FMO DATABASE

FMODB ID: 6YLQZ

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	OptAll
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	-1405149.396077
FMO2-HF: Nuclear repulsion	1339318.509162
FMO2-HF: Total energy	-65830.886916
FMO2-MP2: Total energy	-66014.283264

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.
11.666	16.105	0.219	-2.025	-2.633	0.001

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 : -0.885 / q_NPA : -0.950

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	-0.001	0.006	3.466	-9.128	-7.032	0.001	-1.057	-1.040	0.004
4	A	342	ALA	0	0.017	0.001	2.908	-6.268	-5.372	0.139	-0.266	-0.769	0.001
5	A	343	GLU	-1	-0.794	-0.868	3.196	34.677	36.124	0.079	-0.702	-0.824	-0.004
6	A	344	THR	0	0.017	0.019	5.983	-3.605	-3.605	0.000	0.000	0.000	0.000
7	A	345	ALA	0	0.023	-0.001	8.032	-2.389	-2.389	0.000	0.000	0.000	0.000
8	A	346	SER	0	-0.041	-0.040	7.379	-2.302	-2.302	0.000	0.000	0.000	0.000
9	A	347	LEU	0	0.019	0.019	9.910	-1.909	-1.909	0.000	0.000	0.000	0.000
10	A	348	GLU	-1	-0.786	-0.887	12.184	15.658	15.658	0.000	0.000	0.000	0.000
11	A	349	VAL	0	-0.092	-0.041	13.147	-1.622	-1.622	0.000	0.000	0.000	0.000
12	A	350	ILE	0	-0.004	-0.003	12.776	-1.290	-1.290	0.000	0.000	0.000	0.000
13	A	351	LEU	0	0.035	0.009	15.753	-1.175	-1.175	0.000	0.000	0.000	0.000
14	A	352	LYS	1	0.898	0.957	17.158	-16.663	-16.663	0.000	0.000	0.000	0.000
15	A	353	LYS	1	0.942	0.973	16.156	-17.278	-17.278	0.000	0.000	0.000	0.000
16	A	354	ILE	0	0.034	0.032	19.062	-0.697	-0.697	0.000	0.000	0.000	0.000
17	A	355	ALA	0	0.010	-0.005	22.065	-0.615	-0.615	0.000	0.000	0.000	0.000
18	A	356	ALA	0	0.033	0.004	23.711	-0.502	-0.502	0.000	0.000	0.000	0.000
19	A	357	THR	0	-0.041	-0.026	23.862	-0.487	-0.487	0.000	0.000	0.000	0.000
20	A	358	ILE	0	0.023	-0.010	26.139	-0.430	-0.430	0.000	0.000	0.000	0.000
21	A	359	ILE	0	-0.009	-0.006	27.708	-0.365	-0.365	0.000	0.000	0.000	0.000
22	A	360	SER	0	-0.010	-0.005	29.387	-0.323	-0.323	0.000	0.000	0.000	0.000
23	A	361	PHE	0	-0.044	-0.004	29.353	-0.261	-0.261	0.000	0.000	0.000	0.000
24	A	362	MET	0	-0.031	-0.020	31.524	-0.290	-0.290	0.000	0.000	0.000	0.000
25	A	363	GLN	0	-0.053	-0.029	33.732	-0.184	-0.184	0.000	0.000	0.000	0.000
26	A	364	VAL	0	-0.011	0.014	31.550	-0.222	-0.222	0.000	0.000	0.000	0.000
27	A	365	GLN	0	0.014	-0.003	33.081	0.227	0.227	0.000	0.000	0.000	0.000
28	A	366	LYS	1	0.819	0.890	30.801	-8.732	-8.732	0.000	0.000	0.000	0.000
