FMO DATABASE

FMODB ID: 82RGY

Calculation Name: 3FDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P0DJO8

Base Structure: X-ray

Registration Date: 2023-06-19

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1334922.833883
FMO2-HF: Nuclear repulsion	1277850.399876
FMO2-HF: Total energy	-57072.434007
FMO2-MP2: Total energy	-57238.651061

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:4:SER)

Summations of interaction energy for fragment #1(A:4: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.
-48.415	-50.563	33.268	-18.693	-12.428	-0.045

Interaction energy analysis for fragmet #1(A:4:SER)

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 : -0.019

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	6	ILE	0	0.024	0.016	2.017	-12.244	-7.952	6.198	-5.154	-5.336	0.050
4	A	7	ARG	1	0.805	0.856	3.820	-3.365	-2.933	0.025	-0.143	-0.315	0.002
5	A	8	LYS	1	0.783	0.864	6.421	-0.007	-0.007	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.032	0.019	6.493	-0.232	-0.232	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.040	0.007	7.529	-0.256	-0.256	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.001	0.009	9.788	-0.141	-0.141	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.804	-0.876	11.399	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.023	0.005	10.362	-0.049	-0.049	0.000	0.000	0.000	0.000
11	A	14	LYS	1	0.839	0.896	13.802	-0.206	-0.206	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.798	0.889	15.695	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	16	GLN	0	-0.030	-0.018	16.432	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.016	0.004	17.909	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.865	-0.923	19.900	0.121	0.121	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.112	-0.064	21.457	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	20	PRO	0	0.018	0.039	22.154	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.008	-0.010	22.943	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	22	ASN	0	-0.062	-0.044	23.574	0.001	0.001	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.042	-0.030	22.230	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.053	0.016	19.373	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.030	0.019	17.633	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	26	THR	0	-0.052	-0.017	17.183	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.883	-0.919	16.943	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	28	ILE	0	0.003	0.012	12.345	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.853	0.908	12.394	0.172	0.172	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.754	0.867	13.291	0.161	0.161	0.000	0.000	0.000	0.000
28	A	31	MET	0	-0.002	0.006	8.837	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.018	-0.007	8.506	-0.093	-0.093	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.000	-0.038	8.886	-0.183	-0.183	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.905	-0.928	10.312	-0.324	-0.324	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.059	-0.019	5.139	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.035	-0.009	5.145	-0.571	-0.475	-0.001	-0.001	-0.093	0.000
34	A	37	ILE	0	-0.043	-0.008	3.317	-0.129	0.306	0.019	-0.150	-0.305	0.000
35	A	38	ASP	-1	-0.789	-0.883	6.557	0.026	0.026	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.739	-0.841	9.607	-0.200	-0.200	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.058	-0.017	12.145	0.066	0.066	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.009	-0.049	10.436	0.027	0.027	0.000	0.000	0.000	0.000
39	A	42	ALA	0	-0.001	0.010	9.655	0.085	0.085	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.837	-0.947	11.301	0.004	0.004	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.969	-0.968	14.808	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.016	-0.019	10.728	0.035	0.035	0.000	0.000	0.000	0.000
43	A	46	TYR	0	-0.010	-0.009	14.585	0.020	0.020	0.000	0.000	0.000	0.000
44	A	47	HIS	0	-0.054	-0.024	16.205	0.005	0.005	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.048	0.019	16.737	0.010	0.010	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.035	-0.015	15.505	0.012	0.012	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.005	-0.013	18.715	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.919	-0.962	21.669	0.030	0.030	0.000	0.000	0.000	0.000
49	A	52	PHE	0	-0.055	-0.034	20.099	0.000	0.000	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.019	-0.022	18.756	0.001	0.001	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.012	0.005	24.013	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.060	0.039	26.536	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.072	-0.027	24.714	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.852	-0.947	27.660	0.057	0.057	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.943	-0.962	30.014	0.031	0.031	0.000	0.000	0.000	0.000
56	A	59	HIS	0	-0.139	-0.076	30.690	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.040	-0.024	32.716	0.001	0.001	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.033	0.026	30.431	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	62	ILE	0	0.020	-0.006	23.902	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.856	-0.926	27.959	0.054	0.054	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.843	0.914	30.388	-0.048	-0.048	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.005	-0.013	25.274	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	66	MET	0	-0.034	0.002	25.894	0.001	0.001	0.000	0.000	0.000	0.000
64	A	67	HIS	0	-0.010	0.008	29.171	0.001	0.001	0.000	0.000	0.000	0.000
65	A	68	SER	0	-0.013	0.004	31.495	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.063	-0.056	33.136	0.001	0.001	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.056	0.048	29.137	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.066	-0.034	27.156	0.003	0.003	0.000	0.000	0.000	0.000
