FMO DATABASE

FMODB ID: GYN21

Calculation Name: 3Q47-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q47

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WUD1

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	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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1169439.809529
FMO2-HF: Nuclear repulsion	1115760.589852
FMO2-HF: Total energy	-53679.219677
FMO2-MP2: Total energy	-53834.193006

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(B:24:SER)

Summations of interaction energy for fragment #1(B:24:SER)

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.
-7.737	-6.196	0.037	-0.625	-0.953	0.003

Interaction energy analysis for fragmet #1(B:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.024

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	B	26	SER	0	0.029	-0.024	3.836	-0.318	0.764	-0.015	-0.481	-0.586	0.002
4	B	27	ALA	0	0.045	0.002	6.411	0.628	0.628	0.000	0.000	0.000	0.000
5	B	28	GLN	0	0.069	0.049	9.395	0.294	0.294	0.000	0.000	0.000	0.000
6	B	29	GLU	-1	-0.774	-0.848	7.004	-1.501	-1.501	0.000	0.000	0.000	0.000
7	B	30	LEU	0	-0.057	-0.022	5.992	0.352	0.352	0.000	0.000	0.000	0.000
8	B	31	LYS	1	0.828	0.896	9.505	0.092	0.092	0.000	0.000	0.000	0.000
9	B	32	GLU	-1	-0.854	-0.921	12.628	-0.077	-0.077	0.000	0.000	0.000	0.000
10	B	33	GLN	0	-0.051	-0.034	9.135	0.190	0.190	0.000	0.000	0.000	0.000
11	B	34	GLY	0	0.038	0.014	12.695	0.017	0.017	0.000	0.000	0.000	0.000
12	B	35	ASN	0	0.031	0.022	14.699	-0.015	-0.015	0.000	0.000	0.000	0.000
13	B	36	ARG	1	0.956	0.987	11.762	-0.476	-0.476	0.000	0.000	0.000	0.000
14	B	37	LEU	0	0.007	0.004	13.802	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	38	PHE	0	0.024	0.011	17.801	-0.031	-0.031	0.000	0.000	0.000	0.000
16	B	39	VAL	0	-0.021	-0.004	20.502	-0.026	-0.026	0.000	0.000	0.000	0.000
17	B	40	GLY	0	-0.036	-0.014	20.888	-0.022	-0.022	0.000	0.000	0.000	0.000
18	B	41	ARG	1	0.899	0.947	22.200	-0.235	-0.235	0.000	0.000	0.000	0.000
19	B	42	LYS	1	0.800	0.905	19.283	-0.477	-0.477	0.000	0.000	0.000	0.000
20	B	43	TYR	0	0.078	0.021	19.314	0.040	0.040	0.000	0.000	0.000	0.000
21	B	44	PRO	0	0.087	0.032	19.717	0.017	0.017	0.000	0.000	0.000	0.000
22	B	45	GLU	-1	-0.769	-0.879	15.848	0.611	0.611	0.000	0.000	0.000	0.000
23	B	46	ALA	0	0.006	0.002	14.952	0.100	0.100	0.000	0.000	0.000	0.000
24	B	47	ALA	0	0.013	0.001	15.505	0.024	0.024	0.000	0.000	0.000	0.000
25	B	48	ALA	0	0.023	0.010	13.801	0.005	0.005	0.000	0.000	0.000	0.000
26	B	49	CYS	0	-0.078	-0.038	11.132	0.202	0.202	0.000	0.000	0.000	0.000
27	B	50	TYR	0	0.011	-0.031	11.481	0.010	0.010	0.000	0.000	0.000	0.000
