FMO DATABASE

FMODB ID: KGKM3

Calculation Name: 3LMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LMB

Chain ID: A

ChEMBL ID:

UniProt ID:

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	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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1650750.217656
FMO2-HF: Nuclear repulsion	1584891.655251
FMO2-HF: Total energy	-65858.562405
FMO2-MP2: Total energy	-66046.006838

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.
-7.329	-1.427	2.225	-3.062	-5.063	-0.013

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 : 0.011 / q_NPA : 0.017

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	ALA	0	0.017	0.014	3.740	0.297	3.384	0.495	-1.493	-2.089	-0.001
4	A	4	SER	0	0.001	-0.019	6.216	0.389	0.389	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.078	-0.027	7.432	-0.046	-0.046	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.028	0.000	9.697	-0.096	-0.096	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.096	0.033	13.361	0.006	0.006	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.829	-0.908	15.398	-0.036	-0.036	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.014	0.010	12.272	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.008	0.008	10.434	0.025	0.025	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.024	0.015	13.207	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.795	0.886	16.534	0.037	0.037	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.884	0.952	8.197	-0.098	-0.098	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.021	0.025	14.807	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.939	0.968	16.734	0.036	0.036	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.060	-0.040	17.501	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.018	0.006	15.929	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.010	-0.020	18.289	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.020	-0.009	21.652	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.912	-0.934	19.161	0.033	0.033	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.034	-0.017	17.865	0.000	0.000	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.024	-0.003	21.167	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.059	0.034	24.208	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.005	0.001	26.835	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.026	-0.003	25.096	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.012	-0.008	25.517	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.032	-0.007	28.955	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.051	-0.018	29.804	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.051	0.027	30.819	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.061	-0.037	24.501	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.857	-0.910	25.857	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.025	-0.024	19.532	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.834	-0.879	23.882	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.006	-0.018	23.770	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.050	-0.077	14.362	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.827	-0.899	20.228	-0.126	-0.126	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.002	0.006	16.406	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.855	-0.919	16.924	-0.228	-0.228	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.065	-0.034	19.724	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.064	-0.026	19.114	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.016	0.000	21.765	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.003	0.017	21.678	0.006	0.006	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.042	-0.021	25.549	0.005	0.005	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.046	0.028	28.872	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.007	0.010	31.551	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.007	-0.003	35.193	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.938	-0.967	37.962	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.039	0.022	35.157	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.081	-0.043	33.268	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.011	0.035	36.705	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.043	-0.037	40.349	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.756	-0.872	42.847	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.759	0.861	45.586	0.032	0.032	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.017	-0.018	44.928	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.001	0.016	42.069	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.033	0.010	36.740	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.008	0.005	36.436	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.032	0.007	36.264	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.036	0.020	34.266	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.022	-0.001	32.534	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.019	-0.012	31.491	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.022	-0.043	28.960	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.006	-0.014	28.298	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.018	0.011	26.777	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.010	0.006	26.050	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.010	0.006	24.150	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.002	-0.001	22.329	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.039	0.028	21.328	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	69	CYS	0	-0.019	-0.011	20.736	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.035	-0.016	16.050	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.031	0.003	16.935	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.002	0.024	16.115	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.004	0.002	13.994	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.016	0.026	12.700	-0.090	-0.090	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.036	-0.021	11.390	-0.062	-0.062	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.853	0.911	10.957	0.296	0.296	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.023	-0.032	8.356	-0.165	-0.165	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.016	-0.007	6.796	-0.190	-0.190	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.776	-0.843	7.251	-0.214	-0.214	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.819	-0.893	5.366	-0.586	-0.494	-0.001	-0.005	-0.085	0.000
