FMO DATABASE

FMODB ID: LNV89

Calculation Name: 3HD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD4

Chain ID: A

ChEMBL ID:

UniProt ID: P03416

Base Structure: X-ray

Registration Date: 2023-09-23

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129544.904416
FMO2-HF: Nuclear repulsion	1078891.451449
FMO2-HF: Total energy	-50653.452967
FMO2-MP2: Total energy	-50805.697316

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:64:PRO)

Summations of interaction energy for fragment #1(A:64:PRO)

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.
-3.098	0.445	0.245	-1.474	-2.313	-0.002

Interaction energy analysis for fragmet #1(A:64:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.007

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	66	TYR	0	0.002	0.005	3.297	-2.811	0.633	0.246	-1.469	-2.221	-0.002
4	A	67	SER	0	0.005	-0.008	5.264	0.429	0.528	-0.001	-0.005	-0.092	0.000
5	A	68	TRP	0	0.044	0.009	8.551	0.120	0.120	0.000	0.000	0.000	0.000
6	A	69	PHE	0	0.011	0.008	11.615	0.113	0.113	0.000	0.000	0.000	0.000
7	A	70	SER	0	-0.038	-0.019	11.522	-0.065	-0.065	0.000	0.000	0.000	0.000
8	A	71	GLY	0	0.035	0.020	12.531	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	72	ILE	0	-0.022	-0.003	13.277	0.053	0.053	0.000	0.000	0.000	0.000
10	A	73	THR	0	-0.056	-0.041	15.451	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	74	GLN	0	-0.008	-0.003	16.592	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	75	PHE	0	-0.037	-0.032	19.101	0.018	0.018	0.000	0.000	0.000	0.000
13	A	76	GLN	0	-0.026	-0.006	22.196	0.006	0.006	0.000	0.000	0.000	0.000
14	A	77	LYS	1	0.956	0.968	22.844	0.007	0.007	0.000	0.000	0.000	0.000
15	A	78	GLY	0	0.024	0.006	24.284	0.004	0.004	0.000	0.000	0.000	0.000
16	A	79	LYS	1	0.866	0.954	24.318	0.067	0.067	0.000	0.000	0.000	0.000
17	A	80	GLU	-1	-0.852	-0.931	21.426	-0.140	-0.140	0.000	0.000	0.000	0.000
18	A	81	PHE	0	-0.059	-0.037	17.325	0.001	0.001	0.000	0.000	0.000	0.000
19	A	82	GLN	0	-0.030	-0.019	20.779	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	83	PHE	0	0.005	0.009	19.309	0.004	0.004	0.000	0.000	0.000	0.000
21	A	84	ALA	0	0.029	0.018	24.390	0.000	0.000	0.000	0.000	0.000	0.000
22	A	85	GLU	-1	-0.900	-0.954	26.176	-0.162	-0.162	0.000	0.000	0.000	0.000
23	A	86	GLY	0	0.002	0.009	26.673	0.011	0.011	0.000	0.000	0.000	0.000
24	A	87	GLN	0	-0.051	-0.036	25.672	0.001	0.001	0.000	0.000	0.000	0.000
25	A	88	GLY	0	0.068	0.011	22.027	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	89	VAL	0	-0.033	0.019	19.215	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	90	PRO	0	-0.021	-0.006	16.520	0.033	0.033	0.000	0.000	0.000	0.000
28	A	91	ILE	0	-0.040	-0.003	19.816	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	92	ALA	0	0.024	-0.001	19.411	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	93	ASN	0	-0.022	-0.014	21.540	0.002	0.002	0.000	0.000	0.000	0.000
31	A	94	GLY	0	0.029	0.015	22.510	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	95	ILE	0	-0.012	0.010	18.908	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	96	PRO	0	0.011	0.014	22.673	0.013	0.013	0.000	0.000	0.000	0.000
34	A	97	ALA	0	0.044	0.002	24.544	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	98	SER	0	0.034	0.008	25.871	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	99	GLU	-1	-0.754	-0.869	20.696	-0.304	-0.304	0.000	0.000	0.000	0.000
37	A	100	GLN	0	-0.060	-0.026	20.575	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	101	LYS	1	0.843	0.934	20.019	0.284	0.284	0.000	0.000	0.000	0.000
