FMO DATABASE

FMODB ID: 1726Z

Calculation Name: 3PM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q7PF80

Base Structure: X-ray

Registration Date: 2023-06-21

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1700261.414507
FMO2-HF: Nuclear repulsion	1629131.855423
FMO2-HF: Total energy	-71129.559084
FMO2-MP2: Total energy	-71319.867314

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:1:MET)

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

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.
-3.055	0.526	1.089	-1.832	-2.839	-0.01

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.018

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	3	ASN	0	0.019	0.000	2.719	-1.863	0.837	0.577	-1.543	-1.734	-0.010
4	A	4	PRO	0	0.001	-0.016	2.501	0.503	1.384	0.512	-0.289	-1.105	0.000
5	A	5	CYS	0	-0.045	-0.023	5.457	0.150	0.150	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.029	0.015	7.170	0.280	0.280	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.891	0.954	7.764	0.209	0.209	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.015	0.031	11.181	0.119	0.119	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.032	-0.032	12.859	0.049	0.049	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.024	-0.008	13.462	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.015	-0.009	15.917	0.026	0.026	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.020	0.004	19.063	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.924	0.975	21.291	0.069	0.069	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.078	0.030	21.296	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.054	0.014	19.937	0.018	0.018	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.024	0.019	21.834	0.017	0.017	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.936	-0.973	25.202	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.155	-0.042	20.016	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.008	0.025	21.210	0.023	0.023	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.005	0.022	24.506	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.010	-0.004	21.666	0.006	0.006	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.003	0.002	24.347	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.045	-0.026	24.539	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.043	0.013	23.746	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.018	-0.020	25.772	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.872	-0.923	27.244	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.044	0.000	26.723	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.011	0.001	27.314	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.063	0.027	28.829	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.028	0.012	19.306	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	31	MET	0	0.005	-0.007	24.221	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.019	0.008	25.635	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.097	-0.037	22.483	0.040	0.040	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.021	-0.024	18.835	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.023	-0.025	21.988	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.931	0.987	24.401	0.296	0.296	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.041	0.012	20.453	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.019	0.004	16.336	-0.073	-0.073	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.016	0.010	17.650	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.058	0.015	18.163	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.011	0.000	14.098	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.933	0.956	13.411	0.480	0.480	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.933	0.982	13.119	0.509	0.509	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.002	-0.024	13.311	-0.139	-0.139	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.089	-0.017	9.087	-0.166	-0.166	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.043	-0.021	8.299	-0.686	-0.686	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.060	-0.011	9.695	0.289	0.289	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.925	-0.949	7.084	-1.382	-1.382	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.026	-0.015	7.787	0.380	0.380	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.015	-0.011	9.487	-0.273	-0.273	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.018	0.014	8.687	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.937	0.970	11.033	1.145	1.145	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.009	0.013	13.815	-0.043	-0.043	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.023	0.003	14.659	0.023	0.023	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.008	-0.008	16.471	0.118	0.118	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.012	0.000	18.260	0.049	0.049	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.027	0.003	18.056	0.048	0.048	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.840	-0.922	20.031	-0.364	-0.364	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.029	0.009	22.325	0.031	0.031	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.001	0.014	21.794	0.037	0.037	0.000	0.000	0.000	0.000
61	A	62	ASN	0	0.022	0.003	25.516	0.033	0.033	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.125	-0.062	27.743	0.023	0.023	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.003	-0.007	27.707	0.014	0.014	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.053	-0.023	30.392	0.012	0.012	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.014	0.009	26.756	0.006	0.006	0.000	0.000	0.000	0.000
66	A	67	TYR	0	0.000	0.013	23.972	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	68	SER	0	0.000	-0.003	27.291	0.011	0.011	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.032	-0.012	27.842	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.078	0.025	23.860	0.009	0.009	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.871	0.940	23.978	0.234	0.234	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.027	-0.004	22.489	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.864	-0.924	25.774	-0.158	-0.158	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.921	0.948	25.624	0.158	0.158	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.906	-0.937	27.997	-0.144	-0.144	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.009	-0.004	31.214	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.007	0.003	23.597	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.028	-0.040	28.213	0.002	0.002	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.940	0.979	29.138	0.125	0.125	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.007	-0.002	29.328	0.007	0.007	0.000	0.000	0.000	0.000
