FMO DATABASE

FMODB ID: 8974Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1756789.181423
FMO2-HF: Nuclear repulsion	1688756.405186
FMO2-HF: Total energy	-68032.776237
FMO2-MP2: Total energy	-68228.142832

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.
-15.259	-17.051	19.268	-8.367	-9.11	-0.052

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 : -0.020 / q_NPA : -0.042

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	0.022	-0.012	3.139	-1.291	0.700	0.306	-0.627	-1.671	-0.002
4	A	225	GLU	-1	-0.835	-0.918	3.713	-0.501	-0.367	0.007	0.032	-0.173	0.000
5	A	226	SER	0	-0.010	-0.008	5.697	0.207	0.207	0.000	0.000	0.000	0.000
6	A	227	CYS	0	-0.052	-0.030	3.074	-0.259	-0.116	1.016	-0.292	-0.867	-0.002
7	A	228	ILE	0	0.001	0.008	5.817	0.167	0.167	0.000	0.000	0.000	0.000
8	A	229	ASN	0	-0.035	-0.026	8.471	0.131	0.131	0.000	0.000	0.000	0.000
9	A	230	ARG	1	0.920	0.955	7.065	-0.216	-0.216	0.000	0.000	0.000	0.000
10	A	231	LEU	0	-0.049	-0.027	7.677	0.036	0.036	0.000	0.000	0.000	0.000
11	A	232	ARG	1	0.967	0.984	11.124	0.593	0.593	0.000	0.000	0.000	0.000
12	A	233	GLU	-1	-1.011	-0.987	13.674	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	234	ASP	-1	-0.829	-0.910	14.509	-0.162	-0.162	0.000	0.000	0.000	0.000
14	A	235	ASP	-1	-0.803	-0.891	11.324	0.150	0.150	0.000	0.000	0.000	0.000
15	A	236	THR	0	0.015	-0.015	13.233	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	237	ASP	-1	-0.950	-0.980	12.342	0.216	0.216	0.000	0.000	0.000	0.000
17	A	238	LEU	0	-0.096	-0.040	5.750	0.108	0.108	0.000	0.000	0.000	0.000
18	A	239	LYS	1	0.909	0.971	9.665	-0.158	-0.158	0.000	0.000	0.000	0.000
19	A	240	GLU	-1	-0.960	-0.974	6.387	-0.316	-0.316	0.000	0.000	0.000	0.000
20	A	241	VAL	0	0.028	0.024	3.248	-0.170	0.159	0.022	-0.070	-0.281	0.000
21	A	242	ASN	0	0.027	0.006	3.218	-1.760	-0.562	0.023	-0.533	-0.688	-0.001
22	A	243	ILE	0	0.025	0.010	1.650	-15.390	-21.961	16.434	-6.233	-3.630	-0.048
23	A	244	ASN	0	0.081	0.080	3.925	1.561	1.744	0.000	-0.051	-0.132	0.000
24	A	245	ASN	0	-0.014	-0.013	6.211	0.060	0.060	0.000	0.000	0.000	0.000
25	A	246	MET	0	-0.065	-0.003	2.997	-1.076	-0.347	1.461	-0.588	-1.602	0.001
26	A	247	LYS	1	0.907	0.950	7.100	0.743	0.743	0.000	0.000	0.000	0.000
27	A	248	ARG	1	0.917	0.969	4.625	1.820	1.892	-0.001	-0.005	-0.066	0.000
28	A	249	VAL	0	-0.003	0.009	6.215	0.130	0.130	0.000	0.000	0.000	0.000
29	A	250	SER	0	0.054	0.035	9.461	0.063	0.063	0.000	0.000	0.000	0.000
30	A	251	LYS	1	1.019	0.981	11.607	0.895	0.895	0.000	0.000	0.000	0.000
31	A	252	GLU	-1	-0.918	-0.948	13.779	-0.555	-0.555	0.000	0.000	0.000	0.000
