FMO DATABASE

FMODB ID: NN8JQ

Calculation Name: 1PGV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PGV

Chain ID: A

ChEMBL ID:

UniProt ID: O01479

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1757130.969615
FMO2-HF: Nuclear repulsion	1689097.362124
FMO2-HF: Total energy	-68033.607491
FMO2-MP2: Total energy	-68228.871928

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:222:THR)

Summations of interaction energy for fragment #1(A:222:THR)

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.
-16.311	-16.197	16.951	-7.711	-9.352	-0.051

Interaction energy analysis for fragmet #1(A:222:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.043

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	224	VAL	0	0.020	-0.008	3.346	-1.259	0.717	0.102	-0.660	-1.418	-0.001
4	A	225	GLU	-1	-0.803	-0.889	3.964	-0.510	-0.351	0.002	-0.003	-0.158	0.000
5	A	226	SER	0	0.009	0.015	5.864	0.162	0.162	0.000	0.000	0.000	0.000
6	A	227	CYS	0	-0.061	-0.041	3.186	-0.231	-0.176	1.146	-0.327	-0.874	-0.003
7	A	228	ILE	0	0.000	0.006	5.765	0.143	0.143	0.000	0.000	0.000	0.000
8	A	229	ASN	0	-0.063	-0.045	8.515	0.165	0.165	0.000	0.000	0.000	0.000
9	A	230	ARG	1	0.913	0.927	7.287	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	231	LEU	0	-0.054	-0.031	7.683	0.031	0.031	0.000	0.000	0.000	0.000
11	A	232	ARG	1	0.905	0.940	11.062	0.598	0.598	0.000	0.000	0.000	0.000
12	A	233	GLU	-1	-1.007	-0.983	13.606	-0.112	-0.112	0.000	0.000	0.000	0.000
13	A	234	ASP	-1	-0.811	-0.881	14.535	-0.205	-0.205	0.000	0.000	0.000	0.000
14	A	235	ASP	-1	-0.800	-0.873	11.354	0.045	0.045	0.000	0.000	0.000	0.000
15	A	236	THR	0	0.017	-0.013	13.177	-0.038	-0.038	0.000	0.000	0.000	0.000
16	A	237	ASP	-1	-0.951	-0.972	12.474	0.130	0.130	0.000	0.000	0.000	0.000
17	A	238	LEU	0	-0.097	-0.039	5.571	0.064	0.064	0.000	0.000	0.000	0.000
18	A	239	LYS	1	0.893	0.952	9.532	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	240	GLU	-1	-0.864	-0.920	6.580	-0.540	-0.540	0.000	0.000	0.000	0.000
20	A	241	VAL	0	0.035	0.027	3.313	-0.297	0.034	0.020	-0.073	-0.278	0.000
21	A	242	ASN	0	0.015	-0.003	2.968	-1.312	-0.156	0.049	-0.511	-0.694	-0.001
22	A	243	ILE	0	0.046	0.016	1.700	-15.835	-20.384	13.965	-5.395	-4.021	-0.047
23	A	244	ASN	0	0.078	0.069	3.979	1.604	1.776	0.001	-0.045	-0.127	0.000
24	A	245	ASN	0	-0.019	-0.010	6.164	0.125	0.125	0.000	0.000	0.000	0.000
25	A	246	MET	0	-0.068	-0.001	2.940	-1.114	-0.378	1.667	-0.690	-1.712	0.001
26	A	247	LYS	1	0.878	0.931	7.119	0.680	0.680	0.000	0.000	0.000	0.000
27	A	248	ARG	1	0.926	0.974	4.211	1.155	1.233	-0.001	-0.007	-0.070	0.000
28	A	249	VAL	0	-0.012	0.005	6.187	0.144	0.144	0.000	0.000	0.000	0.000
