FMO DATABASE

FMODB ID: VQLY1

Calculation Name: 3PIW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PIW

Chain ID: A

ChEMBL ID:

UniProt ID: A8E6E2

Base Structure: X-ray

Registration Date: 2023-09-23

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1577557.409368
FMO2-HF: Nuclear repulsion	1513910.824075
FMO2-HF: Total energy	-63646.585293
FMO2-MP2: Total energy	-63828.873565

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:6:CYS)

Summations of interaction energy for fragment #1(A:6:CYS)

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.
-39.955	-29.67	5.648	-3.922	-12.012	0.016

Interaction energy analysis for fragmet #1(A:6:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.094 / q_NPA : -0.023

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	8	MET	0	0.018	0.036	3.885	0.040	1.587	-0.017	-0.726	-0.803	0.003
4	A	9	ARG	1	0.957	0.972	6.601	1.787	1.787	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.916	0.928	8.725	1.314	1.314	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.955	0.980	11.933	1.060	1.060	0.000	0.000	0.000	0.000
7	A	12	HIS	0	0.023	0.030	10.555	0.114	0.114	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.106	0.057	11.910	0.076	0.076	0.000	0.000	0.000	0.000
9	A	14	LYS	1	0.987	0.993	14.570	0.881	0.881	0.000	0.000	0.000	0.000
10	A	15	THR	0	-0.078	-0.054	16.893	0.105	0.105	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.045	0.022	15.553	0.076	0.076	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.014	-0.020	17.655	0.049	0.049	0.000	0.000	0.000	0.000
13	A	18	SER	0	0.008	-0.002	20.122	0.068	0.068	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.075	-0.015	19.187	0.055	0.055	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.057	0.027	18.450	0.048	0.048	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.830	-0.894	22.318	-0.358	-0.358	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.067	-0.052	25.216	0.045	0.045	0.000	0.000	0.000	0.000
18	A	23	MET	0	-0.036	-0.001	20.734	0.031	0.031	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.061	0.040	26.253	0.024	0.024	0.000	0.000	0.000	0.000
20	A	25	GLY	0	-0.040	-0.003	28.593	0.021	0.021	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.015	-0.003	30.185	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	27	PHE	0	0.053	0.037	25.970	0.012	0.012	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.010	0.010	31.931	0.014	0.014	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.971	0.969	34.572	0.147	0.147	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.959	-0.965	36.898	-0.120	-0.120	0.000	0.000	0.000	0.000
26	A	31	CYS	0	0.045	0.014	30.064	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	32	LEU	0	0.007	0.002	30.291	0.004	0.004	0.000	0.000	0.000	0.000
28	A	33	LYS	1	0.930	0.974	33.322	0.123	0.123	0.000	0.000	0.000	0.000
29	A	34	GLU	-1	-0.839	-0.901	32.663	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	35	ASN	0	-0.055	-0.032	32.164	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.033	0.016	28.047	0.014	0.014	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.955	0.982	29.901	0.014	0.014	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.018	-0.011	23.779	0.027	0.027	0.000	0.000	0.000	0.000
34	A	39	THR	0	0.035	0.009	24.549	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.048	0.033	16.209	0.029	0.029	0.000	0.000	0.000	0.000
36	A	41	PRO	0	-0.013	0.013	18.371	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.875	0.897	19.374	0.326	0.326	0.000	0.000	0.000	0.000
38	A	43	TYR	0	0.044	0.024	19.639	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	44	ALA	0	0.002	-0.003	15.673	0.031	0.031	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.016	-0.008	13.645	0.037	0.037	0.000	0.000	0.000	0.000
41	A	46	GLN	0	0.006	0.021	15.993	-0.049	-0.049	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.017	-0.018	14.894	0.033	0.033	0.000	0.000	0.000	0.000
43	A	48	ASN	0	0.013	0.010	16.954	-0.081	-0.081	0.000	0.000	0.000	0.000
