FMO DATABASE

FMODB ID: 2N71R

Calculation Name: 2XSS-A-Xray372

Preferred Name: Phosphodiesterase 5A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2XSS

Chain ID: A

ChEMBL ID: CHEMBL1827

UniProt ID: O76074

Base Structure: X-ray

Registration Date: 2023-09-20

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1402197.532075
FMO2-HF: Nuclear repulsion	1336367.308159
FMO2-HF: Total energy	-65830.223916
FMO2-MP2: Total energy	-66013.666933

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:339:GLU)

Summations of interaction energy for fragment #1(A:339:GLU)

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.
13.181	17.495	0.867	-2.235	-2.945	0.004

Interaction energy analysis for fragmet #1(A:339:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.903 / q_NPA : -0.963

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	341	GLY	0	-0.003	0.001	3.223	-10.011	-6.950	0.009	-1.648	-1.422	0.003
4	A	342	ALA	0	-0.026	-0.015	2.571	-5.232	-4.354	0.858	-0.526	-1.209	0.001
5	A	343	GLU	-1	-0.786	-0.877	4.293	34.706	35.081	0.000	-0.061	-0.314	0.000
6	A	344	THR	0	-0.004	0.019	6.407	-3.390	-3.390	0.000	0.000	0.000	0.000
7	A	345	ALA	0	0.035	0.005	7.870	-2.448	-2.448	0.000	0.000	0.000	0.000
8	A	346	SER	0	-0.056	-0.045	7.474	-2.358	-2.358	0.000	0.000	0.000	0.000
9	A	347	LEU	0	0.034	0.024	10.165	-1.844	-1.844	0.000	0.000	0.000	0.000
10	A	348	GLU	-1	-0.818	-0.908	12.533	15.960	15.960	0.000	0.000	0.000	0.000
11	A	349	VAL	0	-0.078	-0.033	13.611	-1.628	-1.628	0.000	0.000	0.000	0.000
12	A	350	ILE	0	0.015	-0.002	13.502	-1.302	-1.302	0.000	0.000	0.000	0.000
13	A	351	LEU	0	0.039	0.036	16.190	-1.242	-1.242	0.000	0.000	0.000	0.000
14	A	352	LYS	1	0.933	0.966	17.715	-16.294	-16.294	0.000	0.000	0.000	0.000
15	A	353	LYS	1	0.930	0.967	16.609	-17.541	-17.541	0.000	0.000	0.000	0.000
16	A	354	ILE	0	0.043	0.036	19.376	-0.756	-0.756	0.000	0.000	0.000	0.000
17	A	355	ALA	0	0.027	-0.006	22.302	-0.631	-0.631	0.000	0.000	0.000	0.000
18	A	356	ALA	0	0.007	-0.010	23.882	-0.546	-0.546	0.000	0.000	0.000	0.000
19	A	357	THR	0	-0.052	-0.040	24.068	-0.465	-0.465	0.000	0.000	0.000	0.000
20	A	358	ILE	0	0.010	-0.013	26.440	-0.444	-0.444	0.000	0.000	0.000	0.000
21	A	359	ILE	0	0.006	-0.004	28.018	-0.377	-0.377	0.000	0.000	0.000	0.000
22	A	360	SER	0	0.000	0.004	29.700	-0.342	-0.342	0.000	0.000	0.000	0.000
23	A	361	PHE	0	-0.045	-0.018	29.344	-0.305	-0.305	0.000	0.000	0.000	0.000
24	A	362	MET	0	-0.051	-0.023	31.996	-0.312	-0.312	0.000	0.000	0.000	0.000
25	A	363	GLN	0	-0.070	-0.023	34.101	-0.216	-0.216	0.000	0.000	0.000	0.000