28	B	51	GLY	0	0.039	0.027	13.772	-0.066	-0.066	0.000	0.000	0.000	0.000
29	B	52	ARG	1	0.936	0.979	5.313	-3.294	-3.294	0.000	0.000	0.000	0.000
30	B	53	ALA	0	-0.024	-0.012	9.554	-0.052	-0.052	0.000	0.000	0.000	0.000
31	B	54	ILE	0	-0.017	-0.009	11.040	-0.128	-0.128	0.000	0.000	0.000	0.000
32	B	55	THR	0	-0.055	-0.034	10.031	-0.020	-0.020	0.000	0.000	0.000	0.000
33	B	56	ARG	1	0.857	0.925	3.018	-3.288	-2.829	0.052	-0.144	-0.367	0.001
34	B	57	ASN	0	0.030	0.012	9.701	-0.135	-0.135	0.000	0.000	0.000	0.000
35	B	58	PRO	0	0.030	0.028	13.033	0.030	0.030	0.000	0.000	0.000	0.000
36	B	59	LEU	0	0.053	0.031	16.181	0.014	0.014	0.000	0.000	0.000	0.000
37	B	60	VAL	0	0.001	0.011	15.757	-0.022	-0.022	0.000	0.000	0.000	0.000
38	B	61	ALA	0	0.092	0.041	18.553	0.044	0.044	0.000	0.000	0.000	0.000
39	B	62	VAL	0	-0.006	-0.016	19.365	0.029	0.029	0.000	0.000	0.000	0.000
40	B	63	TYR	0	-0.002	-0.006	13.414	0.022	0.022	0.000	0.000	0.000	0.000
41	B	64	TYR	0	-0.001	-0.009	17.690	0.074	0.074	0.000	0.000	0.000	0.000
42	B	65	THR	0	0.010	0.010	20.427	0.014	0.014	0.000	0.000	0.000	0.000
43	B	66	ASN	0	-0.069	-0.033	18.101	-0.018	-0.018	0.000	0.000	0.000	0.000
44	B	67	ARG	1	0.855	0.903	16.846	-0.381	-0.381	0.000	0.000	0.000	0.000
45	B	68	ALA	0	0.039	0.022	20.088	0.010	0.010	0.000	0.000	0.000	0.000
46	B	69	LEU	0	-0.020	0.007	23.556	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	70	CYS	0	-0.075	-0.039	20.331	0.013	0.013	0.000	0.000	0.000	0.000
48	B	71	TYR	0	0.030	-0.003	20.407	0.013	0.013	0.000	0.000	0.000	0.000
49	B	72	LEU	0	0.029	0.014	24.543	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	73	LYS	1	0.879	0.955	25.289	-0.200	-0.200	0.000	0.000	0.000	0.000
51	B	74	MET	0	-0.118	-0.040	21.710	0.013	0.013	0.000	0.000	0.000	0.000
52	B	75	GLN	0	0.010	0.010	26.659	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	76	GLN	0	-0.004	0.003	24.972	0.012	0.012	0.000	0.000	0.000	0.000
54	B	77	PRO	0	0.085	0.033	27.663	0.009	0.009	0.000	0.000	0.000	0.000
55	B	78	GLU	-1	-0.872	-0.935	29.690	0.166	0.166	0.000	0.000	0.000	0.000
56	B	79	GLN	0	-0.007	-0.009	24.267	-0.009	-0.009	0.000	0.000	0.000	0.000
57	B	80	ALA	0	-0.007	-0.002	25.122	0.004	0.004	0.000	0.000	0.000	0.000
58	B	81	LEU	0	0.044	0.025	26.287	-0.012	-0.012	0.000	0.000	0.000	0.000
59	B	82	ALA	0	0.004	-0.001	25.718	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	83	ASP	-1	-0.754	-0.842	21.264	0.286	0.286	0.000	0.000	0.000	0.000
61	B	84	CYS	0	-0.062	-0.030	24.046	-0.017	-0.017	0.000	0.000	0.000	0.000
62	B	85	ARG	1	0.941	0.969	26.793	-0.113	-0.113	0.000	0.000	0.000	0.000
63	B	86	ARG	1	0.922	0.944	21.600	-0.231	-0.231	0.000	0.000	0.000	0.000
