FMO DATABASE

FMODB ID: 7GLQK

Calculation Name: 4D3C-A-Xray372

Preferred Name: Hepatocyte growth factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3C

Chain ID: A

ChEMBL ID: CHEMBL5479

UniProt ID: P14210

Base Structure: X-ray

Registration Date: 2023-06-20

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1301291.204253
FMO2-HF: Nuclear repulsion	1241469.670718
FMO2-HF: Total energy	-59821.533535
FMO2-MP2: Total energy	-59988.411376

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:37:ASN)

Summations of interaction energy for fragment #1(A:37:ASN)

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.
-34.679	-23.029	9.251	-9.768	-11.134	-0.006

Interaction energy analysis for fragmet #1(A:37:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014

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	39	ILE	0	-0.029	-0.020	3.285	-3.379	1.986	-0.042	-2.859	-2.465	0.003
4	A	40	HIS	0	0.007	0.003	3.658	1.446	1.833	0.004	-0.066	-0.325	0.000
5	A	41	GLU	-1	-0.970	-0.969	6.227	-2.909	-2.909	0.000	0.000	0.000	0.000
6	A	42	PHE	0	-0.033	-0.021	8.015	0.613	0.613	0.000	0.000	0.000	0.000
7	A	43	LYS	1	0.890	0.953	10.578	0.248	0.248	0.000	0.000	0.000	0.000
8	A	44	LYS	1	0.948	0.977	11.116	0.476	0.476	0.000	0.000	0.000	0.000
9	A	45	SER	0	0.026	0.016	13.458	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	46	ALA	0	0.002	-0.010	16.299	0.073	0.073	0.000	0.000	0.000	0.000
11	A	47	LYS	1	0.934	0.989	17.194	0.093	0.093	0.000	0.000	0.000	0.000
12	A	48	THR	0	0.029	0.000	18.568	0.030	0.030	0.000	0.000	0.000	0.000
13	A	67	ALA	0	0.028	-0.012	7.545	0.239	0.239	0.000	0.000	0.000	0.000
14	A	68	ASP	-1	-0.759	-0.905	2.242	-6.709	-3.967	6.192	-3.904	-5.030	-0.019
15	A	69	GLN	0	-0.089	-0.041	4.505	0.299	0.593	-0.001	-0.024	-0.269	0.000
16	A	70	CYS	0	-0.060	-0.023	6.317	-0.779	-0.779	0.000	0.000	0.000	0.000
17	A	71	ALA	0	0.108	0.074	5.476	-0.403	-0.403	0.000	0.000	0.000	0.000
18	A	72	ASN	0	0.031	0.090	2.275	-14.545	-11.707	3.099	-2.914	-3.023	0.010
19	A	73	ARG	1	0.879	0.925	5.370	-4.283	-4.259	-0.001	-0.001	-0.022	0.000
20	A	74	CYS	0	-0.114	-0.029	8.764	-0.437	-0.437	0.000	0.000	0.000	0.000
21	A	75	THR	0	0.028	-0.032	6.846	-0.391	-0.391	0.000	0.000	0.000	0.000
22	A	76	ARG	1	0.921	0.959	6.517	-1.972	-1.972	0.000	0.000	0.000	0.000
23	A	77	ASN	0	0.050	0.036	10.375	-0.131	-0.131	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.953	0.986	11.710	-1.838	-1.838	0.000	0.000	0.000	0.000
25	A	79	GLY	0	-0.011	-0.011	13.555	0.104	0.104	0.000	0.000	0.000	0.000
26	A	80	LEU	0	-0.038	-0.010	13.599	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	81	PRO	0	0.018	0.012	17.550	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	82	PHE	0	0.031	0.009	17.365	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	83	THR	0	0.036	0.016	16.688	0.044	0.044	0.000	0.000	0.000	0.000