39	A	102	GLY	0	0.015	0.001	16.574	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	103	TYR	0	-0.035	-0.029	10.168	0.018	0.018	0.000	0.000	0.000	0.000
41	A	104	TRP	0	-0.035	-0.019	13.624	-0.081	-0.081	0.000	0.000	0.000	0.000
42	A	105	TYR	0	0.030	0.001	6.752	0.043	0.043	0.000	0.000	0.000	0.000
43	A	106	ARG	1	0.761	0.864	10.651	0.200	0.200	0.000	0.000	0.000	0.000
44	A	107	HIS	0	0.038	0.020	6.393	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	108	ASN	0	0.046	0.000	9.594	0.077	0.077	0.000	0.000	0.000	0.000
46	A	109	ARG	1	0.861	0.911	11.539	0.027	0.027	0.000	0.000	0.000	0.000
47	A	110	ARG	1	0.887	0.965	11.033	0.073	0.073	0.000	0.000	0.000	0.000
48	A	111	SER	0	-0.029	-0.031	12.611	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	112	PHE	0	-0.007	0.005	13.164	0.032	0.032	0.000	0.000	0.000	0.000
50	A	113	LYS	1	0.841	0.923	15.578	-0.195	-0.195	0.000	0.000	0.000	0.000
51	A	114	THR	0	-0.049	-0.047	17.747	0.014	0.014	0.000	0.000	0.000	0.000
52	A	115	PRO	0	0.014	-0.012	21.002	0.006	0.006	0.000	0.000	0.000	0.000
53	A	116	ASP	-1	-0.785	-0.839	22.795	0.117	0.117	0.000	0.000	0.000	0.000
54	A	117	GLY	0	0.082	0.039	22.331	0.000	0.000	0.000	0.000	0.000	0.000
55	A	118	GLN	0	-0.063	-0.040	22.167	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	119	GLN	0	0.021	0.011	15.793	0.025	0.025	0.000	0.000	0.000	0.000
57	A	120	LYS	1	0.975	0.993	18.993	-0.104	-0.104	0.000	0.000	0.000	0.000
58	A	121	GLN	0	0.055	0.027	17.377	0.002	0.002	0.000	0.000	0.000	0.000
59	A	122	LEU	0	-0.048	-0.025	14.221	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	123	LEU	0	0.009	0.016	16.377	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	124	PRO	0	0.036	0.023	14.095	0.012	0.012	0.000	0.000	0.000	0.000
62	A	125	ARG	1	0.779	0.881	11.047	0.113	0.113	0.000	0.000	0.000	0.000
63	A	126	TRP	0	0.043	0.028	11.336	-0.044	-0.044	0.000	0.000	0.000	0.000
64	A	127	TYR	0	0.041	0.003	8.504	0.093	0.093	0.000	0.000	0.000	0.000
65	A	128	PHE	0	0.059	0.043	11.055	-0.038	-0.038	0.000	0.000	0.000	0.000
66	A	129	TYR	0	-0.022	-0.013	5.682	0.060	0.060	0.000	0.000	0.000	0.000
67	A	130	TYR	0	0.091	0.049	12.167	0.095	0.095	0.000	0.000	0.000	0.000
68	A	131	LEU	0	0.021	0.014	13.611	-0.082	-0.082	0.000	0.000	0.000	0.000
69	A	132	GLY	0	0.049	0.040	14.340	0.040	0.040	0.000	0.000	0.000	0.000
70	A	133	THR	0	-0.060	-0.024	10.614	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	134	GLY	0	0.037	0.008	7.067	0.098	0.098	0.000	0.000	0.000	0.000
72	A	135	PRO	0	-0.084	-0.052	5.169	0.065	0.065	0.000	0.000	0.000	0.000
73	A	136	HIS	0	-0.005	-0.005	6.713	0.177	0.177	0.000	0.000	0.000	0.000
74	A	137	ALA	0	-0.018	0.005	9.429	0.126	0.126	0.000	0.000	0.000	0.000
75	A	138	GLY	0	-0.019	-0.011	11.211	0.072	0.072	0.000	0.000	0.000	0.000
76	A	139	ALA	0	-0.056	-0.014	13.818	0.054	0.054	0.000	0.000	0.000	0.000
77	A	140	SER	0	0.011	0.000	15.684	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	141	TYR	0	-0.003	-0.020	18.809	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	142	GLY	0	0.027	0.009	19.732	0.027	0.027	0.000	0.000	0.000	0.000
80	A	143	ASP	-1	-0.865	-0.911	17.791	-0.259	-0.259	0.000	0.000	0.000	0.000
81	A	144	SER	0	-0.013	-0.013	18.578	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	145	ILE	0	-0.019	-0.002	13.592	0.012	0.012	0.000	0.000	0.000	0.000
83	A	146	GLU	-1	-0.773	-0.868	16.665	-0.173	-0.173	0.000	0.000	0.000	0.000
84	A	147	GLY	0	-0.030	-0.015	14.264	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	148	VAL	0	-0.013	-0.005	12.974	-0.065	-0.065	0.000	0.000	0.000	0.000