80	A	81	TYR	0	0.053	0.021	22.098	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.015	-0.005	28.376	0.009	0.009	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.935	-0.957	31.312	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.010	-0.006	29.047	0.005	0.005	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.058	-0.060	28.956	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.916	0.979	31.613	0.102	0.102	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.039	-0.024	34.915	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.062	-0.005	27.674	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.001	0.003	31.191	0.005	0.005	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.042	0.008	32.075	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.846	-0.931	29.114	-0.039	-0.039	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.041	0.003	23.559	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.003	0.022	28.134	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.987	0.981	28.525	0.059	0.059	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.049	0.047	23.319	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.000	-0.016	24.100	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.049	-0.034	24.829	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.883	-0.938	23.604	-0.079	-0.079	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.020	-0.007	20.663	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.011	-0.024	20.622	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.885	-0.934	22.416	-0.141	-0.141	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.028	0.011	19.675	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	103	CYS	0	-0.017	-0.012	14.192	0.017	0.017	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.012	-0.007	18.395	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.958	0.990	20.002	0.113	0.113	0.000	0.000	0.000	0.000
105	A	106	MET	0	-0.010	0.010	13.748	-0.023	-0.023	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.034	0.040	16.402	-0.033	-0.033	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.975	-0.994	17.735	-0.225	-0.225	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.087	-0.080	16.219	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.030	0.015	12.470	0.007	0.007	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.961	0.977	15.813	0.206	0.206	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.901	-0.946	18.189	-0.300	-0.300	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.946	-0.969	11.107	-1.051	-1.051	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.036	-0.023	15.396	-0.045	-0.045	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.888	-0.965	16.848	-0.361	-0.361	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.041	-0.016	16.874	0.017	0.017	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.032	0.005	16.296	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	118	ALA	0	-0.041	-0.029	16.970	0.004	0.004	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.886	0.947	20.382	0.332	0.332	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.044	0.011	15.328	0.020	0.020	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.016	0.000	19.545	0.018	0.018	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.011	-0.014	19.483	-0.052	-0.052	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.006	0.001	16.522	0.024	0.024	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.073	-0.043	16.816	0.004	0.004	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.916	-0.966	20.040	-0.322	-0.322	0.000	0.000	0.000	0.000
125	A	126	GLY	0	-0.006	-0.003	23.384	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.816	-0.882	17.411	-0.778	-0.778	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.023	-0.014	21.772	0.046	0.046	0.000	0.000	0.000	0.000
128	A	129	ILE	0	-0.018	-0.007	19.116	-0.052	-0.052	0.000	0.000	0.000	0.000
129	A	131	HIS	0	0.052	0.040	19.505	-0.074	-0.074	0.000	0.000	0.000	0.000
130	A	132	PRO	0	0.033	-0.002	15.314	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.026	0.017	16.974	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	134	SER	0	0.045	0.011	19.030	0.019	0.019	0.000	0.000	0.000	0.000
133	A	135	GLY	0	0.008	-0.009	16.071	0.018	0.018	0.000	0.000	0.000	0.000
134	A	136	THR	0	-0.011	-0.003	14.419	-0.042	-0.042	0.000	0.000	0.000	0.000
135	A	137	ILE	0	-0.001	0.003	15.529	0.018	0.018	0.000	0.000	0.000	0.000
136	A	138	LEU	0	0.025	0.007	18.110	0.022	0.022	0.000	0.000	0.000	0.000
137	A	139	ALA	0	-0.027	-0.014	12.807	0.023	0.023	0.000	0.000	0.000	0.000
138	A	141	MET	0	0.017	0.021	15.083	0.055	0.055	0.000	0.000	0.000	0.000
139	A	142	GLY	0	-0.003	0.006	17.677	0.036	0.036	0.000	0.000	0.000	0.000
140	A	143	MET	0	-0.072	-0.039	10.739	0.017	0.017	0.000	0.000	0.000	0.000
141	A	144	THR	0	0.007	-0.004	15.091	0.053	0.053	0.000	0.000	0.000	0.000
142	A	145	LEU	0	-0.011	-0.004	17.135	0.037	0.037	0.000	0.000	0.000	0.000
143	A	146	PHE	0	-0.027	-0.024	16.863	0.025	0.025	0.000	0.000	0.000	0.000
144	A	147	ALA	0	-0.063	-0.033	15.844	0.027	0.027	0.000	0.000	0.000	0.000
145	A	148	GLU	-1	-0.901	-0.948	17.958	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	150	PRO	0	0.022	0.013	23.481	0.016	0.016	0.000	0.000	0.000	0.000
147	A	151	ALA	0	0.049	0.010	25.803	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.844	0.920	26.689	0.022	0.022	0.000	0.000	0.000	0.000
149	A	153	LEU	0	-0.049	-0.026	27.699	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	154	PHE	0	0.023	0.010	20.042	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	155	THR	0	-0.058	-0.047	25.545	0.013	0.013	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.011	-0.010	24.605	0.003	0.003	0.000	0.000	0.000	0.000
153	A	157	ASN	0	0.030	0.008	24.400	0.001	0.001	0.000	0.000	0.000	0.000
154	A	158	ASP	-1	-0.846	-0.929	22.537	0.071	0.071	0.000	0.000	0.000	0.000
155	A	159	ASP	-1	-0.914	-0.969	20.884	-0.023	-0.023	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.023	0.027	18.410	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	162	LYS	1	0.932	0.965	16.351	-0.014	-0.014	0.000	0.000	0.000	0.000
158	A	163	LEU	0	-0.002	-0.003	15.064	-0.012	-0.012	0.000	0.000	0.000	0.000
159	A	164	LYS	1	1.005	1.011	15.102	-0.137	-0.137	0.000	0.000	0.000	0.000
160	A	165	SER	0	-0.026	-0.018	12.483	0.022	0.022	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.038	-0.014	9.812	0.023	0.023	0.000	0.000	0.000	0.000
162	A	167	HIS	1	0.856	0.906	10.244	0.268	0.268	0.000	0.000	0.000	0.000
163	A	168	SER	0	-0.025	0.003	10.400	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	169	LYS	1	0.914	0.960	5.512	-0.390	-0.390	0.000	0.000	0.000	0.000
165	A	171	PRO	0	0.116	0.064	9.427	0.159	0.159	0.000	0.000	0.000	0.000
166	A	172	PHE	0	-0.078	-0.038	12.591	-0.021	-0.021	0.000	0.000	0.000	0.000
167	A	173	LEU	0	0.018	0.027	12.455	0.016	0.016	0.000	0.000	0.000	0.000

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