FMO DATABASE

FMODB ID: 82Z2Y

Calculation Name: 4PTA-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PTA

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1089921.349308
FMO2-HF: Nuclear repulsion	1038749.956578
FMO2-HF: Total energy	-51171.39273
FMO2-MP2: Total energy	-51324.427886

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(D:4:GLN)

Summations of interaction energy for fragment #1(D:4:GLN)

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.
-0.14	1.207	-0.01	-0.564	-0.774	0.002

Interaction energy analysis for fragmet #1(D:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.010

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

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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	D	6	PHE	0	0.041	0.017	3.857	-0.854	0.493	-0.010	-0.564	-0.774	0.002
4	D	7	THR	0	0.022	0.020	5.594	0.199	0.199	0.000	0.000	0.000	0.000
5	D	8	VAL	0	0.026	0.001	7.951	-0.101	-0.101	0.000	0.000	0.000	0.000
6	D	9	GLU	-1	-0.874	-0.934	10.486	0.860	0.860	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.825	-0.901	7.461	1.035	1.035	0.000	0.000	0.000	0.000
8	D	11	ASN	0	0.010	0.012	9.986	-0.065	-0.065	0.000	0.000	0.000	0.000
9	D	12	TYR	0	-0.051	-0.034	12.032	-0.076	-0.076	0.000	0.000	0.000	0.000
10	D	13	LYS	1	0.810	0.890	10.199	-0.945	-0.945	0.000	0.000	0.000	0.000
11	D	14	GLU	-1	-0.941	-0.959	10.325	-0.081	-0.081	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.797	0.901	14.621	-0.096	-0.096	0.000	0.000	0.000	0.000
13	D	16	PHE	0	0.029	0.010	16.210	0.020	0.020	0.000	0.000	0.000	0.000
14	D	17	TYR	0	-0.014	0.001	21.283	-0.022	-0.022	0.000	0.000	0.000	0.000
15	D	18	GLN	0	0.033	0.014	22.044	0.003	0.003	0.000	0.000	0.000	0.000
16	D	19	LEU	0	0.039	0.012	25.848	-0.007	-0.007	0.000	0.000	0.000	0.000
17	D	20	PRO	0	-0.046	-0.011	28.386	-0.006	-0.006	0.000	0.000	0.000	0.000
18	D	21	LYS	1	0.854	0.905	24.939	0.045	0.045	0.000	0.000	0.000	0.000
19	D	22	VAL	0	0.050	0.031	30.889	0.006	0.006	0.000	0.000	0.000	0.000
20	D	23	PHE	0	-0.040	-0.033	33.615	0.002	0.002	0.000	0.000	0.000	0.000
21	D	24	PHE	0	-0.012	-0.018	31.241	0.008	0.008	0.000	0.000	0.000	0.000
22	D	25	THR	0	-0.010	-0.017	34.330	0.001	0.001	0.000	0.000	0.000	0.000
23	D	26	ASN	0	0.035	0.014	37.198	0.003	0.003	0.000	0.000	0.000	0.000
24	D	27	PRO	0	0.000	-0.013	40.001	0.005	0.005	0.000	0.000	0.000	0.000
25	D	28	ASN	0	-0.030	-0.021	42.857	0.005	0.005	0.000	0.000	0.000	0.000
