FMO DATABASE

FMODB ID: 763RK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1400504.361937
FMO2-HF: Nuclear repulsion	1334675.455357
FMO2-HF: Total energy	-65828.906581
FMO2-MP2: Total energy	-66012.353649

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.
18.268	22.783	0.911	-2.4	-3.026	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 : -0.913 / q_NPA : -0.966

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	0.004	0.001	3.356	-9.996	-6.766	0.008	-1.785	-1.454	0.004
4	A	342	ALA	0	-0.031	-0.017	2.552	-4.834	-4.081	0.903	-0.505	-1.150	0.000
5	A	343	GLU	-1	-0.892	-0.955	4.413	34.641	35.173	0.000	-0.110	-0.422	0.000
6	A	344	THR	0	-0.012	0.020	6.370	-2.925	-2.925	0.000	0.000	0.000	0.000
7	A	345	ALA	0	0.050	0.013	8.035	-2.313	-2.313	0.000	0.000	0.000	0.000
8	A	346	SER	0	-0.048	-0.022	7.603	-2.347	-2.347	0.000	0.000	0.000	0.000
9	A	347	LEU	0	0.026	0.020	10.129	-1.774	-1.774	0.000	0.000	0.000	0.000
10	A	348	GLU	-1	-0.881	-0.940	12.495	16.226	16.226	0.000	0.000	0.000	0.000
11	A	349	VAL	0	-0.052	-0.022	13.431	-1.541	-1.541	0.000	0.000	0.000	0.000
12	A	350	ILE	0	0.019	-0.002	13.906	-1.255	-1.255	0.000	0.000	0.000	0.000
13	A	351	LEU	0	0.024	0.025	16.069	-1.218	-1.218	0.000	0.000	0.000	0.000
14	A	352	LYS	1	0.951	0.981	18.235	-15.334	-15.334	0.000	0.000	0.000	0.000
15	A	353	LYS	1	0.910	0.952	16.858	-16.967	-16.967	0.000	0.000	0.000	0.000
16	A	354	ILE	0	0.033	0.026	19.339	-0.718	-0.718	0.000	0.000	0.000	0.000
17	A	355	ALA	0	0.033	-0.007	22.266	-0.616	-0.616	0.000	0.000	0.000	0.000
18	A	356	ALA	0	-0.007	-0.012	23.845	-0.526	-0.526	0.000	0.000	0.000	0.000
19	A	357	THR	0	-0.048	-0.023	24.195	-0.483	-0.483	0.000	0.000	0.000	0.000
20	A	358	ILE	0	-0.001	-0.011	26.403	-0.431	-0.431	0.000	0.000	0.000	0.000
21	A	359	ILE	0	0.007	-0.006	27.854	-0.371	-0.371	0.000	0.000	0.000	0.000
22	A	360	SER	0	-0.040	-0.016	29.664	-0.475	-0.475	0.000	0.000	0.000	0.000
23	A	361	PHE	0	-0.025	-0.011	28.989	-0.261	-0.261	0.000	0.000	0.000	0.000
24	A	362	MET	0	-0.059	-0.032	32.116	-0.357	-0.357	0.000	0.000	0.000	0.000
25	A	363	GLN	0	-0.034	0.004	34.067	-0.160	-0.160	0.000	0.000	0.000	0.000
26	A	364	VAL	0	0.005	0.014	32.068	-0.217	-0.217	0.000	0.000	0.000	0.000
27	A	365	GLN	0	-0.004	-0.011	33.881	0.158	0.158	0.000	0.000	0.000	0.000
28	A	366	LYS	1	0.909	0.955	31.012	-8.400	-8.400	0.000	0.000	0.000	0.000
29	A	367	CYS	0	0.005	0.034	26.677	0.041	0.041	0.000	0.000	0.000	0.000
