FMO DATABASE

FMODB ID: MV2ZZ

Calculation Name: 4YK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YK8

Chain ID: A

ChEMBL ID:

UniProt ID: O36019

Base Structure: X-ray

Registration Date: 2023-06-26

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1588478.086777
FMO2-HF: Nuclear repulsion	1525457.182358
FMO2-HF: Total energy	-63020.904419
FMO2-MP2: Total energy	-63207.249665

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:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-0.566	0.655	-0.005	-0.609	-0.607	0.003

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.014

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	0	HIS	0	0.016	0.013	3.872	-0.175	1.046	-0.005	-0.609	-0.607	0.003
4	A	1	MET	0	-0.015	-0.010	4.975	0.291	0.291	0.000	0.000	0.000	0.000
5	A	2	THR	0	-0.024	-0.021	9.176	0.059	0.059	0.000	0.000	0.000	0.000
6	A	3	ASN	0	-0.066	-0.042	12.875	0.023	0.023	0.000	0.000	0.000	0.000
7	A	4	THR	0	0.011	-0.014	15.084	0.025	0.025	0.000	0.000	0.000	0.000
8	A	5	VAL	0	0.001	0.020	18.344	0.021	0.021	0.000	0.000	0.000	0.000
9	A	6	THR	0	-0.039	-0.024	21.316	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	7	ILE	0	-0.023	-0.011	24.628	0.011	0.011	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.849	-0.908	28.067	-0.130	-0.130	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.010	-0.003	31.591	0.009	0.009	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.821	0.890	34.504	0.108	0.108	0.000	0.000	0.000	0.000
14	A	11	ILE	0	0.020	0.021	36.516	0.006	0.006	0.000	0.000	0.000	0.000
15	A	12	GLY	0	0.066	0.046	40.321	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	13	TYR	0	-0.021	-0.027	42.278	0.002	0.002	0.000	0.000	0.000	0.000
17	A	14	LYS	1	0.786	0.896	43.469	0.059	0.059	0.000	0.000	0.000	0.000
18	A	15	TYR	0	0.041	0.014	42.209	0.002	0.002	0.000	0.000	0.000	0.000
19	A	16	ALA	0	-0.013	0.015	39.149	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	17	ALA	0	0.062	0.020	37.679	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.817	-0.887	37.491	-0.065	-0.065	0.000	0.000	0.000	0.000
22	A	19	VAL	0	0.035	0.011	35.826	0.000	0.000	0.000	0.000	0.000	0.000
23	A	20	VAL	0	0.003	0.005	32.300	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	LYS	1	0.814	0.892	32.745	0.062	0.062	0.000	0.000	0.000	0.000
25	A	22	ALA	0	0.004	0.006	33.313	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	VAL	0	0.035	0.011	29.868	0.000	0.000	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.003	-0.010	27.797	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	25	GLY	0	0.011	0.010	28.433	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	26	VAL	0	0.014	0.002	29.426	0.005	0.005	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.009	0.003	23.717	0.001	0.001	0.000	0.000	0.000	0.000
31	A	28	LEU	0	0.000	-0.004	24.374	0.002	0.002	0.000	0.000	0.000	0.000
32	A	29	PHE	0	-0.028	-0.019	25.822	0.010	0.010	0.000	0.000	0.000	0.000
33	A	30	HIS	0	-0.026	-0.013	24.396	0.019	0.019	0.000	0.000	0.000	0.000
34	A	31	ARG	1	0.773	0.843	18.907	0.139	0.139	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.081	-0.036	21.763	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	33	PHE	0	0.008	0.004	19.356	0.006	0.006	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.036	0.001	24.684	0.010	0.010	0.000	0.000	0.000	0.000
38	A	35	THR	0	-0.008	-0.016	27.248	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	36	VAL	0	0.041	0.028	30.202	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	37	PRO	0	-0.056	-0.017	32.692	0.004	0.004	0.000	0.000	0.000	0.000
41	A	38	ALA	0	0.054	0.018	35.517	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	39	ARG	1	0.857	0.921	36.130	0.017	0.017	0.000	0.000	0.000	0.000
43	A	40	THR	0	0.051	0.023	36.461	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	41	ILE	0	-0.056	-0.016	37.243	0.002	0.002	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.827	-0.893	39.817	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.028	-0.012	39.235	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.026	-0.012	41.001	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	45	ASP	-1	-0.816	-0.849	43.599	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	46	ILE	0	-0.025	0.003	37.747	0.003	0.003	0.000	0.000	0.000	0.000
50	A	47	THR	0	-0.026	-0.037	39.507	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	VAL	0	-0.028	-0.014	34.967	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	49	PRO	0	-0.019	-0.010	32.216	0.004	0.004	0.000	0.000	0.000	0.000