32	A	253	ARG	1	0.905	0.957	9.014	0.870	0.870	0.000	0.000	0.000	0.000
33	A	254	ILE	0	0.022	0.029	8.885	-0.102	-0.102	0.000	0.000	0.000	0.000
34	A	255	ARG	1	0.929	0.956	10.178	0.601	0.601	0.000	0.000	0.000	0.000
35	A	256	SER	0	-0.013	-0.015	10.629	0.054	0.054	0.000	0.000	0.000	0.000
36	A	257	LEU	0	-0.024	-0.010	5.393	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	258	ILE	0	-0.034	-0.020	9.263	0.054	0.054	0.000	0.000	0.000	0.000
38	A	259	GLU	-1	-0.926	-0.966	11.545	-0.467	-0.467	0.000	0.000	0.000	0.000
39	A	260	ALA	0	-0.008	0.001	10.395	0.068	0.068	0.000	0.000	0.000	0.000
40	A	261	ALA	0	-0.022	-0.015	9.991	0.084	0.084	0.000	0.000	0.000	0.000
41	A	262	CYS	0	-0.040	-0.003	11.668	0.073	0.073	0.000	0.000	0.000	0.000
42	A	263	ASN	0	-0.044	-0.022	14.770	0.019	0.019	0.000	0.000	0.000	0.000
43	A	264	SER	0	0.034	0.039	12.742	0.047	0.047	0.000	0.000	0.000	0.000
44	A	265	LYS	1	0.818	0.896	14.688	0.103	0.103	0.000	0.000	0.000	0.000
45	A	266	HIS	0	-0.022	-0.002	14.023	0.053	0.053	0.000	0.000	0.000	0.000
46	A	267	ILE	0	-0.005	0.008	8.729	0.020	0.020	0.000	0.000	0.000	0.000
47	A	268	GLU	-1	-0.914	-0.961	11.607	-0.081	-0.081	0.000	0.000	0.000	0.000
48	A	269	LYS	1	0.909	0.954	9.847	0.157	0.157	0.000	0.000	0.000	0.000
49	A	270	PHE	0	0.062	0.034	6.307	-0.148	-0.148	0.000	0.000	0.000	0.000
50	A	271	SER	0	-0.052	-0.069	6.807	0.453	0.453	0.000	0.000	0.000	0.000
51	A	272	LEU	0	0.026	-0.001	6.538	-0.981	-0.981	0.000	0.000	0.000	0.000
52	A	273	ALA	0	0.042	0.036	8.764	0.308	0.308	0.000	0.000	0.000	0.000
53	A	274	ASN	0	0.006	-0.012	9.601	-0.171	-0.171	0.000	0.000	0.000	0.000
54	A	275	THR	0	-0.025	-0.022	8.133	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	276	ALA	0	-0.086	-0.057	10.844	0.062	0.062	0.000	0.000	0.000	0.000
56	A	277	ILE	0	-0.011	0.012	12.178	0.078	0.078	0.000	0.000	0.000	0.000
57	A	278	SER	0	0.052	0.007	14.898	0.087	0.087	0.000	0.000	0.000	0.000
58	A	279	ASP	-1	-0.710	-0.864	17.908	-0.499	-0.499	0.000	0.000	0.000	0.000
59	A	280	SER	0	-0.114	-0.075	19.244	0.010	0.010	0.000	0.000	0.000	0.000
60	A	281	GLU	-1	-0.886	-0.931	14.410	-0.692	-0.692	0.000	0.000	0.000	0.000
61	A	282	ALA	0	0.065	0.033	15.221	-0.059	-0.059	0.000	0.000	0.000	0.000
62	A	283	ARG	1	0.954	0.980	16.237	0.456	0.456	0.000	0.000	0.000	0.000
63	A	284	GLY	0	0.029	0.022	16.597	0.039	0.039	0.000	0.000	0.000	0.000
64	A	285	LEU	0	-0.010	-0.015	12.373	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	286	ILE	0	-0.023	-0.006	16.172	0.029	0.029	0.000	0.000	0.000	0.000
66	A	287	GLU	-1	-0.896	-0.937	18.539	-0.396	-0.396	0.000	0.000	0.000	0.000