30	A	368	THR	0	-0.006	0.000	25.370	0.106	0.106	0.000	0.000	0.000	0.000
31	A	369	ILE	0	0.012	0.023	20.767	-0.237	-0.237	0.000	0.000	0.000	0.000
32	A	370	PHE	0	-0.002	-0.004	21.880	0.196	0.196	0.000	0.000	0.000	0.000
33	A	371	ILE	0	-0.012	0.000	16.019	-0.195	-0.195	0.000	0.000	0.000	0.000
34	A	372	VAL	0	0.004	-0.011	19.409	-0.139	-0.139	0.000	0.000	0.000	0.000
35	A	373	ASP	-1	-0.881	-0.942	17.055	17.050	17.050	0.000	0.000	0.000	0.000
36	A	374	GLU	-1	-0.971	-1.003	12.857	20.478	20.478	0.000	0.000	0.000	0.000
37	A	375	ASP	-1	-0.935	-0.956	14.480	18.434	18.434	0.000	0.000	0.000	0.000
38	A	376	CYS	0	-0.136	-0.073	17.055	-0.987	-0.987	0.000	0.000	0.000	0.000
39	A	377	SER	0	0.052	-0.003	20.818	0.145	0.145	0.000	0.000	0.000	0.000
40	A	378	ASP	-1	-0.930	-0.936	22.763	10.390	10.390	0.000	0.000	0.000	0.000
41	A	379	SER	0	-0.071	-0.037	22.086	-0.341	-0.341	0.000	0.000	0.000	0.000
42	A	380	PHE	0	-0.042	-0.019	20.921	0.222	0.222	0.000	0.000	0.000	0.000
43	A	381	SER	0	0.037	0.032	15.604	-0.348	-0.348	0.000	0.000	0.000	0.000
44	A	382	SER	0	0.006	0.002	15.437	0.536	0.536	0.000	0.000	0.000	0.000
45	A	383	VAL	0	-0.014	-0.003	18.208	-0.577	-0.577	0.000	0.000	0.000	0.000
46	A	384	PHE	0	0.005	0.016	18.441	-0.140	-0.140	0.000	0.000	0.000	0.000
47	A	385	HIS	1	0.797	0.841	21.463	-10.867	-10.867	0.000	0.000	0.000	0.000
48	A	386	MET	0	0.002	0.013	23.860	0.161	0.161	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.856	-0.900	26.591	9.080	9.080	0.000	0.000	0.000	0.000
50	A	388	CYS	0	-0.008	-0.007	30.300	0.095	0.095	0.000	0.000	0.000	0.000
51	A	389	GLH	0	-0.046	-0.049	33.136	-0.117	-0.117	0.000	0.000	0.000	0.000
52	A	390	GLU	-1	-0.902	-0.938	36.726	7.393	7.393	0.000	0.000	0.000	0.000
53	A	391	LEU	0	-0.030	-0.034	37.097	-0.059	-0.059	0.000	0.000	0.000	0.000
54	A	392	GLU	-1	-0.842	-0.912	40.945	6.666	6.666	0.000	0.000	0.000	0.000
55	A	393	LYS	1	0.895	0.939	43.052	-7.064	-7.064	0.000	0.000	0.000	0.000
56	A	394	SER	0	-0.007	0.013	46.321	-0.150	-0.150	0.000	0.000	0.000	0.000
57	A	395	SER	0	0.010	-0.020	49.551	0.083	0.083	0.000	0.000	0.000	0.000
58	A	396	ASP	-1	-0.807	-0.880	52.478	5.795	5.795	0.000	0.000	0.000	0.000
59	A	397	THR	0	-0.016	-0.041	54.315	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	398	LEU	0	0.042	0.023	56.169	-0.057	-0.057	0.000	0.000	0.000	0.000
61	A	399	THR	0	-0.058	-0.026	51.309	0.047	0.047	0.000	0.000	0.000	0.000
62	A	400	ARG	1	0.929	0.972	48.519	-6.057	-6.057	0.000	0.000	0.000	0.000
