FMO DATABASE

FMODB ID: 98292

Calculation Name: 2D4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4G

Chain ID: A

ChEMBL ID:

UniProt ID: O31629

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1771085.499342
FMO2-HF: Nuclear repulsion	1703818.70125
FMO2-HF: Total energy	-67266.798091
FMO2-MP2: Total energy	-67465.002757

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:1:MET)

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

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.
-25.754	-15.954	19.96	-11.331	-18.425	-0.08

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : 0.001

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	3	TYR	0	0.041	0.008	2.274	-5.501	-0.785	3.496	-2.608	-5.604	-0.016
4	A	4	GLY	0	0.018	-0.004	4.888	0.351	0.410	-0.001	-0.006	-0.052	0.000
5	A	5	ILE	0	-0.014	-0.009	8.623	-0.052	-0.052	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.004	0.018	11.582	0.031	0.031	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.053	0.028	14.533	-0.055	-0.055	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.006	-0.019	13.612	0.047	0.047	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.019	0.011	18.849	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.002	-0.047	22.716	0.008	0.008	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.859	0.900	25.388	-0.097	-0.097	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.910	0.956	26.297	-0.069	-0.069	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.007	0.015	25.196	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.027	-0.032	20.791	0.042	0.042	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.798	-0.890	24.555	0.149	0.149	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.003	0.010	27.528	0.010	0.010	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.050	0.025	24.262	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.051	-0.013	22.408	0.047	0.047	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.106	-0.048	25.381	0.010	0.010	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.029	0.022	27.776	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.798	0.894	18.100	-0.427	-0.427	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.859	0.931	24.417	-0.221	-0.221	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.902	0.961	25.814	-0.202	-0.202	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.002	0.004	26.449	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.711	-0.835	20.129	0.522	0.522	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.032	0.023	19.245	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.004	-0.007	16.253	0.084	0.084	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.009	-0.006	17.240	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.025	-0.013	17.829	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.039	-0.006	13.293	0.035	0.035	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.022	0.000	11.753	0.115	0.115	0.000	0.000	0.000	0.000
32	A	32	PRO	0	0.033	0.035	14.894	-0.049	-0.049	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.028	-0.014	17.296	0.029	0.029	0.000	0.000	0.000	0.000
34	A	34	HIS	1	0.938	0.962	15.262	-0.491	-0.491	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.014	0.003	18.592	0.020	0.020	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.079	-0.050	15.737	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.010	0.028	10.179	-0.053	-0.053	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.885	0.967	11.556	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.015	0.001	12.395	0.043	0.043	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.023	-0.014	8.770	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.007	-0.006	7.229	0.063	0.063	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.881	-0.948	4.260	2.748	3.102	-0.001	-0.075	-0.277	0.000
43	A	43	CYS	0	-0.061	-0.030	2.834	0.009	1.183	0.042	-0.439	-0.776	0.000
44	A	44	ALA	0	0.059	0.028	1.937	-6.282	-8.591	8.579	-3.348	-2.922	-0.036
45	A	45	GLU	-1	-0.866	-0.948	2.381	-16.479	-12.327	3.742	-3.169	-4.724	-0.033
46	A	46	GLU	-1	-0.943	-0.960	3.704	-1.017	-0.848	0.023	-0.013	-0.178	0.000
47	A	47	LYS	1	0.896	0.951	6.477	1.780	1.780	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.019	0.002	5.545	0.340	0.340	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.863	-0.927	7.330	-1.136	-1.136	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.021	-0.010	10.663	0.202	0.202	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.012	0.002	6.474	0.216	0.216	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.035	0.013	9.405	0.219	0.219	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.004	-0.018	11.949	0.180	0.180	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.054	-0.022	13.871	0.089	0.089	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.001	0.008	10.662	0.095	0.095	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.846	0.882	14.304	0.678	0.678	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.053	-0.030	17.684	0.083	0.083	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.020	0.004	15.771	0.044	0.044	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.009	0.010	18.302	0.044	0.044	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.866	0.936	20.133	0.271	0.271	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.850	-0.910	23.280	-0.192	-0.192	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.084	-0.067	21.842	0.022	0.022	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.036	0.016	24.557	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.000	-0.014	24.846	0.008	0.008	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.010	0.035	22.096	0.006	0.006	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.019	0.009	25.803	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.036	-0.018	23.191	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.849	0.908	27.718	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.027	-0.011	25.871	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.015	-0.032	30.454	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.899	0.935	31.919	-0.111	-0.111	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.057	0.039	29.864	0.013	0.013	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.073	-0.038	29.703	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.052	0.002	28.056	0.013	0.013	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.001	0.005	23.133	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.029	0.051	27.639	0.007	0.007	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.025	-0.028	30.062	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.002	0.012	25.327	0.010	0.010	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.035	-0.038	22.959	0.035	0.035	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.006	-0.002	25.771	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.040	