FMO DATABASE

FMODB ID: 22VNR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1731959.819443
FMO2-HF: Nuclear repulsion	1665292.734081
FMO2-HF: Total energy	-66667.085362
FMO2-MP2: Total energy	-66859.132668

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.
-46.632	-49.115	27.339	-13.184	-11.673	-0.021

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 : 0.025 / q_NPA : 0.020

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	0.830	0.910	2.141	-18.734	-24.210	15.962	-5.932	-4.554	0.050
4	B	4	VAL	0	-0.023	-0.003	6.439	-0.689	-0.689	0.000	0.000	0.000	0.000
5	B	5	PRO	0	0.041	0.045	9.993	0.398	0.398	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.898	0.934	11.814	-1.119	-1.119	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.017	0.008	15.131	-0.088	-0.088	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.007	-0.007	17.522	-0.003	-0.003	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.829	-0.921	18.646	0.407	0.407	0.000	0.000	0.000	0.000
10	B	10	HIS	0	0.004	-0.004	20.232	0.031	0.031	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.026	-0.018	19.233	-0.004	-0.004	0.000	0.000	0.000	0.000
12	B	12	GLN	0	0.043	0.024	16.165	0.007	0.007	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.825	0.912	18.541	-0.351	-0.351	0.000	0.000	0.000	0.000
14	B	14	MET	0	-0.022	0.016	21.752	-0.007	-0.007	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.072	0.036	18.994	-0.019	-0.019	0.000	0.000	0.000	0.000
16	B	16	GLN	0	-0.033	0.011	18.955	0.049	0.049	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.847	0.906	21.144	-0.004	-0.004	0.000	0.000	0.000	0.000
18	B	18	GLU	-1	-0.846	-0.914	22.693	-0.133	-0.133	0.000	0.000	0.000	0.000
19	B	19	VAL	0	-0.019	0.000	23.196	0.011	0.011	0.000	0.000	0.000	0.000
20	B	20	THR	0	0.032	0.022	25.196	-0.028	-0.028	0.000	0.000	0.000	0.000
21	B	21	VAL	0	0.101	0.043	26.122	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.007	-0.011	27.131	-0.019	-0.019	0.000	0.000	0.000	0.000
23	B	23	ASP	-1	-0.845	-0.921	27.777	-0.091	-0.091	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.010	-0.015	21.368	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	25	LYS	1	0.837	0.922	24.538	0.162	0.162	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.874	0.940	26.924	0.082	0.082	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.028	-0.015	23.382	0.003	0.003	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.008	0.007	19.843	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	29	ILE	0	-0.004	0.012	23.597	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	30	GLY	0	0.075	0.035	26.913	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.011	-0.012	28.125	0.008	0.008	0.000	0.000	0.000	0.000
32	B	32	ASP	-1	-0.851	-0.898	31.413	-0.066	-0.066	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.998	0.989	30.740	0.021	0.021	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.981	-0.995	30.702	-0.029	-0.029	0.000	0.000	0.000	0.000
35	B	35	TYR	0	-0.089	-0.058	27.582	0.011	0.011	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.872	0.941	26.531	0.091	0.091	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.058	-0.016	20.774	0.024	0.024	0.000	0.000	0.000	0.000
