FMO DATABASE

FMODB ID: GNJ81

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	OptHSide
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	-1332095.954298
FMO2-HF: Nuclear repulsion	1275023.765106
FMO2-HF: Total energy	-57072.189192
FMO2-MP2: Total energy	-57238.441404

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.
-50.895	-48.806	26.915	-16.689	-12.316	-0.038

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 : 0.020 / 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	6	ILE	0	0.047	0.021	2.070	-13.239	-7.965	5.167	-5.075	-5.366	0.051
4	A	7	ARG	1	0.794	0.847	3.844	-3.257	-2.802	0.024	-0.162	-0.317	0.002
5	A	8	LYS	1	0.786	0.866	6.537	0.083	0.083	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.037	0.029	6.861	-0.236	-0.236	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.036	0.005	7.816	-0.251	-0.251	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.005	0.005	10.003	-0.145	-0.145	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.781	-0.869	11.535	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.023	0.014	10.834	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	14	LYS	1	0.832	0.888	14.127	-0.161	-0.161	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.783	0.881	15.810	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	16	GLN	0	-0.035	-0.012	16.975	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.008	0.005	17.991	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.871	-0.917	20.159	0.086	0.086	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.134	-0.070	21.894	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	20	PRO	0	0.003	0.032	22.612	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.038	0.006	23.291	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	22	ASN	0	-0.059	-0.047	24.028	0.001	0.001	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.050	-0.040	22.441	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.044	0.008	19.789	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.037	0.016	17.935	0.000	0.000	0.000	0.000	0.000	0.000
23	A	26	THR	0	-0.047	-0.010	17.466	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.880	-0.922	17.106	-0.049	-0.049	0.000	0.000	0.000	0.000
25	A	28	ILE	0	-0.002	0.010	12.637	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.862	0.925	12.608	0.167	0.167	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.769	0.873	13.215	0.110	0.110	0.000	0.000	0.000	0.000
28	A	31	MET	0	-0.014	0.001	9.112	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	32	ALA	0	0.007	0.000	8.509	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.006	-0.034	8.751	-0.199	-0.199	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.911	-0.933	10.438	-0.262	-0.262	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.053	-0.013	5.310	0.008	0.008	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.045	-0.013	5.451	-0.509	-0.509	0.000	0.000	0.000	0.000
34	A	37	ILE	0	-0.035	-0.011	3.463	-0.197	0.120	0.007	-0.098	-0.227	0.000
35	A	38	ASP	-1	-0.808	-0.895	6.664	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.746	-0.852	9.839	-0.159	-0.159	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.035	-0.007	12.319	0.068	0.068	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.004	-0.042	10.628	0.023	0.023	0.000	0.000	0.000	0.000
39	A	42	ALA	0	-0.005	0.007	9.867	0.083	0.083	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.862	-0.958	11.478	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.966	-0.963	14.990	-0.055	-0.055	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.003	-0.010	10.847	0.036	0.036	0.000	0.000	0.000	0.000
43	A	46	TYR	0	0.036	0.015	14.765	0.020	0.020	0.000	0.000	0.000	0.000
44	A	47	HIS	0	-0.058	-0.037	16.490	0.006	0.006	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.030	0.019	16.763	0.008	0.008	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.045	-0.026	15.823	0.009	0.009	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.004	-0.020	18.997	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.925	-0.955	21.859	0.005	0.005	0.000	0.000	0.000	0.000
49	A	52	PHE	0	-0.049	-0.025	20.333	0.001	0.001	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.014	-0.027	18.997	0.004	0.004	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.021	0.016	24.254	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.038	0.023	26.670	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.061	-0.029	25.121	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.885	-0.955	28.104	0.036	0.036	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.964	-0.963	30.396	0.014	0.014	0.000	0.000	0.000	0.000
56	A	59	HIS	0	-0.147	-0.084	30.886	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.055	-0.031	32.921	0.001	0.001	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.054	0.043	30.427	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	62	ILE	0	0.046	-0.002	24.327	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.940	-0.968	28.352	0.036	0.036	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.894	0.941	30.986	-0.031	-0.031	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.020	-0.002	25.633	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	66	MET	0	-0.023	0.001	25.932	0.001	0.001	0.000	0.000	0.000	0.000
64	A	67	HIS	0	-0.026	-0.005	29.354	0.001	0.001	0.000	0.000	0.000	0.000
65	A	68	SER	0	-0.010	0.016	31.695	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.042	-0.040	33.713	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.053	0.035	29.474	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.065	-0.035	27.479	0.003	0.003	0.000	0.000	0.000	0.000
