FMO DATABASE

FMODB ID: 2NYJR

Calculation Name: 1ZVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KTT6

Base Structure: X-ray

Registration Date: 2023-09-24

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	OptH
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	-981608.008167
FMO2-HF: Nuclear repulsion	933160.407026
FMO2-HF: Total energy	-48447.601141
FMO2-MP2: Total energy	-48589.763827

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-6.773	-5.254	5.255	-2.589	-4.184	0.004

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.029

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	4	ILE	0	0.010	0.005	2.488	-0.882	-0.749	4.385	-1.773	-2.743	0.005
4	A	5	LYS	1	1.026	1.007	2.397	-7.238	-6.055	0.871	-0.771	-1.283	-0.001
5	A	6	SER	0	-0.030	-0.009	4.272	-0.239	-0.036	-0.001	-0.045	-0.158	0.000
6	A	7	LEU	0	0.061	0.040	5.583	-0.190	-0.190	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.914	-0.973	7.851	1.626	1.626	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.014	0.001	6.113	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.025	-0.017	9.422	-0.146	-0.146	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.009	-0.006	11.737	-0.083	-0.083	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.009	0.004	11.450	0.059	0.059	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.079	-0.022	14.209	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.014	-0.006	15.896	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.030	-0.021	18.195	0.009	0.009	0.000	0.000	0.000	0.000
15	A	16	PRO	0	-0.032	-0.003	21.868	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.894	-0.957	24.856	0.092	0.092	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.037	-0.018	28.336	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	MET	0	-0.019	-0.006	31.447	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.036	-0.022	33.968	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.028	0.016	37.700	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.888	-0.940	38.642	0.063	0.063	0.000	0.000	0.000	0.000
22	A	23	TYR	0	0.006	-0.011	37.060	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.038	-0.014	39.907	0.003	0.003	0.000	0.000	0.000	0.000
24	A	25	PHE	0	0.018	0.005	34.461	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	26	CYS	0	-0.010	0.000	40.590	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.033	0.020	42.620	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.008	0.012	44.649	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	ASN	0	0.006	-0.006	46.984	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.055	0.017	48.875	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.003	0.024	48.233	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.056	0.013	42.497	0.001	0.001	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.008	-0.018	46.425	0.001	0.001	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.917	-0.952	49.143	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	TYR	0	-0.015	-0.012	46.895	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.013	-0.018	45.566	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.023	-0.012	47.213	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.032	-0.005	46.827	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.992	-0.987	44.118	0.024	0.024	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.042	-0.005	41.110	0.003	0.003	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.017	-0.004	35.341	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.024	-0.019	35.293	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.000	-0.008	36.942	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	PHE	0	0.009	0.006	33.521	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.855	0.918	38.034	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.913	-0.940	38.051	0.037	0.037	0.000	0.000	0.000	0.000
46	A	47	PRO	0	-0.071	-0.048	39.843	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.912	-0.957	41.613	0.030	0.030	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.007	0.015	43.746	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.108	-0.056	42.033	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	THR	0	0.062	0.036	38.103	0.002	0.002	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.047	-0.028	40.662	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.015	0.020	36.329	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.017	-0.008	39.543	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.840	-0.941	41.516	0.043	0.043	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.015	-0.020	43.061	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.933	-0.967	45.032	0.033	0.033	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.942	0.961	45.649	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.010	0.014	45.870	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	GLN	0	-0.014	0.002	47.938	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.034	-0.010	50.925	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.044	-0.014	50.781	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.051	-0.019	52.802	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.038	-0.027	47.621	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.959	-0.979	49.418	0.034	0.034	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.026	-0.009	44.673	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.016	-0.004	41.300	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.016	0.001	40.451	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.018	0.004	41.191	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.027	-0.015	35.235	0.005	0.005	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.021	-0.001	34.462	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.024	0.016	30.944	0.003	0.003	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.011	-0.004	26.770	0.002	0.002	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.017	0.026	26.442	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.014	-0.015	20.086	0.013	0.013	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.007	0.007	21.959	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.009	-0.003	16.324	0.029	0.029	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.037	-0.008	16.925	-0.047	-0.047	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.077	0.036	14.469	0.028	0.028	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.157	-0.069	11.309	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.038	0.003	5.607	0.007	0.007	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.992	-0.979	9.642	-0.158	-0.158	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.042	0.021	9.301	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.019	-0.013	11.383	0.021	0.021	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.032	0.000	12.530	0.085	0.085	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.027	0.017	14.879	0.031	0.031	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.046	0.015	16.323	0.008	0.008	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.013	-0.005	17.388	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.017	0.040	15.730	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.062	0.019	17.872	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.021	0.009	20.721	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.034	-0.036	20.250	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.848	0.929	20.859	-0.286	-0.286	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.015	-0.013	22.650	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.019	0.011	25.503	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.953	-0.983	22.572	0.272	0.272	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.057	-0.016	25.575	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.031	-0.021	29.239	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.089	-0.040	29.084	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	100	SER	0	-0.030	-0.010	29.289	0.007	0.007	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.034	0.010	27.137	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.043	-0.011	29.047	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.004	-0.009	25.211	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	ILE	0	0.000	0.006	28.526	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.041	0.019	25.901	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	GLY	0	-0.017	-0.007	27.348	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.066	-0.038	26.693	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	TYR	0	-0.016	-0.017	25.335	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	109	HIS	0	0.007	0.010	23.442	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.846	-0.915	22.123	0.094	0.094	0.000	0.000	0.000	0.000
110	A	111	HIS	0	-0.019	-0.006	25.084	0.011	0.011	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.001	-0.009	24.266	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	PHE	0	0.025	0.013	28.737	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.014	0.007	29.734	0.005	0.005	0.000	0.000	0.000	0.000
114	A	115	GLN	0	0.060	0.021	32.778	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.935	0.974	35.511	-0.058	-0.058	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.993	-0.999	37.534	0.088	0.088	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.888	0.950	33.357	-0.113	-0.113	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.036	0.026	32.735	0.009	0.009	0.000	0.000	0.000	0.000
119	A	120	GLN	0	-0.012	-0.010	31.925	0.000	0.000	0.000	0.000	0.000	0.000
120	A	121	GLN	0	0.016	-0.015	31.369	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.018	0.018	28.521	0.012	0.012	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.013	0.014	27.026	0.013	0.013	0.000	0.000	0.000	0.000
123	A	124	GLN	0	-0.018	-0.020	26.603	0.001	0.001	0.000	0.000	0.000	0.000
124	A	125	ALA	0	0.027	0.028	25.384	0.013	0.013	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.008	-0.015	22.275	0.025	0.025	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.006	-0.002	21.690	0.018	0.018	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.898	-0.936	21.379	0.258	0.258	0.000	0.000	0.000	0.000
128	A	129	PHE	0	-0.029	-0.014	16.137	0.027	0.027	0.000	0.000	0.000	0.000
129	A	130	ALA	0	-0.017	0.023	16.773	0.049	0.049	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.071	-0.040	16.632	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)