FMO DATABASE

FMODB ID: JL2K9

Calculation Name: 3ZRI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZRI

Chain ID: A

ChEMBL ID:

UniProt ID:

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1683379.253375
FMO2-HF: Nuclear repulsion	1618580.103293
FMO2-HF: Total energy	-64799.150082
FMO2-MP2: Total energy	-64992.326428

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:-7:HIS)

Summations of interaction energy for fragment #1(A:-7:HIS)

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.
-19.371	-17.505	13.017	-5.736	-9.147	0.033

Interaction energy analysis for fragmet #1(A:-7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.031

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	-5	HIS	0	-0.086	-0.053	1.972	-13.919	-14.055	11.716	-5.351	-6.229	0.037
4	A	-4	HIS	0	-0.035	-0.020	2.480	-2.664	-1.380	1.279	-0.005	-2.558	-0.001
5	A	-3	HIS	0	0.007	0.023	3.427	-3.493	-2.775	0.022	-0.380	-0.360	-0.003
6	A	-2	HIS	0	-0.013	-0.022	5.924	-0.028	-0.028	0.000	0.000	0.000	0.000
7	A	-1	THR	0	-0.036	-0.015	6.770	0.187	0.187	0.000	0.000	0.000	0.000
8	A	0	ASP	-1	-0.862	-0.919	9.780	0.247	0.247	0.000	0.000	0.000	0.000
9	A	1	PRO	0	-0.026	-0.023	12.937	0.029	0.029	0.000	0.000	0.000	0.000
10	A	2	ILE	0	0.019	0.012	15.011	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	3	ARG	1	0.957	0.976	17.055	-0.254	-0.254	0.000	0.000	0.000	0.000
12	A	4	ILE	0	-0.037	-0.027	20.210	0.009	0.009	0.000	0.000	0.000	0.000
13	A	5	GLU	-1	-0.911	-0.943	22.302	0.179	0.179	0.000	0.000	0.000	0.000
14	A	6	LEU	0	0.069	0.021	24.682	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	7	PRO	0	-0.001	-0.014	27.403	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	8	THR	0	-0.003	0.002	25.921	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	9	LEU	0	-0.013	-0.010	26.463	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	10	ILE	0	0.016	0.004	29.889	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	11	ALA	0	-0.051	-0.028	32.208	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	12	LYS	1	0.887	0.964	30.193	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	13	LEU	0	-0.025	0.014	33.914	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	14	ASN	0	0.069	0.039	36.683	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	15	ALA	0	0.023	0.012	40.193	0.001	0.001	0.000	0.000	0.000	0.000
24	A	16	GLN	0	-0.020	-0.011	42.706	0.002	0.002	0.000	0.000	0.000	0.000
25	A	17	SER	0	-0.028	-0.028	39.501	0.002	0.002	0.000	0.000	0.000	0.000
26	A	18	LYS	1	0.941	0.971	37.820	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	19	LEU	0	0.005	0.012	40.501	0.000	0.000	0.000	0.000	0.000	0.000
28	A	20	ALA	0	0.037	0.023	42.695	0.000	0.000	0.000	0.000	0.000	0.000
29	A	21	LEU	0	0.016	0.000	36.372	0.000	0.000	0.000	0.000	0.000	0.000
30	A	22	GLU	-1	-0.918	-0.950	40.379	0.061	0.061	0.000	0.000	0.000	0.000
31	A	23	GLN	0	0.006	-0.016	42.056	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	24	ALA	0	0.011	0.020	40.865	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	25	ALA	0	0.005	-0.003	40.107	0.000	0.000	0.000	0.000	0.000	0.000
34	A	26	SER	0	-0.054	-0.032	41.764	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	27	LEU	0	-0.033	-0.006	44.539	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	28	CYS	0	-0.012	-0.007	40.856	0.000	0.000	0.000	0.000	0.000	0.000