81	A	81	ASN	0	-0.106	-0.049	2.247	-4.012	-2.447	1.418	-0.956	-2.027	-0.005
82	A	82	ILE	0	0.010	0.021	2.888	-2.295	-1.185	0.314	-0.607	-0.817	-0.007
83	A	83	ALA	0	-0.019	-0.006	4.735	0.832	0.880	-0.001	-0.001	-0.045	0.000
84	A	84	CYS	0	-0.045	-0.025	7.239	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.013	0.008	10.638	0.093	0.093	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.065	0.008	13.594	-0.098	-0.098	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.041	-0.010	15.430	0.042	0.042	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.050	0.018	19.203	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.129	-0.062	22.070	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.850	-0.919	23.995	-0.103	-0.103	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.050	0.014	25.503	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.046	0.002	27.956	0.015	0.015	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.023	0.007	30.510	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.871	0.939	32.968	0.061	0.061	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.020	0.004	35.038	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.088	-0.038	36.810	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.001	-0.001	39.786	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	PRO	0	0.031	0.022	39.938	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.015	0.011	36.193	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.037	-0.001	39.476	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.034	0.019	39.233	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.775	0.870	30.812	0.044	0.044	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.009	0.009	31.185	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.777	0.828	30.269	0.066	0.066	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.023	-0.009	27.271	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.028	0.025	26.228	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	CYS	0	-0.063	-0.035	22.146	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	HIS	0	0.046	0.012	21.835	0.016	0.016	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.038	0.001	17.361	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.044	-0.024	17.072	0.016	0.016	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.840	-0.918	18.315	-0.224	-0.224	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.917	-0.960	16.562	-0.296	-0.296	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.929	-0.959	16.252	-0.301	-0.301	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.886	-0.958	17.397	-0.271	-0.271	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.040	-0.023	13.194	-0.049	-0.049	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.020	0.019	12.608	-0.107	-0.107	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.053	-0.032	13.080	-0.072	-0.072	0.000	0.000	0.000	0.000
118	A	118	PHE	0	-0.040	-0.020	12.594	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	119	PHE	0	0.031	-0.001	8.846	-0.072	-0.072	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.779	-0.866	10.458	-0.482	-0.482	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.003	-0.017	12.259	0.093	0.093	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.028	-0.023	7.599	0.106	0.106	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.875	-0.934	7.242	-1.020	-1.020	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.818	0.887	10.573	0.460	0.460	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.820	0.909	13.991	0.309	0.309	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.017	0.006	12.982	0.053	0.053	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.945	0.972	14.029	0.177	0.177	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.002	0.020	14.357	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.877	0.929	16.208	0.188	0.188	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.064	0.054	16.244	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.005	-0.037	19.005	0.022	0.022	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.005	0.014	19.089	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.770	-0.870	22.894	-0.100	-0.100	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.034	0.013	24.703	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.052	-0.025	26.886	0.007	0.007	0.000	0.000	0.000	0.000
136	A	136	ILE	0	-0.006	0.006	29.891	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	TYR	0	0.072	0.019	31.138	0.001	0.001	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.002	-0.015	35.221	0.002	0.002	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.820	-0.892	37.253	-0.051	-0.051	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.002	0.003	35.153	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	CYS	0	-0.054	-0.040	34.372	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.030	0.001	31.537	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.002	0.000	29.048	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.863	0.926	27.585	0.076	0.076	0.000	0.000	0.000	0.000
145	A	145	ILE	0	-0.030	-0.010	26.590	0.007	0.007	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.845	-0.913	29.710	-0.076	-0.076	0.000	0.000	0.000	0.000
147	A	147	PRO	0	0.002	0.000	32.898	0.004	0.004	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.847	-0.931	35.571	-0.070	-0.070	0.000	0.000	0.000	0.000
149	A	149	THR	0	-0.039	-0.014	36.120	0.005	0.005	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.862	0.927	36.649	0.058	0.058	0.000	0.000	0.000	0.000
151	A	151	PRO	0	0.013	0.021	33.978	0.003	0.003	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.026	-0.026	36.210	0.002	0.002	0.000	0.000	0.000	0.000
153	A	153	VAL	0	-0.016	-0.023	33.476	0.003	0.003	0.000	0.000	0.000	0.000
154	A	154	LYS	1	0.850	0.923	30.695	0.098	0.098	0.000	0.000	0.000	0.000
155	A	155	PHE	0	0.011	0.001	24.832	0.006	0.006	0.000	0.000	0.000	0.000
156	A	156	ASN	0	-0.007	-0.009	27.305	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.043	0.026	24.694	0.009	0.009	0.000	0.000	0.000	0.000
158	A	158	GLN	0	-0.007	0.013	22.462	-0.019	-0.019	0.000	0.000	0.000	0.000
159	A	159	TYR	0	0.008	-0.014	18.240	0.019	0.019	0.000	0.000	0.000	0.000
160	A	160	ALA	0	0.001	-0.005	17.566	-0.011	-0.011	0.000	0.000	0.000	0.000
161	A	161	ILE	0	0.021	0.025	10.772	0.025	0.025	0.000	0.000	0.000	0.000
162	A	162	LEU	0	-0.015	-0.023	13.931	0.014	0.014	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.839	0.928	8.908	0.600	0.600	0.000	0.000	0.000	0.000
164	A	164	ASN	0	-0.035	-0.009	10.836	0.131	0.131	0.000	0.000	0.000	0.000

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