FMO DATABASE

FMODB ID: 5J6GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1575319.408224
FMO2-HF: Nuclear repulsion	1511673.904065
FMO2-HF: Total energy	-63645.504159
FMO2-MP2: Total energy	-63827.875266

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.
-42.957	-35.353	8.04	-2.481	-13.168	0.021

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 : -0.155 / q_NPA : -0.073

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	0.051	0.050	3.799	-0.095	1.382	-0.024	-0.555	-0.898	0.001
4	A	9	ARG	1	0.945	0.968	6.546	1.935	1.935	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.996	0.975	9.058	0.926	0.926	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.950	0.972	12.225	1.150	1.150	0.000	0.000	0.000	0.000
7	A	12	HIS	0	-0.003	-0.011	10.708	0.040	0.040	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.122	0.067	11.935	0.064	0.064	0.000	0.000	0.000	0.000
9	A	14	LYS	1	0.947	0.974	14.616	0.799	0.799	0.000	0.000	0.000	0.000
10	A	15	THR	0	-0.059	-0.024	16.998	0.091	0.091	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.036	0.019	15.528	0.066	0.066	0.000	0.000	0.000	0.000
12	A	17	TYR	0	0.029	0.013	17.647	0.058	0.058	0.000	0.000	0.000	0.000
13	A	18	SER	0	-0.004	-0.007	20.054	0.070	0.070	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.039	-0.023	19.265	0.046	0.046	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.044	0.037	18.744	0.036	0.036	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.895	-0.934	22.401	-0.256	-0.256	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.080	-0.054	25.195	0.029	0.029	0.000	0.000	0.000	0.000
18	A	23	MET	0	-0.093	-0.033	20.867	0.031	0.031	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.074	0.033	26.164	0.017	0.017	0.000	0.000	0.000	0.000
20	A	25	GLY	0	-0.049	-0.004	28.771	0.022	0.022	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.038	0.009	30.354	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	27	PHE	0	0.040	0.021	26.326	0.005	0.005	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.018	0.011	32.300	0.013	0.013	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.975	0.968	34.638	0.107	0.107	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.960	-0.978	36.820	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	31	CYS	0	0.079	0.038	30.308	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	32	LEU	0	0.005	0.001	30.058	0.007	0.007	0.000	0.000	0.000	0.000
28	A	33	LYS	1	0.902	0.962	33.256	0.080	0.080	0.000	0.000	0.000	0.000
29	A	34	GLU	-1	-0.932	-0.957	33.447	-0.053	-0.053	0.000	0.000	0.000	0.000
30	A	35	ASN	0	-0.015	-0.007	32.654	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.018	0.014	28.009	0.013	0.013	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.934	0.961	30.315	-0.059	-0.059	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.030	-0.025	23.993	0.028	0.028	0.000	0.000	0.000	0.000
34	A	39	THR	0	0.022	0.024	25.451	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.041	0.016	16.753	0.040	0.040	0.000	0.000	0.000	0.000
36	A	41	PRO	0	-0.022	0.003	18.756	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.991	0.986	19.701	0.100	0.100	0.000	0.000	0.000	0.000
38	A	43	TYR	0	0.034	0.018	19.921	0.005	0.005	0.000	0.000	0.000	0.000
39	A	44	ALA	0	0.007	0.005	16.326	0.053	0.053	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.030	-0.014	13.845	0.113	0.113	0.000	0.000	0.000	0.000
41	A	46	GLN	0	-0.003	0.014	16.008	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.043	-0.019	14.430	0.067	0.067	0.000	0.000	0.000	0.000
43	A	48	ASN	0	0.026	-0.001	16.557	-0.098	-0.098	0.000	0.000	0.000	0.000
44	A	49	ASN	0	0.046	0.020	16.550	0.027	0.027	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.036	0.005	14.076	0.038	0.038	0.000	0.000	0.000	0.000
46	A	51	ASN	0	0.068	0.025	12.523	0.012	0.012	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.038	0.029	12.085	0.107	0.107	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.923	0.972	10.011	0.054	0.054	0.000	0.000	0.000	0.000
