FMO DATABASE

FMODB ID: 661YZ

Calculation Name: 3PNT-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PNT

Chain ID: B

ChEMBL ID:

UniProt ID: D7S065

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1738015.603591
FMO2-HF: Nuclear repulsion	1671348.131719
FMO2-HF: Total energy	-66667.471872
FMO2-MP2: Total energy	-66859.615028

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-42.694	-42.616	23.713	-11.851	-11.939	-0.031

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.013

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	B	3	LYS	1	0.812	0.893	2.103	-16.757	-20.708	13.200	-4.878	-4.371	0.036
4	B	4	VAL	0	-0.002	0.012	6.451	-0.598	-0.598	0.000	0.000	0.000	0.000
5	B	5	PRO	0	0.040	0.043	10.131	0.377	0.377	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.883	0.935	12.092	-1.071	-1.071	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.017	-0.002	15.593	-0.047	-0.047	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.017	-0.015	17.706	-0.015	-0.015	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.799	-0.896	18.468	0.374	0.374	0.000	0.000	0.000	0.000
10	B	10	HIS	0	0.045	0.037	20.674	0.036	0.036	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.041	-0.013	19.363	-0.003	-0.003	0.000	0.000	0.000	0.000
12	B	12	GLN	0	0.028	0.023	16.290	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.788	0.882	18.538	-0.284	-0.284	0.000	0.000	0.000	0.000
14	B	14	MET	0	-0.037	-0.003	21.631	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.088	0.044	19.095	-0.011	-0.011	0.000	0.000	0.000	0.000
16	B	16	GLN	0	-0.024	0.009	18.784	0.033	0.033	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.804	0.893	21.245	0.021	0.021	0.000	0.000	0.000	0.000
18	B	18	GLU	-1	-0.814	-0.892	22.931	-0.174	-0.174	0.000	0.000	0.000	0.000
19	B	19	VAL	0	-0.025	0.003	22.979	0.014	0.014	0.000	0.000	0.000	0.000
20	B	20	THR	0	0.033	-0.007	24.909	-0.031	-0.031	0.000	0.000	0.000	0.000
21	B	21	VAL	0	0.078	0.042	25.832	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.024	0.011	26.903	-0.019	-0.019	0.000	0.000	0.000	0.000
23	B	23	ASP	-1	-0.830	-0.882	27.688	-0.110	-0.110	0.000	0.000	0.000	0.000
24	B	24	LEU	0	0.001	-0.006	21.248	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	25	LYS	1	0.793	0.889	24.507	0.173	0.173	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.849	0.930	26.888	0.094	0.094	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.017	-0.012	23.316	0.004	0.004	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.017	0.004	19.672	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	29	ILE	0	0.022	0.024	23.384	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	30	GLY	0	0.044	0.025	26.664	0.003	0.003	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.029	0.002	27.850	0.010	0.010	0.000	0.000	0.000	0.000
32	B	32	ASP	-1	-0.832	-0.901	31.087	-0.074	-0.074	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.991	0.988	30.600	0.030	0.030	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-1.021	-1.015	30.884	-0.032	-0.032	0.000	0.000	0.000	0.000
35	B	35	TYR	0	-0.057	-0.050	27.613	0.010	0.010	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.820	0.926	26.364	0.095	0.095	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.066	-0.024	20.688	0.024	0.024	0.000	0.000	0.000	0.000
