FMO DATABASE

FMODB ID: 63JZZ

Calculation Name: 3QD7-X-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QD7

Chain ID: X

ChEMBL ID:

UniProt ID: P76053

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1187413.287605
FMO2-HF: Nuclear repulsion	1135499.69335
FMO2-HF: Total energy	-51913.594255
FMO2-MP2: Total energy	-52065.827847

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(X:39:ACE )

Summations of interaction energy for fragment #1(X:39:ACE )

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.
2.276	2.948	-0.004	-0.265	-0.402	0

Interaction energy analysis for fragmet #1(X:39:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / 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].
3	X	41	THR	0	-0.054	-0.036	3.839	1.851	2.523	-0.004	-0.265	-0.402
4	X	42	LEU	0	0.011	0.013	6.631	0.527	0.527	0.000	0.000	0.000
5	X	43	GLN	0	0.044	0.006	8.793	0.132	0.132	0.000	0.000	0.000
6	X	44	LEU	0	-0.038	-0.011	9.910	0.113	0.113	0.000	0.000	0.000
7	X	45	ASP	-1	-0.835	-0.917	6.873	-1.451	-1.451	0.000	0.000	0.000
8	X	46	ASN	0	-0.134	-0.078	9.669	0.168	0.168	0.000	0.000	0.000
9	X	47	PHE	0	0.045	0.010	9.449	0.047	0.047	0.000	0.000	0.000
10	X	48	LEU	0	-0.062	-0.004	13.802	0.048	0.048	0.000	0.000	0.000
11	X	49	THR	0	0.008	0.004	16.265	-0.021	-0.021	0.000	0.000	0.000
12	X	50	THR	0	-0.036	-0.033	19.762	0.013	0.013	0.000	0.000	0.000
13	X	51	GLY	0	0.002	0.008	22.994	0.002	0.002	0.000	0.000	0.000
14	X	52	PHE	0	0.022	-0.020	26.324	0.004	0.004	0.000	0.000	0.000
15	X	53	LEU	0	-0.061	-0.014	25.745	0.004	0.004	0.000	0.000	0.000
16	X	54	ASP	-1	-0.812	-0.902	27.290	-0.022	-0.022	0.000	0.000	0.000
17	X	55	ILE	0	-0.086	-0.056	29.148	0.002	0.002	0.000	0.000	0.000
18	X	56	ILE	0	0.047	0.019	27.452	0.003	0.003	0.000	0.000	0.000
19	X	57	PRO	0	0.025	0.031	31.661	-0.002	-0.002	0.000	0.000	0.000
20	X	58	LEU	0	-0.029	-0.003	33.999	0.003	0.003	0.000	0.000	0.000
21	X	59	SER	0	-0.067	-0.027	35.540	0.002	0.002	0.000	0.000	0.000
22	X	60	GLN	0	0.022	0.017	33.223	0.003	0.003	0.000	0.000	0.000
23	X	61	PRO	0	0.030	0.033	31.607	-0.003	-0.003	0.000	0.000	0.000
24	X	62	LEU	0	0.008	-0.011	24.845	-0.001	-0.001	0.000	0.000	0.000
25	X	63	GLU	-1	-0.961	-0.995	27.491	0.038	0.038	0.000	0.000	0.000
26	X	64	PHE	0	0.023	0.025	20.939	-0.004	-0.004	0.000	0.000	0.000
27	X	65	ARG	1	0.931	0.951	24.665	-0.051	-0.051	0.000	0.000	0.000
