FMO DATABASE

FMODB ID: R5R48

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1204817.620023
FMO2-HF: Nuclear repulsion	1150779.125352
FMO2-HF: Total energy	-54038.494671
FMO2-MP2: Total energy	-54195.840559

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.
-3.415	-6.951	0.319	6.118	-2.9	0.006

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 : 0.008 / q_NPA : 0.008

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	-0.004	-0.001	2.649	7.530	2.369	0.209	6.840	-1.888	0.000
4	A	29	LYS	1	0.913	0.938	4.545	-1.831	-1.621	0.004	-0.064	-0.149	0.000
5	A	30	LEU	0	-0.048	-0.013	7.742	-0.048	-0.048	0.000	0.000	0.000	0.000
6	A	31	ALA	0	0.028	0.009	11.055	-0.177	-0.177	0.000	0.000	0.000	0.000
7	A	32	PRO	0	-0.054	-0.019	14.011	-0.029	-0.029	0.000	0.000	0.000	0.000
8	A	33	PRO	0	-0.030	-0.008	16.920	-0.090	-0.090	0.000	0.000	0.000	0.000
9	A	34	THR	0	0.044	0.008	20.335	0.001	0.001	0.000	0.000	0.000	0.000
10	A	35	ASP	-1	-0.905	-0.921	23.005	0.362	0.362	0.000	0.000	0.000	0.000
11	A	36	VAL	0	-0.048	-0.032	24.579	0.046	0.046	0.000	0.000	0.000	0.000
12	A	37	ARG	1	0.865	0.941	21.995	-0.649	-0.649	0.000	0.000	0.000	0.000
13	A	38	SER	0	0.038	-0.001	26.918	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	39	GLY	0	0.088	0.049	29.769	0.019	0.019	0.000	0.000	0.000	0.000
15	A	40	TYR	0	-0.084	-0.061	26.085	0.023	0.023	0.000	0.000	0.000	0.000
16	A	41	ILE	0	0.028	0.010	28.773	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	42	ARG	1	0.810	0.892	23.407	-0.466	-0.466	0.000	0.000	0.000	0.000
18	A	43	MET	0	-0.040	-0.002	26.016	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	44	VAL	0	0.024	0.000	26.403	0.019	0.019	0.000	0.000	0.000	0.000
20	A	45	LYS	1	0.833	0.909	26.221	-0.284	-0.284	0.000	0.000	0.000	0.000
21	A	46	ASN	0	-0.029	-0.019	19.469	0.032	0.032	0.000	0.000	0.000	0.000
22	A	47	VAL	0	0.088	0.049	21.063	0.012	0.012	0.000	0.000	0.000	0.000
23	A	48	ASN	0	0.021	0.031	16.803	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	49	TYR	0	-0.018	-0.019	20.405	0.080	0.080	0.000	0.000	0.000	0.000
25	A	50	TYR	0	-0.004	-0.006	21.436	-0.066	-0.066	0.000	0.000	0.000	0.000
26	A	51	ILE	0	-0.004	0.006	25.656	0.030	0.030	0.000	0.000	0.000	0.000
27	A	52	ASP	-1	-0.761	-0.855	27.291	0.483	0.483	0.000	0.000	0.000	0.000
28	A	53	SER	0	0.017	-0.007	29.063	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	54	GLU	-1	-0.940	-0.952	31.871	0.342	0.342	0.000	0.000	0.000	0.000
30	A	55	SER	0	-0.092	-0.056	30.223	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	56	ILE	0	-0.065	-0.017	32.380	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	57	TRP	0	0.016	0.011	35.027	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	58	VAL	0	-0.012	-0.007	37.834	0.007	0.007	0.000	0.000	0.000	0.000
34	A	59	ASP	-1	-0.814	-0.910	40.685	0.230	0.230	0.000	0.000	0.000	0.000
35	A	60	ASN	0	-0.029	-0.021	42.042	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	61	GLN	0	-0.075	-0.033	45.018	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	62	GLU	-1	-0.892	-0.949	44.207	0.174	0.174	0.000	0.000	0.000	0.000
38	A	63	PRO	0	0.074	0.036	43.822	0.011	0.011	0.000	0.000	0.000	0.000
39	A	64	GLN	0	-0.008	-0.001	43.042	0.012	0.012	0.000	0.000	0.000	0.000
40	A	65	ILE	0	-0.069	-0.027	38.785	0.013	0.013	0.000	0.000	0.000	0.000
41	A	66	VAL	0	-0.005	-0.002	36.296	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	67	HIS	0	-0.014	-0.007	34.430	0.035	0.035	0.000	0.000	0.000	0.000
