FMO DATABASE

FMODB ID: 98KG2

Calculation Name: 2Z8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q57930

Base Structure: X-ray

Registration Date: 2023-09-23

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1519272.774224
FMO2-HF: Nuclear repulsion	1454734.265838
FMO2-HF: Total energy	-64538.508386
FMO2-MP2: Total energy	-64727.243619

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:3:PRO)

Summations of interaction energy for fragment #1(A:3:PRO)

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.
-8.741	-3.478	6.67	-3.982	-7.953	-0.016

Interaction energy analysis for fragmet #1(A:3:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017

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	5	ILE	0	-0.013	0.000	3.804	-1.175	0.257	-0.017	-0.614	-0.802	0.002
4	A	6	LYS	1	0.962	0.988	6.030	0.826	0.826	0.000	0.000	0.000	0.000
5	A	7	ILE	0	0.022	0.005	9.244	-0.056	-0.056	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.068	-0.041	11.998	0.062	0.062	0.000	0.000	0.000	0.000
7	A	9	ASN	0	-0.063	-0.030	14.484	0.056	0.056	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.036	0.022	16.605	-0.033	-0.033	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.031	-0.013	19.101	0.018	0.018	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.018	0.004	22.235	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.029	0.003	24.619	0.003	0.003	0.000	0.000	0.000	0.000
12	A	14	THR	0	-0.001	-0.017	28.060	0.004	0.004	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.844	0.889	30.980	0.051	0.051	0.000	0.000	0.000	0.000
14	A	16	ILE	0	0.033	0.029	34.757	0.002	0.002	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.120	0.069	37.037	0.004	0.004	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.977	-0.991	39.768	-0.044	-0.044	0.000	0.000	0.000	0.000
17	A	19	ASN	0	-0.052	-0.015	42.293	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.048	0.043	39.290	0.002	0.002	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.868	-0.935	43.633	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.055	-0.063	39.759	0.000	0.000	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.942	-0.963	43.648	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.929	-0.963	46.531	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.037	-0.032	40.454	0.000	0.000	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.014	-0.012	42.658	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.052	-0.010	43.677	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.031	-0.005	43.394	0.001	0.001	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.037	-0.017	37.741	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.895	-0.940	40.511	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.114	-0.063	36.473	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.050	-0.010	38.791	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.901	-0.916	35.875	-0.085	-0.085	0.000	0.000	0.000	0.000
32	A	41	GLY	0	-0.002	-0.030	37.882	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.027	0.015	37.734	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	43	VAL	0	-0.037	-0.011	33.417	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	44	CYS	0	0.057	0.041	34.361	0.003	0.003	0.000	0.000	0.000	0.000
36	A	45	ARG	1	0.842	0.900	30.901	0.092	0.092	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.028	0.033	30.798	0.006	0.006	0.000	0.000	0.000	0.000
