FMO DATABASE

FMODB ID: 66V1Z

Calculation Name: 1PM4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q57221

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	OptHSide
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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-941004.372819
FMO2-HF: Nuclear repulsion	895546.477298
FMO2-HF: Total energy	-45457.895521
FMO2-MP2: Total energy	-45590.683402

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:15:ILE)

Summations of interaction energy for fragment #1(A:15:ILE)

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.
-0.963	0.384	-0.014	-0.556	-0.777	0.001

Interaction energy analysis for fragmet #1(A:15:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.022

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	A	17	ASN	0	0.052	0.037	3.892	-0.578	0.769	-0.014	-0.556	-0.777	0.001
4	A	18	ILE	0	-0.039	-0.011	6.774	0.254	0.254	0.000	0.000	0.000	0.000
5	A	19	ALA	0	0.028	0.028	9.651	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	20	THR	0	0.019	-0.017	12.988	0.061	0.061	0.000	0.000	0.000	0.000
7	A	21	TYR	0	-0.088	-0.058	15.829	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	22	THR	0	0.018	0.001	19.524	0.024	0.024	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.008	0.004	22.575	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	24	THR	0	-0.031	-0.014	26.211	0.013	0.013	0.000	0.000	0.000	0.000
11	A	25	ILE	0	-0.030	0.002	28.295	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	26	GLN	0	0.063	0.006	30.668	0.003	0.003	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.034	0.036	33.921	0.002	0.002	0.000	0.000	0.000	0.000
14	A	28	LYS	1	0.825	0.890	35.303	-0.043	-0.043	0.000	0.000	0.000	0.000
15	A	29	GLY	0	0.022	0.025	33.233	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	30	GLU	-1	-0.832	-0.932	29.603	0.015	0.015	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.023	0.015	25.274	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	32	CYS	0	-0.033	0.016	24.385	0.006	0.006	0.000	0.000	0.000	0.000
19	A	33	ILE	0	0.022	0.018	19.124	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	34	ILE	0	-0.048	-0.030	19.757	0.008	0.008	0.000	0.000	0.000	0.000
21	A	35	GLY	0	0.052	0.031	15.738	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	36	ASN	0	-0.026	-0.042	13.709	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	37	LYS	1	0.865	0.926	15.531	0.218	0.218	0.000	0.000	0.000	0.000
24	A	38	GLU	-1	-0.855	-0.930	17.050	-0.293	-0.293	0.000	0.000	0.000	0.000
25	A	39	GLY	0	-0.025	0.001	17.568	0.004	0.004	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.785	0.875	12.872	0.447	0.447	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.020	-0.027	13.321	0.012	0.012	0.000	0.000	0.000	0.000
28	A	42	ARG	1	0.839	0.921	6.137	0.448	0.448	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.011	0.007	9.361	0.076	0.076	0.000	0.000	0.000	0.000
30	A	44	GLY	0	0.009	-0.001	7.498	-0.151	-0.151	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.793	-0.887	7.943	0.784	0.784	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.064	-0.002	8.793	-0.087	-0.087	0.000	0.000	0.000	0.000
33	A	47	TYR	0	0.025	-0.006	10.310	0.110	0.110	0.000	0.000	0.000	0.000
34	A	48	ALA	0	0.014	0.001	12.228	-0.067	-0.067	0.000	0.000	0.000	0.000
35	A	49	VAL	0	-0.019	-0.004	15.059	0.029	0.029	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.002	0.010	17.534	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	51	HIS	1	0.865	0.918	17.390	-0.243	-0.243	0.000	0.000	0.000	0.000
38	A	52	SER	0	0.032	-0.024	22.630	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	53	THR	0	-0.032	-0.019	25.788	0.008	0.008	0.000	0.000	0.000	0.000
40	A	54	ASN	0	-0.079	-0.041	27.569	0.001	0.001	0.000	0.000	0.000	0.000
41	A	55	VAL	0	0.043	0.012	29.764	0.005	0.005	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.025	-0.012	30.832	0.008	0.008	0.000	0.000	0.000	0.000
43	A	57	ALA	0	-0.030	0.003	28.853	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	58	ASP	-1	-0.843	-0.913	30.342	0.080	0.080	0.000	0.000	0.000	0.000
45	A	59	MET	0	-0.048	-0.036	26.917	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	60	THR	0	-0.043	-0.011	26.404	0.008	0.008	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.016	0.019	18.948	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.015	-0.015	23.421	0.009	0.009	0.000	0.000	0.000	0.000
49	A	63	LEU	0	0.005	0.027	17.060	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	64	LEU	0	-0.020	-0.009	20.849	0.001	0.001	0.000	0.000	0.000	0.000
51	A	65	ARG	1	0.839	0.871	15.183	0.117	0.117	0.000	0.000	0.000	0.000
52	A	66	ASN	0	-0.016	-0.005	21.483	0.013	0.013	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.001	-0.008	22.703	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.027	0.003	24.592	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	69	GLY	0	0.023	0.027	26.201	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	70	ASN	0	-0.047	-0.028	27.974	0.002	0.002	0.000	0.000	0.000	0.000