-0.032	22.292	0.025	0.025	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.017	0.010	25.151	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.028	-0.033	24.270	0.014	0.014	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.034	0.022	25.940	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.829	0.897	26.150	-0.100	-0.100	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.034	0.003	25.901	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.827	-0.890	27.799	0.099	0.099	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.020	0.001	27.455	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.014	-0.034	27.542	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.759	-0.889	27.399	0.028	0.028	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.866	-0.888	26.620	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.023	-0.023	22.605	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.831	0.914	22.486	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.002	-0.009	23.235	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.067	-0.024	18.169	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.013	-0.025	18.770	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.795	-0.904	18.864	0.019	0.019	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.870	0.949	20.037	0.114	0.114	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.023	0.003	13.851	-0.055	-0.055	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.032	0.018	14.972	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.013	-0.012	17.190	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.023	0.002	16.275	-0.044	-0.044	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.033	-0.026	10.850	0.028	0.028	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.035	-0.009	10.383	-0.104	-0.104	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.035	0.001	12.963	0.098	0.098	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.001	-0.013	13.743	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.920	-0.954	15.148	0.105	0.105	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.032	-0.032	16.867	0.023	0.023	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.884	-0.932	18.864	0.158	0.158	0.000	0.000	0.000	0.000
110	A	110	TYR	0	-0.010	0.011	20.395	0.034	0.034	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.045	-0.034	23.302	0.012	0.012	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.026	0.009	19.535	0.020	0.020	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.013	0.016	22.870	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.025	-0.005	22.694	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	HIS	1	0.876	0.931	20.593	-0.288	-0.288	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.010	0.011	21.470	0.015	0.015	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.049	-0.028	20.460	-0.026	-0.026	0.000	0.000	0.000	0.000
118	A	118	VAL	0	-0.036	-0.026	22.425	0.002	0.002	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.028	0.007	24.599	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.080	-0.060	18.102	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.026	-0.011	21.409	0.048	0.048	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.011	0.023	23.734	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.004	-0.024	27.525	0.008	0.008	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.830	-0.926	30.302	0.250	0.250	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.854	-0.900	32.723	0.203	0.203	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.871	-0.941	30.560	0.241	0.241	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.001	0.005	28.631	0.004	0.004	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.013	-0.004	31.750	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.883	-0.937	35.416	0.157	0.157	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.053	-0.030	30.388	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.020	-0.026	31.732	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.005	0.006	34.333	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.022	0.005	34.401	0.001	0.001	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.011	-0.005	30.818	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.914	0.958	34.546	-0.149	-0.149	0.000	0.000	0.000	0.000
136	A	136	MET	0	-0.037	-0.022	35.669	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.054	-0.007	35.558	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.913	-0.960	36.305	0.084	0.084	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.047	-0.034	31.327	0.006	0.006	0.000	0.000	0.000	0.000
140	A	140	SER	0	0.000	0.011	34.529	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.044	-0.034	28.486	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.801	-0.885	31.175	0.049	0.049	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.757	-0.817	25.795	0.080	0.080	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.026	0.001	27.556	0.001	0.001	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.022	0.003	21.233	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.762	-0.853	23.568	-0.056	-0.056	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.831	0.876	19.081	0.043	0.043	0.000	0.000	0.000	0.000
148	A	148	PHE	0	0.010	0.017	14.390	0.046	0.046	0.000	0.000	0.000	0.000
149	A	149	HIS	0	0.003	0.000	13.022	-0.067	-0.067	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.011	0.021	6.789	0.100	0.100	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.037	-0.024	7.695	-0.014	-0.014	0.000	0.000	0.000	0.000
152	A	152	TYR	0	0.058	0.016	2.713	-3.769	-3.553	3.984	-1.280	-2.920	0.007
153	A	153	GLN	0	-0.052	-0.032	4.106	-0.996	-0.665	0.022	-0.099	-0.254	0.000
154	A	154	LEU	0	-0.004	-0.006	4.103	1.742	2.680	0.074	-0.294	-0.718	-0.002
155	A	155	GLU	-1	-0.904	-0.955	6.581	0.805	0.805	0.000	0.000	0.000	0.000
156	A	156	ASN	0	0.008	0.028	8.420	0.117	0.117	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.024	0.017	9.892	-0.213	-0.213	0.000	0.000	0.000	0.000
158	A	158	SER	0	-0.063	-0.043	10.752	-0.061	-0.061	0.000	0.000	0.000	0.000
159	A	159	TRP	0	0.005	0.004	6.227	0.699	0.699	0.000	0.000	0.000	0.000
160	A	160	THR	0	-0.032	-0.016	7.732	-0.455	-0.455	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.024	-0.017	8.066	0.167	0.167	0.000	0.000	0.000	0.000
162	A	162	TYR	0	-0.002	0.010	6.055	-0.142	-0.142	0.000	0.000	0.000	0.000
163	A	163	GLU	-1	-0.774	-0.863	8.795	-0.774	-0.774	0.000	0.000	0.000	0.000
164	A	164	THR	0	-0.038	-0.036	11.941	0.088	0.088	0.000	0.000	0.000	0.000
165	A	165	PHE	0	-0.019	-0.016	11.761	-0.028	-0.028	0.000	0.000	0.000	0.000
166	A	166	LEU	0	-0.014	-0.018	17.281	0.041	0.041	0.000	0.000	0.000	0.000
167	A	167	LEU	0	-0.029	0.003	20.133	-0.021	-0.021	0.000	0.000	0.000	0.000
168	A	168	GLY	0	-0.075	-0.030	22.706	0.000	0.000	0.000	0.000	0.000	0.000

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