FMO DATABASE

FMODB ID: J3MY9

Calculation Name: 4PTA-D-Xray322

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	128
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1094456.890136
FMO2-HF: Nuclear repulsion	1043116.115271
FMO2-HF: Total energy	-51340.774865
FMO2-MP2: Total energy	-51494.475042

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:3:ACE )

Summations of interaction energy for fragment #1(D:3:ACE )

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.
-0.034	1.291	0.003	-0.656	-0.673	-0.001

Interaction energy analysis for fragmet #1(D:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.017

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	5	PHE	0	-0.015	0.009	3.489	0.403	1.728	0.003	-0.656	-0.673	-0.001
4	D	6	PHE	0	0.041	0.023	5.573	-0.182	-0.182	0.000	0.000	0.000	0.000
5	D	7	THR	0	0.019	0.011	6.226	0.200	0.200	0.000	0.000	0.000	0.000
6	D	8	VAL	0	0.032	-0.001	9.010	-0.048	-0.048	0.000	0.000	0.000	0.000
7	D	9	GLU	-1	-0.928	-0.967	10.652	0.151	0.151	0.000	0.000	0.000	0.000
8	D	10	GLU	-1	-0.906	-0.961	8.880	-0.302	-0.302	0.000	0.000	0.000	0.000
9	D	11	ASN	0	0.003	0.006	10.995	0.010	0.010	0.000	0.000	0.000	0.000
10	D	12	TYR	0	-0.053	-0.047	13.623	0.006	0.006	0.000	0.000	0.000	0.000
11	D	13	LYS	1	0.916	0.972	11.454	0.028	0.028	0.000	0.000	0.000	0.000
12	D	14	GLU	-1	-0.935	-0.956	12.248	-0.362	-0.362	0.000	0.000	0.000	0.000
13	D	15	ARG	1	0.836	0.933	16.344	0.081	0.081	0.000	0.000	0.000	0.000
14	D	16	PHE	0	0.011	0.008	17.798	0.016	0.016	0.000	0.000	0.000	0.000
15	D	17	TYR	0	0.006	0.011	22.737	0.003	0.003	0.000	0.000	0.000	0.000
16	D	18	GLN	0	-0.012	-0.024	26.318	0.001	0.001	0.000	0.000	0.000	0.000
17	D	19	LEU	0	0.038	0.004	28.161	0.006	0.006	0.000	0.000	0.000	0.000
18	D	20	PRO	0	-0.051	-0.009	30.757	-0.004	-0.004	0.000	0.000	0.000	0.000
19	D	21	LYS	1	0.963	0.960	28.344	0.093	0.093	0.000	0.000	0.000	0.000
20	D	22	VAL	0	0.054	0.045	33.585	0.003	0.003	0.000	0.000	0.000	0.000
21	D	23	PHE	0	-0.039	-0.035	35.669	0.004	0.004	0.000	0.000	0.000	0.000
22	D	24	PHE	0	-0.040	-0.038	33.509	0.004	0.004	0.000	0.000	0.000	0.000
23	D	25	THR	0	0.041	0.031	37.344	0.000	0.000	0.000	0.000	0.000	0.000
24	D	26	ASN	0	0.004	-0.021	39.983	0.005	0.005	0.000	0.000	0.000	0.000
25	D	27	PRO	0	-0.054	-0.031	42.606	0.001	0.001	0.000	0.000	0.000	0.000
26	D	28	ASN	0	0.007	0.007	45.134	0.003	0.003	0.000	0.000	0.000	0.000
27	D	29	TYR	0	0.012	0.017	40.401	0.000	0.000	0.000	0.000	0.000	0.000
