FMO DATABASE

FMODB ID: 14G4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1090164.325898
FMO2-HF: Nuclear repulsion	1038994.266038
FMO2-HF: Total energy	-51170.059861
FMO2-MP2: Total energy	-51323.200956

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.
1.864	3.318	-0.014	-0.616	-0.823	0.003

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 : 0.015 / q_NPA : -0.004

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	0.034	0.019	3.808	0.566	2.020	-0.014	-0.616	-0.823	0.003
4	D	7	THR	0	0.028	0.013	6.442	-0.548	-0.548	0.000	0.000	0.000	0.000
5	D	8	VAL	0	0.028	-0.002	8.830	-0.156	-0.156	0.000	0.000	0.000	0.000
6	D	9	GLU	-1	-0.930	-0.969	11.620	1.362	1.362	0.000	0.000	0.000	0.000
7	D	10	GLU	-1	-0.906	-0.959	7.589	2.500	2.500	0.000	0.000	0.000	0.000
8	D	11	ASN	0	0.003	0.005	10.542	-0.317	-0.317	0.000	0.000	0.000	0.000
9	D	12	TYR	0	-0.055	-0.048	12.298	-0.218	-0.218	0.000	0.000	0.000	0.000
10	D	13	LYS	1	0.914	0.971	12.336	-1.855	-1.855	0.000	0.000	0.000	0.000
11	D	14	GLU	-1	-0.934	-0.956	10.144	1.667	1.667	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.836	0.933	14.761	-0.788	-0.788	0.000	0.000	0.000	0.000
13	D	16	PHE	0	0.009	0.008	16.197	-0.024	-0.024	0.000	0.000	0.000	0.000
14	D	17	TYR	0	0.007	0.011	21.061	-0.034	-0.034	0.000	0.000	0.000	0.000
15	D	18	GLN	0	-0.013	-0.025	23.405	-0.009	-0.009	0.000	0.000	0.000	0.000
16	D	19	LEU	0	0.038	0.004	25.991	-0.026	-0.026	0.000	0.000	0.000	0.000
17	D	20	PRO	0	-0.048	-0.007	28.361	-0.001	-0.001	0.000	0.000	0.000	0.000
18	D	21	LYS	1	0.959	0.958	24.814	-0.220	-0.220	0.000	0.000	0.000	0.000
19	D	22	VAL	0	0.055	0.045	30.702	-0.003	-0.003	0.000	0.000	0.000	0.000
20	D	23	PHE	0	-0.036	-0.034	33.417	-0.007	-0.007	0.000	0.000	0.000	0.000
21	D	24	PHE	0	-0.040	-0.039	31.359	0.002	0.002	0.000	0.000	0.000	0.000
22	D	25	THR	0	0.039	0.031	34.335	0.001	0.001	0.000	0.000	0.000	0.000
23	D	26	ASN	0	0.005	-0.019	37.072	-0.009	-0.009	0.000	0.000	0.000	0.000
24	D	27	PRO	0	-0.057	-0.034	39.690	0.007	0.007	0.000	0.000	0.000	0.000
25	D	28	ASN	0	0.009	0.008	42.416	0.001	0.001	0.000	0.000	0.000	0.000
26	D	29	TYR	0	0.017	0.021	37.996	0.003	0.003	0.000	0.000	0.000	0.000
27	D	30	LYS	1	0.869	0.945	37.955	-0.111	-0.111	0.000	0.000	0.000	0.000
28	D	31	ASP	-1	-0.934	-0.956	39.507	0.123	0.123	0.000	0.000	0.000	0.000
29	D	32	LEU	0	-0.009	0.005	38.498	0.005	0.005	0.000	0.000	0.000	0.000