26	A	364	VAL	0	0.012	0.018	32.165	-0.218	-0.218	0.000	0.000	0.000	0.000
27	A	365	GLN	0	0.006	-0.003	33.920	0.177	0.177	0.000	0.000	0.000	0.000
28	A	366	LYS	1	0.837	0.907	30.955	-8.675	-8.675	0.000	0.000	0.000	0.000
29	A	367	CYS	0	-0.010	0.029	26.639	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	368	THR	0	-0.022	-0.014	25.257	0.114	0.114	0.000	0.000	0.000	0.000
31	A	369	ILE	0	0.013	0.027	20.717	-0.264	-0.264	0.000	0.000	0.000	0.000
32	A	370	PHE	0	-0.009	-0.008	21.894	0.218	0.218	0.000	0.000	0.000	0.000
33	A	371	ILE	0	-0.012	-0.001	16.009	-0.158	-0.158	0.000	0.000	0.000	0.000
34	A	372	VAL	0	0.003	-0.014	19.409	-0.132	-0.132	0.000	0.000	0.000	0.000
35	A	373	ASP	-1	-0.899	-0.963	16.553	17.235	17.235	0.000	0.000	0.000	0.000
36	A	374	GLU	-1	-0.975	-0.998	12.880	20.435	20.435	0.000	0.000	0.000	0.000
37	A	375	ASP	-1	-0.926	-0.946	14.389	18.264	18.264	0.000	0.000	0.000	0.000
38	A	376	CYS	0	-0.130	-0.070	16.972	-0.945	-0.945	0.000	0.000	0.000	0.000
39	A	377	SER	0	0.028	-0.003	20.736	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	378	ASP	-1	-0.919	-0.937	22.688	10.543	10.543	0.000	0.000	0.000	0.000
41	A	379	SER	0	-0.069	-0.035	22.001	-0.346	-0.346	0.000	0.000	0.000	0.000
42	A	380	PHE	0	-0.035	-0.020	20.920	0.214	0.214	0.000	0.000	0.000	0.000
43	A	381	SER	0	0.044	0.038	15.600	-0.368	-0.368	0.000	0.000	0.000	0.000
44	A	382	SER	0	-0.026	-0.017	15.549	0.643	0.643	0.000	0.000	0.000	0.000
45	A	383	VAL	0	-0.014	-0.006	18.208	-0.607	-0.607	0.000	0.000	0.000	0.000
46	A	384	PHE	0	0.005	0.016	18.495	-0.119	-0.119	0.000	0.000	0.000	0.000
47	A	385	HIS	1	0.811	0.871	21.282	-11.015	-11.015	0.000	0.000	0.000	0.000
48	A	386	MET	0	-0.001	0.012	23.610	0.149	0.149	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.796	-0.856	26.432	9.044	9.044	0.000	0.000	0.000	0.000
50	A	388	CYS	0	-0.025	-0.017	30.144	0.123	0.123	0.000	0.000	0.000	0.000
51	A	389	GLH	0	-0.024	-0.052	32.992	-0.107	-0.107	0.000	0.000	0.000	0.000
52	A	390	GLU	-1	-0.907	-0.943	36.578	7.447	7.447	0.000	0.000	0.000	0.000
53	A	391	LEU	0	0.002	-0.013	36.800	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	392	GLU	-1	-0.778	-0.869	40.789	6.793	6.793	0.000	0.000	0.000	0.000
55	A	393	LYS	1	0.893	0.942	42.573	-7.201	-7.201	0.000	0.000	0.000	0.000
56	A	394	SER	0	-0.004	0.017	46.168	-0.149	-0.149	0.000	0.000	0.000	0.000
57	A	395	SER	0	0.009	-0.019	49.395	0.093	0.093	0.000	0.000	0.000	0.000
58	A	396	ASP	-1	-0.798	-0.879	52.328	5.864	5.864	0.000	0.000	0.000	0.000
