FMO DATABASE

FMODB ID: 52G4Z

Calculation Name: 3DMM-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMM

Chain ID: D

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1015998.02265
FMO2-HF: Nuclear repulsion	967301.048178
FMO2-HF: Total energy	-48696.974472
FMO2-MP2: Total energy	-48837.967064

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(D:1:LEU)

Summations of interaction energy for fragment #1(D:1:LEU)

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.
-22.388	-9.89	11.1	-7.238	-16.357	-0.052

Interaction energy analysis for fragmet #1(D:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.031

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

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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	D	3	GLN	0	0.042	-0.001	3.869	-1.792	-0.483	-0.011	-0.471	-0.827	0.002
4	D	4	THR	0	-0.071	-0.015	5.423	0.716	0.716	0.000	0.000	0.000	0.000
5	D	5	PRO	0	0.077	0.032	9.083	-0.024	-0.024	0.000	0.000	0.000	0.000
6	D	6	SER	0	0.067	0.033	10.395	-0.112	-0.112	0.000	0.000	0.000	0.000
7	D	7	SER	0	-0.056	-0.036	11.342	0.015	0.015	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.029	-0.006	14.626	0.021	0.021	0.000	0.000	0.000	0.000
9	D	9	LEU	0	0.035	0.028	16.563	-0.007	-0.007	0.000	0.000	0.000	0.000
10	D	10	VAL	0	-0.021	-0.018	19.379	0.011	0.011	0.000	0.000	0.000	0.000
11	D	11	GLN	0	0.038	0.018	22.089	0.006	0.006	0.000	0.000	0.000	0.000
12	D	12	THR	0	0.004	-0.045	24.661	-0.021	-0.021	0.000	0.000	0.000	0.000
13	D	13	ASN	0	-0.045	-0.028	26.081	0.013	0.013	0.000	0.000	0.000	0.000
14	D	14	HIS	0	-0.025	0.012	23.709	0.010	0.010	0.000	0.000	0.000	0.000
15	D	15	THR	0	-0.011	-0.026	18.793	-0.004	-0.004	0.000	0.000	0.000	0.000
16	D	16	ALA	0	0.002	0.026	16.652	0.005	0.005	0.000	0.000	0.000	0.000
17	D	17	LYS	1	0.844	0.906	14.275	0.343	0.343	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.025	0.004	8.805	0.047	0.047	0.000	0.000	0.000	0.000
19	D	19	SER	0	-0.032	-0.008	8.497	0.048	0.048	0.000	0.000	0.000	0.000
20	D	20	CYS	0	-0.008	0.008	2.786	-2.622	-2.200	3.869	-1.124	-3.167	-0.002
21	D	21	GLU	-1	-0.849	-0.887	3.576	0.901	1.482	0.007	-0.134	-0.454	0.000
22	D	22	VAL	0	0.008	0.001	2.505	-3.354	0.425	2.413	-2.398	-3.794	-0.022
23	D	23	LYS	1	0.960	0.977	3.153	-7.336	-6.563	0.038	-0.009	-0.801	0.000
24	D	24	SER	0	0.003	-0.010	4.304	-0.609	-0.533	-0.001	-0.010	-0.064	0.000
25	D	25	ILE	0	0.036	0.015	6.126	0.195	0.195	0.000	0.000	0.000	0.000
26	D	26	SER	0	0.034	0.012	9.866	-0.053	-0.053	0.000	0.000	0.000	0.000
27	D	27	LYS	1	0.938	0.975	9.814	0.083	0.083	0.000	0.000	0.000	0.000
28	D	28	LEU	0	0.067	0.055	10.655	-0.034	-0.034	0.000	0.000	0.000	0.000
29	D	29	THR	0	-0.033	-0.018	9.495	0.065	0.065	0.000	0.000	0.000	0.000
30	D	30	SER	0	-0.023	-0.033	8.740	0.026	0.026	0.000	0.000	0.000	0.000
31	D	31	ILE	0	-0.005	0.015	3.742	-0.338	-0.105	0.004	-0.041	-0.196	0.000
32	D	32	TYR	0	0.036	0.003	5.994	0.224	0.224	0.000	0.000	0.000	0.000
33	D	33	TRP	0	0.030	0.008	6.276	-0.425	-0.425	0.000	0.000	0.000	0.000
34	D	34	LEU	0	-0.016	-0.007	7.865	0.153	0.153	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.790	0.863	10.796	0.310	0.310	0.000	0.000	0.000	0.000