38	A	47	SER	0	-0.001	-0.009	30.684	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	48	VAL	0	-0.038	-0.001	29.523	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	49	PRO	0	0.011	-0.009	26.010	0.007	0.007	0.000	0.000	0.000	0.000
41	A	50	LYS	1	0.967	0.978	25.963	0.114	0.114	0.000	0.000	0.000	0.000
42	A	51	VAL	0	-0.013	0.005	25.094	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	52	ALA	0	0.001	-0.002	27.428	0.010	0.010	0.000	0.000	0.000	0.000
44	A	53	LEU	0	0.008	-0.009	28.768	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	54	LEU	0	0.002	0.010	31.394	0.003	0.003	0.000	0.000	0.000	0.000
46	A	55	ILE	0	0.036	0.023	33.272	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	56	PHE	0	-0.004	-0.006	33.386	0.001	0.001	0.000	0.000	0.000	0.000
48	A	57	ARG	1	1.081	1.029	38.197	0.051	0.051	0.000	0.000	0.000	0.000
49	A	58	SER	0	-0.034	-0.007	37.658	0.002	0.002	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.075	0.024	38.581	0.003	0.003	0.000	0.000	0.000	0.000
51	A	60	LYS	1	0.851	0.943	30.584	0.098	0.098	0.000	0.000	0.000	0.000
52	A	61	VAL	0	0.052	0.033	30.966	0.001	0.001	0.000	0.000	0.000	0.000
53	A	62	ASN	0	-0.037	-0.028	28.558	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	63	CYS	0	0.016	0.022	26.797	0.004	0.004	0.000	0.000	0.000	0.000
55	A	64	THR	0	0.009	0.001	24.030	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	65	GLY	0	0.034	0.000	22.772	0.013	0.013	0.000	0.000	0.000	0.000
57	A	66	ALA	0	0.022	0.027	22.274	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	67	LYS	1	0.956	0.963	18.043	0.136	0.136	0.000	0.000	0.000	0.000
59	A	68	SER	0	0.037	0.021	17.295	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.950	0.972	19.308	0.091	0.091	0.000	0.000	0.000	0.000
61	A	70	GLU	-1	-0.849	-0.935	20.657	-0.086	-0.086	0.000	0.000	0.000	0.000
62	A	71	GLU	-1	-0.906	-0.947	22.464	-0.125	-0.125	0.000	0.000	0.000	0.000
63	A	72	ALA	0	0.027	-0.007	23.660	0.007	0.007	0.000	0.000	0.000	0.000
64	A	73	GLU	-1	-0.881	-0.949	25.519	-0.054	-0.054	0.000	0.000	0.000	0.000
65	A	74	ILE	0	-0.031	-0.013	27.243	0.009	0.009	0.000	0.000	0.000	0.000
66	A	75	ALA	0	0.006	-0.008	28.409	0.006	0.006	0.000	0.000	0.000	0.000
67	A	76	ILE	0	0.027	0.009	28.306	0.004	0.004	0.000	0.000	0.000	0.000
68	A	77	LYS	1	0.930	0.973	31.149	0.046	0.046	0.000	0.000	0.000	0.000
69	A	78	LYS	1	0.887	0.952	31.283	0.055	0.055	0.000	0.000	0.000	0.000
70	A	79	ILE	0	0.086	0.050	33.732	0.002	0.002	0.000	0.000	0.000	0.000
71	A	80	ILE	0	-0.012	-0.007	34.436	0.002	0.002	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.902	0.941	37.463	0.029	0.029	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.909	-0.940	38.181	-0.046	-0.046	0.000	0.000	0.000	0.000
74	A	83	LEU	0	-0.004	-0.014	38.820	0.001	0.001	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.898	0.961	41.635	0.026	0.026	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.948	-0.973	43.450	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	86	ALA	0	-0.026	-0.010	45.377	0.002	0.002	0.000	0.000	0.000	0.000
78	A	87	GLY	0	-0.052	-0.011	47.180	0.000	0.000	0.000	0.000	0.000	0.000
79	A	88	ILE	0	-0.002	-0.002	43.211	0.000	0.000	0.000	0.000	0.000	0.000
