FMO DATABASE

FMODB ID: ZV2QN

Calculation Name: 4PNH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PNH

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T109

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1421870.960158
FMO2-HF: Nuclear repulsion	1363519.370965
FMO2-HF: Total energy	-58351.589193
FMO2-MP2: Total energy	-58521.163535

3D Structure Molmil

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
-53.779	-51.126	-0.025	-1.093	-1.535	0.006

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 0.964

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	9	LEU	0	0.008	0.007	3.806	-1.789	0.262	-0.026	-1.024	-1.001	0.006
4	A	10	VAL	0	0.042	0.021	6.469	1.938	1.938	0.000	0.000	0.000	0.000
5	A	11	VAL	0	-0.016	0.001	10.098	0.096	0.096	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.019	0.007	12.751	1.062	1.062	0.000	0.000	0.000	0.000
7	A	13	ASP	-1	-0.786	-0.869	15.688	-13.375	-13.375	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.847	0.898	19.013	12.385	12.385	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.783	-0.882	20.373	-11.232	-11.232	0.000	0.000	0.000	0.000
10	A	16	GLY	0	-0.039	-0.007	24.067	-0.044	-0.044	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.034	0.016	19.163	0.109	0.109	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.016	-0.003	17.108	-0.081	-0.081	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.038	-0.014	21.396	-0.147	-0.147	0.000	0.000	0.000	0.000
14	A	20	VAL	0	-0.015	0.003	24.650	0.130	0.130	0.000	0.000	0.000	0.000
15	A	28	SER	0	-0.014	-0.035	33.692	0.045	0.045	0.000	0.000	0.000	0.000
16	A	29	PRO	0	0.002	-0.007	28.731	-0.142	-0.142	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.772	-0.899	28.173	-10.488	-10.488	0.000	0.000	0.000	0.000
18	A	31	GLU	-1	-0.962	-0.944	29.579	-8.652	-8.652	0.000	0.000	0.000	0.000
19	A	32	TRP	0	-0.053	-0.033	20.961	-0.077	-0.077	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.015	-0.009	27.015	-0.083	-0.083	0.000	0.000	0.000	0.000
21	A	34	ALA	0	0.015	0.009	22.570	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	35	LEU	0	0.024	0.004	24.020	0.459	0.459	0.000	0.000	0.000	0.000
23	A	36	PRO	0	0.052	0.006	23.322	-0.532	-0.532	0.000	0.000	0.000	0.000
24	A	37	GLY	0	0.035	0.018	23.076	-0.335	-0.335	0.000	0.000	0.000	0.000
25	A	38	SER	0	0.007	-0.010	20.051	-0.423	-0.423	0.000	0.000	0.000	0.000
26	A	39	LEU	0	-0.011	0.000	18.408	-0.825	-0.825	0.000	0.000	0.000	0.000
27	A	40	GLU	-1	-0.794	-0.859	17.931	-13.632	-13.632	0.000	0.000	0.000	0.000
28	A	41	ALA	0	-0.011	-0.009	17.367	-0.755	-0.755	0.000	0.000	0.000	0.000
29	A	42	ILE	0	0.009	0.005	13.131	-1.067	-1.067	0.000	0.000	0.000	0.000
30	A	43	ALA	0	0.072	0.048	12.892	-1.482	-1.482	0.000	0.000	0.000	0.000
31	A	44	ARG	1	0.922	0.964	13.536	14.900	14.900	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.013	-0.003	10.841	-0.934	-0.934	0.000	0.000	0.000	0.000
33	A	46	ASN	0	0.002	-0.006	8.955	-0.609	-0.609	0.000	0.000	0.000	0.000
34	A	47	HIS	0	0.003	0.015	8.947	-2.275	-2.275	0.000	0.000	0.000	0.000