53	A	50	THR	0	-0.007	-0.005	34.169	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	51	LEU	0	0.015	0.012	28.446	0.006	0.006	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.006	-0.002	33.144	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.042	0.005	34.005	0.002	0.002	0.000	0.000	0.000	0.000
57	A	54	ALA	0	-0.021	0.003	35.092	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.822	-0.915	29.921	-0.092	-0.092	0.000	0.000	0.000	0.000
59	A	56	LEU	0	0.034	0.030	28.529	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	57	ASN	0	-0.047	-0.042	32.405	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	58	GLU	-1	-0.893	-0.934	35.680	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.051	-0.034	28.606	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	60	LEU	0	-0.017	-0.013	29.721	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	61	ALA	0	0.010	0.002	33.178	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	62	THR	0	-0.032	-0.022	35.499	0.000	0.000	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.865	0.922	27.973	0.147	0.147	0.000	0.000	0.000	0.000
67	A	64	ALA	0	-0.001	0.000	33.803	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	65	ALA	0	-0.006	-0.007	35.095	0.000	0.000	0.000	0.000	0.000	0.000
69	A	66	GLU	-1	-0.936	-0.959	33.630	-0.127	-0.127	0.000	0.000	0.000	0.000
70	A	67	PHE	0	-0.007	-0.004	31.902	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	68	ILE	0	-0.001	-0.002	35.118	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.889	-0.953	38.058	-0.093	-0.093	0.000	0.000	0.000	0.000
73	A	70	THR	0	0.014	0.010	35.957	0.000	0.000	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.076	-0.035	34.316	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	72	ARG	1	0.753	0.853	38.366	0.080	0.080	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.092	-0.064	41.888	0.006	0.006	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.936	-0.952	39.341	-0.106	-0.106	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.001	0.021	36.819	0.000	0.000	0.000	0.000	0.000	0.000
79	A	76	GLY	0	0.001	-0.004	38.766	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	77	ALA	0	-0.064	-0.041	39.654	0.006	0.006	0.000	0.000	0.000	0.000
81	A	78	ASN	0	-0.069	-0.042	34.763	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	79	GLY	0	0.096	0.046	33.066	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	80	GLN	0	-0.069	-0.039	27.120	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	81	MET	0	0.009	0.043	28.830	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	82	ILE	0	-0.002	-0.001	22.623	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	83	LEU	0	0.005	0.020	22.056	0.004	0.004	0.000	0.000	0.000	0.000
87	A	84	LEU	0	-0.037	-0.019	18.516	-0.038	-0.038	0.000	0.000	0.000	0.000
88	A	85	LEU	0	0.024	0.013	17.172	0.043	0.043	0.000	0.000	0.000	0.000
89	A	86	TYR	0	-0.022	-0.054	14.332	-0.089	-0.089	0.000	0.000	0.000	0.000
90	A	87	GLU	-1	-0.787	-0.875	9.680	-0.169	-0.169	0.000	0.000	0.000	0.000
91	A	88	ARG	1	0.853	0.901	13.621	0.058	0.058	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.023	0.015	15.802	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	90	PRO	0	0.137	0.072	17.136	0.014	0.014	0.000	0.000	0.000	0.000
94	A	91	LYS	1	0.952	0.967	18.179	0.132	0.132	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.929	0.954	19.293	0.087	0.087	0.000	0.000	0.000	0.000
96	A	93	SER	0	0.013	0.015	13.930	0.053	0.053	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.061	0.028	14.443	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	95	PHE	0	-0.031	0.011	16.124	0.004	0.004	0.000	0.000	0.000	0.000
99	A	96	GLY	0	0.052	0.016	14.307	0.044	0.044	0.000	0.000	0.000	0.000
100	A	97	LYS	1	0.768	0.889	11.980	0.170	0.170	0.000	0.000	0.000	0.000
101	A	98	GLY	0	0.031	0.025	8.842	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	99	ASN	0	-0.041	-0.030	8.160	-0.332	-0.332	0.000	0.000	0.000	0.000
103	A	100	THR	0	0.014	-0.016	10.826	0.136	0.136	0.000	0.000	0.000	0.000
104	A	101	ILE	0	0.010	0.025	9.377	0.089	0.089	0.000	0.000	0.000	0.000
105	A	102	PRO	0	-0.009	0.011	11.760	0.004	0.004	0.000	0.000	0.000	0.000
106	A	103	TRP	0	0.058	0.034	11.252	-0.098	-0.098	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.762	-0.830	12.339	-0.219	-0.219	0.000	0.000	0.000	0.000