67	A	288	LEU	0	0.026	0.000	12.381	0.011	0.011	0.000	0.000	0.000	0.000
68	A	289	ILE	0	-0.094	-0.051	16.637	0.024	0.024	0.000	0.000	0.000	0.000
69	A	290	GLU	-1	-0.952	-0.980	18.369	-0.277	-0.277	0.000	0.000	0.000	0.000
70	A	291	THR	0	-0.009	0.005	18.984	0.046	0.046	0.000	0.000	0.000	0.000
71	A	292	SER	0	-0.006	-0.001	15.929	0.039	0.039	0.000	0.000	0.000	0.000
72	A	293	PRO	0	0.009	0.012	18.348	0.010	0.010	0.000	0.000	0.000	0.000
73	A	294	SER	0	-0.017	-0.031	15.165	0.032	0.032	0.000	0.000	0.000	0.000
74	A	295	LEU	0	-0.012	0.010	12.171	0.000	0.000	0.000	0.000	0.000	0.000
75	A	296	ARG	1	0.958	0.984	14.845	0.221	0.221	0.000	0.000	0.000	0.000
76	A	297	VAL	0	-0.025	-0.011	12.530	0.032	0.032	0.000	0.000	0.000	0.000
77	A	298	LEU	0	0.049	0.033	12.044	-0.113	-0.113	0.000	0.000	0.000	0.000
78	A	299	ASN	0	-0.013	-0.007	10.658	0.129	0.129	0.000	0.000	0.000	0.000
79	A	300	VAL	0	0.056	0.022	11.257	-0.246	-0.246	0.000	0.000	0.000	0.000
80	A	301	GLU	-1	-0.874	-0.936	13.377	-0.511	-0.511	0.000	0.000	0.000	0.000
81	A	302	SER	0	-0.034	-0.018	13.979	-0.097	-0.097	0.000	0.000	0.000	0.000
82	A	303	ASN	0	-0.068	-0.019	12.580	-0.088	-0.088	0.000	0.000	0.000	0.000
83	A	304	PHE	0	-0.062	-0.049	16.503	0.098	0.098	0.000	0.000	0.000	0.000
84	A	305	LEU	0	-0.005	0.004	16.341	0.021	0.021	0.000	0.000	0.000	0.000
85	A	306	THR	0	-0.027	-0.039	20.321	0.032	0.032	0.000	0.000	0.000	0.000
86	A	307	PRO	0	0.008	0.008	23.625	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	308	GLU	-1	-0.831	-0.930	25.794	-0.282	-0.282	0.000	0.000	0.000	0.000
88	A	309	LEU	0	-0.060	-0.006	19.499	0.003	0.003	0.000	0.000	0.000	0.000
89	A	310	LEU	0	0.007	-0.009	19.419	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	311	ALA	0	0.021	0.017	22.465	0.001	0.001	0.000	0.000	0.000	0.000
91	A	312	ARG	1	0.943	0.973	23.885	0.346	0.346	0.000	0.000	0.000	0.000
92	A	313	LEU	0	-0.018	0.002	17.765	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	314	LEU	0	0.046	0.038	21.388	0.005	0.005	0.000	0.000	0.000	0.000
94	A	315	ARG	1	0.850	0.950	23.210	0.233	0.233	0.000	0.000	0.000	0.000
95	A	316	SER	0	-0.010	-0.034	21.597	0.003	0.003	0.000	0.000	0.000	0.000
96	A	317	THR	0	-0.060	-0.071	20.498	0.013	0.013	0.000	0.000	0.000	0.000
97	A	318	LEU	0	-0.026	-0.022	22.729	0.012	0.012	0.000	0.000	0.000	0.000
98	A	319	VAL	0	-0.018	0.015	24.101	0.020	0.020	0.000	0.000	0.000	0.000
99	A	320	THR	0	0.005	-0.009	20.969	0.020	0.020	0.000	0.000	0.000	0.000
100	A	321	GLN	0	-0.021	0.011	23.494	0.023	0.023	0.000	0.000	0.000	0.000
