FMO DATABASE

FMODB ID: LRRG9

Calculation Name: 2C4F-L-Xray547

Preferred Name: Coagulation factor VII

Target Type: SINGLE PROTEIN

Ligand Name: 2-{[6-{3-[amino(imino)methyl]phenoxy}-4-(diisopropylamino)-3,5-difluoropyridin-2-yl]oxy}-5-[(isobutylamino)carbonyl]ben zoic acid | gamma-carboxy-glutamic acid | 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-d-glucopyranose | alpha-l-fucopyranose | calcium ion

Ligand 3-letter code: GIL | CGU | NAG | GLC | FUC | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C4F

Chain ID: L

ChEMBL ID: CHEMBL3991

UniProt ID: P08709

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-918612.95886
FMO2-HF: Nuclear repulsion	861209.91549
FMO2-HF: Total energy	-57403.04337
FMO2-MP2: Total energy	-57559.136186

3D Structure Molmil

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(L:4:PHE)

Summations of interaction energy for fragment #1(L:4:PHE)

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.
92.351	96.741	0.353	-1.609	-3.134	0

Interaction energy analysis for fragmet #1(L:4:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.943 / q_NPA : 0.951

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	L	6	LEU	0	0.032	0.010	3.551	6.501	8.896	0.041	-0.958	-1.479	0.003
4	L	7	LEU	0	-0.044	-0.026	2.684	5.669	6.957	0.251	-0.506	-1.033	-0.002
5	L	8	LEU	0	0.035	0.030	3.003	2.633	3.340	0.061	-0.145	-0.622	-0.001
6	L	9	ARG	1	0.927	0.981	6.702	30.997	30.997	0.000	0.000	0.000	0.000
7	L	10	PRO	0	0.098	0.052	9.973	-0.638	-0.638	0.000	0.000	0.000	0.000
8	L	11	GLY	0	0.011	0.010	12.598	-0.576	-0.576	0.000	0.000	0.000	0.000
9	L	12	SER	0	0.012	-0.005	13.472	1.155	1.155	0.000	0.000	0.000	0.000
10	L	13	LEU	0	0.060	0.032	14.898	-0.853	-0.853	0.000	0.000	0.000	0.000
11	L	14	LEU	0	0.032	0.020	17.400	-0.124	-0.124	0.000	0.000	0.000	0.000
12	L	15	ARG	1	0.876	0.916	9.466	26.645	26.645	0.000	0.000	0.000	0.000
13	L	16	LEU	0	-0.021	-0.024	9.672	-0.877	-0.877	0.000	0.000	0.000	0.000
14	L	17	CYS	0	-0.085	-0.015	13.022	-1.362	-1.362	0.000	0.000	0.000	0.000
15	L	18	LYS	1	0.967	0.997	16.463	14.484	14.484	0.000	0.000	0.000	0.000
16	L	19	LEU	0	-0.013	0.014	14.689	0.318	0.318	0.000	0.000	0.000	0.000
17	L	20	LEU	0	-0.015	-0.001	9.326	-0.803	-0.803	0.000	0.000	0.000	0.000
18	L	21	GLN	0	0.055	0.029	13.519	0.975	0.975	0.000	0.000	0.000	0.000
19	L	23	SER	0	0.077	0.022	14.065	1.145	1.145	0.000	0.000	0.000	0.000
20	L	24	PHE	0	0.070	0.029	16.006	-0.113	-0.113	0.000	0.000	0.000	0.000
21	L	25	LEU	0	0.010	0.001	15.083	0.389	0.389	0.000	0.000	0.000	0.000
22	L	26	LEU	0	0.004	0.006	10.535	-0.055	-0.055	0.000	0.000	0.000	0.000
23	L	27	ALA	0	0.077	0.029	14.577	0.218	0.218	0.000	0.000	0.000	0.000
