FMO DATABASE

FMODB ID: 899QY

Calculation Name: 4ZYL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZYL

Chain ID: A

ChEMBL ID:

UniProt ID: Q6N5G1

Base Structure: X-ray

Registration Date: 2023-09-21

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1354244.757399
FMO2-HF: Nuclear repulsion	1298352.631823
FMO2-HF: Total energy	-55892.125576
FMO2-MP2: Total energy	-56058.305447

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:LEU)

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

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.
-6.349	-0.585	3.189	-2.516	-6.439	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023

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	9	THR	0	-0.004	-0.018	3.772	-1.228	0.109	0.000	-0.572	-0.766	0.001
4	A	10	VAL	0	-0.041	-0.029	5.753	0.589	0.589	0.000	0.000	0.000	0.000
5	A	11	LEU	0	-0.015	0.013	8.202	0.021	0.021	0.000	0.000	0.000	0.000
6	A	12	VAL	0	-0.006	-0.013	11.104	0.100	0.100	0.000	0.000	0.000	0.000
7	A	13	ALA	0	-0.002	0.005	13.705	0.007	0.007	0.000	0.000	0.000	0.000
8	A	14	GLH	0	-0.021	-0.087	16.756	0.044	0.044	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.803	-0.914	18.155	-0.248	-0.248	0.000	0.000	0.000	0.000
10	A	16	HIS	0	0.058	0.050	20.720	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	17	ASP	-1	-0.817	-0.924	19.430	-0.280	-0.280	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.026	-0.003	19.103	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.820	-0.907	19.027	-0.212	-0.212	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.784	0.894	15.456	0.290	0.290	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.007	0.017	14.371	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	22	ILE	0	0.000	-0.003	15.087	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.004	-0.004	12.181	0.007	0.007	0.000	0.000	0.000	0.000
18	A	24	THR	0	0.002	-0.013	9.819	-0.058	-0.058	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.839	-0.909	10.960	-0.189	-0.189	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.043	-0.020	13.383	0.029	0.029	0.000	0.000	0.000	0.000
21	A	27	PHE	0	0.023	-0.004	7.237	0.040	0.040	0.000	0.000	0.000	0.000
22	A	28	ALA	0	0.003	0.010	9.065	0.035	0.035	0.000	0.000	0.000	0.000
23	A	29	ARG	1	0.847	0.903	10.049	0.194	0.194	0.000	0.000	0.000	0.000
24	A	30	ALA	0	-0.047	-0.018	11.181	0.045	0.045	0.000	0.000	0.000	0.000
25	A	31	SER	0	-0.067	-0.029	9.416	0.061	0.061	0.000	0.000	0.000	0.000
26	A	32	ILE	0	-0.045	-0.009	6.256	0.110	0.110	0.000	0.000	0.000	0.000
27	A	33	SER	0	-0.015	-0.007	2.494	-1.127	-0.383	0.809	-0.285	-1.268	0.001
28	A	34	ALA	0	0.000	-0.016	2.544	-2.245	-0.028	1.922	-1.390	-2.749	-0.017
29	A	35	ASP	-1	-0.833	-0.898	3.042	-3.707	-2.330	0.457	-0.245	-1.590	-0.010
30	A	36	LEU	0	0.014	0.007	4.229	0.278	0.367	0.001	-0.024	-0.066	0.000
31	A	37	ARG	1	0.832	0.928	7.705	1.290	1.290	0.000	0.000	0.000	0.000
32	A	38	PHE	0	0.021	0.000	10.103	0.107	0.107	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.043	-0.020	13.527	0.011	0.011	0.000	0.000	0.000	0.000
34	A	40	SER	0	0.009	-0.023	16.544	0.015	0.015	0.000	0.000	0.000	0.000
35	A	41	ASP	-1	-0.727	-0.867	20.118	-0.225	-0.225	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.004	0.011	20.928	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.890	-0.923	22.372	-0.214	-0.214	0.000	0.000	0.000	0.000
38	A	44	GLN	0	0.039	0.011	18.970	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	45	THR	0	-0.030	-0.030	17.213	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	46	LEU	0	-0.005	-0.009	17.879	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.799	-0.896	19.995	-0.235	-0.235	0.000	0.000	0.000	0.000
42	A	48	TYR	0	-0.010	-0.001	10.043	0.007	0.007	0.000	0.000	0.000	0.000
43	A	49	ILE	0	-0.020	-0.008	15.735	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	50	TYR	0	-0.098	-0.090	16.995	0.012	0.012	0.000	0.000	0.000	0.000