59	A	397	THR	0	0.008	-0.024	54.161	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	398	LEU	0	0.019	0.014	56.051	-0.064	-0.064	0.000	0.000	0.000	0.000
61	A	399	THR	0	-0.056	-0.020	51.129	0.040	0.040	0.000	0.000	0.000	0.000
62	A	400	ARG	1	0.909	0.948	48.204	-6.071	-6.071	0.000	0.000	0.000	0.000
63	A	401	GLU	-1	-0.965	-0.981	49.169	5.684	5.684	0.000	0.000	0.000	0.000
64	A	402	HIS	0	-0.014	0.000	49.358	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.809	-0.892	45.725	6.697	6.697	0.000	0.000	0.000	0.000
66	A	404	ALA	0	-0.015	-0.022	45.541	0.171	0.171	0.000	0.000	0.000	0.000
67	A	405	ASN	0	-0.045	-0.024	45.883	0.137	0.137	0.000	0.000	0.000	0.000
68	A	406	LYS	1	0.820	0.925	42.420	-7.032	-7.032	0.000	0.000	0.000	0.000
69	A	407	ILE	0	0.040	0.015	39.819	0.064	0.064	0.000	0.000	0.000	0.000
70	A	408	ASN	0	-0.032	-0.030	37.591	-0.063	-0.063	0.000	0.000	0.000	0.000
71	A	409	TYR	0	-0.082	-0.048	38.720	0.259	0.259	0.000	0.000	0.000	0.000
72	A	410	MET	0	0.022	0.027	40.299	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	411	TYR	0	0.024	0.005	36.383	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	412	ALA	0	0.043	0.022	39.717	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	413	GLN	0	0.007	-0.006	40.871	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	414	TYR	0	0.008	-0.004	41.731	-0.120	-0.120	0.000	0.000	0.000	0.000
77	A	415	VAL	0	0.034	0.014	39.013	-0.102	-0.102	0.000	0.000	0.000	0.000
78	A	416	LYS	1	0.866	0.940	42.431	-6.481	-6.481	0.000	0.000	0.000	0.000
79	A	417	ASN	0	-0.027	-0.025	45.131	-0.131	-0.131	0.000	0.000	0.000	0.000
80	A	418	THR	0	-0.031	-0.014	44.645	-0.156	-0.156	0.000	0.000	0.000	0.000
81	A	419	MET	0	-0.082	-0.033	45.465	-0.089	-0.089	0.000	0.000	0.000	0.000
82	A	420	GLU	-1	-0.885	-0.942	42.692	6.982	6.982	0.000	0.000	0.000	0.000
83	A	421	PRO	0	0.008	0.003	37.261	0.016	0.016	0.000	0.000	0.000	0.000
84	A	422	LEU	0	-0.069	-0.014	37.066	-0.132	-0.132	0.000	0.000	0.000	0.000
85	A	423	ASN	0	-0.059	-0.046	31.451	0.303	0.303	0.000	0.000	0.000	0.000
86	A	424	ILE	0	-0.024	-0.007	33.222	-0.151	-0.151	0.000	0.000	0.000	0.000
87	A	425	PRO	0	0.005	-0.005	29.917	0.290	0.290	0.000	0.000	0.000	0.000
88	A	426	ASP	-1	-0.750	-0.907	28.903	10.125	10.125	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.037	-0.039	30.577	-0.247	-0.247	0.000	0.000	0.000	0.000
90	A	428	SER	0	-0.021	0.006	32.085	-0.192	-0.192	0.000	0.000	0.000	0.000
91	A	429	LYS	1	0.891	0.937	29.415	-9.857	-9.857	0.000	0.000	0.000	0.000
92	A	430	ASP	-1	-0.817	-0.900	34.619	7.588	7.588	0.000	0.000	0.000	0.000
