FMO DATABASE

FMODB ID: 6N6LZ

Calculation Name: 2FDB-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FDB

Chain ID: M

ChEMBL ID:

UniProt ID: P55075

Base Structure: X-ray

Registration Date: 2023-06-21

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1512948.374065
FMO2-HF: Nuclear repulsion	1452246.48284
FMO2-HF: Total energy	-60701.891224
FMO2-MP2: Total energy	-60878.321289

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(M:32:PHE)

Summations of interaction energy for fragment #1(M:32:PHE)

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.
-6.215	-2.227	0.725	-1.598	-3.115	-0.001

Interaction energy analysis for fragmet #1(M:32:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.021

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	M	34	GLN	0	0.013	-0.002	3.826	-2.551	-1.098	-0.008	-0.590	-0.855	0.003
4	M	35	HIS	0	0.077	0.042	2.554	-2.787	-1.062	0.679	-0.750	-1.653	-0.004
5	M	36	VAL	0	0.039	0.014	3.012	-0.649	0.161	0.054	-0.258	-0.607	0.000
6	M	37	ARG	1	0.880	0.958	5.431	-0.945	-0.945	0.000	0.000	0.000	0.000
7	M	38	GLU	-1	-0.853	-0.915	7.685	0.738	0.738	0.000	0.000	0.000	0.000
8	M	39	GLN	0	0.012	-0.007	7.065	-0.056	-0.056	0.000	0.000	0.000	0.000
9	M	40	SER	0	-0.076	-0.052	8.764	-0.015	-0.015	0.000	0.000	0.000	0.000
10	M	41	LEU	0	-0.088	-0.025	10.975	0.011	0.011	0.000	0.000	0.000	0.000
11	M	42	VAL	0	-0.058	-0.033	13.549	0.003	0.003	0.000	0.000	0.000	0.000
12	M	43	THR	0	-0.067	-0.062	13.938	-0.016	-0.016	0.000	0.000	0.000	0.000
13	M	44	ASP	-1	-0.778	-0.863	10.843	-0.299	-0.299	0.000	0.000	0.000	0.000
14	M	45	GLN	0	-0.093	-0.074	13.658	0.009	0.009	0.000	0.000	0.000	0.000
15	M	46	LEU	0	0.014	0.018	11.946	0.012	0.012	0.000	0.000	0.000	0.000
16	M	47	SER	0	-0.003	0.002	10.813	-0.057	-0.057	0.000	0.000	0.000	0.000
17	M	48	ARG	1	0.945	0.971	13.502	0.248	0.248	0.000	0.000	0.000	0.000
18	M	49	ARG	1	0.777	0.872	14.978	0.120	0.120	0.000	0.000	0.000	0.000
19	M	50	LEU	0	-0.024	-0.007	15.637	0.011	0.011	0.000	0.000	0.000	0.000
20	M	51	ILE	0	0.035	0.007	17.818	0.013	0.013	0.000	0.000	0.000	0.000
21	M	52	ARG	1	0.933	0.977	17.649	0.121	0.121	0.000	0.000	0.000	0.000
22	M	53	THR	0	0.034	0.012	22.923	0.005	0.005	0.000	0.000	0.000	0.000
23	M	54	TYR	0	-0.019	-0.019	22.572	0.001	0.001	0.000	0.000	0.000	0.000
24	M	55	GLN	0	0.008	0.010	28.468	0.005	0.005	0.000	0.000	0.000	0.000
25	M	56	LEU	0	0.012	0.010	26.409	-0.001	-0.001	0.000	0.000	0.000	0.000
26	M	57	TYR	0	0.017	0.014	30.303	0.003	0.003	0.000	0.000	0.000	0.000
27	M	58	SER	0	0.028	0.007	31.916	0.002	0.002	0.000	0.000	0.000	0.000
28	M	59	ARG	1	0.902	0.956	32.487	0.002	0.002	0.000	0.000	0.000	0.000
29	M	60	THR	0	-0.036	-0.016	34.954	0.002	0.002	0.000	0.000	0.000	0.000
30	M	61	SER	0	-0.057	-0.050	37.404	0.000	0.000	0.000	0.000	0.000	0.000
31	M	62	GLY	0	-0.004	0.023	37.793	0.000	0.000	0.000	0.000	0.000	0.000