45	A	51	GLY	0	-0.006	0.017	17.302	0.028	0.028	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.880	0.937	18.180	0.207	0.207	0.000	0.000	0.000	0.000
47	A	53	ASN	0	-0.007	-0.036	20.194	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	54	ARG	1	0.860	0.924	17.095	0.391	0.391	0.000	0.000	0.000	0.000
49	A	55	PHE	0	-0.007	-0.007	14.554	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	56	ALA	0	-0.024	0.001	16.649	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	57	ASP	-1	-0.847	-0.913	14.375	-0.352	-0.352	0.000	0.000	0.000	0.000
52	A	58	ARG	1	0.780	0.876	12.427	0.368	0.368	0.000	0.000	0.000	0.000
53	A	59	GLY	0	-0.014	-0.005	10.702	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	60	ASP	-1	-0.847	-0.910	9.787	-0.891	-0.891	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.030	-0.020	10.165	-0.201	-0.201	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.013	0.036	6.495	0.227	0.227	0.000	0.000	0.000	0.000
57	A	63	TYR	0	0.033	-0.010	9.191	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	64	PRO	0	-0.044	-0.009	8.924	-0.158	-0.158	0.000	0.000	0.000	0.000
59	A	65	ALA	0	0.009	0.008	7.684	0.211	0.211	0.000	0.000	0.000	0.000
60	A	66	ILE	0	-0.039	-0.020	9.304	0.170	0.170	0.000	0.000	0.000	0.000
61	A	67	VAL	0	0.006	-0.003	10.900	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	68	LEU	0	-0.008	0.004	12.518	0.076	0.076	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.008	-0.014	15.260	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	70	ASP	-1	-0.715	-0.813	18.671	-0.176	-0.176	0.000	0.000	0.000	0.000
65	A	71	LEU	0	-0.035	-0.023	20.857	0.006	0.006	0.000	0.000	0.000	0.000
66	A	72	ASN	0	-0.057	-0.028	23.944	0.011	0.011	0.000	0.000	0.000	0.000
67	A	73	MET	0	-0.003	0.062	20.109	0.001	0.001	0.000	0.000	0.000	0.000
68	A	74	PRO	0	-0.006	-0.007	24.353	0.006	0.006	0.000	0.000	0.000	0.000
69	A	75	ARG	1	0.775	0.883	23.496	0.224	0.224	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.015	0.004	21.164	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	77	ASP	-1	-0.793	-0.871	24.830	-0.110	-0.110	0.000	0.000	0.000	0.000
72	A	78	GLY	0	0.042	0.006	23.892	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.900	0.945	24.822	0.082	0.082	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.871	0.912	27.670	0.118	0.118	0.000	0.000	0.000	0.000
75	A	81	VAL	0	0.011	0.011	21.249	0.004	0.004	0.000	0.000	0.000	0.000
76	A	82	VAL	0	0.042	0.016	21.732	0.000	0.000	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.804	0.892	24.042	0.083	0.083	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.023	-0.003	25.250	0.010	0.010	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.025	0.005	19.658	0.008	0.008	0.000	0.000	0.000	0.000
80	A	86	ARG	1	0.763	0.838	20.089	0.115	0.115	0.000	0.000	0.000	0.000
81	A	87	GLN	0	-0.031	-0.008	25.299	0.014	0.014	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.773	-0.816	24.681	-0.088	-0.088	0.000	0.000	0.000	0.000
83	A	89	GLU	-1	-0.837	-0.922	24.883	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	90	THR	0	-0.088	-0.060	22.128	0.004	0.004	0.000	0.000	0.000	0.000
85	A	91	VAL	0	-0.006	-0.006	18.997	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.826	0.914	20.035	0.017	0.017	0.000	0.000	0.000	0.000
87	A	93	HIS	0	-0.011	-0.008	16.227	0.012	0.012	0.000	0.000	0.000	0.000
88	A	94	LEU	0	-0.004	0.012	14.477	0.007	0.007	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.021	0.020	14.481	0.015	0.015	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.006	-0.007	15.092	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	97	ILE	0	-0.033	-0.014	15.589	0.041	0.041	0.000	0.000	0.000	0.000
92	A	98	ALA	0	-0.009	0.005	18.280	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	99	LEU	0	0.020	0.008	16.294	0.009	0.009	0.000	0.000	0.000	0.000