101	A	322	SER	0	0.003	0.008	18.360	0.017	0.017	0.000	0.000	0.000	0.000
102	A	323	ILE	0	-0.051	-0.023	16.934	0.007	0.007	0.000	0.000	0.000	0.000
103	A	324	VAL	0	-0.047	-0.032	18.718	0.035	0.035	0.000	0.000	0.000	0.000
104	A	325	GLU	-1	-0.914	-0.929	15.268	-0.324	-0.324	0.000	0.000	0.000	0.000
105	A	326	PHE	0	0.078	0.044	16.666	-0.070	-0.070	0.000	0.000	0.000	0.000
106	A	327	LYS	1	0.834	0.965	15.105	0.470	0.470	0.000	0.000	0.000	0.000
107	A	328	ALA	0	0.035	0.004	15.868	-0.095	-0.095	0.000	0.000	0.000	0.000
108	A	329	ASP	-1	-0.831	-0.911	17.912	-0.294	-0.294	0.000	0.000	0.000	0.000
109	A	330	ASN	0	-0.057	-0.044	18.391	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	331	GLN	0	-0.005	-0.001	16.919	-0.054	-0.054	0.000	0.000	0.000	0.000
111	A	332	ARG	1	0.914	0.959	20.487	0.395	0.395	0.000	0.000	0.000	0.000
112	A	333	GLN	0	-0.013	-0.016	22.608	0.018	0.018	0.000	0.000	0.000	0.000
113	A	334	SER	0	0.024	0.010	24.777	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	335	VAL	0	-0.011	-0.009	25.794	0.002	0.002	0.000	0.000	0.000	0.000
115	A	336	LEU	0	0.047	0.021	25.094	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	337	GLY	0	0.055	0.028	28.838	0.002	0.002	0.000	0.000	0.000	0.000
117	A	338	ASN	0	0.019	-0.014	32.240	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	339	GLN	0	0.019	0.002	34.064	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	340	VAL	0	0.063	0.043	27.488	0.001	0.001	0.000	0.000	0.000	0.000
120	A	341	GLU	-1	-0.751	-0.875	29.921	-0.194	-0.194	0.000	0.000	0.000	0.000
121	A	342	MET	0	-0.018	-0.017	31.125	0.003	0.003	0.000	0.000	0.000	0.000
122	A	343	ASP	-1	-0.874	-0.904	29.673	-0.232	-0.232	0.000	0.000	0.000	0.000
123	A	344	MET	0	0.024	-0.006	24.392	0.003	0.003	0.000	0.000	0.000	0.000
124	A	345	MET	0	-0.041	0.003	28.801	0.000	0.000	0.000	0.000	0.000	0.000
125	A	346	MET	0	-0.017	-0.001	31.160	0.009	0.009	0.000	0.000	0.000	0.000
126	A	347	ALA	0	-0.013	0.001	27.683	0.004	0.004	0.000	0.000	0.000	0.000
127	A	348	ILE	0	-0.006	-0.020	25.866	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	349	GLU	-1	-0.816	-0.877	28.406	-0.123	-0.123	0.000	0.000	0.000	0.000
129	A	350	GLU	-1	-0.936	-0.957	30.912	-0.153	-0.153	0.000	0.000	0.000	0.000
130	A	351	ASN	0	-0.003	0.016	24.065	0.014	0.014	0.000	0.000	0.000	0.000
131	A	352	GLU	-1	-0.912	-0.965	28.332	-0.114	-0.114	0.000	0.000	0.000	0.000
132	A	353	SER	0	-0.099	-0.069	23.717	0.023	0.023	0.000	0.000	0.000	0.000
133	A	354	LEU	0	-0.069	-0.021	21.676	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	355	LEU	0	-0.037	-0.016	22.475	0.026	0.026	0.000	0.000	0.000	0.000