32	M	63	LYS	1	0.838	0.909	38.221	0.017	0.017	0.000	0.000	0.000	0.000
33	M	64	HIS	0	0.033	0.021	33.583	-0.002	-0.002	0.000	0.000	0.000	0.000
34	M	65	VAL	0	-0.076	-0.037	31.413	0.002	0.002	0.000	0.000	0.000	0.000
35	M	66	GLN	0	0.035	0.013	33.952	-0.005	-0.005	0.000	0.000	0.000	0.000
36	M	67	VAL	0	-0.051	-0.038	32.470	0.004	0.004	0.000	0.000	0.000	0.000
37	M	68	LEU	0	0.042	0.022	35.777	-0.002	-0.002	0.000	0.000	0.000	0.000
38	M	69	ALA	0	0.110	0.050	38.920	0.001	0.001	0.000	0.000	0.000	0.000
39	M	70	ASN	0	-0.016	-0.001	40.955	0.000	0.000	0.000	0.000	0.000	0.000
40	M	71	LYS	1	0.944	0.964	37.516	0.021	0.021	0.000	0.000	0.000	0.000
41	M	72	ARG	1	0.814	0.943	36.920	0.008	0.008	0.000	0.000	0.000	0.000
42	M	73	ILE	0	0.047	0.006	32.952	-0.001	-0.001	0.000	0.000	0.000	0.000
43	M	74	ASN	0	-0.052	-0.030	36.870	0.003	0.003	0.000	0.000	0.000	0.000
44	M	75	ALA	0	0.042	0.018	35.487	-0.002	-0.002	0.000	0.000	0.000	0.000
45	M	76	MET	0	-0.031	-0.024	37.254	0.001	0.001	0.000	0.000	0.000	0.000
46	M	77	ALA	0	0.047	0.059	37.612	0.000	0.000	0.000	0.000	0.000	0.000
47	M	78	GLU	-1	-0.748	-0.869	39.012	-0.022	-0.022	0.000	0.000	0.000	0.000
48	M	79	ASP	-1	-0.810	-0.900	36.877	-0.042	-0.042	0.000	0.000	0.000	0.000
49	M	80	GLY	0	0.013	-0.008	37.032	0.000	0.000	0.000	0.000	0.000	0.000
50	M	81	ASP	-1	-0.850	-0.909	38.240	-0.031	-0.031	0.000	0.000	0.000	0.000
51	M	82	PRO	0	0.047	0.013	37.269	-0.002	-0.002	0.000	0.000	0.000	0.000
52	M	83	PHE	0	0.024	0.012	36.286	-0.002	-0.002	0.000	0.000	0.000	0.000
53	M	84	ALA	0	-0.043	-0.039	34.679	0.002	0.002	0.000	0.000	0.000	0.000
54	M	85	LYS	1	0.828	0.935	32.348	0.043	0.043	0.000	0.000	0.000	0.000
55	M	86	LEU	0	-0.039	-0.022	28.298	0.002	0.002	0.000	0.000	0.000	0.000
56	M	87	ILE	0	0.015	0.000	25.067	-0.005	-0.005	0.000	0.000	0.000	0.000
57	M	88	VAL	0	-0.037	-0.028	21.072	0.005	0.005	0.000	0.000	0.000	0.000
58	M	89	GLU	-1	-0.792	-0.875	19.593	-0.100	-0.100	0.000	0.000	0.000	0.000
59	M	90	THR	0	-0.006	-0.009	15.021	0.006	0.006	0.000	0.000	0.000	0.000
60	M	91	ASP	-1	-0.822	-0.892	16.599	-0.063	-0.063	0.000	0.000	0.000	0.000
61	M	92	THR	0	0.049	0.014	11.521	-0.030	-0.030	0.000	0.000	0.000	0.000
62	M	93	PHE	0	0.025	0.015	6.495	-0.011	-0.011	0.000	0.000	0.000	0.000
63	M	94	GLY	0	0.035	0.013	10.455	0.038	0.038	0.000	0.000	0.000	0.000
64	M	95	SER	0	-0.010	-0.008	12.307	0.013	0.013	0.000	0.000	0.000	0.000
65	M	96	ARG	1	0.879	0.957	14.455	-0.014	-0.014	0.000	0.000	0.000	0.000
66	M	97	VAL	0	0.016	0.006	16.518	-0.019	-0.019	0.000	0.000	0.000	0.000
67	M	98	ARG	1	0.785	0.896	19.244	0.068	0.068	0.000	0.000	0.000	0.000
68	M	99	VAL	0	0.005	-0.007	22.614	-0.007	-0.007	0.000	0.000	0.000	0.000
69	M	100	ARG	1	0.889	0.936	25.655	0.061	0.061	0.000	0.000	0.000	0.000
70	M	101	GLY	0	0.037	0.026	28.289	-0.003	-0.003	0.000	0.000	0.000	0.000
71	M	102	ALA	0	-0.030	-0.027	31.112	0.000	0.000	0.000	0.000	0.000	0.000