38	B	38	THR	0	0.047	0.039	22.041	-0.029	-0.029	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.824	0.898	16.182	0.375	0.375	0.000	0.000	0.000	0.000
40	B	40	ARG	1	0.914	0.946	21.269	-0.044	-0.044	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.908	-0.944	19.721	-0.131	-0.131	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.026	-0.015	20.880	-0.022	-0.022	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.041	-0.010	21.966	0.015	0.015	0.000	0.000	0.000	0.000
44	B	44	MET	0	-0.025	-0.002	23.651	0.010	0.010	0.000	0.000	0.000	0.000
45	B	45	GLY	0	-0.010	-0.012	25.376	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.927	-0.977	27.628	-0.132	-0.132	0.000	0.000	0.000	0.000
47	B	47	ILE	0	-0.043	-0.019	26.397	0.005	0.005	0.000	0.000	0.000	0.000
48	B	48	SER	0	-0.012	-0.032	23.335	0.011	0.011	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.793	-0.866	19.345	-0.387	-0.387	0.000	0.000	0.000	0.000
50	B	50	PRO	0	0.017	-0.003	18.566	-0.005	-0.005	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.794	-0.880	13.777	-0.657	-0.657	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.010	-0.009	14.687	-0.027	-0.027	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.015	-0.002	16.684	0.060	0.060	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.018	0.007	12.650	0.058	0.058	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.822	-0.886	10.429	-0.513	-0.513	0.000	0.000	0.000	0.000
56	B	56	TYR	0	0.003	-0.001	12.124	0.192	0.192	0.000	0.000	0.000	0.000
57	B	57	GLY	0	-0.024	-0.020	14.891	0.110	0.110	0.000	0.000	0.000	0.000
58	B	58	VAL	0	-0.033	-0.035	14.764	0.060	0.060	0.000	0.000	0.000	0.000
59	B	59	TYR	0	0.024	0.008	10.113	-0.016	-0.016	0.000	0.000	0.000	0.000
60	B	60	PRO	0	-0.003	0.002	11.799	0.142	0.142	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.016	-0.008	12.923	0.112	0.112	0.000	0.000	0.000	0.000
62	B	62	PHE	0	0.014	0.013	11.569	0.022	0.022	0.000	0.000	0.000	0.000
63	B	63	ILE	0	0.002	0.001	7.806	0.036	0.036	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.819	0.918	11.732	-0.409	-0.409	0.000	0.000	0.000	0.000
65	B	65	GLY	0	0.043	0.023	14.838	-0.010	-0.010	0.000	0.000	0.000	0.000
66	B	66	TYR	0	-0.017	0.001	16.806	-0.037	-0.037	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.005	-0.027	15.389	-0.035	-0.035	0.000	0.000	0.000	0.000
68	B	68	GLN	0	-0.032	-0.025	17.655	-0.070	-0.070	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.008	-0.003	17.430	-0.026	-0.026	0.000	0.000	0.000	0.000
70	B	70	LYS	1	0.831	0.923	15.455	0.552	0.552	0.000	0.000	0.000	0.000
71	B	71	ALA	0	0.031	0.012	18.060	-0.019	-0.019	0.000	0.000	0.000	0.000
72	B	72	ASN	0	-0.004	0.000	21.461	-0.006	-0.006	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.041	0.016	17.697	0.006	0.006	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.763	-0.851	18.795	-0.550	-0.550	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.887	-0.948	21.736	-0.219	-0.219	0.000	0.000	0.000	0.000
76	B	76	ALA	0	-0.037	-0.021	23.524	0.014	0.014	0.000	0.000	0.000	0.000
77	B	77	LEU	0	-0.016	-0.026	19.519	0.007	0.007	0.000	0.000	0.000	0.000
78	B	78	LEU	0	-0.021	-0.019	24.106	0.006	0.006	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.855	-0.912	26.632	-0.181	-0.181	0.000	0.000	0.000	0.000
