FMO DATABASE

FMODB ID: NNVNQ

Calculation Name: 1ZTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U363

Base Structure: X-ray

Registration Date: 2023-09-20

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040024.385994
FMO2-HF: Nuclear repulsion	992932.983548
FMO2-HF: Total energy	-47091.402446
FMO2-MP2: Total energy	-47232.406349

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:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
-31.918	-36.344	30.962	-14.884	-11.653	-0.055

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.069

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

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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	3	ILE	0	-0.069	-0.027	2.169	-7.166	-3.274	3.630	-3.452	-4.070	0.032
4	A	4	ASP	-1	-0.822	-0.900	3.794	1.325	1.579	0.001	0.066	-0.321	0.001
5	A	5	LYS	1	0.896	0.923	5.294	-1.389	-1.389	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.003	0.011	7.792	-0.227	-0.227	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.011	-0.005	9.958	-0.077	-0.077	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.001	0.006	8.146	-0.088	-0.088	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.932	0.958	10.251	-0.349	-0.349	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.007	0.018	13.089	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.055	0.032	13.651	-0.038	-0.038	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.917	-0.965	14.186	0.061	0.061	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.070	-0.029	15.917	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.020	0.021	18.041	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.004	-0.006	16.496	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.013	-0.026	18.452	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.009	0.018	21.421	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.019	0.008	20.831	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.015	-0.029	22.610	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.001	-0.006	24.427	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.001	0.013	27.086	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.024	0.006	27.045	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.017	-0.017	28.134	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.003	-0.007	30.088	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.860	-0.939	32.401	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.039	-0.014	31.939	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.055	-0.025	32.845	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.003	0.012	35.766	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.914	0.959	35.347	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.005	0.010	34.693	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.056	-0.036	31.094	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.039	0.012	28.624	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.831	-0.897	26.326	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.951	0.984	21.269	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.034	0.024	17.876	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.047	-0.019	18.471	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.017	0.008	10.830	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.017	-0.007	14.249	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.019	-0.029	16.277	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.009	0.018	13.533	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.024	-0.017	12.749	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.020	0.009	13.672	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.036	0.026	16.520	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.005	0.015	9.838	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.910	-0.935	14.289	-0.228	-0.228	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.048	-0.021	15.820	0.015	0.015	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.021	-0.018	16.699	0.003	0.003	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.071	-0.024	17.162	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.081	0.036	12.899	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.016	-0.012	10.844	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.925	0.949	11.104	0.047	0.047	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.032	0.011	11.062	0.040	0.040	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.047	0.015	6.174	0.070	0.070	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.925	0.931	3.608	-1.650	-1.302	0.007	-0.083	-0.271	0.000
55	A	55	ARG	1	0.948	0.960	6.032	-0.372	-0.372	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.001	-0.005	2.276	-0.990	-0.111	2.224	-1.106	-1.998	0.002
57	A	57	ASP	-1	-0.729	-0.852	1.587	-23.271	-33.117	25.101	-10.279	-4.976	-0.090
58	A	58	LYS	1	0.784	0.907	4.405	1.227	1.274	-0.001	-0.030	-0.017	0.000
59	A	59	HIS	0	0.004	-0.007	7.569	0.156	0.156	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.003	0.013	4.921	0.203	0.203	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.853	0.903	6.942	0.358	0.358	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.032	0.022	9.074	0.054	0.054	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.769	-0.882	6.623	0.393	0.393	0.000	0.000	0.000	0.000
64	A	64	TYR	0	0.013	-0.001	5.188	0.261	0.261	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.008	0.008	7.501	0.057	0.057	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.870	-0.943	10.743	0.180	0.180	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.011	-0.007	8.316	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.034	-0.012	10.312	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.022	-0.002	12.132	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.005	0.000	13.027	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.935	0.971	9.315	-0.040	-0.040	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.039	0.017	14.631	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	TRP	0	0.012	0.002	17.838	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.043	-0.026	15.403	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	MET	0	-0.042	-0.004	18.436	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.001	0.006	20.281	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.034	-0.008	19.158	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.022	-0.016	20.566	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.014	0.000	23.583	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.883	-0.954	25.434	0.020	0.020	0.000	0.000	0.000	0.000
81	A	81	ARG	1	1.009	0.992	26.429	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.780	-0.861	26.275	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.048	0.011	22.830	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.001	0.004	24.728	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.850	-0.918	27.154	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.020	-0.005	24.143	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.003	0.012	22.267	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.784	0.877	25.913	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.819	0.904	29.639	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.057	-0.030	26.701	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.038	0.009	26.554	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.016	0.007	29.244	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	PRO	0	0.047	0.017	31.248	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.861	-0.948	30.073	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.046	-0.022	27.267	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.029	-0.020	29.415	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.795	-0.863	31.345	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	98	PHE	0	-0.012	-0.010	26.770	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.068	-0.057	27.706	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.870	0.927	27.857	0.027	0.027	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.891	0.957	24.858	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.942	0.966	21.517	0.038	0.038	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.761	-0.825	21.723	-0.062	-0.062	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.005	0.006	23.655	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.032	0.010	20.625	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.017	0.009	19.786	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.794	0.850	20.720	0.047	0.047	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.032	0.016	23.606	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.015	-0.014	17.980	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.008	0.002	19.374	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	PRO	0	0.025	0.007	20.265	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.000	0.004	19.770	0.003	0.003	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.014	-0.015	14.524	0.002	0.002	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.007	0.014	17.577	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.072	0.051	19.856	0.002	0.002	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.025	-0.013	16.058	0.005	0.005	0.000	0.000	0.000	0.000
117	A	117	SER	0	-0.062	-0.043	15.963	0.000	0.000	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.885	-0.952	17.194	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.830	0.899	20.744	0.005	0.005	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.021	0.001	14.420	0.004	0.004	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.023	-0.013	13.557	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.041	-0.039	19.163	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.042	-0.023	20.494	0.004	0.004	0.000	0.000	0.000	0.000
124	A	124	GLN	0	-0.097	-0.043	17.544	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	125	VAL	0	0.006	0.014	21.669	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:1:SER)