FMO DATABASE

FMODB ID: MNJ3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1519910.845087
FMO2-HF: Nuclear repulsion	1455370.994935
FMO2-HF: Total energy	-64539.850152
FMO2-MP2: Total energy	-64728.535894

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.
-11.372	-4.239	4.08	-3.8	-7.414	-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 : -0.007 / q_NPA : -0.016

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	-0.009	0.003	3.804	-1.556	0.057	-0.020	-0.710	-0.883	0.003
4	A	6	LYS	1	0.961	0.986	6.087	0.680	0.680	0.000	0.000	0.000	0.000
5	A	7	ILE	0	0.013	0.003	9.216	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.062	-0.033	11.894	0.052	0.052	0.000	0.000	0.000	0.000
7	A	9	ASN	0	-0.060	-0.034	14.448	0.046	0.046	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.028	0.020	16.653	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.033	-0.016	19.165	0.011	0.011	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.005	0.004	22.346	0.000	0.000	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.027	-0.010	24.725	0.000	0.000	0.000	0.000	0.000	0.000
12	A	14	THR	0	-0.008	-0.034	28.183	0.005	0.005	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.785	0.861	31.110	0.029	0.029	0.000	0.000	0.000	0.000
14	A	16	ILE	0	0.042	0.026	34.890	0.003	0.003	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.113	0.065	37.151	0.003	0.003	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.891	-0.932	39.904	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	19	ASN	0	-0.079	-0.040	42.426	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.050	0.037	39.550	0.001	0.001	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.810	-0.918	43.731	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.049	-0.049	39.906	0.000	0.000	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.947	-0.962	43.709	-0.035	-0.035	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.925	-0.960	46.575	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.039	-0.032	40.469	0.001	0.001	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.015	-0.010	42.672	0.000	0.000	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.050	-0.012	43.694	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	ILE	0	-0.030	-0.006	42.955	0.001	0.001	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.034	-0.019	37.672	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.887	-0.935	40.520	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.113	-0.065	36.196	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.049	-0.002	38.831	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.850	-0.888	36.201	-0.071	-0.071	0.000	0.000	0.000	0.000
32	A	41	GLY	0	0.018	-0.003	36.957	0.000	0.000	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.053	-0.015	37.796	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	43	VAL	0	-0.035	-0.019	33.475	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	44	CYS	0	0.017	0.030	34.376	0.003	0.003	0.000	0.000	0.000	0.000
36	A	45	ARG	1	0.812	0.877	31.338	0.075	0.075	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.054	0.046	30.724	0.005	0.005	0.000	0.000	0.000	0.000
38	A	47	SER	0	0.006	-0.007	30.637	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	48	VAL	0	-0.013	0.009	29.464	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	49	PRO	0	-0.006	-0.019	25.869	0.007	0.007	0.000	0.000	0.000	0.000