29	A	367	CYS	0	-0.018	0.016	26.305	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	368	THR	0	-0.003	-0.009	24.744	0.067	0.067	0.000	0.000	0.000	0.000
31	A	369	ILE	0	-0.010	0.014	20.183	-0.273	-0.273	0.000	0.000	0.000	0.000
32	A	370	PHE	0	-0.014	-0.006	21.032	0.358	0.358	0.000	0.000	0.000	0.000
33	A	371	ILE	0	-0.025	-0.011	15.527	-0.127	-0.127	0.000	0.000	0.000	0.000
34	A	372	VAL	0	-0.004	-0.007	18.766	0.056	0.056	0.000	0.000	0.000	0.000
35	A	373	ASP	-1	-0.887	-0.958	16.544	17.146	17.146	0.000	0.000	0.000	0.000
36	A	374	GLU	-1	-0.962	-0.990	11.937	20.314	20.314	0.000	0.000	0.000	0.000
37	A	375	ASP	-1	-0.929	-0.948	14.296	18.286	18.286	0.000	0.000	0.000	0.000
38	A	376	CYS	0	-0.116	-0.073	16.724	-0.802	-0.802	0.000	0.000	0.000	0.000
39	A	377	SER	0	0.014	0.004	20.070	-0.199	-0.199	0.000	0.000	0.000	0.000
40	A	378	ASP	-1	-0.925	-0.939	21.641	10.642	10.642	0.000	0.000	0.000	0.000
41	A	379	SER	0	-0.070	-0.049	21.777	-0.344	-0.344	0.000	0.000	0.000	0.000
42	A	380	PHE	0	-0.030	-0.026	19.966	0.081	0.081	0.000	0.000	0.000	0.000
43	A	381	SER	0	0.053	0.055	14.707	-0.363	-0.363	0.000	0.000	0.000	0.000
44	A	382	SER	0	-0.031	-0.035	15.228	0.582	0.582	0.000	0.000	0.000	0.000
45	A	383	VAL	0	-0.015	-0.020	17.643	-0.616	-0.616	0.000	0.000	0.000	0.000
46	A	384	PHE	0	0.022	0.040	18.784	-0.408	-0.408	0.000	0.000	0.000	0.000
47	A	385	HIS	1	0.814	0.870	20.899	-11.115	-11.115	0.000	0.000	0.000	0.000
48	A	386	MET	0	-0.013	0.006	23.398	0.142	0.142	0.000	0.000	0.000	0.000
49	A	387	GLU	-1	-0.773	-0.855	26.338	9.103	9.103	0.000	0.000	0.000	0.000
50	A	388	CYS	0	-0.033	-0.015	30.112	0.140	0.140	0.000	0.000	0.000	0.000
51	A	389	GLH	0	-0.020	-0.028	32.885	-0.101	-0.101	0.000	0.000	0.000	0.000
52	A	390	GLU	-1	-0.865	-0.921	36.557	7.363	7.363	0.000	0.000	0.000	0.000
53	A	391	LEU	0	-0.004	-0.017	37.342	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	392	GLU	-1	-0.776	-0.857	41.314	6.776	6.776	0.000	0.000	0.000	0.000
55	A	393	LYS	1	0.871	0.926	42.341	-7.258	-7.258	0.000	0.000	0.000	0.000
56	A	394	SER	0	0.033	0.035	46.238	-0.145	-0.145	0.000	0.000	0.000	0.000
57	A	395	SER	0	-0.032	-0.047	49.512	0.030	0.030	0.000	0.000	0.000	0.000
58	A	396	ASP	-1	-0.770	-0.851	52.589	5.872	5.872	0.000	0.000	0.000	0.000
59	A	397	THR	0	0.002	-0.003	54.809	0.006	0.006	0.000	0.000	0.000	0.000
60	A	398	LEU	0	0.023	0.005	56.418	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	399	THR	0	-0.069	-0.032	51.054	0.066	0.066	0.000	0.000	0.000	0.000
