FMO DATABASE

FMODB ID: 947L2

Calculation Name: 2D6L-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D6L

Chain ID: X

ChEMBL ID:

UniProt ID: O08573

Base Structure: X-ray

Registration Date: 2023-06-22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1541568.01487
FMO2-HF: Nuclear repulsion	1480164.572522
FMO2-HF: Total energy	-61403.442348
FMO2-MP2: Total energy	-61580.399099

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(X:-1:GLY)

Summations of interaction energy for fragment #1(X:-1:GLY)

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.
11.211	1.673	8.271	4.323	-3.055	-0.021

Interaction energy analysis for fragmet #1(X:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.032

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	X	1	MET	0	-0.023	0.010	2.373	11.969	1.292	7.773	5.197	-2.292	-0.011
4	X	2	ALA	0	0.020	0.010	2.850	-2.375	-1.258	0.499	-0.869	-0.747	-0.010
5	X	3	LEU	0	-0.020	-0.016	5.015	-0.524	-0.502	-0.001	-0.005	-0.016	0.000
6	X	4	PHE	0	-0.013	-0.003	6.998	0.275	0.275	0.000	0.000	0.000	0.000
7	X	5	SER	0	-0.010	-0.014	10.354	-0.149	-0.149	0.000	0.000	0.000	0.000
8	X	6	ALA	0	-0.007	0.000	12.940	0.062	0.062	0.000	0.000	0.000	0.000
9	X	7	GLN	0	-0.002	0.005	15.595	0.045	0.045	0.000	0.000	0.000	0.000
10	X	8	SER	0	0.002	-0.009	16.314	-0.032	-0.032	0.000	0.000	0.000	0.000
11	X	9	PRO	0	-0.002	0.012	15.192	-0.019	-0.019	0.000	0.000	0.000	0.000
12	X	10	TYR	0	0.001	-0.016	17.185	0.047	0.047	0.000	0.000	0.000	0.000
13	X	11	ILE	0	0.012	-0.010	18.030	-0.043	-0.043	0.000	0.000	0.000	0.000
14	X	12	ASN	0	-0.043	-0.039	20.351	0.009	0.009	0.000	0.000	0.000	0.000
15	X	13	PRO	0	-0.006	0.023	21.238	0.021	0.021	0.000	0.000	0.000	0.000
16	X	14	ILE	0	0.019	-0.001	24.221	-0.010	-0.010	0.000	0.000	0.000	0.000
17	X	15	ILE	0	-0.045	-0.008	24.412	-0.003	-0.003	0.000	0.000	0.000	0.000
18	X	16	PRO	0	-0.033	-0.032	28.355	0.009	0.009	0.000	0.000	0.000	0.000
19	X	17	PHE	0	0.031	0.014	23.159	0.006	0.006	0.000	0.000	0.000	0.000
20	X	18	THR	0	-0.007	-0.012	27.102	-0.008	-0.008	0.000	0.000	0.000	0.000
21	X	19	GLY	0	0.002	0.013	25.174	0.013	0.013	0.000	0.000	0.000	0.000
22	X	20	PRO	0	0.024	0.017	24.871	-0.012	-0.012	0.000	0.000	0.000	0.000
23	X	21	ILE	0	-0.029	0.004	20.176	-0.025	-0.025	0.000	0.000	0.000	0.000
24	X	22	GLN	0	-0.003	-0.019	21.911	0.030	0.030	0.000	0.000	0.000	0.000
