FMO DATABASE

FMODB ID: LN759

Calculation Name: 3HDC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HDC

Chain ID: A

ChEMBL ID:

UniProt ID: Q39VV7

Base Structure: X-ray

Registration Date: 2023-09-22

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1421189.931615
FMO2-HF: Nuclear repulsion	1362718.345023
FMO2-HF: Total energy	-58471.586592
FMO2-MP2: Total energy	-58643.568394

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:20:SER)

Summations of interaction energy for fragment #1(A:20: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.
-0.706	0.574	-0.01	-0.604	-0.666	0.002

Interaction energy analysis for fragmet #1(A:20:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.017

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	22	ALA	0	0.017	0.012	3.859	-1.173	0.107	-0.010	-0.604	-0.666	0.002
4	A	23	PRO	0	0.002	-0.004	5.328	0.817	0.817	0.000	0.000	0.000	0.000
5	A	24	GLY	0	0.030	0.017	8.284	-0.178	-0.178	0.000	0.000	0.000	0.000
6	A	25	LYS	1	0.900	0.945	11.877	0.296	0.296	0.000	0.000	0.000	0.000
7	A	26	ALA	0	0.024	0.018	15.337	0.019	0.019	0.000	0.000	0.000	0.000
8	A	27	GLU	-1	-0.938	-0.968	17.060	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	28	SER	0	-0.052	-0.029	20.167	0.031	0.031	0.000	0.000	0.000	0.000
10	A	29	ASP	-1	-0.903	-0.937	21.544	0.112	0.112	0.000	0.000	0.000	0.000
11	A	30	ALA	0	-0.029	-0.024	23.363	0.013	0.013	0.000	0.000	0.000	0.000
12	A	31	PRO	0	-0.026	-0.002	25.481	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	32	LEU	0	-0.004	-0.006	27.408	0.005	0.005	0.000	0.000	0.000	0.000
14	A	33	VAL	0	0.020	0.008	28.957	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	34	ARG	1	0.927	0.955	28.967	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	35	THR	0	0.030	0.010	31.935	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	36	GLY	0	-0.019	-0.003	33.745	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	37	ALA	0	-0.017	-0.004	34.960	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	38	LEU	0	-0.005	-0.004	36.870	0.003	0.003	0.000	0.000	0.000	0.000
20	A	39	ALA	0	0.025	0.016	36.946	0.003	0.003	0.000	0.000	0.000	0.000
21	A	40	PRO	0	0.025	0.018	33.740	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	41	ASN	0	0.030	0.027	36.834	0.003	0.003	0.000	0.000	0.000	0.000
23	A	42	PHE	0	0.009	0.000	38.140	0.004	0.004	0.000	0.000	0.000	0.000
24	A	43	LYS	1	0.921	0.941	40.134	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	44	LEU	0	-0.015	0.011	38.689	0.003	0.003	0.000	0.000	0.000	0.000
26	A	45	PRO	0	0.009	0.012	42.253	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	46	THR	0	-0.009	-0.026	44.579	0.003	0.003	0.000	0.000	0.000	0.000
28	A	47	LEU	0	-0.022	-0.021	46.477	0.001	0.001	0.000	0.000	0.000	0.000
29	A	48	SER	0	0.004	0.011	48.669	0.000	0.000	0.000	0.000	0.000	0.000
30	A	49	GLY	0	-0.016	0.006	48.858	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	50	GLU	-1	-0.769	-0.855	49.647	0.047	0.047	0.000	0.000	0.000	0.000
32	A	51	ASN	0	-0.029	-0.019	47.087	0.003	0.003	0.000	0.000	0.000	0.000
33	A	52	LYS	1	0.850	0.929	46.536	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	53	SER	0	-0.004	-0.023	44.152	0.003	0.003	0.000	0.000	0.000	0.000
35	A	54	LEU	0	0.028	0.016	40.272	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.014	-0.007	43.948	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	56	GLN	0	0.043	0.031	46.387	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	57	TYR	0	0.030	0.010	46.962	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	58	ARG	1	0.882	0.959	42.337	-0.041	-0.041	0.000	0.000	0.000	0.000
40	A	59	GLY	0	0.013	0.006	48.729	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	60	LYS	1	0.799	0.886	49.703	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	61	ILE	0	0.013	0.025	45.288	0.001	0.001	0.000	0.000	0.000	0.000
43	A	62	VAL	0	-0.027	-0.021	43.172	0.001	0.001	0.000	0.000	0.000	0.000
44	A	63	LEU	0	0.013	0.012	41.362	0.001	0.001	0.000	0.000	0.000	0.000
45	A	64	VAL	0	0.005	0.001	37.514	0.000	0.000	0.000	0.000	0.000	0.000
46	A	65	ASN	0	-0.025	-0.019	37.759	0.004	0.004	0.000	0.000	0.000	0.000