49	A	54	THR	0	0.019	0.011	6.924	-0.066	-0.066	0.000	0.000	0.000	0.000
50	A	55	GLY	0	0.045	0.029	8.507	0.447	0.447	0.000	0.000	0.000	0.000
51	A	56	VAL	0	0.013	0.002	11.278	0.077	0.077	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.004	0.003	6.232	-0.154	-0.154	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.861	0.920	6.249	-4.137	-4.137	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.024	0.019	7.795	-0.266	-0.266	0.000	0.000	0.000	0.000
55	A	60	VAL	0	0.016	0.000	9.431	-0.258	-0.258	0.000	0.000	0.000	0.000
56	A	61	TYR	0	-0.032	-0.020	3.492	-0.102	-1.679	0.116	2.330	-0.870	-0.003
57	A	62	LYS	1	0.969	0.969	6.758	-2.770	-2.770	0.000	0.000	0.000	0.000
58	A	63	ILE	0	-0.011	0.014	8.674	-0.131	-0.131	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.051	-0.024	7.968	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.933	-0.973	7.145	-0.544	-0.544	0.000	0.000	0.000	0.000
61	A	66	HIS	0	0.031	0.011	8.995	0.093	0.093	0.000	0.000	0.000	0.000
62	A	67	ILE	0	-0.060	-0.022	12.463	0.040	0.040	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.933	-0.978	10.989	-1.030	-1.030	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.030	0.010	12.159	0.110	0.110	0.000	0.000	0.000	0.000
65	A	70	LEU	0	-0.086	-0.038	14.577	0.063	0.063	0.000	0.000	0.000	0.000
66	A	71	PHE	0	-0.020	-0.037	16.679	0.034	0.034	0.000	0.000	0.000	0.000
67	A	72	ALA	0	0.020	0.024	15.825	0.009	0.009	0.000	0.000	0.000	0.000
68	A	73	ASN	0	-0.020	0.028	17.822	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.837	-0.924	21.047	-0.359	-0.359	0.000	0.000	0.000	0.000
70	A	75	SER	0	-0.049	-0.055	22.973	0.026	0.026	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.078	-0.017	21.339	0.025	0.025	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.001	-0.011	25.690	0.008	0.008	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.878	-0.942	28.425	-0.201	-0.201	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.016	-0.013	30.581	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	80	TRP	0	-0.030	-0.016	23.490	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	81	ASN	0	-0.032	-0.030	27.622	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	82	LYS	1	1.018	0.990	26.238	0.219	0.219	0.000	0.000	0.000	0.000
78	A	83	ARG	1	0.992	1.017	24.711	0.366	0.366	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.860	0.928	23.488	0.326	0.326	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.062	0.027	21.460	-0.056	-0.056	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.824	-0.897	20.106	-0.633	-0.633	0.000	0.000	0.000	0.000
82	A	87	ASN	0	-0.046	-0.036	18.969	-0.089	-0.089	0.000	0.000	0.000	0.000
83	A	88	PHE	0	-0.054	-0.032	16.968	-0.142	-0.142	0.000	0.000	0.000	0.000
84	A	89	GLN	0	0.062	0.022	15.780	-0.130	-0.130	0.000	0.000	0.000	0.000
85	A	90	ASN	0	0.024	0.020	14.277	-0.203	-0.203	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.120	-0.063	13.450	-0.248	-0.248	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.025	0.010	11.342	-0.328	-0.328	0.000	0.000	0.000	0.000
88	A	93	TYR	0	0.102	0.063	9.691	-0.665	-0.665	0.000	0.000	0.000	0.000
89	A	94	ARG	1	0.842	0.909	8.619	1.065	1.065	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.052	-0.035	8.117	-0.708	-0.708	0.000	0.000	0.000	0.000
91	A	96	THR	0	0.054	0.031	5.286	-1.554	-1.452	-0.002	-0.001	-0.099	0.000
92	A	97	LYS	1	0.955	0.975	3.718	-3.446	-3.111	0.045	-0.176	-0.205	-0.002
93	A	98	GLU	-1	-0.909	-0.950	4.350	-5.065	-4.755	-0.002	-0.057	-0.252	0.000
94	A	99	ASN	0	-0.001	-0.015	3.029	-0.512	2.781	2.152	-2.052	-3.393	-0.015
97	A	103	MET	0	-0.028	-0.007	2.102	-11.167	-10.688	4.890	-0.866	-4.504	0.040
98	A	104	ARG	1	0.949	0.983	2.912	-12.728	-10.416	0.652	-0.937	-2.028	0.000
99	A	105	MET	0	-0.065	0.002	2.935	-3.357	-2.484	0.213	-0.167	-0.919	0.000
100	A	106	ARG	1	1.028	1.000	7.258	-1.424	-1.424	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.004	0.012	10.698	-0.214	-0.214	0.000	0.000	0.000	0.000
