FMO DATABASE

FMODB ID: 14M5Z

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	OptH
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	-1331630.27937
FMO2-HF: Nuclear repulsion	1274559.056033
FMO2-HF: Total energy	-57071.223338
FMO2-MP2: Total energy	-57237.476722

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.
-41.662	-28.375	9.259	-11.392	-11.154	-0.025

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 : 0.010

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	0.050	0.026	2.215	-11.974	-5.954	2.964	-4.320	-4.664	0.041
4	A	7	ARG	1	0.837	0.884	3.976	-3.095	-2.698	0.014	-0.141	-0.270	0.001
5	A	8	LYS	1	0.897	0.942	6.673	-0.052	-0.052	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.058	0.045	7.014	-0.214	-0.214	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.035	-0.001	8.011	-0.287	-0.287	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.050	-0.022	10.133	-0.195	-0.195	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.872	-0.930	11.683	0.010	0.010	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.011	0.009	11.098	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	14	LYS	1	0.853	0.919	14.260	-0.205	-0.205	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.897	0.958	15.949	-0.082	-0.082	0.000	0.000	0.000	0.000
13	A	16	GLN	0	-0.017	-0.005	17.109	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.003	0.008	18.011	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.900	-0.957	20.290	0.106	0.106	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.141	-0.071	22.031	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	20	PRO	0	0.003	0.035	22.727	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.044	0.007	23.419	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	22	ASN	0	-0.064	-0.050	24.241	0.004	0.004	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.079	-0.046	22.412	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.059	0.017	20.019	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.040	0.014	18.190	0.005	0.005	0.000	0.000	0.000	0.000
23	A	26	THR	0	-0.048	-0.007	17.714	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	27	GLU	-1	-0.910	-0.952	17.293	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	28	ILE	0	0.026	0.018	12.909	0.000	0.000	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.969	1.004	12.859	0.067	0.067	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.906	0.953	13.423	0.050	0.050	0.000	0.000	0.000	0.000
28	A	31	MET	0	0.014	0.014	9.666	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	32	ALA	0	0.002	0.001	8.738	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.011	-0.001	8.920	-0.144	-0.144	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-1.012	-1.012	10.443	-0.229	-0.229	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.047	-0.014	5.236	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	36	GLY	0	-0.052	-0.018	5.439	-0.396	-0.396	0.000	0.000	0.000	0.000
34	A	37	ILE	0	-0.030	-0.003	3.852	-0.212	0.016	0.001	-0.059	-0.170	0.000
35	A	38	ASP	-1	-0.877	-0.947	6.778	0.006	0.006	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.886	-0.967	9.931	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	40	GLN	0	-0.017	0.001	12.478	0.048	0.048	0.000	0.000	0.000	0.000
38	A	41	THR	0	0.008	-0.014	10.557	0.041	0.041	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.013	0.016	10.148	0.077	0.077	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.865	-0.956	11.688	0.073	0.073	0.000	0.000	0.000	0.000
41	A	44	GLU	-1	-0.982	-0.970	15.162	0.040	0.040	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.003	-0.007	10.957	0.020	0.020	0.000	0.000	0.000	0.000
43	A	46	TYR	0	0.035	0.014	14.973	0.006	0.006	0.000	0.000	0.000	0.000
44	A	47	HIS	0	-0.065	-0.047	16.736	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.043	0.029	16.921	0.001	0.001	0.000	0.000	0.000	0.000
46	A	49	LEU	0	-0.057	-0.027	16.006	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.003	-0.012	19.109	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.914	-0.956	22.001	0.049	0.049	0.000	0.000	0.000	0.000
49	A	52	PHE	0	-0.049	-0.026	20.535	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	53	TYR	0	0.005	-0.020	19.175	0.001	0.001	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.017	0.015	24.367	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.048	0.025	26.778	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.064	-0.033	25.070	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.933	-0.973	28.215	0.050	0.050	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.962	-0.964	30.513	0.036	0.036	0.000	0.000	0.000	0.000
56	A	59	HIS	0	-0.130	-0.068	30.676	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.064	-0.038	33.029	0.000	0.000	0.000	0.000	0.000	0.000
58	A	61	GLY	0	0.061	0.041	30.546	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	62	ILE	0	0.065	0.008	24.764	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.963	-0.979	28.476	0.045	0.045	0.000	0.000	0.000	0.000
61	A	64	LYS	1	0.893	0.941	31.111	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.019	0.002	25.802	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	66	MET	0	-0.022	0.009	25.479	0.000	0.000	0.000	0.000	0.000	0.000
64	A	67	HIS	0	-0.004	0.007	29.464	0.001	0.001	0.000	0.000	0.000	0.000
65	A	68	SER	0	-0.035	-0.007	31.826	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.026	-0.039	33.809	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.057	0.042	29.496	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	71	SER	0	-0.078	-0.043	27.556	0.002	0.002	0.000	0.000	0.000	0.000