28	D	30	LYS	1	0.871	0.947	40.346	0.034	0.034	0.000	0.000	0.000	0.000
29	D	31	ASP	-1	-0.929	-0.953	41.672	-0.021	-0.021	0.000	0.000	0.000	0.000
30	D	32	LEU	0	-0.015	0.002	40.377	0.001	0.001	0.000	0.000	0.000	0.000
31	D	33	SER	0	-0.022	-0.028	40.962	0.000	0.000	0.000	0.000	0.000	0.000
32	D	34	ASN	0	0.056	-0.001	35.624	-0.003	-0.003	0.000	0.000	0.000	0.000
33	D	35	ASP	-1	-0.929	-0.960	36.046	-0.018	-0.018	0.000	0.000	0.000	0.000
34	D	36	ALA	0	0.004	0.002	37.211	-0.001	-0.001	0.000	0.000	0.000	0.000
35	D	37	LYS	1	0.852	0.950	35.536	0.032	0.032	0.000	0.000	0.000	0.000
36	D	38	ILE	0	0.030	0.002	31.347	-0.004	-0.004	0.000	0.000	0.000	0.000
37	D	39	ALA	0	0.000	0.007	33.036	-0.002	-0.002	0.000	0.000	0.000	0.000
38	D	40	TYR	0	-0.037	-0.044	34.640	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	41	ALA	0	0.004	-0.001	30.223	-0.002	-0.002	0.000	0.000	0.000	0.000
40	D	42	ILE	0	-0.017	-0.001	30.152	-0.003	-0.003	0.000	0.000	0.000	0.000
41	D	43	LEU	0	-0.006	-0.026	31.542	0.000	0.000	0.000	0.000	0.000	0.000
42	D	44	ARG	1	0.923	0.971	30.139	0.066	0.066	0.000	0.000	0.000	0.000
43	D	45	ASP	-1	-0.903	-0.952	26.985	-0.064	-0.064	0.000	0.000	0.000	0.000
44	D	46	ARG	1	0.869	0.946	29.600	0.028	0.028	0.000	0.000	0.000	0.000
45	D	47	LEU	0	0.001	0.003	32.123	0.002	0.002	0.000	0.000	0.000	0.000
46	D	48	GLN	0	0.072	0.021	27.580	0.004	0.004	0.000	0.000	0.000	0.000
47	D	49	LEU	0	-0.043	-0.019	30.454	0.003	0.003	0.000	0.000	0.000	0.000
48	D	50	SER	0	0.035	0.016	32.752	0.002	0.002	0.000	0.000	0.000	0.000
49	D	51	ILE	0	0.031	0.026	33.363	0.002	0.002	0.000	0.000	0.000	0.000
50	D	52	LYS	1	0.967	1.001	31.411	0.028	0.028	0.000	0.000	0.000	0.000
51	D	53	ASN	0	-0.142	-0.066	35.129	0.002	0.002	0.000	0.000	0.000	0.000
52	D	54	ASN	0	0.030	0.003	37.953	0.001	0.001	0.000	0.000	0.000	0.000
53	D	55	TRP	0	-0.076	-0.021	38.354	0.001	0.001	0.000	0.000	0.000	0.000
54	D	56	ILE	0	0.002	-0.006	38.388	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	57	ASP	-1	-0.805	-0.877	42.202	-0.027	-0.027	0.000	0.000	0.000	0.000
56	D	58	THR	0	0.011	-0.025	45.502	-0.001	-0.001	0.000	0.000	0.000	0.000
57	D	59	GLU	-1	-0.977	-0.985	47.166	-0.028	-0.028	0.000	0.000	0.000	0.000
58	D	60	GLY	0	-0.014	0.007	43.141	-0.002	-0.002	0.000	0.000	0.000	0.000
59	D	61	ASN	0	-0.082	-0.028	41.422	-0.004	-0.004	0.000	0.000	0.000	0.000
60	D	62	ILE	0	-0.003	-0.004	36.099	0.001	0.001	0.000	0.000	0.000	0.000
61	D	63	TYR	0	-0.016	-0.006	40.114	0.001	0.001	0.000	0.000	0.000	0.000
