FMO DATABASE

FMODB ID: YV8R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1575194.287951
FMO2-HF: Nuclear repulsion	1511548.012161
FMO2-HF: Total energy	-63646.275791
FMO2-MP2: Total energy	-63828.622273

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.
-41.872	-33.208	7.676	-3.59	-12.75	0.024

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 : -0.115 / q_NPA : -0.036

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	0.043	0.047	3.799	-0.125	1.802	-0.029	-0.859	-1.040	0.003
4	A	9	ARG	1	0.922	0.951	6.545	1.712	1.712	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.963	0.957	9.038	1.223	1.223	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.960	0.977	12.207	1.085	1.085	0.000	0.000	0.000	0.000
7	A	12	HIS	0	0.023	0.018	10.571	0.098	0.098	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.114	0.063	11.913	0.079	0.079	0.000	0.000	0.000	0.000
9	A	14	LYS	1	0.971	0.986	14.619	0.893	0.893	0.000	0.000	0.000	0.000
10	A	15	THR	0	-0.079	-0.052	16.986	0.102	0.102	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.043	0.024	15.526	0.076	0.076	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.010	-0.013	17.647	0.050	0.050	0.000	0.000	0.000	0.000
13	A	18	SER	0	-0.018	-0.010	20.054	0.066	0.066	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.041	-0.032	19.308	0.055	0.055	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.049	0.036	18.651	0.043	0.043	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.842	-0.901	22.401	-0.331	-0.331	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.060	-0.050	25.381	0.041	0.041	0.000	0.000	0.000	0.000
18	A	23	MET	0	-0.068	-0.014	20.746	0.037	0.037	0.000	0.000	0.000	0.000
19	A	24	GLY	0	0.073	0.035	26.164	0.022	0.022	0.000	0.000	0.000	0.000
20	A	25	GLY	0	-0.050	-0.004	28.771	0.023	0.023	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.023	0.001	30.354	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	27	PHE	0	0.043	0.028	26.295	0.007	0.007	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.013	0.015	32.300	0.013	0.013	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.976	0.967	34.638	0.137	0.137	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.966	-0.979	36.820	-0.110	-0.110	0.000	0.000	0.000	0.000
26	A	31	CYS	0	0.030	0.005	30.308	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	32	LEU	0	0.017	0.013	30.196	0.006	0.006	0.000	0.000	0.000	0.000
28	A	33	LYS	1	0.915	0.967	33.256	0.111	0.111	0.000	0.000	0.000	0.000
29	A	34	GLU	-1	-0.871	-0.921	33.262	-0.084	-0.084	0.000	0.000	0.000	0.000
30	A	35	ASN	0	-0.025	-0.011	32.654	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.037	0.026	27.975	0.014	0.014	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.939	0.965	30.315	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.036	-0.030	23.970	0.026	0.026	0.000	0.000	0.000	0.000
34	A	39	THR	0	0.027	0.025	25.544	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	40	PHE	0	0.045	0.018	16.736	0.035	0.035	0.000	0.000	0.000	0.000
36	A	41	PRO	0	-0.021	0.003	18.820	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.899	0.919	19.701	0.270	0.270	0.000	0.000	0.000	0.000
38	A	43	TYR	0	0.030	0.013	19.991	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	44	ALA	0	-0.001	0.001	16.368	0.034	0.034	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.024	-0.007	13.903	0.073	0.073	0.000	0.000	0.000	0.000
41	A	46	GLN	0	0.006	0.019	16.196	-0.063	-0.063	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.032	-0.006	14.661	0.037	0.037	0.000	0.000	0.000	0.000
43	A	48	ASN	0	0.020	0.000	16.740	-0.082	-0.082	0.000	0.000	0.000	0.000
44	A	49	ASN	0	0.051	0.021	16.792	0.016	0.016	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.046	0.014	14.076	0.012	0.012	0.000	0.000	0.000	0.000
46	A	51	ASN	0	0.048	0.014	12.680	-0.167	-0.167	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.035	0.025	12.214	0.029	0.029	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.904	0.955	10.190	0.615	0.615	0.000	0.000	0.000	0.000