37	A	29	ILE	0	0.016	0.017	43.017	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	30	GLU	-1	-0.902	-0.919	45.492	0.042	0.042	0.000	0.000	0.000	0.000
39	A	31	ARG	1	0.807	0.884	45.470	-0.047	-0.047	0.000	0.000	0.000	0.000
40	A	32	GLN	0	-0.076	-0.024	45.383	0.000	0.000	0.000	0.000	0.000	0.000
41	A	33	HIS	0	0.035	0.013	41.113	0.002	0.002	0.000	0.000	0.000	0.000
42	A	34	PRO	0	0.026	0.000	37.549	0.000	0.000	0.000	0.000	0.000	0.000
43	A	35	GLU	-1	-0.944	-0.983	32.994	0.088	0.088	0.000	0.000	0.000	0.000
44	A	36	VAL	0	0.025	0.008	36.437	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	37	THR	0	0.001	-0.018	35.535	0.005	0.005	0.000	0.000	0.000	0.000
46	A	38	LEU	0	0.066	0.018	35.366	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	39	GLU	-1	-0.755	-0.862	37.147	0.066	0.066	0.000	0.000	0.000	0.000
48	A	40	HIS	0	0.033	0.031	40.082	0.000	0.000	0.000	0.000	0.000	0.000
49	A	41	TYR	0	-0.040	-0.025	38.359	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	42	LEU	0	-0.011	-0.015	39.876	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	43	ASP	-1	-0.793	-0.886	42.665	0.045	0.045	0.000	0.000	0.000	0.000
52	A	44	VAL	0	0.019	0.028	44.482	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	45	LEU	0	-0.018	-0.014	41.441	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	46	LEU	0	-0.038	-0.007	45.873	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	47	ASP	-1	-0.837	-0.898	48.587	0.041	0.041	0.000	0.000	0.000	0.000
56	A	48	ASN	0	-0.006	0.005	48.104	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	49	PRO	0	-0.049	-0.047	49.997	0.001	0.001	0.000	0.000	0.000	0.000
58	A	50	LEU	0	-0.024	-0.009	50.784	0.000	0.000	0.000	0.000	0.000	0.000
59	A	51	SER	0	0.037	0.035	45.559	0.001	0.001	0.000	0.000	0.000	0.000
60	A	52	ASP	-1	-0.690	-0.818	42.170	0.055	0.055	0.000	0.000	0.000	0.000
61	A	53	VAL	0	0.013	0.004	42.071	0.000	0.000	0.000	0.000	0.000	0.000
62	A	54	ARG	1	0.901	0.952	44.592	-0.041	-0.041	0.000	0.000	0.000	0.000
63	A	55	LEU	0	-0.010	0.008	47.408	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	56	VAL	0	0.005	0.005	42.903	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	57	LEU	0	-0.030	-0.013	45.456	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	58	LYS	1	0.968	0.988	48.082	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	59	GLN	0	-0.045	-0.017	46.713	0.000	0.000	0.000	0.000	0.000	0.000
68	A	60	ALA	0	-0.046	-0.037	47.056	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	61	GLY	0	-0.011	0.012	49.200	0.000	0.000	0.000	0.000	0.000	0.000
70	A	62	LEU	0	-0.055	-0.025	46.893	0.000	0.000	0.000	0.000	0.000	0.000
71	A	63	GLU	-1	-0.907	-0.956	51.036	0.035	0.035	0.000	0.000	0.000	0.000
72	A	64	VAL	0	0.031	-0.003	50.933	0.001	0.001	0.000	0.000	0.000	0.000
73	A	65	ASP	-1	-0.868	-0.928	51.427	0.036	0.036	0.000	0.000	0.000	0.000
74	A	66	GLN	0	-0.053	-0.024	50.774	0.001	0.001	0.000	0.000	0.000	0.000
75	A	67	VAL	0	0.016	0.003	46.143	0.001	0.001	0.000	0.000	0.000	0.000
76	A	68	LYS	1	0.820	0.899	47.688	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	69	GLN	0	-0.047	-0.026	49.081	0.000	0.000	0.000	0.000	0.000	0.000
78	A	70	ALA	0	-0.037	-0.009	46.541	0.000	0.000	0.000	0.000	0.000	0.000
79	A	71	ILE	0	0.055	0.036	43.623	0.001	0.001	0.000	0.000	0.000	0.000
80	A	72	ALA	0	0.015	0.018	45.237	0.001	0.001	0.000	0.000	0.000	0.000