26	D	29	TYR	0	-0.018	-0.007	38.135	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	30	LYS	1	0.840	0.929	38.543	-0.005	-0.005	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.914	-0.945	39.969	0.028	0.028	0.000	0.000	0.000	0.000
29	D	32	LEU	0	-0.007	0.029	38.613	0.003	0.003	0.000	0.000	0.000	0.000
30	D	33	SER	0	-0.028	-0.049	39.449	0.007	0.007	0.000	0.000	0.000	0.000
31	D	34	ASN	0	0.051	-0.008	34.497	-0.008	-0.008	0.000	0.000	0.000	0.000
32	D	35	ASP	-1	-0.800	-0.862	34.917	0.063	0.063	0.000	0.000	0.000	0.000
33	D	36	ALA	0	0.029	0.017	35.997	-0.001	-0.001	0.000	0.000	0.000	0.000
34	D	37	LYS	1	0.806	0.913	33.840	-0.037	-0.037	0.000	0.000	0.000	0.000
35	D	38	ILE	0	0.023	-0.001	30.072	-0.005	-0.005	0.000	0.000	0.000	0.000
36	D	39	ALA	0	0.017	0.000	31.581	-0.003	-0.003	0.000	0.000	0.000	0.000
37	D	40	TYR	0	-0.028	-0.034	32.457	-0.007	-0.007	0.000	0.000	0.000	0.000
38	D	41	ALA	0	0.001	0.000	28.457	-0.009	-0.009	0.000	0.000	0.000	0.000
39	D	42	ILE	0	-0.028	0.001	28.759	-0.007	-0.007	0.000	0.000	0.000	0.000
40	D	43	LEU	0	-0.009	-0.025	29.840	-0.008	-0.008	0.000	0.000	0.000	0.000
41	D	44	ARG	1	0.898	0.940	26.390	0.047	0.047	0.000	0.000	0.000	0.000
42	D	45	ASP	-1	-0.922	-0.953	24.689	-0.023	-0.023	0.000	0.000	0.000	0.000
43	D	46	ARG	1	0.894	0.943	27.557	-0.024	-0.024	0.000	0.000	0.000	0.000
44	D	47	LEU	0	0.019	0.014	30.081	-0.004	-0.004	0.000	0.000	0.000	0.000
45	D	48	GLN	0	0.058	0.029	24.867	0.002	0.002	0.000	0.000	0.000	0.000
46	D	49	LEU	0	-0.030	-0.022	27.470	-0.003	-0.003	0.000	0.000	0.000	0.000
47	D	50	SER	0	0.001	-0.020	30.383	0.003	0.003	0.000	0.000	0.000	0.000
48	D	51	ILE	0	0.006	0.012	30.163	0.000	0.000	0.000	0.000	0.000	0.000
49	D	52	LYS	1	0.903	0.962	29.679	0.039	0.039	0.000	0.000	0.000	0.000
50	D	53	ASN	0	-0.047	-0.019	32.078	0.001	0.001	0.000	0.000	0.000	0.000
51	D	54	ASN	0	-0.020	-0.015	35.334	0.000	0.000	0.000	0.000	0.000	0.000
52	D	55	TRP	0	-0.042	-0.012	36.430	0.005	0.005	0.000	0.000	0.000	0.000
53	D	56	ILE	0	0.031	0.010	35.183	-0.001	-0.001	0.000	0.000	0.000	0.000
54	D	57	ASP	-1	-0.778	-0.860	39.270	-0.045	-0.045	0.000	0.000	0.000	0.000
55	D	58	THR	0	-0.006	-0.026	42.362	-0.004	-0.004	0.000	0.000	0.000	0.000
56	D	59	GLU	-1	-0.924	-0.950	43.715	-0.054	-0.054	0.000	0.000	0.000	0.000
57	D	60	GLY	0	-0.011	0.004	39.599	-0.005	-0.005	0.000	0.000	0.000	0.000
58	D	61	ASN	0	-0.121	-0.059	38.162	-0.004	-0.004	0.000	0.000	0.000	0.000
59	D	62	ILE	0	-0.001	-0.005	33.036	0.003	0.003	0.000	0.000	0.000	0.000
