FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 4GL9N

Calculation Name: 4V7C-A-Other547

Preferred Name:

Target Type:

Ligand Name: (2s)-amino[(4r,6s)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid | (2z)-2-amino-3-(carbamoylamino)prop-2-enoic acid | beta-lysine | diaminopropanoic acid

Ligand 3-letter code: 5OH | UAL | KBE | DPP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V7C

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7J3

Base Structure: ElectronMicroscopy

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 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2363140.659739
FMO2-HF: Nuclear repulsion 2279665.48618
FMO2-HF: Total energy -83475.17356
FMO2-MP2: Total energy -83719.372612


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
254.787255.968-0.01-0.499-0.6720
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.871 / q_NPA : 1.926
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   
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].
3A5THR00.0650.0343.865-1.0780.103-0.010-0.499-0.6720.000
4A6LYS11.0311.0006.33639.10539.1050.0000.0000.0000.000
5A7ARG10.8420.9219.42548.67548.6750.0000.0000.0000.000
6A8MET00.0170.0196.3940.5500.5500.0000.0000.0000.000
7A9ARG10.8410.9115.26267.99367.9930.0000.0000.0000.000
8A10VAL00.0730.0339.5131.6051.6050.0000.0000.0000.000
9A11ILE00.0020.01211.2802.0542.0540.0000.0000.0000.000
10A12ARG10.9340.9666.66765.86765.8670.0000.0000.0000.000
11A13GLU-1-0.949-0.98011.892-40.461-40.4610.0000.0000.0000.000
12A14LYS10.8660.95514.53835.20135.2010.0000.0000.0000.000
13A15VAL0-0.055-0.02213.6481.7131.7130.0000.0000.0000.000
14A16ASP-1-0.798-0.87514.554-34.336-34.3360.0000.0000.0000.000
15A17ALA0-0.057-0.05112.0260.3660.3660.0000.0000.0000.000
16A18THR0-0.115-0.06813.956-0.360-0.3600.0000.0000.0000.000
17A19LYS10.8970.96117.02627.51327.5130.0000.0000.0000.000
18A20GLN0-0.079-0.02918.542-1.662-1.6620.0000.0000.0000.000
19A21TYR00.006-0.01117.8680.6390.6390.0000.0000.0000.000
20A22ASP-1-0.783-0.88822.059-21.495-21.4950.0000.0000.0000.000
21A23ILE00.0240.00124.109-1.151-1.1510.0000.0000.0000.000
22A24ASN0-0.029-0.03725.315-0.132-0.1320.0000.0000.0000.000
23A25GLU-1-0.839-0.92124.093-23.869-23.8690.0000.0000.0000.000
24A26ALA0-0.025-0.02120.374-0.872-0.8720.0000.0000.0000.000
25A27ILE0-0.045-0.01121.410-1.200-1.2000.0000.0000.0000.000
26A28ALA00.0040.01423.9450.0040.0040.0000.0000.0000.000
27A29LEU00.0390.02018.032-0.658-0.6580.0000.0000.0000.000
28A30LEU00.003-0.00418.172-1.466-1.4660.0000.0000.0000.000
29A31LYS10.8040.87518.82422.98622.9860.0000.0000.0000.000
30A32GLU-1-0.929-0.94619.851-28.213-28.2130.0000.0000.0000.000
31A33LEU0-0.070-0.05114.456-2.245-2.2450.0000.0000.0000.000