93	A	431	LYS	1	0.945	0.966	36.982	-7.652	-7.652	0.000	0.000	0.000	0.000
94	A	432	ARG	1	0.852	0.925	38.626	-7.629	-7.629	0.000	0.000	0.000	0.000
95	A	433	PHE	0	-0.038	-0.020	39.082	-0.119	-0.119	0.000	0.000	0.000	0.000
96	A	434	PRO	0	0.039	0.033	39.929	0.183	0.183	0.000	0.000	0.000	0.000
97	A	446	GLN	0	0.031	0.009	26.467	-0.383	-0.383	0.000	0.000	0.000	0.000
98	A	447	CYS	0	-0.030	-0.027	23.379	0.589	0.589	0.000	0.000	0.000	0.000
99	A	448	ILE	0	-0.073	-0.018	24.380	-0.342	-0.342	0.000	0.000	0.000	0.000
100	A	449	ARG	1	0.966	0.985	25.594	-9.172	-9.172	0.000	0.000	0.000	0.000
101	A	450	SER	0	-0.001	0.019	25.721	-0.293	-0.293	0.000	0.000	0.000	0.000
102	A	451	LEU	0	-0.027	-0.022	28.429	0.077	0.077	0.000	0.000	0.000	0.000
103	A	452	LEU	0	0.014	0.022	30.699	-0.105	-0.105	0.000	0.000	0.000	0.000
104	A	453	CYS	0	-0.038	-0.005	32.528	0.023	0.023	0.000	0.000	0.000	0.000
105	A	454	THR	0	0.092	0.039	35.727	-0.095	-0.095	0.000	0.000	0.000	0.000
106	A	455	PRO	0	0.000	0.017	37.669	0.007	0.007	0.000	0.000	0.000	0.000
107	A	456	ILE	0	0.007	0.009	38.724	0.069	0.069	0.000	0.000	0.000	0.000
108	A	457	LYS	1	0.876	0.928	41.883	-7.014	-7.014	0.000	0.000	0.000	0.000
109	A	458	ASN	0	0.078	0.033	45.212	0.120	0.120	0.000	0.000	0.000	0.000
110	A	459	GLY	0	0.089	0.055	47.389	0.016	0.016	0.000	0.000	0.000	0.000
111	A	460	LYS	1	0.898	0.933	48.372	-5.539	-5.539	0.000	0.000	0.000	0.000
112	A	461	LYS	1	0.881	0.935	44.584	-6.834	-6.834	0.000	0.000	0.000	0.000
113	A	462	ASN	0	0.046	0.034	48.664	0.067	0.067	0.000	0.000	0.000	0.000
114	A	463	LYS	1	0.956	0.977	49.874	-6.018	-6.018	0.000	0.000	0.000	0.000
115	A	464	VAL	0	0.006	0.010	44.526	0.086	0.086	0.000	0.000	0.000	0.000
116	A	465	ILE	0	-0.061	-0.038	44.801	-0.140	-0.140	0.000	0.000	0.000	0.000
117	A	466	GLY	0	0.029	0.019	42.820	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	467	VAL	0	-0.028	-0.013	38.635	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	468	CYS	0	0.026	0.029	33.711	0.122	0.122	0.000	0.000	0.000	0.000
120	A	469	GLN	0	0.010	0.002	33.801	-0.149	-0.149	0.000	0.000	0.000	0.000
121	A	470	LEU	0	0.001	0.008	29.016	0.167	0.167	0.000	0.000	0.000	0.000
122	A	471	VAL	0	-0.004	-0.027	27.990	-0.159	-0.159	0.000	0.000	0.000	0.000
123	A	472	ASN	0	-0.015	-0.019	23.941	-0.022	-0.022	0.000	0.000	0.000	0.000
124	A	473	LYS	1	0.873	0.969	22.151	-11.949	-11.949	0.000	0.000	0.000	0.000
125	A	474	MET	0	0.007	-0.006	18.419	0.218	0.218	0.000	0.000	0.000	0.000
126	A	475	GLU	-1	-0.893	-0.917	15.336	15.582	15.582	0.000	0.000	0.000	0.000
