FMO DATABASE

FMODB ID: LN649

Calculation Name: 2D4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4G

Chain ID: A

ChEMBL ID:

UniProt ID: O31629

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	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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1772361.01663
FMO2-HF: Nuclear repulsion	1705096.644567
FMO2-HF: Total energy	-67264.372062
FMO2-MP2: Total energy	-67462.76862

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:1:MET)

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

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.
-21.591	-11.179	14.733	-8.846	-16.299	-0.05

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.008

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	3	TYR	0	0.055	0.011	2.301	-4.692	-0.267	3.297	-2.436	-5.286	-0.013
4	A	4	GLY	0	-0.012	-0.026	4.863	0.328	0.392	-0.001	-0.006	-0.057	0.000
5	A	5	ILE	0	-0.049	-0.096	8.462	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.028	0.826	11.247	0.073	0.073	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.009	0.013	14.340	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.003	-0.017	13.553	0.045	0.045	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.020	0.007	18.945	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.003	-0.045	22.736	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.876	0.907	25.021	-0.105	-0.105	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.958	0.986	26.073	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.015	0.019	25.218	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.018	-0.028	20.988	0.042	0.042	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.803	-0.889	24.307	0.159	0.159	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.001	0.012	27.132	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.053	0.022	24.150	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.081	0.003	22.303	0.045	0.045	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.130	-0.049	25.401	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.028	0.005	27.730	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.774	0.892	18.067	-0.420	-0.420	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.862	0.939	24.599	-0.234	-0.234	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.896	0.951	25.809	-0.193	-0.193	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.036	0.010	26.574	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.709	-0.834	20.199	0.499	0.499	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.046	0.030	19.269	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.015	-0.016	16.390	0.080	0.080	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.037	-0.008	17.423	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.016	-0.017	17.573	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.047	-0.016	13.377	0.039	0.039	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.035	0.009	11.844	0.107	0.107	0.000	0.000	0.000	0.000
32	A	32	PRO	0	0.007	0.024	15.083	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.016	-0.005	17.349	0.016	0.016	0.000	0.000	0.000	0.000
34	A	34	HIS	1	0.959	0.981	15.420	-0.465	-0.465	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.016	-0.006	18.111	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.195	-0.196	14.814	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.142	-0.519	10.306	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	38	ARG	1	1.234	0.961	11.832	0.130	0.130	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.020	-0.007	13.001	0.037	0.037	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.028	-0.012	8.344	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.024	-0.024	7.053	0.085	0.085	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.896	-0.963	3.974	2.361	2.655	-0.001	-0.054	-0.240	0.000
43	A	43	CYS	0	-0.071	0.009	3.521	0.069	0.762	0.005	-0.202	-0.496	0.000
44	A	44	ALA	0	0.068	0.020	2.142	-5.844	-5.218	3.345	-1.975	-1.995	-0.024
45	A	45	GLU	-1	-0.912	-0.987	2.160	-12.982	-10.044	4.007	-2.680	-4.266	-0.020
46	A	46	GLU	-1	-0.908	-0.944	3.497	-1.368	-1.251	0.058	0.073	-0.248	0.000
47	A	47	LYS	1	0.848	0.935	6.571	1.877	1.877	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.027	0.006	5.500	0.160	0.160	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.852	-0.922	7.452	-1.102	-1.102	0.000	0.000	0.000	0.000
50	A	50	GLN	0	0.004	-0.011	11.069	0.110	0.110	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.002	0.012	6.599	0.195	0.195	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.046	0.019	9.322	0.205	0.205	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.019	-0.014	11.837	0.179	0.179	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.049	-0.032	13.919	0.095	0.095	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.001	0.007	10.887	0.091	0.091	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.853	0.899	14.144	0.668	0.668	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.052	-0.042	17.413	0.087	0.087	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.006	0.015	16.229	0.048	0.048	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.014	-0.002	18.167	0.043	0.043	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.840	0.915	20.089	0.276	0.276	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.902	-0.931	23.075	-0.201	-0.201	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.068	-0.043	21.973	0.021	0.021	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.013	-0.001	24.409	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.004	-0.011	24.918	0.007	0.007	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.007	0.022	22.056	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.009	0.008	25.940	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.030	-0.013	23.150	0.008	0.008	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.871	0.921	27.714	-0.040	-0.040	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.027	-0.020	25.700	0.001	0.001	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.020	-0.045	30.199	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.914	0.946	31.487	-0.099	-0.099	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.048	0.042	29.576	0.012	0.012	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.055	-0.033	29.579	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.027	-0.023	28.264	0.014	0.014	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.027	-0.001	23.323	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.021	0.052	27.544	0.007	0.007	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.022	-0.030	29.983	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.008	0.004	25.018	0.006	0.006	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.013	-0.011	22.502	0.019	0.019	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.056	-0.016	25.423	