44	A	49	ASN	0	0.041	0.020	16.646	0.013	0.013	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.059	0.013	14.233	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	51	ASN	0	-0.005	0.005	12.602	-0.199	-0.199	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.068	0.038	12.046	0.028	0.028	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.901	0.955	10.230	0.629	0.629	0.000	0.000	0.000	0.000
49	A	54	THR	0	-0.008	-0.006	7.352	-0.214	-0.214	0.000	0.000	0.000	0.000
50	A	55	GLY	0	0.033	0.024	8.893	0.442	0.442	0.000	0.000	0.000	0.000
51	A	56	VAL	0	0.005	0.001	11.391	0.063	0.063	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.007	-0.002	6.156	-0.130	-0.130	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.865	0.943	6.434	-3.089	-3.089	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.017	0.017	7.783	-0.339	-0.339	0.000	0.000	0.000	0.000
55	A	60	VAL	0	0.005	-0.009	9.213	-0.225	-0.225	0.000	0.000	0.000	0.000
56	A	61	TYR	0	-0.079	-0.072	3.747	-1.381	-1.818	0.114	1.060	-0.738	-0.005
57	A	62	LYS	1	0.892	0.917	6.467	-1.036	-1.036	0.000	0.000	0.000	0.000
58	A	63	ILE	0	-0.015	0.008	8.318	0.033	0.033	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.035	-0.015	7.875	0.130	0.130	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.795	-0.871	6.743	-1.110	-1.110	0.000	0.000	0.000	0.000
61	A	66	HIS	0	0.018	0.006	8.652	0.202	0.202	0.000	0.000	0.000	0.000
62	A	67	ILE	0	-0.036	-0.014	12.186	0.093	0.093	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.855	-0.942	10.336	-1.389	-1.389	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.016	0.001	11.934	0.141	0.141	0.000	0.000	0.000	0.000
65	A	70	LEU	0	-0.073	-0.025	14.350	0.075	0.075	0.000	0.000	0.000	0.000
66	A	71	PHE	0	0.020	-0.013	16.301	0.040	0.040	0.000	0.000	0.000	0.000
67	A	72	ALA	0	-0.028	-0.001	15.335	0.022	0.022	0.000	0.000	0.000	0.000
68	A	73	ASN	0	0.010	0.022	17.425	0.016	0.016	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.818	-0.885	20.928	-0.350	-0.350	0.000	0.000	0.000	0.000
70	A	75	SER	0	-0.035	-0.025	22.880	0.019	0.019	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.060	-0.036	21.596	0.018	0.018	0.000	0.000	0.000	0.000
72	A	77	PRO	0	0.003	-0.008	25.477	0.017	0.017	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.799	-0.888	28.616	-0.206	-0.206	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.010	-0.011	30.408	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	80	TRP	0	-0.033	-0.017	23.063	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	81	ASN	0	-0.029	-0.034	27.777	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.896	0.933	26.273	0.203	0.203	0.000	0.000	0.000	0.000
78	A	83	ARG	1	1.010	1.015	24.535	0.349	0.349	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.818	0.912	23.359	0.355	0.355	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.036	0.015	21.067	-0.064	-0.064	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.798	-0.889	19.869	-0.597	-0.597	0.000	0.000	0.000	0.000
82	A	87	ASN	0	-0.044	-0.023	18.822	-0.073	-0.073	0.000	0.000	0.000	0.000
83	A	88	PHE	0	-0.039	-0.018	16.673	-0.142	-0.142	0.000	0.000	0.000	0.000
84	A	89	GLN	0	0.023	-0.005	15.605	-0.151	-0.151	0.000	0.000	0.000	0.000
85	A	90	ASN	0	-0.015	-0.013	14.149	-0.205	-0.205	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.090	-0.048	13.467	-0.213	-0.213	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.005	0.005	11.258	-0.330	-0.330	0.000	0.000	0.000	0.000
88	A	93	TYR	0	0.088	0.055	9.685	-0.550	-0.550	0.000	0.000	0.000	0.000
89	A	94	ARG	1	0.743	0.845	8.903	1.023	1.023	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.041	-0.027	8.132	-0.671	-0.671	0.000	0.000	0.000	0.000
91	A	96	THR	0	0.031	0.017	5.265	-1.932	-1.840	-0.002	-0.001	-0.089	0.000
92	A	97	LYS	1	0.900	0.958	3.941	-3.181	-2.914	0.019	-0.152	-0.133	-0.001
93	A	98	GLU	-1	-0.838	-0.900	4.946	-3.138	-2.869	-0.002	-0.047	-0.221	0.000
94	A	99	ASN	0	-0.026	-0.030	3.145	-2.128	1.645	2.294	-2.317	-3.750	-0.019
97	A	103	MET	0	0.001	0.012	2.276	-10.784	-8.433	2.987	-1.078	-4.259	0.037
98	A	104	ARG	1	0.949	0.982	3.600	-11.511	-9.977	0.052	-0.483	-1.104	0.001
99	A	105	MET	0	-0.063	-0.014	2.809	-3.059	-2.170	0.203	-0.178	-0.915	0.000