30	D	33	SER	0	-0.026	-0.028	39.489	0.012	0.012	0.000	0.000	0.000	0.000
31	D	34	ASN	0	0.055	-0.002	34.755	0.000	0.000	0.000	0.000	0.000	0.000
32	D	35	ASP	-1	-0.930	-0.961	34.973	0.211	0.211	0.000	0.000	0.000	0.000
33	D	36	ALA	0	0.010	0.005	36.110	0.005	0.005	0.000	0.000	0.000	0.000
34	D	37	LYS	1	0.852	0.951	33.880	-0.175	-0.175	0.000	0.000	0.000	0.000
35	D	38	ILE	0	0.026	0.001	30.227	0.006	0.006	0.000	0.000	0.000	0.000
36	D	39	ALA	0	0.000	0.007	31.644	0.009	0.009	0.000	0.000	0.000	0.000
37	D	40	TYR	0	-0.033	-0.042	32.561	0.004	0.004	0.000	0.000	0.000	0.000
38	D	41	ALA	0	0.001	-0.002	28.441	-0.002	-0.002	0.000	0.000	0.000	0.000
39	D	42	ILE	0	-0.016	-0.001	28.927	0.006	0.006	0.000	0.000	0.000	0.000
40	D	43	LEU	0	-0.008	-0.025	29.898	-0.001	-0.001	0.000	0.000	0.000	0.000
41	D	44	ARG	1	0.932	0.974	27.301	-0.202	-0.202	0.000	0.000	0.000	0.000
42	D	45	ASP	-1	-0.911	-0.956	24.886	0.317	0.317	0.000	0.000	0.000	0.000
43	D	46	ARG	1	0.867	0.946	27.455	-0.228	-0.228	0.000	0.000	0.000	0.000
44	D	47	LEU	0	0.005	0.005	29.954	-0.014	-0.014	0.000	0.000	0.000	0.000
45	D	48	GLN	0	0.070	0.020	24.719	-0.020	-0.020	0.000	0.000	0.000	0.000
46	D	49	LEU	0	-0.044	-0.020	28.672	-0.010	-0.010	0.000	0.000	0.000	0.000
47	D	50	SER	0	0.037	0.017	30.606	-0.008	-0.008	0.000	0.000	0.000	0.000
48	D	51	ILE	0	0.032	0.025	30.482	-0.011	-0.011	0.000	0.000	0.000	0.000
49	D	52	LYS	1	0.965	1.001	29.707	-0.172	-0.172	0.000	0.000	0.000	0.000
50	D	53	ASN	0	-0.142	-0.067	32.766	-0.005	-0.005	0.000	0.000	0.000	0.000
51	D	54	ASN	0	0.027	0.001	35.578	-0.008	-0.008	0.000	0.000	0.000	0.000
52	D	55	TRP	0	-0.080	-0.022	36.532	0.001	0.001	0.000	0.000	0.000	0.000
53	D	56	ILE	0	-0.001	-0.006	35.545	0.005	0.005	0.000	0.000	0.000	0.000
54	D	57	ASP	-1	-0.801	-0.874	39.483	0.060	0.060	0.000	0.000	0.000	0.000
55	D	58	THR	0	0.004	-0.030	42.559	-0.001	-0.001	0.000	0.000	0.000	0.000
56	D	59	GLU	-1	-0.975	-0.984	43.999	0.034	0.034	0.000	0.000	0.000	0.000
57	D	60	GLY	0	-0.015	0.007	40.031	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	61	ASN	0	-0.080	-0.027	38.339	0.006	0.006	0.000	0.000	0.000	0.000
59	D	62	ILE	0	-0.004	-0.005	33.272	0.001	0.001	0.000	0.000	0.000	0.000
60	D	63	TYR	0	-0.016	-0.005	37.403	0.005	0.005	0.000	0.000	0.000	0.000
61	D	64	PHE	0	-0.049	-0.041	33.420	0.006	0.006	0.000	0.000	0.000	0.000
62	D	65	ILE	0	0.023	0.019	38.682	-0.007	-0.007	0.000	0.000	0.000	0.000
