FMO DATABASE

FMODB ID: GYNY1

Calculation Name: 3ASD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ASD

Chain ID: A

ChEMBL ID:

UniProt ID: Q2W8Q0

Base Structure: X-ray

Registration Date: 2023-09-26

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1171121.320805
FMO2-HF: Nuclear repulsion	1119148.475415
FMO2-HF: Total energy	-51972.84539
FMO2-MP2: Total energy	-52128.471273

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:78:PHE)

Summations of interaction energy for fragment #1(A:78:PHE)

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.
-26.871	-20.389	20.141	-8.519	-18.108	0.05

Interaction energy analysis for fragmet #1(A:78:PHE)

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 : 0.011

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	80	VAL	0	0.038	0.007	2.793	-0.378	2.686	0.300	-1.183	-2.182	0.003
4	A	81	ASP	-1	-0.865	-0.920	4.200	-1.606	-1.316	0.001	-0.017	-0.274	0.000
5	A	82	VAL	0	-0.044	-0.040	6.559	0.487	0.487	0.000	0.000	0.000	0.000
6	A	83	ALA	0	-0.041	-0.011	2.599	-0.714	-0.167	1.672	-0.667	-1.552	0.000
7	A	84	LEU	0	0.032	0.023	4.398	-0.019	0.144	-0.001	-0.020	-0.142	0.000
8	A	85	HIS	0	0.013	-0.006	7.345	0.377	0.377	0.000	0.000	0.000	0.000
9	A	86	LEU	0	-0.015	-0.002	5.651	0.171	0.171	0.000	0.000	0.000	0.000
10	A	87	GLY	0	0.040	0.017	7.084	0.154	0.154	0.000	0.000	0.000	0.000
11	A	88	ILE	0	-0.002	-0.005	7.968	0.154	0.154	0.000	0.000	0.000	0.000
12	A	89	ALA	0	-0.008	0.003	11.187	0.080	0.080	0.000	0.000	0.000	0.000
13	A	90	TYR	0	0.008	0.007	8.016	0.115	0.115	0.000	0.000	0.000	0.000
14	A	91	VAL	0	0.022	0.011	11.413	0.043	0.043	0.000	0.000	0.000	0.000
15	A	92	LYS	1	0.794	0.906	13.730	0.137	0.137	0.000	0.000	0.000	0.000
16	A	93	THR	0	-0.049	-0.036	15.176	0.018	0.018	0.000	0.000	0.000	0.000
17	A	94	GLY	0	0.020	0.019	16.627	0.027	0.027	0.000	0.000	0.000	0.000
18	A	95	ALA	0	-0.026	0.002	13.345	0.020	0.020	0.000	0.000	0.000	0.000
19	A	96	VAL	0	0.016	-0.022	12.426	0.008	0.008	0.000	0.000	0.000	0.000
20	A	97	ASP	-1	-0.886	-0.923	12.279	0.357	0.357	0.000	0.000	0.000	0.000
21	A	98	ARG	1	0.994	0.999	8.082	-0.658	-0.658	0.000	0.000	0.000	0.000
22	A	99	GLY	0	-0.020	-0.017	7.575	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	100	THR	0	-0.016	-0.029	7.855	-0.234	-0.234	0.000	0.000	0.000	0.000
24	A	101	GLU	-1	-0.902	-0.941	6.347	1.010	1.010	0.000	0.000	0.000	0.000
25	A	102	LEU	0	-0.067	-0.038	2.522	-0.953	-0.062	0.402	-0.269	-1.025	-0.003
26	A	103	LEU	0	0.005	0.002	4.172	-1.298	-1.071	-0.001	-0.051	-0.176	0.000
27	A	104	GLU	-1	-0.838	-0.898	6.594	-0.172	-0.172	0.000	0.000	0.000	0.000
28	A	105	ARG	1	0.873	0.937	2.224	-21.703	-22.192	17.396	-5.360	-11.547	0.062
29	A	106	SER	0	-0.084	-0.037	2.876	-4.510	-2.810	0.371	-0.929	-1.142	-0.012