64	B	87	ALA	0	-0.013	-0.008	23.796	-0.015	-0.015	0.000	0.000	0.000	0.000
65	B	88	LEU	0	-0.041	-0.023	24.668	-0.018	-0.018	0.000	0.000	0.000	0.000
66	B	89	GLU	-1	-0.964	-0.970	26.158	0.067	0.067	0.000	0.000	0.000	0.000
67	B	90	LEU	0	-0.084	-0.026	20.931	-0.013	-0.013	0.000	0.000	0.000	0.000
68	B	91	ASP	-1	-0.852	-0.944	25.033	-0.012	-0.012	0.000	0.000	0.000	0.000
69	B	92	GLY	0	0.019	0.013	27.127	0.012	0.012	0.000	0.000	0.000	0.000
70	B	93	GLN	0	-0.006	-0.020	30.130	0.008	0.008	0.000	0.000	0.000	0.000
71	B	94	SER	0	0.029	0.032	26.696	0.006	0.006	0.000	0.000	0.000	0.000
72	B	95	VAL	0	0.029	0.020	29.345	0.010	0.010	0.000	0.000	0.000	0.000
73	B	96	LYS	1	0.958	0.966	24.898	-0.084	-0.084	0.000	0.000	0.000	0.000
74	B	97	ALA	0	0.041	0.027	27.097	0.013	0.013	0.000	0.000	0.000	0.000
75	B	98	HIS	0	-0.002	0.001	28.439	0.008	0.008	0.000	0.000	0.000	0.000
76	B	99	PHE	0	-0.010	-0.012	30.988	0.004	0.004	0.000	0.000	0.000	0.000
77	B	100	PHE	0	0.009	-0.019	25.150	0.005	0.005	0.000	0.000	0.000	0.000
78	B	101	LEU	0	0.039	0.040	30.080	0.008	0.008	0.000	0.000	0.000	0.000
79	B	102	GLY	0	0.015	0.000	31.637	0.001	0.001	0.000	0.000	0.000	0.000
80	B	103	GLN	0	-0.037	-0.025	31.790	0.003	0.003	0.000	0.000	0.000	0.000
81	B	104	CYS	0	-0.046	-0.012	30.036	0.008	0.008	0.000	0.000	0.000	0.000
82	B	105	GLN	0	0.019	-0.002	32.704	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	106	LEU	0	-0.037	-0.012	36.086	-0.004	-0.004	0.000	0.000	0.000	0.000
84	B	107	GLU	-1	-0.952	-0.974	32.572	0.163	0.163	0.000	0.000	0.000	0.000
85	B	108	MET	0	-0.057	-0.018	33.900	0.004	0.004	0.000	0.000	0.000	0.000
86	B	109	GLU	-1	-0.821	-0.870	37.307	0.089	0.089	0.000	0.000	0.000	0.000
87	B	110	SER	0	0.006	0.000	38.618	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	111	TYR	0	-0.047	-0.089	40.262	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	112	ASP	-1	-0.794	-0.869	42.340	0.057	0.057	0.000	0.000	0.000	0.000
90	B	113	GLU	-1	-0.867	-0.927	38.574	0.081	0.081	0.000	0.000	0.000	0.000
91	B	114	ALA	0	0.016	0.021	37.772	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	115	ILE	0	-0.019	-0.017	38.678	-0.003	-0.003	0.000	0.000	0.000	0.000
93	B	116	ALA	0	-0.009	0.002	40.616	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	117	ASN	0	0.023	-0.006	35.315	-0.008	-0.008	0.000	0.000	0.000	0.000
95	B	118	LEU	0	0.001	0.007	35.603	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	119	GLN	0	0.014	0.007	37.823	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	120	ARG	1	0.902	0.977	36.386	-0.025	-0.025	0.000	0.000	0.000	0.000
98	B	121	ALA	0	0.026	0.009	34.374	-0.005	-0.005	0.000	0.000	0.000	0.000