63	A	401	GLU	-1	-0.968	-0.984	49.325	5.635	5.635	0.000	0.000	0.000	0.000
64	A	402	HIS	0	-0.022	-0.007	49.415	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.864	-0.929	45.852	6.649	6.649	0.000	0.000	0.000	0.000
66	A	404	ALA	0	-0.057	-0.045	45.704	0.165	0.165	0.000	0.000	0.000	0.000
67	A	405	ASN	0	-0.043	-0.029	46.038	0.162	0.162	0.000	0.000	0.000	0.000
68	A	406	LYS	1	0.975	1.010	42.388	-6.944	-6.944	0.000	0.000	0.000	0.000
69	A	407	ILE	0	0.028	0.016	40.024	0.057	0.057	0.000	0.000	0.000	0.000
70	A	408	ASN	0	0.000	-0.022	37.919	-0.071	-0.071	0.000	0.000	0.000	0.000
71	A	409	TYR	0	-0.067	-0.007	38.878	0.268	0.268	0.000	0.000	0.000	0.000
72	A	410	MET	0	0.018	0.027	40.674	-0.072	-0.072	0.000	0.000	0.000	0.000
73	A	411	TYR	0	0.031	0.009	36.647	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	412	ALA	0	0.039	0.015	39.917	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	413	GLN	0	-0.005	-0.013	41.006	-0.128	-0.128	0.000	0.000	0.000	0.000
76	A	414	TYR	0	-0.021	-0.017	41.744	-0.149	-0.149	0.000	0.000	0.000	0.000
77	A	415	VAL	0	0.034	-0.001	39.158	-0.091	-0.091	0.000	0.000	0.000	0.000
78	A	416	LYS	1	0.904	0.963	42.548	-6.437	-6.437	0.000	0.000	0.000	0.000
79	A	417	ASN	0	-0.026	-0.025	45.247	-0.109	-0.109	0.000	0.000	0.000	0.000
80	A	418	THR	0	-0.026	0.006	44.609	-0.157	-0.157	0.000	0.000	0.000	0.000
81	A	419	MET	0	-0.069	-0.030	45.586	-0.079	-0.079	0.000	0.000	0.000	0.000
82	A	420	GLU	-1	-0.895	-0.953	42.688	6.941	6.941	0.000	0.000	0.000	0.000
83	A	421	PRO	0	0.013	0.006	37.373	0.014	0.014	0.000	0.000	0.000	0.000
84	A	422	LEU	0	-0.053	-0.014	37.237	-0.137	-0.137	0.000	0.000	0.000	0.000
85	A	423	ASN	0	-0.051	-0.023	31.585	0.311	0.311	0.000	0.000	0.000	0.000
86	A	424	ILE	0	0.005	0.002	33.163	-0.149	-0.149	0.000	0.000	0.000	0.000
87	A	425	PRO	0	-0.010	-0.011	30.032	0.288	0.288	0.000	0.000	0.000	0.000
88	A	426	ASP	-1	-0.787	-0.932	29.034	9.974	9.974	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.020	-0.038	30.719	-0.221	-0.221	0.000	0.000	0.000	0.000
90	A	428	SER	0	-0.028	0.000	32.251	-0.243	-0.243	0.000	0.000	0.000	0.000
91	A	429	LYS	1	0.937	0.968	29.824	-9.522	-9.522	0.000	0.000	0.000	0.000
92	A	430	ASP	-1	-0.898	-0.949	34.768	7.552	7.552	0.000	0.000	0.000	0.000
93	A	431	LYS	1	0.951	0.966	37.124	-7.518	-7.518	0.000	0.000	0.000	0.000
94	A	432	ARG	1	0.931	0.980	39.917	-7.333	-7.333	0.000	0.000	0.000	0.000
95	A	433	PHE	0	-0.078	-0.035	39.280	-0.160	-0.160	0.000	0.000	0.000	0.000
