FMO DATABASE

FMODB ID: 7G16K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1729676.950185
FMO2-HF: Nuclear repulsion	1663010.864306
FMO2-HF: Total energy	-66666.085879
FMO2-MP2: Total energy	-66858.105313

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.
-45.674	-47.101	23.801	-11.677	-10.696	-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 : 0.011 / q_NPA : 0.004

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	0.878	0.932	2.395	-19.048	-22.665	12.594	-4.311	-4.665	0.034
4	B	4	VAL	0	-0.005	0.006	5.456	-0.760	-0.760	0.000	0.000	0.000	0.000
5	B	5	PRO	0	0.044	0.048	9.285	0.367	0.367	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.916	0.937	10.932	-0.366	-0.366	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.015	0.014	14.107	-0.145	-0.145	0.000	0.000	0.000	0.000
8	B	8	LEU	0	0.001	-0.004	16.835	0.007	0.007	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.827	-0.928	17.919	0.085	0.085	0.000	0.000	0.000	0.000
10	B	10	HIS	0	-0.003	-0.014	19.489	0.055	0.055	0.000	0.000	0.000	0.000
11	B	11	TYR	0	0.021	-0.010	19.278	0.032	0.032	0.000	0.000	0.000	0.000
12	B	12	GLN	0	-0.008	0.002	14.615	0.109	0.109	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.852	0.926	18.244	-0.184	-0.184	0.000	0.000	0.000	0.000
14	B	14	MET	0	-0.034	0.012	21.481	0.015	0.015	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.047	0.010	18.798	0.000	0.000	0.000	0.000	0.000	0.000
16	B	16	GLN	0	-0.044	0.001	18.831	0.057	0.057	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.899	0.930	20.948	0.017	0.017	0.000	0.000	0.000	0.000
18	B	18	GLU	-1	-0.929	-0.958	22.543	-0.045	-0.045	0.000	0.000	0.000	0.000
19	B	19	VAL	0	-0.009	0.006	23.150	0.002	0.002	0.000	0.000	0.000	0.000
20	B	20	THR	0	0.061	0.038	25.188	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	21	VAL	0	0.103	0.043	26.332	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	22	ASN	0	-0.003	-0.015	27.325	-0.023	-0.023	0.000	0.000	0.000	0.000
23	B	23	ASP	-1	-0.885	-0.952	27.694	-0.109	-0.109	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.034	-0.023	21.576	-0.016	-0.016	0.000	0.000	0.000	0.000
25	B	25	LYS	1	0.894	0.958	24.710	0.156	0.156	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.889	0.959	27.086	0.116	0.116	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.007	-0.008	23.477	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.008	0.015	20.256	-0.021	-0.021	0.000	0.000	0.000	0.000
29	B	29	ILE	0	-0.014	0.014	23.748	-0.023	-0.023	0.000	0.000	0.000	0.000
30	B	30	GLY	0	0.096	0.037	27.053	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	31	SER	0	0.007	-0.008	28.251	0.010	0.010	0.000	0.000	0.000	0.000
32	B	32	ASP	-1	-0.898	-0.943	31.537	-0.118	-0.118	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.997	0.989	30.863	0.108	0.108	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.970	-0.984	30.811	-0.092	-0.092	0.000	0.000	0.000	0.000
35	B	35	TYR	0	-0.059	-0.028	27.755	0.007	0.007	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.876	0.940	26.662	0.183	0.183	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.063	-0.016	20.839	0.018	0.018	0.000	0.000	0.000	0.000