30	A	85	LYS	1	0.906	0.977	14.395	-0.110	-0.110	0.000	0.000	0.000	0.000
31	A	86	ALA	0	0.006	0.004	15.027	-0.108	-0.108	0.000	0.000	0.000	0.000
32	A	87	PHE	0	-0.001	-0.007	8.871	0.211	0.211	0.000	0.000	0.000	0.000
33	A	88	VAL	0	0.018	0.029	14.503	-0.112	-0.112	0.000	0.000	0.000	0.000
34	A	89	PHE	0	0.034	0.007	11.360	0.255	0.255	0.000	0.000	0.000	0.000
35	A	90	ASH	0	0.024	0.003	13.618	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	91	LYS	1	0.896	0.958	14.335	-0.363	-0.363	0.000	0.000	0.000	0.000
37	A	92	ALA	0	0.013	0.025	18.434	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	93	ARG	1	0.948	0.960	19.105	-0.361	-0.361	0.000	0.000	0.000	0.000
39	A	94	LYS	1	0.973	0.998	17.804	-0.559	-0.559	0.000	0.000	0.000	0.000
40	A	95	GLN	0	0.046	0.026	12.820	0.190	0.190	0.000	0.000	0.000	0.000
41	A	97	LEU	0	-0.026	-0.011	13.901	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	98	TRP	0	-0.001	-0.017	10.842	-0.092	-0.092	0.000	0.000	0.000	0.000
43	A	99	PHE	0	0.042	0.016	15.989	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	100	PRO	0	-0.001	0.034	17.541	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	101	PHE	0	0.000	-0.042	19.915	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	102	ASN	0	0.060	0.034	19.102	0.053	0.053	0.000	0.000	0.000	0.000
47	A	103	SER	0	-0.026	0.000	20.680	0.015	0.015	0.000	0.000	0.000	0.000
48	A	104	MET	0	-0.055	-0.020	21.160	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	105	SER	0	-0.051	-0.026	24.298	0.009	0.009	0.000	0.000	0.000	0.000
50	A	117	ASP	-1	-0.924	-0.980	13.768	0.077	0.077	0.000	0.000	0.000	0.000
51	A	118	LEU	0	-0.007	-0.011	15.038	0.134	0.134	0.000	0.000	0.000	0.000
52	A	119	TYR	0	0.007	0.009	9.717	-0.093	-0.093	0.000	0.000	0.000	0.000
53	A	120	GLU	-1	-0.853	-0.938	13.185	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	121	ASN	0	0.059	0.023	12.376	-0.258	-0.258	0.000	0.000	0.000	0.000
55	A	122	LYS	1	0.970	0.970	12.540	1.239	1.239	0.000	0.000	0.000	0.000
56	A	123	ASP	-1	-0.859	-0.905	14.350	-0.579	-0.579	0.000	0.000	0.000	0.000
57	A	124	TYR	0	-0.090	-0.057	16.377	0.098	0.098	0.000	0.000	0.000	0.000
58	A	125	ILE	0	-0.048	-0.029	17.500	0.049	0.049	0.000	0.000	0.000	0.000
59	A	126	ARG	1	0.885	0.939	19.891	0.151	0.151	0.000	0.000	0.000	0.000
60	A	127	ASN	0	-0.014	0.003	19.539	0.042	0.042	0.000	0.000	0.000	0.000
61	A	128	CYS	0	-0.011	-0.004	22.558	0.000	0.000	0.000	0.000	0.000	0.000
62	A	129	ILE	0	-0.037	-0.025	26.277	0.012	0.012	0.000	0.000	0.000	0.000
63	A	130	ILE	0	0.035	-0.011	29.549	0.005	0.005	0.000	0.000	0.000	0.000
64	A	131	GLY	0	0.019	0.010	33.106	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	132	LYS	1	0.980	1.010	34.845	0.117	0.117	0.000	0.000	0.000	0.000