100	A	106	ARG	1	0.969	0.964	7.460	-1.365	-1.365	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.033	0.034	10.718	-0.317	-0.317	0.000	0.000	0.000	0.000
102	A	108	GLN	0	-0.010	-0.022	11.504	-0.117	-0.117	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.040	0.019	14.332	-0.147	-0.147	0.000	0.000	0.000	0.000
104	A	110	THR	0	0.002	0.001	17.695	0.098	0.098	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.021	0.017	19.084	0.025	0.025	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.866	-0.941	12.149	1.656	1.656	0.000	0.000	0.000	0.000
107	A	113	ASP	-1	-0.771	-0.893	15.038	0.468	0.468	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.003	-0.013	9.015	0.042	0.042	0.000	0.000	0.000	0.000
109	A	115	PRO	0	0.020	0.012	13.020	-0.081	-0.081	0.000	0.000	0.000	0.000
110	A	116	ALA	0	0.069	0.039	14.636	-0.090	-0.090	0.000	0.000	0.000	0.000
111	A	117	ARG	1	0.690	0.830	13.379	-0.339	-0.339	0.000	0.000	0.000	0.000
112	A	118	ASP	-1	-0.819	-0.921	11.653	0.968	0.968	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.807	-0.891	13.569	0.595	0.595	0.000	0.000	0.000	0.000
114	A	120	ALA	0	-0.025	0.003	17.073	-0.095	-0.095	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.034	-0.019	12.121	-0.089	-0.089	0.000	0.000	0.000	0.000
116	A	122	LYS	1	0.819	0.901	13.497	-0.983	-0.983	0.000	0.000	0.000	0.000
117	A	123	SER	0	-0.036	-0.028	16.673	-0.051	-0.051	0.000	0.000	0.000	0.000
118	A	124	TYR	0	-0.096	-0.073	17.496	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	125	PHE	0	0.057	0.006	14.607	-0.044	-0.044	0.000	0.000	0.000	0.000
120	A	126	ASN	0	0.038	0.020	18.308	-0.036	-0.036	0.000	0.000	0.000	0.000
121	A	127	LYS	1	0.863	0.941	20.864	0.006	0.006	0.000	0.000	0.000	0.000
122	A	128	LEU	0	0.005	0.010	18.872	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	129	ALA	0	0.058	0.024	20.434	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.065	-0.038	22.403	0.019	0.019	0.000	0.000	0.000	0.000
125	A	131	LEU	0	-0.049	-0.013	25.447	0.007	0.007	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.015	0.014	22.597	0.005	0.005	0.000	0.000	0.000	0.000
127	A	133	ARG	1	0.918	0.959	25.481	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	134	ASN	0	-0.026	-0.026	27.931	0.013	0.013	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.798	0.891	30.184	0.101	0.101	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.868	-0.927	30.624	-0.080	-0.080	0.000	0.000	0.000	0.000
131	A	137	ASN	0	-0.052	-0.028	26.362	-0.021	-0.021	0.000	0.000	0.000	0.000
132	A	138	SER	0	0.029	0.027	28.799	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.056	0.007	29.847	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	141	ALA	0	0.034	0.028	28.228	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	142	TRP	0	0.056	0.012	20.532	-0.030	-0.030	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.764	-0.860	25.531	-0.309	-0.309	0.000	0.000	0.000	0.000
137	A	144	VAL	0	-0.013	-0.002	26.781	-0.023	-0.023	0.000	0.000	0.000	0.000
138	A	145	VAL	0	-0.003	0.001	21.211	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	146	ARG	1	0.723	0.821	22.312	0.291	0.291	0.000	0.000	0.000	0.000
140	A	147	HIS	0	-0.045	-0.020	23.213	-0.028	-0.028	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.825	-0.899	22.174	-0.258	-0.258	0.000	0.000	0.000	0.000
142	A	149	LEU	0	-0.022	-0.015	17.070	-0.037	-0.037	0.000	0.000	0.000	0.000
143	A	150	LEU	0	-0.005	0.009	19.156	-0.085	-0.085	0.000	0.000	0.000	0.000
144	A	151	GLY	0	0.036	0.023	21.283	-0.036	-0.036	0.000	0.000	0.000	0.000
145	A	152	VAL	0	-0.020	-0.009	15.812	-0.031	-0.031	0.000	0.000	0.000	0.000
146	A	153	LEU	0	0.004	-0.007	14.671	-0.085	-0.085	0.000	0.000	0.000	0.000
147	A	154	SER	0	0.013	0.000	17.473	-0.068	-0.068	0.000	0.000	0.000	0.000
148	A	155	ASP	-1	-0.822	-0.884	18.734	-0.394	-0.394	0.000	0.000	0.000	0.000
149	A	156	ILE	0	-0.034	-0.012	12.760	-0.044	-0.044	0.000	0.000	0.000	0.000
150	A	157	ILE	0	-0.094	-0.043	15.150	-0.118	-0.118	0.000	0.000	0.000	0.000
151	A	158	GLN	0	-0.036	-0.015	17.083	-0.098	-0.098	0.000	0.000	0.000	0.000
152	A	159	PRO	0	0.009	0.030	15.766	0.094	0.094	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:CYS)