80	B	80	MET	0	-0.011	0.003	24.492	0.007	0.007	0.000	0.000	0.000	0.000
81	B	81	SER	0	-0.039	-0.005	26.172	0.010	0.010	0.000	0.000	0.000	0.000
82	B	82	ASN	0	-0.045	-0.028	28.192	0.001	0.001	0.000	0.000	0.000	0.000
83	B	83	SER	0	0.003	-0.006	31.111	0.018	0.018	0.000	0.000	0.000	0.000
84	B	84	GLY	0	0.000	0.005	33.400	0.014	0.014	0.000	0.000	0.000	0.000
85	B	85	GLN	0	-0.018	0.003	33.191	0.013	0.013	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.041	0.017	32.088	-0.015	-0.015	0.000	0.000	0.000	0.000
87	B	87	LEU	0	0.035	0.021	29.073	-0.019	-0.019	0.000	0.000	0.000	0.000
88	B	88	ASP	-1	-0.886	-0.948	28.520	-0.219	-0.219	0.000	0.000	0.000	0.000
89	B	89	ILE	0	-0.002	-0.005	27.354	-0.027	-0.027	0.000	0.000	0.000	0.000
90	B	90	TYR	0	-0.003	-0.008	25.781	-0.040	-0.040	0.000	0.000	0.000	0.000
91	B	91	GLN	0	0.013	-0.004	23.807	-0.055	-0.055	0.000	0.000	0.000	0.000
92	B	92	ALA	0	-0.003	-0.007	22.756	-0.037	-0.037	0.000	0.000	0.000	0.000
93	B	93	VAL	0	-0.035	-0.023	21.643	-0.055	-0.055	0.000	0.000	0.000	0.000
94	B	94	GLN	0	0.073	0.037	20.732	-0.106	-0.106	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.028	-0.016	17.879	-0.045	-0.045	0.000	0.000	0.000	0.000
96	B	96	LEU	0	-0.052	-0.029	16.668	-0.088	-0.088	0.000	0.000	0.000	0.000
97	B	97	ASN	0	0.015	0.005	16.085	-0.173	-0.173	0.000	0.000	0.000	0.000
98	B	98	ALA	0	0.036	0.028	15.070	-0.113	-0.113	0.000	0.000	0.000	0.000
99	B	99	GLU	-1	-0.817	-0.888	11.538	-1.254	-1.254	0.000	0.000	0.000	0.000
100	B	100	ASN	0	0.042	0.023	10.910	-0.349	-0.349	0.000	0.000	0.000	0.000
101	B	101	MET	0	-0.013	0.001	11.561	-0.202	-0.202	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.007	-0.003	8.894	-0.162	-0.162	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.070	-0.034	6.927	-0.720	-0.720	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.034	-0.014	6.812	-0.819	-0.819	0.000	0.000	0.000	0.000
105	B	105	TYR	0	-0.031	0.005	7.175	-0.117	-0.117	0.000	0.000	0.000	0.000
106	B	106	TYR	0	-0.033	-0.061	3.503	-0.570	0.139	0.008	-0.225	-0.492	-0.001
107	B	107	GLU	-1	-0.946	-0.970	1.958	-17.022	-17.389	7.357	-3.559	-3.432	-0.042
108	B	108	SER	0	-0.053	-0.043	2.222	-1.492	0.432	3.960	-3.035	-2.849	-0.025
109	B	109	LEU	0	0.002	0.000	3.321	-1.860	-1.133	0.052	-0.433	-0.346	-0.003
110	B	110	PRO	0	-0.059	-0.023	5.886	0.221	0.221	0.000	0.000	0.000	0.000
111	B	111	PHE	0	-0.053	-0.032	8.129	0.189	0.189	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.055	0.028	6.931	-0.277	-0.277	0.000	0.000	0.000	0.000
113	B	113	LEU	0	-0.032	-0.014	12.497	0.155	0.155	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.098	-0.063	16.005	-0.020	-0.020	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.901	0.932	15.062	0.977	0.977	0.000	0.000	0.000	0.000
116	B	116	GLN	0	0.016	0.024	20.620	0.043	0.043	0.000	0.000	0.000	0.000
117	B	117	SER	0	0.015	-0.013	23.474	0.024	0.024	0.000	0.000	0.000	0.000
118	B	118	ILE	0	0.015	0.023	22.104	0.021	0.021	0.000	0.000	0.000	0.000
119	B	119	LEU	0	0.082	0.041	21.637	0.018	0.018	0.000	0.000	0.000	0.000
120	B	120	ALA	0	0.003	0.013	24.621	0.021	0.021	0.000	0.000	0.000	0.000