24	L	28	ARG	1	0.938	0.962	17.904	15.259	15.259	0.000	0.000	0.000	0.000
25	L	29	LEU	0	-0.048	-0.020	13.493	0.607	0.607	0.000	0.000	0.000	0.000
26	L	30	ILE	0	-0.045	-0.016	14.799	0.196	0.196	0.000	0.000	0.000	0.000
27	L	31	PHE	0	0.003	-0.017	18.093	0.522	0.522	0.000	0.000	0.000	0.000
28	L	32	LYS	1	0.854	0.934	18.404	16.069	16.069	0.000	0.000	0.000	0.000
29	L	33	ASP	-1	-0.770	-0.886	22.421	-10.497	-10.497	0.000	0.000	0.000	0.000
30	L	34	ALA	0	0.012	0.021	24.946	-0.307	-0.307	0.000	0.000	0.000	0.000
31	L	35	LEU	0	0.011	0.010	26.643	0.008	0.008	0.000	0.000	0.000	0.000
32	L	36	ARG	1	0.981	0.985	25.656	10.881	10.881	0.000	0.000	0.000	0.000
33	L	37	THR	0	-0.068	-0.039	21.693	-0.156	-0.156	0.000	0.000	0.000	0.000
34	L	38	LYS	1	0.951	0.977	24.193	10.129	10.129	0.000	0.000	0.000	0.000
35	L	39	LEU	0	0.019	0.021	26.712	0.016	0.016	0.000	0.000	0.000	0.000
36	L	40	PHE	0	-0.008	-0.009	20.028	-0.001	-0.001	0.000	0.000	0.000	0.000
37	L	41	TRP	0	0.023	-0.013	18.785	-0.382	-0.382	0.000	0.000	0.000	0.000
38	L	42	ILE	0	-0.011	0.015	24.393	-0.086	-0.086	0.000	0.000	0.000	0.000
39	L	43	SER	0	0.059	0.024	27.359	0.250	0.250	0.000	0.000	0.000	0.000
40	L	44	TYR	0	-0.109	-0.059	17.877	-0.452	-0.452	0.000	0.000	0.000	0.000
41	L	45	SER	0	-0.088	-0.070	22.910	-0.297	-0.297	0.000	0.000	0.000	0.000
42	L	46	ASP	-1	-0.818	-0.877	24.062	-10.262	-10.262	0.000	0.000	0.000	0.000
43	L	47	GLY	0	0.010	0.009	25.796	0.023	0.023	0.000	0.000	0.000	0.000
44	L	48	ASP	-1	-0.856	-0.936	26.781	-10.218	-10.218	0.000	0.000	0.000	0.000
45	L	49	GLN	0	-0.037	-0.032	28.928	-0.110	-0.110	0.000	0.000	0.000	0.000
46	L	50	CYS	0	-0.051	-0.052	32.203	0.435	0.435	0.000	0.000	0.000	0.000
47	L	51	ALA	0	0.027	0.032	28.546	0.153	0.153	0.000	0.000	0.000	0.000
48	L	52	SER	0	-0.086	-0.042	30.475	0.099	0.099	0.000	0.000	0.000	0.000
49	L	53	SER	0	-0.046	-0.021	33.040	0.215	0.215	0.000	0.000	0.000	0.000
50	L	54	PRO	0	0.005	0.011	35.515	0.220	0.220	0.000	0.000	0.000	0.000
51	L	55	CYS	0	-0.099	-0.019	38.387	-0.011	-0.011	0.000	0.000	0.000	0.000
52	L	56	GLN	0	0.069	0.024	40.987	0.087	0.087	0.000	0.000	0.000	0.000
53	L	57	ASN	0	-0.086	-0.059	43.584	0.072	0.072	0.000	0.000	0.000	0.000
54	L	58	GLY	0	0.035	0.020	43.805	0.124	0.124	0.000	0.000	0.000	0.000
55	L	59	GLY	0	-0.011	0.005	43.726	0.019	0.019	0.000	0.000	0.000	0.000
56	L	60	SER	0	-0.025	-0.010	39.912	-0.156	-0.156	0.000	0.000	0.000	0.000
57	L	62	LYS	1	0.912	0.963	34.859	8.692	8.692	0.000	0.000	0.000	0.000
58	L	63	ASP	-1	-0.771	-0.900	31.214	-9.826	-9.826	0.000	0.000	0.000	0.000
59	L	64	GLN	0	-0.093	-0.047	34.185	0.170	0.170	0.000	0.000	0.000	0.000
60	L	65	LEU	0	0.019	0.011	30.864	-0.138	-0.138	0.000	0.000	0.000	0.000