80	A	89	ASP	-1	-0.961	-0.971	44.826	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	90	VAL	0	-0.033	-0.020	39.633	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	91	ILE	0	-0.036	-0.017	36.829	0.003	0.003	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.870	-0.951	37.404	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	93	ASN	0	-0.113	-0.074	33.578	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	94	PRO	0	0.005	0.020	32.807	0.001	0.001	0.000	0.000	0.000	0.000
86	A	95	GLU	-1	-0.935	-0.967	28.974	-0.064	-0.064	0.000	0.000	0.000	0.000
87	A	96	ILE	0	-0.058	-0.008	25.014	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.987	0.982	25.114	0.107	0.107	0.000	0.000	0.000	0.000
89	A	98	ILE	0	0.031	0.013	18.659	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	99	GLN	0	-0.131	-0.097	22.131	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	100	ASN	0	0.017	0.010	18.486	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	101	MET	0	0.003	0.026	14.773	0.006	0.006	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.009	0.023	13.355	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	103	ALA	0	0.006	0.005	9.045	0.034	0.034	0.000	0.000	0.000	0.000
95	A	104	THR	0	-0.067	-0.033	8.485	0.043	0.043	0.000	0.000	0.000	0.000
96	A	105	ALA	0	0.054	0.016	2.994	-0.385	-0.112	0.063	-0.088	-0.247	0.000
97	A	106	ASP	-1	-0.873	-0.942	3.143	-1.213	-0.794	0.017	-0.101	-0.335	0.001
98	A	107	LEU	0	-0.036	-0.016	2.592	-4.128	-1.961	1.380	-1.510	-2.039	-0.017
99	A	108	GLY	0	-0.020	-0.003	3.352	-1.303	-0.393	0.081	-0.391	-0.601	-0.003
100	A	109	ILE	0	-0.061	-0.037	4.839	0.407	0.443	-0.001	-0.003	-0.031	0.000
101	A	110	GLU	-1	-0.897	-0.954	8.118	-0.523	-0.523	0.000	0.000	0.000	0.000
102	A	111	PRO	0	-0.087	-0.040	9.951	0.064	0.064	0.000	0.000	0.000	0.000
103	A	112	ASN	0	0.031	0.019	12.119	0.028	0.028	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.010	-0.026	13.465	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	114	ASP	-1	-0.860	-0.933	16.435	-0.211	-0.211	0.000	0.000	0.000	0.000
106	A	115	ASP	-1	-0.926	-0.957	16.991	-0.200	-0.200	0.000	0.000	0.000	0.000
107	A	116	ILE	0	-0.037	-0.041	12.045	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	117	ALA	0	-0.007	-0.009	16.261	0.010	0.010	0.000	0.000	0.000	0.000
109	A	118	LEU	0	-0.051	-0.001	19.181	0.020	0.020	0.000	0.000	0.000	0.000
110	A	119	MET	0	-0.075	-0.039	17.988	0.015	0.015	0.000	0.000	0.000	0.000
111	A	120	VAL	0	0.000	0.011	14.442	0.000	0.000	0.000	0.000	0.000	0.000
112	A	121	GLU	-1	-0.927	-0.941	17.834	-0.154	-0.154	0.000	0.000	0.000	0.000
113	A	122	GLY	0	-0.033	-0.033	18.507	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.061	-0.051	16.035	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	124	GLU	-1	-0.876	-0.945	18.751	-0.175	-0.175	0.000	0.000	0.000	0.000
116	A	125	TYR	0	-0.069	-0.043	19.202	-0.051	-0.051	0.000	0.000	0.000	0.000
117	A	126	GLU	-1	-0.840	-0.930	20.929	-0.150	-0.150	0.000	0.000	0.000	0.000
118	A	127	PRO	0	-0.020	0.002	21.819	0.000	0.000	0.000	0.000	0.000	0.000
119	A	128	GLU	-1	-0.971	-0.983	23.336	-0.137	-0.137	0.000	0.000	0.000	0.000
120	A	129	GLN	0	-0.064	-0.021	25.692	0.010	0.010	0.000	0.000	0.000	0.000
121	A	130	PHE	0	-0.069	-0.040	18.086	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	131	PRO	0	-0.019	0.017	19.270	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	132	GLY	0	0.001	-0.020	16.401	-0.021	-0.021	0.000	0.000	0.000	0.000
124	A	133	LEU	0	0.007	0.021	14.101	0.029	0.029	0.000	0.000	0.000	0.000