62	D	64	PHE	0	-0.053	-0.042	35.603	0.000	0.000	0.000	0.000	0.000	0.000
63	D	65	ILE	0	0.022	0.015	40.707	0.001	0.001	0.000	0.000	0.000	0.000
64	D	66	TYR	0	0.003	0.004	35.886	0.000	0.000	0.000	0.000	0.000	0.000
65	D	67	THR	0	-0.017	-0.010	41.811	0.001	0.001	0.000	0.000	0.000	0.000
66	D	68	VAL	0	-0.054	-0.054	42.740	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	69	ALA	0	0.072	0.035	42.229	0.000	0.000	0.000	0.000	0.000	0.000
68	D	70	ASP	-1	-0.805	-0.890	38.944	-0.011	-0.011	0.000	0.000	0.000	0.000
69	D	71	LEU	0	0.008	-0.015	37.773	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	72	GLU	-1	-0.847	-0.913	37.984	-0.006	-0.006	0.000	0.000	0.000	0.000
71	D	73	VAL	0	0.010	0.006	34.302	0.001	0.001	0.000	0.000	0.000	0.000
72	D	74	ILE	0	-0.087	-0.042	33.339	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	75	LEU	0	-0.043	-0.033	33.096	-0.002	-0.002	0.000	0.000	0.000	0.000
74	D	76	ASN	0	-0.009	0.017	33.395	0.002	0.002	0.000	0.000	0.000	0.000
75	D	77	CYS	0	-0.094	-0.039	35.471	0.000	0.000	0.000	0.000	0.000	0.000
76	D	78	GLY	0	0.077	0.037	38.875	0.000	0.000	0.000	0.000	0.000	0.000
77	D	79	ASN	0	0.039	-0.014	42.558	-0.002	-0.002	0.000	0.000	0.000	0.000
78	D	80	LYS	1	0.955	0.968	45.101	0.006	0.006	0.000	0.000	0.000	0.000
79	D	81	LYS	1	0.963	0.987	39.618	0.009	0.009	0.000	0.000	0.000	0.000
80	D	82	ILE	0	0.091	0.054	41.581	-0.002	-0.002	0.000	0.000	0.000	0.000
81	D	83	THR	0	-0.063	-0.019	42.922	-0.001	-0.001	0.000	0.000	0.000	0.000
82	D	84	LYS	1	0.868	0.937	42.725	0.015	0.015	0.000	0.000	0.000	0.000
83	D	85	ILE	0	0.035	0.029	38.994	-0.001	-0.001	0.000	0.000	0.000	0.000
84	D	86	LYS	1	0.902	0.958	42.915	0.015	0.015	0.000	0.000	0.000	0.000
85	D	87	LYS	1	0.960	0.979	44.612	0.012	0.012	0.000	0.000	0.000	0.000
86	D	88	GLU	-1	-0.760	-0.878	43.429	-0.021	-0.021	0.000	0.000	0.000	0.000
87	D	89	LEU	0	-0.017	-0.006	39.564	-0.001	-0.001	0.000	0.000	0.000	0.000
88	D	90	GLU	-1	-0.859	-0.939	43.674	-0.020	-0.020	0.000	0.000	0.000	0.000
89	D	91	ASN	0	-0.081	-0.018	46.875	-0.001	-0.001	0.000	0.000	0.000	0.000
90	D	92	VAL	0	0.022	0.019	43.493	0.000	0.000	0.000	0.000	0.000	0.000
91	D	93	ASP	-1	-0.919	-0.951	45.407	-0.028	-0.028	0.000	0.000	0.000	0.000
92	D	94	LEU	0	-0.038	-0.029	39.897	-0.002	-0.002	0.000	0.000	0.000	0.000
93	D	95	LEU	0	-0.062	-0.040	41.469	-0.001	-0.001	0.000	0.000	0.000	0.000
94	D	96	ILE	0	0.052	0.026	43.690	0.002	0.002	0.000	0.000	0.000	0.000
95	D	97	GLN	0	-0.046	-0.039	45.984	0.001	0.001	0.000	0.000	0.000	0.000