121	B	121	ASN	0	-0.038	-0.025	27.851	0.030	0.030	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.044	0.036	23.859	0.018	0.018	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.021	-0.023	27.570	0.017	0.017	0.000	0.000	0.000	0.000
124	B	124	LYS	1	0.839	0.913	29.813	0.254	0.254	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.016	0.009	31.132	0.016	0.016	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.074	0.027	29.256	0.014	0.014	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.834	0.938	32.922	0.266	0.266	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.843	-0.918	36.001	-0.168	-0.168	0.000	0.000	0.000	0.000
129	B	129	ALA	0	0.019	0.001	37.840	-0.003	-0.003	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.063	0.037	40.228	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	131	ILE	0	-0.025	-0.006	33.998	0.000	0.000	0.000	0.000	0.000	0.000
132	B	132	ARG	1	0.780	0.842	33.375	0.241	0.241	0.000	0.000	0.000	0.000
133	B	133	GLU	-1	-0.954	-0.966	36.711	-0.140	-0.140	0.000	0.000	0.000	0.000
134	B	134	ALA	0	-0.024	-0.023	36.940	0.003	0.003	0.000	0.000	0.000	0.000
135	B	135	MET	0	-0.060	-0.037	30.848	-0.002	-0.002	0.000	0.000	0.000	0.000
136	B	136	ALA	0	-0.030	-0.011	34.908	-0.004	-0.004	0.000	0.000	0.000	0.000
137	B	137	HIS	0	-0.016	-0.005	37.081	0.004	0.004	0.000	0.000	0.000	0.000
138	B	138	TYR	0	-0.024	0.000	32.912	0.013	0.013	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.901	0.933	35.030	0.160	0.160	0.000	0.000	0.000	0.000
140	B	140	LEU	0	-0.040	-0.011	35.718	0.010	0.010	0.000	0.000	0.000	0.000
141	B	141	GLY	0	0.033	0.019	34.628	-0.008	-0.008	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.798	-0.923	29.504	-0.141	-0.141	0.000	0.000	0.000	0.000
143	B	143	PHE	0	0.033	0.011	28.880	-0.003	-0.003	0.000	0.000	0.000	0.000
144	B	144	ALA	0	-0.067	-0.028	33.289	-0.002	-0.002	0.000	0.000	0.000	0.000
145	B	145	HIS	0	-0.077	-0.036	33.732	0.007	0.007	0.000	0.000	0.000	0.000
146	B	146	TYR	0	0.000	0.018	28.678	-0.005	-0.005	0.000	0.000	0.000	0.000
147	B	147	GLN	0	-0.020	-0.022	33.878	-0.004	-0.004	0.000	0.000	0.000	0.000
148	B	148	ASP	-1	-0.831	-0.878	29.762	-0.258	-0.258	0.000	0.000	0.000	0.000
149	B	149	THR	0	-0.022	-0.042	32.847	0.003	0.003	0.000	0.000	0.000	0.000
150	B	150	MET	0	0.028	0.018	29.777	-0.016	-0.016	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.007	0.003	30.088	-0.021	-0.021	0.000	0.000	0.000	0.000
152	B	152	ASP	-1	-0.751	-0.843	30.639	-0.242	-0.242	0.000	0.000	0.000	0.000
153	B	153	MET	0	-0.096	-0.037	26.649	-0.026	-0.026	0.000	0.000	0.000	0.000
154	B	154	VAL	0	-0.003	0.003	25.968	-0.036	-0.036	0.000	0.000	0.000	0.000
155	B	155	GLU	-1	-0.806	-0.886	26.273	-0.298	-0.298	0.000	0.000	0.000	0.000
156	B	156	ARG	1	0.836	0.875	25.181	0.282	0.282	0.000	0.000	0.000	0.000
157	B	157	THR	0	-0.039	-0.011	20.840	-0.039	-0.039	0.000	0.000	0.000	0.000
158	B	158	ILE	0	-0.014	-0.002	22.061	-0.052	-0.052	0.000	0.000	0.000	0.000
159	B	159	GLU	-1	-0.961	-0.966	23.550	-0.407	-0.407	0.000	0.000	0.000	0.000
160	B	160	THR	0	-0.103	-0.054	18.932	-0.048	-0.048	0.000	0.000	0.000	0.000
161	B	161	PHE	0	-0.062	-0.038	18.625	-0.074	-0.074	0.000	0.000	0.000	0.000

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