30	A	107	LEU	0	-0.051	-0.033	4.032	0.372	0.461	0.001	-0.023	-0.068	0.000
31	A	108	ALA	0	-0.006	-0.020	6.621	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	109	ASP	-1	-0.892	-0.931	8.382	-0.423	-0.423	0.000	0.000	0.000	0.000
33	A	110	ALA	0	-0.042	-0.014	7.065	0.018	0.018	0.000	0.000	0.000	0.000
34	A	111	PRO	0	-0.038	-0.005	6.952	0.004	0.004	0.000	0.000	0.000	0.000
35	A	112	ASP	-1	-0.766	-0.880	9.776	-0.686	-0.686	0.000	0.000	0.000	0.000
36	A	113	ASN	0	0.016	-0.003	6.533	0.538	0.538	0.000	0.000	0.000	0.000
37	A	114	VAL	0	0.077	0.045	10.308	0.144	0.144	0.000	0.000	0.000	0.000
38	A	115	LYS	1	0.804	0.902	11.817	0.935	0.935	0.000	0.000	0.000	0.000
39	A	116	VAL	0	0.030	0.012	12.021	0.131	0.131	0.000	0.000	0.000	0.000
40	A	117	ALA	0	0.051	0.021	10.783	0.116	0.116	0.000	0.000	0.000	0.000
41	A	118	THR	0	-0.049	-0.041	12.893	0.142	0.142	0.000	0.000	0.000	0.000
42	A	119	VAL	0	-0.022	-0.013	16.222	0.075	0.075	0.000	0.000	0.000	0.000
43	A	120	LEU	0	0.008	0.030	13.273	0.068	0.068	0.000	0.000	0.000	0.000
44	A	121	GLY	0	0.052	0.025	16.238	0.060	0.060	0.000	0.000	0.000	0.000
45	A	122	LEU	0	-0.022	-0.025	17.512	0.057	0.057	0.000	0.000	0.000	0.000
46	A	123	THR	0	-0.018	-0.022	20.363	0.045	0.045	0.000	0.000	0.000	0.000
47	A	124	TYR	0	-0.026	-0.022	15.587	0.054	0.054	0.000	0.000	0.000	0.000
48	A	125	VAL	0	-0.004	0.005	21.051	0.030	0.030	0.000	0.000	0.000	0.000
49	A	126	GLN	0	-0.056	-0.014	23.721	0.013	0.013	0.000	0.000	0.000	0.000
50	A	127	VAL	0	-0.053	-0.030	23.155	0.017	0.017	0.000	0.000	0.000	0.000
51	A	128	GLN	0	0.012	0.013	25.682	0.016	0.016	0.000	0.000	0.000	0.000
52	A	129	LYS	1	0.927	0.985	20.891	0.189	0.189	0.000	0.000	0.000	0.000
53	A	130	TYR	0	0.068	-0.007	20.668	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	131	ASP	-1	-0.842	-0.921	20.071	-0.144	-0.144	0.000	0.000	0.000	0.000
55	A	132	LEU	0	-0.021	-0.009	15.001	0.002	0.002	0.000	0.000	0.000	0.000
56	A	133	ALA	0	-0.023	-0.012	16.080	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	134	VAL	0	0.010	0.015	17.506	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	135	PRO	0	0.021	0.003	13.463	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	136	LEU	0	-0.002	0.009	11.682	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	137	LEU	0	-0.023	-0.021	13.946	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	138	ILE	0	0.002	0.005	14.890	0.002	0.002	0.000	0.000	0.000	0.000
62	A	139	LYS	1	0.822	0.877	10.299	0.099	0.099	0.000	0.000	0.000	0.000
63	A	140	VAL	0	-0.015	-0.011	12.558	-0.056	-0.056	0.000	0.000	0.000	0.000
64	A	141	ALA	0	-0.042	-0.027	14.121	0.007	0.007	0.000	0.000	0.000	0.000
65	A	142	GLU	-1	-0.896	-0.921	13.294	-0.123	-0.123	0.000	0.000	0.000	0.000
