959	0.007	0.007	0.000	0.000	0.000	0.000
73	A	98	ASN	0	0.049	0.037	35.627	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	99	CYS	0	-0.010	-0.038	36.719	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	100	ALA	0	0.000	0.008	40.398	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	101	ASN	0	0.003	-0.018	40.183	0.003	0.003	0.000	0.000	0.000	0.000
77	A	102	TYR	0	-0.001	0.007	36.328	0.004	0.004	0.000	0.000	0.000	0.000
78	A	103	HIS	0	0.014	0.013	35.899	0.019	0.019	0.000	0.000	0.000	0.000
79	A	104	LEU	0	0.008	-0.002	29.228	0.005	0.005	0.000	0.000	0.000	0.000
80	A	105	THR	0	-0.002	-0.002	31.873	0.008	0.008	0.000	0.000	0.000	0.000
81	A	106	GLN	0	0.000	0.032	24.884	0.021	0.021	0.000	0.000	0.000	0.000
82	A	107	VAL	0	-0.080	0.000	28.625	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	108	ARG	1	0.820	0.636	24.637	-0.540	-0.540	0.000	0.000	0.000	0.000
84	A	109	THR	0	0.066	0.263	19.895	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	110	ASP	-1	-0.825	-0.905	20.845	0.661	0.661	0.000	0.000	0.000	0.000
86	A	111	PHE	0	-0.013	-0.019	15.637	0.047	0.047	0.000	0.000	0.000	0.000
87	A	112	TYR	0	0.049	0.038	17.278	-0.095	-0.095	0.000	0.000	0.000	0.000
88	A	113	ASP	-1	-0.786	-0.892	14.589	1.205	1.205	0.000	0.000	0.000	0.000
89	A	114	GLU	-1	-0.905	-0.940	15.477	0.765	0.765	0.000	0.000	0.000	0.000
90	A	115	PHE	0	-0.006	-0.021	14.618	0.040	0.040	0.000	0.000	0.000	0.000
91	A	116	TRP	0	-0.007	-0.021	18.895	-0.060	-0.060	0.000	0.000	0.000	0.000
92	A	117	GLY	0	0.011	0.020	20.634	-0.061	-0.061	0.000	0.000	0.000	0.000
93	A	118	GLN	0	0.034	0.009	21.090	-0.112	-0.112	0.000	0.000	0.000	0.000
94	A	119	GLY	0	0.111	0.059	19.962	0.083	0.083	0.000	0.000	0.000	0.000
95	A	120	LEU	0	-0.068	-0.039	17.739	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	121	ARG	1	0.911	0.961	18.400	-0.523	-0.523	0.000	0.000	0.000	0.000
97	A	122	ALA	0	-0.030	-0.011	16.555	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	123	ALA	0	-0.005	0.000	18.676	0.031	0.031	0.000	0.000	0.000	0.000
99	A	124	PRO	0	-0.025	-0.004	18.756	0.013	0.013	0.000	0.000	0.000	0.000
100	A	125	LYS	1	0.986	0.992	17.699	-0.745	-0.745	0.000	0.000	0.000	0.000
101	A	126	LYS	1	0.977	0.985	21.529	-0.464	-0.464	0.000	0.000	0.000	0.000
102	A	127	GLN	0	0.033	0.020	22.733	0.059	0.059	0.000	0.000	0.000	0.000
103	A	128	LYS	1	0.927	0.967	20.756	-0.697	-0.697	0.000	0.000	0.000	0.000
104	A	129	LYS	1	0.940	0.982	25.106	-0.379	-0.379	0.000	0.000	0.000	0.000
105	A	130	HIS	0	-0.004	-0.003	24.954	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	131	THR	0	0.019	-0.004	29.980	0.015	0.015	0.000	0.000	0.000	0.000
107	A	132	LEU	0	-0.048	-0.010	27.835	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	133	SER	0	0.044	0.020	32.448	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	134	LEU	0	-0.051	-0.023	30.916	0.007	0.007	0.000	0.000	0.000	0.000
110	A	135	THR	0	0.048	0.026	32.836	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	136	PRO	0	0.003	-0.022	33.210	0.019	0.019	0.000	0.000	0.000	0.000
112	A	137	ASP	-1	-0.826	-0.890	32.355	0.259	0.259	0.000	0.000	0.000	0.000
113	A	138	THR	0	0.007	0.007	28.414	0.025	0.025	0.000	0.000	0.000	0.000
114	A	139	THR	0	0.015	-0.011	24.709	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	140	LEU	0	0.013	0.001	25.898	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	141	TYR	0	0.046	0.043	29.187	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	142	ASN	0	0.006	-0.016	31.120	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	143	ALA	0	0.020	0.000	29.697	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	144	ALA	0	0.036	0.018	31.841	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	145	GLN	0	-0.010	0.001	34.770	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	146	ILE	0	0.011	0.013	32.811	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	147	ILE	0	0.026	0.018	33.292	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	149	ALA	0	-0.073	-0.030	39.689	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	150	ASN	0	-0.055	-0.035	38.690	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	151	TYR	0	-0.004	0.007	36.918	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	152	GLY	0	0.014	0.028	41.127	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	153	LYS	1	0.824	0.901	42.876	-0.206	-0.206	0.000	0.000	0.000	0.000
128	A	154	ALA	0	0.019	0.013	44.327	0.006	0.006	0.000	0.000	0.000	0.000
129	A	155	PHE	0	0.032	0.025	45.464	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	156	SER	0	0.019	0.005	42.212	0.006	0.006	0.000	0.000	0.000	0.000
131	A	157	VAL	0	0.017	0.021	44.583	-0.009	-0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:26:ASN)