38	B	38	THR	0	0.038	0.028	21.877	-0.027	-0.027	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.835	0.889	16.143	0.349	0.349	0.000	0.000	0.000	0.000
40	B	40	ARG	1	0.900	0.939	21.290	-0.054	-0.054	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.879	-0.934	19.480	-0.110	-0.110	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.016	-0.020	20.760	-0.020	-0.020	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.041	-0.012	21.781	0.016	0.016	0.000	0.000	0.000	0.000
44	B	44	MET	0	-0.037	-0.003	23.548	0.004	0.004	0.000	0.000	0.000	0.000
45	B	45	GLY	0	-0.024	-0.025	25.343	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.905	-0.968	27.824	-0.133	-0.133	0.000	0.000	0.000	0.000
47	B	47	ILE	0	-0.031	-0.003	26.389	0.004	0.004	0.000	0.000	0.000	0.000
48	B	48	SER	0	0.005	-0.027	23.275	0.019	0.019	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.795	-0.863	19.232	-0.373	-0.373	0.000	0.000	0.000	0.000
50	B	50	PRO	0	0.007	-0.015	18.457	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.816	-0.876	13.953	-0.575	-0.575	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.010	-0.005	14.641	-0.027	-0.027	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.012	0.002	16.543	0.043	0.043	0.000	0.000	0.000	0.000
54	B	54	LEU	0	0.001	0.002	12.501	0.045	0.045	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.804	-0.873	10.375	-0.390	-0.390	0.000	0.000	0.000	0.000
56	B	56	TYR	0	-0.023	-0.028	12.358	0.201	0.201	0.000	0.000	0.000	0.000
57	B	57	GLY	0	-0.014	-0.019	15.195	0.099	0.099	0.000	0.000	0.000	0.000
58	B	58	VAL	0	-0.009	-0.006	14.547	0.053	0.053	0.000	0.000	0.000	0.000
59	B	59	TYR	0	0.014	0.009	10.005	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	PRO	0	-0.010	-0.008	11.856	0.130	0.130	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.016	-0.004	13.112	0.105	0.105	0.000	0.000	0.000	0.000
62	B	62	PHE	0	0.001	0.000	11.617	0.028	0.028	0.000	0.000	0.000	0.000
63	B	63	ILE	0	0.001	-0.005	7.970	0.033	0.033	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.832	0.918	11.957	-0.275	-0.275	0.000	0.000	0.000	0.000
65	B	65	GLY	0	0.041	0.030	15.220	0.013	0.013	0.000	0.000	0.000	0.000
66	B	66	TYR	0	-0.031	-0.001	16.959	-0.024	-0.024	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.006	-0.030	15.199	-0.031	-0.031	0.000	0.000	0.000	0.000
68	B	68	GLN	0	-0.015	-0.021	17.434	-0.075	-0.075	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.016	0.000	17.439	-0.019	-0.019	0.000	0.000	0.000	0.000
70	B	70	LYS	1	0.807	0.906	15.139	0.608	0.608	0.000	0.000	0.000	0.000
71	B	71	ALA	0	0.035	0.023	17.816	-0.020	-0.020	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.002	-0.022	21.270	-0.011	-0.011	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.023	0.006	17.593	0.010	0.010	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.773	-0.858	18.610	-0.585	-0.585	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.891	-0.950	21.422	-0.239	-0.239	0.000	0.000	0.000	0.000
76	B	76	ALA	0	-0.012	-0.002	23.635	0.013	0.013	0.000	0.000	0.000	0.000
77	B	77	LEU	0	-0.016	-0.016	19.446	0.008	0.008	0.000	0.000	0.000	0.000