62	A	400	ARG	1	0.890	0.931	48.395	-6.102	-6.102	0.000	0.000	0.000	0.000
63	A	401	GLU	-1	-0.939	-0.965	49.777	5.657	5.657	0.000	0.000	0.000	0.000
64	A	402	HIS	0	-0.022	0.004	49.705	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	403	ASP	-1	-0.798	-0.892	46.150	6.682	6.682	0.000	0.000	0.000	0.000
66	A	404	ALA	0	-0.031	-0.020	46.035	0.180	0.180	0.000	0.000	0.000	0.000
67	A	405	ASN	0	-0.037	-0.013	46.669	0.112	0.112	0.000	0.000	0.000	0.000
68	A	406	LYS	1	0.776	0.881	42.903	-6.993	-6.993	0.000	0.000	0.000	0.000
69	A	407	ILE	0	0.045	0.023	40.282	0.096	0.096	0.000	0.000	0.000	0.000
70	A	408	ASN	0	-0.014	-0.022	37.600	-0.071	-0.071	0.000	0.000	0.000	0.000
71	A	409	TYR	0	-0.056	-0.046	38.696	0.273	0.273	0.000	0.000	0.000	0.000
72	A	410	MET	0	-0.016	0.007	40.511	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	411	TYR	0	0.009	-0.006	37.053	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	412	ALA	0	0.057	0.022	39.693	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	413	GLN	0	0.001	-0.002	40.976	-0.147	-0.147	0.000	0.000	0.000	0.000
76	A	414	TYR	0	0.030	0.011	42.157	-0.120	-0.120	0.000	0.000	0.000	0.000
77	A	415	VAL	0	0.027	0.018	39.359	-0.132	-0.132	0.000	0.000	0.000	0.000
78	A	416	LYS	1	0.847	0.914	42.780	-6.485	-6.485	0.000	0.000	0.000	0.000
79	A	417	ASN	0	-0.029	-0.018	45.416	-0.171	-0.171	0.000	0.000	0.000	0.000
80	A	418	THR	0	-0.034	-0.024	44.861	-0.136	-0.136	0.000	0.000	0.000	0.000
81	A	419	MET	0	-0.073	-0.026	46.197	-0.091	-0.091	0.000	0.000	0.000	0.000
82	A	420	GLU	-1	-0.832	-0.913	43.219	6.932	6.932	0.000	0.000	0.000	0.000
83	A	421	PRO	0	-0.013	-0.017	37.741	0.004	0.004	0.000	0.000	0.000	0.000
84	A	422	LEU	0	-0.059	-0.006	37.339	-0.148	-0.148	0.000	0.000	0.000	0.000
85	A	423	ASN	0	-0.055	-0.042	31.524	0.291	0.291	0.000	0.000	0.000	0.000
86	A	424	ILE	0	-0.021	-0.007	33.165	-0.232	-0.232	0.000	0.000	0.000	0.000
87	A	425	PRO	0	0.018	-0.002	30.098	0.274	0.274	0.000	0.000	0.000	0.000
88	A	426	ASP	-1	-0.731	-0.887	29.035	10.277	10.277	0.000	0.000	0.000	0.000
89	A	427	VAL	0	-0.003	-0.006	30.925	-0.290	-0.290	0.000	0.000	0.000	0.000
90	A	428	SER	0	-0.060	-0.019	32.124	-0.213	-0.213	0.000	0.000	0.000	0.000
91	A	429	LYS	1	0.858	0.923	30.111	-9.855	-9.855	0.000	0.000	0.000	0.000
92	A	430	ASP	-1	-0.765	-0.861	35.255	7.602	7.602	0.000	0.000	0.000	0.000
93	A	431	LYS	1	0.874	0.917	37.776	-7.812	-7.812	0.000	0.000	0.000	0.000
94	A	432	ARG	1	0.853	0.919	38.708	-7.731	-7.731	0.000	0.000	0.000	0.000