81	A	73	SER	0	-0.136	-0.066	47.070	0.000	0.000	0.000	0.000	0.000	0.000
82	A	74	THR	0	-0.102	-0.078	41.956	0.001	0.001	0.000	0.000	0.000	0.000
83	A	75	TYR	0	-0.033	-0.037	42.519	0.003	0.003	0.000	0.000	0.000	0.000
84	A	76	SER	0	-0.044	-0.012	41.712	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	77	ARG	1	0.951	0.968	43.787	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	78	GLU	-1	-0.857	-0.923	45.156	0.044	0.044	0.000	0.000	0.000	0.000
87	A	79	GLN	0	-0.103	-0.060	39.926	0.001	0.001	0.000	0.000	0.000	0.000
88	A	80	VAL	0	0.016	0.001	44.071	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	81	LEU	0	-0.041	-0.004	41.289	0.002	0.002	0.000	0.000	0.000	0.000
90	A	82	ASP	-1	-0.901	-0.940	39.126	0.056	0.056	0.000	0.000	0.000	0.000
91	A	83	THR	0	-0.060	-0.041	35.819	0.000	0.000	0.000	0.000	0.000	0.000
92	A	84	TYR	0	-0.028	-0.014	38.718	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	85	PRO	0	0.031	0.021	37.663	0.004	0.004	0.000	0.000	0.000	0.000
94	A	86	ALA	0	-0.001	0.009	33.403	0.000	0.000	0.000	0.000	0.000	0.000
95	A	87	PHE	0	-0.007	-0.016	32.373	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	88	SER	0	0.052	0.035	31.951	0.005	0.005	0.000	0.000	0.000	0.000
97	A	89	PRO	0	0.002	-0.016	26.525	0.004	0.004	0.000	0.000	0.000	0.000
98	A	90	LEU	0	0.011	0.024	27.631	0.006	0.006	0.000	0.000	0.000	0.000
99	A	91	LEU	0	0.034	0.009	29.214	0.002	0.002	0.000	0.000	0.000	0.000
100	A	92	VAL	0	0.003	-0.002	26.645	0.001	0.001	0.000	0.000	0.000	0.000
101	A	93	GLU	-1	-0.879	-0.917	24.179	0.140	0.140	0.000	0.000	0.000	0.000
102	A	94	LEU	0	0.008	0.007	26.681	0.004	0.004	0.000	0.000	0.000	0.000
103	A	95	LEU	0	-0.009	0.000	29.804	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	96	GLN	0	0.002	0.014	21.397	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	97	GLU	-1	-0.823	-0.875	25.706	0.136	0.136	0.000	0.000	0.000	0.000
106	A	98	ALA	0	0.032	0.023	27.701	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	99	TRP	0	0.037	0.029	27.419	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	100	LEU	0	-0.016	0.001	24.222	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	101	LEU	0	0.022	0.019	28.036	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	102	SER	0	-0.019	-0.044	30.984	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	103	SER	0	-0.074	-0.033	29.245	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	104	THR	0	-0.043	-0.038	27.590	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	105	GLU	-1	-0.857	-0.915	31.018	0.084	0.084	0.000	0.000	0.000	0.000
114	A	106	LEU	0	-0.049	-0.013	33.538	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	107	GLU	-1	-0.960	-0.954	35.032	0.052	0.052	0.000	0.000	0.000	0.000
116	A	108	GLN	0	-0.033	-0.029	35.549	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	109	ALA	0	-0.039	-0.023	35.140	0.004	0.004	0.000	0.000	0.000	0.000
118	A	110	GLU	-1	-0.872	-0.936	35.691	0.061	0.061	0.000	0.000	0.000	0.000
119	A	111	LEU	0	-0.055	-0.030	32.127	0.001	0.001	0.000	0.000	0.000	0.000
120	A	112	ARG	1	0.833	0.890	35.618	-0.058	-0.058	0.000	0.000	0.000	0.000
121	A	113	SER	0	0.006	-0.044	37.776	0.004	0.004	0.000	0.000	0.000	0.000
122	A	114	GLY	0	0.028	0.010	39.264	0.001	0.001	0.000	0.000	0.000	0.000
123	A	115	ALA	0	-0.022	-0.010	35.024	0.001	0.001	0.000	0.000	0.000	0.000
124	A	116	ILE	0	0.004	-0.010	34.331	0.005	0.005	0.000	0.000	0.000	0.000