36	D	36	GLU	-1	-0.848	-0.916	13.645	-0.455	-0.455	0.000	0.000	0.000	0.000
37	D	37	ARG	1	0.816	0.896	15.192	0.338	0.338	0.000	0.000	0.000	0.000
38	D	38	GLN	0	-0.038	-0.038	18.882	0.036	0.036	0.000	0.000	0.000	0.000
39	D	39	ASP	-1	-0.821	-0.924	20.888	-0.236	-0.236	0.000	0.000	0.000	0.000
40	D	40	PRO	0	-0.055	-0.032	24.542	0.010	0.010	0.000	0.000	0.000	0.000
41	D	41	LYS	1	0.880	0.946	26.277	0.213	0.213	0.000	0.000	0.000	0.000
42	D	42	ASP	-1	-0.919	-0.950	24.319	-0.207	-0.207	0.000	0.000	0.000	0.000
43	D	43	LYS	1	0.819	0.924	16.138	0.385	0.385	0.000	0.000	0.000	0.000
44	D	44	TYR	0	-0.014	-0.031	19.099	0.003	0.003	0.000	0.000	0.000	0.000
45	D	45	PHE	0	-0.013	-0.013	10.906	-0.042	-0.042	0.000	0.000	0.000	0.000
46	D	46	GLU	-1	-0.761	-0.810	15.105	-0.319	-0.319	0.000	0.000	0.000	0.000
47	D	47	PHE	0	-0.040	-0.025	12.111	-0.076	-0.076	0.000	0.000	0.000	0.000
48	D	48	LEU	0	0.007	0.020	12.651	0.049	0.049	0.000	0.000	0.000	0.000
49	D	49	ALA	0	0.043	0.001	12.298	0.066	0.066	0.000	0.000	0.000	0.000
50	D	50	SER	0	-0.030	-0.008	10.502	-0.090	-0.090	0.000	0.000	0.000	0.000
51	D	51	TRP	0	0.057	0.031	10.635	0.071	0.071	0.000	0.000	0.000	0.000
52	D	52	SER	0	0.000	0.006	11.055	-0.046	-0.046	0.000	0.000	0.000	0.000
53	D	53	SER	0	-0.030	-0.026	13.301	0.043	0.043	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.033	-0.010	15.118	0.015	0.015	0.000	0.000	0.000	0.000
55	D	55	LYS	1	0.943	0.963	17.185	0.243	0.243	0.000	0.000	0.000	0.000
56	D	56	GLY	0	0.047	0.045	16.920	0.011	0.011	0.000	0.000	0.000	0.000
57	D	57	VAL	0	-0.017	-0.021	14.825	-0.035	-0.035	0.000	0.000	0.000	0.000
58	D	58	LEU	0	-0.032	-0.005	15.055	0.045	0.045	0.000	0.000	0.000	0.000
59	D	59	TYR	0	-0.017	-0.033	15.234	-0.044	-0.044	0.000	0.000	0.000	0.000
60	D	60	GLY	0	0.041	0.024	16.797	0.015	0.015	0.000	0.000	0.000	0.000
61	D	61	GLU	-1	-0.812	-0.919	17.890	-0.210	-0.210	0.000	0.000	0.000	0.000
62	D	62	SER	0	-0.059	-0.044	18.881	0.014	0.014	0.000	0.000	0.000	0.000
63	D	63	VAL	0	-0.015	-0.009	17.016	0.004	0.004	0.000	0.000	0.000	0.000
64	D	64	ASP	-1	-0.756	-0.845	20.296	-0.217	-0.217	0.000	0.000	0.000	0.000
65	D	65	LYS	1	0.789	0.874	22.630	0.223	0.223	0.000	0.000	0.000	0.000
66	D	66	LYS	1	0.848	0.939	21.232	0.296	0.296	0.000	0.000	0.000	0.000
67	D	67	ARG	1	0.808	0.877	21.898	0.234	0.234	0.000	0.000	0.000	0.000
68	D	68	ASN	0	-0.014	0.002	20.785	-0.008	-0.008	0.000	0.000	0.000	0.000
69	D	69	ILE	0	0.017	0.019	15.285	-0.024	-0.024	0.000	0.000	0.000	0.000
70	D	70	ILE	0	0.010	0.013	16.808	0.026	0.026	0.000	0.000	0.000	0.000
71	D	71	LEU	0	-0.009	-0.001	11.148	-0.047	-0.047	0.000	0.000	0.000	0.000
72	D	72	GLU	-1	-0.783	-0.875	12.714	-0.294	-0.294	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.041	0.011	11.899	-0.078	-0.078	0.000	0.000	0.000	0.000
74	D	74	SER	0	-0.015	0.003	9.796	-0.054	-0.054	0.000	0.000	0.000	0.000
75	D	75	ASP	-1	-0.906	-0.946	9.726	-0.288	-0.288	0.000	0.000	0.000	0.000
76	D	76	SER	0	-0.015	-0.033	10.619	0.085	0.085	0.000	0.000	0.000	0.000
77	D	77	ARG	1	0.842	0.913	7.283	-0.574	-0.574	0.000	0.000	0.000	0.000
78	D	78	ARG	1	0.825	0.899	6.393	0.086	0.086	0.000	0.000	0.000	0.000
79	D	79	PRO	0	-0.012	0.015	5.895	0.051	0.051	0.000	0.000	0.000	0.000