49	A	54	THR	0	0.018	0.011	6.830	-0.268	-0.268	0.000	0.000	0.000	0.000
50	A	55	GLY	0	0.053	0.031	8.649	0.468	0.468	0.000	0.000	0.000	0.000
51	A	56	VAL	0	0.005	0.000	11.339	0.117	0.117	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.003	0.003	6.372	-0.109	-0.109	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.878	0.940	6.185	-3.905	-3.905	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.017	0.016	7.795	-0.202	-0.202	0.000	0.000	0.000	0.000
55	A	60	VAL	0	0.012	0.000	9.512	-0.207	-0.207	0.000	0.000	0.000	0.000
56	A	61	TYR	0	-0.085	-0.062	3.773	-0.920	-1.116	0.073	0.726	-0.602	-0.003
57	A	62	LYS	1	0.892	0.921	6.758	-1.572	-1.572	0.000	0.000	0.000	0.000
58	A	63	ILE	0	-0.017	0.008	8.674	-0.102	-0.102	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.040	-0.018	7.945	0.031	0.031	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.803	-0.886	7.123	-0.826	-0.826	0.000	0.000	0.000	0.000
61	A	66	HIS	0	0.027	0.008	8.995	0.118	0.118	0.000	0.000	0.000	0.000
62	A	67	ILE	0	-0.045	-0.013	12.473	0.056	0.056	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.930	-0.975	10.967	-1.107	-1.107	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.021	0.002	12.151	0.118	0.118	0.000	0.000	0.000	0.000
65	A	70	LEU	0	-0.078	-0.031	14.577	0.068	0.068	0.000	0.000	0.000	0.000
66	A	71	PHE	0	0.001	-0.028	16.679	0.036	0.036	0.000	0.000	0.000	0.000
67	A	72	ALA	0	0.014	0.024	15.834	0.014	0.014	0.000	0.000	0.000	0.000
68	A	73	ASN	0	-0.019	0.013	17.822	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.811	-0.875	21.056	-0.364	-0.364	0.000	0.000	0.000	0.000
70	A	75	SER	0	-0.039	-0.038	22.973	0.026	0.026	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.088	-0.045	21.464	0.022	0.022	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.004	-0.011	25.690	0.012	0.012	0.000	0.000	0.000	0.000
73	A	78	GLU	-1	-0.869	-0.938	28.425	-0.205	-0.205	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.008	-0.004	30.581	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	80	TRP	0	-0.033	-0.012	23.272	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	81	ASN	0	-0.020	-0.027	27.667	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	82	LYS	1	0.987	0.977	26.238	0.214	0.214	0.000	0.000	0.000	0.000
78	A	83	ARG	1	0.997	1.011	24.711	0.356	0.356	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.842	0.933	23.488	0.345	0.345	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.047	0.018	21.441	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.808	-0.891	20.106	-0.619	-0.619	0.000	0.000	0.000	0.000
82	A	87	ASN	0	-0.046	-0.028	18.969	-0.071	-0.071	0.000	0.000	0.000	0.000
83	A	88	PHE	0	-0.053	-0.032	16.928	-0.141	-0.141	0.000	0.000	0.000	0.000
84	A	89	GLN	0	0.041	0.000	15.785	-0.140	-0.140	0.000	0.000	0.000	0.000
85	A	90	ASN	0	-0.016	-0.006	14.277	-0.217	-0.217	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.107	-0.055	13.450	-0.228	-0.228	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.018	0.005	11.431	-0.321	-0.321	0.000	0.000	0.000	0.000
88	A	93	TYR	0	0.081	0.052	9.809	-0.622	-0.622	0.000	0.000	0.000	0.000
89	A	94	ARG	1	0.766	0.862	8.619	0.948	0.948	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.046	-0.034	8.117	-0.674	-0.674	0.000	0.000	0.000	0.000
91	A	96	THR	0	0.084	0.054	5.284	-1.661	-1.561	-0.002	-0.001	-0.097	0.000
92	A	97	LYS	1	0.937	0.971	3.718	-3.816	-3.491	0.046	-0.168	-0.203	-0.002
93	A	98	GLU	-1	-0.858	-0.918	4.328	-4.579	-4.240	-0.001	-0.062	-0.275	0.000
94	A	99	ASN	0	-0.009	-0.021	3.104	-0.666	2.705	1.975	-2.043	-3.303	-0.015
97	A	103	MET	0	-0.014	-0.004	2.098	-10.652	-10.774	5.051	-0.310	-4.619	0.040
98	A	104	ARG	1	0.942	0.979	3.110	-12.539	-10.522	0.334	-0.692	-1.660	0.001
99	A	105	MET	0	-0.070	-0.011	2.783	-3.272	-2.369	0.229	-0.181	-0.951	0.000
100	A	106	ARG	1	1.017	0.998	7.464	-1.081	-1.081	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.028	0.033	10.718	-0.340	-0.340	0.000	0.000	0.000	0.000