47	A	66	PHE	0	0.001	0.000	33.902	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	67	TRP	0	-0.028	-0.031	35.272	0.005	0.005	0.000	0.000	0.000	0.000
49	A	68	ALA	0	0.027	-0.007	34.604	0.001	0.001	0.000	0.000	0.000	0.000
50	A	69	SER	0	-0.061	-0.061	36.616	0.000	0.000	0.000	0.000	0.000	0.000
51	A	70	TRP	0	0.047	0.027	30.229	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	71	CYS	0	-0.031	0.006	33.230	0.001	0.001	0.000	0.000	0.000	0.000
53	A	72	PRO	0	0.011	0.000	34.392	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	73	TYR	0	0.091	0.037	31.838	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	74	CYS	0	-0.057	-0.006	35.312	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	75	ARG	1	0.815	0.907	38.107	-0.103	-0.103	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.862	-0.951	39.067	0.087	0.087	0.000	0.000	0.000	0.000
58	A	77	GLU	-1	-0.791	-0.890	38.725	0.083	0.083	0.000	0.000	0.000	0.000
59	A	78	MET	0	-0.046	-0.008	41.217	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	79	PRO	0	0.016	0.000	44.372	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	80	SER	0	0.026	-0.002	44.442	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	81	MET	0	-0.028	-0.013	40.633	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	82	ASP	-1	-0.769	-0.875	45.638	0.048	0.048	0.000	0.000	0.000	0.000
64	A	83	ARG	1	0.780	0.845	47.930	-0.055	-0.055	0.000	0.000	0.000	0.000
65	A	84	LEU	0	-0.006	0.006	45.289	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	85	VAL	0	-0.025	0.001	47.726	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.737	0.835	50.305	-0.050	-0.050	0.000	0.000	0.000	0.000
68	A	87	SER	0	-0.048	-0.011	51.647	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	88	PHE	0	-0.009	-0.021	49.425	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	89	PRO	0	0.030	0.013	54.155	0.000	0.000	0.000	0.000	0.000	0.000
71	A	90	LYS	1	0.980	0.980	55.281	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	91	GLY	0	0.040	0.023	52.943	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	92	ASP	-1	-0.857	-0.914	52.458	0.033	0.033	0.000	0.000	0.000	0.000
74	A	93	LEU	0	0.012	0.019	45.920	0.000	0.000	0.000	0.000	0.000	0.000
75	A	94	VAL	0	-0.034	-0.018	47.258	0.000	0.000	0.000	0.000	0.000	0.000
76	A	95	VAL	0	0.071	0.040	43.365	0.002	0.002	0.000	0.000	0.000	0.000
77	A	96	LEU	0	-0.064	-0.025	42.277	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	97	ALA	0	0.066	0.039	41.243	0.004	0.004	0.000	0.000	0.000	0.000
79	A	98	VAL	0	0.011	0.004	37.084	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	99	ASN	0	-0.049	-0.026	37.712	0.007	0.007	0.000	0.000	0.000	0.000
81	A	100	VAL	0	0.038	0.002	32.675	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	101	GLU	-1	-0.757	-0.836	34.220	0.111	0.111	0.000	0.000	0.000	0.000
83	A	102	LYS	1	0.957	0.972	34.419	-0.122	-0.122	0.000	0.000	0.000	0.000
84	A	103	ARG	1	0.946	0.963	37.010	-0.086	-0.086	0.000	0.000	0.000	0.000
85	A	104	PHE	0	0.042	0.035	40.691	0.001	0.001	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.044	0.034	40.901	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	106	GLU	-1	-0.764	-0.891	43.547	0.060	0.060	0.000	0.000	0.000	0.000
88	A	107	LYS	1	0.903	0.940	46.978	-0.070	-0.070	0.000	0.000	0.000	0.000
89	A	108	TYR	0	0.062	0.027	42.610	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	109	ARG	1	0.839	0.925	45.455	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	110	ARG	1	0.851	0.913	49.555	-0.059	-0.059	0.000	0.000	0.000	0.000
92	A	111	ALA	0	0.027	0.032	48.947	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	112	PRO	0	0.005	0.017	50.983	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	113	VAL	0	-0.008	-0.005	47.825	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	114	SER	0	-0.008	-0.002	51.004	0.000	0.000	0.000	0.000	0.000	0.000
96	A	115	PHE	0	-0.029	-0.027	45.594	0.000	0.000	0.000	0.000	0.000	0.000
97	A	116	ASN	0	-0.037	-0.026	46.487	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	117	PHE	0	0.022	0.003	43.812	0.003	0.003	0.000	0.000	0.000	0.000