41	A	50	LYS	1	0.971	0.978	25.943	0.095	0.095	0.000	0.000	0.000	0.000
42	A	51	VAL	0	-0.018	-0.001	25.055	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	52	ALA	0	0.014	0.012	27.410	0.007	0.007	0.000	0.000	0.000	0.000
44	A	53	LEU	0	0.003	-0.007	28.793	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	54	LEU	0	0.003	0.009	31.428	0.001	0.001	0.000	0.000	0.000	0.000
46	A	55	ILE	0	0.037	0.021	33.323	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	56	PHE	0	0.004	0.001	33.209	0.000	0.000	0.000	0.000	0.000	0.000
48	A	57	ARG	1	1.015	0.999	38.287	0.036	0.036	0.000	0.000	0.000	0.000
49	A	58	SER	0	-0.027	-0.007	37.808	0.002	0.002	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.068	0.036	38.699	0.003	0.003	0.000	0.000	0.000	0.000
51	A	60	LYS	1	0.864	0.943	30.339	0.073	0.073	0.000	0.000	0.000	0.000
52	A	61	VAL	0	0.050	0.035	31.177	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	62	ASN	0	-0.030	-0.023	28.688	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	63	CYS	0	-0.003	0.010	26.847	0.003	0.003	0.000	0.000	0.000	0.000
55	A	64	THR	0	0.012	0.003	24.064	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	65	GLY	0	0.043	0.007	22.784	0.011	0.011	0.000	0.000	0.000	0.000
57	A	66	ALA	0	-0.003	0.015	22.278	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	67	LYS	1	0.880	0.910	18.027	0.085	0.085	0.000	0.000	0.000	0.000
59	A	68	SER	0	0.031	0.013	17.311	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.910	0.940	19.352	0.020	0.020	0.000	0.000	0.000	0.000
61	A	70	GLU	-1	-0.811	-0.909	20.861	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	71	GLU	-1	-0.821	-0.890	22.373	-0.085	-0.085	0.000	0.000	0.000	0.000
63	A	72	ALA	0	0.036	-0.002	23.706	0.002	0.002	0.000	0.000	0.000	0.000
64	A	73	GLU	-1	-0.860	-0.935	25.568	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	74	ILE	0	-0.029	-0.014	27.288	0.005	0.005	0.000	0.000	0.000	0.000
66	A	75	ALA	0	-0.010	-0.009	28.440	0.003	0.003	0.000	0.000	0.000	0.000
67	A	76	ILE	0	0.026	0.008	28.291	0.001	0.001	0.000	0.000	0.000	0.000
68	A	77	LYS	1	0.930	0.971	30.925	0.013	0.013	0.000	0.000	0.000	0.000
69	A	78	LYS	1	0.862	0.942	30.910	0.032	0.032	0.000	0.000	0.000	0.000
70	A	79	ILE	0	0.072	0.044	34.272	0.001	0.001	0.000	0.000	0.000	0.000
71	A	80	ILE	0	-0.020	-0.013	34.439	0.001	0.001	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.920	0.954	37.516	0.009	0.009	0.000	0.000	0.000	0.000
73	A	82	GLU	-1	-0.901	-0.944	38.073	-0.029	-0.029	0.000	0.000	0.000	0.000
74	A	83	LEU	0	-0.002	-0.016	39.117	0.001	0.001	0.000	0.000	0.000	0.000
75	A	84	LYS	1	0.807	0.896	41.694	0.008	0.008	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.949	-0.971	43.519	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	86	ALA	0	-0.028	-0.012	45.427	0.001	0.001	0.000	0.000	0.000	0.000
78	A	87	GLY	0	-0.052	-0.010	47.208	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	88	ILE	0	-0.013	-0.008	43.366	0.000	0.000	0.000	0.000	0.000	0.000
80	A	89	ASP	-1	-0.950	-0.965	44.912	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	90	VAL	0	-0.046	-0.030	39.760	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	91	ILE	0	-0.040	-0.015	36.934	0.003	0.003	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.796	-0.888	37.515	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	93	ASN	0	-0.111	-0.069	33.824	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	94	PRO	0	0.012	0.026	32.593	0.002	0.002	0.000	0.000	0.000	0.000
