FMO DATABASE

FMODB ID: 3J72L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1417594.337337
FMO2-HF: Nuclear repulsion	1359122.941374
FMO2-HF: Total energy	-58471.395963
FMO2-MP2: Total energy	-58643.324205

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.
0.089	1.479	-0.025	-0.606	-0.759	0.003

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 : -0.028 / q_NPA : -0.026

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	0.011	0.008	3.800	0.462	1.852	-0.025	-0.606	-0.759	0.003
4	A	23	PRO	0	0.018	0.009	6.368	0.142	0.142	0.000	0.000	0.000	0.000
5	A	24	GLY	0	0.036	0.017	9.001	-0.238	-0.238	0.000	0.000	0.000	0.000
6	A	25	LYS	1	0.900	0.943	12.594	-0.051	-0.051	0.000	0.000	0.000	0.000
7	A	26	ALA	0	0.014	0.009	15.342	0.043	0.043	0.000	0.000	0.000	0.000
8	A	27	GLU	-1	-0.939	-0.966	17.248	0.132	0.132	0.000	0.000	0.000	0.000
9	A	28	SER	0	-0.059	-0.032	20.378	0.037	0.037	0.000	0.000	0.000	0.000
10	A	29	ASP	-1	-0.881	-0.940	21.828	0.247	0.247	0.000	0.000	0.000	0.000
11	A	30	ALA	0	-0.048	-0.011	23.679	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	31	PRO	0	-0.010	-0.005	25.591	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	32	LEU	0	-0.010	-0.013	27.446	0.002	0.002	0.000	0.000	0.000	0.000
14	A	33	VAL	0	0.023	0.009	28.700	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	34	ARG	1	0.933	0.961	28.723	-0.062	-0.062	0.000	0.000	0.000	0.000
16	A	35	THR	0	0.018	0.003	31.640	0.000	0.000	0.000	0.000	0.000	0.000
17	A	36	GLY	0	-0.015	-0.005	33.704	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	37	ALA	0	-0.020	-0.004	34.833	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	38	LEU	0	-0.016	-0.012	36.746	0.001	0.001	0.000	0.000	0.000	0.000
20	A	39	ALA	0	0.005	0.006	36.826	0.005	0.005	0.000	0.000	0.000	0.000
21	A	40	PRO	0	0.021	0.019	33.744	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	41	ASN	0	0.025	0.023	36.745	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	42	PHE	0	0.023	0.005	38.328	0.008	0.008	0.000	0.000	0.000	0.000
24	A	43	LYS	1	0.949	0.968	40.345	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	44	LEU	0	-0.016	0.009	38.801	0.005	0.005	0.000	0.000	0.000	0.000
26	A	45	PRO	0	-0.015	0.006	42.482	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	46	THR	0	0.001	-0.023	44.911	0.002	0.002	0.000	0.000	0.000	0.000
28	A	47	LEU	0	-0.014	-0.017	46.650	0.002	0.002	0.000	0.000	0.000	0.000
29	A	48	SER	0	-0.013	-0.003	49.073	0.000	0.000	0.000	0.000	0.000	0.000
30	A	49	GLY	0	-0.010	0.007	49.209	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	50	GLU	-1	-0.760	-0.840	50.285	0.057	0.057	0.000	0.000	0.000	0.000
32	A	51	ASN	0	-0.039	-0.030	47.052	0.005	0.005	0.000	0.000	0.000	0.000
33	A	52	LYS	1	0.856	0.926	46.641	-0.060	-0.060	0.000	0.000	0.000	0.000
34	A	53	SER	0	-0.021	-0.024	44.482	0.004	0.004	0.000	0.000	0.000	0.000
35	A	54	LEU	0	0.033	0.015	40.100	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.022	-0.021	43.841	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	56	GLN	0	0.044	0.031	45.912	0.000	0.000	0.000	0.000	0.000	0.000
38	A	57	TYR	0	0.011	-0.002	46.667	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	58	ARG	1	0.950	0.994	42.395	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	59	GLY	0	0.002	0.002	48.479	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	60	LYS	1	0.818	0.910	49.239	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	61	ILE	0	0.014	0.024	44.727	0.002	0.002	0.000	0.000	0.000	0.000
43	A	62	VAL	0	-0.023	-0.018	43.017	0.001	0.001	0.000	0.000	0.000	0.000
44	A	63	LEU	0	0.003	0.014	41.062	0.001	0.001	0.000	0.000	0.000	0.000
45	A	64	VAL	0	-0.007	-0.010	37.309	0.001	0.001	0.000	0.000	0.000	0.000
46	A	65	ASN	0	-0.001	-0.005	37.435	0.004	0.004	0.000	0.000	0.000	0.000
47	A	66	PHE	0	-0.014	0.000	33.779	0.002	0.002	0.000	0.000	0.000	0.000
48	A	67	TRP	0	-0.012	-0.022	35.278	0.000	0.000	0.000	0.000	0.000	0.000
49	A	68	ALA	0	0.043	0.003	34.743	0.005	0.005	0.000	0.000	0.000	0.000