57	A	71	GLY	0	0.015	0.016	28.252	0.006	0.006	0.000	0.000	0.000	0.000
58	A	72	TRP	0	-0.017	-0.006	21.390	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	73	GLY	0	0.025	0.007	25.242	0.006	0.006	0.000	0.000	0.000	0.000
60	A	74	GLU	-1	-0.818	-0.878	24.243	0.042	0.042	0.000	0.000	0.000	0.000
61	A	75	ILE	0	-0.027	-0.001	18.842	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.856	0.911	17.918	-0.138	-0.138	0.000	0.000	0.000	0.000
63	A	77	ARG	1	0.844	0.880	22.693	-0.061	-0.061	0.000	0.000	0.000	0.000
64	A	78	ASN	0	-0.009	0.002	20.726	0.003	0.003	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.827	-0.906	23.505	0.117	0.117	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.002	-0.001	23.296	0.016	0.016	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.836	-0.915	21.458	0.192	0.192	0.000	0.000	0.000	0.000
68	A	82	LYS	1	0.774	0.888	20.713	-0.136	-0.136	0.000	0.000	0.000	0.000
69	A	83	PRO	0	-0.026	-0.018	15.274	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.027	0.019	16.637	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	85	LYS	1	0.842	0.891	10.300	-0.789	-0.789	0.000	0.000	0.000	0.000
72	A	86	TYR	0	-0.071	-0.074	13.618	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.859	-0.886	11.167	0.162	0.162	0.000	0.000	0.000	0.000
74	A	88	ASP	-1	-0.760	-0.831	12.372	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.016	-0.053	8.827	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	90	TYR	0	-0.036	-0.004	13.407	0.000	0.000	0.000	0.000	0.000	0.000
77	A	91	THR	0	0.035	0.018	15.156	-0.027	-0.027	0.000	0.000	0.000	0.000
78	A	92	SER	0	0.000	0.009	16.982	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	93	GLY	0	0.033	0.025	16.177	0.000	0.000	0.000	0.000	0.000	0.000
80	A	94	LEU	0	-0.025	-0.013	16.445	0.028	0.028	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.036	0.046	16.558	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	96	TRP	0	-0.065	-0.041	11.601	0.018	0.018	0.000	0.000	0.000	0.000
83	A	97	ILE	0	-0.020	-0.016	18.595	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	98	TRP	0	0.067	0.040	14.004	0.031	0.031	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.865	0.910	20.649	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	100	ILE	0	0.025	0.018	22.380	0.014	0.014	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.828	0.908	25.667	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	102	ASN	0	0.004	-0.012	29.206	0.015	0.015	0.000	0.000	0.000	0.000
89	A	103	ASN	0	-0.031	-0.026	30.412	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.103	0.075	33.545	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.054	-0.045	35.548	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.877	-0.914	35.409	0.054	0.054	0.000	0.000	0.000	0.000
93	A	107	THR	0	-0.012	-0.002	34.025	0.001	0.001	0.000	0.000	0.000	0.000
94	A	108	SER	0	0.019	0.010	30.481	0.004	0.004	0.000	0.000	0.000	0.000
95	A	109	ASN	0	0.035	0.031	25.286	0.005	0.005	0.000	0.000	0.000	0.000
96	A	110	TYR	0	0.011	0.027	23.034	0.006	0.006	0.000	0.000	0.000	0.000
97	A	111	SER	0	0.040	-0.005	20.167	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	112	LEU	0	-0.021	-0.004	17.756	0.016	0.016	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.803	-0.886	13.955	0.232	0.232	0.000	0.000	0.000	0.000
100	A	114	ALA	0	0.000	-0.020	13.616	0.035	0.035	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.022	-0.009	7.906	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	116	VAL	0	-0.021	-0.005	9.760	0.039	0.039	0.000	0.000	0.000	0.000
103	A	117	HIS	0	0.022	-0.016	8.004	-0.073	-0.073	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.839	-0.891	10.314	-0.575	-0.575	0.000	0.000	0.000	0.000
105	A	119	ASP	-1	-0.895	-0.947	10.992	-0.616	-0.616	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.823	0.898	13.460	0.097	0.097	0.000	0.000	0.000	0.000
107	A	121	GLU	-1	-0.855	-0.921	16.197	-0.210	-0.210	0.000	0.000	0.000	0.000
108	A	122	ASP	-1	-0.894	-0.953	19.589	-0.076	-0.076	0.000	0.000	0.000	0.000
109	A	123	SER	0	-0.089	-0.042	22.234	0.013	0.013	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.732	-0.834	17.961	-0.183	-0.183	0.000	0.000	0.000	0.000
111	A	125	VAL	0	-0.044	-0.014	21.120	0.015	0.015	0.000	0.000	0.000	0.000
112	A	126	LEU	0	-0.004	0.001	23.817	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	127	THR	0	-0.007	-0.008	26.170	0.008	0.008	0.000	0.000	0.000	0.000
114	A	128	LYS	1	0.882	0.932	29.051	0.036	0.036	0.000	0.000	0.000	0.000
115	A	130	PRO	0	0.024	0.004	26.676	0.000	0.000	0.000	0.000	0.000	0.000
116	A	131	VAL	0	0.007	0.013	29.720	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ILE)