78	B	78	LEU	0	-0.018	-0.019	23.993	0.005	0.005	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.838	-0.907	26.453	-0.188	-0.188	0.000	0.000	0.000	0.000
80	B	80	MET	0	-0.011	0.000	24.374	0.007	0.007	0.000	0.000	0.000	0.000
81	B	81	SER	0	-0.041	-0.008	26.049	0.014	0.014	0.000	0.000	0.000	0.000
82	B	82	ASN	0	-0.032	-0.034	28.091	0.007	0.007	0.000	0.000	0.000	0.000
83	B	83	SER	0	-0.034	-0.018	30.984	0.019	0.019	0.000	0.000	0.000	0.000
84	B	84	GLY	0	0.011	0.008	33.158	0.014	0.014	0.000	0.000	0.000	0.000
85	B	85	GLN	0	-0.008	0.003	33.038	0.011	0.011	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.037	0.007	32.012	-0.015	-0.015	0.000	0.000	0.000	0.000
87	B	87	LEU	0	0.021	0.011	29.305	-0.017	-0.017	0.000	0.000	0.000	0.000
88	B	88	ASP	-1	-0.876	-0.947	28.475	-0.225	-0.225	0.000	0.000	0.000	0.000
89	B	89	ILE	0	-0.003	0.001	27.123	-0.029	-0.029	0.000	0.000	0.000	0.000
90	B	90	TYR	0	0.023	0.008	25.730	-0.039	-0.039	0.000	0.000	0.000	0.000
91	B	91	GLN	0	0.001	-0.011	23.416	-0.044	-0.044	0.000	0.000	0.000	0.000
92	B	92	ALA	0	-0.019	-0.012	22.598	-0.040	-0.040	0.000	0.000	0.000	0.000
93	B	93	VAL	0	-0.017	-0.009	21.499	-0.055	-0.055	0.000	0.000	0.000	0.000
94	B	94	GLN	0	0.069	0.033	20.625	-0.106	-0.106	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.018	-0.024	17.865	-0.046	-0.046	0.000	0.000	0.000	0.000
96	B	96	LEU	0	-0.058	-0.032	16.697	-0.092	-0.092	0.000	0.000	0.000	0.000
97	B	97	ASN	0	0.010	0.000	16.269	-0.167	-0.167	0.000	0.000	0.000	0.000
98	B	98	ALA	0	0.011	0.015	15.114	-0.101	-0.101	0.000	0.000	0.000	0.000
99	B	99	GLU	-1	-0.804	-0.888	11.675	-1.236	-1.236	0.000	0.000	0.000	0.000
100	B	100	ASN	0	0.019	0.015	11.061	-0.324	-0.324	0.000	0.000	0.000	0.000
101	B	101	MET	0	-0.006	-0.001	11.399	-0.209	-0.209	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.014	0.005	8.949	-0.151	-0.151	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.035	-0.020	6.890	-0.659	-0.659	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.044	-0.024	6.696	-0.701	-0.701	0.000	0.000	0.000	0.000
105	B	105	TYR	0	-0.042	0.000	7.202	0.200	0.200	0.000	0.000	0.000	0.000
106	B	106	TYR	0	-0.024	-0.055	3.439	-0.323	0.491	0.009	-0.280	-0.542	-0.001
107	B	107	GLU	-1	-0.932	-0.946	1.971	-15.403	-16.202	8.208	-3.586	-3.823	-0.040
108	B	108	SER	0	-0.070	-0.048	2.379	-1.359	1.290	2.024	-2.236	-2.437	-0.018
109	B	109	LEU	0	0.005	0.002	2.955	-3.116	-1.751	0.272	-0.871	-0.766	-0.008
110	B	110	PRO	0	-0.057	-0.027	5.701	0.264	0.264	0.000	0.000	0.000	0.000
111	B	111	PHE	0	-0.043	-0.020	8.114	0.199	0.199	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.075	0.041	6.719	-0.302	-0.302	0.000	0.000	0.000	0.000
113	B	113	LEU	0	-0.008	-0.006	12.333	0.152	0.152	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.046	-0.028	16.052	-0.013	-0.013	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.842	0.891	15.074	0.984	0.984	0.000	0.000	0.000	0.000
116	B	116	GLN	0	0.018	0.026	20.045	0.059	0.059	0.000	0.000	0.000	0.000
117	B	117	SER	0	0.017	-0.011	23.063	0.033	0.033	0.000	0.000	0.000	0.000
118	B	118	ILE	0	0.012	0.020	21.982	0.029	0.029	0.000	0.000	0.000	0.000
119	B	119	LEU	0	0.076	0.042	21.685	0.026	0.026	0.000	0.000	0.000	0.000
120	B	120	ALA	0	0.001	0.013	24.531	0.025	0.025	0.000	0.000	0.000	0.000
