FMO DATABASE

FMODB ID: 3J4RL

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1771786.983288
FMO2-HF: Nuclear repulsion	1704524.799086
FMO2-HF: Total energy	-67262.184202
FMO2-MP2: Total energy	-67460.801482

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.
-17.983	-7.557	11.991	-7.665	-14.753	-0.039

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 : 0.020 / q_NPA : 0.009

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	0.048	0.013	2.275	-5.063	-0.690	3.632	-2.545	-5.459	-0.016
4	A	4	GLY	0	-0.003	-0.059	4.794	0.403	0.474	-0.001	-0.008	-0.062	0.000
5	A	5	ILE	0	0.053	-0.178	8.376	-0.086	-0.086	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.007	0.730	11.165	0.074	0.074	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.013	0.004	14.239	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.010	-0.018	13.639	0.047	0.047	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.021	0.010	18.824	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.023	-0.015	22.616	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.939	0.949	24.893	-0.063	-0.063	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.940	0.973	25.942	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.017	0.026	25.052	0.008	0.008	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.028	-0.042	20.901	0.042	0.042	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.819	-0.908	24.177	0.132	0.132	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.015	0.008	26.999	0.010	0.010	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.041	0.015	24.001	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.123	0.023	22.041	0.040	0.040	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.138	-0.049	25.271	0.010	0.010	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.011	-0.002	27.611	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.772	0.889	17.777	-0.350	-0.350	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.890	0.954	24.500	-0.199	-0.199	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.883	0.941	25.837	-0.166	-0.166	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.044	0.014	26.464	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.739	-0.856	20.138	0.417	0.417	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.040	0.026	19.408	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.001	-0.009	16.393	0.071	0.071	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.079	-0.023	17.363	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.040	-0.028	18.286	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.007	0.004	13.385	0.039	0.039	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.041	0.006	12.020	0.091	0.091	0.000	0.000	0.000	0.000
32	A	32	PRO	0	0.002	0.035	14.949	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.003	0.000	17.220	0.010	0.010	0.000	0.000	0.000	0.000
34	A	34	HIS	1	0.938	0.966	15.403	-0.344	-0.344	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.002	0.002	18.014	0.018	0.018	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.167	-0.123	13.858	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.518	-0.438	9.819	-0.135	-0.135	0.000	0.000	0.000	0.000
38	A	38	ARG	1	1.551	1.068	11.728	0.285	0.285	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.017	-0.026	12.942	0.020	0.020	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.011	0.005	8.301	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.011	-0.024	6.524	0.151	0.151	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.889	-0.955	4.021	1.559	1.890	0.001	-0.079	-0.253	0.000
43	A	43	CYS	0	-0.066	0.024	3.510	0.243	0.945	0.004	-0.213	-0.494	0.000
44	A	44	ALA	0	0.053	0.004	2.131	-5.530	-5.072	3.466	-1.964	-1.960	-0.023
45	A	45	GLU	-1	-0.912	-0.983	2.393	-9.610	-6.889	1.677	-1.495	-2.903	-0.006
46	A	46	GLU	-1	-0.918	-0.945	3.525	-1.390	-1.311	0.060	0.105	-0.244	0.000
47	A	47	LYS	1	0.841	0.923	6.573	1.909	1.909	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.025	0.006	5.459	0.121	0.121	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.842	-0.918	7.342	-1.053	-1.053	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.004	0.000	10.927	0.090	0.090	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.011	0.021	6.528	0.200	0.200	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.055	0.021	9.165	0.221	0.221	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.042	-0.034	11.672	0.193	0.193	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.045	-0.037	13.884	0.103	0.103	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.008	0.014	10.741	0.091	0.091	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.962	0.979	14.366	0.718	0.718	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.088	-0.048	17.224	0.106	0.106	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.022	0.019	16.479	0.054	0.054	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.015	-0.006	18.130	0.043	0.043	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.938	0.969	20.044	0.314	0.314	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-1.017	-0.993	22.933	-0.220	-0.220	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.048	-0.022	22.009	0.019	0.019	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.003	-0.010	24.359	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.002	-0.010	24.852	0.003	0.003	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.001	0.008	21.846	0.007	0.007	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.033	0.028	25.855	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.040	-0.021	23.023	0.007	0.007	0.000	0.000	0.000	0.000
68	A	68	LYS	1	1.016	1.006	27.613	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.033	-0.028	25.324	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.022	-0.024	30.101	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.965	0.966	31.382	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.059	0.050	29.229	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.068	-0.041	29.481	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.015	-0.034	28.183	0.013	0.013	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.023	0.001	23.000	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.025	0.053	27.471	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.025	-0.035	29.914	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.012	0.008	24.971	0.006	0.006	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.012	-0.015	22.062	0.006	0.006	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.056	-0.012	25.494	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.037	-0.038	22.091	0.019	0.019	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.016	0.009	24.924	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.040	-0.042	24.126	0.008	0.008	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.027	0.016	25.468	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.882	0.919	25.955	-0.056	-0.056	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.005	0.007	25.531	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.911	-0.973	27.498	0.038	0.038	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.040	-0.009	27.349	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.053	0.027	27.405	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.836	-0.928	27.534	-0.041	-0.041	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.899	-0.930	26.282	-0.067	-0.067	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.022	-0.023	22.191	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.899	0.967	22.483	0.033	0.033	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.023	-0.010	23.354	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.045	-0.022	18.288	-0.022	-0.022	0.000	0.000	0.000	0.000