99	B	122	TYR	0	0.000	0.001	35.773	-0.007	-0.007	0.000	0.000	0.000	0.000
100	B	123	SER	0	-0.040	-0.035	38.727	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	124	LEU	0	-0.022	0.006	33.382	-0.005	-0.005	0.000	0.000	0.000	0.000
102	B	125	ALA	0	0.009	-0.006	35.023	-0.006	-0.006	0.000	0.000	0.000	0.000
103	B	126	LYS	1	0.912	0.966	35.964	-0.020	-0.020	0.000	0.000	0.000	0.000
104	B	127	GLU	-1	-0.905	-0.951	37.705	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	128	GLN	0	-0.067	-0.042	32.099	-0.005	-0.005	0.000	0.000	0.000	0.000
106	B	129	ARG	1	0.901	0.960	35.236	0.018	0.018	0.000	0.000	0.000	0.000
107	B	130	LEU	0	-0.012	-0.002	31.236	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	131	ASN	0	0.009	-0.009	34.647	0.007	0.007	0.000	0.000	0.000	0.000
109	B	132	PHE	0	0.000	-0.006	30.286	0.001	0.001	0.000	0.000	0.000	0.000
110	B	133	GLY	0	0.068	0.045	35.287	0.006	0.006	0.000	0.000	0.000	0.000
111	B	134	ASP	-1	-0.806	-0.901	38.565	0.046	0.046	0.000	0.000	0.000	0.000
112	B	135	ASP	-1	-0.886	-0.922	34.072	0.076	0.076	0.000	0.000	0.000	0.000
113	B	136	ILE	0	-0.019	-0.022	34.834	0.005	0.005	0.000	0.000	0.000	0.000
114	B	137	PRO	0	0.009	0.005	37.885	0.002	0.002	0.000	0.000	0.000	0.000
115	B	138	SER	0	-0.008	-0.019	39.454	0.001	0.001	0.000	0.000	0.000	0.000
116	B	139	ALA	0	-0.002	0.005	36.930	0.003	0.003	0.000	0.000	0.000	0.000
117	B	140	LEU	0	-0.009	-0.010	38.977	0.001	0.001	0.000	0.000	0.000	0.000
118	B	141	ARG	1	0.786	0.876	41.627	-0.052	-0.052	0.000	0.000	0.000	0.000
119	B	142	ILE	0	0.008	0.007	39.524	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	143	ALA	0	0.052	0.026	40.216	0.001	0.001	0.000	0.000	0.000	0.000
121	B	144	LYS	1	0.879	0.935	42.089	-0.049	-0.049	0.000	0.000	0.000	0.000
122	B	145	LYS	1	0.944	0.977	45.602	-0.062	-0.062	0.000	0.000	0.000	0.000
123	B	146	LYS	1	0.886	0.956	42.240	-0.090	-0.090	0.000	0.000	0.000	0.000
124	B	147	ARG	1	0.858	0.899	44.945	-0.057	-0.057	0.000	0.000	0.000	0.000
125	B	148	TRP	0	-0.044	-0.017	46.410	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	149	ASN	0	0.015	-0.014	47.538	-0.004	-0.004	0.000	0.000	0.000	0.000
127	B	150	SER	0	-0.040	-0.011	46.447	0.000	0.000	0.000	0.000	0.000	0.000
128	B	151	ILE	0	0.006	-0.005	48.530	-0.001	-0.001	0.000	0.000	0.000	0.000
129	B	152	GLU	-1	-0.814	-0.894	51.793	0.052	0.052	0.000	0.000	0.000	0.000
130	B	153	GLU	-1	-0.879	-0.933	47.576	0.082	0.082	0.000	0.000	0.000	0.000
131	B	154	ARG	1	0.802	0.901	46.253	-0.078	-0.078	0.000	0.000	0.000	0.000
132	B	155	ARG	1	0.829	0.933	53.727	-0.054	-0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:24:SER)