43	A	68	PHE	0	0.033	0.007	29.400	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	69	ASP	-1	-0.795	-0.889	26.659	0.564	0.564	0.000	0.000	0.000	0.000
45	A	70	ALA	0	-0.047	-0.016	24.945	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	71	VAL	0	-0.017	-0.017	21.755	0.043	0.043	0.000	0.000	0.000	0.000
47	A	72	VAL	0	-0.035	-0.013	17.672	-0.040	-0.040	0.000	0.000	0.000	0.000
48	A	73	ASN	0	0.057	0.028	17.243	0.156	0.156	0.000	0.000	0.000	0.000
49	A	74	MET	0	-0.037	-0.020	12.279	-0.060	-0.060	0.000	0.000	0.000	0.000
50	A	75	ASP	-1	-0.796	-0.917	11.845	1.298	1.298	0.000	0.000	0.000	0.000
51	A	76	ARG	1	0.829	0.892	6.056	-2.173	-2.173	0.000	0.000	0.000	0.000
52	A	77	GLY	0	0.000	0.010	7.081	-0.549	-0.549	0.000	0.000	0.000	0.000
53	A	78	LEU	0	-0.017	-0.003	6.573	1.343	1.343	0.000	0.000	0.000	0.000
54	A	79	TYR	0	0.027	0.012	3.077	-4.970	-3.555	0.106	-0.658	-0.863	0.006
55	A	80	VAL	0	-0.052	-0.023	8.413	-0.361	-0.361	0.000	0.000	0.000	0.000
56	A	81	TYR	0	-0.033	-0.038	11.659	-0.325	-0.325	0.000	0.000	0.000	0.000
57	A	82	PRO	0	-0.013	-0.019	12.898	0.074	0.074	0.000	0.000	0.000	0.000
58	A	83	GLU	-1	-0.767	-0.838	13.452	0.800	0.800	0.000	0.000	0.000	0.000
59	A	84	PRO	0	0.025	-0.001	9.089	0.174	0.174	0.000	0.000	0.000	0.000
60	A	85	LYS	1	0.888	0.935	8.073	-0.330	-0.330	0.000	0.000	0.000	0.000
61	A	86	ARG	1	0.796	0.903	9.155	-0.997	-0.997	0.000	0.000	0.000	0.000
62	A	87	TYR	0	0.005	0.003	7.260	0.213	0.213	0.000	0.000	0.000	0.000
63	A	88	ALA	0	-0.023	-0.006	9.397	-0.391	-0.391	0.000	0.000	0.000	0.000
64	A	89	ARG	1	0.902	0.922	11.051	-1.192	-1.192	0.000	0.000	0.000	0.000
65	A	90	SER	0	-0.035	-0.027	13.357	-0.179	-0.179	0.000	0.000	0.000	0.000
66	A	91	VAL	0	-0.023	-0.016	16.172	0.090	0.090	0.000	0.000	0.000	0.000
67	A	92	ARG	1	0.772	0.868	18.521	-0.670	-0.670	0.000	0.000	0.000	0.000
68	A	93	GLN	0	-0.068	-0.063	21.544	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	94	TYR	0	0.092	0.052	24.412	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	95	LYS	1	0.812	0.890	24.367	-0.575	-0.575	0.000	0.000	0.000	0.000
71	A	96	ILE	0	0.024	0.016	30.229	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	97	LEU	0	-0.036	-0.005	33.959	0.004	0.004	0.000	0.000	0.000	0.000
73	A	98	ASN	0	0.057	0.030	35.466	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	99	CYS	0	-0.014	-0.027	36.617	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	100	ALA	0	0.007	0.007	40.529	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	101	ASN	0	-0.017	-0.022	40.229	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	102	TYR	0	0.006	0.001	36.146	0.000	0.000	0.000	0.000	0.000	0.000
78	A	103	HIS	0	0.013	0.019	35.793	0.018	0.018	0.000	0.000	0.000	0.000
79	A	104	LEU	0	0.013	0.002	29.217	0.004	0.004	0.000	0.000	0.000	0.000
80	A	105	THR	0	-0.010	0.001	31.671	0.008	0.008	0.000	0.000	0.000	0.000
81	A	106	GLN	0	-0.023	0.003	24.892	0.021	0.021	0.000	0.000	0.000	0.000
82	A	107	VAL	0	0.014	-0.005	28.628	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	108	ARG	1	0.851	0.891	24.164	-0.579	-0.579	0.000	0.000	0.000	0.000
84	A	109	THR	0	-0.049	-0.014	19.191	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	110	ASP	-1	-0.792	-0.853	20.137	0.709	0.709	0.000	0.000	0.000	0.000
86	A	111	PHE	0	0.007	-0.007	15.072	0.020	0.020	0.000	0.000	0.000	0.000
87	A	112	TYR	0	0.046	0.027	16.257	-0.103	-0.103	0.000	0.000	0.000	0.000
88	A	113	ASP	-1	-0.744	-0.873	14.030	1.347	1.347	0.000	0.000	0.000	0.000