61	L	66	GLN	0	-0.024	-0.009	31.304	0.523	0.523	0.000	0.000	0.000	0.000
62	L	67	SER	0	-0.100	-0.055	33.575	0.329	0.329	0.000	0.000	0.000	0.000
63	L	68	TYR	0	-0.032	-0.048	35.257	-0.233	-0.233	0.000	0.000	0.000	0.000
64	L	69	ILE	0	-0.021	-0.005	37.520	0.223	0.223	0.000	0.000	0.000	0.000
65	L	71	PHE	0	-0.023	-0.011	40.994	0.166	0.166	0.000	0.000	0.000	0.000
66	L	72	CYS	0	-0.034	0.013	43.906	-0.190	-0.190	0.000	0.000	0.000	0.000
67	L	73	LEU	0	0.042	0.024	46.531	0.083	0.083	0.000	0.000	0.000	0.000
68	L	74	PRO	0	0.008	-0.018	49.105	0.029	0.029	0.000	0.000	0.000	0.000
69	L	75	ALA	0	0.035	0.039	52.584	0.085	0.085	0.000	0.000	0.000	0.000
70	L	76	PHE	0	-0.025	-0.017	49.263	0.033	0.033	0.000	0.000	0.000	0.000
71	L	77	GLU	-1	-0.829	-0.908	49.844	-5.878	-5.878	0.000	0.000	0.000	0.000
72	L	78	GLY	0	0.011	0.011	48.990	-0.021	-0.021	0.000	0.000	0.000	0.000
73	L	79	ARG	1	0.924	0.960	42.135	7.273	7.273	0.000	0.000	0.000	0.000
74	L	80	ASN	0	0.012	-0.013	41.728	-0.367	-0.367	0.000	0.000	0.000	0.000
75	L	82	GLU	-1	-0.728	-0.856	46.365	-6.847	-6.847	0.000	0.000	0.000	0.000
76	L	83	THR	0	-0.024	0.001	47.927	0.131	0.131	0.000	0.000	0.000	0.000
77	L	84	HIS	1	0.879	0.936	49.678	6.180	6.180	0.000	0.000	0.000	0.000
78	L	85	LYS	1	0.886	0.923	53.651	5.893	5.893	0.000	0.000	0.000	0.000
79	L	86	ASP	-1	-0.900	-0.949	56.509	-5.524	-5.524	0.000	0.000	0.000	0.000
80	L	87	ASP	-1	-0.940	-0.974	55.718	-5.610	-5.610	0.000	0.000	0.000	0.000
81	L	88	GLN	0	-0.068	-0.030	56.654	0.075	0.075	0.000	0.000	0.000	0.000
82	L	89	LEU	0	-0.026	0.006	60.332	0.078	0.078	0.000	0.000	0.000	0.000
83	L	90	ILE	0	0.001	-0.011	62.268	0.071	0.071	0.000	0.000	0.000	0.000
84	L	91	CYS	0	0.029	0.008	65.640	-0.023	-0.023	0.000	0.000	0.000	0.000
85	L	92	VAL	0	-0.041	-0.016	63.953	0.031	0.031	0.000	0.000	0.000	0.000
86	L	93	ASN	0	-0.054	-0.026	61.605	-0.038	-0.038	0.000	0.000	0.000	0.000
87	L	94	GLU	-1	-0.872	-0.940	64.568	-4.830	-4.830	0.000	0.000	0.000	0.000
88	L	95	ASN	0	-0.032	-0.017	67.086	0.045	0.045	0.000	0.000	0.000	0.000
89	L	96	GLY	0	0.038	0.021	67.223	0.062	0.062	0.000	0.000	0.000	0.000
90	L	97	GLY	0	0.008	-0.006	68.273	-0.008	-0.008	0.000	0.000	0.000	0.000
91	L	98	CYS	0	-0.083	-0.018	69.127	-0.013	-0.013	0.000	0.000	0.000	0.000
92	L	99	GLU	-1	-0.788	-0.889	72.852	-4.112	-4.112	0.000	0.000	0.000	0.000
93	L	100	GLN	0	-0.026	-0.014	75.499	0.048	0.048	0.000	0.000	0.000	0.000
94	L	101	TYR	0	-0.027	-0.009	76.495	-0.004	-0.004	0.000	0.000	0.000	0.000
95	L	103	SER	0	-0.034	-0.021	73.236	0.072	0.072	0.000	0.000	0.000	0.000
96	L	104	ASP	-1	-0.751	-0.867	67.987	-4.772	-4.772	0.000	0.000	0.000	0.000
97	L	105	HIS	0	-0.050	-0.015	69.210	0.109	0.109	0.000	0.000	0.000	0.000