32A34ALA0-0.0030.01514.805-2.482-2.4820.0000.0000.0000.000
33A35THR00.0130.00214.7220.0130.0130.0000.0000.0000.000
34A36ALA0-0.067-0.02215.191-0.626-0.6260.0000.0000.0000.000
35A37LYS10.9460.96216.57934.37134.3710.0000.0000.0000.000
36A38PHE00.0280.00715.8820.8540.8540.0000.0000.0000.000
37A39VAL00.0480.03220.200-0.976-0.9760.0000.0000.0000.000
38A40GLU-1-0.768-0.88315.343-37.912-37.9120.0000.0000.0000.000
39A41SER0-0.011-0.01818.3251.8921.8920.0000.0000.0000.000
40A42VAL0-0.0100.00217.869-1.819-1.8190.0000.0000.0000.000
41A43ASP-1-0.886-0.94915.874-31.748-31.7480.0000.0000.0000.000
42A44VAL00.002-0.00817.262-0.933-0.9330.0000.0000.0000.000
43A45ALA0-0.011-0.00314.4530.5010.5010.0000.0000.0000.000
44A46VAL00.021-0.00116.4970.2570.2570.0000.0000.0000.000
45A47ASN0-0.0050.00416.4340.3460.3460.0000.0000.0000.000
46A48LEU00.0310.00418.2381.0061.0060.0000.0000.0000.000
47A49GLY0-0.033-0.01121.883-0.363-0.3630.0000.0000.0000.000
48A50ILE0-0.100-0.06423.6871.1401.1400.0000.0000.0000.000
49A51ASP-1-0.839-0.91523.866-22.536-22.5360.0000.0000.0000.000
50A52ALA0-0.003-0.01121.9900.4790.4790.0000.0000.0000.000
51A53ARG10.8640.93121.15324.31524.3150.0000.0000.0000.000
52A54LYS10.8900.94226.23319.11519.1150.0000.0000.0000.000
53A55SER00.0110.01229.357-0.311-0.3110.0000.0000.0000.000
54A56ASP-1-0.855-0.93431.638-17.698-17.6980.0000.0000.0000.000
55A57GLN00.014-0.00328.3660.1810.1810.0000.0000.0000.000
56A58ASN0-0.047-0.01326.965-0.449-0.4490.0000.0000.0000.000
57A59VAL00.0090.01825.3890.6430.6430.0000.0000.0000.000
58A60ARG10.8920.93425.92519.26519.2650.0000.0000.0000.000
59A61GLY00.0300.02228.1080.7910.7910.0000.0000.0000.000
60A62ALA0-0.041-0.02428.857-0.645-0.6450.0000.0000.0000.000
61A63THR0-0.0210.00528.2070.4440.4440.0000.0000.0000.000
62A64VAL00.0380.00430.242-0.400-0.4000.0000.0000.0000.000
63A65LEU0-0.0040.01826.349-0.012-0.0120.0000.0000.0000.000
64A66PRO00.0050.01430.5160.3280.3280.0000.0000.0000.000
65A67HIS0-0.0060.00030.5010.9370.9370.0000.0000.0000.000
66A68GLY00.0310.02330.794-0.217-0.2170.0000.0000.0000.000
67A69THR0-0.002-0.02226.065-0.434-0.4340.0000.0000.0000.000
68A70GLY00.0340.02425.830-0.861-0.8610.0000.0000.0000.000
69A71ARG10.8310.89423.92023.31323.3130.0000.0000.0000.000
70A72SER00.0390.02527.6910.3290.3290.0000.0000.0000.000
71A73VAL00.0140.02428.205-0.629-0.6290.0000.0000.0000.000
72A74ARG10.8960.94430.21519.00919.0090.0000.0000.0000.000
73A75VAL00.0210.00631.823-0.388-0.3880.0000.0000.0000.000
74A76ALA00.0240.02134.3000.4490.4490.0000.0000.0000.000
75A77VAL0-0.048-0.03336.021-0.220-0.2200.0000.0000.0000.000
76A78PHE00.0140.01436.4080.2130.2130.0000.0000.0000.000
77A79THR0-0.054-0.04140.9420.0250.0250.0000.0000.0000.000