66	A	133	GLY	0	0.031	0.017	31.118	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	134	GLY	0	0.023	0.009	30.606	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	135	SER	0	-0.064	-0.053	29.332	0.001	0.001	0.000	0.000	0.000	0.000
69	A	136	TYR	0	0.079	0.049	22.400	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	137	LYS	1	0.904	0.955	22.319	0.196	0.196	0.000	0.000	0.000	0.000
71	A	138	GLY	0	0.054	0.037	20.120	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	139	THR	0	0.026	-0.010	15.482	0.011	0.011	0.000	0.000	0.000	0.000
73	A	140	VAL	0	-0.014	0.009	18.271	-0.073	-0.073	0.000	0.000	0.000	0.000
74	A	141	SER	0	0.023	0.010	18.544	0.037	0.037	0.000	0.000	0.000	0.000
75	A	142	ILE	0	-0.013	-0.007	20.152	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	143	THR	0	0.023	0.020	23.707	0.014	0.014	0.000	0.000	0.000	0.000
77	A	144	LYS	1	1.004	1.005	27.049	0.236	0.236	0.000	0.000	0.000	0.000
78	A	145	SER	0	-0.021	0.002	29.484	0.002	0.002	0.000	0.000	0.000	0.000
79	A	146	GLY	0	0.002	0.000	25.942	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	147	ILE	0	-0.037	-0.026	25.659	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	148	LYS	1	0.968	0.988	19.276	0.660	0.660	0.000	0.000	0.000	0.000
82	A	149	CYS	0	-0.014	-0.023	23.455	0.022	0.022	0.000	0.000	0.000	0.000
83	A	150	GLN	0	0.005	-0.002	23.681	-0.035	-0.035	0.000	0.000	0.000	0.000
84	A	151	PRO	0	-0.048	-0.041	22.708	0.011	0.011	0.000	0.000	0.000	0.000
85	A	152	TRP	0	0.013	0.008	24.234	0.040	0.040	0.000	0.000	0.000	0.000
86	A	153	SER	0	-0.050	-0.030	24.158	0.018	0.018	0.000	0.000	0.000	0.000
87	A	154	SER	0	-0.038	-0.008	26.305	0.024	0.024	0.000	0.000	0.000	0.000
88	A	155	MET	0	0.002	-0.001	28.005	0.002	0.002	0.000	0.000	0.000	0.000
89	A	156	ILE	0	0.016	0.039	29.728	0.008	0.008	0.000	0.000	0.000	0.000
90	A	157	PRO	0	0.007	-0.022	28.940	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	158	HIS	1	0.816	0.931	31.031	0.283	0.283	0.000	0.000	0.000	0.000
92	A	159	GLU	-1	-0.830	-0.900	32.469	-0.163	-0.163	0.000	0.000	0.000	0.000
93	A	160	HIS	0	-0.018	-0.015	30.213	0.013	0.013	0.000	0.000	0.000	0.000
94	A	161	SER	0	0.040	0.027	34.741	0.002	0.002	0.000	0.000	0.000	0.000
95	A	162	PHE	0	-0.014	-0.027	31.377	0.007	0.007	0.000	0.000	0.000	0.000
96	A	163	LEU	0	0.067	0.038	30.649	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	164	PRO	0	0.076	0.017	27.105	0.010	0.010	0.000	0.000	0.000	0.000
98	A	165	SER	0	-0.058	-0.023	29.658	0.016	0.016	0.000	0.000	0.000	0.000
99	A	166	SER	0	-0.032	-0.011	32.594	0.010	0.010	0.000	0.000	0.000	0.000
100	A	167	TYR	0	-0.015	0.015	31.305	0.005	0.005	0.000	0.000	0.000	0.000
101	A	168	ARG	1	1.018	1.015	30.001	0.053	0.053	0.000	0.000	0.000	0.000
102	A	169	GLY	0	0.009	0.005	28.015	0.003	0.003	0.000	0.000	0.000	0.000