86	A	149	PHE	0	0.004	0.007	15.374	0.040	0.040	0.000	0.000	0.000	0.000
87	A	150	TRP	0	0.002	-0.006	15.361	-0.039	-0.039	0.000	0.000	0.000	0.000
88	A	151	VAL	0	-0.037	-0.013	18.328	0.026	0.026	0.000	0.000	0.000	0.000
89	A	152	ALA	0	0.044	0.004	20.469	-0.027	-0.027	0.000	0.000	0.000	0.000
90	A	153	ASN	0	-0.011	-0.001	23.166	0.026	0.026	0.000	0.000	0.000	0.000
91	A	154	SER	0	0.034	-0.007	26.136	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	155	GLN	0	-0.063	-0.021	28.797	0.007	0.007	0.000	0.000	0.000	0.000
93	A	156	ALA	0	-0.019	0.002	23.863	0.001	0.001	0.000	0.000	0.000	0.000
94	A	157	ASP	-1	-0.792	-0.862	25.993	-0.188	-0.188	0.000	0.000	0.000	0.000
95	A	158	THR	0	-0.006	-0.016	22.617	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	159	ASN	0	-0.062	-0.032	22.651	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	160	THR	0	-0.034	-0.038	22.539	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	161	ARG	1	0.831	0.903	14.345	0.463	0.463	0.000	0.000	0.000	0.000
99	A	162	SER	0	-0.045	-0.044	16.891	0.017	0.017	0.000	0.000	0.000	0.000
100	A	163	ASP	-1	-0.900	-0.952	17.760	-0.290	-0.290	0.000	0.000	0.000	0.000
101	A	164	ILE	0	-0.109	-0.044	15.215	0.008	0.008	0.000	0.000	0.000	0.000
102	A	165	VAL	0	0.005	0.005	12.717	-0.053	-0.053	0.000	0.000	0.000	0.000
103	A	166	GLU	-1	-0.791	-0.903	8.569	-1.579	-1.579	0.000	0.000	0.000	0.000
104	A	167	ARG	1	0.787	0.891	7.856	0.734	0.734	0.000	0.000	0.000	0.000
105	A	168	ASP	-1	-0.742	-0.827	8.306	-0.361	-0.361	0.000	0.000	0.000	0.000
106	A	169	PRO	0	-0.075	-0.055	6.372	0.081	0.081	0.000	0.000	0.000	0.000
107	A	170	SER	0	-0.094	-0.056	9.451	0.096	0.096	0.000	0.000	0.000	0.000
108	A	171	SER	0	-0.048	-0.043	12.513	0.003	0.003	0.000	0.000	0.000	0.000
109	A	172	HIS	0	-0.007	-0.003	12.953	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	173	GLU	-1	-0.900	-0.937	11.721	-0.070	-0.070	0.000	0.000	0.000	0.000
111	A	174	ALA	0	-0.053	-0.020	10.455	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	175	ILE	0	0.023	0.014	12.418	0.078	0.078	0.000	0.000	0.000	0.000
113	A	176	PRO	0	-0.029	-0.036	15.452	-0.031	-0.031	0.000	0.000	0.000	0.000
114	A	177	THR	0	0.028	0.007	15.622	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	178	ARG	1	0.827	0.902	18.071	0.159	0.159	0.000	0.000	0.000	0.000
116	A	179	PHE	0	0.033	0.008	19.504	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	180	ALA	0	0.065	0.042	24.037	0.012	0.012	0.000	0.000	0.000	0.000
118	A	181	PRO	0	0.011	-0.007	27.475	0.000	0.000	0.000	0.000	0.000	0.000
119	A	182	GLY	0	0.033	0.022	30.411	0.001	0.001	0.000	0.000	0.000	0.000
120	A	183	THR	0	-0.054	-0.023	24.245	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	184	VAL	0	-0.028	-0.010	27.370	0.005	0.005	0.000	0.000	0.000	0.000
122	A	185	LEU	0	0.007	0.003	22.745	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	186	PRO	0	-0.012	0.026	21.276	0.015	0.015	0.000	0.000	0.000	0.000
124	A	187	GLN	0	0.058	0.007	24.042	0.006	0.006	0.000	0.000	0.000	0.000
125	A	188	GLY	0	0.009	-0.004	24.665	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	189	PHE	0	0.011	0.007	18.467	0.001	0.001	0.000	0.000	0.000	0.000
127	A	190	TYR	0	-0.038	-0.023	17.873	0.009	0.009	0.000	0.000	0.000	0.000
128	A	191	VAL	0	0.029	0.015	18.201	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	192	GLU	-1	-0.753	-0.836	14.411	-0.033	-0.033	0.000	0.000	0.000	0.000
130	A	193	GLY	0	0.049	0.035	17.366	-0.021	-0.021	0.000	0.000	0.000	0.000
131	A	194	SER	0	-0.032	0.000	19.237	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:PRO)