FMO DATABASE

FMODB ID: R5MV8

Calculation Name: 2D4P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071882.596007
FMO2-HF: Nuclear repulsion	1022379.650795
FMO2-HF: Total energy	-49502.945212
FMO2-MP2: Total energy	-49649.852796

3D Structure Molmil

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.
-53.896	-43.089	29.755	-15.464	-25.099	-0.123

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 : -0.031 / q_NPA : -0.015

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	0.031	0.007	3.191	-6.161	-1.369	1.260	-2.492	-3.560	0.004
4	A	4	ARG	1	0.723	0.811	5.752	-0.521	-0.521	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.052	0.026	9.083	0.082	0.082	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.041	-0.011	11.488	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.009	-0.044	13.165	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.774	-0.867	16.390	0.221	0.221	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.836	-0.897	16.908	0.223	0.223	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.772	-0.840	12.781	0.364	0.364	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.004	-0.006	14.488	0.046	0.046	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.876	-0.942	16.532	0.160	0.160	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.826	0.904	10.074	-0.155	-0.155	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.001	-0.002	11.683	0.088	0.088	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.029	-0.032	13.435	0.039	0.039	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.853	0.912	11.230	0.159	0.159	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.067	-0.008	8.527	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.036	0.003	12.418	0.047	0.047	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.041	0.020	15.587	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.938	0.957	17.504	-0.098	-0.098	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.877	0.942	17.352	-0.386	-0.386	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.075	0.052	19.169	0.053	0.053	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.002	0.007	16.366	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.022	0.008	19.660	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.092	0.033	21.069	0.027	0.027	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.002	0.004	22.324	0.010	0.010	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.001	-0.007	20.887	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.014	0.031	16.785	0.023	0.023	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.838	0.867	18.895	-0.175	-0.175	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.065	-0.029	21.465	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.006	-0.018	17.124	0.005	0.005	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.015	0.019	16.939	0.032	0.032	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.918	0.966	17.979	-0.256	-0.256	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.053	-0.022	18.515	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.017	0.015	17.651	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.812	0.890	16.068	-0.436	-0.436	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.018	0.017	13.903	0.060	0.060	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.041	-0.013	8.853	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.007	-0.010	7.414	0.090	0.090	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.011	0.010	3.208	-0.665	-0.119	0.158	-0.169	-0.536	0.001
41	A	41	GLU	-1	-0.797	-0.885	3.089	0.031	0.896	0.046	-0.280	-0.631	0.000
42	A	42	GLU	-1	-0.818	-0.900	1.814	-34.822	-32.738	20.984	-11.704	-11.365	-0.124
43	A	43	GLY	0	0.020	0.013	3.244	1.567	1.340	0.083	0.518	-0.375	-0.001
44	A	44	GLU	-1	-0.861	-0.939	5.733	0.273	0.273	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.783	-0.843	6.485	-0.154	-0.154	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.010	-0.011	5.559	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.014	-0.007	2.422	-1.659	-0.556	1.885	-0.568	-2.420	0.004
48	A	48	GLY	0	0.051	-0.003	5.527	0.360	0.453	-0.001	-0.013	-0.078	0.000
49	A	49	PHE	0	-0.044	-0.010	7.187	-0.258	-0.258	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.029	0.015	9.775	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.051	-0.020	12.232	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.044	0.010	15.752	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.025	-0.019	17.608	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.017	0.014	20.899	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.020	-0.011	23.637	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	56	TRP	0	-0.029	-0.009	26.753	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.007	-0.009	28.802	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.018	-0.001	31.766	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.977	-0.989	33.274	0.131	0.131	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.042	0.038	29.589	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.002	-0.018	25.151	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.002	-0.009	23.811	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.040	-0.018	18.346	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.006	0.011	20.895	0.011	0.011	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.009	-0.017	14.664	0.025	0.025	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.060	-0.023	17.868	-0.039	-0.039	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.756	0.843	15.201	-0.521	-0.521	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.019	0.029	9.985	0.042	0.042	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.776	-0.845	11.066	0.393	0.393	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.024	-0.016	7.524	0.497	0.497	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.776	0.886	5.530	-0.478	-0.478	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.052	0.033	2.371	-0.114	0.527	0.312	-0.323	-0.630	-0.002
73	A	73	VAL	0	0.064	0.036	5.421	0.920	0.920	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.965	-0.971	2.765	-10.316	-8.063	1.425	-1.116	-2.562	-0.011
75	A	75	ALA	0	0.009	-0.006	2.925	0.826	1.957	3.559	-2.095	-2.595	0.006
76	A	76	LEU	0	-0.013	-0.007	3.641	0.813	-1.661	0.044	2.778	-0.347	0.000
77	A	77	ARG	1	0.865	0.915	7.202	-0.634	-0.634	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.001	0.003	5.852	-0.529	-0.529	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.021	-0.007	6.315	-0.655	-0.655	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.039	-0.008	8.327	-0.430	-0.430	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.912	0.954	6.025	-1.131	-1.131	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.037	-0.002	8.977	-0.177	-0.177	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.002	-0.004	11.017	-0.157	-0.157	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.040	0.033	13.806	-0.107	-0.107	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.826	0.901	13.931	-0.552	-0.552	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.006	0.000	15.164	-0.067	-0.067	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.024	-0.022	16.892	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.038	0.008	18.096	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.855	-0.908	17.980	0.403	0.403	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.080	-0.039	21.117	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.010	0.008	23.109	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.099	-0.052	22.167	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.022	0.005	24.073	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.862	-0.912	23.305	0.239	0.239	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.015	-0.002	17.239	0.018	0.018	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.022	0.014	20.676	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.013	-0.009	15.133	0.046	0.046	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.014	-0.006	19.642	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.001	0.000	17.050	0.034	0.034	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.849	-0.920	19.228	0.177	0.177	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.026	-0.002	18.957	0.021	0.021	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.913	-0.950	20.011	0.061	0.061	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.802	0.894	13.107	-0.554	-0.554	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.835	0.883	15.576	-0.064	-0.064	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.839	-0.921	8.481	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.009	-0.010	11.417	0.086	0.086	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.845	-0.909	12.763	0.163	0.163	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.925	-0.965	11.729	-0.143	-0.143	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.016	-0.027	9.915	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.004	-0.011	11.710	0.019	0.019	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.977	0.997	15.011	-0.100	-0.100	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.063	-0.032	12.548	-0.034	-0.034	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.801	-0.872	10.893	0.613	0.613	0.000	0.000	0.000	0.000
114	A	114	GLY	0	-0.015	0.003	14.680	0.016	0.016	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.020	-0.006	14.990	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.001	0.001	19.238	-0.030	-0.030	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.032	-0.027	19.601	0.017	0.017	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.022	0.036	23.575	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.044	-0.035	26.882	0.008	0.008	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.010	-0.006	28.198	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.040	0.027	28.053	0.006	0.006	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.019	-0.003	24.956	0.004	0.004	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.015	0.010	28.670	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.012	-0.007	27.920	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.977	0.990	31.370	-0.105	-0.105	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.001	-0.001	30.212	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.025	-0.015	32.917	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.028	0.022	33.282	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.025	-0.013	31.645	0.007	0.007	0.000	0.000	0.000	0.000
130	A	130	ARG	1	1.006	1.006	34.403	-0.106	-0.106	0.000	0.000	0.000	0.000

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