102	A	108	GLN	0	-0.035	-0.039	11.627	-0.121	-0.121	0.000	0.000	0.000	0.000
103	A	109	GLY	0	-0.018	0.002	14.319	-0.094	-0.094	0.000	0.000	0.000	0.000
104	A	110	THR	0	0.026	0.007	17.323	0.094	0.094	0.000	0.000	0.000	0.000
105	A	111	VAL	0	0.003	0.008	19.659	0.035	0.035	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.879	-0.943	12.797	1.674	1.674	0.000	0.000	0.000	0.000
107	A	113	ASP	-1	-0.782	-0.898	14.596	0.587	0.587	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.025	-0.029	9.266	0.090	0.090	0.000	0.000	0.000	0.000
109	A	115	PRO	0	0.029	0.019	13.154	-0.059	-0.059	0.000	0.000	0.000	0.000
110	A	116	ALA	0	0.069	0.039	14.690	-0.087	-0.087	0.000	0.000	0.000	0.000
111	A	117	ARG	1	0.711	0.831	13.377	-0.474	-0.474	0.000	0.000	0.000	0.000
112	A	118	ASP	-1	-0.846	-0.931	11.733	1.248	1.248	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.815	-0.900	13.662	0.642	0.642	0.000	0.000	0.000	0.000
114	A	120	ALA	0	-0.034	-0.011	17.217	-0.105	-0.105	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.019	-0.020	12.639	-0.102	-0.102	0.000	0.000	0.000	0.000
116	A	122	LYS	1	0.835	0.919	13.849	-1.104	-1.104	0.000	0.000	0.000	0.000
117	A	123	SER	0	-0.042	-0.024	16.889	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	124	TYR	0	-0.088	-0.070	17.854	-0.038	-0.038	0.000	0.000	0.000	0.000
119	A	125	PHE	0	0.073	0.014	14.971	-0.052	-0.052	0.000	0.000	0.000	0.000
120	A	126	ASN	0	0.030	0.019	18.557	-0.044	-0.044	0.000	0.000	0.000	0.000
121	A	127	LYS	1	0.914	0.965	20.991	-0.066	-0.066	0.000	0.000	0.000	0.000
122	A	128	LEU	0	0.010	0.012	19.281	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	129	ALA	0	0.054	0.026	20.619	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	130	THR	0	-0.060	-0.040	22.599	0.011	0.011	0.000	0.000	0.000	0.000
125	A	131	LEU	0	-0.035	-0.001	25.766	0.003	0.003	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.010	0.007	22.738	0.002	0.002	0.000	0.000	0.000	0.000
127	A	133	ARG	1	0.932	0.981	25.501	-0.038	-0.038	0.000	0.000	0.000	0.000
128	A	134	ASN	0	-0.042	-0.038	28.195	0.009	0.009	0.000	0.000	0.000	0.000
129	A	135	LYS	1	0.800	0.896	30.346	0.084	0.084	0.000	0.000	0.000	0.000
130	A	136	ASP	-1	-0.894	-0.939	30.933	-0.069	-0.069	0.000	0.000	0.000	0.000
131	A	137	ASN	0	-0.040	-0.030	26.251	-0.024	-0.024	0.000	0.000	0.000	0.000
132	A	138	SER	0	0.039	0.034	29.083	-0.019	-0.019	0.000	0.000	0.000	0.000
133	A	139	PHE	0	0.080	0.013	30.039	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	141	ALA	0	0.014	0.020	28.514	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	142	TRP	0	0.062	0.018	20.956	-0.027	-0.027	0.000	0.000	0.000	0.000
136	A	143	GLU	-1	-0.780	-0.869	25.860	-0.288	-0.288	0.000	0.000	0.000	0.000
137	A	144	VAL	0	-0.007	0.000	26.951	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	145	VAL	0	0.003	0.004	21.477	-0.014	-0.014	0.000	0.000	0.000	0.000
139	A	146	ARG	1	0.749	0.852	22.634	0.279	0.279	0.000	0.000	0.000	0.000
140	A	147	HIS	0	-0.032	-0.017	23.354	-0.026	-0.026	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.846	-0.904	22.463	-0.202	-0.202	0.000	0.000	0.000	0.000
142	A	149	LEU	0	-0.023	-0.019	17.372	-0.030	-0.030	0.000	0.000	0.000	0.000
143	A	150	LEU	0	-0.017	0.002	19.536	-0.071	-0.071	0.000	0.000	0.000	0.000
144	A	151	GLY	0	0.030	0.016	21.568	-0.038	-0.038	0.000	0.000	0.000	0.000
145	A	152	VAL	0	-0.006	0.004	16.255	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	153	LEU	0	0.002	-0.016	14.962	-0.071	-0.071	0.000	0.000	0.000	0.000
147	A	154	SER	0	0.005	0.000	17.873	-0.068	-0.068	0.000	0.000	0.000	0.000
148	A	155	ASP	-1	-0.814	-0.881	19.143	-0.337	-0.337	0.000	0.000	0.000	0.000
149	A	156	ILE	0	-0.053	-0.022	13.199	-0.051	-0.051	0.000	0.000	0.000	0.000
150	A	157	ILE	0	-0.089	-0.040	15.260	-0.124	-0.124	0.000	0.000	0.000	0.000
151	A	158	GLN	0	-0.037	-0.014	16.935	-0.117	-0.117	0.000	0.000	0.000	0.000
152	A	159	PRO	0	0.021	0.036	15.669	0.084	0.084	0.000	0.000	0.000	0.000

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