121	B	121	ASN	0	-0.045	-0.031	27.716	0.043	0.043	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.068	0.049	23.962	0.018	0.018	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.042	-0.031	27.436	0.017	0.017	0.000	0.000	0.000	0.000
124	B	124	LYS	1	0.832	0.916	29.739	0.263	0.263	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.029	0.018	30.939	0.017	0.017	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.054	0.015	28.853	0.015	0.015	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.859	0.937	32.645	0.258	0.258	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.850	-0.907	35.964	-0.165	-0.165	0.000	0.000	0.000	0.000
129	B	129	ALA	0	0.005	-0.009	37.635	-0.004	-0.004	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.042	0.024	40.031	0.001	0.001	0.000	0.000	0.000	0.000
131	B	131	ILE	0	-0.035	-0.010	33.634	0.000	0.000	0.000	0.000	0.000	0.000
132	B	132	ARG	1	0.758	0.835	33.136	0.236	0.236	0.000	0.000	0.000	0.000
133	B	133	GLU	-1	-0.890	-0.939	36.552	-0.136	-0.136	0.000	0.000	0.000	0.000
134	B	134	ALA	0	-0.024	-0.017	37.140	0.003	0.003	0.000	0.000	0.000	0.000
135	B	135	MET	0	-0.044	-0.023	30.408	-0.003	-0.003	0.000	0.000	0.000	0.000
136	B	136	ALA	0	-0.019	-0.003	34.626	-0.002	-0.002	0.000	0.000	0.000	0.000
137	B	137	HIS	0	-0.036	-0.030	36.645	0.003	0.003	0.000	0.000	0.000	0.000
138	B	138	TYR	0	-0.033	-0.014	33.010	0.011	0.011	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.838	0.900	34.736	0.154	0.154	0.000	0.000	0.000	0.000
140	B	140	LEU	0	-0.028	-0.005	35.943	0.011	0.011	0.000	0.000	0.000	0.000
141	B	141	GLY	0	0.028	0.011	34.492	-0.008	-0.008	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.783	-0.917	29.570	-0.132	-0.132	0.000	0.000	0.000	0.000
143	B	143	PHE	0	0.014	0.002	28.843	-0.002	-0.002	0.000	0.000	0.000	0.000
144	B	144	ALA	0	-0.044	-0.014	33.251	-0.001	-0.001	0.000	0.000	0.000	0.000
145	B	145	HIS	0	-0.069	-0.032	33.714	0.008	0.008	0.000	0.000	0.000	0.000
146	B	146	TYR	0	0.002	0.020	28.262	-0.002	-0.002	0.000	0.000	0.000	0.000
147	B	147	GLN	0	-0.005	-0.010	33.736	-0.003	-0.003	0.000	0.000	0.000	0.000
148	B	148	ASP	-1	-0.813	-0.876	30.108	-0.240	-0.240	0.000	0.000	0.000	0.000
149	B	149	THR	0	-0.026	-0.036	33.065	0.004	0.004	0.000	0.000	0.000	0.000
150	B	150	MET	0	0.015	0.019	29.640	-0.015	-0.015	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.004	0.003	29.917	-0.021	-0.021	0.000	0.000	0.000	0.000
152	B	152	ASP	-1	-0.759	-0.848	30.328	-0.233	-0.233	0.000	0.000	0.000	0.000
153	B	153	MET	0	-0.078	-0.020	26.475	-0.026	-0.026	0.000	0.000	0.000	0.000
154	B	154	VAL	0	0.006	0.025	25.722	-0.036	-0.036	0.000	0.000	0.000	0.000
155	B	155	GLU	-1	-0.803	-0.876	25.983	-0.294	-0.294	0.000	0.000	0.000	0.000
156	B	156	ARG	1	0.834	0.861	25.205	0.261	0.261	0.000	0.000	0.000	0.000
157	B	157	THR	0	-0.031	-0.015	20.724	-0.042	-0.042	0.000	0.000	0.000	0.000
158	B	158	ILE	0	-0.039	-0.014	21.817	-0.053	-0.053	0.000	0.000	0.000	0.000
159	B	159	GLU	-1	-0.941	-0.967	23.407	-0.389	-0.389	0.000	0.000	0.000	0.000
160	B	160	THR	0	-0.099	-0.045	18.329	-0.051	-0.051	0.000	0.000	0.000	0.000
161	B	161	PHE	0	-0.061	-0.042	18.589	-0.075	-0.075	0.000	0.000	0.000	0.000

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