29	A	250	SER	0	0.069	0.035	9.494	0.051	0.051	0.000	0.000	0.000	0.000
30	A	251	LYS	1	1.000	0.976	11.855	0.846	0.846	0.000	0.000	0.000	0.000
31	A	252	GLU	-1	-0.875	-0.914	13.972	-0.600	-0.600	0.000	0.000	0.000	0.000
32	A	253	ARG	1	0.860	0.918	9.276	0.727	0.727	0.000	0.000	0.000	0.000
33	A	254	ILE	0	-0.001	0.005	8.947	-0.113	-0.113	0.000	0.000	0.000	0.000
34	A	255	ARG	1	0.877	0.922	10.338	0.577	0.577	0.000	0.000	0.000	0.000
35	A	256	SER	0	-0.003	-0.001	10.856	0.040	0.040	0.000	0.000	0.000	0.000
36	A	257	LEU	0	-0.011	-0.005	5.304	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	258	ILE	0	-0.043	-0.031	9.325	0.038	0.038	0.000	0.000	0.000	0.000
38	A	259	GLU	-1	-0.865	-0.919	11.602	-0.492	-0.492	0.000	0.000	0.000	0.000
39	A	260	ALA	0	0.008	0.007	10.401	0.068	0.068	0.000	0.000	0.000	0.000
40	A	261	ALA	0	-0.026	-0.016	9.983	0.077	0.077	0.000	0.000	0.000	0.000
41	A	262	CYS	0	-0.083	-0.035	11.746	0.042	0.042	0.000	0.000	0.000	0.000
42	A	263	ASN	0	-0.041	-0.020	14.872	0.042	0.042	0.000	0.000	0.000	0.000
43	A	264	SER	0	0.028	0.031	12.792	0.046	0.046	0.000	0.000	0.000	0.000
44	A	265	LYS	1	0.761	0.852	14.772	0.159	0.159	0.000	0.000	0.000	0.000
45	A	266	HIS	0	-0.001	0.002	14.064	0.053	0.053	0.000	0.000	0.000	0.000
46	A	267	ILE	0	-0.002	0.013	8.404	0.006	0.006	0.000	0.000	0.000	0.000
47	A	268	GLU	-1	-0.870	-0.925	11.511	-0.152	-0.152	0.000	0.000	0.000	0.000
48	A	269	LYS	1	0.791	0.886	9.833	0.341	0.341	0.000	0.000	0.000	0.000
49	A	270	PHE	0	0.061	0.033	6.413	-0.192	-0.192	0.000	0.000	0.000	0.000
50	A	271	SER	0	-0.048	-0.058	6.803	0.484	0.484	0.000	0.000	0.000	0.000
51	A	272	LEU	0	0.030	0.005	6.608	-0.963	-0.963	0.000	0.000	0.000	0.000
52	A	273	ALA	0	0.041	0.041	8.825	0.332	0.332	0.000	0.000	0.000	0.000
53	A	274	ASN	0	0.018	-0.002	9.604	-0.153	-0.153	0.000	0.000	0.000	0.000
54	A	275	THR	0	-0.011	-0.019	8.099	0.027	0.027	0.000	0.000	0.000	0.000
55	A	276	ALA	0	-0.086	-0.061	10.855	0.067	0.067	0.000	0.000	0.000	0.000
56	A	277	ILE	0	-0.005	0.017	12.010	0.081	0.081	0.000	0.000	0.000	0.000
57	A	278	SER	0	0.031	-0.010	14.912	0.078	0.078	0.000	0.000	0.000	0.000
58	A	279	ASP	-1	-0.730	-0.871	17.848	-0.480	-0.480	0.000	0.000	0.000	0.000
59	A	280	SER	0	-0.104	-0.075	19.510	0.009	0.009	0.000	0.000	0.000	0.000
60	A	281	GLU	-1	-0.831	-0.877	14.391	-0.619	-0.619	0.000	0.000	0.000	0.000
61	A	282	ALA	0	0.052	0.026	15.165	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	283	ARG	1	0.968	0.984	16.185	0.432	0.432	0.000	0.000	0.000	0.000
63	A	284	GLY	0	0.021	0.020	16.623	0.036	0.036	0.000	0.000	0.000	0.000
