FMO DATABASE

FMODB ID: VR8Q1

Calculation Name: 3PNT-B-Xray318

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	161
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1729716.508714
FMO2-HF: Nuclear repulsion	1663050.649636
FMO2-HF: Total energy	-66665.859078
FMO2-MP2: Total energy	-66857.863538

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.
-226.27	-223.706	23.977	-13.425	-13.115	-0.101

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 : 1 / q_Mulliken : 0.801 / q_NPA : 0.886

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	0.880	0.934	2.573	38.874	38.264	6.577	-2.302	-3.665	0.023
4	B	4	VAL	0	0.005	0.014	5.312	0.769	0.794	0.000	-0.004	-0.020	0.000
5	B	5	PRO	0	0.045	0.049	9.137	0.755	0.755	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.919	0.940	10.837	21.725	21.725	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.019	0.015	14.047	-0.422	-0.422	0.000	0.000	0.000	0.000
8	B	8	LEU	0	0.002	-0.004	16.721	-0.279	-0.279	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.826	-0.927	17.817	-16.155	-16.155	0.000	0.000	0.000	0.000
10	B	10	HIS	0	-0.003	-0.013	19.362	0.080	0.080	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.024	-0.009	19.133	0.591	0.591	0.000	0.000	0.000	0.000
12	B	12	GLN	0	-0.012	0.001	14.494	0.385	0.385	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.851	0.925	18.237	14.915	14.915	0.000	0.000	0.000	0.000
14	B	14	MET	0	-0.032	0.014	21.604	0.510	0.510	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.045	0.010	18.872	0.383	0.383	0.000	0.000	0.000	0.000
16	B	16	GLN	0	-0.048	-0.001	18.971	-0.827	-0.827	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.904	0.932	21.064	12.580	12.580	0.000	0.000	0.000	0.000
18	B	18	GLU	-1	-0.931	-0.959	22.610	-11.668	-11.668	0.000	0.000	0.000	0.000
19	B	19	VAL	0	-0.012	0.004	23.190	0.439	0.439	0.000	0.000	0.000	0.000
20	B	20	THR	0	0.062	0.037	25.193	-0.239	-0.239	0.000	0.000	0.000	0.000
21	B	21	VAL	0	0.104	0.044	26.231	-0.316	-0.316	0.000	0.000	0.000	0.000
22	B	22	ASN	0	-0.001	-0.014	27.220	-0.108	-0.108	0.000	0.000	0.000	0.000
23	B	23	ASP	-1	-0.884	-0.952	27.628	-10.413	-10.413	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.037	-0.025	21.488	-0.312	-0.312	0.000	0.000	0.000	0.000
25	B	25	LYS	1	0.894	0.959	24.601	9.987	9.987	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.891	0.960	26.968	9.517	9.517	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.007	-0.009	23.391	-0.057	-0.057	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.007	0.016	20.139	-0.260	-0.260	0.000	0.000	0.000	0.000
29	B	29	ILE	0	-0.011	0.016	23.626	-0.100	-0.100	0.000	0.000	0.000	0.000
30	B	30	GLY	0	0.096	0.036	26.922	-0.072	-0.072	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.007	-0.008	28.144	0.323	0.323	0.000	0.000	0.000	0.000
32	B	32	ASP	-1	-0.897	-0.943	31.435	-9.192	-9.192	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.997	0.989	30.780	9.278	9.278	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.971	-0.984	30.750	-9.470	-9.470	0.000	0.000	0.000	0.000
35	B	35	TYR	0	-0.058	-0.028	27.676	-0.101	-0.101	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.871	0.938	26.580	10.153	10.153	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.058	-0.015	20.779	0.007	0.007	0.000	0.000	0.000	0.000