135	A	356	ARG	1	0.852	0.904	18.552	0.218	0.218	0.000	0.000	0.000	0.000
136	A	357	VAL	0	0.084	0.041	20.742	-0.036	-0.036	0.000	0.000	0.000	0.000
137	A	358	GLY	0	-0.077	-0.061	19.580	0.022	0.022	0.000	0.000	0.000	0.000
138	A	359	ILE	0	0.072	0.012	20.458	-0.044	-0.044	0.000	0.000	0.000	0.000
139	A	360	SER	0	-0.019	0.009	23.279	0.031	0.031	0.000	0.000	0.000	0.000
140	A	361	PHE	0	0.021	0.006	26.209	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	362	ALA	0	-0.040	-0.039	29.543	0.012	0.012	0.000	0.000	0.000	0.000
142	A	363	SER	0	-0.032	-0.015	32.721	0.017	0.017	0.000	0.000	0.000	0.000
143	A	364	MET	0	0.011	-0.011	34.145	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	365	GLU	-1	-0.856	-0.923	36.000	-0.121	-0.121	0.000	0.000	0.000	0.000
145	A	366	ALA	0	0.066	0.018	31.695	0.000	0.000	0.000	0.000	0.000	0.000
146	A	367	ARG	1	0.884	0.945	31.183	0.136	0.136	0.000	0.000	0.000	0.000
147	A	368	HIS	0	0.034	0.022	32.154	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	369	ARG	1	0.847	0.891	34.174	0.129	0.129	0.000	0.000	0.000	0.000
149	A	370	VAL	0	-0.016	0.002	27.557	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	371	SER	0	-0.089	-0.050	29.917	0.001	0.001	0.000	0.000	0.000	0.000
151	A	372	GLU	-1	-0.897	-0.955	30.948	-0.090	-0.090	0.000	0.000	0.000	0.000
152	A	373	ALA	0	-0.007	0.010	30.397	0.005	0.005	0.000	0.000	0.000	0.000
153	A	374	LEU	0	-0.044	-0.023	25.300	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	375	GLU	-1	-0.910	-0.953	28.529	-0.089	-0.089	0.000	0.000	0.000	0.000
155	A	376	ARG	1	0.818	0.914	30.612	0.144	0.144	0.000	0.000	0.000	0.000
156	A	377	ASN	0	-0.034	-0.040	27.125	0.020	0.020	0.000	0.000	0.000	0.000
157	A	378	TYR	0	-0.013	-0.015	26.383	0.010	0.010	0.000	0.000	0.000	0.000
158	A	379	GLU	-1	-0.807	-0.904	28.808	-0.044	-0.044	0.000	0.000	0.000	0.000
159	A	380	ARG	1	0.920	0.984	28.383	0.130	0.130	0.000	0.000	0.000	0.000
160	A	381	VAL	0	-0.047	-0.030	26.132	0.009	0.009	0.000	0.000	0.000	0.000
161	A	382	ARG	1	0.825	0.896	29.309	0.053	0.053	0.000	0.000	0.000	0.000
162	A	383	LEU	0	0.050	0.017	31.275	0.010	0.010	0.000	0.000	0.000	0.000
163	A	384	ARG	1	0.945	0.981	26.770	0.074	0.074	0.000	0.000	0.000	0.000
164	A	385	ARG	1	0.881	0.945	24.915	0.052	0.052	0.000	0.000	0.000	0.000
165	A	386	LEU	0	-0.041	-0.013	31.401	0.009	0.009	0.000	0.000	0.000	0.000
166	A	387	GLY	0	0.014	0.029	34.537	0.004	0.004	0.000	0.000	0.000	0.000
167	A	388	LYS	1	0.909	0.953	36.033	0.050	0.050	0.000	0.000	0.000	0.000

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