25	X	23	GLY	0	0.015	0.013	22.008	-0.005	-0.005	0.000	0.000	0.000	0.000
26	X	24	GLY	0	0.020	0.017	23.871	0.008	0.008	0.000	0.000	0.000	0.000
27	X	25	LEU	0	-0.070	-0.046	19.358	-0.018	-0.018	0.000	0.000	0.000	0.000
28	X	26	GLN	0	0.005	-0.003	18.910	0.033	0.033	0.000	0.000	0.000	0.000
29	X	27	GLU	-1	-0.836	-0.895	16.891	-0.244	-0.244	0.000	0.000	0.000	0.000
30	X	28	GLY	0	-0.022	-0.025	13.777	0.027	0.027	0.000	0.000	0.000	0.000
31	X	29	LEU	0	-0.065	-0.018	12.652	-0.088	-0.088	0.000	0.000	0.000	0.000
32	X	30	GLN	0	0.007	-0.011	8.067	-0.056	-0.056	0.000	0.000	0.000	0.000
33	X	31	VAL	0	0.022	0.011	12.598	0.030	0.030	0.000	0.000	0.000	0.000
34	X	32	THR	0	0.002	-0.002	10.427	-0.018	-0.018	0.000	0.000	0.000	0.000
35	X	33	LEU	0	-0.011	0.004	13.632	0.093	0.093	0.000	0.000	0.000	0.000
36	X	34	GLN	0	0.077	0.062	13.770	-0.146	-0.146	0.000	0.000	0.000	0.000
37	X	35	GLY	0	0.019	0.001	16.291	0.075	0.075	0.000	0.000	0.000	0.000
38	X	36	THR	0	-0.036	-0.003	19.736	-0.018	-0.018	0.000	0.000	0.000	0.000
39	X	37	THR	0	0.013	0.025	22.535	0.020	0.020	0.000	0.000	0.000	0.000
40	X	38	LYS	1	0.899	0.971	24.979	0.204	0.204	0.000	0.000	0.000	0.000
41	X	39	SER	0	0.085	0.016	28.434	-0.011	-0.011	0.000	0.000	0.000	0.000
42	X	40	PHE	0	-0.001	0.000	30.466	0.002	0.002	0.000	0.000	0.000	0.000
43	X	41	ALA	0	-0.021	0.001	29.144	0.006	0.006	0.000	0.000	0.000	0.000
44	X	42	GLN	0	0.045	0.013	31.158	-0.001	-0.001	0.000	0.000	0.000	0.000
45	X	43	ARG	1	0.883	0.895	30.217	0.161	0.161	0.000	0.000	0.000	0.000
46	X	44	PHE	0	-0.050	-0.014	22.624	0.010	0.010	0.000	0.000	0.000	0.000
47	X	45	VAL	0	0.011	0.013	27.095	-0.002	-0.002	0.000	0.000	0.000	0.000
48	X	46	VAL	0	-0.013	0.003	21.109	-0.002	-0.002	0.000	0.000	0.000	0.000
49	X	47	ASN	0	0.043	0.030	24.489	-0.008	-0.008	0.000	0.000	0.000	0.000
50	X	48	PHE	0	0.034	0.021	19.075	-0.005	-0.005	0.000	0.000	0.000	0.000
51	X	49	GLN	0	-0.052	-0.057	24.920	0.003	0.003	0.000	0.000	0.000	0.000
52	X	50	ASN	0	0.067	0.040	27.830	-0.014	-0.014	0.000	0.000	0.000	0.000
53	X	51	SER	0	-0.006	-0.007	30.026	0.013	0.013	0.000	0.000	0.000	0.000
54	X	52	PHE	0	0.062	0.011	31.284	-0.010	-0.010	0.000	0.000	0.000	0.000
55	X	53	ASN	0	-0.003	0.003	32.783	-0.008	-0.008	0.000	0.000	0.000	0.000
56	X	54	GLY	0	0.049	0.039	32.512	0.000	0.000	0.000	0.000	0.000	0.000