95	A	433	PHE	0	-0.020	-0.010	39.378	-0.104	-0.104	0.000	0.000	0.000	0.000
96	A	434	PRO	0	0.031	0.026	40.337	0.173	0.173	0.000	0.000	0.000	0.000
97	A	446	GLN	0	0.020	0.011	27.291	-0.425	-0.425	0.000	0.000	0.000	0.000
98	A	447	CYS	0	-0.038	-0.026	24.011	0.553	0.553	0.000	0.000	0.000	0.000
99	A	448	ILE	0	-0.046	-0.009	24.628	-0.437	-0.437	0.000	0.000	0.000	0.000
100	A	449	ARG	1	0.973	0.974	26.255	-9.260	-9.260	0.000	0.000	0.000	0.000
101	A	450	SER	0	0.007	0.024	26.102	-0.385	-0.385	0.000	0.000	0.000	0.000
102	A	451	LEU	0	-0.023	-0.023	28.855	0.060	0.060	0.000	0.000	0.000	0.000
103	A	452	LEU	0	-0.001	0.013	30.973	-0.074	-0.074	0.000	0.000	0.000	0.000
104	A	453	CYS	0	-0.054	-0.005	32.887	0.025	0.025	0.000	0.000	0.000	0.000
105	A	454	THR	0	0.093	0.042	36.073	-0.098	-0.098	0.000	0.000	0.000	0.000
106	A	455	PRO	0	0.006	0.020	38.134	0.032	0.032	0.000	0.000	0.000	0.000
107	A	456	ILE	0	-0.013	0.002	39.080	0.029	0.029	0.000	0.000	0.000	0.000
108	A	457	LYS	1	0.847	0.915	42.105	-7.024	-7.024	0.000	0.000	0.000	0.000
109	A	458	ASN	0	0.041	0.006	45.244	0.124	0.124	0.000	0.000	0.000	0.000
110	A	459	GLY	0	0.070	0.036	47.396	0.038	0.038	0.000	0.000	0.000	0.000
111	A	460	LYS	1	0.896	0.945	48.398	-5.534	-5.534	0.000	0.000	0.000	0.000
112	A	461	LYS	1	0.906	0.944	44.885	-6.816	-6.816	0.000	0.000	0.000	0.000
113	A	462	ASN	0	0.037	0.033	48.795	0.073	0.073	0.000	0.000	0.000	0.000
114	A	463	LYS	1	0.967	0.984	50.190	-6.032	-6.032	0.000	0.000	0.000	0.000
115	A	464	VAL	0	0.015	0.023	44.953	0.099	0.099	0.000	0.000	0.000	0.000
116	A	465	ILE	0	-0.076	-0.050	45.109	-0.167	-0.167	0.000	0.000	0.000	0.000
117	A	466	GLY	0	0.041	0.025	43.112	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	467	VAL	0	-0.033	-0.014	38.789	-0.045	-0.045	0.000	0.000	0.000	0.000
119	A	468	CYS	0	0.025	0.030	33.939	0.118	0.118	0.000	0.000	0.000	0.000
120	A	469	GLN	0	0.029	-0.003	34.397	-0.166	-0.166	0.000	0.000	0.000	0.000
121	A	470	LEU	0	-0.010	0.003	29.194	0.161	0.161	0.000	0.000	0.000	0.000
122	A	471	VAL	0	0.005	-0.025	28.617	-0.207	-0.207	0.000	0.000	0.000	0.000
123	A	472	ASN	0	-0.008	-0.009	24.330	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	473	LYS	1	0.858	0.946	22.593	-11.970	-11.970	0.000	0.000	0.000	0.000
125	A	474	MET	0	-0.005	-0.015	18.852	0.187	0.187	0.000	0.000	0.000	0.000
126	A	475	GLU	-1	-0.877	-0.915	15.625	15.345	15.345	0.000	0.000	0.000	0.000
127	A	476	GLU	-1	-0.800	-0.895	16.383	14.812	14.812	0.000	0.000	0.000	0.000