38	B	38	THR	0	0.032	0.033	22.050	-0.449	-0.449	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.914	0.953	16.322	18.150	18.150	0.000	0.000	0.000	0.000
40	B	40	ARG	1	0.910	0.947	21.259	12.884	12.884	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.893	-0.942	20.101	-15.418	-15.418	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.002	-0.010	20.737	-0.629	-0.629	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.030	-0.009	21.873	0.400	0.400	0.000	0.000	0.000	0.000
44	B	44	MET	0	0.002	0.015	23.511	0.438	0.438	0.000	0.000	0.000	0.000
45	B	45	GLY	0	-0.015	-0.009	25.298	-0.491	-0.491	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.908	-0.970	27.560	-10.363	-10.363	0.000	0.000	0.000	0.000
47	B	47	ILE	0	-0.057	-0.021	26.092	0.333	0.333	0.000	0.000	0.000	0.000
48	B	48	SER	0	-0.036	-0.053	23.379	-0.200	-0.200	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.782	-0.881	19.053	-16.858	-16.858	0.000	0.000	0.000	0.000
50	B	50	PRO	0	0.020	-0.009	18.440	-0.737	-0.737	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.859	-0.924	13.474	-23.058	-23.058	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.017	-0.008	14.691	-1.438	-1.438	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.016	-0.004	16.734	-0.178	-0.178	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.038	0.001	12.770	-0.020	-0.020	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.814	-0.842	10.556	-28.756	-28.756	0.000	0.000	0.000	0.000
56	B	56	TYR	0	0.006	0.004	12.194	-1.076	-1.076	0.000	0.000	0.000	0.000
57	B	57	GLY	0	0.005	0.000	14.923	1.016	1.016	0.000	0.000	0.000	0.000
58	B	58	VAL	0	-0.033	-0.037	14.905	0.084	0.084	0.000	0.000	0.000	0.000
59	B	59	TYR	0	0.016	0.006	9.709	-0.351	-0.351	0.000	0.000	0.000	0.000
60	B	60	PRO	0	0.002	0.002	11.689	-0.122	-0.122	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.008	-0.003	12.803	0.673	0.673	0.000	0.000	0.000	0.000
62	B	62	PHE	0	0.009	0.015	11.500	0.719	0.719	0.000	0.000	0.000	0.000
63	B	63	ILE	0	-0.009	-0.001	7.964	0.210	0.210	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.826	0.919	11.751	17.599	17.599	0.000	0.000	0.000	0.000
65	B	65	GLY	0	0.038	0.025	14.876	1.124	1.124	0.000	0.000	0.000	0.000
66	B	66	TYR	0	-0.010	0.007	16.863	0.625	0.625	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.016	-0.035	15.560	0.068	0.068	0.000	0.000	0.000	0.000
68	B	68	GLN	0	0.040	0.011	17.646	-0.447	-0.447	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.001	0.004	17.375	0.136	0.136	0.000	0.000	0.000	0.000
70	B	70	LYS	1	0.841	0.936	15.446	17.148	17.148	0.000	0.000	0.000	0.000
71	B	71	ALA	0	0.031	0.008	18.188	0.174	0.174	0.000	0.000	0.000	0.000
72	B	72	ASN	0	0.028	0.016	21.579	0.449	0.449	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.029	0.007	17.472	0.381	0.381	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.799	-0.895	18.797	-15.485	-15.485	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.910	-0.958	21.801	-10.825	-10.825	0.000	0.000	0.000	0.000
76	B	76	ALA	0	-0.038	-0.021	23.545	0.442	0.442	0.000	0.000	0.000	0.000
77	B	77	LEU	0	-0.019	-0.026	19.481	0.332	0.332	0.000	0.000	0.000	0.000