63	D	66	TYR	0	0.004	0.005	34.227	0.011	0.011	0.000	0.000	0.000	0.000
64	D	67	THR	0	-0.059	-0.034	40.375	-0.006	-0.006	0.000	0.000	0.000	0.000
65	D	68	VAL	0	-0.016	-0.034	41.645	0.005	0.005	0.000	0.000	0.000	0.000
66	D	69	ALA	0	0.066	0.032	41.725	0.005	0.005	0.000	0.000	0.000	0.000
67	D	70	ASP	-1	-0.816	-0.896	37.834	0.160	0.160	0.000	0.000	0.000	0.000
68	D	71	LEU	0	0.013	-0.010	36.927	0.011	0.011	0.000	0.000	0.000	0.000
69	D	72	GLU	-1	-0.842	-0.913	37.160	0.162	0.162	0.000	0.000	0.000	0.000
70	D	73	VAL	0	0.004	0.003	33.847	0.010	0.010	0.000	0.000	0.000	0.000
71	D	74	ILE	0	-0.084	-0.042	32.204	0.016	0.016	0.000	0.000	0.000	0.000
72	D	75	LEU	0	-0.040	-0.030	32.270	0.014	0.014	0.000	0.000	0.000	0.000
73	D	76	ASN	0	-0.012	0.015	33.158	0.000	0.000	0.000	0.000	0.000	0.000
74	D	77	CYS	0	-0.093	-0.038	35.169	-0.004	-0.004	0.000	0.000	0.000	0.000
75	D	78	GLY	0	0.075	0.036	38.567	-0.005	-0.005	0.000	0.000	0.000	0.000
76	D	79	ASN	0	0.043	-0.010	42.275	-0.002	-0.002	0.000	0.000	0.000	0.000
77	D	80	LYS	1	0.953	0.966	44.535	-0.123	-0.123	0.000	0.000	0.000	0.000
78	D	81	LYS	1	0.962	0.986	39.331	-0.196	-0.196	0.000	0.000	0.000	0.000
79	D	82	ILE	0	0.089	0.053	40.614	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	83	THR	0	-0.060	-0.017	41.991	-0.007	-0.007	0.000	0.000	0.000	0.000
81	D	84	LYS	1	0.868	0.936	41.978	-0.160	-0.160	0.000	0.000	0.000	0.000
82	D	85	ILE	0	0.024	0.023	37.936	-0.003	-0.003	0.000	0.000	0.000	0.000
83	D	86	LYS	1	0.911	0.962	41.673	-0.128	-0.128	0.000	0.000	0.000	0.000
84	D	87	LYS	1	0.967	0.983	43.107	-0.107	-0.107	0.000	0.000	0.000	0.000
85	D	88	GLU	-1	-0.766	-0.881	42.208	0.142	0.142	0.000	0.000	0.000	0.000
86	D	89	LEU	0	-0.018	-0.008	37.908	-0.002	-0.002	0.000	0.000	0.000	0.000
87	D	90	GLU	-1	-0.876	-0.944	41.845	0.098	0.098	0.000	0.000	0.000	0.000
88	D	91	ASN	0	-0.083	-0.020	44.899	-0.003	-0.003	0.000	0.000	0.000	0.000
89	D	92	VAL	0	0.016	0.016	41.442	-0.003	-0.003	0.000	0.000	0.000	0.000
90	D	93	ASP	-1	-0.920	-0.951	42.969	0.083	0.083	0.000	0.000	0.000	0.000
91	D	94	LEU	0	-0.039	-0.031	37.656	0.002	0.002	0.000	0.000	0.000	0.000
92	D	95	LEU	0	-0.072	-0.044	39.210	0.007	0.007	0.000	0.000	0.000	0.000
93	D	96	ILE	0	0.049	0.024	41.521	-0.007	-0.007	0.000	0.000	0.000	0.000
94	D	97	GLN	0	-0.011	-0.026	43.804	0.007	0.007	0.000	0.000	0.000	0.000
95	D	98	LYS	1	0.980	1.000	45.912	-0.074	-0.074	0.000	0.000	0.000	0.000