69	A	72	TRP	0	-0.035	-0.029	20.598	0.009	0.009	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.072	0.059	25.619	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.834	0.897	25.114	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	75	ILE	0	0.066	0.037	22.256	0.003	0.003	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.738	-0.844	21.446	0.087	0.087	0.000	0.000	0.000	0.000
74	A	77	LEU	0	-0.029	-0.023	20.298	0.015	0.015	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.824	-0.906	19.916	0.013	0.013	0.000	0.000	0.000	0.000
76	A	79	LEU	0	0.031	0.024	16.047	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.030	-0.011	15.714	0.025	0.025	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.037	-0.039	15.267	0.024	0.024	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.044	0.033	14.221	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	83	CYS	0	-0.028	-0.015	11.352	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	84	TYR	0	-0.024	-0.055	10.230	0.080	0.080	0.000	0.000	0.000	0.000
82	A	85	GLN	0	-0.047	-0.022	10.486	0.020	0.020	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.057	0.033	6.733	-0.079	-0.079	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.019	0.002	5.831	-0.274	-0.274	0.000	0.000	0.000	0.000
85	A	88	ILE	0	-0.070	-0.043	6.149	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.038	-0.011	7.622	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.872	-0.899	1.605	-31.203	-36.791	21.499	-10.585	-5.326	-0.084
88	A	91	ASP	-1	-0.936	-0.966	3.021	-1.368	0.078	0.219	-0.753	-0.912	-0.007
89	A	92	MET	0	-0.051	-0.009	4.147	0.437	0.622	-0.001	-0.016	-0.168	0.000
90	A	93	LYS	1	0.813	0.885	6.128	-0.496	-0.496	0.000	0.000	0.000	0.000
91	A	94	VAL	0	0.029	-0.009	9.680	0.042	0.042	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.020	-0.009	12.417	0.013	0.013	0.000	0.000	0.000	0.000
93	A	96	ASP	-1	-0.769	-0.877	8.758	0.309	0.309	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.011	0.023	8.540	0.042	0.042	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.018	-0.026	10.554	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	99	GLU	-1	-0.879	-0.923	12.689	0.160	0.160	0.000	0.000	0.000	0.000
97	A	100	MET	0	0.006	0.037	7.531	0.071	0.071	0.000	0.000	0.000	0.000
98	A	101	LEU	0	0.031	0.007	11.045	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	102	SER	0	-0.026	-0.021	13.773	-0.066	-0.066	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.049	-0.033	17.094	0.006	0.006	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.096	-0.052	17.064	-0.030	-0.030	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.801	-0.871	11.994	0.323	0.323	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.019	0.006	10.022	-0.030	-0.030	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.833	0.914	14.674	-0.147	-0.147	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.048	0.040	13.060	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	109	PHE	0	0.039	0.020	14.893	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.004	0.009	19.223	0.006	0.006	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.787	0.866	20.430	-0.096	-0.096	0.000	0.000	0.000	0.000
109	A	112	THR	0	0.049	0.011	20.281	0.016	0.016	0.000	0.000	0.000	0.000
110	A	113	PRO	0	0.128	0.060	16.948	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.016	-0.012	18.540	0.000	0.000	0.000	0.000	0.000	0.000
112	A	115	GLN	0	-0.017	0.007	21.383	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	116	LEU	0	0.061	0.052	16.507	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	117	GLN	0	0.077	0.057	16.395	0.010	0.010	0.000	0.000	0.000	0.000
115	A	118	ASN	0	-0.052	-0.048	18.921	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.027	-0.028	21.719	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.082	0.058	14.769	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	121	TYR	0	0.008	-0.012	17.279	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.893	0.952	21.767	-0.059	-0.059	0.000	0.000	0.000	0.000
120	A	123	LEU	0	0.048	0.029	20.373	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	124	LYS	1	0.906	0.962	17.040	-0.056	-0.056	0.000	0.000	0.000	0.000
122	A	125	LYS	1	0.845	0.936	22.353	-0.035	-0.035	0.000	0.000	0.000	0.000
123	A	126	GLU	-1	-0.901	-0.947	25.467	0.000	0.000	0.000	0.000	0.000	0.000
124	A	127	LEU	0	-0.121	-0.063	27.364	0.000	0.000	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.056	-0.026	24.701	0.001	0.001	0.000	0.000	0.000	0.000
126	A	129	GLN	0	0.068	0.035	27.305	0.001	0.001	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.019	0.012	23.617	0.005	0.005	0.000	0.000	0.000	0.000
128	A	131	GLU	-1	-0.942	-0.979	26.141	0.010	0.010	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.812	-0.898	28.234	0.031	0.031	0.000	0.000	0.000	0.000
130	A	133	ILE	0	-0.042	-0.009	27.596	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	134	PRO	0	0.015	0.007	30.346	0.003	0.003	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.790	0.884	30.350	-0.044	-0.044	0.000	0.000	0.000	0.000
133	A	136	ASN	0	-0.045	-0.017	33.349	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	137	LYS	1	0.985	0.988	35.640	-0.023	-0.023	0.000	0.000	0.000	0.000
135	A	138	PRO	0	0.021	0.015	37.221	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.029	0.011	38.880	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	140	ARG	1	0.957	0.967	42.361	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	141	LYS	1	0.950	0.986	39.969	-0.024	-0.024	0.000	0.000	0.000	0.000
139	A	142	ARG	1	0.970	0.982	45.853	-0.016	-0.016	0.000	0.000	0.000	0.000
140	A	143	LYS	1	1.043	1.027	49.288	-0.013	-0.013	0.000	0.000	0.000	0.000

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