FMO DATABASE

FMODB ID: JL8V9

Calculation Name: 4YIF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YIF

Chain ID: A

ChEMBL ID:

UniProt ID: P9WMF1

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:

Apendix: None

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1093872.396002
FMO2-HF: Nuclear repulsion	1040227.690215
FMO2-HF: Total energy	-53644.705787
FMO2-MP2: Total energy	-53800.078022

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:4:SER)

Summations of interaction energy for fragment #1(A:4: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.
-5.218	-2.509	0.018	-1.122	-1.605	0.001

Interaction energy analysis for fragmet #1(A:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.000

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	6	ALA	0	0.013	0.010	3.657	-0.510	1.250	-0.003	-0.837	-0.921	0.001
4	A	7	ARG	1	0.841	0.888	3.475	-4.036	-3.368	0.022	-0.199	-0.490	0.000
5	A	8	LEU	0	0.022	0.022	4.535	-0.221	0.060	-0.001	-0.086	-0.194	0.000
6	A	9	ALA	0	0.031	0.013	6.434	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.012	-0.006	8.155	-0.065	-0.065	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.841	-0.900	8.657	1.263	1.263	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.021	0.012	10.313	-0.109	-0.109	0.000	0.000	0.000	0.000
10	A	13	SER	0	0.023	0.019	12.195	-0.070	-0.070	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.015	-0.012	13.385	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.006	-0.007	14.279	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	16	VAL	0	0.063	0.033	16.025	-0.035	-0.035	0.000	0.000	0.000	0.000
14	A	17	MET	0	-0.001	0.012	17.916	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.908	0.951	16.401	-0.431	-0.431	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.026	0.018	20.044	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	20	SER	0	0.010	-0.010	21.706	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.914	0.962	23.474	-0.186	-0.186	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.038	0.017	24.705	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	23	LEU	0	0.030	0.013	24.457	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.941	0.974	24.981	-0.103	-0.103	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.073	-0.041	28.377	0.000	0.000	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.855	0.917	28.896	-0.081	-0.081	0.000	0.000	0.000	0.000
24	A	27	ASN	0	0.036	0.032	32.170	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.043	0.025	34.752	0.004	0.004	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.010	-0.001	38.455	0.001	0.001	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.007	-0.003	39.466	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	31	PRO	0	-0.008	0.001	41.556	0.004	0.004	0.000	0.000	0.000	0.000
29	A	32	VAL	0	0.025	0.017	38.830	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.014	0.002	37.286	0.003	0.003	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.017	-0.017	30.511	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	35	SER	0	0.000	0.003	33.870	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	36	GLN	0	0.052	0.030	35.059	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.039	0.017	34.602	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.095	-0.049	31.923	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.061	0.027	33.860	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.015	0.000	36.459	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.036	-0.043	32.706	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.027	-0.036	33.091	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.033	-0.014	35.009	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.051	-0.029	38.004	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	45	ASN	0	-0.068	-0.035	32.665	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.817	-0.881	32.368	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	47	GLY	0	-0.002	0.018	36.658	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	48	ALA	0	-0.005	-0.012	40.349	0.003	0.003	0.000	0.000	0.000	0.000
46	A	49	MET	0	-0.002	0.005	35.994	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	THR	0	0.027	0.024	42.066	0.002	0.002	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.038	0.004	41.637	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	GLY	0	-0.040	-0.016	40.694	0.003	0.003	0.000	0.000	0.000	0.000
50	A	53	ALA	0	0.020	0.012	38.348	0.002	0.002	0.000	0.000	0.000	0.000
51	A	54	LEU	0	0.092	0.037	36.545	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	ALA	0	-0.062	-0.027	35.944	0.003	0.003	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.022	-0.014	33.565	0.005	0.005	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.733	0.838	28.345	0.023	0.023	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.776	-0.864	31.065	0.029	0.029	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.905	0.968	24.528	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.013	0.006	31.641	0.010	0.010	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.982	0.976	34.145	-0.059	-0.059	0.000	0.000	0.000	0.000
59	A	62	PRO	0	0.090	0.035	37.355	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	PRO	0	-0.009	0.009	40.550	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	64	SER	0	0.024	0.018	37.992	0.002	0.002	0.000	0.000	0.000	0.000
62	A	65	MET	0	-0.009	0.015	36.925	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	THR	0	0.013	-0.013	40.071	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.926	0.962	42.654	-0.044	-0.044	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.011	0.018	38.265	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.038	0.006	41.663	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	70	ALA	0	-0.001	-0.001	43.839	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	71	SER	0	0.030	0.004	43.544	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.020	-0.010	40.393	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.031	-0.011	44.921	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.911	-0.953	48.449	0.025	0.025	0.000	0.000	0.000	0.000