78A80GLN00.0290.00044.4240.1530.1530.0000.0000.0000.000
79A81GLY00.0500.02748.1230.0360.0360.0000.0000.0000.000
80A82ALA00.0740.02950.509-0.139-0.1390.0000.0000.0000.000
81A83ASN0-0.002-0.00446.2330.0770.0770.0000.0000.0000.000
82A84ALA00.0050.01246.073-0.366-0.3660.0000.0000.0000.000
83A85GLU-1-0.909-0.95646.849-12.085-12.0850.0000.0000.0000.000
84A86ALA00.010-0.00247.525-0.182-0.1820.0000.0000.0000.000
85A87ALA0-0.016-0.00642.691-0.252-0.2520.0000.0000.0000.000
86A88LYS10.9380.96043.25613.43213.4320.0000.0000.0000.000
87A89ALA00.0280.01444.822-0.164-0.1640.0000.0000.0000.000
88A90ALA0-0.098-0.03842.660-0.008-0.0080.0000.0000.0000.000
89A91GLY00.0430.02041.111-0.205-0.2050.0000.0000.0000.000
90A92ALA0-0.052-0.02538.472-0.479-0.4790.0000.0000.0000.000
91A93GLU-1-0.872-0.92734.875-16.926-16.9260.0000.0000.0000.000
92A94LEU0-0.008-0.00337.3320.2400.2400.0000.0000.0000.000
93A95VAL0-0.018-0.01639.398-0.203-0.2030.0000.0000.0000.000
94A96GLY00.0060.02541.4400.2430.2430.0000.0000.0000.000
95A97MET00.007-0.00242.7190.0460.0460.0000.0000.0000.000
96A98GLU-1-0.839-0.92844.094-13.527-13.5270.0000.0000.0000.000
97A99ASP-1-0.909-0.96144.751-12.847-12.8470.0000.0000.0000.000
98A100LEU00.0040.00644.818-0.035-0.0350.0000.0000.0000.000
99A101ALA00.0110.00440.316-0.375-0.3750.0000.0000.0000.000
100A102ASP-1-0.880-0.95739.599-15.336-15.3360.0000.0000.0000.000
101A103GLN0-0.016-0.01940.064-0.344-0.3440.0000.0000.0000.000
102A104ILE00.0050.00035.711-0.306-0.3060.0000.0000.0000.000
103A105LYS10.8090.91034.77916.69216.6920.0000.0000.0000.000
104A106LYS10.8950.96335.71314.81414.8140.0000.0000.0000.000
105A107GLY00.0330.01435.379-0.247-0.2470.0000.0000.0000.000
106A108GLU-1-0.907-0.93035.150-16.574-16.5740.0000.0000.0000.000
107A109MET0-0.066-0.03530.883-0.266-0.2660.0000.0000.0000.000
108A110ASN0-0.004-0.00330.421-0.590-0.5900.0000.0000.0000.000
109A111PHE0-0.003-0.02230.2150.5520.5520.0000.0000.0000.000
110A112ASP-1-0.830-0.89326.421-22.861-22.8610.0000.0000.0000.000
111A113VAL0-0.073-0.04527.565-0.549-0.5490.0000.0000.0000.000
112A114VAL00.0050.01730.2310.4390.4390.0000.0000.0000.000
113A115ILE0-0.038-0.01933.324-0.196-0.1960.0000.0000.0000.000
114A116ALA00.0310.00736.1770.1470.1470.0000.0000.0000.000
115A117SER00.033-0.01139.253-0.046-0.0460.0000.0000.0000.000
116A118PRO00.001-0.01642.186-0.081-0.0810.0000.0000.0000.000
117A119ASP-1-0.845-0.88243.166-13.205-13.2050.0000.0000.0000.000
118A120ALA00.0580.04142.9600.2110.2110.0000.0000.0000.000
119A121MET0-0.033-0.02036.631-0.381-0.3810.0000.0000.0000.000
120A122ARG10.7930.87740.27312.81612.8160.0000.0000.0000.000
121A123VAL00.0140.02241.604-0.082-0.0820.0000.0000.0000.000