35	A	48	ALA	0	-0.010	0.006	9.891	-0.295	-0.295	0.000	0.000	0.000	0.000
36	A	49	GLY	0	-0.023	-0.019	6.085	-1.622	-1.622	0.000	0.000	0.000	0.000
37	A	50	TYR	0	-0.051	-0.028	4.503	-6.596	-6.421	-0.001	-0.010	-0.164	0.000
38	A	51	ARG	1	0.872	0.923	3.481	43.377	43.804	0.002	-0.059	-0.370	0.000
39	A	52	VAL	0	0.026	0.008	6.023	0.689	0.689	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.013	0.018	8.884	0.700	0.700	0.000	0.000	0.000	0.000
41	A	54	VAL	0	-0.015	-0.007	11.387	0.937	0.937	0.000	0.000	0.000	0.000
42	A	55	ALA	0	0.000	-0.016	15.129	0.256	0.256	0.000	0.000	0.000	0.000
43	A	56	THR	0	0.042	0.014	17.323	0.830	0.830	0.000	0.000	0.000	0.000
44	A	57	ASN	0	0.039	0.026	20.802	0.006	0.006	0.000	0.000	0.000	0.000
45	A	58	GLN	0	0.076	0.024	23.522	0.328	0.328	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.055	-0.033	25.652	0.456	0.456	0.000	0.000	0.000	0.000
47	A	60	GLY	0	-0.037	-0.036	27.118	0.430	0.430	0.000	0.000	0.000	0.000
48	A	61	ILE	0	0.005	0.021	24.754	-0.172	-0.172	0.000	0.000	0.000	0.000
49	A	62	GLY	0	0.006	-0.013	28.548	0.240	0.240	0.000	0.000	0.000	0.000
50	A	63	ARG	1	0.882	0.930	31.150	8.585	8.585	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.010	0.012	30.434	0.211	0.211	0.000	0.000	0.000	0.000
52	A	65	LEU	0	-0.017	0.018	31.463	0.114	0.114	0.000	0.000	0.000	0.000
53	A	66	PHE	0	-0.021	-0.024	27.708	-0.100	-0.100	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.754	-0.836	31.855	-9.331	-9.331	0.000	0.000	0.000	0.000
55	A	68	MET	0	0.056	-0.003	25.612	-0.299	-0.299	0.000	0.000	0.000	0.000
56	A	69	ALA	0	-0.025	0.005	28.561	-0.380	-0.380	0.000	0.000	0.000	0.000
57	A	70	THR	0	-0.018	-0.036	29.569	-0.199	-0.199	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.008	-0.004	24.022	-0.298	-0.298	0.000	0.000	0.000	0.000
59	A	72	ASN	0	-0.061	-0.039	24.785	-0.851	-0.851	0.000	0.000	0.000	0.000
60	A	73	ALA	0	0.014	0.021	24.701	-0.447	-0.447	0.000	0.000	0.000	0.000
61	A	74	MET	0	0.044	0.045	24.169	-0.278	-0.278	0.000	0.000	0.000	0.000
62	A	75	HIS	0	0.039	0.011	17.042	-0.230	-0.230	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.020	-0.011	20.795	-0.546	-0.546	0.000	0.000	0.000	0.000
64	A	77	LYS	1	0.837	0.912	22.814	10.298	10.298	0.000	0.000	0.000	0.000
65	A	78	MET	0	-0.029	-0.014	18.448	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	79	HIS	0	-0.024	-0.007	16.017	-0.709	-0.709	0.000	0.000	0.000	0.000
67	A	80	ARG	1	0.926	0.946	19.252	11.017	11.017	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.024	0.002	21.133	0.169	0.169	0.000	0.000	0.000	0.000
69	A	82	ALA	0	0.020	0.010	16.119	0.033	0.033	0.000	0.000	0.000	0.000
70	A	83	ALA	0	0.016	0.006	17.988	-0.225	-0.225	0.000	0.000	0.000	0.000
71	A	84	ALA	0	-0.046	-0.009	18.958	0.101	0.101	0.000	0.000	0.000	0.000
72	A	85	VAL	0	-0.032	-0.015	18.161	0.407	0.407	0.000	0.000	0.000	0.000
73	A	86	GLY	0	-0.019	0.004	16.946	-0.327	-0.327	0.000	0.000	0.000	0.000
74	A	87	GLY	0	-0.014	0.003	13.867	-0.947	-0.947	0.000	0.000	0.000	0.000
75	A	88	ARG	1	0.806	0.871	9.612	23.446	23.446	0.000	0.000	0.000	0.000
