FMO DATABASE

FMODB ID: R8GR8

Calculation Name: 3A7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7L

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6T9

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	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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1038300.492562
FMO2-HF: Nuclear repulsion	990341.667585
FMO2-HF: Total energy	-47958.824978
FMO2-MP2: Total energy	-48099.734218

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:SER)

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

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.
-17.874	-9.153	4.346	-4.982	-8.083	-0.016

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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	VAL	0	0.046	0.044	3.887	0.728	2.739	-0.009	-1.013	-0.989	0.004
4	A	4	PRO	0	0.003	0.012	6.445	-0.207	-0.207	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.026	-0.003	9.969	0.043	0.043	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-1.021	-1.002	12.313	-0.068	-0.068	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.056	-0.006	10.485	0.032	0.032	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.814	0.895	13.513	0.112	0.112	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.037	-0.007	7.873	0.097	0.097	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.020	-0.003	12.121	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.916	0.942	11.226	0.156	0.156	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.903	-0.942	11.062	-0.219	-0.219	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.028	0.043	6.292	0.143	0.143	0.000	0.000	0.000	0.000
14	A	14	GLH	0	-0.004	-0.013	8.939	0.173	0.173	0.000	0.000	0.000	0.000
15	A	15	TRP	0	-0.042	-0.022	9.415	-0.112	-0.112	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.014	-0.002	11.674	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.873	0.912	14.930	-0.083	-0.083	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.797	0.915	17.049	0.036	0.036	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.746	-0.830	20.749	0.040	0.040	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.037	-0.039	23.035	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.881	-0.919	26.421	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.056	-0.031	25.884	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.081	-0.053	24.707	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.004	-0.027	19.405	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.041	-0.015	16.762	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.007	0.004	15.418	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.066	0.031	13.300	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.019	0.026	9.853	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.005	-0.025	5.133	-0.001	0.054	-0.001	-0.002	-0.051	0.000
30	A	30	GLU	-1	-0.837	-0.924	2.439	-1.033	0.152	1.290	-0.879	-1.596	0.001
31	A	31	HIS	0	-0.029	-0.032	2.380	-12.043	-8.161	2.329	-2.445	-3.767	-0.021
32	A	32	ALA	0	0.032	0.020	3.408	-0.960	-0.665	0.110	-0.052	-0.352	0.002
33	A	33	GLN	0	-0.016	0.002	5.642	-0.334	-0.334	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.902	-0.936	5.099	0.395	0.395	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.058	-0.035	6.297	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.003	0.000	8.638	0.022	0.022	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.070	-0.023	10.427	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.939	-0.976	11.905	0.190	0.190	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.013	0.013	12.076	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.070	-0.044	15.795	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.041	-0.018	19.030	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.002	-0.013	17.015	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.905	-0.931	19.766	0.038	0.038	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.029	-0.025	20.472	0.006	0.006	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.006	0.015	22.117	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.953	-0.982	25.141	0.021	0.021	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.012	-0.015	27.284	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.050	-0.022	29.149	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.023	-0.002	28.013	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.073	-0.045	28.560	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.013	0.001	24.196	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.049	-0.056	26.389	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.042	-0.018	22.436	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.035	-0.017	20.699	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.812	-0.881	21.759	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.953	-0.973	21.137	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	CYS	0	-0.098	-0.050	20.239	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.022	0.007	18.742	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.015	-0.002	18.553	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.000	0.005	14.780	0.014	0.014	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.905	-0.964	16.679	0.039	0.039	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.038	-0.007	14.809	0.008	0.008	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.049	-0.027	16.596	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.756	0.889	10.962	-0.092	-0.092	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.052	-0.020	14.832	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.037	0.022	16.891	0.016	0.016	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.052	-0.033	14.180	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.825	-0.876	16.176	0.009	0.009	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.023	-0.005	14.649	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.011	-0.017	16.315	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.035	0.030	17.934	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.048	-0.027	16.591	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.043	-0.032	18.687	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.001	-0.036	22.215	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.023	-0.026	25.735	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.955	-0.967	27.061	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.049	0.023	23.235	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.023	-0.018	25.630	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.050	-0.036	24.550	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.049	0.023	22.497	0.002	0.002	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.043	-0.025	17.719	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.871	-0.940	21.526	0.060	0.060	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.023	-0.005	21.289	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.022	-0.010	16.894	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.042	-0.029	20.463	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-1.018	-1.002	23.562	0.063	0.063	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.086	-0.064	19.837	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.006	0.012	17.894	0.014	0.014	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.801	-0.891	15.228	0.161	0.161	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.027	-0.011	13.912	0.035	0.035	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.025	-0.016	11.247	0.040	0.040	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.019	-0.033	9.580	0.056	0.056	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.027	-0.012	9.289	0.054	0.054	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.923	-0.963	10.533	0.158	0.158	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.058	0.050	6.879	-0.075	-0.075	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.044	-0.046	5.076	-0.134	-0.090	-0.001	-0.007	-0.035	0.000
97	A	97	ALA	0	-0.068	-0.042	11.140	-0.081	-0.081	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.014	-0.010	14.348	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.014	0.015	12.990	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.104	-0.035	13.878	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.030	0.017	14.096	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	102	PHE	0	0.024	0.003	17.766	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.830	0.914	19.456	-0.047	-0.047	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.029	0.019	20.915	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.927	0.964	23.502	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.018	0.017	24.249	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.028	-0.028	26.022	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.884	-0.915	27.552	-0.041	-0.041	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.799	-0.885	25.530	-0.035	-0.035	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.077	-0.060	25.835	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.747	-0.847	23.298	-0.043	-0.043	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.012	-0.011	20.883	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.992	-0.985	20.311	-0.095	-0.095	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.058	-0.021	19.825	-0.015	-0.015	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.060	-0.017	16.297	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.006	0.009	11.394	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.860	-0.931	13.677	-0.232	-0.232	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.043	0.021	9.714	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	119	THR	0	0.031	0.019	9.106	-0.092	-0.092	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.048	-0.021	10.689	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.015	-0.026	4.704	0.105	0.205	-0.001	-0.010	-0.089	0.000
122	A	122	GLU	-1	-0.899	-0.965	5.733	-1.514	-1.514	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.005	-0.007	6.804	-0.083	-0.083	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.019	-0.005	9.129	0.097	0.097	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.036	-0.025	2.490	-1.423	-0.274	0.629	-0.574	-1.204	-0.002
126	A	126	GLU	-1	-1.034	-1.010	6.208	-0.357	-0.357	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-1.022	-0.992	8.295	-0.166	-0.166	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.948	-0.959	7.252	-0.988	-0.988	0.000	0.000	0.000	0.000

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