57	X	55	ASN	0	-0.018	-0.016	33.553	-0.003	-0.003	0.000	0.000	0.000	0.000
58	X	56	ASP	-1	-0.827	-0.906	32.985	-0.123	-0.123	0.000	0.000	0.000	0.000
59	X	57	ILE	0	-0.091	-0.035	28.346	-0.008	-0.008	0.000	0.000	0.000	0.000
60	X	58	ALA	0	0.085	0.041	26.286	0.002	0.002	0.000	0.000	0.000	0.000
61	X	59	PHE	0	-0.012	-0.006	20.884	-0.008	-0.008	0.000	0.000	0.000	0.000
62	X	60	HIS	0	-0.061	-0.018	25.702	-0.004	-0.004	0.000	0.000	0.000	0.000
63	X	61	PHE	0	0.055	0.013	21.405	-0.007	-0.007	0.000	0.000	0.000	0.000
64	X	62	ASN	0	-0.011	-0.022	25.254	0.012	0.012	0.000	0.000	0.000	0.000
65	X	63	PRO	0	0.020	0.010	24.210	0.014	0.014	0.000	0.000	0.000	0.000
66	X	64	ARG	1	0.833	0.916	27.219	0.197	0.197	0.000	0.000	0.000	0.000
67	X	65	PHE	0	-0.033	-0.034	26.033	-0.001	-0.001	0.000	0.000	0.000	0.000
68	X	66	GLU	-1	-0.802	-0.876	31.552	-0.152	-0.152	0.000	0.000	0.000	0.000
69	X	67	GLU	-1	-0.850	-0.920	34.081	-0.158	-0.158	0.000	0.000	0.000	0.000
70	X	68	GLY	0	0.020	0.018	33.892	0.000	0.000	0.000	0.000	0.000	0.000
71	X	69	GLY	0	-0.067	-0.033	30.135	-0.011	-0.011	0.000	0.000	0.000	0.000
72	X	70	TYR	0	-0.080	-0.051	28.941	-0.006	-0.006	0.000	0.000	0.000	0.000
73	X	71	VAL	0	-0.012	-0.015	24.434	-0.004	-0.004	0.000	0.000	0.000	0.000
74	X	72	VAL	0	-0.021	0.011	27.667	0.004	0.004	0.000	0.000	0.000	0.000
75	X	73	CYS	0	-0.045	-0.004	25.356	-0.028	-0.028	0.000	0.000	0.000	0.000
76	X	74	ASN	0	0.025	-0.006	27.704	0.015	0.015	0.000	0.000	0.000	0.000
77	X	75	THR	0	0.011	0.009	28.933	-0.016	-0.016	0.000	0.000	0.000	0.000
78	X	76	LYS	1	0.803	0.916	31.035	0.155	0.155	0.000	0.000	0.000	0.000
79	X	77	GLN	0	0.050	0.019	33.326	-0.008	-0.008	0.000	0.000	0.000	0.000
80	X	78	ASN	0	-0.017	-0.002	35.848	0.007	0.007	0.000	0.000	0.000	0.000
81	X	79	GLY	0	0.015	-0.002	37.457	0.005	0.005	0.000	0.000	0.000	0.000
82	X	80	GLN	0	-0.063	-0.039	38.324	0.001	0.001	0.000	0.000	0.000	0.000
83	X	81	TRP	0	-0.002	-0.014	31.485	-0.008	-0.008	0.000	0.000	0.000	0.000
84	X	82	GLY	0	0.048	0.038	34.799	0.008	0.008	0.000	0.000	0.000	0.000
85	X	83	PRO	0	0.022	0.019	34.245	-0.001	-0.001	0.000	0.000	0.000	0.000
86	X	84	GLU	-1	-0.765	-0.878	32.574	-0.180	-0.180	0.000	0.000	0.000	0.000
87	X	85	GLU	-1	-0.841	-0.899	27.617	-0.221	-0.221	0.000	0.000	0.000	0.000
88	X	86	ARG	1	0.841	0.905	29.159	0.150	0.150	0.000	0.000	0.000	0.000
89	X	87	LYS	1	0.878	0.958	22.514	0.362	0.362	0.000	0.000	0.000	0.000