72	A	75	MET	0	-0.107	-0.049	43.552	0.000	0.000	0.000	0.000	0.000	0.000
73	A	76	GLY	0	0.027	0.031	48.379	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	77	PHE	0	-0.030	0.003	43.550	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.011	-0.006	43.585	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.777	-0.869	46.577	0.003	0.003	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.801	0.901	48.649	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.041	0.015	47.853	0.001	0.001	0.000	0.000	0.000	0.000
79	A	82	PRO	0	-0.044	0.003	47.401	0.001	0.001	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.088	0.045	48.181	0.002	0.002	0.000	0.000	0.000	0.000
81	A	84	PRO	0	-0.009	-0.011	45.534	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.075	-0.041	47.297	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.844	-0.934	50.193	0.013	0.013	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.026	0.011	51.238	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	88	ARG	1	0.875	0.948	46.046	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	89	GLN	0	-0.009	-0.025	46.729	0.001	0.001	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.024	0.000	48.635	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	91	LEU	0	0.010	0.002	44.339	0.002	0.002	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.019	-0.002	44.312	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	SER	0	0.031	-0.028	44.307	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.002	0.013	41.219	0.003	0.003	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.024	-0.033	44.521	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.802	-0.916	45.420	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	97	SER	0	-0.033	-0.006	45.805	0.001	0.001	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.047	0.017	43.609	0.002	0.002	0.000	0.000	0.000	0.000
96	A	99	ALA	0	0.040	0.017	41.381	0.001	0.001	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.788	-0.884	40.960	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	101	LEU	0	-0.004	0.011	39.863	0.001	0.001	0.000	0.000	0.000	0.000
99	A	102	VAL	0	0.005	0.012	35.941	0.003	0.003	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.795	0.886	36.735	0.004	0.004	0.000	0.000	0.000	0.000
101	A	104	ALA	0	-0.007	-0.009	37.560	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	105	ALA	0	-0.020	-0.024	35.239	0.002	0.002	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.853	0.921	32.504	0.023	0.023	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.818	0.901	32.921	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	108	ALA	0	0.080	0.044	33.911	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.882	0.941	29.371	-0.022	-0.022	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.036	0.017	29.316	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.915	-0.957	30.237	0.003	0.003	0.000	0.000	0.000	0.000
109	A	112	TRP	0	0.034	0.020	25.956	0.007	0.007	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.008	-0.015	23.519	0.006	0.006	0.000	0.000	0.000	0.000
111	A	114	ALA	0	0.008	0.007	26.860	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.854	-0.920	29.024	0.040	0.040	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.823	0.911	24.896	-0.052	-0.052	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.033	0.014	22.508	0.000	0.000	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.014	0.023	25.187	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.076	-0.043	25.606	0.000	0.000	0.000	0.000	0.000	0.000
117	A	120	LEU	0	0.001	0.031	20.723	0.008	0.008	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.004	-0.039	20.345	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.925	0.950	23.217	0.081	0.081	0.000	0.000	0.000	0.000
120	A	123	SER	0	0.103	0.047	19.237	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.815	-0.883	17.887	-0.034	-0.034	0.000	0.000	0.000	0.000
122	A	125	ARG	1	0.825	0.907	18.999	0.036	0.036	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.836	-0.902	20.343	-0.157	-0.157	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.004	0.010	14.208	-0.024	-0.024	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.011	-0.018	16.858	-0.014	-0.014	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.824	0.903	18.474	0.154	0.154	0.000	0.000	0.000	0.000
127	A	130	SER	0	0.034	0.003	16.890	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	131	ALA	0	-0.014	-0.008	15.271	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	132	ALA	0	-0.038	-0.016	16.573	0.011	0.011	0.000	0.000	0.000	0.000
130	A	133	ASP	-1	-0.884	-0.936	20.052	-0.178	-0.178	0.000	0.000	0.000	0.000
131	A	134	LEU	0	-0.020	-0.017	13.915	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	135	MET	0	-0.072	-0.040	16.453	0.023	0.023	0.000	0.000	0.000	0.000
133	A	136	LEU	0	0.009	0.007	18.232	0.021	0.021	0.000	0.000	0.000	0.000
134	A	137	ALA	0	0.015	0.013	18.507	0.007	0.007	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.084	-0.047	13.653	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	139	VAL	0	-0.084	-0.038	17.838	0.028	0.028	0.000	0.000	0.000	0.000
137	A	140	ASP	-1	-0.922	-0.953	21.269	-0.118	-0.118	0.000	0.000	0.000	0.000
138	A	141	GLU	-1	-0.885	-0.906	23.409	-0.036	-0.036	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.038	-0.025	23.320	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.032	-0.015	25.618	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:SER)