60	D	63	TYR	0	-0.035	-0.006	37.291	0.006	0.006	0.000	0.000	0.000	0.000
61	D	64	PHE	0	-0.024	-0.008	33.226	0.000	0.000	0.000	0.000	0.000	0.000
62	D	65	ILE	0	-0.005	0.008	38.426	0.001	0.001	0.000	0.000	0.000	0.000
63	D	66	TYR	0	0.025	0.022	33.435	0.005	0.005	0.000	0.000	0.000	0.000
64	D	67	THR	0	-0.072	-0.077	39.860	0.001	0.001	0.000	0.000	0.000	0.000
65	D	68	VAL	0	-0.006	-0.020	41.187	0.001	0.001	0.000	0.000	0.000	0.000
66	D	69	ALA	0	0.083	0.041	41.151	0.002	0.002	0.000	0.000	0.000	0.000
67	D	70	ASP	-1	-0.839	-0.880	37.526	0.023	0.023	0.000	0.000	0.000	0.000
68	D	71	LEU	0	0.014	-0.010	36.460	0.003	0.003	0.000	0.000	0.000	0.000
69	D	72	GLU	-1	-0.795	-0.888	36.968	0.047	0.047	0.000	0.000	0.000	0.000
70	D	73	VAL	0	-0.018	-0.004	33.280	0.007	0.007	0.000	0.000	0.000	0.000
71	D	74	ILE	0	-0.054	-0.026	32.028	0.006	0.006	0.000	0.000	0.000	0.000
72	D	75	LEU	0	-0.014	-0.008	32.086	0.002	0.002	0.000	0.000	0.000	0.000
73	D	76	ASN	0	-0.017	0.008	32.356	0.007	0.007	0.000	0.000	0.000	0.000
74	D	77	CYS	0	-0.095	-0.043	34.445	0.003	0.003	0.000	0.000	0.000	0.000
75	D	78	GLY	0	0.086	0.051	37.950	-0.005	-0.005	0.000	0.000	0.000	0.000
76	D	79	ASN	0	-0.026	-0.050	41.600	-0.003	-0.003	0.000	0.000	0.000	0.000
77	D	80	LYS	1	0.963	0.985	43.962	-0.040	-0.040	0.000	0.000	0.000	0.000
78	D	81	LYS	1	0.864	0.925	37.829	-0.069	-0.069	0.000	0.000	0.000	0.000
79	D	82	ILE	0	0.037	0.023	39.629	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	83	THR	0	-0.074	-0.050	41.656	-0.006	-0.006	0.000	0.000	0.000	0.000
81	D	84	LYS	1	0.815	0.903	41.202	-0.049	-0.049	0.000	0.000	0.000	0.000
82	D	85	ILE	0	0.015	0.007	37.483	-0.003	-0.003	0.000	0.000	0.000	0.000
83	D	86	LYS	1	0.861	0.930	41.218	-0.014	-0.014	0.000	0.000	0.000	0.000
84	D	87	LYS	1	0.984	0.991	42.874	-0.020	-0.020	0.000	0.000	0.000	0.000
85	D	88	GLU	-1	-0.764	-0.850	41.847	0.030	0.030	0.000	0.000	0.000	0.000
86	D	89	LEU	0	-0.002	-0.001	37.523	-0.003	-0.003	0.000	0.000	0.000	0.000
87	D	90	GLU	-1	-0.852	-0.928	41.583	-0.003	-0.003	0.000	0.000	0.000	0.000
88	D	91	ASN	0	-0.103	-0.037	44.727	-0.001	-0.001	0.000	0.000	0.000	0.000
89	D	92	VAL	0	0.021	0.013	41.506	0.000	0.000	0.000	0.000	0.000	0.000
90	D	93	ASP	-1	-0.900	-0.941	42.842	-0.019	-0.019	0.000	0.000	0.000	0.000
91	D	94	LEU	0	-0.030	-0.014	37.548	-0.004	-0.004	0.000	0.000	0.000	0.000
92	D	95	LEU	0	-0.076	-0.046	38.872	-0.001	-0.001	0.000	0.000	0.000	0.000
93	D	96	ILE	0	0.060	0.028	41.259	0.001	0.001	0.000	0.000	0.000	0.000