64	A	285	LEU	0	-0.005	-0.015	12.209	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	286	ILE	0	-0.021	-0.009	16.128	0.025	0.025	0.000	0.000	0.000	0.000
66	A	287	GLU	-1	-0.856	-0.909	18.608	-0.411	-0.411	0.000	0.000	0.000	0.000
67	A	288	LEU	0	0.039	0.016	12.261	0.011	0.011	0.000	0.000	0.000	0.000
68	A	289	ILE	0	-0.088	-0.049	16.627	0.018	0.018	0.000	0.000	0.000	0.000
69	A	290	GLU	-1	-0.952	-0.974	18.301	-0.283	-0.283	0.000	0.000	0.000	0.000
70	A	291	THR	0	-0.023	-0.013	19.001	0.046	0.046	0.000	0.000	0.000	0.000
71	A	292	SER	0	0.010	0.007	15.847	0.037	0.037	0.000	0.000	0.000	0.000
72	A	293	PRO	0	0.008	0.010	18.317	0.010	0.010	0.000	0.000	0.000	0.000
73	A	294	SER	0	-0.028	-0.039	15.079	0.034	0.034	0.000	0.000	0.000	0.000
74	A	295	LEU	0	-0.031	-0.007	12.137	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	296	ARG	1	0.931	0.970	14.690	0.296	0.296	0.000	0.000	0.000	0.000
76	A	297	VAL	0	-0.023	-0.014	12.854	0.035	0.035	0.000	0.000	0.000	0.000
77	A	298	LEU	0	0.047	0.030	11.896	-0.128	-0.128	0.000	0.000	0.000	0.000
78	A	299	ASN	0	-0.032	-0.033	10.849	0.119	0.119	0.000	0.000	0.000	0.000
79	A	300	VAL	0	0.053	0.021	11.313	-0.244	-0.244	0.000	0.000	0.000	0.000
80	A	301	GLU	-1	-0.860	-0.916	13.429	-0.510	-0.510	0.000	0.000	0.000	0.000
81	A	302	SER	0	-0.031	-0.021	13.997	-0.091	-0.091	0.000	0.000	0.000	0.000
82	A	303	ASN	0	-0.073	-0.025	12.528	-0.064	-0.064	0.000	0.000	0.000	0.000
83	A	304	PHE	0	-0.051	-0.042	16.532	0.093	0.093	0.000	0.000	0.000	0.000
84	A	305	LEU	0	-0.007	0.005	16.137	0.022	0.022	0.000	0.000	0.000	0.000
85	A	306	THR	0	-0.022	-0.033	20.269	0.031	0.031	0.000	0.000	0.000	0.000
86	A	307	PRO	0	0.018	0.013	23.481	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	308	GLU	-1	-0.844	-0.935	25.735	-0.275	-0.275	0.000	0.000	0.000	0.000
88	A	309	LEU	0	-0.056	-0.008	19.357	0.001	0.001	0.000	0.000	0.000	0.000
89	A	310	LEU	0	0.000	-0.011	19.378	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	311	ALA	0	0.014	0.012	22.311	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	312	ARG	1	0.960	0.978	23.902	0.334	0.334	0.000	0.000	0.000	0.000
92	A	313	LEU	0	-0.026	-0.003	17.708	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	314	LEU	0	0.049	0.030	21.266	0.001	0.001	0.000	0.000	0.000	0.000
94	A	315	ARG	1	0.827	0.927	23.055	0.234	0.234	0.000	0.000	0.000	0.000
95	A	316	SER	0	-0.003	-0.022	21.415	0.003	0.003	0.000	0.000	0.000	0.000
96	A	317	THR	0	-0.051	-0.051	20.276	0.010	0.010	0.000	0.000	0.000	0.000
97	A	318	LEU	0	-0.044	-0.027	22.604	0.010	0.010	0.000	0.000	0.000	0.000
98	A	319	VAL	0	-0.016	0.013	24.110	0.020	0.020	0.000	0.000	0.000	0.000
99	A	320	THR	0	0.009	0.000	20.970	0.020	0.020	0.000	0.000	0.000	0.000