28	X	66	ARG	1	0.887	0.966	17.357	-0.111	-0.111	0.000	0.000	0.000
29	X	67	GLU	-1	-0.906	-0.963	24.082	0.065	0.065	0.000	0.000	0.000
30	X	68	GLY	0	-0.011	-0.008	24.798	0.009	0.009	0.000	0.000	0.000
31	X	69	LEU	0	-0.052	-0.014	21.937	0.013	0.013	0.000	0.000	0.000
32	X	70	GLN	0	0.018	0.005	24.653	0.001	0.001	0.000	0.000	0.000
33	X	71	HIS	0	0.042	0.000	26.556	0.001	0.001	0.000	0.000	0.000
34	X	72	GLY	0	0.028	0.017	28.041	-0.004	-0.004	0.000	0.000	0.000
35	X	73	VAL	0	-0.060	-0.024	22.576	0.001	0.001	0.000	0.000	0.000
36	X	74	LEU	0	0.046	0.005	24.786	0.002	0.002	0.000	0.000	0.000
37	X	75	ASP	-1	-0.859	-0.924	27.096	0.067	0.067	0.000	0.000	0.000
38	X	76	LYS	1	0.767	0.905	18.969	-0.187	-0.187	0.000	0.000	0.000
39	X	77	LEU	0	-0.016	-0.009	22.951	0.001	0.001	0.000	0.000	0.000
40	X	78	ARG	1	0.974	0.992	25.431	-0.055	-0.055	0.000	0.000	0.000
41	X	79	SER	0	-0.048	-0.047	28.501	-0.005	-0.005	0.000	0.000	0.000
42	X	80	GLY	0	0.038	0.065	24.558	0.005	0.005	0.000	0.000	0.000
43	X	81	LYS	1	0.919	0.955	23.444	-0.109	-0.109	0.000	0.000	0.000
44	X	82	TYR	0	-0.007	-0.021	21.693	0.013	0.013	0.000	0.000	0.000
45	X	83	PRO	0	-0.033	-0.010	20.667	-0.010	-0.010	0.000	0.000	0.000
46	X	84	GLN	0	0.080	0.028	21.787	0.006	0.006	0.000	0.000	0.000
47	X	85	GLN	0	0.049	0.027	17.377	-0.026	-0.026	0.000	0.000	0.000
48	X	86	ALA	0	-0.030	-0.003	16.826	0.012	0.012	0.000	0.000	0.000
49	X	87	SER	0	-0.058	-0.034	18.335	-0.004	-0.004	0.000	0.000	0.000
50	X	88	LEU	0	0.061	0.047	16.300	-0.008	-0.008	0.000	0.000	0.000
51	X	89	ASN	0	-0.020	-0.024	19.212	-0.002	-0.002	0.000	0.000	0.000
52	X	90	LEU	0	0.061	0.013	19.023	-0.012	-0.012	0.000	0.000	0.000
53	X	91	LEU	0	-0.051	-0.019	22.767	-0.004	-0.004	0.000	0.000	0.000
54	X	92	ARG	1	0.899	0.937	26.097	0.033	0.033	0.000	0.000	0.000
55	X	93	GLN	0	0.076	0.057	22.186	-0.013	-0.013	0.000	0.000	0.000
56	X	94	PRO	0	0.043	0.027	23.789	0.007	0.007	0.000	0.000	0.000
57	X	95	VAL	0	0.062	0.018	23.130	-0.006	-0.006	0.000	0.000	0.000
58	X	96	GLU	-1	-0.812	-0.903	18.954	-0.201	-0.201	0.000	0.000	0.000
59	X	97	GLU	-1	-0.936	-0.969	19.106	-0.206	-0.206	0.000	0.000	0.000
60	X	98	CYS	0	-0.046	-0.016	18.368	-0.003	-0.003	0.000	0.000	0.000
61	X	99	ARG	1	0.840	0.905	15.948	0.231	0.231	0.000	0.000	0.000
62	X	100	LYS	1	0.936	0.975	14.378	0.229	0.229	0.000	0.000	0.000
63	X	101	MET	0	-0.007	-0.001	13.390	-0.025	-0.025	0.000	0.000	0.000