90	X	88	MET	0	0.025	0.015	27.741	-0.007	-0.007	0.000	0.000	0.000	0.000
91	X	89	GLN	0	0.023	-0.016	23.292	-0.013	-0.013	0.000	0.000	0.000	0.000
92	X	90	MET	0	0.005	0.021	25.853	-0.021	-0.021	0.000	0.000	0.000	0.000
93	X	91	PRO	0	-0.045	-0.006	20.286	0.008	0.008	0.000	0.000	0.000	0.000
94	X	92	PHE	0	0.012	0.001	19.589	-0.036	-0.036	0.000	0.000	0.000	0.000
95	X	93	GLN	0	0.041	0.006	22.931	0.034	0.034	0.000	0.000	0.000	0.000
96	X	94	LYS	1	0.885	0.929	24.883	0.178	0.178	0.000	0.000	0.000	0.000
97	X	95	GLY	0	0.009	-0.003	26.919	0.007	0.007	0.000	0.000	0.000	0.000
98	X	96	MET	0	-0.023	0.015	21.861	0.006	0.006	0.000	0.000	0.000	0.000
99	X	97	PRO	0	-0.026	-0.029	18.292	-0.005	-0.005	0.000	0.000	0.000	0.000
100	X	98	PHE	0	-0.038	-0.021	17.334	-0.007	-0.007	0.000	0.000	0.000	0.000
101	X	99	GLU	-1	-0.794	-0.874	10.177	-1.713	-1.713	0.000	0.000	0.000	0.000
102	X	100	LEU	0	-0.055	-0.026	14.645	-0.034	-0.034	0.000	0.000	0.000	0.000
103	X	101	CYS	0	-0.034	-0.009	11.527	-0.040	-0.040	0.000	0.000	0.000	0.000
104	X	102	PHE	0	0.020	0.017	13.898	0.024	0.024	0.000	0.000	0.000	0.000
105	X	103	LEU	0	0.034	0.012	11.486	-0.023	-0.023	0.000	0.000	0.000	0.000
106	X	104	VAL	0	0.000	0.009	14.677	0.065	0.065	0.000	0.000	0.000	0.000
107	X	105	GLN	0	-0.012	-0.008	15.180	-0.057	-0.057	0.000	0.000	0.000	0.000
108	X	106	ARG	1	0.874	0.907	17.644	0.163	0.163	0.000	0.000	0.000	0.000
109	X	107	SER	0	0.014	0.007	20.931	0.022	0.022	0.000	0.000	0.000	0.000
110	X	108	GLU	-1	-0.791	-0.881	19.335	-0.313	-0.313	0.000	0.000	0.000	0.000
111	X	109	PHE	0	0.040	0.032	18.805	-0.028	-0.028	0.000	0.000	0.000	0.000
112	X	110	LYS	1	0.826	0.896	15.050	0.449	0.449	0.000	0.000	0.000	0.000
113	X	111	VAL	0	-0.012	-0.001	16.268	-0.050	-0.050	0.000	0.000	0.000	0.000
114	X	112	MET	0	-0.006	0.004	11.045	0.083	0.083	0.000	0.000	0.000	0.000
115	X	113	VAL	0	0.011	0.006	14.800	0.016	0.016	0.000	0.000	0.000	0.000
116	X	114	ASN	0	0.007	-0.011	13.747	-0.012	-0.012	0.000	0.000	0.000	0.000
117	X	115	LYS	1	0.859	0.902	7.127	2.294	2.294	0.000	0.000	0.000	0.000
118	X	116	LYS	1	0.948	0.994	11.303	0.630	0.630	0.000	0.000	0.000	0.000
119	X	117	PHE	0	0.010	-0.005	14.165	0.015	0.015	0.000	0.000	0.000	0.000
120	X	118	PHE	0	-0.002	-0.005	15.746	0.067	0.067	0.000	0.000	0.000	0.000
121	X	119	VAL	0	-0.001	-0.009	19.127	0.060	0.060	0.000	0.000	0.000	0.000