69	A	72	TRP	0	-0.017	-0.026	20.551	0.013	0.013	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.065	0.052	25.511	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.797	0.874	24.771	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	75	ILE	0	0.077	0.042	21.968	0.006	0.006	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.733	-0.837	21.093	0.133	0.133	0.000	0.000	0.000	0.000
74	A	77	LEU	0	-0.022	-0.022	19.948	0.022	0.022	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.824	-0.887	19.660	0.052	0.052	0.000	0.000	0.000	0.000
76	A	79	LEU	0	0.044	0.033	15.724	0.003	0.003	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.032	-0.011	15.434	0.034	0.034	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.052	-0.045	14.999	0.033	0.033	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.052	0.032	13.938	0.006	0.006	0.000	0.000	0.000	0.000
80	A	83	CYS	0	-0.030	-0.017	11.135	0.004	0.004	0.000	0.000	0.000	0.000
81	A	84	TYR	0	-0.028	-0.058	10.039	0.120	0.120	0.000	0.000	0.000	0.000
82	A	85	GLN	0	-0.046	-0.021	10.483	0.030	0.030	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.045	0.024	6.437	-0.053	-0.053	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.022	0.005	5.684	-0.272	-0.272	0.000	0.000	0.000	0.000
85	A	88	ILE	0	-0.061	-0.041	6.244	0.038	0.038	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.044	-0.019	7.565	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.839	-0.878	1.549	-31.073	-39.818	26.891	-12.616	-5.530	-0.092
88	A	91	ASP	-1	-0.943	-0.966	3.112	0.036	1.229	0.137	-0.618	-0.712	-0.005
89	A	92	MET	0	-0.049	-0.012	4.546	0.427	0.576	-0.001	-0.011	-0.137	0.000
90	A	93	LYS	1	0.819	0.881	6.427	-0.580	-0.580	0.000	0.000	0.000	0.000
91	A	94	VAL	0	0.032	-0.002	9.885	0.049	0.049	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.011	-0.001	12.320	0.015	0.015	0.000	0.000	0.000	0.000
93	A	96	ASP	-1	-0.761	-0.868	8.875	0.386	0.386	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.008	0.020	8.508	0.071	0.071	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.025	-0.023	10.528	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	99	GLU	-1	-0.877	-0.924	12.692	0.218	0.218	0.000	0.000	0.000	0.000
97	A	100	MET	0	0.000	0.040	7.262	0.081	0.081	0.000	0.000	0.000	0.000
98	A	101	LEU	0	0.036	0.009	10.775	-0.052	-0.052	0.000	0.000	0.000	0.000
99	A	102	SER	0	-0.031	-0.031	13.416	-0.089	-0.089	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.038	-0.036	16.820	0.006	0.006	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.097	-0.056	16.928	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.792	-0.863	11.795	0.458	0.458	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.029	-0.005	9.490	-0.039	-0.039	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.820	0.908	14.157	-0.198	-0.198	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.053	0.042	12.766	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	109	PHE	0	0.041	0.026	14.836	-0.046	-0.046	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.007	0.008	19.130	0.006	0.006	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.773	0.873	20.143	-0.138	-0.138	0.000	0.000	0.000	0.000
109	A	112	THR	0	0.041	0.007	20.089	0.021	0.021	0.000	0.000	0.000	0.000
110	A	113	PRO	0	0.103	0.055	16.897	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.023	-0.018	18.444	0.001	0.001	0.000	0.000	0.000	0.000
112	A	115	GLN	0	-0.019	0.001	21.344	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	116	LEU	0	0.063	0.057	16.141	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	117	GLN	0	0.079	0.059	16.449	0.014	0.014	0.000	0.000	0.000	0.000
115	A	118	ASN	0	-0.033	-0.036	18.887	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.031	-0.019	21.584	-0.019	-0.019	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.082	0.052	14.501	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	121	TYR	0	-0.013	-0.023	17.290	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.897	0.948	21.685	-0.093	-0.093	0.000	0.000	0.000	0.000
120	A	123	LEU	0	0.040	0.031	20.422	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	124	LYS	1	0.888	0.948	16.804	-0.144	-0.144	0.000	0.000	0.000	0.000
122	A	125	LYS	1	0.868	0.947	22.132	-0.067	-0.067	0.000	0.000	0.000	0.000
123	A	126	GLU	-1	-0.915	-0.956	25.553	0.032	0.032	0.000	0.000	0.000	0.000
124	A	127	LEU	0	-0.100	-0.052	27.387	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.059	-0.024	24.506	0.000	0.000	0.000	0.000	0.000	0.000
126	A	129	GLN	0	0.061	0.031	27.044	0.003	0.003	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.021	0.014	23.280	0.007	0.007	0.000	0.000	0.000	0.000
128	A	131	GLU	-1	-0.931	-0.972	25.748	0.035	0.035	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.805	-0.898	27.580	0.059	0.059	0.000	0.000	0.000	0.000
130	A	133	ILE	0	-0.024	0.007	27.310	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	134	PRO	0	0.048	0.018	30.005	0.004	0.004	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.775	0.869	30.550	-0.066	-0.066	0.000	0.000	0.000	0.000
133	A	136	ASN	0	-0.025	-0.015	33.035	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	137	LYS	1	0.930	0.969	35.224	-0.040	-0.040	0.000	0.000	0.000	0.000
135	A	138	PRO	0	0.039	0.015	37.072	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.021	0.011	38.845	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	140	ARG	1	0.971	0.976	42.275	-0.030	-0.030	0.000	0.000	0.000	0.000
138	A	141	LYS	1	0.909	0.964	39.892	-0.041	-0.041	0.000	0.000	0.000	0.000
139	A	142	ARG	1	0.960	0.980	45.725	-0.027	-0.027	0.000	0.000	0.000	0.000
140	A	143	LYS	1	1.044	1.028	49.186	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:SER)