FMO DATABASE

FMODB ID: Q1MJY

Calculation Name: 2D4P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4P

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIW0

Base Structure: X-ray

Registration Date: 2023-03-13

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	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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071491.843603
FMO2-HF: Nuclear repulsion	1021988.787339
FMO2-HF: Total energy	-49503.056265
FMO2-MP2: Total energy	-49649.938812

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.
-47.424	-37.083	27.739	-14.026	-24.055	-0.112

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 : 0.008 / q_NPA : 0.011

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	PHE	0	0.039	0.011	3.026	-5.331	-1.711	2.486	-2.352	-3.754	0.002
4	A	4	ARG	1	0.708	0.805	5.715	-0.383	-0.383	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.053	0.018	9.228	0.090	0.090	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.036	-0.012	11.827	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.007	-0.034	13.503	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.770	-0.861	16.660	0.196	0.196	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.835	-0.900	16.917	0.202	0.202	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.748	-0.832	12.785	0.330	0.330	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.009	-0.004	14.623	0.044	0.044	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.872	-0.933	16.511	0.162	0.162	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.804	0.884	10.086	-0.159	-0.159	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.003	0.002	11.869	0.097	0.097	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.018	-0.043	13.570	0.024	0.024	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.834	0.892	11.257	0.048	0.048	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.055	-0.001	8.426	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.043	-0.001	12.483	0.025	0.025	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.053	0.027	15.707	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.919	0.945	17.594	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.861	0.926	17.027	-0.348	-0.348	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.079	0.053	19.134	0.046	0.046	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.006	0.003	16.395	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.020	0.016	19.699	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.088	0.031	21.414	0.022	0.022	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.002	0.004	22.592	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.016	0.003	21.051	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.002	0.022	17.111	0.020	0.020	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.848	0.869	19.378	-0.158	-0.158	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.071	-0.022	21.954	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.023	-0.008	17.445	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.027	0.027	16.992	0.027	0.027	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.887	0.940	18.028	-0.221	-0.221	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.041	-0.022	18.760	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.001	0.011	18.279	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.831	0.901	16.338	-0.362	-0.362	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.004	0.009	14.363	0.051	0.051	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.037	-0.014	9.250	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.005	-0.007	7.759	0.080	0.080	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.019	0.013	3.346	-0.539	-0.085	0.087	-0.124	-0.417	0.000
41	A	41	GLU	-1	-0.804	-0.876	3.249	0.406	1.014	0.020	-0.165	-0.463	0.000
42	A	42	GLU	-1	-0.814	-0.909	1.840	-27.643	-25.196	15.973	-8.933	-9.487	-0.105
43	A	43	GLY	0	0.007	0.004	3.517	0.975	1.100	0.034	0.086	-0.246	0.000
44	A	44	GLU	-1	-0.869	-0.924	5.986	0.239	0.239	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.786	-0.841	6.723	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.014	-0.010	5.545	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.034	0.007	2.259	-1.428	-1.185	4.077	-0.917	-3.403	0.006
48	A	48	GLY	0	0.044	-0.008	5.205	0.046	0.136	-0.002	-0.030	-0.059	0.000
49	A	49	PHE	0	-0.043	-0.015	7.002	-0.235	-0.235	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.022	0.009	9.765	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.033	-0.011	12.308	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.032	0.008	15.997	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.027	-0.017	17.978	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.023	0.012	21.381	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.017	-0.011	23.957	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	TRP	0	-0.037	-0.020	27.093	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.018	-0.013	28.518	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.017	-0.002	31.879	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.972	-0.989	33.805	0.104	0.104	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.053	0.045	30.072	0.006	0.006	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.005	-0.015	25.602	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.021	-0.023	24.096	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.022	-0.015	18.664	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.005	0.014	20.688	0.012	0.012	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.033	-0.010	14.715	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.050	-0.014	17.836	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.742	0.846	15.297	-0.455	-0.455	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.022	0.022	9.865	0.038	0.038	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.755	-0.826	11.057	0.303	0.303	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.024	-0.010	7.482	0.460	0.460	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.753	0.872	5.549	-0.624	-0.624	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.064	0.037	2.451	-0.425	0.272	0.260	-0.340	-0.617	-0.002
73	A	73	VAL	0	0.028	0.020	5.379	0.791	0.870	-0.001	-0.002	-0.076	0.000
74	A	74	GLU	-1	-0.960	-0.972	2.590	-10.960	-8.755	2.111	-1.462	-2.853	-0.017
75	A	75	ALA	0	0.013	0.001	3.015	0.563	1.848	2.651	-1.599	-2.337	0.004
76	A	76	LEU	0	-0.007	-0.007	3.751	0.244	-1.306	0.044	1.819	-0.313	0.000
77	A	77	ARG	1	0.865	0.921	7.243	-0.309	-0.309	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.010	-0.002	5.843	-0.475	-0.437	-0.001	-0.007	-0.030	0.000
79	A	79	LEU	0	-0.038	-0.015	6.424	-0.621	-0.621	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.025	-0.003	8.490	-0.358	-0.358	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.895	0.940	6.084	-0.740	-0.740	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.022	0.008	9.297	-0.137	-0.137	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.014	-0.008	11.344	-0.128	-0.128	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.046	0.027	14.289	-0.081	-0.081	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.813	0.894	14.295	-0.447	-0.447	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.012	-0.007	15.406	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.013	-0.012	17.179	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.037	0.010	18.576	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.848	-0.910	17.857	0.338	0.338	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.066	-0.031	21.227	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.021	-0.001	23.487	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.094	-0.037	22.274	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.018	0.007	24.514	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.835	-0.897	23.499	0.182	0.182	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.014	-0.010	17.271	0.019	0.019	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.011	0.011	20.651	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.022	-0.003	14.876	0.042	0.042	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.026	-0.012	19.399	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.017	-0.008	16.744	0.018	0.018	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.837	-0.915	18.670	0.138	0.138	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.004	-0.003	18.412	0.016	0.016	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.897	-0.951	19.496	0.018	0.018	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.821	0.910	13.075	-0.462	-0.462	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.819	0.882	14.701	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.820	-0.914	8.354	-0.225	-0.225	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.007	-0.011	10.847	0.089	0.089	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.832	-0.907	12.516	0.085	0.085	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.935	-0.969	11.583	-0.275	-0.275	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.019	-0.029	9.706	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.001	-0.009	11.472	0.029	0.029	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.982	0.998	14.856	-0.015	-0.015	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.059	-0.033	12.321	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.811	-0.877	11.011	0.357	0.357	0.000	0.000	0.000	0.000
114	A	114	GLY	0	-0.008	0.005	14.822	0.018	0.018	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.029	-0.013	14.986	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.000	0.005	19.177	-0.024	-0.024	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.024	-0.025	19.102	0.018	0.018	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.024	0.029	23.144	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.043	-0.025	26.869	0.006	0.006	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.019	0.004	28.282	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.035	0.008	28.194	0.004	0.004	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.013	0.002	24.566	0.002	0.002	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.016	0.016	28.405	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.004	-0.009	27.970	0.009	0.009	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.959	0.977	31.340	-0.085	-0.085	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.017	0.013	30.214	0.005	0.005	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.013	-0.017	32.870	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.002	0.019	33.738	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.004	-0.011	31.622	0.008	0.008	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.995	1.007	34.637	-0.089	-0.089	0.000	0.000	0.000	0.000

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