125	A	134	VAL	0	-0.038	-0.025	15.324	-0.057	-0.057	0.000	0.000	0.000	0.000
126	A	135	TYR	0	0.031	0.005	12.177	0.022	0.022	0.000	0.000	0.000	0.000
127	A	136	ARG	1	0.937	0.978	15.430	0.190	0.190	0.000	0.000	0.000	0.000
128	A	137	LEU	0	0.010	0.011	12.137	0.006	0.006	0.000	0.000	0.000	0.000
129	A	138	ASP	-1	-0.880	-0.950	16.722	-0.196	-0.196	0.000	0.000	0.000	0.000
130	A	139	ASP	-1	-0.928	-0.941	17.747	-0.155	-0.155	0.000	0.000	0.000	0.000
131	A	140	PRO	0	-0.008	-0.008	13.446	0.000	0.000	0.000	0.000	0.000	0.000
132	A	141	LYS	1	0.960	0.981	16.201	0.171	0.171	0.000	0.000	0.000	0.000
133	A	142	VAL	0	-0.058	-0.026	12.741	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	143	VAL	0	-0.004	-0.001	15.780	0.026	0.026	0.000	0.000	0.000	0.000
135	A	144	VAL	0	-0.005	-0.014	10.432	-0.049	-0.049	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.026	0.001	12.715	0.062	0.062	0.000	0.000	0.000	0.000
137	A	146	ILE	0	0.029	0.009	9.676	-0.134	-0.134	0.000	0.000	0.000	0.000
138	A	147	PHE	0	-0.009	-0.014	11.503	0.105	0.105	0.000	0.000	0.000	0.000
139	A	148	GLY	0	0.089	0.039	11.863	-0.064	-0.064	0.000	0.000	0.000	0.000
140	A	149	SER	0	0.025	0.008	11.041	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	150	GLY	0	0.082	0.047	8.653	-0.013	-0.013	0.000	0.000	0.000	0.000
142	A	151	LYS	1	0.886	0.962	7.399	0.293	0.293	0.000	0.000	0.000	0.000
143	A	152	VAL	0	0.004	0.009	6.144	0.112	0.112	0.000	0.000	0.000	0.000
144	A	153	VAL	0	-0.061	-0.045	8.788	-0.026	-0.026	0.000	0.000	0.000	0.000
145	A	154	ILE	0	0.014	0.017	7.259	0.047	0.047	0.000	0.000	0.000	0.000
146	A	155	THR	0	-0.034	-0.016	11.522	0.057	0.057	0.000	0.000	0.000	0.000
147	A	156	GLY	0	0.053	0.003	15.142	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	157	LEU	0	-0.016	0.012	11.382	0.028	0.028	0.000	0.000	0.000	0.000
149	A	158	LYS	1	0.935	0.958	15.910	0.205	0.205	0.000	0.000	0.000	0.000
150	A	159	SER	0	0.012	-0.009	15.812	0.031	0.031	0.000	0.000	0.000	0.000
151	A	160	GLU	-1	-0.856	-0.944	11.753	-0.314	-0.314	0.000	0.000	0.000	0.000
152	A	161	GLU	-1	-0.932	-0.959	10.899	-0.190	-0.190	0.000	0.000	0.000	0.000
153	A	162	ASP	-1	-0.839	-0.936	11.237	-0.304	-0.304	0.000	0.000	0.000	0.000
154	A	163	ALA	0	0.003	0.000	9.215	-0.057	-0.057	0.000	0.000	0.000	0.000
155	A	164	LYS	1	0.967	0.972	6.351	-0.013	-0.013	0.000	0.000	0.000	0.000
156	A	165	ARG	1	0.810	0.915	7.329	0.105	0.105	0.000	0.000	0.000	0.000
157	A	166	ALA	0	0.009	-0.002	9.816	0.008	0.008	0.000	0.000	0.000	0.000
158	A	167	LEU	0	0.024	0.009	2.014	-0.579	-0.347	2.109	-0.727	-1.614	0.001
159	A	168	LYS	1	0.793	0.881	5.762	-0.110	-0.110	0.000	0.000	0.000	0.000
160	A	169	LYS	1	0.919	0.947	6.742	0.359	0.359	0.000	0.000	0.000	0.000
161	A	170	ILE	0	0.032	0.042	7.270	0.056	0.056	0.000	0.000	0.000	0.000
162	A	171	LEU	0	-0.032	-0.023	2.129	-0.434	-0.691	3.039	-0.546	-2.236	0.000
163	A	172	ASP	-1	-0.867	-0.909	6.301	0.029	0.029	0.000	0.000	0.000	0.000
164	A	173	THR	0	0.059	0.016	9.061	0.067	0.067	0.000	0.000	0.000	0.000
165	A	174	ILE	0	0.001	-0.010	7.984	0.029	0.029	0.000	0.000	0.000	0.000
166	A	175	LYS	1	0.851	0.929	4.621	0.313	0.364	-0.001	-0.002	-0.048	0.000
167	A	176	GLU	-1	-0.974	-0.988	10.505	-0.151	-0.151	0.000	0.000	0.000	0.000
168	A	177	VAL	0	-0.011	0.018	13.094	0.028	0.028	0.000	0.000	0.000	0.000
169	A	178	GLN	0	-0.033	0.002	12.187	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:PRO)