122A124VAL00.0160.00735.948-0.294-0.2940.0000.0000.0000.000
123A125GLY0-0.019-0.01136.351-0.523-0.5230.0000.0000.0000.000
124A126GLN0-0.0010.01036.393-0.369-0.3690.0000.0000.0000.000
125A127LEU00.0670.02436.305-0.294-0.2940.0000.0000.0000.000
126A128GLY00.0820.04233.723-0.434-0.4340.0000.0000.0000.000
127A129GLN0-0.032-0.02230.660-0.432-0.4320.0000.0000.0000.000
128A130VAL0-0.009-0.00529.251-0.713-0.7130.0000.0000.0000.000
129A131LEU00.0460.02928.653-0.727-0.7270.0000.0000.0000.000
130A132GLY00.0100.00227.774-0.582-0.5820.0000.0000.0000.000
131A133PRO0-0.045-0.02624.028-0.558-0.5580.0000.0000.0000.000
132A134ARG10.9230.95622.93721.82721.8270.0000.0000.0000.000
133A135GLY00.0050.01624.409-0.287-0.2870.0000.0000.0000.000
134A136LEU0-0.009-0.00125.4250.4790.4790.0000.0000.0000.000
135A137MET0-0.0350.00228.5860.5190.5190.0000.0000.0000.000
136A138PRO00.0110.01631.016-0.235-0.2350.0000.0000.0000.000
137A139ASN0-0.022-0.03932.0560.0520.0520.0000.0000.0000.000
138A140PRO00.0890.04334.040-0.274-0.2740.0000.0000.0000.000
139A141LYS10.9110.96730.83818.47518.4750.0000.0000.0000.000
140A142VAL0-0.076-0.05228.693-0.395-0.3950.0000.0000.0000.000
141A143GLY00.0630.03931.570-0.240-0.2400.0000.0000.0000.000
142A144THR00.000-0.00131.9420.0560.0560.0000.0000.0000.000
143A145VAL00.003-0.00435.1160.1330.1330.0000.0000.0000.000
144A146THR00.007-0.01538.2400.0840.0840.0000.0000.0000.000
145A147PRO00.0420.02141.260-0.060-0.0600.0000.0000.0000.000
146A148ASN00.0140.02741.5960.1650.1650.0000.0000.0000.000
147A149VAL00.0300.00140.807-0.324-0.3240.0000.0000.0000.000
148A150ALA00.0310.01040.848-0.323-0.3230.0000.0000.0000.000
149A151GLU-1-0.891-0.92340.428-14.491-14.4910.0000.0000.0000.000
150A152ALA00.0200.00737.160-0.365-0.3650.0000.0000.0000.000
151A153VAL0-0.002-0.01436.366-0.559-0.5590.0000.0000.0000.000
152A154LYS10.8950.97036.74013.96013.9600.0000.0000.0000.000
153A155ASN00.0260.01435.340-0.097-0.0970.0000.0000.0000.000
154A156ALA00.005-0.00632.457-0.523-0.5230.0000.0000.0000.000
155A157LYS10.7760.87732.32517.03017.0300.0000.0000.0000.000
156A158ALA00.0030.01434.092-0.175-0.1750.0000.0000.0000.000
157A159GLY0-0.023-0.00230.330-0.287-0.2870.0000.0000.0000.000
158A160GLN0-0.031-0.02430.030-0.211-0.2110.0000.0000.0000.000
159A161VAL0-0.0040.01124.142-0.291-0.2910.0000.0000.0000.000
160A162ARG10.8650.92026.70021.54221.5420.0000.0000.0000.000
161A163TYR00.0280.01724.034-0.894-0.8940.0000.0000.0000.000
162A164ARG10.9550.94823.14223.58123.5810.0000.0000.0000.000
163A165ASN00.0140.02921.201-0.228-0.2280.0000.0000.0000.000
164A166ASP-1-0.768-0.89016.581-30.336-30.3360.0000.0000.0000.000
165A167LYS10.9690.96716.66931.45131.4510.0000.0000.0000.000