38	B	38	THR	0	0.032	0.032	22.276	-0.035	-0.035	0.000	0.000	0.000	0.000
39	B	39	ARG	1	0.918	0.956	16.866	0.757	0.757	0.000	0.000	0.000	0.000
40	B	40	ARG	1	0.910	0.947	21.446	0.219	0.219	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.891	-0.942	20.282	-0.467	-0.467	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.001	-0.010	21.233	-0.045	-0.045	0.000	0.000	0.000	0.000
43	B	43	TYR	0	-0.030	-0.010	22.366	0.023	0.023	0.000	0.000	0.000	0.000
44	B	44	MET	0	-0.002	0.013	24.049	0.022	0.022	0.000	0.000	0.000	0.000
45	B	45	GLY	0	-0.012	-0.007	25.837	-0.019	-0.019	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.906	-0.969	28.045	-0.231	-0.231	0.000	0.000	0.000	0.000
47	B	47	ILE	0	-0.062	-0.023	26.266	0.018	0.018	0.000	0.000	0.000	0.000
48	B	48	SER	0	-0.034	-0.052	23.488	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.787	-0.882	19.345	-0.651	-0.651	0.000	0.000	0.000	0.000
50	B	50	PRO	0	0.019	-0.010	18.590	-0.023	-0.023	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.858	-0.924	14.002	-1.201	-1.201	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.015	-0.006	14.788	-0.073	-0.073	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.015	-0.004	16.790	0.060	0.060	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.048	-0.004	12.880	0.086	0.086	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.809	-0.841	10.608	-1.442	-1.442	0.000	0.000	0.000	0.000
56	B	56	TYR	0	0.013	0.007	12.201	0.074	0.074	0.000	0.000	0.000	0.000
57	B	57	GLY	0	-0.009	-0.006	14.925	0.148	0.148	0.000	0.000	0.000	0.000
58	B	58	VAL	0	-0.034	-0.038	14.957	0.092	0.092	0.000	0.000	0.000	0.000
59	B	59	TYR	0	0.020	0.008	9.827	0.050	0.050	0.000	0.000	0.000	0.000
60	B	60	PRO	0	0.012	0.008	11.605	0.232	0.232	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.018	-0.008	12.680	0.187	0.187	0.000	0.000	0.000	0.000
62	B	62	PHE	0	0.006	0.012	11.464	0.058	0.058	0.000	0.000	0.000	0.000
63	B	63	ILE	0	0.000	0.004	7.841	0.099	0.099	0.000	0.000	0.000	0.000
64	B	64	LYS	1	0.827	0.919	11.625	-0.338	-0.338	0.000	0.000	0.000	0.000
65	B	65	GLY	0	0.037	0.024	14.755	-0.037	-0.037	0.000	0.000	0.000	0.000
66	B	66	TYR	0	-0.011	0.007	16.747	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.016	-0.034	15.518	-0.066	-0.066	0.000	0.000	0.000	0.000
68	B	68	GLN	0	0.039	0.010	17.620	-0.068	-0.068	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.005	0.003	17.330	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	70	LYS	1	0.850	0.940	15.529	0.297	0.297	0.000	0.000	0.000	0.000
71	B	71	ALA	0	0.029	0.007	18.264	-0.030	-0.030	0.000	0.000	0.000	0.000
72	B	72	ASN	0	0.027	0.016	21.682	-0.008	-0.008	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.035	0.011	17.577	-0.008	-0.008	0.000	0.000	0.000	0.000
74	B	74	GLU	-1	-0.809	-0.901	18.932	-0.355	-0.355	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.906	-0.957	21.943	-0.151	-0.151	0.000	0.000	0.000	0.000
76	B	76	ALA	0	-0.041	-0.020	23.674	0.006	0.006	0.000	0.000	0.000	0.000
77	B	77	LEU	0	-0.015	-0.025	19.641	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	78	LEU	0	-0.025	-0.020	24.291	0.002	0.002	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.877	-0.938	26.825	-0.163	-0.163	0.000	0.000	0.000	0.000