78	B	78	LEU	0	-0.018	-0.016	24.131	0.392	0.392	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.880	-0.939	26.658	-9.903	-9.903	0.000	0.000	0.000	0.000
80	B	80	MET	0	-0.040	-0.012	24.668	0.248	0.248	0.000	0.000	0.000	0.000
81	B	81	SER	0	-0.029	-0.004	26.210	0.344	0.344	0.000	0.000	0.000	0.000
82	B	82	ASN	0	-0.073	-0.043	28.178	0.296	0.296	0.000	0.000	0.000	0.000
83	B	83	SER	0	-0.019	-0.016	31.141	0.420	0.420	0.000	0.000	0.000	0.000
84	B	84	GLY	0	0.006	0.015	33.398	0.285	0.285	0.000	0.000	0.000	0.000
85	B	85	GLN	0	-0.006	0.002	33.084	0.348	0.348	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.038	0.017	32.051	-0.326	-0.326	0.000	0.000	0.000	0.000
87	B	87	LEU	0	0.031	0.017	28.896	-0.367	-0.367	0.000	0.000	0.000	0.000
88	B	88	ASP	-1	-0.882	-0.945	28.484	-10.648	-10.648	0.000	0.000	0.000	0.000
89	B	89	ILE	0	0.001	-0.004	27.330	-0.531	-0.531	0.000	0.000	0.000	0.000
90	B	90	TYR	0	0.001	-0.004	25.527	-0.609	-0.609	0.000	0.000	0.000	0.000
91	B	91	GLN	0	0.025	-0.004	23.636	-0.841	-0.841	0.000	0.000	0.000	0.000
92	B	92	ALA	0	-0.011	-0.005	22.723	-0.772	-0.772	0.000	0.000	0.000	0.000
93	B	93	VAL	0	-0.018	-0.011	21.603	-0.807	-0.807	0.000	0.000	0.000	0.000
94	B	94	GLN	0	0.039	0.015	20.838	-1.345	-1.345	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.036	-0.025	17.831	-1.031	-1.031	0.000	0.000	0.000	0.000
96	B	96	LEU	0	-0.040	-0.028	16.630	-1.299	-1.299	0.000	0.000	0.000	0.000
97	B	97	ASN	0	0.043	0.029	16.002	-1.473	-1.473	0.000	0.000	0.000	0.000
98	B	98	ALA	0	0.032	0.020	15.116	-1.424	-1.424	0.000	0.000	0.000	0.000
99	B	99	GLU	-1	-0.838	-0.913	11.527	-24.424	-24.424	0.000	0.000	0.000	0.000
100	B	100	ASN	0	0.045	0.020	10.818	-3.811	-3.811	0.000	0.000	0.000	0.000
101	B	101	MET	0	-0.027	-0.002	11.329	-2.000	-2.000	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.012	-0.005	8.807	-3.034	-3.034	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.067	-0.034	6.243	-6.849	-6.849	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.018	-0.004	6.548	-6.407	-6.407	0.000	0.000	0.000	0.000
105	B	105	TYR	0	-0.031	0.007	6.917	-2.252	-2.252	0.000	0.000	0.000	0.000
106	B	106	TYR	0	-0.059	-0.101	3.359	-8.839	-7.589	0.012	-0.525	-0.737	-0.003
107	B	107	GLU	-1	-0.957	-0.970	1.750	-128.464	-129.622	13.882	-7.268	-5.457	-0.092
108	B	108	SER	0	-0.054	-0.039	2.260	-6.766	-4.390	3.478	-2.928	-2.926	-0.026
109	B	109	LEU	0	0.017	0.006	3.352	-8.383	-7.702	0.028	-0.398	-0.310	-0.003
110	B	110	PRO	0	-0.062	-0.026	5.967	1.713	1.713	0.000	0.000	0.000	0.000
111	B	111	PHE	0	-0.055	-0.030	8.053	2.540	2.540	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.070	0.030	6.988	-2.565	-2.565	0.000	0.000	0.000	0.000
113	B	113	LEU	0	-0.009	-0.002	12.542	1.573	1.573	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.119	-0.047	16.039	0.453	0.453	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.984	0.980	15.127	19.597	19.597	0.000	0.000	0.000	0.000
116	B	116	GLN	0	0.007	0.031	20.608	0.530	0.530	0.000	0.000	0.000	0.000
117	B	117	SER	0	0.025	-0.020	23.449	0.382	0.382	0.000	0.000	0.000	0.000
118	B	118	ILE	0	0.017	0.028	22.140	0.392	0.392	0.000	0.000	0.000	0.000
119	B	119	LEU	0	0.088	0.040	21.168	0.297	0.297	0.000	0.000	0.000	0.000
120	B	120	ALA	0	-0.012	-0.002	24.566	0.411	0.411	0.000	0.000	0.000	0.000