166A168ASN0-0.130-0.07215.296-0.208-0.2080.0000.0000.0000.000
167A169GLY00.0650.03918.4780.5860.5860.0000.0000.0000.000
168A170ILE0-0.074-0.01814.232-0.123-0.1230.0000.0000.0000.000
169A171ILE00.0000.00017.5821.2441.2440.0000.0000.0000.000
170A172HIS00.021-0.00114.0190.1050.1050.0000.0000.0000.000
171A173THR0-0.041-0.00617.9821.0131.0130.0000.0000.0000.000
172A174THR00.0070.01019.910-0.245-0.2450.0000.0000.0000.000
173A175ILE0-0.005-0.01421.2751.0791.0790.0000.0000.0000.000
174A176GLY00.0770.04322.9261.1041.1040.0000.0000.0000.000
175A177LYS10.8360.94022.21323.64623.6460.0000.0000.0000.000
176A178VAL00.0480.01819.5010.5600.5600.0000.0000.0000.000
177A179ASP-1-0.941-0.96821.956-22.149-22.1490.0000.0000.0000.000
178A180PHE00.0240.01825.3000.5400.5400.0000.0000.0000.000
179A181ASP-1-0.786-0.86726.575-20.254-20.2540.0000.0000.0000.000
180A182ALA00.0390.01326.866-0.282-0.2820.0000.0000.0000.000
181A183ASP-1-0.851-0.93227.932-19.503-19.5030.0000.0000.0000.000
182A184LYS10.8320.90229.47118.61918.6190.0000.0000.0000.000
183A185LEU0-0.022-0.01423.177-0.248-0.2480.0000.0000.0000.000
184A186LYS10.9420.99226.74819.15219.1520.0000.0000.0000.000
185A187GLU-1-0.848-0.93128.271-18.670-18.6700.0000.0000.0000.000
186A188ASN0-0.064-0.03826.9140.7230.7230.0000.0000.0000.000
187A189LEU0-0.018-0.01622.222-0.558-0.5580.0000.0000.0000.000
188A190GLU-1-0.844-0.93725.741-19.981-19.9810.0000.0000.0000.000
189A191ALA0-0.0020.00528.6800.3150.3150.0000.0000.0000.000
190A192LEU0-0.025-0.00923.0030.2530.2530.0000.0000.0000.000
191A193LEU0-0.010-0.00622.998-0.053-0.0530.0000.0000.0000.000
192A194VAL00.0430.01726.6190.2320.2320.0000.0000.0000.000
193A195ALA00.0220.01228.6570.5260.5260.0000.0000.0000.000
194A196LEU0-0.014-0.01822.8540.1660.1660.0000.0000.0000.000
195A197LYS10.9010.96227.56020.43320.4330.0000.0000.0000.000
196A198LYS10.9370.97830.11517.04317.0430.0000.0000.0000.000
197A199ALA0-0.050-0.02429.3770.5550.5550.0000.0000.0000.000
198A200LYS10.9210.98729.43618.37618.3760.0000.0000.0000.000
199A201PRO0-0.0200.01329.1990.5600.5600.0000.0000.0000.000
200A202THR00.033-0.00732.073-0.302-0.3020.0000.0000.0000.000
201A203GLN00.0330.03033.060-0.238-0.2380.0000.0000.0000.000
202A204ALA0-0.025-0.01029.037-0.372-0.3720.0000.0000.0000.000
203A205LYS10.9660.98330.55217.36417.3640.0000.0000.0000.000
204A206GLY00.0210.01428.805-0.557-0.5570.0000.0000.0000.000
205A207VAL00.0240.00024.9540.3750.3750.0000.0000.0000.000
206A208TYR00.002-0.01625.109-0.790-0.7900.0000.0000.0000.000
207A209ILE00.0050.01622.796-0.588-0.5880.0000.0000.0000.000
208A210LYS10.8970.95619.54527.70027.7000.0000.0000.0000.000
209A211LYS10.9310.97115.26933.88233.8820.0000.0000.0000.000
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