80	B	80	MET	0	-0.033	-0.008	24.807	0.001	0.001	0.000	0.000	0.000	0.000
81	B	81	SER	0	-0.039	-0.008	26.395	0.006	0.006	0.000	0.000	0.000	0.000
82	B	82	ASN	0	-0.072	-0.044	28.361	0.001	0.001	0.000	0.000	0.000	0.000
83	B	83	SER	0	-0.017	-0.015	31.315	0.017	0.017	0.000	0.000	0.000	0.000
84	B	84	GLY	0	0.007	0.015	33.571	0.012	0.012	0.000	0.000	0.000	0.000
85	B	85	GLN	0	-0.004	0.004	33.253	0.010	0.010	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.037	0.016	32.232	-0.015	-0.015	0.000	0.000	0.000	0.000
87	B	87	LEU	0	0.034	0.019	29.057	-0.020	-0.020	0.000	0.000	0.000	0.000
88	B	88	ASP	-1	-0.884	-0.945	28.652	-0.244	-0.244	0.000	0.000	0.000	0.000
89	B	89	ILE	0	-0.004	-0.007	27.502	-0.027	-0.027	0.000	0.000	0.000	0.000
90	B	90	TYR	0	0.003	-0.004	25.913	-0.036	-0.036	0.000	0.000	0.000	0.000
91	B	91	GLN	0	0.028	-0.002	23.788	-0.066	-0.066	0.000	0.000	0.000	0.000
92	B	92	ALA	0	-0.009	-0.003	22.892	-0.041	-0.041	0.000	0.000	0.000	0.000
93	B	93	VAL	0	-0.030	-0.018	21.789	-0.049	-0.049	0.000	0.000	0.000	0.000
94	B	94	GLN	0	0.047	0.016	21.037	-0.107	-0.107	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.034	-0.021	17.994	-0.068	-0.068	0.000	0.000	0.000	0.000
96	B	96	LEU	0	-0.047	-0.031	16.809	-0.090	-0.090	0.000	0.000	0.000	0.000
97	B	97	ASN	0	0.034	0.023	16.210	-0.129	-0.129	0.000	0.000	0.000	0.000
98	B	98	ALA	0	0.032	0.022	15.271	-0.134	-0.134	0.000	0.000	0.000	0.000
99	B	99	GLU	-1	-0.829	-0.907	11.732	-1.182	-1.182	0.000	0.000	0.000	0.000
100	B	100	ASN	0	0.027	0.010	11.023	-0.357	-0.357	0.000	0.000	0.000	0.000
101	B	101	MET	0	-0.032	-0.005	11.674	-0.221	-0.221	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.018	-0.001	8.956	-0.323	-0.323	0.000	0.000	0.000	0.000
103	B	103	LEU	0	-0.063	-0.032	6.478	-0.915	-0.915	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.032	-0.013	6.845	-0.807	-0.807	0.000	0.000	0.000	0.000
105	B	105	TYR	0	-0.039	0.000	7.366	-0.173	-0.173	0.000	0.000	0.000	0.000
106	B	106	TYR	0	-0.067	-0.106	3.808	-1.023	-0.415	0.004	-0.171	-0.441	0.000
107	B	107	GLU	-1	-0.959	-0.975	2.104	-17.352	-16.021	4.388	-2.685	-3.034	-0.033
108	B	108	SER	0	-0.067	-0.046	1.654	1.807	1.607	6.789	-4.232	-2.357	-0.020
109	B	109	LEU	0	0.021	0.004	3.505	-1.962	-1.511	0.026	-0.278	-0.199	-0.002
110	B	110	PRO	0	-0.055	-0.023	6.098	0.479	0.479	0.000	0.000	0.000	0.000
111	B	111	PHE	0	-0.060	-0.034	8.104	0.221	0.221	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.072	0.033	7.154	-0.305	-0.305	0.000	0.000	0.000	0.000
113	B	113	LEU	0	-0.015	-0.004	12.703	0.150	0.150	0.000	0.000	0.000	0.000
114	B	114	ASN	0	-0.118	-0.047	16.206	-0.015	-0.015	0.000	0.000	0.000	0.000
115	B	115	ARG	1	0.977	0.976	15.339	0.847	0.847	0.000	0.000	0.000	0.000
116	B	116	GLN	0	-0.001	0.026	20.802	0.007	0.007	0.000	0.000	0.000	0.000
117	B	117	SER	0	0.028	-0.019	23.649	0.014	0.014	0.000	0.000	0.000	0.000
118	B	118	ILE	0	0.026	0.033	22.321	0.012	0.012	0.000	0.000	0.000	0.000
119	B	119	LEU	0	0.071	0.031	21.389	0.006	0.006	0.000	0.000	0.000	0.000
120	B	120	ALA	0	-0.012	-0.003	24.777	0.012	0.012	0.000	0.000	0.000	0.000