64	X	102	VAL	0	0.015	0.008	13.981	0.020	0.020	0.000	0.000	0.000
65	X	103	PHE	0	0.022	0.025	8.295	0.092	0.092	0.000	0.000	0.000
66	X	104	SER	0	-0.013	-0.002	9.266	0.061	0.061	0.000	0.000	0.000
67	X	105	PHE	0	-0.004	-0.007	9.595	0.072	0.072	0.000	0.000	0.000
68	X	106	ILE	0	-0.031	-0.016	10.821	0.072	0.072	0.000	0.000	0.000
69	X	107	GLN	0	0.018	0.008	5.685	0.421	0.421	0.000	0.000	0.000
70	X	108	GLN	0	-0.006	0.011	6.955	0.192	0.192	0.000	0.000	0.000
71	X	109	ALA	0	-0.015	-0.018	8.714	0.096	0.096	0.000	0.000	0.000
72	X	110	LEU	0	-0.032	-0.015	8.161	0.014	0.014	0.000	0.000	0.000
73	X	111	ALA	0	-0.003	0.009	5.658	0.080	0.080	0.000	0.000	0.000
74	X	112	ASP	-1	-0.909	-0.943	7.587	0.319	0.319	0.000	0.000	0.000
75	X	113	GLY	0	-0.072	-0.035	11.017	-0.080	-0.080	0.000	0.000	0.000
76	X	114	LEU	0	-0.035	-0.026	12.991	-0.081	-0.081	0.000	0.000	0.000
77	X	115	ARG	1	0.930	0.964	14.747	-0.184	-0.184	0.000	0.000	0.000
78	X	116	ASN	0	-0.015	-0.011	17.469	-0.006	-0.006	0.000	0.000	0.000
79	X	117	VAL	0	0.019	0.025	15.335	0.002	0.002	0.000	0.000	0.000
80	X	118	LEU	0	-0.046	-0.020	18.670	-0.006	-0.006	0.000	0.000	0.000
81	X	119	ILE	0	0.032	0.017	17.753	-0.007	-0.007	0.000	0.000	0.000
82	X	120	ILE	0	-0.005	-0.007	21.237	0.000	0.000	0.000	0.000	0.000
83	X	121	HIS	0	0.048	0.011	23.963	-0.006	-0.006	0.000	0.000	0.000
84	X	122	GLY	0	-0.012	-0.011	25.516	-0.006	-0.006	0.000	0.000	0.000
85	X	123	LYS	1	0.901	0.952	29.205	-0.002	-0.002	0.000	0.000	0.000
86	X	124	GLY	0	0.035	0.023	32.525	-0.003	-0.003	0.000	0.000	0.000
87	X	125	ARG	1	0.892	0.934	34.259	0.014	0.014	0.000	0.000	0.000
88	X	126	ASP	-1	-0.792	-0.907	36.948	-0.021	-0.021	0.000	0.000	0.000
89	X	127	ASP	-1	-0.816	-0.920	35.076	-0.014	-0.014	0.000	0.000	0.000
90	X	128	LYS	1	0.934	0.971	33.763	0.027	0.027	0.000	0.000	0.000
91	X	129	SER	0	-0.022	0.006	34.038	-0.004	-0.004	0.000	0.000	0.000
92	X	130	HIS	0	0.023	-0.012	26.649	0.003	0.003	0.000	0.000	0.000
93	X	131	ALA	0	0.011	0.004	28.787	-0.002	-0.002	0.000	0.000	0.000
94	X	132	ASN	0	-0.006	-0.019	28.461	0.005	0.005	0.000	0.000	0.000
95	X	133	ILE	0	-0.001	0.014	27.253	0.001	0.001	0.000	0.000	0.000
96	X	134	VAL	0	0.014	-0.006	23.367	-0.002	-0.002	0.000	0.000	0.000
97	X	135	ARG	1	0.778	0.878	24.172	0.004	0.004	0.000	0.000	0.000
98	X	136	SER	0	0.013	0.010	25.221	0.006	0.006	0.000	0.000	0.000
99	X	137	TYR	0	0.044	0.021	22.048	-0.001	-0.001	0.000	0.000	0.000