102	A	108	GLN	0	-0.009	-0.016	11.170	-0.177	-0.177	0.000	0.000	0.000	0.000
103	A	109	GLY	0	-0.024	0.001	14.269	-0.124	-0.124	0.000	0.000	0.000	0.000
104	A	110	THR	0	0.018	0.000	17.250	0.090	0.090	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.009	0.011	19.564	0.015	0.015	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.881	-0.945	12.945	1.981	1.981	0.000	0.000	0.000	0.000
107	A	113	ASP	-1	-0.791	-0.907	14.378	1.036	1.036	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.031	-0.034	9.360	0.107	0.107	0.000	0.000	0.000	0.000
109	A	115	PRO	0	0.023	0.015	13.154	-0.075	-0.075	0.000	0.000	0.000	0.000
110	A	116	ALA	0	0.089	0.050	14.690	-0.098	-0.098	0.000	0.000	0.000	0.000
111	A	117	ARG	1	0.723	0.849	13.391	-0.862	-0.862	0.000	0.000	0.000	0.000
112	A	118	ASP	-1	-0.906	-0.963	11.934	1.476	1.476	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.875	-0.934	13.662	0.722	0.722	0.000	0.000	0.000	0.000
114	A	120	ALA	0	-0.040	-0.023	17.217	-0.120	-0.120	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.024	-0.027	12.725	-0.116	-0.116	0.000	0.000	0.000	0.000
116	A	122	LYS	1	0.961	0.993	13.414	-1.243	-1.243	0.000	0.000	0.000	0.000
117	A	123	SER	0	-0.018	0.000	16.889	-0.088	-0.088	0.000	0.000	0.000	0.000
118	A	124	TYR	0	-0.092	-0.060	17.977	-0.046	-0.046	0.000	0.000	0.000	0.000
119	A	125	PHE	0	0.070	0.013	14.964	-0.059	-0.059	0.000	0.000	0.000	0.000
120	A	126	ASN	0	0.035	0.021	18.557	-0.053	-0.053	0.000	0.000	0.000	0.000
121	A	127	LYS	1	0.914	0.965	20.991	-0.173	-0.173	0.000	0.000	0.000	0.000
122	A	128	LEU	0	0.015	0.015	19.321	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	129	ALA	0	0.059	0.029	20.658	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.060	-0.036	22.599	0.004	0.004	0.000	0.000	0.000	0.000
125	A	131	LEU	0	-0.037	-0.001	25.762	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.018	0.007	22.708	0.000	0.000	0.000	0.000	0.000	0.000
127	A	133	ARG	1	0.928	0.975	25.135	-0.085	-0.085	0.000	0.000	0.000	0.000
128	A	134	ASN	0	-0.040	-0.035	28.195	0.004	0.004	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.873	0.939	30.345	0.036	0.036	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.879	-0.930	31.045	-0.050	-0.050	0.000	0.000	0.000	0.000
131	A	137	ASN	0	-0.031	-0.024	26.157	-0.028	-0.028	0.000	0.000	0.000	0.000
132	A	138	SER	0	0.020	0.030	29.083	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.080	0.014	30.039	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	141	ALA	0	-0.019	0.002	28.396	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	142	TRP	0	0.047	0.013	21.248	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.816	-0.905	25.860	-0.237	-0.237	0.000	0.000	0.000	0.000
137	A	144	VAL	0	-0.015	0.001	26.827	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	145	VAL	0	0.004	0.003	21.474	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	146	ARG	1	0.775	0.887	22.634	0.246	0.246	0.000	0.000	0.000	0.000
140	A	147	HIS	0	-0.030	-0.016	23.354	-0.017	-0.017	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.858	-0.921	22.477	-0.095	-0.095	0.000	0.000	0.000	0.000
142	A	149	LEU	0	-0.021	-0.019	17.464	-0.016	-0.016	0.000	0.000	0.000	0.000
143	A	150	LEU	0	-0.014	0.002	19.536	-0.059	-0.059	0.000	0.000	0.000	0.000
144	A	151	GLY	0	0.028	0.015	21.568	-0.028	-0.028	0.000	0.000	0.000	0.000
145	A	152	VAL	0	0.004	0.009	16.264	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	153	LEU	0	-0.004	-0.018	15.186	-0.047	-0.047	0.000	0.000	0.000	0.000
147	A	154	SER	0	-0.008	-0.005	17.873	-0.056	-0.056	0.000	0.000	0.000	0.000
148	A	155	ASP	-1	-0.882	-0.938	19.201	-0.170	-0.170	0.000	0.000	0.000	0.000
149	A	156	ILE	0	-0.071	-0.028	13.123	-0.022	-0.022	0.000	0.000	0.000	0.000
150	A	157	ILE	0	-0.094	-0.045	15.260	-0.087	-0.087	0.000	0.000	0.000	0.000
151	A	158	GLN	0	-0.064	-0.033	16.935	-0.061	-0.061	0.000	0.000	0.000	0.000
152	A	159	PRO	0	0.021	0.037	15.791	0.065	0.065	0.000	0.000	0.000	0.000

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