96	D	99	ARG	1	0.929	0.981	47.856	-0.073	-0.073	0.000	0.000	0.000	0.000
97	D	100	GLN	0	-0.017	-0.002	48.030	-0.002	-0.002	0.000	0.000	0.000	0.000
98	D	101	GLY	0	0.054	0.034	47.631	0.004	0.004	0.000	0.000	0.000	0.000
99	D	102	LEU	0	-0.026	-0.051	49.457	-0.003	-0.003	0.000	0.000	0.000	0.000
100	D	103	ASN	0	0.021	0.013	49.128	0.003	0.003	0.000	0.000	0.000	0.000
101	D	104	LYS	1	0.968	0.988	45.181	-0.107	-0.107	0.000	0.000	0.000	0.000
102	D	105	PRO	0	-0.023	-0.021	45.502	0.005	0.005	0.000	0.000	0.000	0.000
103	D	106	ASN	0	0.027	0.006	44.953	-0.007	-0.007	0.000	0.000	0.000	0.000
104	D	107	LEU	0	0.021	0.031	42.922	0.004	0.004	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.075	-0.038	39.951	-0.001	-0.001	0.000	0.000	0.000	0.000
106	D	109	TYR	0	-0.017	-0.030	39.944	0.002	0.002	0.000	0.000	0.000	0.000
107	D	110	LEU	0	0.005	0.010	33.876	0.000	0.000	0.000	0.000	0.000	0.000
108	D	111	LEU	0	-0.010	0.014	37.902	-0.008	-0.008	0.000	0.000	0.000	0.000
109	D	112	LYS	1	0.956	0.987	33.489	-0.079	-0.079	0.000	0.000	0.000	0.000
110	D	113	PRO	0	0.016	0.011	34.263	-0.005	-0.005	0.000	0.000	0.000	0.000
111	D	114	ALA	0	0.012	0.012	37.380	-0.006	-0.006	0.000	0.000	0.000	0.000
112	D	115	ILE	0	0.015	-0.006	34.592	0.008	0.008	0.000	0.000	0.000	0.000
113	D	116	THR	0	-0.024	-0.009	38.295	-0.010	-0.010	0.000	0.000	0.000	0.000
114	D	117	LYS	1	1.007	0.971	38.887	-0.030	-0.030	0.000	0.000	0.000	0.000
115	D	118	ASN	0	-0.010	0.006	39.261	0.005	0.005	0.000	0.000	0.000	0.000
116	D	119	ASP	-1	-0.711	-0.840	36.505	0.102	0.102	0.000	0.000	0.000	0.000
117	D	120	ILE	0	-0.009	0.000	34.217	0.006	0.006	0.000	0.000	0.000	0.000
118	D	121	TYR	0	0.027	0.023	34.470	0.002	0.002	0.000	0.000	0.000	0.000
119	D	122	GLU	-1	-0.932	-0.985	35.475	0.108	0.108	0.000	0.000	0.000	0.000
120	D	123	ILE	0	-0.065	-0.039	30.439	0.011	0.011	0.000	0.000	0.000	0.000
121	D	124	ASP	-1	-0.876	-0.931	30.763	0.084	0.084	0.000	0.000	0.000	0.000
122	D	125	LYS	1	0.879	0.939	30.980	-0.088	-0.088	0.000	0.000	0.000	0.000
123	D	126	ALA	0	-0.031	-0.018	31.218	0.007	0.007	0.000	0.000	0.000	0.000
124	D	127	GLU	-1	-0.917	-0.941	26.732	0.178	0.178	0.000	0.000	0.000	0.000
125	D	128	ASN	0	-0.100	-0.054	26.612	-0.007	-0.007	0.000	0.000	0.000	0.000
126	D	129	GLU	-1	-0.974	-0.975	27.050	0.128	0.128	0.000	0.000	0.000	0.000

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