50	A	69	SER	0	-0.049	-0.053	36.634	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	70	TRP	0	0.036	0.019	30.442	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	71	CYS	0	-0.024	0.008	33.005	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	72	PRO	0	0.019	-0.002	34.238	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	73	TYR	0	0.097	0.038	31.377	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	74	CYS	0	-0.047	-0.002	35.097	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	75	ARG	1	0.831	0.922	37.775	-0.080	-0.080	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.894	-0.955	39.071	0.053	0.053	0.000	0.000	0.000	0.000
58	A	77	GLU	-1	-0.814	-0.905	38.373	0.062	0.062	0.000	0.000	0.000	0.000
59	A	78	MET	0	-0.040	-0.010	41.241	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	79	PRO	0	0.012	-0.003	43.935	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	80	SER	0	0.027	0.009	43.641	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	81	MET	0	-0.019	-0.006	40.365	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	82	ASP	-1	-0.773	-0.877	45.359	0.041	0.041	0.000	0.000	0.000	0.000
64	A	83	ARG	1	0.803	0.870	47.239	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	84	LEU	0	-0.014	0.002	45.095	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	85	VAL	0	-0.018	-0.006	47.419	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.728	0.836	50.010	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	87	SER	0	-0.070	-0.020	51.551	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	88	PHE	0	-0.008	-0.007	49.297	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	89	PRO	0	0.038	0.019	53.658	0.000	0.000	0.000	0.000	0.000	0.000
71	A	90	LYS	1	1.007	0.989	54.842	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	91	GLY	0	-0.003	-0.006	53.043	0.000	0.000	0.000	0.000	0.000	0.000
73	A	92	ASP	-1	-0.844	-0.917	52.317	0.032	0.032	0.000	0.000	0.000	0.000
74	A	93	LEU	0	-0.005	0.011	45.548	0.000	0.000	0.000	0.000	0.000	0.000
75	A	94	VAL	0	-0.037	-0.015	46.830	0.000	0.000	0.000	0.000	0.000	0.000
76	A	95	VAL	0	0.063	0.036	43.065	0.001	0.001	0.000	0.000	0.000	0.000
77	A	96	LEU	0	-0.048	-0.018	42.124	0.000	0.000	0.000	0.000	0.000	0.000
78	A	97	ALA	0	0.053	0.030	41.072	0.003	0.003	0.000	0.000	0.000	0.000
79	A	98	VAL	0	0.005	-0.003	37.442	0.000	0.000	0.000	0.000	0.000	0.000
80	A	99	ASN	0	-0.054	-0.042	37.758	0.008	0.008	0.000	0.000	0.000	0.000
81	A	100	VAL	0	0.027	-0.008	32.836	0.001	0.001	0.000	0.000	0.000	0.000
82	A	101	GLU	-1	-0.788	-0.846	34.584	0.112	0.112	0.000	0.000	0.000	0.000
83	A	102	LYS	1	0.980	0.991	34.920	-0.151	-0.151	0.000	0.000	0.000	0.000
84	A	103	ARG	1	0.935	0.962	37.065	-0.098	-0.098	0.000	0.000	0.000	0.000
85	A	104	PHE	0	0.039	0.022	40.500	0.000	0.000	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.028	0.023	41.004	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	106	GLU	-1	-0.791	-0.910	43.568	0.060	0.060	0.000	0.000	0.000	0.000
88	A	107	LYS	1	0.919	0.956	46.993	-0.068	-0.068	0.000	0.000	0.000	0.000
89	A	108	TYR	0	0.033	0.012	43.078	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	109	ARG	1	0.904	0.958	46.347	-0.075	-0.075	0.000	0.000	0.000	0.000
91	A	110	ARG	1	0.865	0.922	49.887	-0.056	-0.056	0.000	0.000	0.000	0.000
92	A	111	ALA	0	0.011	0.023	49.024	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	112	PRO	0	0.011	0.024	51.047	0.000	0.000	0.000	0.000	0.000	0.000
94	A	113	VAL	0	0.001	-0.003	47.708	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	114	SER	0	-0.020	-0.007	50.595	0.001	0.001	0.000	0.000	0.000	0.000
96	A	115	PHE	0	-0.018	-0.018	45.421	0.001	0.001	0.000	0.000	0.000	0.000
97	A	116	ASN	0	-0.054	-0.028	46.554	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	117	PHE	0	0.024	0.002	43.706	0.003	0.003	0.000	0.000	0.000	0.000
99	A	118	LEU	0	0.001	0.000	41.949	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	119	SER	0	-0.025	-0.005	40.339	0.003	0.003	0.000	0.000	0.000	0.000