127	A	476	GLU	-1	-0.811	-0.918	16.043	14.937	14.937	0.000	0.000	0.000	0.000
128	A	477	ASN	0	-0.032	-0.023	8.795	1.021	1.021	0.000	0.000	0.000	0.000
129	A	478	THR	0	-0.016	-0.007	10.581	0.936	0.936	0.000	0.000	0.000	0.000
130	A	479	GLY	0	0.041	0.035	13.026	-0.063	-0.063	0.000	0.000	0.000	0.000
131	A	480	LYS	1	0.946	0.970	14.804	-15.726	-15.726	0.000	0.000	0.000	0.000
132	A	481	VAL	0	0.010	0.006	17.958	0.021	0.021	0.000	0.000	0.000	0.000
133	A	482	LYS	1	0.770	0.865	19.069	-14.155	-14.155	0.000	0.000	0.000	0.000
134	A	483	PRO	0	0.023	0.005	23.105	-0.238	-0.238	0.000	0.000	0.000	0.000
135	A	484	PHE	0	0.014	0.026	25.638	0.393	0.393	0.000	0.000	0.000	0.000
136	A	485	ASN	0	-0.010	-0.030	26.350	-0.450	-0.450	0.000	0.000	0.000	0.000
137	A	486	ARG	1	1.014	1.004	28.985	-8.832	-8.832	0.000	0.000	0.000	0.000
138	A	487	ASN	0	-0.033	-0.011	28.065	-0.357	-0.357	0.000	0.000	0.000	0.000
139	A	488	ASP	-1	-0.758	-0.858	26.257	11.164	11.164	0.000	0.000	0.000	0.000
140	A	489	GLU	-1	-0.817	-0.916	29.307	8.630	8.630	0.000	0.000	0.000	0.000
141	A	490	GLN	0	0.015	0.005	32.317	-0.260	-0.260	0.000	0.000	0.000	0.000
142	A	491	PHE	0	-0.036	-0.017	29.268	-0.144	-0.144	0.000	0.000	0.000	0.000
143	A	492	LEU	0	0.011	-0.008	31.981	-0.100	-0.100	0.000	0.000	0.000	0.000
144	A	493	GLU	-1	-0.921	-0.970	33.431	7.823	7.823	0.000	0.000	0.000	0.000
145	A	494	ALA	0	-0.032	-0.013	34.931	-0.231	-0.231	0.000	0.000	0.000	0.000
146	A	495	PHE	0	-0.022	-0.007	31.336	-0.122	-0.122	0.000	0.000	0.000	0.000
147	A	496	VAL	0	0.023	-0.007	35.294	-0.116	-0.116	0.000	0.000	0.000	0.000
148	A	497	ILE	0	-0.005	0.005	38.083	-0.251	-0.251	0.000	0.000	0.000	0.000
149	A	498	PHE	0	-0.003	-0.005	34.530	-0.206	-0.206	0.000	0.000	0.000	0.000
150	A	499	CYS	0	-0.024	0.002	36.904	-0.041	-0.041	0.000	0.000	0.000	0.000
151	A	500	GLY	0	0.009	0.011	39.569	-0.127	-0.127	0.000	0.000	0.000	0.000
152	A	501	LEU	0	-0.003	-0.010	43.117	-0.155	-0.155	0.000	0.000	0.000	0.000
153	A	502	GLY	0	0.003	0.018	41.632	-0.109	-0.109	0.000	0.000	0.000	0.000
154	A	503	ILE	0	0.023	-0.007	40.528	-0.131	-0.131	0.000	0.000	0.000	0.000
155	A	504	GLN	0	-0.010	-0.027	43.969	-0.082	-0.082	0.000	0.000	0.000	0.000
156	A	505	ASN	0	-0.013	0.002	45.379	-0.250	-0.250	0.000	0.000	0.000	0.000
157	A	506	THR	0	-0.025	-0.003	44.678	-0.061	-0.061	0.000	0.000	0.000	0.000
158	A	507	GLN	0	-0.118	-0.046	47.105	-0.112	-0.112	0.000	0.000	0.000	0.000
159	A	508	MET	0	-0.001	0.006	49.775	-0.139	-0.139	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:339:GLU)