66	A	143	ALA	0	0.047	0.024	11.542	0.021	0.021	0.000	0.000	0.000	0.000
67	A	144	ASN	0	-0.052	-0.033	13.615	0.035	0.035	0.000	0.000	0.000	0.000
68	A	145	PRO	0	0.016	0.019	17.177	0.033	0.033	0.000	0.000	0.000	0.000
69	A	146	ILE	0	0.053	0.017	19.758	0.035	0.035	0.000	0.000	0.000	0.000
70	A	147	ASN	0	0.022	0.019	19.426	0.042	0.042	0.000	0.000	0.000	0.000
71	A	148	PHE	0	0.042	0.012	22.046	0.005	0.005	0.000	0.000	0.000	0.000
72	A	149	ASN	0	0.024	0.001	23.709	0.025	0.025	0.000	0.000	0.000	0.000
73	A	150	VAL	0	0.029	0.027	18.146	0.013	0.013	0.000	0.000	0.000	0.000
74	A	151	ARG	1	0.920	0.975	20.272	0.221	0.221	0.000	0.000	0.000	0.000
75	A	152	PHE	0	0.017	0.014	23.293	0.019	0.019	0.000	0.000	0.000	0.000
76	A	153	ARG	1	0.880	0.930	22.852	0.226	0.226	0.000	0.000	0.000	0.000
77	A	154	LEU	0	0.041	0.033	19.507	0.007	0.007	0.000	0.000	0.000	0.000
78	A	155	GLY	0	0.042	0.022	22.508	0.018	0.018	0.000	0.000	0.000	0.000
79	A	156	VAL	0	-0.036	-0.022	26.034	0.012	0.012	0.000	0.000	0.000	0.000
80	A	157	ALA	0	0.010	0.002	22.696	0.010	0.010	0.000	0.000	0.000	0.000
81	A	158	LEU	0	-0.013	-0.008	21.751	0.011	0.011	0.000	0.000	0.000	0.000
82	A	159	ASP	-1	-0.800	-0.869	24.999	-0.064	-0.064	0.000	0.000	0.000	0.000
83	A	160	ASN	0	-0.035	-0.028	26.759	0.000	0.000	0.000	0.000	0.000	0.000
84	A	161	LEU	0	-0.059	-0.025	22.119	0.004	0.004	0.000	0.000	0.000	0.000
85	A	162	GLY	0	0.017	0.013	26.597	0.012	0.012	0.000	0.000	0.000	0.000
86	A	163	ARG	1	0.767	0.853	19.848	0.064	0.064	0.000	0.000	0.000	0.000
87	A	164	PHE	0	0.044	0.011	27.265	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	165	ASP	-1	-0.771	-0.886	29.443	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	166	GLU	-1	-0.785	-0.848	22.465	-0.046	-0.046	0.000	0.000	0.000	0.000
90	A	167	ALA	0	-0.017	-0.004	25.870	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	168	ILE	0	-0.003	-0.008	27.429	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	169	ASP	-1	-0.816	-0.900	26.822	-0.053	-0.053	0.000	0.000	0.000	0.000
93	A	170	SER	0	-0.038	-0.037	23.884	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	171	PHE	0	-0.020	-0.025	25.691	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	172	LYS	1	0.860	0.928	29.014	0.048	0.048	0.000	0.000	0.000	0.000
96	A	173	ILE	0	-0.002	0.005	23.702	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	174	ALA	0	-0.021	-0.012	26.954	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	175	LEU	0	-0.033	-0.031	28.017	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	176	GLY	0	-0.010	-0.003	30.164	0.004	0.004	0.000	0.000	0.000	0.000
100	A	177	LEU	0	-0.055	-0.016	24.729	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	178	ARG	1	0.851	0.905	29.042	0.177	0.177	0.000	0.000	0.000	0.000