96	A	96	ASN	0	0.020	-0.009	18.747	-0.037	-0.037	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.861	-0.947	18.827	-0.087	-0.087	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.921	0.973	19.512	0.201	0.201	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.038	-0.014	14.342	-0.062	-0.062	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.030	0.012	14.975	-0.045	-0.045	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.016	0.024	17.012	0.009	0.009	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.032	0.005	16.087	-0.058	-0.058	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.023	-0.023	10.973	0.030	0.030	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.052	-0.018	10.162	-0.121	-0.121	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.035	-0.006	12.995	0.081	0.081	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.024	-0.021	14.098	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.975	-0.997	15.350	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.037	-0.032	17.125	0.025	0.025	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.945	-0.967	18.369	0.059	0.059	0.000	0.000	0.000	0.000
110	A	110	TYR	0	0.054	0.046	20.467	0.014	0.014	0.000	0.000	0.000	0.000
111	A	111	ASN	0	0.003	-0.032	22.465	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.001	0.053	19.485	0.016	0.016	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.017	-0.006	22.397	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.004	0.018	22.292	0.024	0.024	0.000	0.000	0.000	0.000
115	A	115	HIS	1	0.850	0.905	20.007	-0.172	-0.172	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.036	0.025	21.075	0.006	0.006	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.024	-0.012	20.117	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	118	VAL	0	-0.034	-0.025	22.172	0.007	0.007	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.033	0.010	24.427	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.077	-0.048	18.047	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.002	0.000	21.305	0.023	0.023	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.004	0.023	23.352	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.061	0.041	27.109	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.820	-0.931	29.859	0.207	0.207	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.908	-0.952	32.400	0.158	0.158	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.932	-0.963	30.030	0.226	0.226	0.000	0.000	0.000	0.000
127	A	127	HIS	0	0.009	0.019	28.771	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.002	-0.010	31.660	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.905	-0.939	35.269	0.139	0.139	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.036	-0.021	30.174	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.024	-0.025	31.744	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	132	GLY	0	0.005	0.019	33.930	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.015	0.007	34.210	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.041	-0.038	30.713	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.915	0.976	34.556	-0.108	-0.108	0.000	0.000	0.000	0.000
136	A	136	MET	0	-0.044	-0.027	35.461	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.027	0.006	35.298	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.914	-0.970	35.864	0.058	0.058	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.059	-0.009	31.210	0.005	0.005	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.022	-0.018	34.527	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.101	-0.055	28.171	0.001	0.001	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.919	-0.966	30.996	0.005	0.005	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.762	-0.840	25.690	0.034	0.034	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.044	0.019	27.461	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.043	-0.013	21.145	0.001	0.001	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.811	-0.918	23.542	-0.108	-0.108	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.883	0.929	18.923	0.101	0.101	0.000	0.000	0.000	0.000
148	A	148	PHE	0	-0.008	0.008	14.058	0.046	0.046	0.000	0.000	0.000	0.000
149	A	149	HIS	0	-0.005	-0.001	12.495	-0.054	-0.054	0.000	0.000	0.000	0.000
150	A	150	LEU	0	0.053	0.050	6.886	0.046	0.046	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.059	-0.036	7.325	0.011	0.011	0.000	0.000	0.000	0.000
152	A	152	TYR	0	0.070	0.029	2.589	-3.426	-2.632	3.131	-1.255	-2.670	0.007
153	A	153	GLN	0	-0.092	-0.040	4.054	-0.275	0.024	0.006	-0.072	-0.233	0.000
154	A	154	LEU	0	-0.005	0.002	4.492	1.628	2.226	0.015	-0.139	-0.475	-0.001
155	A	155	GLU	-1	-0.879	-0.940	6.767	1.230	1.230	0.000	0.000	0.000	0.000
156	A	156	ASN	0	0.002	0.018	8.899	0.122	0.122	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.030	0.013	9.807	-0.251	-0.251	0.000	0.000	0.000	0.000
158	A	158	SER	0	-0.077	-0.055	10.733	-0.119	-0.119	0.000	0.000	0.000	0.000
159	A	159	TRP	0	-0.007	-0.008	6.052	0.598	0.598	0.000	0.000	0.000	0.000
160	A	160	THR	0	-0.001	0.003	7.663	-0.435	-0.435	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.022	-0.024	8.040	0.099	0.099	0.000	0.000	0.000	0.000
162	A	162	TYR	0	-0.036	-0.010	6.531	-0.081	-0.081	0.000	0.000	0.000	0.000
163	A	163	GLU	-1	-0.876	-0.952	8.628	-0.886	-0.886	0.000	0.000	0.000	0.000
164	A	164	THR	0	-0.044	-0.037	11.550	0.073	0.073	0.000	0.000	0.000	0.000
165	A	165	PHE	0	-0.013	-0.010	11.806	-0.023	-0.023	0.000	0.000	0.000	0.000
166	A	166	LEU	0	-0.018	-0.021	17.010	0.043	0.043	0.000	0.000	0.000	0.000
167	A	167	LEU	0	-0.059	-0.005	20.046	-0.020	-0.020	0.000	0.000	0.000	0.000
168	A	168	GLY	0	-0.009	0.010	22.698	0.019	0.019	0.000	0.000	0.000	0.000

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