100	A	321	GLN	0	-0.036	0.006	23.319	0.022	0.022	0.000	0.000	0.000	0.000
101	A	322	SER	0	-0.004	0.020	19.167	0.011	0.011	0.000	0.000	0.000	0.000
102	A	323	ILE	0	-0.027	-0.017	16.766	0.004	0.004	0.000	0.000	0.000	0.000
103	A	324	VAL	0	-0.047	-0.035	18.606	0.038	0.038	0.000	0.000	0.000	0.000
104	A	325	GLU	-1	-0.882	-0.913	15.611	-0.366	-0.366	0.000	0.000	0.000	0.000
105	A	326	PHE	0	0.067	0.038	16.704	-0.075	-0.075	0.000	0.000	0.000	0.000
106	A	327	LYS	1	0.794	0.906	15.218	0.468	0.468	0.000	0.000	0.000	0.000
107	A	328	ALA	0	0.022	0.004	15.911	-0.095	-0.095	0.000	0.000	0.000	0.000
108	A	329	ASP	-1	-0.735	-0.852	17.950	-0.307	-0.307	0.000	0.000	0.000	0.000
109	A	330	ASN	0	-0.051	-0.040	18.403	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	331	GLN	0	0.017	0.014	17.034	-0.046	-0.046	0.000	0.000	0.000	0.000
111	A	332	ARG	1	0.917	0.955	20.509	0.366	0.366	0.000	0.000	0.000	0.000
112	A	333	GLN	0	-0.012	-0.013	22.624	0.022	0.022	0.000	0.000	0.000	0.000
113	A	334	SER	0	0.015	0.005	24.808	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	335	VAL	0	-0.013	-0.012	25.813	0.001	0.001	0.000	0.000	0.000	0.000
115	A	336	LEU	0	0.047	0.025	25.120	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	337	GLY	0	0.057	0.028	28.880	0.002	0.002	0.000	0.000	0.000	0.000
117	A	338	ASN	0	0.014	-0.016	32.289	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	339	GLN	0	0.019	0.003	34.028	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	340	VAL	0	0.057	0.039	27.501	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	341	GLU	-1	-0.767	-0.883	29.882	-0.197	-0.197	0.000	0.000	0.000	0.000
121	A	342	MET	0	-0.019	-0.014	31.177	0.002	0.002	0.000	0.000	0.000	0.000
122	A	343	ASP	-1	-0.828	-0.890	29.465	-0.232	-0.232	0.000	0.000	0.000	0.000
123	A	344	MET	0	-0.007	-0.011	24.371	0.000	0.000	0.000	0.000	0.000	0.000
124	A	345	MET	0	-0.030	0.005	28.676	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	346	MET	0	-0.020	-0.002	31.165	0.009	0.009	0.000	0.000	0.000	0.000
126	A	347	ALA	0	-0.015	-0.002	27.548	0.004	0.004	0.000	0.000	0.000	0.000
127	A	348	ILE	0	-0.004	-0.020	25.786	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	349	GLU	-1	-0.816	-0.871	28.249	-0.133	-0.133	0.000	0.000	0.000	0.000
129	A	350	GLU	-1	-0.908	-0.946	30.699	-0.173	-0.173	0.000	0.000	0.000	0.000
130	A	351	ASN	0	-0.005	0.010	23.868	0.012	0.012	0.000	0.000	0.000	0.000
131	A	352	GLU	-1	-0.827	-0.913	28.164	-0.128	-0.128	0.000	0.000	0.000	0.000
132	A	353	SER	0	-0.091	-0.064	23.474	0.022	0.022	0.000	0.000	0.000	0.000