94	D	97	GLN	0	-0.024	-0.018	43.885	0.000	0.000	0.000	0.000	0.000	0.000
95	D	98	LYS	1	0.948	1.002	44.399	0.033	0.033	0.000	0.000	0.000	0.000
96	D	99	ARG	1	0.895	0.959	47.415	0.005	0.005	0.000	0.000	0.000	0.000
97	D	100	GLN	0	-0.003	0.006	48.163	0.003	0.003	0.000	0.000	0.000	0.000
98	D	101	GLY	0	0.052	0.026	47.630	0.000	0.000	0.000	0.000	0.000	0.000
99	D	102	LEU	0	-0.028	-0.047	49.665	0.001	0.001	0.000	0.000	0.000	0.000
100	D	103	ASN	0	0.025	0.006	49.348	-0.002	-0.002	0.000	0.000	0.000	0.000
101	D	104	LYS	1	0.964	0.991	45.137	-0.012	-0.012	0.000	0.000	0.000	0.000
102	D	105	PRO	0	0.005	-0.007	45.618	0.000	0.000	0.000	0.000	0.000	0.000
103	D	106	ASN	0	-0.010	0.005	45.273	-0.005	-0.005	0.000	0.000	0.000	0.000
104	D	107	LEU	0	0.050	0.036	42.847	0.001	0.001	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.046	-0.027	40.029	0.001	0.001	0.000	0.000	0.000	0.000
106	D	109	TYR	0	-0.029	-0.054	39.812	-0.001	-0.001	0.000	0.000	0.000	0.000
107	D	110	LEU	0	0.012	0.007	34.040	0.005	0.005	0.000	0.000	0.000	0.000
108	D	111	LEU	0	0.004	0.013	37.997	-0.006	-0.006	0.000	0.000	0.000	0.000
109	D	112	LYS	1	0.945	0.987	34.548	0.081	0.081	0.000	0.000	0.000	0.000
110	D	113	PRO	0	0.025	0.015	34.613	0.001	0.001	0.000	0.000	0.000	0.000
111	D	114	ALA	0	0.016	0.015	37.499	-0.007	-0.007	0.000	0.000	0.000	0.000
112	D	115	ILE	0	0.018	-0.006	34.720	0.002	0.002	0.000	0.000	0.000	0.000
113	D	116	THR	0	-0.028	-0.035	38.649	-0.001	-0.001	0.000	0.000	0.000	0.000
114	D	117	LYS	1	1.002	0.969	39.054	0.048	0.048	0.000	0.000	0.000	0.000
115	D	118	ASN	0	-0.007	0.015	39.657	0.001	0.001	0.000	0.000	0.000	0.000
116	D	119	ASP	-1	-0.701	-0.817	36.542	-0.018	-0.018	0.000	0.000	0.000	0.000
117	D	120	ILE	0	-0.001	0.010	34.281	0.001	0.001	0.000	0.000	0.000	0.000
118	D	121	TYR	0	0.035	0.028	34.510	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	122	GLU	-1	-0.911	-0.966	35.702	0.007	0.007	0.000	0.000	0.000	0.000
120	D	123	ILE	0	-0.038	-0.024	30.264	0.006	0.006	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.883	-0.940	31.009	-0.055	-0.055	0.000	0.000	0.000	0.000
122	D	125	LYS	1	0.784	0.881	31.336	-0.003	-0.003	0.000	0.000	0.000	0.000
123	D	126	ALA	0	-0.030	-0.007	31.046	0.009	0.009	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.843	-0.902	25.716	-0.025	-0.025	0.000	0.000	0.000	0.000
125	D	128	ASN	0	-0.022	-0.006	26.697	-0.014	-0.014	0.000	0.000	0.000	0.000
126	D	129	GLU	-1	-0.951	-0.963	27.393	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:4:GLN)