76	A	89	ILE	0	0.019	0.012	10.942	-0.892	-0.892	0.000	0.000	0.000	0.000
77	A	90	ASP	-1	-0.836	-0.907	8.626	-28.000	-28.000	0.000	0.000	0.000	0.000
78	A	91	ALA	0	-0.013	0.003	11.728	0.112	0.112	0.000	0.000	0.000	0.000
79	A	92	VAL	0	-0.004	0.004	13.695	0.034	0.034	0.000	0.000	0.000	0.000
80	A	93	PHE	0	0.012	-0.010	16.490	0.542	0.542	0.000	0.000	0.000	0.000
81	A	94	PHE	0	0.024	0.006	20.148	-0.131	-0.131	0.000	0.000	0.000	0.000
82	A	95	CYS	0	0.052	0.037	21.929	0.677	0.677	0.000	0.000	0.000	0.000
83	A	112	MET	0	-0.029	-0.012	19.306	0.389	0.389	0.000	0.000	0.000	0.000
84	A	113	MET	0	0.054	0.022	15.378	-0.561	-0.561	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.953	0.961	16.716	11.868	11.868	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.047	0.032	17.458	-0.074	-0.074	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.038	-0.010	12.684	-0.865	-0.865	0.000	0.000	0.000	0.000
88	A	117	ALA	0	-0.001	-0.018	12.073	-1.643	-1.643	0.000	0.000	0.000	0.000
89	A	118	GLU	-1	-0.942	-0.945	12.186	-18.539	-18.539	0.000	0.000	0.000	0.000
90	A	119	ARG	1	0.882	0.953	11.722	20.798	20.798	0.000	0.000	0.000	0.000
91	A	120	PHE	0	-0.078	-0.050	7.636	-1.174	-1.174	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.892	-0.933	6.536	-34.044	-34.044	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.075	-0.058	5.566	-6.348	-6.348	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.788	-0.891	7.586	-19.928	-19.928	0.000	0.000	0.000	0.000
95	A	124	PRO	0	-0.018	-0.015	10.047	-0.620	-0.620	0.000	0.000	0.000	0.000
96	A	125	ALA	0	-0.003	0.010	12.752	0.685	0.685	0.000	0.000	0.000	0.000
97	A	126	ASP	-1	-0.966	-0.971	8.862	-25.485	-25.485	0.000	0.000	0.000	0.000
98	A	127	THR	0	-0.117	-0.066	9.707	-2.571	-2.571	0.000	0.000	0.000	0.000
99	A	128	PRO	0	-0.045	-0.002	11.138	1.743	1.743	0.000	0.000	0.000	0.000
100	A	129	VAL	0	0.001	-0.002	13.591	-0.959	-0.959	0.000	0.000	0.000	0.000
101	A	130	VAL	0	-0.013	-0.007	15.645	0.905	0.905	0.000	0.000	0.000	0.000
102	A	131	GLY	0	0.058	0.019	18.185	-0.110	-0.110	0.000	0.000	0.000	0.000
103	A	132	ASP	-1	-0.701	-0.819	21.435	-11.095	-11.095	0.000	0.000	0.000	0.000
104	A	133	SER	0	-0.060	-0.021	24.554	0.609	0.609	0.000	0.000	0.000	0.000
105	A	134	LEU	0	0.100	0.048	25.151	-0.422	-0.422	0.000	0.000	0.000	0.000
106	A	135	ARG	1	0.777	0.862	21.965	12.422	12.422	0.000	0.000	0.000	0.000
107	A	136	ASP	-1	-0.835	-0.913	19.779	-14.708	-14.708	0.000	0.000	0.000	0.000
108	A	137	LEU	0	0.039	0.036	20.573	-0.483	-0.483	0.000	0.000	0.000	0.000
109	A	138	GLN	0	0.031	0.014	22.303	-0.161	-0.161	0.000	0.000	0.000	0.000
110	A	139	ALA	0	-0.048	-0.028	22.377	-0.047	-0.047	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.004	-0.008	18.856	-0.362	-0.362	0.000	0.000	0.000	0.000
112	A	141	ALA	0	0.016	0.006	18.833	-0.503	-0.503	0.000	0.000	0.000	0.000
113	A	142	ALA	0	-0.058	-0.022	20.922	0.025	0.025	0.000	0.000	0.000	0.000
114	A	143	LEU	0	-0.045	-0.033	16.246	0.127	0.127	0.000	0.000	0.000	0.000