96	A	434	PRO	0	0.054	0.041	40.088	0.177	0.177	0.000	0.000	0.000	0.000
97	A	446	GLN	0	-0.009	-0.016	26.493	-0.247	-0.247	0.000	0.000	0.000	0.000
98	A	447	CYS	0	-0.033	-0.012	23.581	0.582	0.582	0.000	0.000	0.000	0.000
99	A	448	ILE	0	-0.040	-0.005	24.690	-0.305	-0.305	0.000	0.000	0.000	0.000
100	A	449	ARG	1	0.973	0.987	25.759	-9.091	-9.091	0.000	0.000	0.000	0.000
101	A	450	SER	0	-0.005	0.027	25.877	-0.295	-0.295	0.000	0.000	0.000	0.000
102	A	451	LEU	0	-0.029	-0.020	28.565	0.081	0.081	0.000	0.000	0.000	0.000
103	A	452	LEU	0	0.018	0.026	30.875	-0.103	-0.103	0.000	0.000	0.000	0.000
104	A	453	CYS	0	-0.047	-0.008	32.640	0.026	0.026	0.000	0.000	0.000	0.000
105	A	454	THR	0	0.079	0.028	35.310	-0.122	-0.122	0.000	0.000	0.000	0.000
106	A	455	PRO	0	-0.005	0.017	37.767	0.011	0.011	0.000	0.000	0.000	0.000
107	A	456	ILE	0	-0.006	0.011	38.880	0.065	0.065	0.000	0.000	0.000	0.000
108	A	457	LYS	1	0.893	0.938	41.972	-6.932	-6.932	0.000	0.000	0.000	0.000
109	A	458	ASN	0	0.067	0.029	45.288	0.114	0.114	0.000	0.000	0.000	0.000
110	A	459	GLY	0	0.075	0.046	47.446	0.014	0.014	0.000	0.000	0.000	0.000
111	A	460	LYS	1	0.894	0.932	48.430	-5.518	-5.518	0.000	0.000	0.000	0.000
112	A	461	LYS	1	0.944	0.968	44.136	-6.875	-6.875	0.000	0.000	0.000	0.000
113	A	462	ASN	0	0.026	0.018	48.731	0.066	0.066	0.000	0.000	0.000	0.000
114	A	463	LYS	1	0.944	0.971	49.960	-5.960	-5.960	0.000	0.000	0.000	0.000
115	A	464	VAL	0	0.001	0.011	44.697	0.088	0.088	0.000	0.000	0.000	0.000
116	A	465	ILE	0	-0.064	-0.043	44.974	-0.140	-0.140	0.000	0.000	0.000	0.000
117	A	466	GLY	0	0.026	0.018	42.928	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	467	VAL	0	-0.012	-0.004	38.829	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	468	CYS	0	0.005	0.018	34.345	0.135	0.135	0.000	0.000	0.000	0.000
120	A	469	GLN	0	0.042	0.012	33.930	-0.169	-0.169	0.000	0.000	0.000	0.000
121	A	470	LEU	0	-0.002	0.008	29.028	0.166	0.166	0.000	0.000	0.000	0.000
122	A	471	VAL	0	0.001	-0.023	27.942	-0.154	-0.154	0.000	0.000	0.000	0.000
123	A	472	ASN	0	-0.006	-0.017	24.049	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	473	LYS	1	0.898	0.988	22.845	-11.647	-11.647	0.000	0.000	0.000	0.000
125	A	474	MET	0	0.003	-0.010	18.581	0.197	0.197	0.000	0.000	0.000	0.000
126	A	475	GLU	-1	-0.954	-0.964	15.014	16.331	16.331	0.000	0.000	0.000	0.000
127	A	476	GLU	-1	-0.865	-0.941	16.144	14.494	14.494	0.000	0.000	0.000	0.000