72	M	103	GLU	-1	-0.879	-0.929	32.066	-0.043	-0.043	0.000	0.000	0.000	0.000
73	M	104	THR	0	-0.018	-0.011	35.266	0.000	0.000	0.000	0.000	0.000	0.000
74	M	105	GLY	0	0.046	0.035	32.024	0.001	0.001	0.000	0.000	0.000	0.000
75	M	106	LEU	0	-0.076	-0.035	31.793	0.001	0.001	0.000	0.000	0.000	0.000
76	M	107	TYR	0	0.039	0.009	25.170	-0.001	-0.001	0.000	0.000	0.000	0.000
77	M	108	ILE	0	0.006	0.004	28.523	0.006	0.006	0.000	0.000	0.000	0.000
78	M	109	CYS	0	-0.034	-0.005	27.792	-0.001	-0.001	0.000	0.000	0.000	0.000
79	M	110	MET	0	-0.004	0.030	28.758	0.003	0.003	0.000	0.000	0.000	0.000
80	M	111	ASN	0	0.032	0.015	30.032	0.005	0.005	0.000	0.000	0.000	0.000
81	M	112	LYS	1	1.076	1.023	32.329	-0.025	-0.025	0.000	0.000	0.000	0.000
82	M	113	LYS	1	0.896	0.953	33.310	-0.022	-0.022	0.000	0.000	0.000	0.000
83	M	114	GLY	0	0.051	0.026	32.328	0.000	0.000	0.000	0.000	0.000	0.000
84	M	115	LYS	1	0.889	0.954	33.411	-0.008	-0.008	0.000	0.000	0.000	0.000
85	M	116	LEU	0	0.069	0.038	30.562	0.000	0.000	0.000	0.000	0.000	0.000
86	M	117	ILE	0	-0.076	-0.059	32.754	0.000	0.000	0.000	0.000	0.000	0.000
87	M	118	ALA	0	0.082	0.050	32.522	-0.001	-0.001	0.000	0.000	0.000	0.000
88	M	119	LYS	1	0.799	0.893	29.163	0.007	0.007	0.000	0.000	0.000	0.000
89	M	120	SER	0	0.074	0.034	31.814	-0.002	-0.002	0.000	0.000	0.000	0.000
90	M	121	ASN	0	0.049	0.029	28.776	-0.008	-0.008	0.000	0.000	0.000	0.000
91	M	122	GLY	0	0.026	-0.003	27.018	0.006	0.006	0.000	0.000	0.000	0.000
92	M	123	LYS	1	0.982	0.994	20.356	0.038	0.038	0.000	0.000	0.000	0.000
93	M	124	GLY	0	0.022	0.012	23.562	0.002	0.002	0.000	0.000	0.000	0.000
94	M	125	LYS	1	1.006	0.990	19.431	-0.074	-0.074	0.000	0.000	0.000	0.000
95	M	126	ASP	-1	-0.831	-0.905	23.048	0.004	0.004	0.000	0.000	0.000	0.000
96	M	127	CYS	0	-0.090	-0.053	24.861	-0.001	-0.001	0.000	0.000	0.000	0.000
97	M	128	VAL	0	0.005	0.017	18.659	-0.007	-0.007	0.000	0.000	0.000	0.000
98	M	129	PHE	0	-0.044	-0.026	21.246	0.014	0.014	0.000	0.000	0.000	0.000
99	M	130	THR	0	0.047	0.031	16.697	-0.012	-0.012	0.000	0.000	0.000	0.000
100	M	131	GLU	-1	-0.873	-0.927	18.508	-0.054	-0.054	0.000	0.000	0.000	0.000
101	M	132	ILE	0	0.009	0.001	18.445	-0.003	-0.003	0.000	0.000	0.000	0.000
102	M	133	VAL	0	0.010	0.003	19.703	-0.004	-0.004	0.000	0.000	0.000	0.000
103	M	134	LEU	0	-0.030	-0.025	21.618	0.006	0.006	0.000	0.000	0.000	0.000
104	M	135	GLU	-1	-0.789	-0.890	23.805	0.029	0.029	0.000	0.000	0.000	0.000
105	M	136	ASN	0	-0.083	-0.041	25.314	-0.007	-0.007	0.000	0.000	0.000	0.000
106	M	137	ASN	0	-0.001	-0.014	25.324	-0.007	-0.007	0.000	0.000	0.000	0.000
107	M	138	TYR	0	-0.004	0.002	26.414	-0.006	-0.006	0.000	0.000	0.000	0.000
108	M	139	THR	0	-0.025	-0.015	23.351	-0.002	-0.002	0.000	0.000	0.000	0.000
109	M	140	ALA	0	0.024	0.014	23.984	0.004	0.004	0.000	0.000	0.000	0.000
110	M	141	LEU	0	0.012	0.006	22.482	-0.004	-0.004	0.000	0.000	0.000	0.000