96	D	98	LYS	1	0.968	0.991	47.952	0.025	0.025	0.000	0.000	0.000	0.000
97	D	99	ARG	1	0.947	0.996	50.004	0.016	0.016	0.000	0.000	0.000	0.000
98	D	100	GLN	0	-0.059	-0.053	49.648	0.002	0.002	0.000	0.000	0.000	0.000
99	D	101	GLY	0	0.040	0.029	51.213	0.000	0.000	0.000	0.000	0.000	0.000
100	D	102	LEU	0	0.014	0.006	53.413	0.001	0.001	0.000	0.000	0.000	0.000
101	D	103	ASN	0	0.026	0.001	51.558	-0.001	-0.001	0.000	0.000	0.000	0.000
102	D	104	LYS	1	0.903	0.948	48.593	0.007	0.007	0.000	0.000	0.000	0.000
103	D	105	PRO	0	0.057	0.040	47.153	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	106	ASN	0	-0.043	-0.039	46.637	-0.001	-0.001	0.000	0.000	0.000	0.000
105	D	107	LEU	0	0.049	0.042	44.990	0.000	0.000	0.000	0.000	0.000	0.000
106	D	108	LEU	0	-0.088	-0.044	41.649	0.000	0.000	0.000	0.000	0.000	0.000
107	D	109	TYR	0	-0.004	-0.023	42.330	0.000	0.000	0.000	0.000	0.000	0.000
108	D	110	LEU	0	0.006	0.011	36.140	0.001	0.001	0.000	0.000	0.000	0.000
109	D	111	LEU	0	-0.012	0.013	40.268	-0.001	-0.001	0.000	0.000	0.000	0.000
110	D	112	LYS	1	0.959	0.989	36.885	0.052	0.052	0.000	0.000	0.000	0.000
111	D	113	PRO	0	0.015	0.011	37.148	0.002	0.002	0.000	0.000	0.000	0.000
112	D	114	ALA	0	0.012	0.013	40.307	-0.001	-0.001	0.000	0.000	0.000	0.000
113	D	115	ILE	0	0.016	-0.006	38.101	-0.002	-0.002	0.000	0.000	0.000	0.000
114	D	116	THR	0	-0.022	-0.010	42.039	0.002	0.002	0.000	0.000	0.000	0.000
115	D	117	LYS	1	1.007	0.971	43.054	0.036	0.036	0.000	0.000	0.000	0.000
116	D	118	ASN	0	-0.010	0.006	43.725	-0.001	-0.001	0.000	0.000	0.000	0.000
117	D	119	ASP	-1	-0.711	-0.840	40.137	-0.043	-0.043	0.000	0.000	0.000	0.000
118	D	120	ILE	0	-0.011	-0.001	38.942	-0.002	-0.002	0.000	0.000	0.000	0.000
119	D	121	TYR	0	0.030	0.025	38.861	-0.002	-0.002	0.000	0.000	0.000	0.000
120	D	122	GLU	-1	-0.932	-0.985	39.666	-0.044	-0.044	0.000	0.000	0.000	0.000
121	D	123	ILE	0	-0.069	-0.041	34.172	-0.001	-0.001	0.000	0.000	0.000	0.000
122	D	124	ASP	-1	-0.874	-0.931	34.731	-0.068	-0.068	0.000	0.000	0.000	0.000
123	D	125	LYS	1	0.879	0.941	35.100	0.052	0.052	0.000	0.000	0.000	0.000
124	D	126	ALA	0	-0.028	-0.015	34.294	0.000	0.000	0.000	0.000	0.000	0.000
125	D	127	GLU	-1	-0.917	-0.942	30.639	-0.088	-0.088	0.000	0.000	0.000	0.000
126	D	128	ASN	0	-0.104	-0.061	30.550	-0.009	-0.009	0.000	0.000	0.000	0.000
127	D	129	GLU	-1	-0.916	-0.959	30.585	-0.075	-0.075	0.000	0.000	0.000	0.000
128	D	130	NME	0	-0.060	-0.013	33.168	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:ACE )