122	X	120	GLN	0	0.022	0.004	19.540	-0.064	-0.064	0.000	0.000	0.000	0.000
123	X	121	TYR	0	-0.018	-0.025	21.121	0.025	0.025	0.000	0.000	0.000	0.000
124	X	122	GLN	0	0.034	0.017	23.062	-0.013	-0.013	0.000	0.000	0.000	0.000
125	X	123	HIS	0	-0.037	-0.022	21.157	0.018	0.018	0.000	0.000	0.000	0.000
126	X	124	ARG	1	0.828	0.893	26.062	0.202	0.202	0.000	0.000	0.000	0.000
127	X	125	VAL	0	-0.018	-0.001	28.733	0.015	0.015	0.000	0.000	0.000	0.000
128	X	126	PRO	0	0.002	-0.008	27.645	-0.013	-0.013	0.000	0.000	0.000	0.000
129	X	127	TYR	0	0.031	0.015	21.767	-0.001	-0.001	0.000	0.000	0.000	0.000
130	X	128	HIS	0	0.034	0.016	24.561	-0.017	-0.017	0.000	0.000	0.000	0.000
131	X	129	LEU	0	-0.052	-0.021	25.520	0.008	0.008	0.000	0.000	0.000	0.000
132	X	130	VAL	0	-0.032	0.000	23.909	0.001	0.001	0.000	0.000	0.000	0.000
133	X	131	ASP	-1	-0.767	-0.857	24.842	-0.160	-0.160	0.000	0.000	0.000	0.000
134	X	132	THR	0	-0.054	-0.029	25.966	0.006	0.006	0.000	0.000	0.000	0.000
135	X	133	ILE	0	-0.016	-0.003	20.325	-0.016	-0.016	0.000	0.000	0.000	0.000
136	X	134	ALA	0	0.014	0.001	24.285	0.017	0.017	0.000	0.000	0.000	0.000
137	X	135	VAL	0	-0.007	0.000	22.498	-0.017	-0.017	0.000	0.000	0.000	0.000
138	X	136	SER	0	-0.001	0.001	25.818	0.024	0.024	0.000	0.000	0.000	0.000
139	X	137	GLY	0	0.079	0.041	28.069	-0.014	-0.014	0.000	0.000	0.000	0.000
140	X	138	CYS	0	-0.034	-0.012	29.600	0.005	0.005	0.000	0.000	0.000	0.000
141	X	139	LEU	0	0.002	-0.010	23.039	-0.010	-0.010	0.000	0.000	0.000	0.000
142	X	140	LYS	1	0.946	0.981	22.525	0.268	0.268	0.000	0.000	0.000	0.000
143	X	141	LEU	0	0.040	0.016	19.799	-0.030	-0.030	0.000	0.000	0.000	0.000
144	X	142	SER	0	-0.100	-0.066	18.237	0.027	0.027	0.000	0.000	0.000	0.000
145	X	143	PHE	0	0.043	0.010	12.722	0.044	0.044	0.000	0.000	0.000	0.000
146	X	144	ILE	0	0.001	0.008	16.478	-0.047	-0.047	0.000	0.000	0.000	0.000
147	X	145	THR	0	0.014	0.004	11.844	0.027	0.027	0.000	0.000	0.000	0.000
148	X	146	PHE	0	0.020	0.006	14.074	-0.055	-0.055	0.000	0.000	0.000	0.000
149	X	147	GLN	0	0.017	0.008	7.295	-0.166	-0.166	0.000	0.000	0.000	0.000
150	X	148	THR	0	0.060	0.031	11.281	-0.025	-0.025	0.000	0.000	0.000	0.000
151	X	149	GLN	0	0.052	0.015	7.735	-0.100	-0.100	0.000	0.000	0.000	0.000
152	X	150	ASN	0	-0.018	0.012	9.986	0.208	0.208	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:-1:GLY)