86	A	95	GLU	-1	-0.816	-0.905	29.040	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	96	ILE	0	-0.033	0.003	25.344	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.835	0.916	24.944	0.050	0.050	0.000	0.000	0.000	0.000
89	A	98	ILE	0	0.037	0.011	18.814	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	99	GLN	0	-0.066	-0.052	22.282	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	100	ASN	0	0.037	0.019	18.615	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	101	MET	0	0.006	0.018	14.767	0.011	0.011	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.006	0.024	13.266	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	103	ALA	0	0.006	0.004	9.232	0.043	0.043	0.000	0.000	0.000	0.000
95	A	104	THR	0	-0.040	-0.024	8.434	0.048	0.048	0.000	0.000	0.000	0.000
96	A	105	ALA	0	0.034	0.009	2.940	-0.332	-0.023	0.068	-0.109	-0.268	0.001
97	A	106	ASP	-1	-0.878	-0.938	3.278	-1.664	-1.235	0.017	-0.105	-0.341	0.001
98	A	107	LEU	0	-0.025	-0.014	2.674	-4.372	-2.122	1.426	-1.505	-2.170	-0.017
99	A	108	GLY	0	-0.021	-0.004	3.160	-2.034	-0.906	0.133	-0.538	-0.723	-0.005
100	A	109	ILE	0	-0.067	-0.040	4.630	0.537	0.576	-0.001	-0.007	-0.032	0.000
101	A	110	GLU	-1	-0.883	-0.944	7.908	-0.603	-0.603	0.000	0.000	0.000	0.000
102	A	111	PRO	0	-0.067	-0.031	9.956	0.066	0.066	0.000	0.000	0.000	0.000
103	A	112	ASN	0	-0.037	-0.030	12.238	0.038	0.038	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.020	-0.024	13.761	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	114	ASP	-1	-0.849	-0.931	16.557	-0.242	-0.242	0.000	0.000	0.000	0.000
106	A	115	ASP	-1	-0.866	-0.922	17.128	-0.245	-0.245	0.000	0.000	0.000	0.000
107	A	116	ILE	0	-0.028	-0.036	12.093	0.002	0.002	0.000	0.000	0.000	0.000
108	A	117	ALA	0	-0.004	-0.002	16.378	0.015	0.015	0.000	0.000	0.000	0.000
109	A	118	LEU	0	-0.057	-0.006	19.297	0.024	0.024	0.000	0.000	0.000	0.000
110	A	119	MET	0	-0.074	-0.035	18.078	0.017	0.017	0.000	0.000	0.000	0.000
111	A	120	VAL	0	-0.010	0.005	14.555	0.001	0.001	0.000	0.000	0.000	0.000
112	A	121	GLU	-1	-0.919	-0.939	17.936	-0.154	-0.154	0.000	0.000	0.000	0.000
113	A	122	GLY	0	-0.045	-0.036	18.598	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.060	-0.057	16.038	-0.031	-0.031	0.000	0.000	0.000	0.000
115	A	124	GLU	-1	-0.883	-0.945	18.855	-0.180	-0.180	0.000	0.000	0.000	0.000
116	A	125	TYR	0	-0.058	-0.045	19.182	-0.051	-0.051	0.000	0.000	0.000	0.000
117	A	126	GLU	-1	-0.796	-0.904	21.044	-0.160	-0.160	0.000	0.000	0.000	0.000
118	A	127	PRO	0	-0.019	0.008	22.086	0.001	0.001	0.000	0.000	0.000	0.000
119	A	128	GLU	-1	-0.977	-0.980	23.449	-0.147	-0.147	0.000	0.000	0.000	0.000
120	A	129	GLN	0	-0.107	-0.054	25.810	0.014	0.014	0.000	0.000	0.000	0.000
121	A	130	PHE	0	-0.077	-0.048	18.284	0.001	0.001	0.000	0.000	0.000	0.000
122	A	131	PRO	0	-0.006	0.019	19.214	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	132	GLY	0	-0.008	-0.019	16.510	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	133	LEU	0	-0.003	0.015	14.151	0.030	0.030	0.000	0.000	0.000	0.000
125	A	134	VAL	0	-0.034	-0.021	15.427	-0.052	-0.052	0.000	0.000	0.000	0.000