80	D	80	PHE	0	0.032	-0.007	8.313	-0.181	-0.181	0.000	0.000	0.000	0.000
81	D	81	LEU	0	-0.027	0.001	10.376	0.036	0.036	0.000	0.000	0.000	0.000
82	D	82	SER	0	-0.028	-0.043	12.056	0.007	0.007	0.000	0.000	0.000	0.000
83	D	83	ILE	0	0.021	0.010	14.675	0.011	0.011	0.000	0.000	0.000	0.000
84	D	84	MET	0	0.016	0.004	17.997	0.018	0.018	0.000	0.000	0.000	0.000
85	D	85	ASN	0	-0.020	-0.007	21.627	0.005	0.005	0.000	0.000	0.000	0.000
86	D	86	VAL	0	-0.002	0.026	19.598	0.004	0.004	0.000	0.000	0.000	0.000
87	D	87	LYS	1	0.975	0.974	22.746	0.201	0.201	0.000	0.000	0.000	0.000
88	D	88	PRO	0	0.058	0.038	23.158	-0.025	-0.025	0.000	0.000	0.000	0.000
89	D	89	GLU	-1	-0.839	-0.924	23.732	-0.220	-0.220	0.000	0.000	0.000	0.000
90	D	90	ASP	-1	-0.903	-0.943	19.704	-0.326	-0.326	0.000	0.000	0.000	0.000
91	D	91	SER	0	-0.017	0.000	18.934	-0.046	-0.046	0.000	0.000	0.000	0.000
92	D	92	ASP	-1	-0.733	-0.850	16.760	-0.356	-0.356	0.000	0.000	0.000	0.000
93	D	93	PHE	0	-0.011	-0.004	12.929	-0.004	-0.004	0.000	0.000	0.000	0.000
94	D	94	TYR	0	-0.007	-0.021	11.300	-0.003	-0.003	0.000	0.000	0.000	0.000
95	D	95	PHE	0	-0.003	0.002	7.291	-0.106	-0.106	0.000	0.000	0.000	0.000
96	D	97	ALA	0	0.010	0.001	3.681	-0.586	-0.316	0.011	-0.065	-0.216	0.000
97	D	98	THR	0	-0.019	-0.017	2.574	-2.424	-0.658	1.354	-1.097	-2.023	-0.011
98	D	99	VAL	0	0.008	0.005	4.326	-0.028	0.044	0.000	-0.027	-0.046	0.000
99	D	100	GLY	0	0.046	0.024	7.817	0.058	0.058	0.000	0.000	0.000	0.000
100	D	101	SER	0	-0.033	-0.005	9.841	-0.019	-0.019	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.035	0.010	13.364	0.055	0.055	0.000	0.000	0.000	0.000
102	D	103	LYS	1	0.926	0.966	7.045	-0.436	-0.436	0.000	0.000	0.000	0.000
103	D	104	MET	0	0.044	0.024	7.278	-0.026	-0.026	0.000	0.000	0.000	0.000
104	D	105	VAL	0	-0.068	-0.043	2.355	-0.805	0.036	1.337	-0.410	-1.767	-0.001
105	D	106	PHE	0	0.050	0.018	3.580	-0.876	-0.023	0.034	-0.259	-0.627	-0.002
106	D	107	GLY	0	0.028	0.000	2.466	-4.106	-2.200	1.995	-1.989	-1.912	-0.015
107	D	108	THR	0	-0.021	-0.022	3.298	1.298	0.915	0.050	0.796	-0.463	-0.001
108	D	109	GLY	0	0.005	0.015	5.958	0.539	0.539	0.000	0.000	0.000	0.000
109	D	110	THR	0	-0.042	-0.037	8.159	-0.037	-0.037	0.000	0.000	0.000	0.000
110	D	111	LYS	1	0.874	0.954	10.775	0.388	0.388	0.000	0.000	0.000	0.000
111	D	112	LEU	0	0.003	0.019	14.422	0.037	0.037	0.000	0.000	0.000	0.000
112	D	113	THR	0	-0.052	-0.046	16.385	0.028	0.028	0.000	0.000	0.000	0.000
113	D	114	VAL	0	0.007	0.015	20.173	0.001	0.001	0.000	0.000	0.000	0.000
114	D	115	VAL	0	0.013	0.011	22.977	0.009	0.009	0.000	0.000	0.000	0.000
115	D	116	ASP	-1	-0.815	-0.890	26.627	-0.156	-0.156	0.000	0.000	0.000	0.000
116	D	117	VAL	0	-0.030	-0.017	29.728	0.007	0.007	0.000	0.000	0.000	0.000
117	D	118	LEU	0	0.007	0.001	25.994	-0.008	-0.008	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.011	-0.014	29.225	0.006	0.006	0.000	0.000	0.000	0.000
119	D	120	THR	0	0.001	0.023	30.322	-0.001	-0.001	0.000	0.000	0.000	0.000
120	D	121	THR	0	-0.019	-0.031	31.177	0.003	0.003	0.000	0.000	0.000	0.000
121	D	122	ALA	0	-0.004	0.015	33.960	-0.001	-0.001	0.000	0.000	0.000	0.000
122	D	123	PRO	0	0.017	0.014	37.247	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:LEU)