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.040	-0.041	22.129	0.021	0.021	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.019	0.013	25.011	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.046	-0.045	24.242	0.012	0.012	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.033	0.015	25.578	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.834	0.882	26.060	-0.086	-0.086	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.017	0.010	25.602	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.818	-0.882	27.596	0.081	0.081	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.030	-0.004	27.437	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.007	-0.032	27.479	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.816	-0.920	27.596	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.866	-0.893	26.397	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.019	-0.018	22.619	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.904	0.955	22.541	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.008	-0.013	23.395	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.061	-0.028	18.291	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.008	-0.017	18.791	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.801	-0.906	18.857	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.884	0.955	20.051	0.146	0.146	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.031	-0.011	14.267	-0.059	-0.059	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.051	0.029	15.012	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.004	0.023	17.087	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.048	0.013	16.213	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.029	-0.022	11.020	0.024	0.024	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.049	-0.016	10.117	-0.111	-0.111	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.028	-0.001	13.112	0.087	0.087	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.014	-0.016	14.051	-0.033	-0.033	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.998	-1.006	15.290	0.018	0.018	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.012	-0.039	17.054	0.030	0.030	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.929	-0.982	18.311	0.118	0.118	0.000	0.000	0.000	0.000
110	A	110	TYR	0	0.045	0.053	20.399	0.016	0.016	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.025	-0.018	22.504	0.008	0.008	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.019	0.061	19.485	0.021	0.021	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.014	-0.008	22.453	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.011	0.006	22.364	0.028	0.028	0.000	0.000	0.000	0.000
115	A	115	HIS	1	0.863	0.923	20.301	-0.254	-0.254	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.024	0.020	21.177	0.012	0.012	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.022	-0.013	20.307	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	118	VAL	0	-0.024	-0.017	22.281	0.009	0.009	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.027	0.011	24.536	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.077	-0.048	18.098	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.011	-0.002	21.192	0.033	0.033	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.003	0.019	23.292	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.066	0.035	27.054	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.822	-0.926	29.788	0.238	0.238	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.925	-0.959	32.328	0.184	0.184	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.903	-0.957	30.382	0.247	0.247	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.005	0.011	28.820	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	128	SER	0	0.003	-0.006	31.721	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.910	-0.941	35.358	0.155	0.155	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.041	-0.023	30.320	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.019	-0.017	31.853	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.001	0.014	34.029	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.027	-0.001	34.315	0.001	0.001	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.017	-0.032	30.713	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.908	0.974	34.662	-0.135	-0.135	0.000	0.000	0.000	0.000
136	A	136	MET	0	-0.031	-0.020	35.564	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.042	-0.001	35.391	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.920	-0.969	35.977	0.079	0.079	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.046	-0.024	31.330	0.006	0.006	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.003	0.010	34.624	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	HIS	0	-0.072	-0.055	28.431	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.819	-0.905	31.112	0.039	0.039	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.769	-0.823	25.699	0.075	0.075	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.035	0.013	27.619	0.001	0.001	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.026	-0.004	21.244	0.001	0.001	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.762	-0.857	23.672	-0.060	-0.060	0.000	0.000	0.000	0.000
147	A	147	ARG	1	0.829	0.872	18.926	0.046	0.046	0.000	0.000	0.000	0.000
148	A	148	PHE	0	0.003	0.013	14.169	0.046	0.046	0.000	0.000	0.000	0.000
149	A	149	HIS	0	-0.015	-0.010	12.638	-0.054	-0.054	0.000	0.000	0.000	0.000
150	A	150	LEU	0	0.024	0.042	6.874	0.055	0.055	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.039	-0.020	7.445	-0.013	-0.013	0.000	0.000	0.000	0.000
152	A	152	TYR	0	0.058	0.011	2.608	-3.749	-3.446	3.993	-1.321	-2.974	0.008
153	A	153	GLN	0	-0.082	-0.037	4.167	-0.603	-0.315	0.008	-0.075	-0.221	0.000
154	A	154	LEU	0	-0.005	0.002	4.404	1.626	2.290	0.022	-0.170	-0.516	-0.001
155	A	155	GLU	-1	-0.875	-0.938	6.714	1.109	1.109	0.000	0.000	0.000	0.000
156	A	156	ASN	0	-0.008	0.010	8.709	0.110	0.110	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.014	0.011	9.707	-0.248	-0.248	0.000	0.000	0.000	0.000
158	A	158	SER	0	-0.049	-0.037	10.652	-0.077	-0.077	0.000	0.000	0.000	0.000
159	A	159	TRP	0	-0.015	-0.005	5.902	0.658	0.658	0.000	0.000	0.000	0.000
160	A	160	THR	0	0.003	0.008	7.706	-0.498	-0.498	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.027	-0.026	8.168	0.146	0.146	0.000	0.000	0.000	0.000
162	A	162	TYR	0	-0.014	0.002	6.364	-0.107	-0.107	0.000	0.000	0.000	0.000
163	A	163	GLU	-1	-0.777	-0.876	8.827	-0.784	-0.784	0.000	0.000	0.000	0.000
164	A	164	THR	0	-0.053	-0.036	11.761	0.076	0.076	0.000	0.000	0.000	0.000
165	A	165	PHE	0	0.000	-0.009	11.641	-0.034	-0.034	0.000	0.000	0.000	0.000
166	A	166	LEU	0	-0.002	-0.010	17.161	0.044	0.044	0.000	0.000	0.000	0.000
167	A	167	LEU	0	-0.046	-0.006	19.845	-0.019	-0.019	0.000	0.000	0.000	0.000
168	A	168	GLY	0	-0.035	-0.004	22.766	0.011	0.011	0.000	0.000	0.000	0.000

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