126	A	135	TYR	0	0.030	0.003	11.948	0.019	0.019	0.000	0.000	0.000	0.000
127	A	136	ARG	1	0.937	0.979	15.509	0.181	0.181	0.000	0.000	0.000	0.000
128	A	137	LEU	0	0.011	0.016	12.071	0.006	0.006	0.000	0.000	0.000	0.000
129	A	138	ASP	-1	-0.890	-0.960	16.779	-0.168	-0.168	0.000	0.000	0.000	0.000
130	A	139	ASP	-1	-0.867	-0.906	17.643	-0.098	-0.098	0.000	0.000	0.000	0.000
131	A	140	PRO	0	-0.022	-0.006	13.528	0.001	0.001	0.000	0.000	0.000	0.000
132	A	141	LYS	1	0.957	0.980	16.435	0.131	0.131	0.000	0.000	0.000	0.000
133	A	142	VAL	0	-0.057	-0.027	12.960	0.002	0.002	0.000	0.000	0.000	0.000
134	A	143	VAL	0	-0.005	-0.002	15.932	0.018	0.018	0.000	0.000	0.000	0.000
135	A	144	VAL	0	-0.005	-0.014	10.492	-0.038	-0.038	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.017	0.009	12.758	0.053	0.053	0.000	0.000	0.000	0.000
137	A	146	ILE	0	0.029	0.008	9.875	-0.125	-0.125	0.000	0.000	0.000	0.000
138	A	147	PHE	0	-0.009	-0.011	11.605	0.108	0.108	0.000	0.000	0.000	0.000
139	A	148	GLY	0	0.083	0.038	11.973	-0.076	-0.076	0.000	0.000	0.000	0.000
140	A	149	SER	0	0.009	-0.001	10.959	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	150	GLY	0	0.072	0.044	8.450	-0.037	-0.037	0.000	0.000	0.000	0.000
142	A	151	LYS	1	0.908	0.969	7.498	0.281	0.281	0.000	0.000	0.000	0.000
143	A	152	VAL	0	0.005	0.006	5.933	0.119	0.119	0.000	0.000	0.000	0.000
144	A	153	VAL	0	-0.064	-0.047	8.720	0.002	0.002	0.000	0.000	0.000	0.000
145	A	154	ILE	0	0.018	0.020	7.466	0.045	0.045	0.000	0.000	0.000	0.000
146	A	155	THR	0	-0.033	-0.019	11.608	0.062	0.062	0.000	0.000	0.000	0.000
147	A	156	GLY	0	0.048	0.013	15.238	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	157	LEU	0	-0.014	0.010	11.437	0.028	0.028	0.000	0.000	0.000	0.000
149	A	158	LYS	1	0.859	0.913	16.084	0.156	0.156	0.000	0.000	0.000	0.000
150	A	159	SER	0	-0.027	-0.038	15.734	0.034	0.034	0.000	0.000	0.000	0.000
151	A	160	GLU	-1	-0.798	-0.916	11.826	-0.134	-0.134	0.000	0.000	0.000	0.000
152	A	161	GLU	-1	-0.927	-0.952	10.985	0.037	0.037	0.000	0.000	0.000	0.000
153	A	162	ASP	-1	-0.810	-0.899	11.297	-0.177	-0.177	0.000	0.000	0.000	0.000
154	A	163	ALA	0	0.014	0.004	9.460	-0.058	-0.058	0.000	0.000	0.000	0.000
155	A	164	LYS	1	0.909	0.941	6.631	-0.212	-0.212	0.000	0.000	0.000	0.000
156	A	165	ARG	1	0.788	0.878	7.328	0.018	0.018	0.000	0.000	0.000	0.000
157	A	166	ALA	0	0.009	-0.006	9.935	-0.015	-0.015	0.000	0.000	0.000	0.000
158	A	167	LEU	0	0.024	0.012	2.224	-0.847	-0.141	0.992	-0.447	-1.251	0.001
159	A	168	LYS	1	0.810	0.902	6.229	-0.257	-0.257	0.000	0.000	0.000	0.000
160	A	169	LYS	1	0.898	0.937	7.067	0.236	0.236	0.000	0.000	0.000	0.000
161	A	170	ILE	0	0.028	0.033	7.420	0.034	0.034	0.000	0.000	0.000	0.000
162	A	171	LEU	0	0.021	0.008	2.261	-0.898	-0.239	1.465	-0.379	-1.746	0.000
163	A	172	ASP	-1	-0.849	-0.909	6.378	0.019	0.019	0.000	0.000	0.000	0.000
164	A	173	THR	0	0.063	0.029	9.339	0.061	0.061	0.000	0.000	0.000	0.000
165	A	174	ILE	0	0.030	0.005	8.171	0.030	0.030	0.000	0.000	0.000	0.000
166	A	175	LYS	1	0.758	0.871	5.968	0.487	0.487	0.000	0.000	0.000	0.000
167	A	176	GLU	-1	-0.981	-0.988	10.585	-0.153	-0.153	0.000	0.000	0.000	0.000
168	A	177	VAL	0	-0.029	0.006	13.186	0.031	0.031	0.000	0.000	0.000	0.000
169	A	178	GLN	0	-0.028	0.004	12.239	0.006	0.006	0.000	0.000	0.000	0.000

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