FMO DATABASE

FMODB ID: 98972

Calculation Name: 3MAB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MAB

Chain ID: A

ChEMBL ID:

UniProt ID:

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	OptH
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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-579494.888475
FMO2-HF: Nuclear repulsion	546526.70389
FMO2-HF: Total energy	-32968.184585
FMO2-MP2: Total energy	-33065.353181

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:3:LEU)

Summations of interaction energy for fragment #1(A:3: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.
-6.856	-2.404	3.623	-2.256	-5.817	0.001

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.038

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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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	5	ASN	0	0.030	0.004	3.316	-2.386	-0.417	0.090	-0.989	-1.070	-0.001
4	A	6	LEU	0	0.008	-0.008	5.880	0.465	0.465	0.000	0.000	0.000	0.000
5	A	7	SER	0	-0.086	-0.044	7.583	0.218	0.218	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.937	-0.966	7.038	-1.757	-1.757	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.057	-0.012	5.987	0.224	0.224	0.000	0.000	0.000	0.000
8	A	10	PRO	0	0.019	0.001	9.692	0.028	0.028	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.066	-0.045	13.243	0.017	0.017	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.016	0.030	10.449	0.034	0.034	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.033	0.031	13.053	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.966	0.957	13.120	0.590	0.590	0.000	0.000	0.000	0.000
13	A	15	VAL	0	0.049	0.029	15.602	-0.035	-0.035	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.066	0.044	14.811	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.842	-0.925	9.519	-1.218	-1.218	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.066	-0.047	12.813	0.010	0.010	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.848	-0.919	15.191	-0.324	-0.324	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.025	-0.014	10.652	0.018	0.018	0.000	0.000	0.000	0.000
19	A	21	ILE	0	-0.004	-0.001	10.044	0.019	0.019	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.894	0.935	12.337	0.389	0.389	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.028	0.034	14.901	0.035	0.035	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.075	-0.041	12.854	0.028	0.028	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.042	-0.010	8.992	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.913	0.938	7.216	0.584	0.584	0.000	0.000	0.000	0.000
25	A	27	THR	0	0.016	0.020	2.398	-0.990	-0.579	1.612	-0.547	-1.476	0.002
26	A	28	PRO	0	0.043	-0.001	2.525	-0.771	0.272	0.617	-0.323	-1.336	0.001
27	A	29	VAL	0	-0.019	-0.002	2.476	-0.783	0.134	1.304	-0.378	-1.842	-0.001
28	A	30	GLU	-1	-0.829	-0.901	4.327	-0.777	-0.665	0.000	-0.019	-0.093	0.000
29	A	31	LEU	0	0.017	0.009	6.631	0.061	0.061	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.897	0.927	7.274	-0.259	-0.259	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.942	-0.947	8.488	0.042	0.042	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.081	-0.035	10.357	0.012	0.012	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.022	0.021	11.976	0.025	0.025	0.000	0.000	0.000	0.000
34	A	36	SER	0	-0.039	-0.054	13.814	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.845	0.908	15.574	0.028	0.028	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.768	-0.862	16.007	-0.139	-0.139	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.017	-0.013	13.223	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	40	PHE	0	-0.020	-0.021	15.239	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.014	0.006	18.389	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.877	0.931	14.264	0.195	0.195	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.019	-0.017	15.407	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	44	TRP	0	-0.051	-0.032	18.974	0.005	0.005	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.960	-0.968	21.836	-0.149	-0.149	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.104	-0.043	18.906	0.016	0.016	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.873	-0.915	22.428	-0.199	-0.199	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.018	0.003	23.649	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.136	-0.081	25.449	0.010	0.010	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.015	0.020	19.898	0.005	0.005	0.000	0.000	0.000	0.000
49	A	51	CYS	0	-0.003	-0.004	23.147	0.022	0.022	0.000	0.000	0.000	0.000
50	A	52	MET	0	0.021	0.023	22.957	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.049	-0.048	23.211	0.005	0.005	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.779	-0.896	19.406	-0.239	-0.239	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.019	0.025	18.436	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.081	-0.052	18.733	0.010	0.010	0.000	0.000	0.000	0.000
55	A	57	ALA	0	-0.030	-0.014	16.846	0.011	0.011	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.042	0.016	13.423	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.800	-0.876	14.007	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.007	-0.010	15.551	0.029	0.029	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.012	0.004	10.943	0.027	0.027	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.039	-0.016	10.905	0.033	0.033	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.112	-0.080	11.666	0.084	0.084	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.014	0.014	12.042	0.052	0.052	0.000	0.000	0.000	0.000
63	A	65	ILE	0	-0.039	-0.015	12.803	0.017	0.017	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.965	0.978	16.158	0.040	0.040	0.000	0.000	0.000	0.000
65	A	67	TRP	0	0.066	0.017	18.111	0.032	0.032	0.000	0.000	0.000	0.000
66	A	68	HIS	0	-0.050	-0.029	19.797	0.014	0.014	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.050	-0.029	21.722	0.008	0.008	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.011	0.018	18.756	0.013	0.013	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.851	-0.925	22.309	0.017	0.017	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.891	-0.969	24.901	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	73	ALA	0	-0.022	-0.011	26.715	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.893	0.950	20.181	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.975	0.983	24.209	0.026	0.026	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.024	0.010	25.532	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.868	-0.908	22.951	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.025	0.007	20.320	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.966	0.969	24.236	0.043	0.043	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.913	0.959	27.504	0.018	0.018	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.036	0.018	22.112	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	HIS	0	0.073	0.051	25.294	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.053	-0.052	26.652	0.002	0.002	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.100	-0.053	27.950	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.034	0.031	24.860	0.002	0.002	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.926	-0.957	28.251	-0.111	-0.111	0.000	0.000	0.000	0.000
85	A	87	GLY	0	-0.081	-0.037	31.071	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:3:LEU)