89	A	114	GLU	-1	-0.848	-0.897	15.003	0.778	0.778	0.000	0.000	0.000	0.000
90	A	115	PHE	0	-0.002	-0.002	14.216	0.101	0.101	0.000	0.000	0.000	0.000
91	A	116	TRP	0	0.029	0.012	18.322	-0.070	-0.070	0.000	0.000	0.000	0.000
92	A	117	GLY	0	0.009	0.017	20.114	-0.066	-0.066	0.000	0.000	0.000	0.000
93	A	118	GLN	0	0.018	0.001	20.680	-0.105	-0.105	0.000	0.000	0.000	0.000
94	A	119	GLY	0	0.092	0.046	19.561	0.088	0.088	0.000	0.000	0.000	0.000
95	A	120	LEU	0	-0.048	-0.030	17.328	-0.065	-0.065	0.000	0.000	0.000	0.000
96	A	121	ARG	1	0.902	0.959	17.650	-0.565	-0.565	0.000	0.000	0.000	0.000
97	A	122	ALA	0	-0.014	0.002	16.048	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	123	ALA	0	-0.005	-0.010	18.131	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	124	PRO	0	-0.024	0.008	18.265	0.035	0.035	0.000	0.000	0.000	0.000
100	A	125	LYS	1	0.985	0.973	17.409	-0.803	-0.803	0.000	0.000	0.000	0.000
101	A	126	LYS	1	0.983	0.990	21.232	-0.490	-0.490	0.000	0.000	0.000	0.000
102	A	127	GLN	0	0.024	0.025	22.577	0.043	0.043	0.000	0.000	0.000	0.000
103	A	128	LYS	1	0.947	0.970	20.891	-0.695	-0.695	0.000	0.000	0.000	0.000
104	A	129	LYS	1	0.906	0.965	25.021	-0.402	-0.402	0.000	0.000	0.000	0.000
105	A	130	HIS	0	0.005	0.006	25.134	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	131	THR	0	0.022	0.003	29.985	0.017	0.017	0.000	0.000	0.000	0.000
107	A	132	LEU	0	-0.030	-0.006	27.630	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	133	SER	0	0.031	0.007	32.200	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	134	LEU	0	-0.063	-0.025	30.850	0.004	0.004	0.000	0.000	0.000	0.000
110	A	135	THR	0	0.064	0.034	32.339	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	136	PRO	0	0.040	-0.010	33.246	0.019	0.019	0.000	0.000	0.000	0.000
112	A	137	ASP	-1	-0.825	-0.895	32.289	0.235	0.235	0.000	0.000	0.000	0.000
113	A	138	THR	0	-0.024	0.005	28.546	0.024	0.024	0.000	0.000	0.000	0.000
114	A	139	THR	0	0.023	-0.007	24.768	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	140	LEU	0	0.000	0.003	25.678	0.001	0.001	0.000	0.000	0.000	0.000
116	A	141	TYR	0	0.035	0.033	29.091	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	142	ASN	0	0.005	-0.018	30.626	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	143	ALA	0	0.019	-0.004	29.422	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	144	ALA	0	0.051	0.020	31.575	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	145	GLN	0	-0.014	0.000	34.499	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	146	ILE	0	0.008	0.011	32.399	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	147	ILE	0	0.041	0.024	33.428	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	149	ALA	0	-0.060	-0.009	39.415	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	150	ASN	0	-0.064	-0.034	38.589	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	151	TYR	0	-0.002	0.001	36.626	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	152	GLY	0	0.021	0.018	40.839	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	153	LYS	1	0.807	0.878	42.452	-0.203	-0.203	0.000	0.000	0.000	0.000
128	A	154	ALA	0	0.012	0.012	44.001	0.006	0.006	0.000	0.000	0.000	0.000
129	A	155	PHE	0	0.039	0.030	45.561	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	156	SER	0	0.011	-0.001	41.939	0.007	0.007	0.000	0.000	0.000	0.000
131	A	157	VAL	0	0.021	0.028	44.498	-0.009	-0.009	0.000	0.000	0.000	0.000

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