94	A	100	SER	0	0.025	0.004	20.775	0.001	0.001	0.000	0.000	0.000	0.000
95	A	101	THR	0	0.021	0.009	24.383	0.005	0.005	0.000	0.000	0.000	0.000
96	A	102	SER	0	-0.048	-0.015	26.838	0.013	0.013	0.000	0.000	0.000	0.000
97	A	103	GLU	-1	-0.847	-0.920	28.737	-0.068	-0.068	0.000	0.000	0.000	0.000
98	A	104	SER	0	-0.044	-0.014	30.680	0.009	0.009	0.000	0.000	0.000	0.000
99	A	105	ALA	0	0.094	0.036	31.753	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	106	LYS	1	0.938	0.986	33.027	0.051	0.051	0.000	0.000	0.000	0.000
101	A	107	HIS	0	0.071	0.034	29.747	0.000	0.000	0.000	0.000	0.000	0.000
102	A	108	ILE	0	0.032	0.032	27.763	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	109	THR	0	-0.020	-0.027	28.678	0.001	0.001	0.000	0.000	0.000	0.000
104	A	110	GLU	-1	-0.904	-0.947	30.866	-0.080	-0.080	0.000	0.000	0.000	0.000
105	A	111	ALA	0	0.028	0.018	25.348	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	112	TYR	0	0.029	0.014	24.297	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	113	SER	0	-0.073	-0.022	27.640	0.003	0.003	0.000	0.000	0.000	0.000
108	A	114	ILE	0	-0.054	-0.034	26.142	0.002	0.002	0.000	0.000	0.000	0.000
109	A	115	GLY	0	0.039	0.030	25.957	0.000	0.000	0.000	0.000	0.000	0.000
110	A	116	PHE	0	-0.010	-0.002	20.422	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	117	ASN	0	0.016	0.019	19.156	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	118	ALA	0	0.017	0.003	19.632	0.018	0.018	0.000	0.000	0.000	0.000
113	A	119	TYR	0	-0.007	-0.029	21.400	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	120	LEU	0	-0.025	-0.005	18.095	0.014	0.014	0.000	0.000	0.000	0.000
115	A	121	VAL	0	0.028	0.005	21.942	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	122	LYS	1	0.763	0.850	20.862	0.191	0.191	0.000	0.000	0.000	0.000
117	A	123	PRO	0	-0.021	-0.005	20.561	0.010	0.010	0.000	0.000	0.000	0.000
118	A	124	ALA	0	0.031	0.027	23.190	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	125	ASN	0	-0.043	-0.022	23.393	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	126	ILE	0	0.035	0.010	17.576	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.006	0.004	18.831	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	128	ASP	-1	-0.821	-0.923	20.209	-0.070	-0.070	0.000	0.000	0.000	0.000
123	A	129	TYR	0	0.009	-0.008	17.203	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	130	VAL	0	0.023	0.013	15.045	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	131	GLU	-1	-0.795	-0.876	15.959	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	132	ALA	0	-0.030	-0.003	18.199	0.012	0.012	0.000	0.000	0.000	0.000
127	A	133	ILE	0	-0.015	-0.010	12.160	0.006	0.006	0.000	0.000	0.000	0.000
128	A	134	ARG	1	0.842	0.898	13.520	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	135	SER	0	-0.039	-0.005	14.585	0.039	0.039	0.000	0.000	0.000	0.000
130	A	136	LEU	0	-0.007	0.001	13.508	0.022	0.022	0.000	0.000	0.000	0.000
131	A	137	TRP	0	0.059	0.010	6.002	-0.069	-0.069	0.000	0.000	0.000	0.000
132	A	138	HIS	0	0.055	0.030	12.309	0.075	0.075	0.000	0.000	0.000	0.000
133	A	139	PHE	0	-0.006	0.003	14.314	0.045	0.045	0.000	0.000	0.000	0.000
134	A	140	TRP	0	-0.004	-0.032	13.244	0.037	0.037	0.000	0.000	0.000	0.000
135	A	141	MET	0	-0.046	-0.009	7.645	0.059	0.059	0.000	0.000	0.000	0.000
136	A	142	ASN	0	-0.055	-0.029	10.763	0.196	0.196	0.000	0.000	0.000	0.000
137	A	143	THR	0	-0.080	-0.032	13.012	0.001	0.001	0.000	0.000	0.000	0.000
138	A	144	ALA	0	-0.018	0.003	15.459	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	145	SER	0	-0.033	-0.033	14.104	0.066	0.066	0.000	0.000	0.000	0.000
140	A	146	LEU	0	-0.008	0.006	9.804	-0.048	-0.048	0.000	0.000	0.000	0.000
141	A	147	PRO	0	-0.016	0.003	13.717	0.058	0.058	0.000	0.000	0.000	0.000
142	A	148	THR	0	-0.014	-0.013	12.329	0.013	0.013	0.000	0.000	0.000	0.000
143	A	149	THR	0	0.007	0.024	13.943	0.022	0.022	0.000	0.000	0.000	0.000

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