FMO DATABASE

FMODB ID: 4JJ6N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-891535.841494
FMO2-HF: Nuclear repulsion	847420.410187
FMO2-HF: Total energy	-44115.431307
FMO2-MP2: Total energy	-44244.226494

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.
-15.938	-343.056	577.774	-226.503	-24.153	-0.118

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 : -0.150 / q_NPA : -0.166

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	0.093	0.038	2.584	-5.283	-2.549	1.653	-1.798	-2.589	-0.007
4	A	5	LEU	0	-0.087	-0.039	3.069	0.411	1.222	0.094	-0.234	-0.670	-0.001
5	A	6	THR	0	0.014	-0.010	4.700	1.057	1.160	-0.001	-0.018	-0.084	0.000
6	A	7	ASP	-1	-0.867	-0.921	6.951	-0.121	-0.121	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.029	0.026	7.870	0.185	0.185	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.071	-0.048	7.429	0.282	0.282	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.002	-0.006	10.540	0.203	0.203	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.845	-0.913	12.521	-0.408	-0.408	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.074	-0.041	13.334	0.101	0.101	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.075	-0.043	13.970	0.084	0.084	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.840	-0.915	16.621	-0.296	-0.296	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.090	-0.026	18.031	0.056	0.056	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.032	-0.023	19.820	0.037	0.037	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.939	0.979	19.724	0.265	0.265	0.000	0.000	0.000	0.000
17	A	18	PHE	0	0.028	0.027	16.745	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	TRP	0	0.028	0.007	19.923	0.009	0.009	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.057	-0.054	20.512	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.031	-0.009	15.492	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.056	0.033	18.501	0.021	0.021	0.000	0.000	0.000	0.000
22	A	23	TRP	0	0.015	-0.010	14.147	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.131	-0.074	19.851	0.029	0.029	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.851	-0.936	20.430	-0.157	-0.157	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.852	-0.923	19.196	-0.249	-0.249	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.014	-0.006	18.709	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.845	0.919	18.917	0.146	0.146	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.973	1.003	13.363	0.303	0.303	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.052	-0.029	15.131	-0.057	-0.057	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.060	0.036	11.250	0.021	0.021	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.070	-0.044	17.118	0.016	0.016	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.082	0.059	13.282	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	34	PRO	0	0.064	0.034	16.733	0.059	0.059	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.002	-0.009	18.442	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.947	0.964	17.976	0.405	0.405	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.089	-0.044	21.496	0.029	0.029	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.953	0.967	25.005	0.193	0.193	0.000	0.000	0.000	0.000
38	A	39	ARG	1	1.016	1.005	23.791	0.264	0.264	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.855	-0.931	26.545	-0.164	-0.164	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.957	0.971	26.920	0.145	0.145	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.006	0.018	23.471	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	43	PRO	0	-0.031	-0.019	26.709	0.014	0.014	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.902	-0.958	27.980	-0.160	-0.160	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.047	-0.014	27.956	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.080	-0.033	23.155	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.797	-0.899	20.290	-0.277	-0.277	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.909	-0.988	19.052	-0.441	-0.441	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.023	0.003	11.600	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	50	TYR	0	-0.052	-0.051	13.457	-0.089	-0.089	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.891	-0.932	14.649	-0.454	-0.454	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.077	0.038	15.159	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.063	-0.034	7.039	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.040	-0.028	10.770	-0.133	-0.133	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.908	-0.967	12.549	-0.358	-0.358	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.876	-0.939	8.134	-0.643	-0.643	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.854	0.913	7.830	1.004	1.004	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.856	0.935	9.226	0.508	0.508	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.926	0.969	10.616	0.389	0.389	0.000	0.000	0.000	0.000
59	A	60	HIS	0	-0.078	-0.026	6.208	0.342	0.342	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.015	-0.005	8.340	0.066	0.066	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.066	-0.024	5.945	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.010	0.009	10.207	0.039	0.039	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.823	-0.910	12.817	-0.484	-0.484	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.046	-0.025	12.751	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	66	PRO	0	0.019	0.007	15.228	0.046	0.046	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.882	-0.939	18.331	-0.213	-0.213	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.026	-0.007	19.602	0.005	0.005	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.958	-0.980	14.549	-0.552	-0.552	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.001	-0.013	17.007	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.128	0.052	13.761	-0.050	-0.050	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.044	-0.001	12.997	-0.085	-0.085	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.079	-0.047	13.721	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	74	CYS	0	0.002	0.013	10.299	-0.098	-0.098	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.085	0.046	9.061	-0.137	-0.137	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.007	-0.004	8.956	-0.167	-0.167	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.851	0.916	10.335	0.618	0.618	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.040	0.024	3.622	0.090	0.365	0.006	-0.061	-0.220	0.000
78	A	79	LEU	0	0.066	0.033	5.532	-0.244	-0.244	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.892	0.943	7.022	0.849	0.849	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.093	-0.047	6.971	0.112	0.112	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.043	0.021	2.327	-5.275	-0.034	0.761	-4.461	-1.541	-0.005
82	A	83	ASN	0	-0.028	-0.006	4.360	0.151	0.202	-0.001	-0.016	-0.035	0.000
83	A	84	ARG	0	0.147	0.189	1.129	-8.846	-345.179	575.262	-219.915	-19.014	-0.105
84	A	85	ALA	0	0.003	-0.003	6.197	0.017	0.017	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.872	0.945	9.769	0.259	0.259	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.054	-0.036	12.757	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.842	-0.909	16.290	-0.150	-0.150	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.887	0.965	19.767	0.147	0.147	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.061	0.023	23.155	0.011	0.011	0.000	0.000	0.000	0.000
90	A	91	PHE	0	0.037	-0.001	19.409	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.079	-0.035	20.274	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	93	ILE	0	0.065	0.040	22.812	0.022	0.022	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.000	-0.015	24.597	-0.019	-0.019	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.996	1.012	25.798	0.225	0.225	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.037	0.018	27.880	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.939	0.979	30.577	0.182	0.182	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.000	0.006	22.417	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.883	0.952	22.785	0.256	0.256	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.007	0.019	20.965	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.043	-0.033	17.134	0.074	0.074	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.929	0.963	17.768	0.229	0.229	0.000	0.000	0.000	0.000
102	A	103	TRP	0	-0.023	-0.019	11.331	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.017	-0.005	14.264	0.030	0.030	0.000	0.000	0.000	0.000
104	A	105	MET	0	0.029	0.028	8.238	0.073	0.073	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.066	-0.019	8.190	0.062	0.062	0.000	0.000	0.000	0.000

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