102	A	179	PRO	0	0.053	0.038	32.520	0.003	0.003	0.000	0.000	0.000	0.000
103	A	180	ASN	0	0.049	0.003	35.479	0.010	0.010	0.000	0.000	0.000	0.000
104	A	181	GLU	-1	-0.746	-0.834	32.187	-0.156	-0.156	0.000	0.000	0.000	0.000
105	A	182	GLY	0	0.075	0.036	35.219	0.002	0.002	0.000	0.000	0.000	0.000
106	A	183	LYS	1	0.818	0.886	31.526	0.159	0.159	0.000	0.000	0.000	0.000
107	A	184	VAL	0	-0.008	-0.001	30.769	0.000	0.000	0.000	0.000	0.000	0.000
108	A	185	HIS	0	0.017	0.019	33.287	0.009	0.009	0.000	0.000	0.000	0.000
109	A	186	ARG	1	0.939	0.957	36.439	0.092	0.092	0.000	0.000	0.000	0.000
110	A	187	ALA	0	-0.017	-0.001	32.112	0.004	0.004	0.000	0.000	0.000	0.000
111	A	188	ILE	0	-0.005	0.001	32.445	0.005	0.005	0.000	0.000	0.000	0.000
112	A	189	ALA	0	-0.006	0.004	34.039	0.007	0.007	0.000	0.000	0.000	0.000
113	A	190	PHE	0	0.035	0.003	35.699	0.006	0.006	0.000	0.000	0.000	0.000
114	A	191	SER	0	0.000	-0.014	31.953	0.002	0.002	0.000	0.000	0.000	0.000
115	A	192	TYR	0	-0.097	-0.068	34.063	0.003	0.003	0.000	0.000	0.000	0.000
116	A	193	GLU	-1	-0.866	-0.926	36.910	-0.036	-0.036	0.000	0.000	0.000	0.000
117	A	194	GLN	0	-0.105	-0.060	33.392	0.006	0.006	0.000	0.000	0.000	0.000
118	A	195	MET	0	-0.048	0.017	33.743	0.002	0.002	0.000	0.000	0.000	0.000
119	A	196	GLY	0	0.019	0.018	37.314	0.005	0.005	0.000	0.000	0.000	0.000
120	A	197	ARG	1	0.738	0.825	33.841	0.028	0.028	0.000	0.000	0.000	0.000
121	A	198	HIS	0	0.018	-0.021	40.726	0.000	0.000	0.000	0.000	0.000	0.000
122	A	199	GLU	-1	-0.982	-0.983	43.285	-0.026	-0.026	0.000	0.000	0.000	0.000
123	A	200	GLU	-1	-0.807	-0.882	37.953	-0.032	-0.032	0.000	0.000	0.000	0.000
124	A	201	ALA	0	-0.001	0.005	39.698	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	202	LEU	0	0.002	0.006	40.695	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	203	PRO	0	-0.011	-0.015	41.678	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	204	HIS	1	0.854	0.934	36.688	0.062	0.062	0.000	0.000	0.000	0.000
128	A	205	PHE	0	0.041	0.014	40.186	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	206	LYS	1	0.936	0.974	42.403	0.041	0.041	0.000	0.000	0.000	0.000
130	A	207	LYS	1	0.926	0.981	39.763	0.077	0.077	0.000	0.000	0.000	0.000
131	A	208	ALA	0	-0.022	-0.028	39.572	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	209	ASN	0	-0.087	-0.046	40.934	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	210	GLU	-1	-0.881	-0.930	43.976	-0.064	-0.064	0.000	0.000	0.000	0.000
134	A	211	LEU	0	-0.151	-0.060	38.749	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	212	ASP	-1	-0.920	-0.960	41.412	-0.102	-0.102	0.000	0.000	0.000	0.000
136	A	213	GLU	-1	-0.940	-0.974	43.872	-0.078	-0.078	0.000	0.000	0.000	0.000
137	A	214	GLY	0	-0.090	-0.021	47.233	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:78:PHE)