125	A	117	PHE	0	0.025	0.011	35.293	0.002	0.002	0.000	0.000	0.000	0.000
126	A	118	LEU	0	0.029	0.018	35.513	0.000	0.000	0.000	0.000	0.000	0.000
127	A	119	ALA	0	-0.011	0.008	31.335	0.002	0.002	0.000	0.000	0.000	0.000
128	A	120	ALA	0	0.011	-0.003	32.534	0.003	0.003	0.000	0.000	0.000	0.000
129	A	121	LEU	0	-0.030	-0.012	34.320	0.000	0.000	0.000	0.000	0.000	0.000
130	A	122	THR	0	-0.050	-0.045	31.748	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	123	ARG	1	0.851	0.923	25.046	-0.127	-0.127	0.000	0.000	0.000	0.000
132	A	124	ALA	0	0.045	0.023	31.728	0.001	0.001	0.000	0.000	0.000	0.000
133	A	125	ASP	-1	-0.938	-0.979	30.013	0.096	0.096	0.000	0.000	0.000	0.000
134	A	126	ARG	1	0.804	0.905	25.606	-0.118	-0.118	0.000	0.000	0.000	0.000
135	A	127	TYR	0	-0.073	-0.094	27.261	0.000	0.000	0.000	0.000	0.000	0.000
136	A	128	LEU	0	-0.024	0.004	32.867	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	129	SER	0	-0.011	-0.021	36.479	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	130	PHE	0	0.033	0.001	38.608	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	131	LYS	1	0.967	0.975	39.938	-0.045	-0.045	0.000	0.000	0.000	0.000
140	A	132	LEU	0	0.017	0.010	40.742	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	133	ILE	0	-0.016	0.004	36.355	0.000	0.000	0.000	0.000	0.000	0.000
142	A	134	SER	0	-0.038	-0.023	40.383	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	135	LEU	0	-0.069	-0.020	43.743	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	136	PHE	0	0.039	0.000	40.867	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	137	GLU	-1	-0.906	-0.942	42.166	0.053	0.053	0.000	0.000	0.000	0.000
146	A	138	GLY	0	-0.023	-0.004	43.293	0.000	0.000	0.000	0.000	0.000	0.000
147	A	139	ILE	0	-0.022	0.000	42.392	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	140	ASN	0	0.005	0.000	42.029	0.002	0.002	0.000	0.000	0.000	0.000
149	A	141	ARG	1	0.876	0.928	36.790	-0.067	-0.067	0.000	0.000	0.000	0.000
150	A	142	GLU	-1	-0.863	-0.932	37.885	0.066	0.066	0.000	0.000	0.000	0.000
151	A	143	ASN	0	-0.032	-0.023	39.468	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	144	LEU	0	0.020	0.013	40.201	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	145	LYS	1	0.863	0.902	32.867	-0.086	-0.086	0.000	0.000	0.000	0.000
154	A	146	LYS	1	0.880	0.953	38.730	-0.050	-0.050	0.000	0.000	0.000	0.000
155	A	147	HIS	0	-0.010	-0.025	40.781	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	148	PHE	0	0.041	0.042	39.225	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	149	ALA	0	0.035	-0.008	42.196	-0.001	-0.001	0.000	0.000	0.000	0.000
158	A	150	MET	0	-0.051	-0.020	43.944	-0.003	-0.003	0.000	0.000	0.000	0.000
159	A	151	ILE	0	-0.052	-0.017	44.296	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	152	LEU	0	-0.047	-0.008	42.343	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	153	SER	0	0.019	0.004	46.620	0.000	0.000	0.000	0.000	0.000	0.000
162	A	154	ASP	-1	-0.940	-0.967	48.950	0.035	0.035	0.000	0.000	0.000	0.000
163	A	155	SER	0	-0.066	-0.048	45.556	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	156	ALA	0	-0.021	-0.029	48.226	-0.001	-0.001	0.000	0.000	0.000	0.000
165	A	157	GLU	-1	-0.812	-0.881	42.081	0.058	0.058	0.000	0.000	0.000	0.000
166	A	158	THR	0	-0.025	0.012	43.520	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-7:HIS)