98	L	106	THR	0	0.032	0.018	66.601	-0.044	-0.044	0.000	0.000	0.000	0.000
99	L	107	GLY	0	0.012	0.003	65.186	0.047	0.047	0.000	0.000	0.000	0.000
100	L	108	THR	0	-0.046	-0.021	66.226	-0.012	-0.012	0.000	0.000	0.000	0.000
101	L	109	LYS	1	0.966	0.996	66.545	4.644	4.644	0.000	0.000	0.000	0.000
102	L	110	ARG	1	0.846	0.924	67.814	4.701	4.701	0.000	0.000	0.000	0.000
103	L	111	SER	0	-0.041	-0.042	69.875	0.011	0.011	0.000	0.000	0.000	0.000
104	L	113	ARG	1	0.872	0.920	75.161	4.198	4.198	0.000	0.000	0.000	0.000
105	L	114	CYS	0	-0.089	-0.035	77.190	-0.009	-0.009	0.000	0.000	0.000	0.000
106	L	115	HIS	1	0.851	0.924	81.456	3.781	3.781	0.000	0.000	0.000	0.000
107	L	116	GLU	-1	-0.809	-0.919	84.150	-3.731	-3.731	0.000	0.000	0.000	0.000
108	L	117	GLY	0	0.033	0.022	87.851	0.003	0.003	0.000	0.000	0.000	0.000
109	L	118	TYR	0	-0.050	-0.014	84.110	-0.003	-0.003	0.000	0.000	0.000	0.000
110	L	119	SER	0	-0.047	-0.017	84.617	0.015	0.015	0.000	0.000	0.000	0.000
111	L	120	LEU	0	0.007	-0.004	77.087	-0.016	-0.016	0.000	0.000	0.000	0.000
112	L	121	LEU	0	0.008	0.010	78.796	0.040	0.040	0.000	0.000	0.000	0.000
113	L	122	ALA	0	-0.003	-0.016	78.547	-0.034	-0.034	0.000	0.000	0.000	0.000
114	L	123	ASP	-1	-0.795	-0.862	73.709	-4.310	-4.310	0.000	0.000	0.000	0.000
115	L	124	GLY	0	-0.037	-0.015	73.417	-0.069	-0.069	0.000	0.000	0.000	0.000
116	L	125	VAL	0	-0.080	-0.068	71.017	-0.049	-0.049	0.000	0.000	0.000	0.000
117	L	126	SER	0	0.011	-0.016	74.465	-0.006	-0.006	0.000	0.000	0.000	0.000
118	L	128	THR	0	0.042	0.033	80.789	0.008	0.008	0.000	0.000	0.000	0.000
119	L	129	PRO	0	-0.005	-0.013	84.010	0.014	0.014	0.000	0.000	0.000	0.000
120	L	130	THR	0	-0.071	-0.049	87.375	0.013	0.013	0.000	0.000	0.000	0.000
121	L	131	VAL	0	-0.029	-0.018	90.259	0.046	0.046	0.000	0.000	0.000	0.000
122	L	132	GLU	-1	-0.873	-0.920	91.928	-3.350	-3.350	0.000	0.000	0.000	0.000
123	L	133	TYR	0	-0.052	-0.038	92.762	-0.026	-0.026	0.000	0.000	0.000	0.000
124	L	134	PRO	0	-0.007	0.016	87.811	0.006	0.006	0.000	0.000	0.000	0.000
125	L	135	CYS	0	-0.009	-0.016	86.625	-0.005	-0.005	0.000	0.000	0.000	0.000
126	L	136	GLY	0	-0.005	-0.006	85.202	-0.043	-0.043	0.000	0.000	0.000	0.000
127	L	137	LYS	1	0.914	0.969	82.643	3.841	3.841	0.000	0.000	0.000	0.000
128	L	138	ILE	0	-0.020	-0.013	85.889	0.043	0.043	0.000	0.000	0.000	0.000
129	L	139	PRO	0	0.044	0.005	88.843	-0.004	-0.004	0.000	0.000	0.000	0.000
130	L	140	ILE	0	-0.053	-0.018	91.189	0.019	0.019	0.000	0.000	0.000	0.000
131	L	141	LEU	0	-0.101	-0.058	86.069	0.001	0.001	0.000	0.000	0.000	0.000
132	L	142	GLU	-2	-1.806	-1.882	85.988	-7.513	-7.513	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:4:PHE)