101	A	120	ASP	-1	-0.764	-0.900	34.981	0.127	0.127	0.000	0.000	0.000	0.000
102	A	121	ALA	0	0.004	0.008	36.199	0.008	0.008	0.000	0.000	0.000	0.000
103	A	122	THR	0	-0.010	-0.015	35.112	0.006	0.006	0.000	0.000	0.000	0.000
104	A	123	GLY	0	0.047	0.037	32.168	0.011	0.011	0.000	0.000	0.000	0.000
105	A	124	GLN	0	-0.015	-0.012	30.380	0.002	0.002	0.000	0.000	0.000	0.000
106	A	125	VAL	0	-0.036	-0.024	32.752	0.000	0.000	0.000	0.000	0.000	0.000
107	A	126	GLN	0	0.020	-0.011	30.268	0.000	0.000	0.000	0.000	0.000	0.000
108	A	127	GLN	0	-0.010	0.000	25.899	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	128	ARG	1	0.849	0.911	28.644	-0.115	-0.115	0.000	0.000	0.000	0.000
110	A	129	TYR	0	-0.035	-0.039	30.729	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	130	GLY	0	0.013	0.018	27.066	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	131	ALA	0	-0.022	0.009	27.182	0.001	0.001	0.000	0.000	0.000	0.000
113	A	132	ASN	0	-0.035	-0.027	23.347	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	133	ARG	1	0.952	0.981	23.757	-0.144	-0.144	0.000	0.000	0.000	0.000
115	A	134	LEU	0	-0.016	0.015	27.962	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	135	PRO	0	0.046	0.002	31.651	0.001	0.001	0.000	0.000	0.000	0.000
117	A	136	ASP	-1	-0.794	-0.883	30.468	0.106	0.106	0.000	0.000	0.000	0.000
118	A	137	THR	0	-0.017	0.002	33.101	0.000	0.000	0.000	0.000	0.000	0.000
119	A	138	PHE	0	-0.013	-0.009	30.815	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	139	ILE	0	0.014	0.012	36.466	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	140	VAL	0	-0.031	-0.015	39.101	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	141	ASP	-1	-0.752	-0.877	41.152	0.037	0.037	0.000	0.000	0.000	0.000
123	A	142	ARG	1	0.890	0.928	44.004	-0.027	-0.027	0.000	0.000	0.000	0.000
124	A	143	LYS	1	0.933	0.956	45.479	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	144	GLY	0	-0.001	0.003	43.135	0.001	0.001	0.000	0.000	0.000	0.000
126	A	145	ILE	0	-0.027	-0.002	38.836	0.005	0.005	0.000	0.000	0.000	0.000
127	A	146	ILE	0	0.000	0.015	34.506	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	147	ARG	1	0.904	0.936	36.995	-0.032	-0.032	0.000	0.000	0.000	0.000
129	A	148	GLN	0	-0.005	-0.011	34.710	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	149	ARG	1	0.906	0.968	27.108	-0.090	-0.090	0.000	0.000	0.000	0.000
131	A	150	VAL	0	-0.032	-0.021	33.014	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	151	THR	0	-0.032	-0.035	28.093	0.005	0.005	0.000	0.000	0.000	0.000
133	A	152	GLY	0	-0.006	-0.001	31.363	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	153	GLY	0	-0.020	-0.002	32.791	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	154	ILE	0	-0.042	-0.019	36.086	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	155	GLU	-1	-0.790	-0.883	38.458	0.036	0.036	0.000	0.000	0.000	0.000
137	A	156	TRP	0	-0.037	-0.061	37.944	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	157	ASP	-1	-0.795	-0.872	43.416	0.029	0.029	0.000	0.000	0.000	0.000
139	A	158	ALA	0	0.015	0.018	43.752	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	159	PRO	0	0.057	0.012	45.832	0.001	0.001	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.963	0.977	39.460	-0.011	-0.011	0.000	0.000	0.000	0.000
142	A	161	VAL	0	0.025	0.025	41.290	0.000	0.000	0.000	0.000	0.000	0.000
143	A	162	VAL	0	0.044	0.024	43.854	0.001	0.001	0.000	0.000	0.000	0.000
144	A	163	SER	0	-0.032	-0.021	46.737	0.000	0.000	0.000	0.000	0.000	0.000
145	A	164	TYR	0	0.032	0.015	38.960	0.001	0.001	0.000	0.000	0.000	0.000
146	A	165	LEU	0	0.027	0.016	43.065	0.001	0.001	0.000	0.000	0.000	0.000
147	A	166	LYS	1	0.926	0.968	45.929	-0.023	-0.023	0.000	0.000	0.000	0.000
148	A	167	SER	0	-0.112	-0.051	45.472	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	168	LEU	0	-0.065	-0.040	42.897	0.000	0.000	0.000	0.000	0.000	0.000
150	A	169	GLU	-1	-0.931	-0.937	47.238	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)