69	A	72	TRP	0	-0.031	-0.028	20.800	0.010	0.010	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.070	0.053	25.701	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.929	0.961	25.186	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	75	ILE	0	0.075	0.046	22.444	0.005	0.005	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.741	-0.850	21.532	0.116	0.116	0.000	0.000	0.000	0.000
74	A	77	LEU	0	-0.044	-0.032	20.368	0.019	0.019	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.902	-0.953	20.018	0.060	0.060	0.000	0.000	0.000	0.000
76	A	79	LEU	0	0.039	0.028	15.990	0.007	0.007	0.000	0.000	0.000	0.000
77	A	80	LEU	0	-0.053	-0.027	15.853	0.034	0.034	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.029	-0.032	15.356	0.028	0.028	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.066	0.043	14.312	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	83	CYS	0	-0.028	-0.013	11.489	0.029	0.029	0.000	0.000	0.000	0.000
81	A	84	TYR	0	-0.020	-0.048	10.324	0.102	0.102	0.000	0.000	0.000	0.000
82	A	85	GLN	0	-0.051	-0.025	10.488	0.024	0.024	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.062	0.034	6.806	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.024	0.006	5.890	-0.169	-0.169	0.000	0.000	0.000	0.000
85	A	88	ILE	0	-0.081	-0.046	6.082	-0.063	-0.063	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.047	-0.019	7.517	-0.062	-0.062	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.891	-0.929	2.034	-22.969	-18.023	6.058	-6.057	-4.947	-0.060
88	A	91	ASP	-1	-0.931	-0.966	2.995	-1.971	-0.458	0.222	-0.797	-0.938	-0.007
89	A	92	MET	0	-0.054	-0.009	3.961	0.344	0.527	0.000	-0.018	-0.165	0.000
90	A	93	LYS	1	0.916	0.957	6.181	-0.409	-0.409	0.000	0.000	0.000	0.000
91	A	94	VAL	0	0.040	0.001	9.721	0.043	0.043	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.039	-0.023	12.435	0.016	0.016	0.000	0.000	0.000	0.000
93	A	96	ASP	-1	-0.849	-0.935	8.662	0.260	0.260	0.000	0.000	0.000	0.000
94	A	97	ILE	0	-0.012	0.010	8.603	0.038	0.038	0.000	0.000	0.000	0.000
95	A	98	SER	0	-0.022	-0.035	10.498	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	99	GLU	-1	-0.882	-0.943	12.639	0.144	0.144	0.000	0.000	0.000	0.000
97	A	100	MET	0	0.020	0.042	7.792	0.060	0.060	0.000	0.000	0.000	0.000
98	A	101	LEU	0	0.020	0.004	11.246	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	102	SER	0	-0.033	-0.024	13.853	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	103	LEU	0	-0.065	-0.040	16.950	0.003	0.003	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.078	-0.034	16.994	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.805	-0.882	11.798	0.268	0.268	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.026	0.002	10.168	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.849	0.928	14.761	-0.145	-0.145	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.044	0.037	13.261	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	109	PHE	0	0.033	0.024	15.187	-0.036	-0.036	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.010	0.006	19.333	0.001	0.001	0.000	0.000	0.000	0.000
108	A	111	LYS	1	0.820	0.891	20.508	-0.118	-0.118	0.000	0.000	0.000	0.000
109	A	112	THR	0	0.053	0.011	20.166	0.015	0.015	0.000	0.000	0.000	0.000
110	A	113	PRO	0	0.111	0.047	16.956	0.000	0.000	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.015	-0.012	18.453	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	115	GLN	0	-0.021	0.013	21.320	0.000	0.000	0.000	0.000	0.000	0.000
113	A	116	LEU	0	0.066	0.050	16.262	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	117	GLN	0	0.081	0.062	16.458	0.012	0.012	0.000	0.000	0.000	0.000
115	A	118	ASN	0	-0.047	-0.043	18.894	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.034	-0.029	21.763	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.071	0.049	15.131	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	121	TYR	0	0.007	-0.014	16.989	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	122	LYS	1	0.894	0.950	21.792	-0.070	-0.070	0.000	0.000	0.000	0.000
120	A	123	LEU	0	0.049	0.029	20.240	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	124	LYS	1	0.928	0.977	17.468	-0.070	-0.070	0.000	0.000	0.000	0.000
122	A	125	LYS	1	0.842	0.935	22.319	-0.049	-0.049	0.000	0.000	0.000	0.000
123	A	126	GLU	-1	-0.896	-0.946	25.442	0.020	0.020	0.000	0.000	0.000	0.000
124	A	127	LEU	0	-0.121	-0.060	27.351	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.054	-0.025	24.691	0.000	0.000	0.000	0.000	0.000	0.000
126	A	129	GLN	0	0.059	0.034	27.330	0.001	0.001	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.017	0.009	23.739	0.004	0.004	0.000	0.000	0.000	0.000
128	A	131	GLU	-1	-0.960	-1.002	26.219	0.031	0.031	0.000	0.000	0.000	0.000
129	A	132	ASP	-1	-0.812	-0.903	28.339	0.054	0.054	0.000	0.000	0.000	0.000
130	A	133	ILE	0	-0.042	-0.005	27.590	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	134	PRO	0	0.010	0.003	30.406	0.003	0.003	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.788	0.882	30.642	-0.055	-0.055	0.000	0.000	0.000	0.000
133	A	136	ASN	0	-0.047	-0.017	33.423	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	137	LYS	1	0.977	0.981	35.629	-0.030	-0.030	0.000	0.000	0.000	0.000
135	A	138	PRO	0	0.014	0.016	37.157	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.025	0.006	38.827	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	140	ARG	1	0.945	0.963	42.312	-0.021	-0.021	0.000	0.000	0.000	0.000
138	A	141	LYS	1	1.000	1.010	39.874	-0.030	-0.030	0.000	0.000	0.000	0.000
139	A	142	ARG	1	0.963	0.978	45.823	-0.021	-0.021	0.000	0.000	0.000	0.000
140	A	143	LYS	1	1.037	1.024	49.254	-0.016	-0.016	0.000	0.000	0.000	0.000

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