108	A	105	GLN	0	-0.018	-0.005	15.848	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	106	TRP	0	0.006	-0.007	18.890	0.011	0.011	0.000	0.000	0.000	0.000
110	A	107	ILE	0	0.015	0.005	21.951	0.008	0.008	0.000	0.000	0.000	0.000
111	A	108	LEU	0	0.050	0.019	24.929	0.011	0.011	0.000	0.000	0.000	0.000
112	A	109	HIS	0	0.026	0.025	28.511	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	110	THR	0	-0.004	-0.014	30.332	0.013	0.013	0.000	0.000	0.000	0.000
114	A	111	THR	0	-0.038	-0.029	33.885	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	112	ILE	0	-0.011	-0.003	37.255	0.005	0.005	0.000	0.000	0.000	0.000
116	A	113	LEU	0	-0.051	-0.016	40.448	0.000	0.000	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.816	-0.889	43.689	-0.070	-0.070	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.799	-0.887	46.653	-0.065	-0.065	0.000	0.000	0.000	0.000
119	A	116	GLY	0	-0.006	-0.006	50.112	0.001	0.001	0.000	0.000	0.000	0.000
120	A	117	ASP	-1	-0.863	-0.965	49.489	-0.051	-0.051	0.000	0.000	0.000	0.000
121	A	118	SER	0	0.004	0.010	44.534	0.000	0.000	0.000	0.000	0.000	0.000
122	A	119	TYR	0	-0.080	-0.044	44.769	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	120	GLN	0	-0.022	-0.028	44.662	0.002	0.002	0.000	0.000	0.000	0.000
124	A	121	GLU	-1	-0.844	-0.923	42.372	-0.062	-0.062	0.000	0.000	0.000	0.000
125	A	122	SER	0	-0.006	-0.034	40.496	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	123	SER	0	-0.018	-0.043	39.790	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	124	LEU	0	0.015	0.017	39.673	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	125	SER	0	-0.043	-0.005	35.757	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	126	LEU	0	-0.009	-0.008	34.985	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	127	GLU	-1	-0.908	-0.961	34.886	-0.056	-0.056	0.000	0.000	0.000	0.000
131	A	128	ALA	0	0.018	0.014	34.313	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	129	ALA	0	0.008	0.002	31.159	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	130	VAL	0	-0.005	-0.014	30.092	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	131	GLU	-1	-0.877	-0.927	30.426	-0.064	-0.064	0.000	0.000	0.000	0.000
135	A	132	GLN	0	-0.008	-0.014	27.856	0.003	0.003	0.000	0.000	0.000	0.000
136	A	133	ILE	0	-0.031	-0.003	25.702	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	134	VAL	0	0.006	0.008	25.491	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	135	GLN	0	-0.059	-0.038	26.193	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	136	ALA	0	-0.014	-0.011	22.101	0.002	0.002	0.000	0.000	0.000	0.000
140	A	137	VAL	0	-0.072	-0.036	21.144	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	138	ASN	0	-0.054	-0.049	21.359	0.023	0.023	0.000	0.000	0.000	0.000
142	A	139	LEU	0	-0.002	0.030	21.008	0.012	0.012	0.000	0.000	0.000	0.000
143	A	140	ARG	1	0.852	0.890	16.061	0.058	0.058	0.000	0.000	0.000	0.000
144	A	141	SER	0	0.040	0.013	15.487	0.006	0.006	0.000	0.000	0.000	0.000
145	A	142	LEU	0	0.000	0.010	15.551	0.019	0.019	0.000	0.000	0.000	0.000
146	A	143	SER	0	-0.070	-0.027	13.837	0.030	0.030	0.000	0.000	0.000	0.000
147	A	144	TYR	0	-0.099	-0.077	9.143	0.171	0.171	0.000	0.000	0.000	0.000
148	A	145	LEU	0	0.039	0.044	12.543	-0.088	-0.088	0.000	0.000	0.000	0.000
149	A	146	PRO	0	0.008	0.020	11.803	0.076	0.076	0.000	0.000	0.000	0.000
150	A	147	PRO	0	0.015	0.027	11.370	0.016	0.016	0.000	0.000	0.000	0.000
151	A	148	VAL	0	0.052	0.031	14.363	-0.052	-0.052	0.000	0.000	0.000	0.000
152	A	149	ALA	0	-0.047	-0.013	14.843	0.016	0.016	0.000	0.000	0.000	0.000
153	A	150	MET	0	-0.024	-0.031	16.962	-0.027	-0.027	0.000	0.000	0.000	0.000
154	A	151	ASP	-1	-0.887	-0.939	20.407	0.043	0.043	0.000	0.000	0.000	0.000
155	A	152	SER	0	-0.079	-0.041	23.731	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	153	GLY	0	0.024	0.021	22.965	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	154	ASN	0	0.022	0.001	22.274	0.002	0.002	0.000	0.000	0.000	0.000
158	A	155	TYR	0	-0.003	-0.019	15.790	-0.009	-0.009	0.000	0.000	0.000	0.000
159	A	156	PRO	0	-0.058	-0.030	17.572	-0.003	-0.003	0.000	0.000	0.000	0.000
160	A	157	TYR	0	0.019	0.024	18.873	-0.034	-0.034	0.000	0.000	0.000	0.000
161	A	158	GLU	-1	-0.914	-0.940	20.711	-0.268	-0.268	0.000	0.000	0.000	0.000
162	A	159	ILE	0	0.015	0.010	23.029	-0.009	-0.009	0.000	0.000	0.000	0.000
163	A	160	VAL	0	0.008	0.007	23.080	0.012	0.012	0.000	0.000	0.000	0.000
164	A	161	THR	0	0.044	0.022	26.230	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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