121	B	121	ASN	0	-0.052	-0.023	28.046	0.022	0.022	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.041	0.031	23.986	0.012	0.012	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.002	0.000	27.680	0.012	0.012	0.000	0.000	0.000	0.000
124	B	124	LYS	1	0.880	0.935	29.951	0.208	0.208	0.000	0.000	0.000	0.000
125	B	125	ALA	0	0.034	0.016	31.284	0.013	0.013	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.074	0.030	29.278	0.011	0.011	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.845	0.949	33.047	0.229	0.229	0.000	0.000	0.000	0.000
128	B	128	ASP	-1	-0.843	-0.916	36.126	-0.165	-0.165	0.000	0.000	0.000	0.000
129	B	129	ALA	0	0.023	-0.001	37.964	-0.007	-0.007	0.000	0.000	0.000	0.000
130	B	130	HIS	0	0.068	0.041	40.344	-0.005	-0.005	0.000	0.000	0.000	0.000
131	B	131	ILE	0	-0.029	-0.009	34.131	-0.004	-0.004	0.000	0.000	0.000	0.000
132	B	132	ARG	1	0.799	0.861	33.642	0.243	0.243	0.000	0.000	0.000	0.000
133	B	133	GLU	-1	-0.948	-0.962	36.821	-0.162	-0.162	0.000	0.000	0.000	0.000
134	B	134	ALA	0	-0.019	-0.022	36.918	0.000	0.000	0.000	0.000	0.000	0.000
135	B	135	MET	0	-0.062	-0.039	30.929	-0.006	-0.006	0.000	0.000	0.000	0.000
136	B	136	ALA	0	-0.030	-0.009	34.983	-0.009	-0.009	0.000	0.000	0.000	0.000
137	B	137	HIS	0	-0.027	-0.012	37.219	0.001	0.001	0.000	0.000	0.000	0.000
138	B	138	TYR	0	-0.019	0.004	33.257	0.014	0.014	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.910	0.951	35.680	0.210	0.210	0.000	0.000	0.000	0.000
140	B	140	LEU	0	-0.037	-0.011	35.784	0.009	0.009	0.000	0.000	0.000	0.000
141	B	141	GLY	0	0.031	0.016	34.911	-0.012	-0.012	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.828	-0.937	29.934	-0.270	-0.270	0.000	0.000	0.000	0.000
143	B	143	PHE	0	0.048	0.015	28.963	-0.005	-0.005	0.000	0.000	0.000	0.000
144	B	144	ALA	0	-0.064	-0.028	33.639	0.002	0.002	0.000	0.000	0.000	0.000
145	B	145	HIS	0	-0.083	-0.036	34.117	0.010	0.010	0.000	0.000	0.000	0.000
146	B	146	TYR	0	-0.006	0.016	28.743	-0.005	-0.005	0.000	0.000	0.000	0.000
147	B	147	GLN	0	-0.050	-0.047	34.171	0.004	0.004	0.000	0.000	0.000	0.000
148	B	148	ASP	-1	-0.817	-0.896	29.752	-0.335	-0.335	0.000	0.000	0.000	0.000
149	B	149	THR	0	-0.026	-0.003	33.102	0.000	0.000	0.000	0.000	0.000	0.000
150	B	150	MET	0	0.030	0.019	29.860	-0.019	-0.019	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.015	-0.009	30.215	-0.019	-0.019	0.000	0.000	0.000	0.000
152	B	152	ASP	-1	-0.789	-0.885	30.792	-0.291	-0.291	0.000	0.000	0.000	0.000
153	B	153	MET	0	-0.082	-0.044	26.866	-0.030	-0.030	0.000	0.000	0.000	0.000
154	B	154	VAL	0	-0.025	-0.010	26.083	-0.039	-0.039	0.000	0.000	0.000	0.000
155	B	155	GLU	-1	-0.849	-0.924	26.360	-0.313	-0.313	0.000	0.000	0.000	0.000
156	B	156	ARG	1	0.898	0.927	25.246	0.376	0.376	0.000	0.000	0.000	0.000
157	B	157	THR	0	-0.012	0.007	20.876	-0.042	-0.042	0.000	0.000	0.000	0.000
158	B	158	ILE	0	-0.013	0.038	22.138	-0.043	-0.043	0.000	0.000	0.000	0.000
159	B	159	GLU	-1	-0.976	-0.974	23.636	-0.417	-0.417	0.000	0.000	0.000	0.000
160	B	160	THR	0	-0.134	-0.106	18.915	-0.030	-0.030	0.000	0.000	0.000	0.000
161	B	161	PHE	0	-0.069	-0.037	19.006	-0.051	-0.051	0.000	0.000	0.000	0.000

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