133	A	354	LEU	0	-0.063	-0.020	21.204	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	355	LEU	0	-0.026	-0.014	22.481	0.028	0.028	0.000	0.000	0.000	0.000
135	A	356	ARG	1	0.830	0.893	18.114	0.267	0.267	0.000	0.000	0.000	0.000
136	A	357	VAL	0	0.072	0.031	20.780	-0.037	-0.037	0.000	0.000	0.000	0.000
137	A	358	GLY	0	-0.086	-0.045	19.610	0.024	0.024	0.000	0.000	0.000	0.000
138	A	359	ILE	0	0.065	0.011	20.485	-0.041	-0.041	0.000	0.000	0.000	0.000
139	A	360	SER	0	-0.031	0.003	23.306	0.032	0.032	0.000	0.000	0.000	0.000
140	A	361	PHE	0	0.032	0.015	26.225	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	362	ALA	0	-0.031	-0.027	29.567	0.012	0.012	0.000	0.000	0.000	0.000
142	A	363	SER	0	-0.033	-0.019	32.741	0.017	0.017	0.000	0.000	0.000	0.000
143	A	364	MET	0	0.006	-0.013	34.173	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	365	GLU	-1	-0.854	-0.915	36.026	-0.126	-0.126	0.000	0.000	0.000	0.000
145	A	366	ALA	0	0.062	0.018	31.790	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	367	ARG	1	0.860	0.927	31.048	0.146	0.146	0.000	0.000	0.000	0.000
147	A	368	HIS	0	0.010	0.018	32.179	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	369	ARG	1	0.833	0.860	34.323	0.136	0.136	0.000	0.000	0.000	0.000
149	A	370	VAL	0	-0.021	-0.002	27.591	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	371	SER	0	0.000	-0.007	29.951	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	372	GLU	-1	-0.936	-0.968	30.973	-0.100	-0.100	0.000	0.000	0.000	0.000
152	A	373	ALA	0	0.000	0.012	30.503	0.005	0.005	0.000	0.000	0.000	0.000
153	A	374	LEU	0	-0.032	-0.015	25.258	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	375	GLU	-1	-0.923	-0.958	28.564	-0.110	-0.110	0.000	0.000	0.000	0.000
155	A	376	ARG	1	0.806	0.899	30.549	0.159	0.159	0.000	0.000	0.000	0.000
156	A	377	ASN	0	-0.032	-0.035	27.134	0.021	0.021	0.000	0.000	0.000	0.000
157	A	378	TYR	0	0.006	-0.005	26.323	0.007	0.007	0.000	0.000	0.000	0.000
158	A	379	GLU	-1	-0.764	-0.852	28.836	-0.061	-0.061	0.000	0.000	0.000	0.000
159	A	380	ARG	1	0.835	0.933	27.870	0.155	0.155	0.000	0.000	0.000	0.000
160	A	381	VAL	0	-0.043	-0.027	26.055	0.008	0.008	0.000	0.000	0.000	0.000
161	A	382	ARG	1	0.776	0.849	29.346	0.070	0.070	0.000	0.000	0.000	0.000
162	A	383	LEU	0	0.045	0.013	31.298	0.010	0.010	0.000	0.000	0.000	0.000
163	A	384	ARG	1	0.945	0.980	26.745	0.101	0.101	0.000	0.000	0.000	0.000
164	A	385	ARG	1	0.887	0.949	25.017	0.082	0.082	0.000	0.000	0.000	0.000
165	A	386	LEU	0	-0.039	-0.014	31.428	0.008	0.008	0.000	0.000	0.000	0.000
166	A	387	GLY	0	0.008	0.025	34.533	0.005	0.005	0.000	0.000	0.000	0.000
167	A	388	LYS	1	0.910	0.955	36.008	0.068	0.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:222:THR)