121	B	121	ASN	0	-0.057	-0.027	27.843	0.633	0.633	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.041	0.032	23.784	0.337	0.337	0.000	0.000	0.000	0.000
123	B	123	THR	0	0.006	0.005	27.453	0.376	0.376	0.000	0.000	0.000	0.000
124	B	124	LYS	1	0.876	0.933	29.731	9.419	9.419	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.034	0.015	31.077	0.330	0.330	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.072	0.030	29.063	0.277	0.277	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.846	0.950	32.830	9.455	9.455	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.842	-0.916	35.905	-7.971	-7.971	0.000	0.000	0.000	0.000
129	B	129	ALA	0	0.021	-0.002	37.752	-0.117	-0.117	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.064	0.039	40.135	-0.081	-0.081	0.000	0.000	0.000	0.000
131	B	131	ILE	0	-0.028	-0.008	33.929	-0.094	-0.094	0.000	0.000	0.000	0.000
132	B	132	ARG	1	0.799	0.861	33.418	9.241	9.241	0.000	0.000	0.000	0.000
133	B	133	GLU	-1	-0.947	-0.961	36.612	-7.557	-7.557	0.000	0.000	0.000	0.000
134	B	134	ALA	0	-0.018	-0.022	36.725	-0.011	-0.011	0.000	0.000	0.000	0.000
135	B	135	MET	0	-0.065	-0.040	30.671	-0.122	-0.122	0.000	0.000	0.000	0.000
136	B	136	ALA	0	-0.029	-0.008	34.684	-0.158	-0.158	0.000	0.000	0.000	0.000
137	B	137	HIS	0	-0.028	-0.012	36.884	0.041	0.041	0.000	0.000	0.000	0.000
138	B	138	TYR	0	-0.016	0.005	33.052	0.212	0.212	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.907	0.951	35.286	8.746	8.746	0.000	0.000	0.000	0.000
140	B	140	LEU	0	-0.038	-0.013	35.584	0.158	0.158	0.000	0.000	0.000	0.000
141	B	141	GLY	0	0.027	0.015	34.526	-0.269	-0.269	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.828	-0.938	29.394	-10.779	-10.779	0.000	0.000	0.000	0.000
143	B	143	PHE	0	0.047	0.015	28.630	-0.004	-0.004	0.000	0.000	0.000	0.000
144	B	144	ALA	0	-0.061	-0.026	33.133	0.146	0.146	0.000	0.000	0.000	0.000
145	B	145	HIS	0	-0.085	-0.037	33.591	0.285	0.285	0.000	0.000	0.000	0.000
146	B	146	TYR	0	-0.007	0.015	28.220	-0.092	-0.092	0.000	0.000	0.000	0.000
147	B	147	GLN	0	-0.050	-0.047	33.675	0.127	0.127	0.000	0.000	0.000	0.000
148	B	148	ASP	-1	-0.818	-0.896	29.304	-10.793	-10.793	0.000	0.000	0.000	0.000
149	B	149	THR	0	-0.026	-0.004	32.634	-0.076	-0.076	0.000	0.000	0.000	0.000
150	B	150	MET	0	0.024	0.016	29.558	-0.351	-0.351	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.014	-0.008	29.864	-0.333	-0.333	0.000	0.000	0.000	0.000
152	B	152	ASP	-1	-0.788	-0.885	30.417	-9.978	-9.978	0.000	0.000	0.000	0.000
153	B	153	MET	0	-0.088	-0.047	26.428	-0.525	-0.525	0.000	0.000	0.000	0.000
154	B	154	VAL	0	-0.025	-0.011	25.683	-0.616	-0.616	0.000	0.000	0.000	0.000
155	B	155	GLU	-1	-0.849	-0.923	26.133	-10.380	-10.380	0.000	0.000	0.000	0.000
156	B	156	ARG	1	0.896	0.926	24.874	11.420	11.420	0.000	0.000	0.000	0.000
157	B	157	THR	0	-0.023	-0.001	20.523	-0.619	-0.619	0.000	0.000	0.000	0.000
158	B	158	ILE	0	-0.021	0.034	21.879	-0.601	-0.601	0.000	0.000	0.000	0.000
159	B	159	GLU	-1	-0.980	-0.975	23.405	-12.127	-12.127	0.000	0.000	0.000	0.000
160	B	160	THR	0	-0.163	-0.124	18.637	-0.479	-0.479	0.000	0.000	0.000	0.000
161	B	161	PHE	-1	-0.992	-0.996	18.783	-16.155	-16.155	0.000	0.000	0.000	0.000

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