FMO DATABASE

FMODB ID: YVV92

Calculation Name: 4P55-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P55

Chain ID: A

ChEMBL ID:

UniProt ID: Q2HR71

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-894076.020684
FMO2-HF: Nuclear repulsion	849959.028141
FMO2-HF: Total energy	-44116.992542
FMO2-MP2: Total energy	-44245.766134

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:SER)

Summations of interaction energy for fragment #1(A:2: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.
-25.948	-26.687	21.996	-10.229	-11.027	-0.091

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.071

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	4	TRP	0	0.092	0.053	3.018	-3.534	-0.866	0.186	-1.116	-1.738	-0.004
4	A	5	LEU	0	-0.058	-0.029	3.140	0.702	1.481	0.050	-0.265	-0.565	0.000
5	A	6	THR	0	-0.014	-0.028	4.633	0.259	0.345	-0.001	-0.009	-0.075	0.000
6	A	7	ASP	-1	-0.857	-0.928	6.433	-0.681	-0.681	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.000	0.003	8.344	0.316	0.316	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.052	-0.033	7.432	0.343	0.343	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.006	0.001	10.448	0.226	0.226	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.848	-0.912	12.483	-0.537	-0.537	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.079	-0.033	13.391	0.146	0.146	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.088	-0.038	13.518	0.105	0.105	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.851	-0.922	16.444	-0.578	-0.578	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.070	-0.049	17.687	0.082	0.082	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.024	-0.009	19.690	0.049	0.049	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.862	0.929	19.984	0.265	0.265	0.000	0.000	0.000	0.000
17	A	18	PHE	0	0.036	0.020	16.961	0.027	0.027	0.000	0.000	0.000	0.000
18	A	19	TRP	0	0.001	-0.011	19.832	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.034	-0.047	20.483	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.033	-0.004	15.750	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.062	0.031	18.602	0.025	0.025	0.000	0.000	0.000	0.000
22	A	23	TRP	0	0.007	-0.019	13.566	-0.057	-0.057	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.111	-0.059	19.411	0.059	0.059	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.795	-0.897	20.328	-0.385	-0.385	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.806	-0.894	19.007	-0.481	-0.481	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.070	-0.029	18.480	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.789	0.884	19.271	0.374	0.374	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.948	0.976	14.163	0.788	0.788	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.006	-0.001	15.114	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.032	0.017	10.999	0.041	0.041	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.040	-0.038	16.998	0.028	0.028	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.066	0.048	13.583	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	34	PRO	0	0.034	0.021	17.007	0.048	0.048	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.031	0.028	18.860	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.931	0.955	18.002	0.137	0.137	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.005	0.007	22.010	0.014	0.014	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.914	0.960	25.671	0.140	0.140	0.000	0.000	0.000	0.000
38	A	39	ARG	1	1.027	1.018	23.038	0.127	0.127	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.795	-0.898	26.592	-0.131	-0.131	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.782	0.858	27.146	0.106	0.106	0.000	0.000	0.000	0.000
41	A	42	MET	0	0.000	0.022	23.639	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	43	PRO	0	0.001	-0.004	27.177	0.015	0.015	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.759	-0.863	28.120	-0.130	-0.130	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.022	0.012	28.265	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.078	-0.035	23.286	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.763	-0.864	20.426	-0.209	-0.209	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.891	-0.973	18.794	-0.270	-0.270	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.025	0.002	11.662	0.019	0.019	0.000	0.000	0.000	0.000
49	A	50	TYR	0	-0.063	-0.051	13.771	-0.058	-0.058	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.805	-0.893	14.531	-0.071	-0.071	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.037	0.029	15.398	0.023	0.023	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.004	-0.001	7.037	0.032	0.032	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.050	-0.034	10.753	0.018	0.018	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.829	-0.911	12.498	-0.045	-0.045	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.805	-0.874	9.086	-0.280	-0.280	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.789	0.881	8.056	-0.145	-0.145	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.756	0.870	9.389	0.176	0.176	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.769	0.842	11.390	0.271	0.271	0.000	0.000	0.000	0.000
59	A	60	HIS	0	-0.070	-0.030	6.559	0.091	0.091	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.014	0.000	8.429	0.296	0.296	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.043	-0.017	5.768	0.088	0.088	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.028	0.009	10.369	-0.150	-0.150	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.821	-0.891	12.612	0.115	0.115	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.035	-0.015	12.898	0.034	0.034	0.000	0.000	0.000	0.000
65	A	66	PRO	0	0.017	-0.001	15.268	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.896	-0.944	18.495	0.076	0.076	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.026	-0.011	19.755	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.822	-0.876	13.968	0.087	0.087	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.002	-0.012	16.721	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.103	0.051	13.785	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.038	-0.012	12.948	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.072	-0.030	13.968	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	74	CYS	0	0.011	0.014	10.292	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.073	0.033	9.022	0.093	0.093	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.001	-0.005	9.187	-0.134	-0.134	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.753	0.827	10.683	-0.210	-0.210	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.053	0.032	3.867	-0.127	0.058	0.000	-0.024	-0.161	0.000
78	A	79	LEU	0	0.044	0.017	5.900	0.124	0.124	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.842	0.921	7.068	0.085	0.085	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.040	-0.028	6.119	-0.240	-0.240	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.002	0.013	2.516	0.030	1.048	0.600	-0.641	-0.977	0.004
82	A	83	ASN	0	-0.032	-0.014	4.198	-1.689	-1.629	-0.001	-0.018	-0.040	0.000
83	A	84	ARG	0	0.112	0.101	1.817	-23.828	-29.363	21.162	-8.156	-7.471	-0.091
84	A	85	ALA	0	-0.024	-0.008	6.481	0.400	0.400	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.856	0.917	9.751	0.839	0.839	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.017	-0.016	13.031	0.045	0.045	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.776	-0.859	16.448	-0.432	-0.432	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.919	0.967	20.115	0.203	0.203	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.028	0.020	23.522	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	91	PHE	0	0.068	0.005	19.646	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.068	-0.021	19.984	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	93	ILE	0	0.038	0.023	22.224	0.018	0.018	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.007	-0.021	24.540	0.008	0.008	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.997	1.007	25.595	0.247	0.247	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.045	0.028	27.915	0.008	0.008	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.848	0.897	30.464	0.131	0.131	0.000	0.000	0.000	0.000
97	A	98	MET	0	-0.013	0.015	22.787	0.003	0.003	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.874	0.942	23.354	0.179	0.179	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.036	-0.001	20.899	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.025	-0.017	16.816	0.059	0.059	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.881	0.941	17.877	0.387	0.387	0.000	0.000	0.000	0.000
102	A	103	TRP	0	-0.050	-0.019	11.303	0.020	0.020	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.026	-0.010	14.070	0.066	0.066	0.000	0.000	0.000	0.000
104	A	105	MET	0	0.020	0.025	8.090	0.078	0.078	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.073	-0.044	8.540	0.120	0.120	0.000	0.000	0.000	0.000

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