128	A	477	ASN	0	-0.027	-0.008	9.113	0.570	0.570	0.000	0.000	0.000	0.000
129	A	478	THR	0	-0.028	-0.015	10.947	1.409	1.409	0.000	0.000	0.000	0.000
130	A	479	GLY	0	0.047	0.037	13.386	0.283	0.283	0.000	0.000	0.000	0.000
131	A	480	LYS	1	0.945	0.962	14.903	-15.730	-15.730	0.000	0.000	0.000	0.000
132	A	481	VAL	0	-0.007	-0.002	18.298	0.000	0.000	0.000	0.000	0.000	0.000
133	A	482	LYS	1	0.782	0.869	19.762	-14.040	-14.040	0.000	0.000	0.000	0.000
134	A	483	PRO	0	0.027	0.000	23.573	-0.254	-0.254	0.000	0.000	0.000	0.000
135	A	484	PHE	0	0.009	0.030	26.024	0.385	0.385	0.000	0.000	0.000	0.000
136	A	485	ASN	0	0.000	-0.015	26.892	-0.460	-0.460	0.000	0.000	0.000	0.000
137	A	486	ARG	1	0.998	0.985	29.151	-8.820	-8.820	0.000	0.000	0.000	0.000
138	A	487	ASN	0	-0.037	-0.023	28.371	-0.377	-0.377	0.000	0.000	0.000	0.000
139	A	488	ASP	-1	-0.762	-0.856	26.450	11.307	11.307	0.000	0.000	0.000	0.000
140	A	489	GLU	-1	-0.840	-0.916	29.503	8.683	8.683	0.000	0.000	0.000	0.000
141	A	490	GLN	0	0.041	0.021	32.637	-0.227	-0.227	0.000	0.000	0.000	0.000
142	A	491	PHE	0	-0.016	0.005	29.441	-0.146	-0.146	0.000	0.000	0.000	0.000
143	A	492	LEU	0	0.011	-0.006	32.260	-0.140	-0.140	0.000	0.000	0.000	0.000
144	A	493	GLU	-1	-0.920	-0.974	33.663	7.817	7.817	0.000	0.000	0.000	0.000
145	A	494	ALA	0	-0.021	-0.011	35.061	-0.222	-0.222	0.000	0.000	0.000	0.000
146	A	495	PHE	0	-0.018	-0.011	31.235	-0.140	-0.140	0.000	0.000	0.000	0.000
147	A	496	VAL	0	0.017	-0.008	35.468	-0.132	-0.132	0.000	0.000	0.000	0.000
148	A	497	ILE	0	-0.007	0.010	38.351	-0.250	-0.250	0.000	0.000	0.000	0.000
149	A	498	PHE	0	0.007	0.000	34.651	-0.211	-0.211	0.000	0.000	0.000	0.000
150	A	499	CYS	0	-0.027	0.002	36.919	-0.060	-0.060	0.000	0.000	0.000	0.000
151	A	500	GLY	0	0.030	0.010	39.642	-0.132	-0.132	0.000	0.000	0.000	0.000
152	A	501	LEU	0	-0.008	-0.008	43.178	-0.177	-0.177	0.000	0.000	0.000	0.000
153	A	502	GLY	0	0.028	0.032	41.892	-0.131	-0.131	0.000	0.000	0.000	0.000
154	A	503	ILE	0	-0.007	0.002	40.971	-0.112	-0.112	0.000	0.000	0.000	0.000
155	A	504	GLN	0	0.020	-0.012	44.386	-0.082	-0.082	0.000	0.000	0.000	0.000
156	A	505	ASN	0	-0.044	-0.030	46.072	-0.226	-0.226	0.000	0.000	0.000	0.000
157	A	506	THR	0	-0.038	-0.023	44.474	-0.064	-0.064	0.000	0.000	0.000	0.000
158	A	507	GLN	0	-0.069	-0.035	46.929	-0.101	-0.101	0.000	0.000	0.000	0.000
159	A	508	MET	0	-0.040	0.002	49.891	-0.145	-0.145	0.000	0.000	0.000	0.000

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