100	X	138	VAL	0	-0.030	-0.007	20.108	0.000	0.000	0.000	0.000	0.000
101	X	139	ALA	0	-0.001	0.000	20.784	0.010	0.010	0.000	0.000	0.000
102	X	140	ARG	1	0.887	0.969	20.901	0.059	0.059	0.000	0.000	0.000
103	X	141	TRP	0	-0.030	-0.016	17.012	0.003	0.003	0.000	0.000	0.000
104	X	142	LEU	0	-0.012	-0.006	16.644	0.012	0.012	0.000	0.000	0.000
105	X	143	THR	0	-0.060	-0.039	17.383	0.022	0.022	0.000	0.000	0.000
106	X	144	GLU	-1	-0.750	-0.882	16.204	-0.050	-0.050	0.000	0.000	0.000
107	X	145	PHE	0	-0.020	0.001	10.280	0.002	0.002	0.000	0.000	0.000
108	X	146	ASP	-1	-0.815	-0.922	12.864	0.229	0.229	0.000	0.000	0.000
109	X	147	ASP	-1	-0.865	-0.919	10.731	0.488	0.488	0.000	0.000	0.000
110	X	148	VAL	0	-0.029	0.003	13.980	-0.001	-0.001	0.000	0.000	0.000
111	X	149	GLN	0	0.002	-0.009	16.652	-0.015	-0.015	0.000	0.000	0.000
112	X	150	ALA	0	0.023	-0.002	19.911	-0.015	-0.015	0.000	0.000	0.000
113	X	151	TYR	0	-0.010	-0.006	20.960	0.008	0.008	0.000	0.000	0.000
114	X	152	CYS	0	-0.015	-0.008	23.350	-0.002	-0.002	0.000	0.000	0.000
115	X	153	THR	0	-0.019	0.011	26.244	-0.002	-0.002	0.000	0.000	0.000
116	X	154	ALA	0	0.020	0.025	26.904	0.005	0.005	0.000	0.000	0.000
117	X	155	LEU	0	0.059	0.019	28.591	-0.005	-0.005	0.000	0.000	0.000
118	X	156	PRO	0	0.014	-0.017	31.064	-0.002	-0.002	0.000	0.000	0.000
119	X	157	HIS	0	-0.015	0.004	30.621	-0.006	-0.006	0.000	0.000	0.000
120	X	158	HIS	0	0.031	0.035	27.157	0.001	0.001	0.000	0.000	0.000
121	X	159	GLY	0	0.049	0.023	27.913	-0.001	-0.001	0.000	0.000	0.000
122	X	160	GLY	0	-0.045	-0.019	30.237	-0.005	-0.005	0.000	0.000	0.000
123	X	161	SER	0	0.017	-0.011	30.005	0.000	0.000	0.000	0.000	0.000
124	X	162	GLY	0	-0.049	-0.016	29.731	-0.003	-0.003	0.000	0.000	0.000
125	X	163	ALA	0	0.006	0.013	25.465	-0.005	-0.005	0.000	0.000	0.000
126	X	164	CYS	0	-0.027	0.001	23.123	0.003	0.003	0.000	0.000	0.000
127	X	165	TYR	0	0.022	0.002	22.789	0.000	0.000	0.000	0.000	0.000
128	X	166	VAL	0	0.057	0.014	17.466	-0.004	-0.004	0.000	0.000	0.000
129	X	167	ALA	0	-0.055	-0.029	19.593	0.013	0.013	0.000	0.000	0.000
130	X	168	LEU	0	0.043	0.013	13.684	-0.009	-0.009	0.000	0.000	0.000
131	X	169	ARG	1	0.802	0.875	13.825	-0.318	-0.318	0.000	0.000	0.000
132	X	170	LYS	1	0.842	0.919	14.034	-0.295	-0.295	0.000	0.000	0.000
133	X	171	NME	0	0.065	0.050	11.482	-0.027	-0.027	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:39:ACE )