115	A	144	GLY	0	0.015	0.024	17.112	-0.648	-0.648	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.029	-0.013	12.624	-0.494	-0.494	0.000	0.000	0.000	0.000
117	A	146	ARG	1	0.986	0.995	15.431	18.736	18.736	0.000	0.000	0.000	0.000
118	A	147	PRO	0	-0.020	-0.005	17.193	-0.467	-0.467	0.000	0.000	0.000	0.000
119	A	148	HIS	0	-0.024	-0.040	17.123	-0.295	-0.295	0.000	0.000	0.000	0.000
120	A	149	LEU	0	-0.013	-0.016	20.479	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	150	VAL	0	-0.019	-0.007	21.260	0.048	0.048	0.000	0.000	0.000	0.000
122	A	151	LEU	0	-0.057	-0.029	24.045	0.368	0.368	0.000	0.000	0.000	0.000
123	A	152	THR	0	0.012	-0.002	24.922	0.355	0.355	0.000	0.000	0.000	0.000
124	A	153	GLY	0	0.036	0.015	27.295	-0.152	-0.152	0.000	0.000	0.000	0.000
125	A	154	LYS	1	0.756	0.846	26.672	11.294	11.294	0.000	0.000	0.000	0.000
126	A	155	GLY	0	0.096	0.049	27.895	0.158	0.158	0.000	0.000	0.000	0.000
127	A	156	LYS	1	0.897	0.954	28.527	9.689	9.689	0.000	0.000	0.000	0.000
128	A	157	LYS	1	0.951	0.978	31.890	8.904	8.904	0.000	0.000	0.000	0.000
129	A	158	THR	0	-0.056	-0.066	27.734	0.255	0.255	0.000	0.000	0.000	0.000
130	A	159	LEU	0	-0.014	-0.010	29.339	0.038	0.038	0.000	0.000	0.000	0.000
131	A	160	ALA	0	-0.047	-0.021	31.264	0.107	0.107	0.000	0.000	0.000	0.000
132	A	161	ALA	0	-0.050	-0.017	33.412	0.198	0.198	0.000	0.000	0.000	0.000
133	A	162	GLY	0	0.022	0.029	32.674	0.140	0.140	0.000	0.000	0.000	0.000
134	A	163	GLY	0	-0.005	-0.006	32.424	-0.023	-0.023	0.000	0.000	0.000	0.000
135	A	164	LEU	0	-0.058	-0.033	26.661	-0.269	-0.269	0.000	0.000	0.000	0.000
136	A	165	PRO	0	0.010	-0.006	24.267	0.196	0.196	0.000	0.000	0.000	0.000
137	A	166	GLU	-1	-0.879	-0.919	26.040	-10.483	-10.483	0.000	0.000	0.000	0.000
138	A	167	GLY	0	-0.005	0.013	23.038	0.117	0.117	0.000	0.000	0.000	0.000
139	A	168	THR	0	-0.076	-0.058	22.249	-0.740	-0.740	0.000	0.000	0.000	0.000
140	A	169	ARG	1	0.841	0.904	19.461	14.783	14.783	0.000	0.000	0.000	0.000
141	A	170	VAL	0	0.017	0.007	23.119	-0.141	-0.141	0.000	0.000	0.000	0.000
142	A	171	HIS	0	0.024	0.025	20.892	-0.329	-0.329	0.000	0.000	0.000	0.000
143	A	172	ASP	-1	-0.814	-0.924	24.336	-9.925	-9.925	0.000	0.000	0.000	0.000
144	A	173	ASP	-1	-0.821	-0.931	24.000	-12.010	-12.010	0.000	0.000	0.000	0.000
145	A	174	LEU	0	0.025	0.013	16.877	-0.340	-0.340	0.000	0.000	0.000	0.000
146	A	175	ARG	1	0.811	0.877	19.325	11.584	11.584	0.000	0.000	0.000	0.000
147	A	176	ALA	0	-0.019	-0.012	20.452	-0.323	-0.323	0.000	0.000	0.000	0.000
148	A	177	PHE	0	0.011	0.013	14.106	-0.229	-0.229	0.000	0.000	0.000	0.000
149	A	178	ALA	0	0.033	0.024	15.727	-0.533	-0.533	0.000	0.000	0.000	0.000
150	A	179	LEU	0	-0.068	-0.034	16.235	-0.557	-0.557	0.000	0.000	0.000	0.000
151	A	180	ASP	-1	-0.839	-0.915	18.535	-14.456	-14.456	0.000	0.000	0.000	0.000
152	A	181	PHE	0	-0.004	-0.020	10.433	-0.492	-0.492	0.000	0.000	0.000	0.000
153	A	182	LEU	0	-0.088	-0.041	11.345	-1.011	-1.011	0.000	0.000	0.000	0.000
154	A	183	SER	0	-0.024	-0.014	14.755	0.970	0.970	0.000	0.000	0.000	0.000
155	A	184	LYN	0	-0.031	0.030	12.619	0.117	0.117	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)