103	A	170	LYS	1	0.904	0.947	28.097	0.127	0.127	0.000	0.000	0.000	0.000
104	A	171	ASP	-1	-0.875	-0.915	22.417	-0.286	-0.286	0.000	0.000	0.000	0.000
105	A	172	LEU	0	0.024	0.038	24.945	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	173	GLN	0	0.017	-0.006	20.815	0.031	0.031	0.000	0.000	0.000	0.000
107	A	174	GLU	-1	-0.920	-0.962	17.583	-0.480	-0.480	0.000	0.000	0.000	0.000
108	A	175	ASN	0	-0.005	0.003	19.755	0.017	0.017	0.000	0.000	0.000	0.000
109	A	176	TYR	0	0.007	0.002	16.520	-0.055	-0.055	0.000	0.000	0.000	0.000
110	A	177	CYS	0	-0.022	-0.014	22.065	0.017	0.017	0.000	0.000	0.000	0.000
111	A	178	ARG	1	0.708	0.824	21.578	0.331	0.331	0.000	0.000	0.000	0.000
112	A	179	ASN	0	0.043	0.047	27.645	0.008	0.008	0.000	0.000	0.000	0.000
113	A	180	PRO	0	-0.016	-0.019	30.401	0.016	0.016	0.000	0.000	0.000	0.000
114	A	181	ARG	1	0.904	0.929	32.479	0.138	0.138	0.000	0.000	0.000	0.000
115	A	182	GLY	0	-0.027	0.007	34.735	0.007	0.007	0.000	0.000	0.000	0.000
116	A	183	GLU	-1	-0.936	-0.979	35.656	-0.159	-0.159	0.000	0.000	0.000	0.000
117	A	184	GLU	-1	-0.870	-0.961	36.412	-0.134	-0.134	0.000	0.000	0.000	0.000
118	A	185	GLY	0	0.001	0.018	36.118	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	186	GLY	0	0.035	0.032	32.824	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	187	PRO	0	-0.122	-0.078	28.126	0.003	0.003	0.000	0.000	0.000	0.000
121	A	188	TRP	0	0.066	0.044	29.913	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	190	PHE	0	0.015	0.004	28.500	0.016	0.016	0.000	0.000	0.000	0.000
123	A	191	THR	0	-0.006	-0.027	27.813	-0.030	-0.030	0.000	0.000	0.000	0.000
124	A	192	SER	0	-0.047	-0.036	25.642	0.014	0.014	0.000	0.000	0.000	0.000
125	A	193	ASN	0	0.065	0.022	27.789	0.002	0.002	0.000	0.000	0.000	0.000
126	A	194	PRO	0	0.014	-0.016	30.864	0.012	0.012	0.000	0.000	0.000	0.000
127	A	195	GLU	-1	-0.930	-0.954	33.813	-0.220	-0.220	0.000	0.000	0.000	0.000
128	A	196	VAL	0	0.021	0.032	33.040	0.012	0.012	0.000	0.000	0.000	0.000
129	A	197	ARG	1	0.884	0.963	33.176	0.173	0.173	0.000	0.000	0.000	0.000
130	A	198	TYR	0	-0.024	-0.032	32.162	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	199	GLU	-1	-0.809	-0.914	31.006	-0.292	-0.292	0.000	0.000	0.000	0.000
132	A	200	VAL	0	0.009	0.002	30.674	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	202	ASP	-1	-0.920	-0.950	27.617	-0.314	-0.314	0.000	0.000	0.000	0.000
134	A	203	ILE	0	-0.069	-0.040	24.397	-0.038	-0.038	0.000	0.000	0.000	0.000
135	A	204	PRO	0	0.089	0.059	25.543	0.023	0.023	0.000	0.000	0.000	0.000
136	A	205	GLN	0	-0.020	-0.013	27.833	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	207	SER	0	-0.006	0.003	29.993	0.000	0.000	0.000	0.000	0.000	0.000
138	A	208	GLU	-1	-0.900	-0.935	30.694	-0.233	-0.233	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:ASN)