FMO DATABASE

FMODB ID: 6YMNZ

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	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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-982312.860115
FMO2-HF: Nuclear repulsion	933864.379511
FMO2-HF: Total energy	-48448.480604
FMO2-MP2: Total energy	-48590.655916

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.
-11.338	-6.685	3.68	-3.418	-4.916	0.015

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 : -0.001 / q_NPA : -0.025

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	0.008	0.002	2.761	-2.198	0.177	1.378	-1.502	-2.250	0.005
4	A	5	LYS	1	1.026	1.019	2.147	-9.579	-7.565	2.304	-1.874	-2.445	0.010
5	A	6	SER	0	-0.027	-0.011	4.123	-0.129	0.073	-0.001	-0.038	-0.164	0.000
6	A	7	LEU	0	0.036	0.029	5.580	0.210	0.210	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.893	-0.966	7.482	1.537	1.537	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.016	0.001	5.969	0.069	0.069	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.040	-0.018	9.427	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.007	-0.001	11.608	0.031	0.031	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.003	0.006	11.383	0.088	0.088	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.079	-0.029	13.790	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.021	-0.009	15.651	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.029	-0.018	18.187	0.037	0.037	0.000	0.000	0.000	0.000
15	A	16	PRO	0	-0.026	0.000	21.776	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.846	-0.918	24.848	-0.035	-0.035	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.038	-0.022	28.230	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	19	MET	0	-0.017	-0.001	29.729	0.002	0.002	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.022	-0.014	33.808	0.004	0.004	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.031	0.015	37.532	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.805	-0.877	38.626	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	TYR	0	-0.014	-0.021	36.901	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.024	-0.011	39.885	0.004	0.004	0.000	0.000	0.000	0.000
24	A	25	PHE	0	0.011	0.004	34.357	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	26	CYS	0	-0.021	0.002	40.558	0.004	0.004	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.044	0.023	42.590	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.009	0.011	44.616	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.002	-0.011	46.919	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.037	0.011	48.638	0.002	0.002	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.029	0.002	47.871	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.061	0.007	41.864	0.001	0.001	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.039	-0.025	45.856	0.000	0.000	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.874	-0.942	48.436	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	35	TYR	0	0.002	-0.001	46.432	0.003	0.003	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.003	-0.007	44.497	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.045	-0.017	46.539	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.006	0.005	46.393	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.946	-0.954	43.598	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.030	-0.001	40.749	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.008	-0.005	35.139	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.027	-0.017	35.018	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.008	-0.004	36.515	0.006	0.006	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.005	0.001	33.174	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.881	0.946	37.760	0.053	0.053	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.857	-0.893	38.221	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	47	PRO	0	-0.070	-0.044	39.960	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.900	-0.955	41.593	-0.040	-0.040	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.005	0.004	43.751	0.003	0.003	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.121	-0.052	41.513	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	51	THR	0	0.037	-0.002	37.771	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.052	-0.030	40.457	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.015	0.017	36.293	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.012	-0.013	39.442	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.840	-0.931	41.486	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.019	-0.022	42.947	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.868	-0.917	45.010	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.886	0.918	44.565	0.025	0.025	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.007	0.007	45.815	0.000	0.000	0.000	0.000	0.000	0.000
59	A	60	GLN	0	-0.037	-0.016	47.916	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.090	-0.045	50.901	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.044	-0.014	50.623	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.050	-0.018	52.688	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.040	-0.025	47.483	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.964	-0.983	49.456	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.011	-0.017	44.748	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.004	0.001	41.328	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.015	-0.003	40.424	0.001	0.001	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.018	0.010	41.157	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.019	-0.013	35.055	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.000	-0.011	34.571	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.004	0.012	30.680	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.008	-0.004	26.817	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.019	0.016	26.005	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.014	-0.018	20.385	0.012	0.012	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.002	-0.009	21.415	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.010	0.000	15.732	0.014	0.014	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.042	-0.011	16.235	-0.042	-0.042	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.074	0.025	13.566	0.032	0.032	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.166	-0.071	10.576	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.032	-0.008	4.542	-0.248	-0.186	-0.001	-0.004	-0.057	0.000
81	A	82	GLU	-1	-0.979	-0.960	8.472	-1.089	-1.089	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.035	0.013	8.894	-0.238	-0.238	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.023	-0.015	10.972	0.181	0.181	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.039	0.002	12.485	0.038	0.038	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.021	0.016	14.830	0.061	0.061	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.058	0.014	16.289	0.029	0.029	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.018	-0.004	17.313	0.023	0.023	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.013	0.031	15.674	0.029	0.029	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.063	0.022	17.818	0.026	0.026	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.013	0.009	20.677	0.010	0.010	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.034	-0.033	20.200	0.007	0.007	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.807	0.918	20.750	-0.127	-0.127	0.000	0.000	0.000	0.000
93	A	94	LEU	0	0.002	-0.006	22.594	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.016	0.008	25.441	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.935	-0.975	21.996	0.141	0.141	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.057	-0.010	25.877	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.022	-0.017	29.180	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.082	-0.039	29.095	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	100	SER	0	-0.008	0.006	29.234	0.001	0.001	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.009	-0.006	27.053	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.046	-0.018	29.002	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.003	-0.008	25.304	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.006	0.003	28.495	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.039	0.021	25.503	0.000	0.000	0.000	0.000	0.000	0.000
105	A	106	GLY	0	-0.007	-0.003	26.856	0.006	0.006	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.071	-0.042	26.124	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	TYR	0	-0.018	-0.015	24.312	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	109	HIS	0	0.010	0.007	22.799	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.837	-0.916	22.331	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	111	HIS	0	-0.007	0.008	24.785	0.018	0.018	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.001	-0.008	24.238	0.000	0.000	0.000	0.000	0.000	0.000
112	A	113	PHE	0	0.028	0.018	28.711	0.006	0.006	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.010	0.007	29.760	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	GLN	0	0.005	-0.011	32.741	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.857	0.911	35.474	0.000	0.000	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.930	-0.964	37.502	0.023	0.023	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.860	0.931	33.143	-0.034	-0.034	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.038	0.026	32.697	0.003	0.003	0.000	0.000	0.000	0.000
119	A	120	GLN	0	-0.015	-0.015	31.897	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	121	GLN	0	-0.022	-0.018	30.747	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.032	0.017	28.487	0.008	0.008	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.010	0.008	26.994	0.003	0.003	0.000	0.000	0.000	0.000
123	A	124	GLN	0	-0.015	-0.014	26.580	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	125	ALA	0	0.007	0.017	25.349	0.010	0.010	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.003	-0.009	22.467	0.011	0.011	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.009	0.002	21.667	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.847	-0.914	21.331	0.145	0.145	0.000	0.000	0.000	0.000
128	A	129	PHE	0	-0.020	-0.017	15.994	0.024	0.024	0.000	0.000	0.000	0.000
129	A	130	ALA	0	-0.016	0.026	16.755	0.033	0.033	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.088	-0.050	16.615	0.020	0.020	0.000	0.000	0.000	0.000

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