128	A	477	ASN	0	-0.023	-0.024	8.916	0.919	0.919	0.000	0.000	0.000	0.000
129	A	478	THR	0	-0.027	-0.007	10.713	0.952	0.952	0.000	0.000	0.000	0.000
130	A	479	GLY	0	0.046	0.039	13.166	-0.052	-0.052	0.000	0.000	0.000	0.000
131	A	480	LYS	1	0.942	0.963	14.933	-15.775	-15.775	0.000	0.000	0.000	0.000
132	A	481	VAL	0	-0.003	0.005	18.104	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	482	LYS	1	0.872	0.936	20.356	-13.226	-13.226	0.000	0.000	0.000	0.000
134	A	483	PRO	0	0.020	-0.008	23.220	-0.228	-0.228	0.000	0.000	0.000	0.000
135	A	484	PHE	0	0.018	0.026	25.731	0.381	0.381	0.000	0.000	0.000	0.000
136	A	485	ASN	0	-0.002	-0.018	25.526	-0.429	-0.429	0.000	0.000	0.000	0.000
137	A	486	ARG	1	1.057	1.020	29.052	-8.669	-8.669	0.000	0.000	0.000	0.000
138	A	487	ASN	0	-0.015	-0.001	27.206	-0.445	-0.445	0.000	0.000	0.000	0.000
139	A	488	ASP	-1	-0.787	-0.881	26.514	10.868	10.868	0.000	0.000	0.000	0.000
140	A	489	GLU	-1	-0.866	-0.957	29.368	8.426	8.426	0.000	0.000	0.000	0.000
141	A	490	GLN	0	-0.010	-0.007	32.464	-0.287	-0.287	0.000	0.000	0.000	0.000
142	A	491	PHE	0	-0.052	-0.026	29.247	-0.137	-0.137	0.000	0.000	0.000	0.000
143	A	492	LEU	0	0.002	-0.009	31.949	-0.091	-0.091	0.000	0.000	0.000	0.000
144	A	493	GLU	-1	-0.893	-0.961	33.497	7.790	7.790	0.000	0.000	0.000	0.000
145	A	494	ALA	0	-0.035	-0.020	35.025	-0.225	-0.225	0.000	0.000	0.000	0.000
146	A	495	PHE	0	-0.026	-0.006	31.987	-0.117	-0.117	0.000	0.000	0.000	0.000
147	A	496	VAL	0	0.020	-0.012	35.350	-0.115	-0.115	0.000	0.000	0.000	0.000
148	A	497	ILE	0	-0.011	0.000	38.154	-0.252	-0.252	0.000	0.000	0.000	0.000
149	A	498	PHE	0	-0.004	-0.006	34.707	-0.189	-0.189	0.000	0.000	0.000	0.000
150	A	499	CYS	0	-0.016	0.014	36.890	-0.045	-0.045	0.000	0.000	0.000	0.000
151	A	500	GLY	0	0.005	0.007	39.641	-0.122	-0.122	0.000	0.000	0.000	0.000
152	A	501	LEU	0	0.011	-0.003	43.181	-0.140	-0.140	0.000	0.000	0.000	0.000
153	A	502	GLY	0	0.000	0.017	41.701	-0.102	-0.102	0.000	0.000	0.000	0.000
154	A	503	ILE	0	0.012	-0.014	40.665	-0.128	-0.128	0.000	0.000	0.000	0.000
155	A	504	GLN	0	-0.026	-0.028	44.054	-0.095	-0.095	0.000	0.000	0.000	0.000
156	A	505	ASN	0	-0.007	0.007	45.592	-0.226	-0.226	0.000	0.000	0.000	0.000
157	A	506	THR	0	-0.008	0.003	44.898	-0.081	-0.081	0.000	0.000	0.000	0.000
158	A	507	GLN	0	-0.105	-0.045	47.189	-0.132	-0.132	0.000	0.000	0.000	0.000
159	A	508	MET	0	-0.015	0.003	49.867	-0.149	-0.149	0.000	0.000	0.000	0.000

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