111	M	142	GLN	0	0.033	0.031	21.077	0.000	0.000	0.000	0.000	0.000	0.000
112	M	143	ASN	0	-0.035	-0.030	22.312	0.001	0.001	0.000	0.000	0.000	0.000
113	M	144	ALA	0	0.068	0.033	19.924	0.009	0.009	0.000	0.000	0.000	0.000
114	M	145	LYS	1	0.870	0.952	21.536	-0.022	-0.022	0.000	0.000	0.000	0.000
115	M	146	TYR	0	0.001	-0.019	24.185	0.010	0.010	0.000	0.000	0.000	0.000
116	M	147	GLU	-1	-0.724	-0.859	19.753	0.060	0.060	0.000	0.000	0.000	0.000
117	M	148	GLY	0	0.041	0.042	24.060	0.001	0.001	0.000	0.000	0.000	0.000
118	M	149	TRP	0	-0.117	-0.063	27.071	-0.007	-0.007	0.000	0.000	0.000	0.000
119	M	150	TYR	0	0.044	0.007	24.172	-0.002	-0.002	0.000	0.000	0.000	0.000
120	M	151	MET	0	-0.053	-0.007	26.896	-0.001	-0.001	0.000	0.000	0.000	0.000
121	M	152	ALA	0	0.027	0.004	29.517	0.000	0.000	0.000	0.000	0.000	0.000
122	M	153	PHE	0	-0.009	-0.012	31.995	-0.001	-0.001	0.000	0.000	0.000	0.000
123	M	154	THR	0	-0.021	-0.005	36.060	0.001	0.001	0.000	0.000	0.000	0.000
124	M	155	ARG	1	0.990	0.991	39.377	0.004	0.004	0.000	0.000	0.000	0.000
125	M	156	LYS	1	0.962	0.970	41.425	-0.002	-0.002	0.000	0.000	0.000	0.000
126	M	157	GLY	0	0.090	0.049	39.145	-0.001	-0.001	0.000	0.000	0.000	0.000
127	M	158	ARG	1	0.922	0.967	39.508	-0.001	-0.001	0.000	0.000	0.000	0.000
128	M	159	PRO	0	0.037	0.019	36.381	0.001	0.001	0.000	0.000	0.000	0.000
129	M	160	ARG	1	0.766	0.866	35.551	-0.011	-0.011	0.000	0.000	0.000	0.000
130	M	161	LYS	1	0.916	0.948	34.913	-0.011	-0.011	0.000	0.000	0.000	0.000
131	M	162	GLY	0	0.118	0.048	31.974	0.001	0.001	0.000	0.000	0.000	0.000
132	M	163	SER	0	0.005	0.014	32.406	0.002	0.002	0.000	0.000	0.000	0.000
133	M	164	LYS	1	0.902	0.951	34.460	-0.028	-0.028	0.000	0.000	0.000	0.000
134	M	165	THR	0	-0.056	-0.035	31.095	-0.002	-0.002	0.000	0.000	0.000	0.000
135	M	166	ARG	1	0.975	0.980	30.700	-0.031	-0.031	0.000	0.000	0.000	0.000
136	M	167	GLN	0	0.060	0.015	23.815	-0.006	-0.006	0.000	0.000	0.000	0.000
137	M	168	HIS	0	0.106	0.054	28.926	-0.008	-0.008	0.000	0.000	0.000	0.000
138	M	169	GLN	0	-0.004	0.016	31.656	-0.001	-0.001	0.000	0.000	0.000	0.000
139	M	170	ARG	1	1.043	1.001	32.650	-0.006	-0.006	0.000	0.000	0.000	0.000
140	M	171	GLU	-1	-0.816	-0.882	33.944	0.008	0.008	0.000	0.000	0.000	0.000
141	M	172	VAL	0	-0.039	-0.019	28.882	-0.003	-0.003	0.000	0.000	0.000	0.000
142	M	173	HIS	0	-0.018	0.021	29.058	-0.005	-0.005	0.000	0.000	0.000	0.000
143	M	174	PHE	0	-0.040	-0.027	27.977	-0.001	-0.001	0.000	0.000	0.000	0.000
144	M	175	MET	0	0.043	0.034	28.396	0.001	0.001	0.000	0.000	0.000	0.000
145	M	176	LYS	1	0.799	0.895	21.416	0.063	0.063	0.000	0.000	0.000	0.000
146	M	177	ARG	1	0.858	0.904	27.641	0.038	0.038	0.000	0.000	0.000	0.000
147	M	178	LEU	0	0.070	0.034	28.153	-0.001	-0.001	0.000	0.000	0.000	0.000
148	M	179	PRO	0	0.007	0.009	29.493	0.006	0.006	0.000	0.000	0.000	0.000
149	M	180	ARG	1	0.936	0.984	32.640	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(M:32:PHE)