99	A	118	LEU	0	0.005	0.000	41.888	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	119	SER	0	-0.018	-0.012	40.022	0.003	0.003	0.000	0.000	0.000	0.000
101	A	120	ASP	-1	-0.767	-0.885	34.561	0.096	0.096	0.000	0.000	0.000	0.000
102	A	121	ALA	0	-0.014	-0.004	35.854	0.007	0.007	0.000	0.000	0.000	0.000
103	A	122	THR	0	-0.012	-0.008	34.790	0.003	0.003	0.000	0.000	0.000	0.000
104	A	123	GLY	0	0.036	0.023	31.764	0.006	0.006	0.000	0.000	0.000	0.000
105	A	124	GLN	0	-0.007	-0.008	30.127	0.000	0.000	0.000	0.000	0.000	0.000
106	A	125	VAL	0	-0.053	-0.036	32.822	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	126	GLN	0	0.016	-0.017	30.073	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	127	GLN	0	-0.001	0.006	26.196	0.001	0.001	0.000	0.000	0.000	0.000
109	A	128	ARG	1	0.851	0.914	28.515	-0.073	-0.073	0.000	0.000	0.000	0.000
110	A	129	TYR	0	-0.035	-0.038	31.049	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	130	GLY	0	0.035	0.027	27.045	0.000	0.000	0.000	0.000	0.000	0.000
112	A	131	ALA	0	0.005	0.028	26.966	0.013	0.013	0.000	0.000	0.000	0.000
113	A	132	ASN	0	-0.079	-0.053	24.221	0.011	0.011	0.000	0.000	0.000	0.000
114	A	133	ARG	1	0.934	0.969	23.898	-0.196	-0.196	0.000	0.000	0.000	0.000
115	A	134	LEU	0	0.012	0.024	28.344	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	135	PRO	0	0.049	0.015	31.969	0.006	0.006	0.000	0.000	0.000	0.000
117	A	136	ASP	-1	-0.810	-0.896	30.929	0.120	0.120	0.000	0.000	0.000	0.000
118	A	137	THR	0	-0.007	0.010	33.517	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	138	PHE	0	0.002	-0.003	31.045	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	139	ILE	0	0.007	0.008	36.740	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	140	VAL	0	-0.022	-0.015	39.215	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	141	ASP	-1	-0.740	-0.863	41.432	0.034	0.034	0.000	0.000	0.000	0.000
123	A	142	ARG	1	0.845	0.905	44.491	-0.029	-0.029	0.000	0.000	0.000	0.000
124	A	143	LYS	1	0.879	0.928	45.768	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	144	GLY	0	0.003	-0.001	43.227	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	145	ILE	0	-0.040	-0.006	38.971	0.002	0.002	0.000	0.000	0.000	0.000
127	A	146	ILE	0	0.006	0.008	34.445	0.001	0.001	0.000	0.000	0.000	0.000
128	A	147	ARG	1	0.880	0.928	37.198	-0.036	-0.036	0.000	0.000	0.000	0.000
129	A	148	GLN	0	0.000	-0.004	35.331	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	149	ARG	1	0.885	0.957	27.347	-0.114	-0.114	0.000	0.000	0.000	0.000
131	A	150	VAL	0	-0.027	-0.017	33.813	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	151	THR	0	-0.028	-0.035	28.608	0.002	0.002	0.000	0.000	0.000	0.000
133	A	152	GLY	0	-0.009	0.005	31.826	0.003	0.003	0.000	0.000	0.000	0.000
134	A	153	GLY	0	-0.011	-0.001	33.123	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	154	ILE	0	-0.038	-0.021	36.792	0.001	0.001	0.000	0.000	0.000	0.000
136	A	155	GLU	-1	-0.781	-0.857	39.187	0.060	0.060	0.000	0.000	0.000	0.000
137	A	156	TRP	0	-0.020	-0.047	38.347	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	157	ASP	-1	-0.794	-0.870	43.825	0.049	0.049	0.000	0.000	0.000	0.000
139	A	158	ALA	0	0.038	0.022	44.421	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	159	PRO	0	0.031	-0.002	46.422	0.000	0.000	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.960	0.981	40.299	-0.050	-0.050	0.000	0.000	0.000	0.000
142	A	161	VAL	0	0.024	0.023	41.867	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	162	VAL	0	0.039	0.026	44.330	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	163	SER	0	-0.027	-0.012	47.552	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	164	TYR	0	0.028	0.011	39.502	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	165	LEU	0	0.031	0.019	43.300	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	166	LYS	1	0.903	0.960	46.340	-0.037	-0.037	0.000	0.000	0.000	0.000
148	A	167	SER	0	-0.089	-0.045	45.988	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	168	LEU	0	-0.066	-0.032	43.140	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	169	GLU	-1	-0.853	-0.901	47.392	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:20:SER)